scholarly journals Pan-Cancer Analysis of m5C Regulator Genes Reveals Consistent Epigenetic Landscape Changes in Multiple Cancers

2020 ◽  
Author(s):  
Chen Xue ◽  
Qingmiao Shi ◽  
Chunting Zhang ◽  
Juan Li ◽  
Yuting He
Keyword(s):  
Landscape Changes ◽  
Epigenetic Landscape ◽  
Multiple Cancers ◽  
Regulator Genes ◽  
Pan Cancer

scholarly journals Transcriptome Analysis of Recurrently Deregulated Genes across Multiple Cancers Identifies New Pan-Cancer Biomarkers

2015 ◽  
Vol 76 (2) ◽  
pp. 216-226 ◽  
Author(s):  
Bogumil Kaczkowski ◽  
Yuji Tanaka ◽  
Hideya Kawaji ◽  
Albin Sandelin ◽  
Robin Andersson ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Cancer Biomarkers ◽  
Multiple Cancers ◽  
Pan Cancer

Pan-cancer analysis indicates that MYBL2 is associated with the prognosis and immunotherapy of multiple cancers as an oncogene

Cell Cycle ◽  
2021 ◽  
pp. 1-18
Author(s):  
Xingjie Chen ◽  
Yalin Lu ◽  
Hao Yu ◽  
Kangjie Du ◽  
Yu Zhang ◽  
...  
Keyword(s):  
Multiple Cancers ◽  
Pan Cancer

Epigenetic Landscape Changes Due to Acupuncture Treatment: From Clinical to Basic Research

2020 ◽  
Vol 26 (8) ◽  
pp. 633-640 ◽  
Author(s):  
Hao Hong ◽  
Xin-yue Jing ◽  
Shu-bao Liu ◽  
Yong-jun Peng ◽  
Bing-mei Zhu
Keyword(s):  
Acupuncture Treatment ◽  
Basic Research ◽  
Landscape Changes ◽  
Epigenetic Landscape

Somatic gene mutation signatures predict cancer type and prognosis in multiple cancers with pan-cancer 1000 gene panel

2020 ◽  
Vol 470 ◽  
pp. 181-190 ◽  
Author(s):  
Hai-Long Wang ◽  
Peng-Fei Liu ◽  
Jie Yue ◽  
Wen-Hua Jiang ◽  
Yun-Long Cui ◽  
...  
Keyword(s):  
Gene Mutation ◽  
Gene Panel ◽  
Cancer Type ◽  
Multiple Cancers ◽  
Somatic Gene ◽  
Somatic Gene Mutation ◽  
Pan Cancer

scholarly journals Pan-cancer analysis of m5C regulator genes reveals consistent epigenetic landscape changes in multiple cancers

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Yuting He ◽  
Xiao Yu ◽  
Menggang Zhang ◽  
Wenzhi Guo
Keyword(s):  
Copy Number Variations ◽  
Regulatory Genes ◽  
The Cancer Genome Atlas ◽  
Cancer Pathogenesis ◽  
Cancer Genome Atlas ◽  
Cancer Types ◽  
Reversible Modification ◽  
Regulator Genes ◽  
Modified Nucleobases ◽  
Pan Cancer

Abstract Background 5-Methylcytosine (m5C) is a reversible modification to both DNA and various cellular RNAs. However, its roles in developing human cancers are poorly understood, including the effects of mutant m5C regulators and the outcomes of modified nucleobases in RNAs. Methods Based on The Cancer Genome Atlas (TCGA) database, we uncovered that mutations and copy number variations (CNVs) of m5C regulatory genes were significantly correlated across many cancer types. We then assessed the correlation between the expression of individual m5C regulators and the activity of related hallmark pathways of cancers. Results After validating m5C regulators’ expression based on their contributions to cancer development and progression, we observed their upregulation within tumor-specific processes. Notably, our research connected aberrant alterations to m5C regulatory genes with poor clinical outcomes among various tumors that may drive cancer pathogenesis and/or survival. Conclusion Our results offered strong evidence and clinical implications for the involvement of m5C regulators.

scholarly journals Pan-cancer analysis of mRNA stability for decoding tumour post-transcriptional programs

2021 ◽  
Author(s):  
Gabrielle Perron ◽  
Pouria Jandaghi ◽  
Maryam Rajaee ◽  
Rached Alkallas ◽  
Yasser Riazalhosseini ◽  
...  
Keyword(s):  
Mrna Stability ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Critical Role ◽  
Rna Stability ◽  
Cancer Type ◽  
Multiple Cancers ◽  
Transcriptional Changes ◽  
Potential Factors ◽  
Pan Cancer

AbstractRNA stability is a crucial and often overlooked determinant of gene expression. Some of the regulators of mRNA stability are long known as key oncogenic or tumour suppressor factors. Nonetheless, the extent to which mRNA stability contributes to transcriptome remodeling in cancer is unknown, and the factors that modulate mRNA stability during cancer development and progression are largely uncharacterized. Here, by decoupling transcriptional and post-transcriptional effects in RNA-seq data of 7760 samples from 18 cancer types, we present a pan-cancer view of the mRNA stability changes that accompany tumour development and progression. We show that thousands of genes are dysregulated at the mRNA stability level, and identify the potential factors that drive these changes, including >80 RNA-binding proteins (RBPs) and microRNAs (miRNAs). Most RBPs and miRNAs have cancer type-specific activities, but a few show recurrent inactivation across multiple cancers, including the RBFOX family of RBPs and miR-29. Analysis of cell lines with phenotypic activation or inhibition of RBFOX1 and miR-29 confirms their role in modulation of genes that are dysregulated across multiple cancers, with functions in calcium signaling, extracellular matrix organization, and stemness. Overall, our study highlights the critical role of mRNA stability in shaping the tumour transcriptome, with recurrent post-transcriptional changes that are ~30% as frequent as transcriptional events. These results provide a resource for systematic interrogation of cancer-associated stability drivers and pathways.

scholarly journals Molecular Mechanisms of PD-1 and PD-L1 Activity on a Pan-Cancer Basis: A Bioinformatic Exploratory Study

2021 ◽  
Vol 22 (11) ◽  
pp. 5478
Author(s):  
Siddarth Kannan ◽  
Geraldine Martina O’Connor ◽  
Emyr Yosef Bakker
Keyword(s):  
Clinical Relevance ◽  
Molecular Mechanisms ◽  
Patient Survival ◽  
Drug Repurposing ◽  
Immune Checkpoint Blockade ◽  
Multiple Cancers ◽  
Significant Survival ◽  
Cancer Types ◽  
Repurposed Drugs ◽  
Pan Cancer

Immune checkpoint blockade targeting PD-1 (PDCD1)/PD-L1 (CD274) is increasingly used for multiple cancers. However, efficacy and adverse-related events vary significantly. This bioinformatic study interrogated molecular differences pertaining to PDCD1/CD274 and their correlated genes on a pan-cancer basis to identify differences between cancer types. Patient RNA-seq data from fifteen cancer types were accessed on cBioPortal to determine the role of PDCD1/CD274 in patient survival and to identify positively and negatively correlated genes, which were also assessed for clinical relevance. Genes correlating with PDCD1/CD274 across multiple cancers were taken forward for drug repurposing via DRUGSURV and microRNA analysis using miRDB and miRabel. MicroRNAs were also screened for clinical relevance using OncomiR. Forty genes were consistently correlated with PDCD1/CD274 across multiple cancers, with the cancers themselves exhibiting a differential role for the correlated genes in terms of patient survival. Esophageal and renal cancers in particular stood out in this regard as having a unique survival profile. Forty-nine putative microRNAs were identified as being linked to the PDCD1/CD274 network, which were taken forward and further assessed for clinical relevance using OncomiR and previously published literature. One hundred and thirty significant survival associations for 46 microRNAs across fourteen groups of cancers were identified. Finally, a total of 23 putative repurposed drugs targeting multiple components of the PDCD1/CD274 network were identified, which may represent immunotherapeutic adjuvants. Taken together, these results shed light on the varying PDCD1/CD274 networks between individual cancers and signpost a need for more cancer-specific investigations and treatments.

scholarly journals Comprehensive Pan-Cancer Analysis and the Regulatory Mechanism of ASF1B, a Gene Associated With Thyroid Cancer Prognosis in the Tumor Micro-Environment

2021 ◽  
Vol 11 ◽  
Author(s):  
Jing Ma ◽  
Wei Han ◽  
Kai Lu
Keyword(s):  
Gene Expression ◽  
Survival Analysis ◽  
Thyroid Cancer ◽  
Prognostic Marker ◽  
Enrichment Analysis ◽  
Differential Analysis ◽  
Expression Levels ◽  
Multiple Cancers ◽  
Mtorc1 Signaling ◽  
Pan Cancer

BackgroundThe incidence of thyroid cancer, whose local recurrence and metastasis lead to death, has always been high and the pathogenesis of papillary thyroid carcinoma (PTC) has not been clearly elucidated. Therefore, the research for more accurate prognosis-related predictive biomarkers is imminent, and a key gene can often be a prognostic marker for multiple tumors.MethodsGene expression profiles of various cancers in the TCGA and GTEx databases were downloaded, and genes significantly associated with the prognosis of THCA were identified by combining differential analysis with survival analysis. Then, a series of bioinformatics tools and methods were used to analyze the expression of the gene in each cancer and the correlation of each expression with prognosis, tumor immune microenvironment, immune neoantigens, immune checkpoints, DNA repair genes, and methyltransferases respectively. The possible biological mechanisms were also investigated by GSEA enrichment analysis.Results656 differentially expressed genes were identified from two datasets and 960 DEGs that were associated with disease-free survival in THCA patients were screened via survival analysis. The former and the latter were crossed to obtain 7 key genes, and the gene with the highest risk factor, ASF1B, was selected for this study. Differential analysis of multiple databases showed that ASF1B was commonly and highly expressed in pan-cancer. Survival analysis showed that high ASF1B expression was significantly associated with poor patient prognosis in multiple cancers. In addition, ASF1B expression levels were found to be associated with tumor immune infiltration in THCA, KIRC, LGG, and LIHC, and with tumor microenvironment in BRCA, LUSC, STAD, UCEC, and KIRC. Further analysis of the relationship between ASF1B expression and immune checker gene expression suggested that ASF1B may regulate tumor immune patterns in most tumors by regulating the expression levels of specific immune checker genes. Finally, GSEA enrichment analysis showed that ASF1B high expression was mainly enriched in cell cycle, MTORC1 signaling system, E2F targets, and G2M checkpoints pathways.ConclusionsASF1B may be an independent prognostic marker for predicting the prognosis of THCA patients. The pan-cancer analysis suggested that ASF1B may play an important role in the tumor micro-environment and tumor immunity and it has the potential of serving as a predictive biomarker for multiple cancers.

scholarly journals Pan-cancer analysis of m5C regulator genes reveals consistent epigenetic landscape changes in multiple cancers

2021 ◽  
Author(s):  
Yuting He ◽  
Xiao Yu ◽  
Menggang Zhang ◽  
Wenzhi Guo
Keyword(s):  
Copy Number Variations ◽  
Regulatory Genes ◽  
The Cancer Genome Atlas ◽  
Cancer Pathogenesis ◽  
Cancer Genome Atlas ◽  
Cancer Types ◽  
Reversible Modification ◽  
Regulator Genes ◽  
Modified Nucleobases ◽  
Pan Cancer

Abstract Backgroud5-methylcytosine (m5C) is a reversible modification to both DNA and various cellular RNAs. However, its roles in developing human cancers are poorly understood, including the effects of mutant m5C regulators and the outcomes of modified nucleobases in RNAs. Methods Based on The Cancer Genome Atlas (TCGA) database, we uncovered that mutations and copy number variations (CNVs) of m5C regulatory genes were significantly correlated across 33 cancer types. We then assessed the correlation between the expression of individual m5C regulators and the activity of related hallmark pathways of cancers. After validating m5C regulators' expression based on their contributions to cancer development and progression, we observed their up-regulation within tumor-specific processes. Results Notably, our research connected aberrant alterations to m5C regulatory genes with poor clinical outcomes among various tumors that may drive cancer pathogenesis and/or survival. Conclusions Our results offered strong evidence and clinical implications for the involvement of m5C regulators.

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