Bioinformatic tools for epitranscriptomics

Taguchi, Y-h.

doi:10.1152/ajpcell.00437.2022

Cited by 6 publications

(2 citation statements)

References 102 publications

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“…Conventional sequencing techniques such as bulk RNA-seq and scRNA-seq quantify and normalize for mRNA expression but are not specifically developed to detect RNA modifications. Taguchi et al recently reviewed developments in epitranscriptome spatial detection and data analysis [ 41 ]. Advancements in de novo sequencing will be discussed later in this review.…”

Section: Rna Modification Patterns In Gliomamentioning

confidence: 99%

The epitranscriptome of high-grade gliomas: a promising therapeutic target with implications from the tumor microenvironment to endogenous retroviruses

Ramsoomair,

Ceccarelli,

Heiss

et al. 2023

J Transl Med

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Glioblastoma (GBM) comprises 45.6% of all primary malignant brain cancers and is one of the most common and aggressive intracranial tumors in adults. Intratumoral heterogeneity with a wide range of proteomic, genetic, and epigenetic dysregulation contributes to treatment resistance and poor prognosis, thus demanding novel therapeutic approaches. To date, numerous clinical trials have been developed to target the proteome and epigenome of high-grade gliomas with promising results. However, studying RNA modifications, or RNA epitranscriptomics, is a new frontier within neuro-oncology. RNA epitranscriptomics was discovered in the 1970s, but in the last decade, the extent of modification of mRNA and various non-coding RNAs has emerged and been implicated in transposable element activation and many other oncogenic processes within the tumor microenvironment. This review provides background information and discusses the therapeutic potential of agents modulating epitranscriptomics in high-grade gliomas. A particular emphasis will be placed on how combination therapies that include immune agents targeting hERV-mediated viral mimicry could improve the treatment of GBM.

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Section: Rna Modification Patterns In Gliomamentioning

confidence: 99%

The epitranscriptome of high-grade gliomas: a promising therapeutic target with implications from the tumor microenvironment to endogenous retroviruses

Ramsoomair,

Ceccarelli,

Heiss

et al. 2023

J Transl Med

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“…Recently, with the advancements in bioinformatics, there's been an upsurge in accessible data and refined algorithmic frameworks. This evolution equips researchers with the tools to efficiently pinpoint and validate potential biological targets (Taguchi, 2023).…”

Section: Introductionmentioning

confidence: 99%

Histone ubiquitination-related gene CUL4B promotes lung adenocarcinoma progression and cisplatin resistance

Yin,

Zhang,

Zeng

et al. 2023

Front. Genet.

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Background: The role of the histone ubiquitination-related gene in the cisplatin resistance of lung adenocarcinoma (LUAD) remains an intricate subject.Methods: We accessed transcriptome data of both wild type and cisplatin-resistant cells from the GSE108214 dataset, and garnered transcriptome and clinical data of LUAD patients from The Cancer Genome Atlas (TCGA) database. Utilizing the R software, we analyzed these public datasets in depth. Real-time Quantitative PCR (qPCR) was used to detect the RNA level of CUL4B. Effect of CUL4B on cell proliferation was evaluated using CCK8 and colony formation assay. Effect of CUL4B on cell invasion was evaluated using transwell assay. Cisplatin sensitivity was evaluated by calculating IC50.Results: Our analysis shed light on the significance of the histone ubiquitination-related gene, CUL4B, in relation to cisplatin resistance and the overall survival rates of LUAD patients. Notably, CUL4B was found to be overexpressed in both lung cancer tissues and cells. Meanwhile, in vitro experiments indicated can CUL4B significantly promote the proliferation, invasion and migration of lung cancer cells. Furthermore, suppressing CUL4B expression led to a noticeable reduction in the IC50 value of cisplatin in lung cancer cells. A deep dive into biological enrichment analysis revealed that among patients exhibiting high CUL4B expression, there was a pronounced activation of the G2M checkpoint and the PI3K/AKT/mTOR signaling pathways. Immune microenvironment analysis has revealed that patients with elevated CUL4B expression may exhibit increased infiltration of M2 macrophages, coupled with a reduced infiltration of CD8+ T cells and activated NK cells. Notably, we observed higher CUL4B expression among those who responded positively to immunotherapy.Conclusion: These findings underscore the significance of CUL4B in the resistance to cisplatin in lung cancer, highlighting its potential as a therapeutic target.

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Statistical modeling of single-cell epitranscriptomics enabled trajectory and regulatory inference of RNA methylation

Wang,

Zhou

et al. 2024

Cell Genomics

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Bioinformatic tools for epitranscriptomics

Cited by 6 publications

References 102 publications

The epitranscriptome of high-grade gliomas: a promising therapeutic target with implications from the tumor microenvironment to endogenous retroviruses

The epitranscriptome of high-grade gliomas: a promising therapeutic target with implications from the tumor microenvironment to endogenous retroviruses

Histone ubiquitination-related gene CUL4B promotes lung adenocarcinoma progression and cisplatin resistance

Statistical modeling of single-cell epitranscriptomics enabled trajectory and regulatory inference of RNA methylation

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