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Arumuganainar D. Extra Tree Classifier Predicts an Interactome Hub Gene as HSPB1 in Oral Cancer: A Bioinformatics Analysis. Cureus 2024; 16:e59863. [PMID: 38854307 PMCID: PMC11157462 DOI: 10.7759/cureus.59863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 05/07/2024] [Indexed: 06/11/2024] Open
Abstract
Introduction Oral cancer is a significant global health issue that is mainly caused by factors, such as smoking, alcohol consumption, poor oral hygiene, age, and the human papillomavirus. Unfortunately, delayed diagnosis contributes to high rates of illness and mortality. However, saliva shows promise as a potential source for early detection, prognosis, and treatment. By analyzing the proteins and their interactions in saliva, we can gain insights that can assist in early detection and prediction. In this study, we aim to identify and predict the key genes, known as hub genes, in the salivary transcriptomics data of oral cancer patients and healthy individuals. Methods The data used for the analysis were obtained from salivaryproteome.org (https://salivaryproteome.org/) . The retrieved data consisted of individuals with oral cancer who were assigned unique identification numbers (IDs) 1025, 1030, 1027, and 1029, while the healthy individuals were assigned IDs 4256, 4257, 4255, and 4258, respectively. Differential gene expression analysis was used to identify genes that showed significant differences between the two groups. Uniformity and clustering were assessed through heatmaps and principal component analysis. Protein-protein interactions were investigated using the STRING database and Cytoscape. In addition, machine learning algorithms were employed to identify key genes involved in the interatomic interactions by analyzing transcriptomics data generated from the differential gene expression analysis. Results The accuracy and class accuracy of the extra tree classifier showed 98% and 97% in predicting interactomic hub genes, and HSPB1 was identified as a hub gene using Cytohubba from Cytoscape. Conclusion The predictive extra tree classifier, with its high accuracy in analysing interactomic hub genes in oral cancer, can potentially improve diagnosis and treatment strategies.
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Affiliation(s)
- Deepavalli Arumuganainar
- Department of Periodontics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, IND
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Hasanlu M, Amiri-Dashatan N, Farahani M, Koushki M, Ahmadi H, Parsamanesh N, Ahmadi NA. Comprehensive Analysis of the Expression, Prognosis, and Immune Infiltrates for Chromodomain-Helicase-DNA-Binding Proteins in Breast Tumor. Asian Pac J Cancer Prev 2024; 25:1547-1558. [PMID: 38809626 PMCID: PMC11318824 DOI: 10.31557/apjcp.2024.25.5.1547] [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: 09/01/2023] [Accepted: 05/04/2024] [Indexed: 05/31/2024] Open
Abstract
BACKGROUND Several recent studies suggest that chromodomain-helicase -DNA-binding domains (CHDs) are linked with cancers. We explored the association between chromodomain-Helicase-DNA-binding domain proteins and breast cancer (BrCa) and introduced potential prognostic markers using various databases. MATERIALS AND METHODS We analyzed the expression of the CHD family and their prognostic value in BrCa by mining UALCAN, TIMER, and Kaplan-Meier plotter databases. The association of CHD expression and immune infiltrating abundance was studied via the TIMER database. In addition, microRNAs related to the CHD family were identified by using the MirTarBase online database. RESULTS The present study indicated that compared to normal tissues, BrCa tissues showed increased mRNA levels of CHD3/4/7 but decreased CHD2/5/9 expression. Interestingly, We also found a positive correlation between CHD gene expression and the infiltration of macrophage, neutrophil, and dendritic cells in BrCa, except CHD3/5. The Kaplan-Meier Plotter analysis suggested that high expression levels of CHD1/2/3/4/6/8/9 were significantly related to shorter relapse-free survival (RFS), while higher mRNA expression of CHD1, CHD2, CHD8, and CHD9 was significantly associated with longer overall survival of BrCa patients. The miRNAs of hsa-miR-615-3p and hsa-let-7b-5p were identified as being more correlated with the CHD family. CONCLUSION The altered expression of some CHD members was significantly related to clinical cancer outcomes, and CHD1/2/8/9 could serve as potential prognostic biomarkers to improve the survival of BrCa patients. However, to evaluate the studied CHD members in detail are needed further investigations including experimental validation.
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Affiliation(s)
- Masoumeh Hasanlu
- Department of Internal Medicine, Vali-e-Asr Hospital, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Nasrin Amiri-Dashatan
- Zanjan Metabolic Diseases Research Center, Zanjan University of Medical Sciences, Zanjan, Iran.
| | - Masoumeh Farahani
- Skin Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mehdi Koushki
- Department of Clinical Biochemistry, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran.
| | - Hesameddin Ahmadi
- Laser Application in Medical Sciences Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
- Micro Nano System Laboratory (MNSL), Department of Mechanical Engineering, Sharif University of Technology, Tehran, Iran.
| | - Negin Parsamanesh
- Zanjan Metabolic Diseases Research Center, Zanjan University of Medical Sciences, Zanjan, Iran.
- Department of Genetics and Molecular Medicine, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran.
| | - Nayeb Ali Ahmadi
- Proteomics Research Center, Department of Medical Laboratory Sciences, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Ohmuro-Matsuyama Y, Gomi K, Shimoda T, Yamaji H, Ueda H. Improving the Stability of Protein-Protein Interaction Assay FlimPIA Using a Thermostabilized Firefly Luciferase. Front Bioeng Biotechnol 2021; 9:778120. [PMID: 34858964 PMCID: PMC8631863 DOI: 10.3389/fbioe.2021.778120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 10/27/2021] [Indexed: 11/13/2022] Open
Abstract
The protein–protein interaction assay is a key technology in various fields, being applicable in drug screening as well as in diagnosis and inspection, wherein the stability of assays is important. In a previous study, we developed a unique protein–protein interaction assay “FlimPIA” based on the functional complementation of mutant firefly luciferases (Fluc). The catalytic step of Fluc was divided into two half steps: D-luciferin was adenylated in the first step, while adenylated luciferin was oxidized in the second step. We constructed two mutants of Fluc from Photinus pyralis (Ppy); one mutant named Donor is defective in the second half reaction, while the other mutant named Acceptor exhibited low activity in the first half reaction. To date, Ppy has been used in the system; however, its thermostability is low. In this study, to improve the stability of the system, we applied Fluc from thermostabilized Luciola lateralis to FlimPIA. We screened suitable mutants as probes for FlimPIA and obtained Acceptor and Donor candidates. We detected the interaction of FKBP12-FRB with FlimPIA using these candidates. Furthermore, after the incubation of the probes at 37°C for 1 h, the luminescence signal of the new system was 2.4-fold higher than that of the previous system, showing significant improvement in the stability of the assay.
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Affiliation(s)
- Yuki Ohmuro-Matsuyama
- Laboratory of Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan.,Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan.,Technology Research Laboratory, Shimadzu Corporation, Kyoto, Japan
| | | | - Takuya Shimoda
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan
| | - Hideki Yamaji
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan
| | - Hiroshi Ueda
- Laboratory of Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
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Salarić I, Karmelić I, Lovrić J, Baždarić K, Rožman M, Čvrljević I, Zajc I, Brajdić D, Macan D. Salivary melatonin in oral squamous cell carcinoma patients. Sci Rep 2021; 11:13201. [PMID: 34168230 PMCID: PMC8225878 DOI: 10.1038/s41598-021-92649-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 06/09/2021] [Indexed: 12/12/2022] Open
Abstract
Melatonin's role in circadian rhythm is well documented, as are its' anti-oxidant, oncostatic and anti-inflammatory properties. Poor sleep quality has been associated as a potential risk factor for several malignancies, including head and neck cancers. The purpose of this study is to determine salivary melatonin (MLT) levels in oral squamous cell carcinoma (OSCC) patients, compare the salivary MLT levels with those in healthy individuals and compare the salivary and serum levels in OSCC patients. Furthermore, the aim is to investigate the potential relationship between sleep quality and salivary MLT levels in OSCC patients. Unstimulated (UWS) and stimulated (SWS) whole saliva was sampled from patients with T1N0M0 and T2N0M0 OSCC (N = 34) and 33 sex and age matched healthy subjects. Serum samples were taken from 11 OSCC patients. Sleep quality was measured using Pittsburgh Sleep Quality Index (PSQI) questionnaire. Melatonin levels in UWS and SWS were significantly higher in the OSCC group. Sleep quality was significantly lower in patients with OSCC (P = 0.0001). ROC analysis was found to be significant (P < 0.001) in evaluating MLT concentration limit in diagnosing OSCC. The expected relationship between sleep quality and salivary MLT levels in OSCC patients was not observed. Our results suggest salivary MLT as a potential biomarker that might facilitate non-invasive detection of early stage OSCC.
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Affiliation(s)
- Ivan Salarić
- Department of Oral Surgery, University of Zagreb School of Dental Medicine, Av. Gojka Šuška 6, 10000, Zagreb, Croatia
- Department of Maxillofacial and Oral Surgery, University Hospital Dubrava, Zagreb, Croatia
| | - Ivana Karmelić
- Department of Medical Chemistry, Biochemistry and Clinical Chemistry, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Jasna Lovrić
- Department of Medical Chemistry, Biochemistry and Clinical Chemistry, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Ksenija Baždarić
- Department of Medical Informatics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Marko Rožman
- Department of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Igor Čvrljević
- Department of Maxillofacial and Oral Surgery, University Hospital Dubrava, Zagreb, Croatia
| | - Ivan Zajc
- Department of Oral Surgery, University of Zagreb School of Dental Medicine, Av. Gojka Šuška 6, 10000, Zagreb, Croatia
- Department of Maxillofacial and Oral Surgery, University Hospital Dubrava, Zagreb, Croatia
| | - Davor Brajdić
- Department of Oral Surgery, University of Zagreb School of Dental Medicine, Av. Gojka Šuška 6, 10000, Zagreb, Croatia
- Department of Maxillofacial and Oral Surgery, University Hospital Dubrava, Zagreb, Croatia
| | - Darko Macan
- Department of Oral Surgery, University of Zagreb School of Dental Medicine, Av. Gojka Šuška 6, 10000, Zagreb, Croatia.
- Department of Maxillofacial and Oral Surgery, University Hospital Dubrava, Zagreb, Croatia.
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Keinänen A, Uittamo J, Marinescu-Gava M, Kainulainen S, Snäll J. Preoperative C-reactive protein to albumin ratio and oral health in oral squamous cell carcinoma patients. BMC Oral Health 2021; 21:132. [PMID: 33740951 PMCID: PMC7977568 DOI: 10.1186/s12903-021-01516-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 03/09/2021] [Indexed: 01/15/2023] Open
Abstract
Background The C-reactive protein to albumin (CRP/alb) ratio can predict early survival of a hospitalized patient. We evaluated factors that influence the preoperative CRP/alb ratio in oral squamous cell carcinoma (OSCC) patients and in particular clarified the role of oral health to this ratio. Materials and methods Data from surgically treated OSCC patients were collected retrospectively. The outcome variables were preoperative CRP/alb ratio, CRP level, and alb level. The studied predictors were total number of teeth, periodontal stability, marginal bone loss, tumour stage, T-class, lymph node status, and site. The statistical significance of age, sex, comorbidity combination of age and disease history (Charlson Comorbidity Index [CCI]), smoking, and alcohol history for outcome variables were evaluated. Patient 3-month mortality and occurrence of postoperative infections were recorded. Results A total of 159 patients were included in the study. The early mortality was 3.8%. CRP/alb was higher in these patients than in those who survived. The only independent variables for CRP/alb changes were CCI and heavy alcohol use. The CRP/alb ratio was significantly lower in non-heavy alcohol users (odds ratio [OR] 0.114, 95% confidence interval [CI] 0.024–0.541; adjusted p = 0.006) than in other patients. Patients with CCI 0–1 were more likely to have a lower CRP/alb ratio than patients with CCI ≥ 5 (OR 0.033, 95% CI 0.004–0.284; adjusted p = 0.002). In addition, high CRP/alb ratio associated with postoperative infections (p = 0.026). Conclusions The CRP/alb ratio was high in OSCC patients with combined comorbities of age and disease history and in patients with heavy alcohol use. Oral health or tumour-related variables did not independently affect the CRP/alb ratio. The CRP/alb ratio appears suitable for prediction of OSCC patient early survival.
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Affiliation(s)
- Arvi Keinänen
- Department of Oral and Maxillofacial Diseases, University of Helsinki and Helsinki University Hospital, P.O. Box 220, 00029, Helsinki, Finland.
| | - Johanna Uittamo
- Department of Oral and Maxillofacial Diseases, University of Helsinki and Helsinki University Hospital, P.O. Box 220, 00029, Helsinki, Finland
| | - Magdalena Marinescu-Gava
- Department of Oral and Maxillofacial Diseases, University of Helsinki and Helsinki University Hospital, P.O. Box 220, 00029, Helsinki, Finland.,HUS Radiology (Medical Imaging Center), Helsinki, Finland.,Finnish Student Health Service, Helsinki, Finland
| | - Satu Kainulainen
- Department of Oral and Maxillofacial Diseases, University of Helsinki and Helsinki University Hospital, P.O. Box 220, 00029, Helsinki, Finland
| | - Johanna Snäll
- Department of Oral and Maxillofacial Diseases, University of Helsinki and Helsinki University Hospital, P.O. Box 220, 00029, Helsinki, Finland
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Roi A, Roi CI, Negruțiu ML, Riviș M, Sinescu C, Rusu LC. The Challenges of OSCC Diagnosis: Salivary Cytokines as Potential Biomarkers. J Clin Med 2020; 9:jcm9092866. [PMID: 32899735 PMCID: PMC7565402 DOI: 10.3390/jcm9092866] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/17/2020] [Accepted: 09/01/2020] [Indexed: 01/17/2023] Open
Abstract
Fast, economic, and noninvasive, molecular analysis of saliva has the potential to become a diagnostic tool of reference for several local and systemic diseases, oral cancer included. The diagnosis of Oral Squamous Cell Carcinoma (OSCC) can be performed using high specificity and sensibility biomarkers that can be encountered in the biological fluids. Recent advances in salivary proteomics have underlined the potential use of salivary biomarkers as early diagnosis screening tools for oral neoplasia. In this respect, over 100 salivary molecules have been described and proposed as oral cancer biomarkers, out of which cytokines are among the most promising. Besides being directly involved in inflammation and immune response, the role of salivary cytokines in tumor growth and progression linked them to the incidence of oral malignant lesions. This review summarizes the existing studies based on the use of salivary cytokines as potential oral cancer biomarkers, their involvement in the malignant process based on their type, and ther influence upon prognostic and metastatic rates.
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Affiliation(s)
- Alexandra Roi
- Department of Oral Pathology, "Victor Babeș" University of Medicine and Pharmacy Timisoara, Romania, Eftimie Murgu Sq. no.2, 300041 Timisoara, Romania
| | - Ciprian Ioan Roi
- Department of Anaesthesiology and Oral Surgery, "Victor Babeș" University of Medicine and Pharmacy Timisoara, Romania, Eftimie Murgu Sq. no.2, 300041 Timisoara, Romania
| | - Meda Lavinia Negruțiu
- Department of Propedeutics, "Victor Babeș" University of Medicine and Pharmacy Timisoara, Romania, Eftimie Murgu Sq. no.2, 300041 Timisoara, Romania
| | - Mircea Riviș
- Department of Anaesthesiology and Oral Surgery, "Victor Babeș" University of Medicine and Pharmacy Timisoara, Romania, Eftimie Murgu Sq. no.2, 300041 Timisoara, Romania
| | - Cosmin Sinescu
- Department of Propedeutics, "Victor Babeș" University of Medicine and Pharmacy Timisoara, Romania, Eftimie Murgu Sq. no.2, 300041 Timisoara, Romania
| | - Laura-Cristina Rusu
- Department of Oral Pathology, "Victor Babeș" University of Medicine and Pharmacy Timisoara, Romania, Eftimie Murgu Sq. no.2, 300041 Timisoara, Romania
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Amiri-Dashatan N, Koushki M, Jalilian A, Ahmadi NA, Rezaei-Tavirani M. Integrated Bioinformatics Analysis of mRNAs and miRNAs Identified Potential Biomarkers of Oral Squamous Cell Carcinoma. Asian Pac J Cancer Prev 2020; 21:1841-1848. [PMID: 32597160 PMCID: PMC7568896 DOI: 10.31557/apjcp.2020.21.6.1841] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 06/28/2020] [Indexed: 12/21/2022] Open
Abstract
Background: Oral cancer is a frequently encountered neoplasm of the head and neck region, being the eighth most common type of human malignancy worldwide. Despite improvement in its control, morbidity and mortality, rates have improved little in the past decades. The present investigations about gene interaction and pathways still could not clear the appearance and development of oral squamous cell carcinoma (OSCC), completely. The aim of this study is to investigate the key genes and microRNAs interaction in OSCC. Materials and Methods: The microarray datasets GSE13601 and GSE98463, including mRNA and miRNA profiles, were extracted from the GEO database and were analyzed using GEO2R. Functional and pathway enrichment analyses were performed by using the DAVID database. The protein-protein interaction (PPI) network was constructed and analyzed using STRING database and Cytoscape software, respectively. Finally, miRDB was applied to predict the targets of the differentially expressed miRNAs (DEMs). Results: Totally, 97 differentially expressed genes (DEGs) were found in OSCC, including 66 up-regulated and 31 down-regulated genes. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses showed that up-regulated genes were significantly enriched in movement of cell or subcellular component, cell adhesion, biological adhesion, cellular localization, apoptotic signaling pathway, while the downregulated genes were enriched in muscle system process and oxidation-reduction process. From the PPI network, the top 10 nodes with the highest degree were detected as hub genes. In addition, 18 DEMs were screened, which included 7 up-regulated and 11 down-regulated miRNAs. STAT1 was potentially targeted by three miRNAs, including has-miR- 6825-5P, has-miR-4495, and has-miR-5580-3P. Conclusion: The roles of DEMs such as hsa-mir-5580-3p in OSCC through interactions with DEGs CD44, ACLY, ACTR3, STAT1, LAMC2 and YWHAZ may offer a suitable candidate biomarker pattern for diagnosis, prognosis and treatment processes in OSCC.
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Affiliation(s)
- Nasrin Amiri-Dashatan
- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mehdi Koushki
- Department of Clinical Biochemistry, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
| | - Ali Jalilian
- Department of Clinical Biochemistry, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
| | - Nayeb Ali Ahmadi
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran.
| | - Mostafa Rezaei-Tavirani
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran.
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Zamanian Azodi M, Rezaei Tavirani M, Rezaei Tavirani M. Identification of the Key Genes of Autism Spectrum Disorder Through Protein-Protein Interaction Network. Galen Med J 2019; 8:e1367. [PMID: 34466502 PMCID: PMC8343959 DOI: 10.31661/gmj.v0i0.1367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 10/09/2018] [Accepted: 11/17/2018] [Indexed: 12/01/2022] Open
Abstract
Background: Currently, the prevalence of autism spectrum disorder (ASD) is increasing, which widely spurs the interest in the molecular investigation. Thereby, a better understanding of the given disorder mechanisms is likely to be achieved. Bioinformatics suiting protein-protein interactions analysis via the application of high-throughput studies, such as protein array, is one of these achievements. Materials and Methods: The gene expression data from Gene Expression Omnibus (GEO) database were downloaded, and the expression profile of patients with developmental delay and autistic features were analyzed via Cytoscape and its relevant plug-ins. Results: Our findings indicated that EGFR, ACTB, RHOA, CALM1, MAPK1, and JUN genes as the hub-bottlenecks and their related terms could be important in ASD risk. In other words, any expression modification in these genes could trigger dysfunctions in the corresponding biological processes. Conclusion: We suggest that differentially expressed genes could be used as suitable targets for ASD after being validated.
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Affiliation(s)
- Mona Zamanian Azodi
- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mostafa Rezaei Tavirani
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Majid Rezaei Tavirani
- Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Correspondence to: Majid Rezaei Tavirani, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran Telephon Number: 09183420279 Email Address:
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