Comprehensive characterization of a drug-resistance-related ceRNA network across 15 anti-cancer drug categories

Liu, Bing; Zhou, Xiaorui; Wu, Dongyuan; Shen, Xiaopei; Mi, Kai; Qu, Zhengyi; Jiang, Yanan; Shang, Desi

doi:10.1016/j.omtn.2021.02.011

Cited by 9 publications

(5 citation statements)

References 55 publications

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“…The method used to identify clinically actionable genes (CAGs) is described in our previous work [ 15 ]. CAGs contain 135 target therapeutic genes ( http://archive.broadinstitute.org/cancer/cga/target ) [ 16 ] and 19 immunotherapeutic genes [ 17 ].…”

Section: Methodsmentioning

confidence: 99%

Comprehensive molecular characterization of hypertension-related genes in cancer

et al. 2022

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Background During cancer treatment, patients have a significantly higher risk of developing cardiovascular complications such as hypertension. In this study, we investigated the internal relationships between hypertension and different types of cancer. Methods First, we comprehensively characterized the involvement of 10 hypertension-related genes across 33 types of cancer. The somatic copy number alteration (CNA) and single nucleotide variant (SNV) of each gene were identified for each type of cancer. Then, the expression patterns of hypertension-related genes were analyzed across 14 types of cancer. The hypertension-related genes were aberrantly expressed in different types of cancer, and some were associated with the overall survival of patients or the cancer stage. Subsequently, the interactions between hypertension-related genes and clinically actionable genes (CAGs) were identified by analyzing the co-expressions and protein–protein interactions. Results We found that certain hypertension-related genes were correlated with CAGs. Next, the pathways associated with hypertension-related genes were identified. The positively correlated pathways included epithelial to mesenchymal transition, hormone androgen receptor, and receptor tyrosine kinase, and the negatively correlated pathways included apoptosis, cell cycle, and DNA damage response. Finally, the correlations between hypertension-related genes and drug sensitivity were evaluated for different drugs and different types of cancer. The hypertension-related genes were all positively or negatively correlated with the resistance of cancer to the majority of anti-cancer drugs. These results highlight the importance of hypertension-related genes in cancer. Conclusions This study provides an approach to characterize the relationship between hypertension-related genes and cancers in the post-genomic era.

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Section: Methodsmentioning

confidence: 99%

Comprehensive molecular characterization of hypertension-related genes in cancer

et al. 2022

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“…The ceRNA network comprises protein-coding mRNAs as well as non-coding RNAs, including long non-coding RNAs (lncRNAs), circRNAs, and pseudogene RNAs. Via the ceRNA network, non-coding RNAs could contribute to anti-cancer drug resistance [ 141 ]. In recent years, the studies on the mechanism of action of circRNA in drug resistance are mostly based on the ceRNA network.…”

Section: Mechanismsmentioning

confidence: 99%

Circular RNAs and Drug Resistance in Genitourinary Cancers: A Literature Review

Long

Shi

et al. 2022

Cancers

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In recent years, systematic treatment has made great progress in genitourinary tumors. However, some patients develop resistance to the treatments, resulting in an increase in mortality. Circular RNAs (circRNAs) form a class of non-coding RNAs with high stability and significant clinical relevance. Accumulating evidence indicates that circRNAs play a vital role in cancer development and tumor chemotherapy resistance. This review summarizes the molecular and cellular mechanisms of drug resistance mediated by circRNAs to common drugs used in the treatment of genitourinary tumors. Several circRNAs were identified to regulate the responsiveness to systemic treatments in genitourinary tumors, including chemotherapies such as cisplatin and targeted therapies such as enzalutamide. Canonically, cicrRNAs participate in the competing endogenous RNA (ceRNA) network, or in some cases directly interact with proteins, regulate downstream pathways, and even some circRNAs have the potential to produce proteins or polypeptides. Several cellular mechanisms were involved in circRNA-dependent drug resistance, including autophagy, cancer stem cells, epithelial-mesenchymal transition, and exosomes. The potential clinical prospect of circRNAs in regulating tumor drug resistance was also discussed.

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“…Leonardo Salmena et al proposed the “competing endogenous RNA” (ceRNA) hypothesis in 2011, and, since then, ceRNA-related research has developed rapidly and made great contributions to revealing the occurrence and development of diseases [ 27 ], prognosis [ 28 ], and therapeutic response [ 29 ]. The ceRNA hypothesis proposes that RNAs, including messenger RNAs (mRNAs) and ncRNAs, expressed concurrently and with a similar complement of MREs, are capable of indirectly regulating one another by competing for a shared, limited pool of miRNA molecules [ 30 , 31 ].…”

Section: Introductionmentioning

confidence: 99%

Integrative Analysis and Experimental Validation of Competing Endogenous RNAs in Obstructive Sleep Apnea

Zhu

Liu

et al. 2023

Biomolecules

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Background: Obstructive sleep apnea (OSA) is highly prevalent yet underdiagnosed. This study aimed to develop a predictive signature, as well as investigate competing endogenous RNAs (ceRNAs) and their potential functions in OSA. Methods: The GSE135917, GSE38792, and GSE75097 datasets were collected from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database. Weighted gene correlation network analysis (WGCNA) and differential expression analysis were used to identify OSA-specific mRNAs. Machine learning methods were applied to establish a prediction signature for OSA. Furthermore, several online tools were used to establish the lncRNA-mediated ceRNAs in OSA. The hub ceRNAs were screened using the cytoHubba and validated by real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Correlations between ceRNAs and the immune microenvironment of OSA were also investigated. Results: Two gene co-expression modules closely related to OSA and 30 OSA-specific mRNAs were obtained. They were significantly enriched in the antigen presentation and lipoprotein metabolic process categories. A signature that consisted of five mRNAs was established, which showed a good diagnostic performance in both independent datasets. A total of twelve lncRNA-mediated ceRNA regulatory pathways in OSA were proposed and validated, including three mRNAs, five miRNAs, and three lncRNAs. Of note, we found that upregulation of lncRNAs in ceRNAs could lead to activation of the nuclear factor kappa B (NF-κB) pathway. In addition, mRNAs in the ceRNAs were closely correlated to the increased infiltration level of effector memory of CD4 T cells and CD56bright natural killer cells in OSA. Conclusions: In conclusion, our research opens new possibilities for diagnosis of OSA. The newly discovered lncRNA-mediated ceRNA networks and their links to inflammation and immunity may provide potential research spots for future studies.

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Comprehensive characterization of a drug-resistance-related ceRNA network across 15 anti-cancer drug categories

Cited by 9 publications

References 55 publications

Comprehensive molecular characterization of hypertension-related genes in cancer

Comprehensive molecular characterization of hypertension-related genes in cancer

Circular RNAs and Drug Resistance in Genitourinary Cancers: A Literature Review

Integrative Analysis and Experimental Validation of Competing Endogenous RNAs in Obstructive Sleep Apnea

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