scholarly journals The Association of Sex-biased ATRX Mutation in Female Gastric Cancer Patients With Enhanced Immunotherapy-related Anticancer Immunity  

2020 ◽  
Author(s):  
You Ge ◽  
Feiran Wei ◽  
Guoping Du ◽  
Gaoqiang Fei ◽  
Wei Li ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Enrichment Analysis ◽  
Genetic Alterations ◽  
Gene Set Enrichment Analysis ◽  
Gene Set Enrichment ◽  
Female Patients ◽  
Male Patients ◽  
Ifn Γ ◽  
Sex Biases ◽  
Anticancer Immunity

Abstract Background: Genetic alterations have been proven to be the promising biomarkers for ICI response. However, sex biases in genetic alterations have been often ignored in the field of immunotherapy, which might specially influence the anticancer immunity and immunotherapy efficacy in male or female patients. Here, we have systematically evaluated the effect of the sex biases in somatic mutation of gastric cancer (GC) patients on the anticancer immunity and clinical benefit to immunotherapy. Methods: Genomic and transcriptomic data of gastric cancer were downloaded from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC). We also obtained the genomic and clinical data of a MSKCC ICI-treated cohort from cbioportal database. GC male and female-derived tumor somatic mutation profiles were compared by maftools R package. Single sample gene set enrichment analysis (ssGSEA) was conducted to calculate the score of the anticancer immunity indicators including IFN-γ signaling, cytolytic activity (CYT) and antigen presenting machinery (APM). Results: ATRX was found to mutate more frequently in female GC patients compared to male patients (FDR = 0.0108). Female GC patients with ATRX mutation manifested significantly more MSI-high subtypes, increased TMB and PDL1 expression as well as higher scores of IFN-γ signaling, CYT and APM. Gene set enrichment analysis (GSEA) has shown that ATRX mutation might enhance the immunogenicity and anticancer immunity through affecting DNA damage repair pathways. In the ICI-treated cohort from MSKCC, GC patients with ATRX mutation were associated with prolonged overall survival. When stratifying the entire ICI-treated cohort by sex, female patients with ATRX mutation obtained significantly better survival benefits than that of ATRX mutant male patients (Female patients, HR of ATRX MT vs WT = 0.636, 95%CI = 0.455-0.890, P = 0.023; Male patients, HR of ATRX MT vs WT = 0.929, 95%CI = 0.596-1.362, P = 0.712). Conclusions: ATRX mutation might serve as a potential predictive biomarker for favorable clinical benefit to ICI in female GC patients. ATRX mutation could be applied in combination with other biomarkers of ICI response to better identify the female GC patients who will derive greater benefits from ICI therapy.

scholarly journals The association of sex-biased ATRX mutation in female gastric cancer patients with enhanced immunotherapy-related anticancer immunity

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
You Ge ◽  
Feiran Wei ◽  
Guoping Du ◽  
Gaoqiang Fei ◽  
Wei Li ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Enrichment Analysis ◽  
Genetic Alterations ◽  
Gene Set Enrichment Analysis ◽  
Gene Set Enrichment ◽  
Female Patients ◽  
Male Patients ◽  
Ifn Γ ◽  
Sex Biases ◽  
Anticancer Immunity

Abstract Background Genetic alterations have been proven to be the promising biomarkers for ICI response. However, sex biases in genetic alterations have been often ignored in the field of immunotherapy, which might specially influence the anticancer immunity and immunotherapy efficacy in male or female patients. Here, we have systematically evaluated the effect of the sex biases in somatic mutation of gastric cancer (GC) patients on the anticancer immunity and clinical benefit to immunotherapy. Methods Genomic and transcriptomic data of gastric cancer were downloaded from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC). We also obtained the genomic and clinical data of a MSKCC ICI-treated cohort from cbioportal database. GC male and female-derived tumor somatic mutation profiles were compared by maftools R package. Single sample gene set enrichment analysis (ssGSEA) was conducted to calculate the score of the anticancer immunity indicators including IFN-γ signaling, cytolytic activity (CYT) and antigen presenting machinery (APM). Results ATRX was found to mutate more frequently in female GC patients compared to male patients (FDR = 0.0108). Female GC patients with ATRX mutation manifested significantly more MSI-high subtypes, increased TMB and PDL1 expression as well as higher scores of IFN-γ signaling, CYT and APM. Gene set enrichment analysis (GSEA) has shown that ATRX mutation might enhance the immunogenicity and anticancer immunity through affecting DNA damage repair pathways. In the ICI-treated cohort from MSKCC, GC patients with ATRX mutation were associated with prolonged overall survival. When stratifying the entire ICI-treated cohort by sex, female patients with ATRX mutation obtained significantly better survival benefits than that of ATRX mutant male patients (Female patients, HR of ATRX MT vs WT = 0.636, 95%CI = 0.455–0.890, P = 0.023; Male patients, HR of ATRX MT vs WT = 0.929, 95%CI = 0.596–1.362, P = 0.712). Conclusions ATRX mutation might serve as a potential predictive biomarker for favorable clinical benefit to ICI in female GC patients. ATRX mutation could be applied in combination with other biomarkers of ICI response to better identify the female GC patients who will derive greater benefits from ICI therapy.

scholarly journals Infiltration of Immunoinflammatory Cells and Related Chemokine/Interleukin Expression in Different Gastric Immune Microenvironments

2020 ◽  
Vol 2020 ◽  
pp. 1-13
Author(s):  
Ang Wang ◽  
Siru Nie ◽  
Zhi Lv ◽  
Jing Wen ◽  
Yuan Yuan
Keyword(s):  
Gastric Cancer ◽  
Gastric Mucosa ◽  
Immune Cell ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Upward Trend ◽  
Immune Microenvironment ◽  
Gene Set Enrichment ◽  
Expression Characteristic ◽  
Precancerous Stage

Gastric mucosal immune microenvironment plays an important role in the occurrence and development of diseases such as inflammation and cancer. In the present study, single-sample gene set enrichment analysis (ssGSEA) was used to evaluate the expression of cytokines and the degree of immune cell infiltration in four different gastric mucosa tissues from normal gastric mucosa, simple gastritis, and atrophic gastritis to gastric cancer. Here, we show the immune microenvironments of these four gastric mucosae were significantly different. From inflammation to gastric cancer, most immunoinflammatory cells showed a downward trend such as central memory CD4 T cell. Instead, several cells showed an upward trend such as macrophage. Additionally, we found some chemokines/interleukins were illustrated to be low expressed (or highly expressed) in precancerous stage and highly expressed (or low expressed) in postcancerous stage, which demonstrated an opposite expression characteristic in pre-/postcancerous stage.

scholarly journals Expression Profiles and Prognostic Values of BOLA Family members in Ovarian Cancer

2020 ◽  
Author(s):  
Mingyang Zhu ◽  
Shiqi Xiao
Keyword(s):  
Ovarian Cancer ◽  
Metal Ion ◽  
Expression Profiles ◽  
Family Members ◽  
Enrichment Analysis ◽  
Genetic Alterations ◽  
Gene Set Enrichment Analysis ◽  
Gene Set Enrichment ◽  
Gene Set ◽  
Protein Disulfide Oxidoreductase

Abstract Background: The BOLA gene family, comprising 3 members, is mainly involved in the regulation of intracellular iron homeostasis. Emerging evidence suggests that BOLA family member 2 play vital roles in tumorigenesis and progression of hepatic cellular carcinoma. However, little known about its roles in ovarian cancer. Methods: In present study, we investigated the expression profiles, prognostic roles, and genetic alterations of three BOLA family members in patients with ovarian cancer through several public databases, containing Oncomine and Gene Expression Profiling Interactive Analysis, Human Protein Atlas, Kaplan–Meier plotter and cBioPortal. Then, we constructed the protein–protein interaction networks of BOLA proteins and their interactors by using String database and Cytoscape software. In addition, we performed the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment by the Annotation, Visualization, and Integrated Discovery database. Finally, we explored the mechanisms underlying the involvement of BOLA family members in OC by using gene set enrichment analysis. Results: The mRNA and protein expression levels of BOLA2 and BOLA3 were heavily higher in ovarian cancer tissues than that in normal ovarian tissues. Dysregulated mRNA expressions of three BOLA family members were significantly associated with prognosis in overall or subgroup analysis. Moreover, genetic alterations also occurred in three BOLA family members in ovarian cancer. Network analysis and enrichment analysis indicated that three BOLA family members and their 20 interactors were mainly associated with metal-ion binding and protein disulfide oxidoreductase activity. Gene set enrichment analysis indicated that BOLA family members were mainly associated with oxidative phosphorylation, proteasome, protein export and glutathione metabolism in ovarian cancer. Conclusions: In brief, the present comprehensive bioinformatics analysis revealed that BOLA1, 2, and 3 may be new prognostic biomarkers, and BOLA2 and BOLA3 may be a potential therapeutic target of precision therapy for patients with ovarian cancer, but further studies are demanded to certify this notion.

scholarly journals Expression profiles and prognostic values of BolA family members in ovarian cancer

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Mingyang Zhu ◽  
Shiqi Xiao
Keyword(s):  
Ovarian Cancer ◽  
Metal Ion ◽  
Expression Profiles ◽  
Family Members ◽  
Enrichment Analysis ◽  
Genetic Alterations ◽  
Gene Set Enrichment Analysis ◽  
Gene Set Enrichment ◽  
Gene Set ◽  
Protein Disulfide Oxidoreductase

Abstract Background The BOLA gene family, comprising three members, is mainly involved in regulating intracellular iron homeostasis. Emerging evidence suggests that BolA family member 2 plays a vital role in tumorigenesis and hepatic cellular carcinoma progression. However, there was less known about its role in ovarian cancer. Methods In the present study, we investigated the expression profiles, prognostic roles, and genetic alterations of three BolA family members in patients with ovarian cancer through several public databases, containing Oncomine and Gene Expression Profiling Interactive Analysis, Human Protein Atlas, Kaplan–Meier plotter and cBioPortal. Then, we constructed the protein-protein interaction networks of BOLA proteins and their interactors by using the String database and Cytoscape software. In addition, we performed the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment by the Annotation, Visualization, and Integrated Discovery database. Finally, we explored the mechanisms underlying BolA family members’ involvement in OC by using gene set enrichment analysis. Results The mRNA and protein expression levels of BOLA2 and BOLA3 were heavily higher in ovarian cancer tissues than in normal ovarian tissues. Dysregulated mRNA expressions of three BolA family members were significantly associated with prognosis in overall or subgroup analysis. Moreover, genetic alterations also occurred in three BolA family members in ovarian cancer. GO analysis indicated that BolA family members might regulate the function of metal ion binding and protein disulfide oxidoreductase activity. Gene set enrichment analysis indicated that BolA family members were mainly associated with oxidative phosphorylation, proteasome, protein export, and glutathione metabolism in ovarian cancer. Conclusion In brief, our finding may contribute to increasing currently limited prognostic biomarkers and treatment options for ovarian cancer.

scholarly journals Mining the TCGA Database for Microenvironment‐Related Genes with Prognostic Value in Gastric Cancer

2021 ◽  
Author(s):  
Ting Liu ◽  
Zheng Gong ◽  
Hong Zhang ◽  
Yi Wan ◽  
Ming-Han Ren ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Distant Metastasis ◽  
Clinical Stage ◽  
Enrichment Analysis ◽  
Clinicopathological Characteristics ◽  
Gene Set Enrichment Analysis ◽  
The Cancer Genome Atlas ◽  
Gene Set Enrichment ◽  
Gene Set ◽  
Protein Protein Interaction

Abstract BackgroundGastric cancer (GC) is the fifth most common cancer worldwide. Previous studies have suggested that the tumor microenvironment (TME) plays an important role in the development and prognosis of GC. In this study, we aimed to identify genes in tumor-infiltrating immune cells (TICs) that influence the progression and prognosis of GC. MethodsWe used the ESTIMATE algorithm to calculate the scores of the stromal and immune components of the TME in 407 GC samples collected from The Cancer Genome Atlas (TCGA) database.The differentially expressed genes (DEGs) were intersected by a protein-protein interaction (PPI) network and analyzed by univariate Cox regression.Further analysis showed the correlation between MCEMP1 and the clinicopathological characteristics of GC patients (clinical stage, distant metastasis) and survival.Then we used Gene set enrichment analysis (GSEA) and CIBERSORT analysis to examine the relationship between MCEMP1 and the TME.ResultsThe analysis revealed that the expression of MCEMP1 was positively correlated with the clinicopathological characteristics of GC patients (clinical stage, distant metastasis) and negatively correlated with survival. Gene set enrichment analysis (GSEA) indicated that gene sets in the MCEMP1 high expression group were concentrated mainly in immune-related pathways. CIBERSORT analysis of the proportion of TICs revealed that neutrophils and M2 macrophages were positively correlated with MCEMP1 expression, suggesting that MCEMP1 is responsible for preservation of the immune-dominant status of the TME. ConclusionHigh MCEMP1 expression might be a biomarker of a poor prognosis in GC patients and provide a clue regarding the different statuses of the TME, offering additional insight into therapy for GC.

scholarly journals HTRA3 Is a Prognostic Biomarker and Associated With Immune Infiltrates in Gastric Cancer

2020 ◽  
Vol 10 ◽  
Author(s):  
Ce Ji ◽  
Li-Sha Sun ◽  
Fei Xing ◽  
Nan Niu ◽  
Hong-Li Gao ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Multivariate Analysis ◽  
Confidence Interval ◽  
Enrichment Analysis ◽  
Hazard Ratio ◽  
Gene Set Enrichment Analysis ◽  
Signal Pathways ◽  
Gene Set Enrichment ◽  
Gene Set ◽  
The Impact

HtrA serine peptidase 3 (HTRA3) participates in multiple signal pathways and plays an important regulatory role in various malignancies; however, its role on prognosis and immune infiltrates in gastric cancer (GC) remains unclear. The study investigated HTRA3 expression in tumor tissues and its association with immune infiltrates, and determined its prognostic roles in GC patients. Patients with GC were collected from the cancer genome atlas (TCGA). We compared the expression of HTRA3 in GC and normal gastric mucosa tissues with Wilcoxon rank sum test. And logistic regression was used to evaluate the relationship between HTRA3 and clinicopathological characters. Gene ontology (GO) term analysis, Gene set enrichment analysis (GSEA), and single-sample Gene Set Enrichment Analysis (ssGSEA) was conducted to explain the enrichmental pathways and functions and quantify the extent of immune cells infiltration for HTRA3. Kaplan-Meier analysis and Cox regression were performed to evaluate the correlation between HTRA3 and survival rates. A nomogram, based on Cox multivariate analysis, was used to predict the impact of HTRA3 on prognosis. High HTRA3 expression was significantly correlated with tumor histological type, histological grade, clinical stage, T stage, and TP53 status (P < 0.05). HTRA3-high GC patients had a lower 10-year progression-free interval [PFI; hazard ratio (HR): 1.46; 95% confidence interval (CI): 1.02–2.08; P = 0.038], disease-specific survival (DSS; HR: 1.65; CI: 1.08–2.52; P = 0.021) and overall survival (OS; HR: 1.59; CI: 1.14–2.22; P = 0.006). Multivariate survival analysis showed that HTRA3 was an independent prognostic marker for PFI (HR: 1.456; CI: 1.021–2.078; P = 0.038), DSS (HR: 1.650; CI: 1.079–2.522; P = 0.021) and OS [hazard ratio (HR): 1.590; 95% confidence interval (CI):1.140–2.219; P = 0.006]. The C-indexes and calibration plots of the nomogram based on multivariate analysis indicated an effective predictive performance for GC patients. GSEA showed that High HTRA3 expression may activate NF-κB pathway, YAP1/WWTR1/TAZ pathway, and TGFβ pathway. There was a negative correlation between the HTRA3 expression and the abundances of adaptive immunocytes (T helper cell 17 cells) and a positive correlation with abundances of innate immunocytes (natural killer cells, macrophages etc.). HTRA3 plays a vital role in GC progression and prognosis and could be a moderate biomarker for prediction for survival after gastrectomy.

Diagnostic and prognostic value of HOXC family members in gastric cancer

2021 ◽  
Author(s):  
Mei-Qian Wang ◽  
Qi-Yun Yin ◽  
Yi-Ru Chen ◽  
Sen-Lin Zhu
Keyword(s):  
Gastric Cancer ◽  
Operating Characteristic ◽  
Characteristic Curve ◽  
Family Members ◽  
Enrichment Analysis ◽  
Diagnostic Value ◽  
Gene Set Enrichment Analysis ◽  
Gene Set Enrichment ◽  
Hox Clusters ◽  
Diagnostic And Prognostic Value

Aims: HOX clusters encode proteins that play pivotal roles in regulating transcription factors and many other proteins during embryogenesis. However, little is known about the diagnostic and prognostic values of HOXC family members in gastric cancer (GC). Materials and methods: The authors evaluated the data in patients with GC based on bioinformatics analysis. Results: HOXC6/8/9/10/11/13 were overexpressed in GC and associated with a poor prognosis. HOXC4/5 were downregulated in GC tissues. Receiver operating characteristic curve analysis demonstrated that they have high diagnostic value. In addition, HOXC4/5/6/9/10/11/13 were negatively correlated with DNA methylation level. The gene set enrichment analysis results implied that they play essential roles in multiple biological processes underlying tumorigenesis. Conclusion: HOXC family members are potential targets for diagnosis and may work as prognostic biomarkers of GC.

scholarly journals Identification the ferroptosis-related gene signature in Gastric cancer based on weighted gene co-expression network analysis (WGCNA)

2021 ◽  
Author(s):  
Feng Wang ◽  
Cheng Chen ◽  
Wei-Peng Chen ◽  
Zu-Ling Li ◽  
Hui Cheng
Keyword(s):  
Gastric Cancer ◽  
Prognostic Model ◽  
Biological Function ◽  
Cox Regression ◽  
Prognostic Index ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Gene Set Enrichment ◽  
Analysis Survival ◽  
Blue Module

Abstract Background Ferroptosis is a mode of regulated cell death that depends on iron, plays pivotal roles in regulating various biological process in human cancers. However, the role of ferroptosis in Gastric cancer (GC) remains unclear. Methods A total of 2721 differentially expressed genes (DEGs) were filtered base on The Cancer Genome Atlas (TCGA) (n = 375) dataset. Gene modules were identified based on co-expression network analysis (WGCNA). Functional analysis was performed to explore the biological function. Lasso-penalized and univariate Cox regression (UCR) analysis, survival genes were screened out to construct a prognostic model, which validated by the GSE43292 dataset. Gene set enrichment analysis (GSEA) for prognostic index was performed. Finally, the correlations of ferroptosis and immune cells were assessed through the TIMER database. Results Compared to normal specimens, 1063 highly upregulated and 1658 downregulated genes respectively and their normal counterparts in GC specimens were screened. WGCNA analysis was used and identified 7 modules, of which, blue module with the most significant enrichment result was selected. By taking intersections of blue module and differentially expressed ferroptosis-related genes (DEFRGs), we got 23 common genes. Functional analysis was performed to explore the biological function of the interested genes, and with the consequences Lasso-penalized and univariate Cox regression (UCR) analysis, survival genes were screened out to construct a prognostic model based on 3 genes (SLC1A5, ANGPTL4, and CGAS), which could play a role in predicting the survival of GC patients. UCR and multivariate Cox regression (MCR) analysis revealed that the prognostic index could be used as independent prognostic indicators and validated using another GSE84437 dataset. Notably, patients in high-risk groups had higher levels of higher mutation frequencies such as TTN and TP53.Mechanistically. Gene set enrichment analysis (GSEA) unveiled several significant and pathways involved in GC. TIMER analysis demonstrated that risk score strongly correlated with Macrophage and CD4 + T cells infiltration. In addition, high- and low-risk group illustrated different distributions in different immune status. Conclusions In this study, a novel FRGs signature was built. It could accurately predict GC prognosis and pave the new way for diagnosis and therapy strategy. May reflect the status of tumor immune microenvironment.

scholarly journals Elevated TUBA1A Might Indicate the Clinical Outcomes of Patients with Gastric Cancer, Being Associated with the Infiltration of Macrophages in the Tumor Immune Microenvironment

2020 ◽  
Vol 29 (4) ◽  
pp. 509-522
Author(s):  
Dazhi Wang ◽  
Zheng Jiao ◽  
Yinghui Ji ◽  
Shuyu Zhang
Keyword(s):  
Gastric Cancer ◽  
Tumor Microenvironment ◽  
Single Cell ◽  
Single Cells ◽  
Enrichment Analysis ◽  
Clinicopathological Features ◽  
Gene Set Enrichment Analysis ◽  
Regulation Mechanism ◽  
Gene Set Enrichment ◽  
Gene Set

Background and Aims: TUBA1A belongs to the tubulin superfamily, and its role in gastric cancer (GC) remains unclear. This study assessed the expression and effect of TUBA1A in GC, as well as its association with survival and clinicopathological features. Gene set enrichment analysis (GSEA) results revealed that high TUBA1A expression was associated with multiple pathways, including those that contributed to the infiltration of macrophages in the tumor microenvironment. Since increased infiltration of macrophages can lead to oxaliplatin resistance, we analyzed the association between TUBA1A, the infiltration of macrophages to the tumor microenvironment, and the inhibitory concentration 50% (IC50) of oxaliplatin. In addition, we analyzed the possible epigenetic regulation mechanism. Methods: A total of 1,881 samples, including 1,618 patients with GC and 263 normal samples, were examined. The associations between clinicopathological features and TUBA1A were assessed by chi-square test, survival was assessed by Kaplan-Meier analysis, and gene set enrichment analysis (GSEA) was performed to explore the potential mechanisms. The associations between TUBA1A and immune infiltration of M0-, M1-, and M2- polarized macrophages were examined by applying deconvolution’s quantification and Pearson’s correlation analysis. The association of TUBA1A with the IC50 of oxaliplatin was analyzed by Pearson correlation test. The mechanisms of TUBA1A dysregulation were studied by analyzing methylation data. A single-cell TUBA1A mRNA expression map of the stomach was drawn from the analysis of stomach single-cell RNA sequencing data that included more than 13,000 single cells of 17 stomach cell types. Results: TUBA1A expression was elevated in GC (p<0.01) and indicated poorer overall survival (p<0.001), first progression survival (p<0.001), and post-progression survival (p<0.01). High TUBA1A expression was significantly correlated with more aggressive clinicopathological features of GC patients (p<0.001). Elevated TUBA1A contributes to the infiltration of macrophages to the tumor microenvironment (p<0.001) and increased the IC50 of oxaliplatin in vitro (p<0.05), while hypomethylation was shown to contribute to the upregulation of TUBA1A (p<0.05). Conclusions: TUBA1A might be a potential prognostic marker and therapeutic target in GC. TUBA1A is significantly associated with the infiltration of M2-polarized macrophages in GC, and the IC50 of oxaliplatin. Hypomethylation contributes to the upregulation of TUBA1A in GC.

Identification of key mRNAs, miRNAs, and mRNA-miRNA network involved in papillary thyroid carcinoma

2020 ◽  
Vol 15 ◽  
Author(s):  
Wei Han ◽  
Dongchen Lu ◽  
Chonggao Wang ◽  
Mengdi Cui ◽  
Kai Lu
Keyword(s):  
Papillary Thyroid Carcinoma ◽  
Thyroid Carcinoma ◽  
Differential Expression Analysis ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Integrated Analysis ◽  
Papillary Thyroid ◽  
Gene Set Enrichment ◽  
Mirna Expression Data

Background: In the past decades, the incidence of thyroid cancer (TC) has been gradually increasing, owing to the widespread use of ultrasound scanning devices. However, the key mRNAs, miRNAs, and mRNA-miRNA network in papillary thyroid carcinoma (PTC) has not been fully understood. Material and Methods: In this study, multiple bioinformatics methods were employed, including differential expression analysis, gene set enrichment analysis, and miRNA-mRNA interaction network construction. Results: First, we investigated the key miRNAs that regulated significantly more differentially expressed genes based on GSEA method. Second, we searched for the key miRNAs based on the mRNA-miRNA interaction subnetwork involved in PTC. We identified hsa-mir-1275, hsa-mir-1291, hsa-mir-206 and hsa-mir-375 as the key miRNAs involved in PTC pathogenesis. Conclusion: The integrated analysis of the gene and miRNA expression data not only identified key mRNAs, miRNAs, and mRNA-miRNA network involved in papillary thyroid carcinoma, but also improved our understanding of the pathogenesis of PTC.

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