REIA: A database for cancer A-to-I RNA editing with interactive analysis

Zhu, Hao; Huang, Lu Sheng S.; Liu, Songbin; Dai, Zhiming; Songyang, Zhou; Weng, Zhihui; Xiong, Yuanyan

doi:10.7150/ijbs.69458

Cited by 8 publications

(10 citation statements)

References 78 publications

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“…The majority of RESs were found in the 3’UTR, followed by introns ( Figure 1B ); however, LAML RESs were mostly found in introns (mRNAs or noncoding RNAs), probably because it is the only blood cancer here, as opposed to other solid tumors. This pattern was also observed for A-to-I events, obtained from the previous study of A-to-I editing sites by our group ( 19 ) ( Figure S1B ). Moreover, LAML RESs showed the highest editing levels (EL) among all cancer types, while COAD and READ showed the lowest ELs ( Figure 1C ).…”

Section: Resultssupporting

confidence: 86%

Pan-cancer investigation of C-to-U editing reveals its important role in cancer development and new targets for cancer treatment

Guo

Li²,

Zhao³

et al. 2023

Front. Oncol.

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RNA editing is prevalent in the transcriptome and is important for multiple cellular processes. C-to-U RNA editing sites (RES) are relatively rare and understudied in humans, compared to A-to-I editing. However, the functional impact of C-to-U editing in human cancers also remains elusive. Here, we conducted the first comprehensive survey of pan-cancer C-to-U RESs. Surprisingly, we found that the same subset of RESs were associated with multiple features, including patient survival, cancer stemness, tumor mutation burden (TMB), and tumor-infiltrated immune cell compositions (ICC), suggesting an RES-mediated close relationship between these features. For example, editing sites for GALM or IFI6 that led to higher expression were linked to lower survival and more cancer stemness. Also, TMB was found to be lower in prostate cancer cases with ICC-associated RESs in CAVIN1 or VWA8 or higher in prostate cancer cases with thymoma. With experimental support, we also found RESs in CST3, TPI1, or TNC that are linked to immune checkpoint blockade by anti-PD1. We also confirmed through experiments that two C-to-U RESs in CSNK2B or RPS14 had different effects on colon cancer cells. Patients with CSNK2B editing, which increased the expression of the oncogene CLDN18, had a lower response to drugs. On the other hand, drugs worked better on people who had RPS14 editing, which greatly increased ribosome production. In summary, our study demonstrated the important roles of C-to-U RESs across cancers and shed light on personalized cancer therapy.

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Section: Resultssupporting

confidence: 86%

Pan-cancer investigation of C-to-U editing reveals its important role in cancer development and new targets for cancer treatment

Guo

Li²,

Zhao³

et al. 2023

Front. Oncol.

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“…The role of RNA editing in cancer is still not fully understood, although it has long been associated with malignancy [ 27 , 29 , 113 ]. Aberrant expression of ADARs has been observed in various cancers.…”

Section: Biological Functions Of Rna Editingmentioning

confidence: 99%

“…The extent of RNA editing and the significance of RNA editing sites vary among different types of cancer. A-to-I RNA editing, which accounts for nearly 90% of all RNA editing events, has been the main focus of studies on the link between RNA editing and cancer, with less research on APOBEC-catalyzed RNA editing in cancer cells [ 113 ]. Current understanding suggests that RNA editing plays a crucial role in carcinogenesis through multiple mechanisms.…”

Section: Biological Functions Of Rna Editingmentioning

confidence: 99%

RNA editing enzymes: structure, biological functions and applications

Zhang,

Zhu,

Gao

et al. 2024

Cell Biosci

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With the advancement of sequencing technologies and bioinformatics, over than 170 different RNA modifications have been identified. However, only a few of these modifications can lead to base pair changes, which are called RNA editing. RNA editing is a ubiquitous modification in mammalian transcriptomes and is an important co/posttranscriptional modification that plays a crucial role in various cellular processes. There are two main types of RNA editing events: adenosine to inosine (A-to-I) editing, catalyzed by ADARs on double-stranded RNA or ADATs on tRNA, and cytosine to uridine (C-to-U) editing catalyzed by APOBECs. This article provides an overview of the structure, function, and applications of RNA editing enzymes. We discuss the structural characteristics of three RNA editing enzyme families and their catalytic mechanisms in RNA editing. We also explain the biological role of RNA editing, particularly in innate immunity, cancer biogenesis, and antiviral activity. Additionally, this article describes RNA editing tools for manipulating RNA to correct disease-causing mutations, as well as the potential applications of RNA editing enzymes in the field of biotechnology and therapy.

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“… [ 12 ] REIA http://bioinfo-sysu.com/reia An interactive web server can be used to explore the relationship between A-to-I RNA editing sites and cancer. [ 14 ] SPRINT http://sprint.tianlab.cn An SNP-free method to recognize RNA editing sites (RESs). [ 16 ] RED-ML https://github.com/BGIRED/RED-ML Machine learning-based RNA editing detection.…”

Section: A-to-i Rna Editingmentioning

confidence: 99%

The role of ADAR1 through and beyond its editing activity in cancer

Jiao,

Xu,

Liu

et al. 2024

Cell Commun Signal

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Adenosine-to-inosine (A-to-I) editing of RNA, catalyzed by adenosine deaminase acting on RNA (ADAR) enzymes, is a prevalent RNA modification in mammals. It has been shown that A-to-I editing plays a critical role in multiple diseases, such as cardiovascular disease, neurological disorder, and particularly cancer. ADARs are the family of enzymes, including ADAR1, ADAR2, and ADAR3, that catalyze the occurrence of A-to-I editing. Notably, A-to-I editing is mainly catalyzed by ADAR1. Given the significance of A-to-I editing in disease development, it is important to unravel the complex roles of ADAR1 in cancer for the development of novel therapeutic interventions.In this review, we briefly describe the progress of research on A-to-I editing and ADARs in cancer, mainly focusing on the role of ADAR1 in cancer from both editing-dependent and independent perspectives. In addition, we also summarized the factors affecting the expression and editing activity of ADAR1 in cancer.

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REIA: A database for cancer A-to-I RNA editing with interactive analysis

Cited by 8 publications

References 78 publications

Pan-cancer investigation of C-to-U editing reveals its important role in cancer development and new targets for cancer treatment

Pan-cancer investigation of C-to-U editing reveals its important role in cancer development and new targets for cancer treatment

RNA editing enzymes: structure, biological functions and applications

The role of ADAR1 through and beyond its editing activity in cancer

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