Screening differentially expressed genes between endometriosis and ovarian cancer to find new biomarkers for endometriosis

Lu, Zhenzhen; Gao, Ying

doi:10.1080/07853890.2021.1966087

Cited by 20 publications

(12 citation statements)

References 73 publications

(83 reference statements)

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“…Furthermore, one of the tumor necrosis factor receptors, TNFRSF4, could be a useful target for immunotherapy of HNSCC [34]. Although there are no published reports on GAST and IGHM for HNSCC, these genes may be related to tumorigenesis and development [35,36]. In general, these previous findings emphasize the importance of these seven genes in HNSCC prognosis prediction.…”

Section: Discussionmentioning

confidence: 92%

Seven Immune-Related Genes’ Prognostic Value and Correlation with Treatment Outcome in Head and Neck Squamous Cell Carcinoma

Shen

Guo

et al. 2023

Mediators of Inflammation

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Background. Head and neck squamous cell carcinoma (HNSCC) is a growing concern worldwide, due to its poor prognosis, low responsiveness to treatment, and drug resistance. Since immunotherapy effectively improves HNSCC patients’ survival status, it is important to continuously explore new immune-related predictive factors to accurately predict the immune landscape and clinical outcomes of individuals suffering from HNSCC. Methods. The HNSCC transcriptome profiling of RNA-sequencing data was retrieved from TCGA database, and the microarray of GSE27020 was obtained from the GEO database for validation. The differentially expressed genes (DEGs) between HNSCC and normal samples were identified by multiple test corrections in TCGA database. The univariate and multivariate Cox analyses were performed to identify proper immune-related genes (IRGs) to construct a risk model. The Cox regression coefficient was employed for calculation of the risk score (RS) of IRG signature. The median value of RS was utilized as a basis to classify individuals with HNSCC into high- and low-risk groups. The Kaplan-Meier (K-M) survival analysis and receiver operating characteristic (ROC) curves were employed for the identification of the prognostic significance and precision of the IRG signature. The signature was also evaluated based on clinical variables, predictive nomogram, mutation analysis, infiltrating immune cells, immune-related pathways, and chemotherapeutic efficacy. The protein-protein interaction (PPI) network and functional enrichment pathway investigations were utilized to explore possible potential molecular mechanisms. Finally, the hub gene’s differential mRNA expression levels were evaluated by means of the Gene Expression Profiling Interactive Analysis (GEPIA), and the Human Protein Atlas (HPA) was utilized for the validation of their translational levels. Results. Collectively, 1593 DEGs between HNSCC and normal samples were identified, of which 136 IRGs were differentially expressed. Then, the 136 immune-related DEGs were mostly enriched in the cytokine-related signaling pathways by GO and KEGG analyses. After that, a valuable signature based on seven genes (DKK1, GAST, IGHM, IL12RB2, SLURP1, STC2, and TNFRSF4) was designed. The HNSCC patients into the low-risk group and the high-risk group were divided by using the median RS; the HNSCC patients in the high-risk group had a worse survival than those in the low-risk group. The risk signature was verified to be an independent predictive marker for HNSCC patients. Meanwhile, the RS had the largest contribution to survival of these patients based on the predictive nomogram. In addition, the low-risk HNSCC patients exhibited significantly enriched immune cells, along with an association with high chemosensitivity. Conclusion. The constructed gene signature can independently function as a predictive indicator for the clinical features of HNSCC patients. The low-risk HNSCC subjects might benefit from immunotherapy and chemotherapy.

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Section: Discussionmentioning

confidence: 92%

Seven Immune-Related Genes’ Prognostic Value and Correlation with Treatment Outcome in Head and Neck Squamous Cell Carcinoma

Shen

Guo

et al. 2023

Mediators of Inflammation

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“…IGHM is an immune-related gene encoding the C region of the µ heavy chain and defines its isoform ( 62 ). It significantly affects the density of infiltrating CD20 + B cells in tumor tissues ( 63 ). In addition, Pocha et al revealed that a high expression of surfactant genes, including SFTPB , was associated with intratumoral T-cell infiltration and a low immunosuppressive microenvironment in LUAD ( 64 ).…”

Section: Discussionmentioning

confidence: 99%

Integrating single-cell and bulk RNA sequencing to develop a cancer-associated fibroblast-related signature for immune infiltration prediction and prognosis in lung adenocarcinoma

Huang¹,

Xiao²,

Shi³

et al. 2023

J Thorac Dis

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Background: An accumulating amount of studies are highlighting the impacts of cancer-associated fibroblasts (CAFs) on the initiation, metastasis, invasion, and immune evasion of lung cancer. However, it is still unclear how to tailor treatment regimens based on the transcriptomic characteristics of CAFs in the tumor microenvironment of patients with lung cancer.Methods: Our study examined single-cell RNA-sequencing data from the Gene Expression Omnibus (GEO) database to identify expression profiles for CAF marker genes and constructed a prognostic signature of lung adenocarcinoma using these genes in The Cancer Genome Atlas (TCGA) database. The signature was validated in 3 independent GEO cohorts. Univariate and multivariate analyses were used to confirm the clinical significance of the signature. Next, multiple differential gene enrichment analysis methods were used to explore the biological pathways related to the signature. Six algorithms were used to assess the relative proportion of infiltrating immune cells, and the relationship between the signature and immunotherapy response of lung adenocarcinoma (LUAD) was explored based on the tumor immune dysfunction and exclusion (TIDE) algorithm. Results:The signature related to CAFs in this study showed good accuracy and predictive capacity. In all clinical subgroups, the high-risk patients had a poor prognosis. The univariate and multivariate analyses confirmed that the signature was an independent prognostic marker. Moreover, the signature was closely associated with particular biological pathways related to cell cycle, DNA replication, carcinogenesis, and immune response. The 6 algorithms used to assess the relative proportion of infiltrating immune cells indicated that a lower infiltration of immune cells in the tumor microenvironment was associated with highrisk scores. Importantly, we found a negative correlation between TIDE, exclusion score, and risk score.Conclusions: Our study constructed a prognostic signature based on CAF marker genes useful for prognosis and immune infiltration estimation of lung adenocarcinoma. This tool could enhance therapy efficacy and allow individualized treatments.

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“…Therefore, we hope to find markers of tissue and blood coexistence for BRCA identification and diagnosis. Furthermore, we searched for “tissue-blood shared miRNAs as cancer biomarkers” regarding BRCA or other carcinomas, but there were only a few studies that focus on marker miRNAs that work in both tissues and blood [ 40 , 41 , 42 , 43 , 44 ]. Thereby, we hope to fill the gap of miRNAs shared by tissues and blood as tumor biomarkers.…”

Section: Introductionmentioning

confidence: 99%

Integrated Tissue and Blood miRNA Expression Profiles Identify Novel Biomarkers for Accurate Non-Invasive Diagnosis of Breast Cancer: Preliminary Results and Future Clinical Implications

Gao²,

Liu³

et al. 2022

Genes

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We aimed to identify miRNAs that were closely related to breast cancer (BRCA). By integrating several methods including significance analysis of microarrays, fold change, Pearson’s correlation analysis, t test, and receiver operating characteristic analysis, we developed a decision-tree-based scoring algorithm, called Optimized Scoring Mechanism for Primary Synergy MicroRNAs (O-PSM). Five synergy miRNAs (hsa-miR-139-5p, hsa-miR-331-3p, hsa-miR-342-5p, hsa-miR-486-5p, and hsa-miR-654-3p) were identified using O-PSM, which were used to distinguish normal samples from pathological ones, and showed good results in blood data and in multiple sets of tissue data. These five miRNAs showed accurate categorization efficiency in BRCA typing and staging and had better categorization efficiency than experimentally verified miRNAs. In the Protein-Protein Interaction (PPI) network, the target genes of hsa-miR-342-5p have the most regulatory relationships, which regulate carcinogenesis proliferation and metastasis by regulating Glycosaminoglycan biosynthesis and the Rap1 signaling pathway. Moreover, hsa-miR-342-5p showed potential clinical application in survival analysis. We also used O-PSM to generate an R package uploaded on github (SuFei-lab/OPSM accessed on 22 October 2021). We believe that miRNAs included in O-PSM could have clinical implications for diagnosis, prognostic stratification and treatment of BRCA, proposing potential significant biomarkers that could be utilized to design personalized treatment plans in BRCA patients in the future.

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Screening differentially expressed genes between endometriosis and ovarian cancer to find new biomarkers for endometriosis

Cited by 20 publications

References 73 publications

Seven Immune-Related Genes’ Prognostic Value and Correlation with Treatment Outcome in Head and Neck Squamous Cell Carcinoma

Seven Immune-Related Genes’ Prognostic Value and Correlation with Treatment Outcome in Head and Neck Squamous Cell Carcinoma

Integrating single-cell and bulk RNA sequencing to develop a cancer-associated fibroblast-related signature for immune infiltration prediction and prognosis in lung adenocarcinoma

Integrated Tissue and Blood miRNA Expression Profiles Identify Novel Biomarkers for Accurate Non-Invasive Diagnosis of Breast Cancer: Preliminary Results and Future Clinical Implications

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