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Article ; Online: Investigating the causal relationship between human blood/urine metabolites and periodontal disease using two-sample Mendelian randomization.

Yin, Xinhai / Wu, Yadong / Song, Jukun

Health science reports

2024 Volume 7, Issue 3, Page(s) e1895

Abstract: Background and aims: The aim is to investigate the cause-and-effect connection between metabolites found in blood/urine and the likelihood of developing periodontal disease (PD) through the utilization of a two-sample Mendelian randomization (MR) method. ...

Abstract	Background and aims: The aim is to investigate the cause-and-effect connection between metabolites found in blood/urine and the likelihood of developing periodontal disease (PD) through the utilization of a two-sample Mendelian randomization (MR) method. Methods: Using an inverse variance weighted (IVW) method and two additional two-sample MR models, we examined the relationship between blood/urine metabolites and PD by analyzing data from a comprehensive metabolome-based genome-wide association study and the Genome-Wide Association Studies (GWAS) of PD. To assess the consistency and dependability of the findings, diversity, cross-effects, and sensitivity analyses were conducted. Results: Out of the 35 metabolites found in blood and urine, a total of eight metabolites (C-reactive protein, Potassium in urine, Urea, Cystatin C, Non-albumin protein, Creatinine, estimated Glomerular Filtration Rate, and Phosphate) displayed a possible causal connection with the risk of dental caries/PD using the inverse variance weighted (IVW) method ( Conclusion: Based on the available evidence, it is not possible to establish a significant causal link between the 35 blood metabolites and the likelihood of developing dental caries and PD.
Language	English
Publishing date	2024-03-10
Publishing country	United States
Document type	Journal Article
ISSN	2398-8835
ISSN (online)	2398-8835
DOI	10.1002/hsr2.1895
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Article ; Online: Relationship between periodontitis and COVID-19: A bidirectional two-sample Mendelian randomization study.

Song, Jukun / Wu, Yadong / Yin, Xinhai / Zhang, Junmei

Health science reports

2023 Volume 6, Issue 8, Page(s) e1413

Abstract: Background and aims: Coronavirus disease (COVID-19) is a major danger to world health and has been linked to periodontitis in a number of epidemiological observational studies. However, it is unclear whether COVID-19 causes periodontitis. COVID-19's ... ...

Abstract	Background and aims: Coronavirus disease (COVID-19) is a major danger to world health and has been linked to periodontitis in a number of epidemiological observational studies. However, it is unclear whether COVID-19 causes periodontitis. COVID-19's causal influence on periodontitis was determined using bidirectional Mendelian randomization (MR). Methods: Large-scale COVID-19 and periodontitis genome wide association study data were analyzed. Inverse variance weighting, MR-Egger, weighted median, and MR-PRESSO were used to estimate causal effects. Sensitivity studies were conducted using the Cochran's Q test, the MR-Egger intercept test, the MR-PRESSO, and the leave-one-out (LOO) analysis. Further investigation of potential mediating factors was performed using risk factor analysis. Results: The MR presented no causal relationship between periodontitis and hospitalization for COVID-19 (odds ratio [OR] = 0.97, 95% confidence interval [CI] 0.78-1.20; Conclusion: Periodontitis had no link to the risk of COVID-19 hospitalization, susceptibility, or severity. However, the substance in COVID-19 that is responsible for this effect must be studied further.
Language	English
Publishing date	2023-08-08
Publishing country	United States
Document type	Journal Article
ISSN	2398-8835
ISSN (online)	2398-8835
DOI	10.1002/hsr2.1413
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Article ; Online: Integrated analysis of NET-DNA receptor CCDC25 in malignant tumors: Pan-cancer analysis.

Cheng, Xianlin / Yin, Xinhai / Song, Jukun

Health science reports

2023 Volume 6, Issue 10, Page(s) e1621

Abstract: Background: Previously, it was reported that the coiled-coil domain containing 25 (CCDC25) plays a role in the formation of neutrophil extracellular traps (NETs). This study systematically analyzed the expression profiles of CCDC25 in 30 different types ...

Abstract	Background: Previously, it was reported that the coiled-coil domain containing 25 (CCDC25) plays a role in the formation of neutrophil extracellular traps (NETs). This study systematically analyzed the expression profiles of CCDC25 in 30 different types of cancer and one type of blood cancer, acute myeloid leukemia. Methods: The GTEx and CCLE databases were used to evaluate the distribution of CCDC25 expression in both normal tissue and cancer cell lines. A comparison was performed between normal tissue and tumor tissue to analyze the differential expression of CCDC25. We assessed the impact of CCDC25 on the clinical outlook in the TCGA pan-cancer data set by analyzing the Kaplan-Meier survival plot and conducting COX regression analysis. Moreover, the association between the expression levels of CCDC25 and the tumor microenvironment in multiple cancers was conducted. Additionally, the investigation also examined the link between CCDC25 and immune neoantigen, tumor mutational burden, microsatellite instability, mismatch repair genes (MMRs), HLA-related genes, and DNA methyltransferase (DNMT). Results: CCDC25 was expressed in nearly all of the 31 normal tissues while exhibiting a moderate to low level of expression in cancer cell lines. While abnormal expression was detected in the majority of malignancies, there was no link found between elevated CCDC25 levels and overall survival, disease-free survival, recurrence-free survival, and disease-free interval in the TCGA comprehensive cancer data set. Nevertheless, the expression of CCDC25 exhibited a notable link with the infiltration levels of activated CD4 memory T cells, quiescent mast cells, dendritic cells in an activated state, T cells that assist in follicle development, M2 macrophages, and neutrophils in various tumors. Conclusions: In most cancers, the results indicate that there is no link between CCDC25 and prognosis. However, CCDC25 can be targeted for therapeutic purposes concerning metastasis and immune infiltration.
Language	English
Publishing date	2023-10-12
Publishing country	United States
Document type	Journal Article
ISSN	2398-8835
ISSN (online)	2398-8835
DOI	10.1002/hsr2.1621
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Article ; Online: Mendelian Randomisation Study on Association of Gut Microbiota and Periodontitis.

Song, Jukun / Wu, Yadong / Yin, Xinhai / Ma, Hong / Zhang, Junmei

International dental journal

2023 Volume 73, Issue 6, Page(s) 847–853

Abstract: Objective: Several studies have demonstrated the possible association between gut microbiota and periodontitis. The mechanism by which gut microbiota contribute to periodontitis remains unknown.: Methods: A 2-sample Mendelian randomisation (MR) study ...

Abstract	Objective: Several studies have demonstrated the possible association between gut microbiota and periodontitis. The mechanism by which gut microbiota contribute to periodontitis remains unknown. Methods: A 2-sample Mendelian randomisation (MR) study was conducted using publicly available Genome-Wide Association Studies (GWAS) data of European ancestry. The relationships between gut microbiota and tooth loss and periodontitis were assessed using summary-level data. Moreover, inverse variance weighted (IVW), MR-Egger, weighted median, and simple Mendelian were used. The results were further validated using sensitivity analyses. Results: A total of 211 gut microbiota were studied, including 9 phyla, 16 classes, 20 orders, 35 families, and 131 genera. The IVW method identified 16 bacterial genera related to the risk of periodontitis and tooth loss. Lactobacillaceae was associated with an increased risk of periodontitis (odds ratio [OR], 1.40, 95% confidence interval [CI], 1.03-1.91, P<.001) and tooth loss (OR, 1.12; 95% CIs, 1.02-1.24, P = .002), whereas Lachnospiraceae UCG008 was linked to a lower risk of tooth loss (P = .041). There was no heterogeneity and horizontal pleiotropy in the sensitivity analysis. Conclusions: Several microorganisms were identified to be linked to the risk of periodontitis. Furthermore, the findings improved our understanding of gut microbiota and periodontitis pathology.
MeSH term(s)	Humans ; Gastrointestinal Microbiome ; Genome-Wide Association Study ; Odds Ratio ; Periodontitis/complications ; Periodontitis/genetics ; Tooth Loss ; Mendelian Randomization Analysis
Language	English
Publishing date	2023-06-12
Publishing country	England
Document type	Journal Article
ZDB-ID	218262-2
ISSN	1875-595X ; 0020-6539
ISSN (online)	1875-595X
ISSN	0020-6539
DOI	10.1016/j.identj.2023.05.002
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Article ; Online: The causal links between gut microbiota and COVID-19: A Mendelian randomization study.

Song, Jukun / Wu, Yadong / Yin, Xinhai / Ma, Hong / Zhang, Junmei

Journal of medical virology

2023 Volume 95, Issue 5, Page(s) e28784

Abstract: Several studies have shown a possible correlation between gut microbiota and COVID-19. However, the cause-and-effect relationship between the two has not been investigated. We conducted a two-sample Mendelian randomization study (MR) study using publicly ...

Abstract	Several studies have shown a possible correlation between gut microbiota and COVID-19. However, the cause-and-effect relationship between the two has not been investigated. We conducted a two-sample Mendelian randomization study (MR) study using publicly available GWAS data. Inverse variance weighted (IVW) analysis was the main MR analysis technique and was supplemented with other sensitivity analyses. Forty-two bacterial genera were associated with COVID-19 susceptibility, hospitalization, and severity in the IVW method. Among these gut microbiota, five gut microbiota (genus unknowngenus [id.1000005472], family unknownfamily [id.1000005471], genus Tyzzerella3, order MollicutesRF9.id.11579, and phylum Actinobacteria) were significantly associated with COVID-19 hospitalization and severity. Three gut microbiota (class Negativicutes, order Selenomonadales, and class Actinobacteria) were significantly associated with COVID-19 hospitalization and susceptibility, while two microbiota (class Negativicutes and order Selenomonadales) were significantly associated with COVID-19 hospitalization and severity, and susceptibility. Sensitivity analysis did not detect any heterogeneity and horizontal pleiotropy. Our findings demonstrated that several microorganisms were causally linked to COVID-19, and improved our understanding of the relationship between gut microbiota and COVID-19 pathology.
MeSH term(s)	Humans ; Gastrointestinal Microbiome/genetics ; Mendelian Randomization Analysis ; COVID-19 ; Microbiota ; Dietary Supplements ; Genome-Wide Association Study ; Polymorphism, Single Nucleotide
Language	English
Publishing date	2023-05-22
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	752392-0
ISSN	1096-9071 ; 0146-6615
ISSN (online)	1096-9071
ISSN	0146-6615
DOI	10.1002/jmv.28784
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Zs.A 1320: Show issues

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Article ; Online: Overexpression of YTHDC2 contributes to the progression of prostate cancer and predicts poor outcomes in patients with prostate cancer.

Song, Jukun / You, Ganhua / Yin, Xinhai / Zhu, Guohua / Wang, Wei / Yu, Yongwei / Zhu, Jianguo

Journal of biochemical and molecular toxicology

2023 Volume 37, Issue 4, Page(s) e23308

Abstract: YTH domain-containing protein 2 (YTHDC2), a member of N6-methyladenosine (m6A) readers, has been reported to be closely associated with multiple cancer types. However, very little is known about the YTHDC2 gene and its involvement in prostate cancer. ... ...

Abstract	YTH domain-containing protein 2 (YTHDC2), a member of N6-methyladenosine (m6A) readers, has been reported to be closely associated with multiple cancer types. However, very little is known about the YTHDC2 gene and its involvement in prostate cancer. YTHDC2 protein expression level was analyzed and correlated to clinical outcomes in prostate cancer patients who underwent prostatectomy in Guizhou Provincial People's Hospital. The YTHDC2 expression level was also detected in prostate cancer cell lines and an immortalized prostate epithelial cell line BPH-1 and RWPE1 by quantitative real-time reverse transcription polymerase chain reaction. Furthermore, we established stable cell lines (DU145 and PC-3) transfected with either empty vector or the full-length YTHDC2 gene and conducted cell function assays in vitro. Fisher's exact test and Pearson χ
MeSH term(s)	Male ; Humans ; Prostatic Hyperplasia/metabolism ; Cell Line, Tumor ; Prostatic Neoplasms/metabolism ; Prostate/metabolism ; Prostate/surgery ; Prostatectomy/methods ; RNA Helicases/metabolism
Chemical Substances	YTHDC2 protein, human (EC 3.6.4.13) ; RNA Helicases (EC 3.6.4.13)
Language	English
Publishing date	2023-01-16
Publishing country	United States
Document type	Journal Article
ZDB-ID	1410020-4
ISSN	1099-0461 ; 1095-6670
ISSN (online)	1099-0461
ISSN	1095-6670
DOI	10.1002/jbt.23308
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Zs.A 2201: Show issues

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Article ; Online: Systematic analysis of the function and prognostic value of RNA binding protein in head and neck squamous cell carcinoma.

Duan, Xiaofeng / Cheng, Xianlin / Yin, Xinhai / Ke, Zhao / Song, Jukun

European archives of oto-rhino-laryngology : official journal of the European Federation of Oto-Rhino-Laryngological Societies (EUFOS) : affiliated with the German Society for Oto-Rhino-Laryngology - Head and Neck Surgery

2021 Volume 279, Issue 3, Page(s) 1535–1547

Abstract: Objective: Dysregulation of RNA binding proteins (RBPs) plays an important role in controlling processes in cancer development. However, the function of RBPs has not been thoroughly and systematically documented in head and neck cancer. We aim to ... ...

Abstract	Objective: Dysregulation of RNA binding proteins (RBPs) plays an important role in controlling processes in cancer development. However, the function of RBPs has not been thoroughly and systematically documented in head and neck cancer. We aim to explore the role of RPB in the pathogenesis of HNSC. Methods: We obtained HNSC gene expression data and corresponding clinical information from The Cancer Genome Atlas (TCGA) and the GEO databases, and identified aberrantly expressed RBPs between tumors and normal tissues. Meanwhile, we performed a series of bioinformatics to explore the function and prognostic value of these RBPs. Results: A total of 249 abnormally expressed RBPs were identified, including 101 downregulated RBPs and 148 upregulated RBPs. Using least absolute shrinkage and selection operator (LASSO) and univariate Cox regression analysis, the 15 RPBs were identified as hub genes. With the 15 RPBS, the prognostic prediction model was constructed. Further analysis showed that the high-risk score of the patients expressed a better survival outcome. The prediction model was validated in another HNSC dataset, and similar findings were observed. Conclusions: Our results provide novel insights into the pathogenesis of HNSC. The fifteen RBP gene signature exhibited the predictive value of moderate HNSC prognosis, and have potential application value in clinical decision-making and individualized treatment.
MeSH term(s)	Gene Expression Regulation, Neoplastic ; Head and Neck Neoplasms/genetics ; Humans ; Prognosis ; RNA-Binding Proteins/genetics ; Squamous Cell Carcinoma of Head and Neck/genetics
Chemical Substances	RNA-Binding Proteins
Language	English
Publishing date	2021-07-04
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1017359-6
ISSN	1434-4726 ; 0937-4477
ISSN (online)	1434-4726
ISSN	0937-4477
DOI	10.1007/s00405-021-06929-9
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Article ; Online: Effects of CPAP on the transcriptional signatures in patients with obstructive sleep apnea via coexpression network analysis.

Peng, Juxiang / Song, Jukun / Zhou, Jing / Yin, Xinhai / Song, Jinlin

Journal of cellular biochemistry

2019 Volume 120, Issue 6, Page(s) 9277–9290

Abstract: A growing number of studies provide epidemiological evidence linking obstructive sleep apnea (OSA) with a number of chronic disorders. Transcriptional analyses have been conducted to analyze the gene expression data. However, the weighted gene ... ...

Abstract	A growing number of studies provide epidemiological evidence linking obstructive sleep apnea (OSA) with a number of chronic disorders. Transcriptional analyses have been conducted to analyze the gene expression data. However, the weighted gene coexpression network analysis (WGCNA) method has not been applied to determine the transcriptional consequence of continuous positive airway pressure (CPAP) therapy in patients with severe OSA. The aim of this study was to identify key pathways and genes in patients with OSA that are influenced by CPAP treatment and uncover/unveil potential molecular mechanisms using WGCNA. We analyzed the microarray data of OSA (GSE 49800) listed in the Gene Expression Omnibus database. Coexpression modules were constructed using WGCNA. In addition, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis were also conducted. After the initial data processing, 5101 expressed gene profiles were identified. Next, a weighted gene coexpression network was established and 16 modules of coexpressed genes were identified. The interaction analysis demonstrated a relative independence of gene expression in these modules. The black module, tan module, midnightblue module, pink module, and greenyellow module were significantly associated with the alterations in circulating leukocyte gene expression at baseline and after exposure to CPAP. The five hub genes were considered to be candidate OSA-related genes after CPAP treatment. Functional enrichment analysis revealed that steroid biosynthesis, amino sugar and nucleotide sugar metabolism, protein processing in the endoplasmic reticulum, and the insulin signaling pathway play critical roles in the development of OSA in circulating leukocyte gene expression at baseline and after exposure to CPAP. Using this new systems biology approach, we identified several genes and pathways that appear to be critical to OSA after CPAP treatment, and these findings provide a better understanding of OSA pathogenesis.
MeSH term(s)	Continuous Positive Airway Pressure/methods ; Female ; Gene Expression Regulation/genetics ; Gene Ontology ; Gene Regulatory Networks/genetics ; Humans ; Leukocytes/metabolism ; Leukocytes/pathology ; Male ; Middle Aged ; Sleep Apnea, Obstructive/genetics ; Sleep Apnea, Obstructive/pathology ; Sleep Apnea, Obstructive/therapy
Language	English
Publishing date	2019-02-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	392402-6
ISSN	1097-4644 ; 0730-2312
ISSN (online)	1097-4644
ISSN	0730-2312
DOI	10.1002/jcb.28203
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Zs.A 1114: Show issues

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Article ; Online: miRNA-Based Feature Classifier Is Associated with Tumor Mutational Burden in Head and Neck Squamous Cell Carcinoma.

Xia, Yu / Wang, Qi / Huang, Xiaolin / Yin, Xinhai / Song, Jukun / Ke, Zhao / Duan, Xiaofeng

BioMed research international

2020 Volume 2020, Page(s) 1686480

Abstract: Tumor mutation burden (TMB) is considered to be an independent genetic biomarker that can predict the tumor patient's response to immune checkpoint inhibitors (ICIs). Meanwhile, microRNA (miRNA) plays a key role in regulating the anticancer immune ... ...

Abstract	Tumor mutation burden (TMB) is considered to be an independent genetic biomarker that can predict the tumor patient's response to immune checkpoint inhibitors (ICIs). Meanwhile, microRNA (miRNA) plays a key role in regulating the anticancer immune response. However, the correlation between miRNA expression patterns and TMB is not elucidated in HNSCC. In the HNSCC cohort of the TCGA dataset, miRNAs that were differentially expressed in high TMB and low TMB samples were screened. The least absolute contraction and selection operator (LASSO) method is used to construct a miRNA-based feature classifier to predict the TMB level in the training set. The test set is used to verify the classifier. The correlation between the miRNA-based classifier index and the expression of three immune checkpoints (PD1, PDL1, and CTLA4) was explored. We further perform functional enrichment analysis on the miRNA contained in the miRNA-based feature classifier. Twenty-five differentially expressed miRNAs are used to build miRNA-based feature classifiers to predict TMB levels. The accuracy of the 25-miRNA-based signature classifier is 0.822 in the training set, 0.702 in the test set, and 0.774 in the total set. The miRNA-based feature classifier index showed a low correlation with PD1 and PDL1, but no correlation with CTLA4. The enrichment analysis of these 25 miRNAs shows that they are involved in many immune-related biological processes and cancer-related pathways. The miRNA expression patterns are related to tumor mutation burden, and miRNA-based feature classifiers can be used as biomarkers to predict TMB levels in HNSCC.
MeSH term(s)	Aged ; Biomarkers, Tumor/genetics ; Biomarkers, Tumor/immunology ; Female ; Head and Neck Neoplasms/genetics ; Head and Neck Neoplasms/metabolism ; Head and Neck Neoplasms/therapy ; Humans ; Immunotherapy ; Machine Learning ; Male ; MicroRNAs/analysis ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Middle Aged ; Mutation/genetics ; Regression Analysis ; Squamous Cell Carcinoma of Head and Neck/genetics ; Squamous Cell Carcinoma of Head and Neck/metabolism ; Squamous Cell Carcinoma of Head and Neck/therapy
Chemical Substances	Biomarkers, Tumor ; MicroRNAs
Language	English
Publishing date	2020-12-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	2698540-8
ISSN	2314-6141 ; 2314-6133
ISSN (online)	2314-6141
ISSN	2314-6133
DOI	10.1155/2020/1686480
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Article ; Online: The relationship between tooth loss and mortality from all causes, cardiovascular diseases, and coronary heart disease in the general population: systematic review and dose-response meta-analysis of prospective cohort studies.

Peng, Juxiang / Song, Jukun / Han, Jing / Chen, Zhu / Yin, Xinhai / Zhu, Jianguo / Song, Jinlin

Bioscience reports

2019 Volume 39, Issue 1

Abstract: Background: ...

Abstract	Background:
MeSH term(s)	Alcohol Drinking/physiopathology ; Cardiovascular Diseases/complications ; Cardiovascular Diseases/mortality ; Cardiovascular Diseases/pathology ; Female ; Humans ; Male ; Marital Status/statistics & numerical data ; Prospective Studies ; Regression Analysis ; Risk Factors ; Smoking/physiopathology ; Social Class ; Survival Analysis ; Tooth Loss/complications ; Tooth Loss/mortality ; Tooth Loss/pathology
Language	English
Publishing date	2019-01-11
Publishing country	England
Document type	Journal Article ; Meta-Analysis ; Research Support, Non-U.S. Gov't ; Systematic Review
ZDB-ID	764946-0
ISSN	1573-4935 ; 0144-8463
ISSN (online)	1573-4935
ISSN	0144-8463
DOI	10.1042/BSR20181773
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