Detecting and Characterizing A-To-I microRNA Editing in Cancer

Marceca, Gioacchino P.; Tomasello, Luisa; Distefano, Rosario; Acunzo, Mario; Croce, Carlo M.; Nigita, Giovanni

doi:10.3390/cancers13071699

Cited by 20 publications

(17 citation statements)

References 115 publications

(125 reference statements)

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“…RNA editing is often found in the binding domain of miRNAs and mRNA 61 and in pri-miRNA 19 . About 20% of pri-miRNAs are edited 62 , of which more than 550 positions are edited in human context 20 . Again, its association with the miRNA expression needs further studies.…”

Section: Resultsmentioning

confidence: 99%

“…Although these databases had offered the retrieval of these editing sites, they did not provide a functional analysis for them. The A-to-I editing sites were long known to be closely connected with features of many omics: the A-to-I editing sites have a complementary relationship with the DNA mutation of hepatocellular carcinoma (HCC) risk genes in HCC patients 18 ; those sites in the 3'UTR region can also affect the miRNA expression in a variety of cancers 19 , 20 ; and they can even be used as the indicator to build a cancer prognostic model 12 . Furthermore, the A-to-I RNA editing contributes to the protein diversity of cancer.…”

Section: Introductionmentioning

confidence: 99%

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

Zhu¹,

Huang²,

Liu³

et al. 2022

Int. J. Biol. Sci.

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Epitranscriptomic changes caused by adenosine-to-inosine (A-to-I) RNA editing contribute to the pathogenesis of human cancers; however, only a small fraction of the millions editing sites detected so far has clear functionality. To facilitate more in-depth studies on the editing, this paper offers REIA ( http://bioinfo-sysu.com/reia ), an interactive web server that analyses and visualizes the association between human cancers and A-to-I RNA editing sites (RESs). As a comprehensive database, REIA curates not only 8,447,588 RESs from 9,895 patients across 34 cancers, where 33 are from TCGA and 1 from GEO, but also 13 different types of multi-omic data for the cancers. As an interactive server, REIA provides various options for the user to specify the interested sites, to browse their annotation/editing level/profile in cancer, and to compare the difference in multi-omic features between editing and non-editing groups. From the editing profiles, REIA further detects 658 peptides that are supported by mass spectrum data but not yet covered in any prior works.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Zhu¹,

Huang²,

Liu³

et al. 2022

Int. J. Biol. Sci.

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show abstract

“…APA is an mRNArelated process that produces multiple transcriptional subtypes through selecting alternate (proximal or distal) polyadenylation signals on the 3′-UTR of pre-mRNAs and even proteomic diversity (Akman and Erson-Bensan, 2014). A-to-I editing consists of the irreversible conversion of adenosine to inosine catalyzed by adenosine deaminase acting on RNA (ADAR) enzymes (Marceca et al, 2021). These RNA modification patterns participate in various physiological processes and play important regulatory roles in diseases including cancers, neurologic and metabolic diseases (Wilkinson et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

The Identification of Two RNA Modification Patterns and Tumor Microenvironment Infiltration Characterization of Lung Adenocarcinoma

Lin

Pan

et al. 2022

Front. Genet.

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Background: RNA modification plays an important role in many diseases. A comprehensive study of tumor microenvironment (TME) characteristics mediated by RNA modification regulators will improve the understanding of TME immune regulation.Methods: We selected 26 RNA modification “writers” of lung adenocarcinoma (LUAD) samples and performed unsupervised clustering analysis to explore RNA modification patterns in LUAD. Differentially expressed genes (DEGs) with RNA modification patterns were screened to develop a “writers” of RNA modification score (WM score) system. The infiltration ratio of TME cell subsets was analyzed by CIBERSORT.Results: We identified two RNA modification modes showing different characteristics of overall survival (OS) and TME cell infiltration. According to WM score, LUAD patients were divided into a high-WM score group and a low-WM score group. High-scored patients had a poor prognosis and higher tumor mutation burden (TMB), they were more sensitive to four LUAD therapies (erlotinib, XA V939, gefitinib, and KU-55933) and more clinically responsive to PD-L1 treatment. Those with a low WM score showed higher stromal scores, ESTIMATE scores, and survival chance.Conclusion: Our work revealed the potential role of RNA modification patterns in TME, genetic variation, targeted inhibitor therapy, and immunotherapy. Identifying RNA modification pattern of LUAD patients help understand the characteristics of TME and may promote the development of immunotherapy strategies.

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“…A background noise resulting from single‐nucleotide polymorphisms, somatic mutations, pseudogenes, and sequencing errors impede inosine positioning as well. [ 57 ]…”

Section: Internal Rna Modificationsmentioning

confidence: 99%

Shaping the Bacterial Epitranscriptome—5′‐Terminal and Internal RNA Modifications

2021

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All domains of life utilize a diverse set of modified ribonucleotides that can impact the sequence, structure, function, stability, and the fate of RNAs, as well as their interactions with other molecules. Today, more than 160 different RNA modifications are known that decorate the RNA at the 5′‐terminus or internal RNA positions. The boost of next‐generation sequencing technologies sets the foundation to identify and study the functional role of RNA modifications. The recent advances in the field of RNA modifications reveal a novel regulatory layer between RNA modifications and proteins, which is central to developing a novel concept called “epitranscriptomics.” The majority of RNA modifications studies focus on the eukaryotic epitranscriptome. In contrast, RNA modifications in prokaryotes are poorly characterized. This review outlines the current knowledge of the prokaryotic epitranscriptome focusing on mRNA modifications. Here, it is described that several internal and 5′‐terminal RNA modifications either present or likely present in prokaryotic mRNA. Thereby, the individual techniques to identify these epitranscriptomic modifications, their writers, readers and erasers, and their proposed functions are explored. Besides that, still unanswered questions in the field of prokaryotic epitranscriptomics are pointed out, and its future perspectives in the dawn of next‐generation sequencing technologies are outlined.

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Detecting and Characterizing A-To-I microRNA Editing in Cancer

Cited by 20 publications

References 115 publications

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

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

The Identification of Two RNA Modification Patterns and Tumor Microenvironment Infiltration Characterization of Lung Adenocarcinoma

Shaping the Bacterial Epitranscriptome—5′‐Terminal and Internal RNA Modifications

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