RNA Editing and Drug Discovery for Cancer Therapy

Huang, Wei-Chieh; Tseng, Chao-Neng; Tang, Jen‐Yang; Yang, Cheng‐Hong; Liang, Shih‐Shin; Chang, Hsueh-Wei

doi:10.1155/2013/804505

Cited by 9 publications

(12 citation statements)

References 62 publications

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“…The next-generation sequencing used in the study permitted comparing genomic DNA and RNA sequencing data from the same individuals. These preliminary findings, however obtained from noncancerous samples, may indicate that the ADARmediated RNA editing may change the sequence of THRB pre-mRNA post-transcriptionally (Ramaswami et al, 2012) and that this process may be impaired in numerous cancers (Huang et al, 2013).…”

Section: Thrb (Thyroid Hormone Receptor Beta)mentioning

confidence: 99%

“…Adenosine (A) to inosine (I) RNA editing of AZIN1 was demonstrated to be increased in the hepatocellular carcinoma and suggested as a potential driver in the pathogenesis of human cancers, particularly HCC. ADAR1-mediated A-to-I RNA editing was shown to change the RNA nucleotide sequence relative to that of the encoding DNA that was reported to result in cancer development and progression (Huang et al, 2013). ADAR belongs to the family of RNA specific adenosine deaminase, which acts on double-stranded RNA (dsRNA) substrats including those created by long naturally occurring antisence transcripts (cis-and trans-NATs) such as Rev-erbα/TRα2 or intra-THRB transcripts (see diagram 1).…”

Section: Thrb (Thyroid Hormone Receptor Beta)mentioning

confidence: 99%

See 1 more Smart Citation

THRB (Thyroid Hormone Receptor, Beta)

Master¹,

Nauman²

2014

Atlas of Genetics and Cytogenetics in Oncology and Haematology

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Section: Thrb (Thyroid Hormone Receptor Beta)mentioning

confidence: 99%

Section: Thrb (Thyroid Hormone Receptor Beta)mentioning

confidence: 99%

THRB (Thyroid Hormone Receptor, Beta)

Master¹,

Nauman²

2014

Atlas of Genetics and Cytogenetics in Oncology and Haematology

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“…12,[16][17][18] In particular, diverse cancer-related RNA editing sites have been identified in many oncogenes like glioma associated oncogene 1 (GLI1). 19) Some RNA editing sites have an impact on drug discovery. 20) Gene products like isoforms are created by RNA editing affecting drug activities.…”

Section: Rna Editingmentioning

confidence: 99%

“…20) Gene products like isoforms are created by RNA editing affecting drug activities. 19) Recent development of high-throughput DNA and RNA sequencing technologies have contributed to the identification of new RNA editing sites and editing types such as T to C, T to A, C to A, C to T, G to T, C to G and G to C. 21) The results from these new techniques suggest that RNA editing is strongly connected to human phenotypes including several diseases. 22) Currently, one big challenge in RNA editing research is the correct identification of RNA editing sites from noisy RNA-Seq data by discriminating true RNA editing sites from Single Nucleotide Polymorphisms (SNPs) and technical artifacts caused by sequencing and analysis error.…”

Section: Rna Editingmentioning

confidence: 99%

Bioinformatics Approaches for the Identification and Annotation of RNA Editing Sites

Lee

Kim

2013

J Genet Med

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deletion editing (insertion or deletion of nucleotides). With the development of high-throughput next-generation sequencing technologies, increasing numbers of RNA editing sites are rapidly being discovered. Accordingly, many bioinformatics tools and algorithms to identify novel RNA editing sites and semantic annotation of known information are increasingly being introduced. Each method, however, is not free from limitations. For example, numerous false positives are found in the newly discovered sites. 2-4)It is in part due to the limitation of the currently available highthroughput sequencing technologies and in part due to the incompleteness of bioinformatics analysis methods.This review summarizes modern bioinformatics approaches that discover and annotate RNA editing sites. Analytic methods do not work alone solely on RNA sequencing data. This review also includes the strategic steps used in the analysis of RNA editing, related bioinformatics resources that are useful in the analysis of RNA editing and methods to compare the analysis to further improve the analysis results. Post-transcriptional nucleotide sequence modification of transcripts by RNA editing is an important molecular mechanism in the regulation of protein function and is associated with a variety of human disease phenotypes. Identification of RNA editing sites is the basic step for studying RNA editing. Databases and bioinformatics resources are used to annotate and evaluate as well as identify RNA editing sites. No method is free of limitations. Correctly establishing an analytic pipeline and strategic application of both experimental and bioinformatics methods constitute the first step in investigating RNA editing. This review summarizes modern bioinformatics approaches and related resources for RNA editing research. Bioinformatics Approaches for the Identification and

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“…RNA editing is a common and essential post-transcriptional alteration of RNA sequences, affecting millions of bases, expanding the transcriptome diversity and the functions of RNA transcripts [1]. Although several types of RNA editing have been characterized, conversion of adenosine residues to inosine (A to I) is the most frequent type of editing in humans, which is catalyzed by the double stranded RNA (dsRNA) speci c adenosine deaminase that act on RNA (ADAR) family [2,3]. Resulting inosine is recognized by most of the biological machineries as a guanosine (G), consequently, editing could have protein recoding outcome, generating proteomic and phenotypic diversity [4].…”

Section: Introductionmentioning

confidence: 99%

Comprehensive Characterization of RNA Editing in Primary Gastric Adenocarcinoma through RNA-seq Data Analysis

Behroozi

Shahbazi²,

Bakhtiarizadeh

et al. 2020

Preprint

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RNA editing is a post-transcriptional nucleotide modification in humans. Of the various types of RNA editing, the adenosine to inosine substitution is the most widespread in higher eukaryotes, which is mediated by ADAR family enzyme. Inosine is recognized by the biological machineries as guanosine, therefore, editing can potentially rendering substantial functional effects throughout the genome, depending on where it located. RNA editing could contribute to cancer by either exclusive editing of tumor suppressor/promoting genes or by introducing transcriptomic diversity to promote cancer progression. Here, we provided a comprehensive overview of the RNA editing sites in gastric adenocarcinoma and highlighted some of their possible contributions to gastric cancer. RNA-seq data corresponding to 8 gastric adenocarcinoma and their paired non-tumor counterparts were retrieved from GEO database. After pre-possessing and variant calling steps, a stringent filtering pipeline was employed to distinguish potential RNA editing sites from SNPs. The identified potential editing sites were annotated and compared with those in DARNED database. Totally, 12362 high-confidence adenosine to inosine RNA editing sites were detected across all samples. Of these, 12105 and 257 were known and novel editing events, respectively. These editing sites were unevenly distributed across genomic regions, nearly half of them were located in 3´UTR. Indeed, 4868, 3985 and 3509 editing sites were found to be common in both tissue, normal specific and cancer specific, respectively. Further analysis revealed significant number of differentially edited events among these sites, which were located in protein coding genes and microRNAs. Given the distinct pattern of RNA editing in gastric adenocarcinoma and adjacent normal tissue, edited sites have the potential to serve as biomarkers and therapeutic targets in gastric cancer diagnose, management and treatment.

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RNA Editing and Drug Discovery for Cancer Therapy

Cited by 9 publications

References 62 publications

THRB (Thyroid Hormone Receptor, Beta)

THRB (Thyroid Hormone Receptor, Beta)

Bioinformatics Approaches for the Identification and Annotation of RNA Editing Sites

Comprehensive Characterization of RNA Editing in Primary Gastric Adenocarcinoma through RNA-seq Data Analysis

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