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Article ; Online: Integrated analysis of NET‐DNA receptor CCDC25 in malignant tumors

Xianlin Cheng / Xinhai Yin / Jukun Song

Health Science Reports, Vol 6, Iss 10, Pp n/a-n/a (2023)

Pan‐cancer analysis

2023

Abstract: 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 ... ...

Abstract	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.
Keywords	immune neoantigen ; microsatellite instability ; NET‐DNA receptor ; TMB ; Medicine ; R
Subject code	616 ; 610
Language	English
Publishing date	2023-10-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Pyroptosis‐related gene signatures are associated with prognosis and tumor microenvironment infiltration in head and neck cancer

Yan Long / Yadong Wu / Juxiang Peng / Jukun Song / Na Li

Health Science Reports, Vol 6, Iss 10, Pp n/a-n/a (2023)

2023

Abstract: Abstract Background and Aims Recent studies have highlighted the biological significance of pyroptosis in cancer development. Nevertheless, it is still uncertain if pyroptosis also plays a part in immune modulation and the creation of the tumor ... ...

Abstract	Abstract Background and Aims Recent studies have highlighted the biological significance of pyroptosis in cancer development. Nevertheless, it is still uncertain if pyroptosis also plays a part in immune modulation and the creation of the tumor microenvironment (TME). Methods The pyroptosis regulatory genes (PRGs) were comprehensively assessed in 1938 head and neck cancer samples, and systematically correlated these modification patterns with the infiltration characteristics of TME cells. The unsupervised consensus analysis method was used to identify specific pyroptosis clusters. The single‐sample gene set enrichment analysis and CIBERSOFT algorithms were used to evaluate the infiltration levels of various immune cell subsets. A principal component analysis algorithm was used to construct the pyrolysis potential index (PPI) to quantify the pyrolysis regulation patterns in head and neck squamous cell carcinoma (HNSC). Results Pyrophosphate regulatory genes (PRGs) are often upregulated in tumors due to mutations. PRGs relate to various clinical outcomes and pathways. Molecular subtyping identified pyroptosis patterns, which align with three tumor immunophenotypes: immune‐inflamed, immune‐excluded, and immune‐desert. The PPI measures pyrolysis roles, showing higher PPI in tumor samples linked to subtypes and clinical characteristics. Lower PPI correlates with longer survival, increased immune activity, more tumor mutations, high PD‐L1 expression, and mutations in significant genes like PIK3CA. Such patients also experience enhanced immune responses in immunotherapy trials. Conclusion We conducted a comprehensive examination of pyroptosis in HNSC and developed a PPI indicator that shows a strong correlation with the variety and intricacy of the TME.
Keywords	head and neck squamous cell carcinoma ; immunotherapy ; mutation burden ; pyroptosis ; tumor microenvironment ; Medicine ; R
Subject code	616
Language	English
Publishing date	2023-10-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Integrating GWAS and proteome data to identify novel drug targets for MU

Yadong Wu / Jukun Song / Manyi Liu / Hong Ma / Junmei Zhang

Scientific Reports, Vol 13, Iss 1, Pp 1-

2023 Volume 8

Abstract: Abstract Mouth ulcers have been associated with numerous loci in genome wide association studies (GWAS). Nonetheless, it remains unclear what mechanisms are involved in the pathogenesis of mouth ulcers at these loci, as well as what the most effective ... ...

Abstract	Abstract Mouth ulcers have been associated with numerous loci in genome wide association studies (GWAS). Nonetheless, it remains unclear what mechanisms are involved in the pathogenesis of mouth ulcers at these loci, as well as what the most effective ulcer drugs are. Thus, we aimed to screen hub genes responsible for mouth ulcer pathogenesis. We conducted an imputed/in-silico proteome-wide association study to discover candidate genes that impact the development of mouth ulcers and affect the expression and concentration of associated proteins in the bloodstream. The integrative analysis revealed that 35 genes play a significant role in the development of mouth ulcers, both in terms of their protein and transcriptional levels. Following this analysis, the researchers identified 6 key genes, namely BTN3A3, IL12B, BPI, FAM213A, PLXNB2, and IL22RA2, which were related to the onset of mouth ulcers. By combining with multidimensional data, six genes were found to correlate with mouth ulcer pathogenesis, which can be useful for further biological and therapeutic research.
Keywords	Medicine ; R ; Science ; Q
Subject code	572
Language	English
Publishing date	2023-06-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The peripheral immune cell counts and mouth ulcers

Yajing Wang / Yuanyuan Hu / Mengxuan Shen / Yang Cai / Zhiyuan Li / Changyue Xue / Xu Tan / Jukun Song

Heliyon, Vol 10, Iss 1, Pp e23430- (2024)

A two-sample Mendelian randomization study

1481

Abstract: Objective: This study explored the causal association of peripheral immune cell counts with mouth ulcers (MUs) by two-sample Mendelian Randomization. Design: The counts of 12 circulating immune cell types (leukocytes, lymphocytes, monocytes, eosinophils, ...

Abstract	Objective: This study explored the causal association of peripheral immune cell counts with mouth ulcers (MUs) by two-sample Mendelian Randomization. Design: The counts of 12 circulating immune cell types (leukocytes, lymphocytes, monocytes, eosinophils, neutrophils, basophils, CD4+ cells, CD8+ cells, unswitched memory B cells, NK cells, B cells and a derived ratio (CD4+/CD8+)) were determined as the exposure. MUs were the outcome. The analysis was conducted mostly using the inverse-variance weighted (IVW) approach. MR Egger, weighted median, weighted mode and simple mode were used to detect the horizontal pleiotropy. Results: The IVW results for leukocytes and lymphocyte counts were OR = 0.93, 95 % CI = 0.88–0.98, p = 0.0115 and OR = 0.91, 95 % CI: 0.84–0.98, p = 0.0150, respectively. The Wald ratio result for CD4+ cell and CD8+ cell counts were OR = 0.70, 95 % CI: 0.65–0.75, p = 1.05 × 10−20 and OR = 1.25, 95 % CI: 1.19–1.31, p = 9.99 × 10−21, respectively. Conclusions: This study supports a causal effect of peripheral immune cell counts on MUs. Higher leukocyte, lymphocyte and CD4+ cell counts can protect against MUs, but higher CD8+ cell counts enhance the risk of MUs. This finding confirms host immune factors play a crucial role in the aetiology of MUs.
Keywords	Peripheral immune cell counts ; Mouth ulcers ; Two-sample mendelian randomization (MR) ; Lymphocyte ; CD4+ cell ; CD8+ cell ; Science (General) ; Q1-390 ; Social sciences (General) ; H1-99
Subject code	570
Language	English
Publishing date	2024-01-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Understanding the consequences of leisure sedentary behavior on periodontitis

Zhonghua Zhang / Ming Ding / Hui Ding / Yuyan Qian / Jiaxing Hu / Jukun Song / Zhu Chen

Heliyon, Vol 9, Iss 12, Pp e23118- (2023)

A two-step, multivariate Mendelian randomization study

2023

Abstract: Background: The relationship between leisure sedentary behavior (LSB) and periodontitis risk remains unclear in terms of causality and the potential mediating effects of intermediate factors. Materials and methods: Using the aggregate data of several ... ...

Abstract	Background: The relationship between leisure sedentary behavior (LSB) and periodontitis risk remains unclear in terms of causality and the potential mediating effects of intermediate factors. Materials and methods: Using the aggregate data of several large-scale genetic association studies from participants of European descent, we conducted a univariate, two-step, and multivariate Mendelian random (MR) analysis to infer the overall effect of LSB on periodontitis, and quantified the intermediary proportion of intermediary traits such as smoking. Results: Our findings indicated that per 1-SD increase (1.87 h) in leisure screen time (LST), there was a 23 % increase in the risk of periodontitis. [odds ratios (95 % CI) = 1.23 (1.04–1.44), p = 0.013]. Smoking was found to partially mediate the overall causal effect of LST on periodontitis, with a mediation rate of 20.7 % (95 % CI: 4.9%–35.5 %). Multivariate MR analysis demonstrated that the causal effect of LST on periodontitis was weakened when adjusting for smoking, resulting in an odds ratio of 1.19 (95 % CI: 1.01–1.39, p = 0.049) for each 1 standard deviation increase in exposure. Conclusion: The study provides evidence of a potential causal relationship between LSB characterized by LST and periodontitis, thereby further supporting the notion that reducing LSB is beneficial for health. Furthermore, it confirms the role of smoking as a mediator in this process, suggesting that inhibiting smoking behavior among individuals with long-term LSB may serve as a strategy to mitigate the risk of periodontitis.
Keywords	Leisure sedentary behavior ; Mendelian randomization ; Periodontitis ; Smoking ; Intermediary analysis ; Science (General) ; Q1-390 ; Social sciences (General) ; H1-99
Subject code	150
Language	English
Publishing date	2023-12-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Combined Analysis of the Aberrant Epigenetic Alteration of Pancreatic Ductal Adenocarcinoma

Rui Xu / Qiuyan Xu / Guanglei Huang / Xinhai Yin / Jianguo Zhu / Yikun Peng / Jukun Song

BioMed Research International, Vol

2019 Volume 2019

Abstract: Background. Pancreatic ductal adenocarcinoma (PDAC) remains one of the most fatal malignancies due to its high morbidity and mortality. DNA methylation exerts a vital part in the development of PDAC. However, a mechanistic role of mutual interactions ... ...

Abstract	Background. Pancreatic ductal adenocarcinoma (PDAC) remains one of the most fatal malignancies due to its high morbidity and mortality. DNA methylation exerts a vital part in the development of PDAC. However, a mechanistic role of mutual interactions between DNA methylation and mRNA as epigenetic regulators on transcriptomic alterations and its correlation with clinical outcomes such as survival have remained largely uncovered in cancer. Therefore, elucidation of aberrant epigenetic alteration in the development of PDAC is an urgent problem to be solved. In this work, we conduct an integrative epigenetic analysis of PDAC to identify aberrant DNA methylation-driven cancer genes during the occurrence of cancer. Methods. DNA methylation matrix and mRNA profile were obtained from the TCGA database. The integration of methylation and gene expression datasets was analyzed using an R package MethylMix. The genes with hypomethylation/hypermethylation were further validated in the Kaplan–Meier analysis. The correlation analysis of gene expression and aberrant DNA methylation was also conducted. We performed a pathway analysis on aberrant DNG methylation genes identified by MethylMix criteria using ConsensusPathDB. Results. 188 patients with both methylation data and mRNA data were considered eligible. A mixture model was constructed, and differential methylation genes in normal and tumor groups using the Wilcoxon rank test was performed. With the inclusion criteria, 95 differential methylation genes were detected. Among these genes, 74 hypermethylation and 21 hypomethylation genes were found. The pathway analysis revealed an increase in hypermethylation of genes involved in ATP-sensitive potassium channels, Robo4, and VEGF signaling pathways crosstalk, and generic transcription pathway. Conclusion. Integrated analysis of the aberrant epigenetic alteration in pancreatic ductal adenocarcinoma indicated that differentially methylated genes could play a vital role in the occurrence of PDAC by bioinformatics analysis. The ...
Keywords	Medicine ; R
Subject code	570
Language	English
Publishing date	2019-01-01T00:00:00Z
Publisher	Hindawi Limited
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Audio / Video ; Online: Image_1_Systematic Analysis of Coronavirus Disease 2019 (COVID-19) Receptor ACE2 in Malignant Tumors

Jukun Song / Jing Han / Feng Liu / Xianlin Chen / Shenqi Qian / Yadong Wang / Zhenyu Jia / Xiaofeng Duan / Xiangyan Zhang / Jianguo Zhu

Pan-Cancer Analysis.tif

2020

Abstract: Background Coronavirus disease 2019 (COVID-19) was first detected in patients with pneumonia in December 2019 in China and it spread rapidly to the rest of the world becoming a global pandemic. Several observational studies have reported that cancer is a ...

Abstract	Background Coronavirus disease 2019 (COVID-19) was first detected in patients with pneumonia in December 2019 in China and it spread rapidly to the rest of the world becoming a global pandemic. Several observational studies have reported that cancer is a risk factor for COVID-19. On the other hand, ACE2, a receptor for the SARS-CoV-2 virus, was found to be aberrantly expressed in many tumors. However, the characterization of aberrant ACE2 expression in malignant tumors has not been elucidated. Here, we conducted a systematic analysis of the ACE2 expression profile across 31 types of tumors. Methods Distribution of ACE2 expression was analyzed using the GTEx, CCLE, TCGA pan-cancer databases. We evaluated the effect of ACE2 on clinical prognosis using the Kaplan-Meier survival plot and COX regression analysis. Correlation between ACE2 and immune infiltration levels was investigated in various cancer types. Additionally, the correlation between ACE2 and immune neoantigen, TMB, microsatellite instability, Mismatch Repair Genes (MMRs), HLA gene members, and DNA Methyltransferase (DNMT) was investigated. The frequency of ACE2 gene mutation in various tumors was analyzed. Functional enrichment analysis was conducted in various cancer types using the GSEA method. Results In normal tissues, ACE2 was highly expressed in almost all 31 organs tested. In cancer cell lines, the expression level of ACE2 was low to medium. Although aberrant expression was observed in most cancer types, high expression of ACE2 was not linked to OS, DFS, RFS, and DFI in most tumors in TCGA pan-cancer data. We found that ACE2 expression was significantly correlated with the infiltrating levels of macrophages and dendritic cells, CD4+ T cells, CD8+ T cells, and B cells in multiple tumors. A positive correlation between ACE2 expression and immune neoantigen, TMB, and microsatellite instability was found in multiple cancers. GSEA analysis which was carried out to determine the effect of ACE2 on tumors indicated that several cancer-associated pathways and immune-related pathways were hyperactivated in the high ACE2 expression group of most tumors. Conclusion These findings suggest that ACE2 is not correlated with prognosis in most cancer types. However, elevated ACE2 is significantly correlated with immune infiltrating levels, including those of CD8+ T cells, CD4+ T cells, macrophages, neutrophils, and DCs in multiple cancers, especially in lung and breast cancer patients. These findings suggest that ACE2 may affect the tumor environment in cancer patients with COVID-19.
Keywords	Biochemistry ; Molecular Biology ; Structural Biology ; Enzymes ; Protein Trafficking ; Proteomics and Intermolecular Interactions (excl. Medical Proteomics) ; Receptors and Membrane Biology ; Signal Transduction ; Structural Biology (incl. Macromolecular Modelling) ; Synthetic Biology ; COVID-19 ; ACE2 ; Pan-cancer analysis ; SARS-CoV-2 ; TCGA ; covid19
Publishing date	2020-10-23T07:34:30Z
Publishing country	uk
Document type	Audio / Video ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Systematic Analysis of Coronavirus Disease 2019 (COVID-19) Receptor ACE2 in Malignant Tumors

Jukun Song / Jing Han / Feng Liu / Xianlin Chen / Shenqi Qian / Yadong Wang / Zhenyu Jia / Xiaofeng Duan / Xiangyan Zhang / Jianguo Zhu

Frontiers in Molecular Biosciences, Vol

Pan-Cancer Analysis

2020 Volume 7

Abstract: BackgroundCoronavirus disease 2019 (COVID-19) was first detected in patients with pneumonia in December 2019 in China and it spread rapidly to the rest of the world becoming a global pandemic. Several observational studies have reported that cancer is a ... ...

Abstract	BackgroundCoronavirus disease 2019 (COVID-19) was first detected in patients with pneumonia in December 2019 in China and it spread rapidly to the rest of the world becoming a global pandemic. Several observational studies have reported that cancer is a risk factor for COVID-19. On the other hand, ACE2, a receptor for the SARS-CoV-2 virus, was found to be aberrantly expressed in many tumors. However, the characterization of aberrant ACE2 expression in malignant tumors has not been elucidated. Here, we conducted a systematic analysis of the ACE2 expression profile across 31 types of tumors.MethodsDistribution of ACE2 expression was analyzed using the GTEx, CCLE, TCGA pan-cancer databases. We evaluated the effect of ACE2 on clinical prognosis using the Kaplan-Meier survival plot and COX regression analysis. Correlation between ACE2 and immune infiltration levels was investigated in various cancer types. Additionally, the correlation between ACE2 and immune neoantigen, TMB, microsatellite instability, Mismatch Repair Genes (MMRs), HLA gene members, and DNA Methyltransferase (DNMT) was investigated. The frequency of ACE2 gene mutation in various tumors was analyzed. Functional enrichment analysis was conducted in various cancer types using the GSEA method.ResultsIn normal tissues, ACE2 was highly expressed in almost all 31 organs tested. In cancer cell lines, the expression level of ACE2 was low to medium. Although aberrant expression was observed in most cancer types, high expression of ACE2 was not linked to OS, DFS, RFS, and DFI in most tumors in TCGA pan-cancer data. We found that ACE2 expression was significantly correlated with the infiltrating levels of macrophages and dendritic cells, CD4+ T cells, CD8+ T cells, and B cells in multiple tumors. A positive correlation between ACE2 expression and immune neoantigen, TMB, and microsatellite instability was found in multiple cancers. GSEA analysis which was carried out to determine the effect of ACE2 on tumors indicated that several cancer-associated pathways and ...
Keywords	COVID-19 ; ACE2 ; Pan-cancer analysis ; SARS-CoV-2 ; TCGA ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2020-10-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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