4.7 Article

Pharmacoepitranscriptomic landscape revealing m6A modification could be a drug-effect biomarker for cancer treatment

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

m6A-Atlas: a comprehensive knowledgebase for unraveling the N6-methyladenosine (m6A) epitranscriptome

Yujiao Tang et al.

Summary: N-6-Methyladenosine (m(6)A) is the most prevalent RNA modification on mRNAs and lncRNAs, and m(6)A-Atlas is a comprehensive knowledgebase for unraveling the m(6)A epitranscriptome. It features a high-confidence collection of m(6)A sites and quantitative epitranscriptome profiles, offering novel features like conservation among vertebrate species and potential pathogenesis inference from disease-associated genetic mutations. The user-friendly interface allows for querying, visualization, and sharing of annotated m(6)A epitranscriptomes.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemistry & Molecular Biology

RMDisease: a database of genetic variants that affect RNA modifications, with implications for epitranscriptome pathogenesis

Kunqi Chen et al.

Summary: Recent studies suggest a significant role of RNA modifications in biological mechanisms and disease progression. RMDisease is a database containing information on 202,307 human SNPs that may affect RNA modifications, with 4,289 disease-associated SNPs potentially playing a role in disease pathogenesis, along with essential post-transcriptional regulation information.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemical Research Methods

ConsRM: collection and large-scale prediction of the evolutionarily conserved RNA methylation sites, with implications for the functional epitranscriptome

Bowen Song et al.

Summary: The study compared the human and mouse m(6)A epitranscriptomes and developed a novel scoring framework, ConsRM, to measure the conservation degree of m(6)A sites. Experimental results demonstrated that ConsRM outperformed well-adopted conservation scores in distinguishing conserved and unconserved m(6)A sites, with higher ConsRM scores indicating potential functional importance. An online database with conservation metrics of 177,998 human m(6)A sites was developed for conservation analysis and functional prioritization.

BRIEFINGS IN BIOINFORMATICS (2021)

Article Pharmacology & Pharmacy

An Evidence-Based Framework for Evaluating Pharmacogenomics Knowledge for Personalized Medicine

Michelle Whirl-Carrillo et al.

Summary: Clinical annotations in PharmGKB summarize the association between variant-drug pairs and are assigned a level of evidence. To ensure consistency and transparency, a scoring system has been developed to automate LOE assignment. This system improves the quality and reliability of clinical annotations.

CLINICAL PHARMACOLOGY & THERAPEUTICS (2021)

Review Genetics & Heredity

The epitranscriptome beyond m6A

David Wiener et al.

Summary: This Perspective reviews efforts to map six different RNA modifications and how they differ from N-6-methyladenosine. The authors discuss technical and analytical challenges of characterizing the epitranscriptome and provide their conclusions on the abundance and distribution of these modifications. The article highlights commonalities and differences among the modifications in comparison to m(6)A, speculating on their origins and functional abilities over evolutionary timescales.

NATURE REVIEWS GENETICS (2021)

Review Spectroscopy

MASS SPECTROMETRY-BASED PERSONALIZED DRUG THERAPY

Jia-Jia Cui et al.

MASS SPECTROMETRY REVIEWS (2020)

Review Oncology

Role of RNA modifications in cancer

Isaia Barbieri et al.

NATURE REVIEWS CANCER (2020)

Article Biotechnology & Applied Microbiology

REPIC: a database for exploring the N6-methyladenosine methylome

Shun Liu et al.

GENOME BIOLOGY (2020)

Article Medicine, General & Internal

Pharmacogenomics

Dan M. Roden et al.

LANCET (2019)

Article Biochemistry & Molecular Biology

MODOMICS: a database of RNA modification pathways. 2017 update

Pietro Boccaletto et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Biochemistry & Molecular Biology

DrugBank 5.0: a major update to the DrugBank database for 2018

David S. Wishart et al.

NUCLEIC ACIDS RESEARCH (2018)

Review Multidisciplinary Sciences

RNA modifications modulate gene expression during development

Michaela Frye et al.

SCIENCE (2018)

Review Biochemistry & Molecular Biology

Dynamic RNA Modifications in Gene Expression Regulation

Ian A. Roundtree et al.

Review Genetics & Heredity

The genetics of drug efficacy: opportunities and challenges

Matthew R. Nelson et al.

NATURE REVIEWS GENETICS (2016)

Review Oncology

Biomarker development in the precision medicine era: lung cancer as a case study

Ashley J. Vargas et al.

NATURE REVIEWS CANCER (2016)

Review Multidisciplinary Sciences

Pharmacogenomics in the clinic

Mary V. Relling et al.

NATURE (2015)

Article Biochemistry & Molecular Biology

Genomics of Drug Sensitivity in Cancer (GDSC): a resource for therapeutic biomarker discovery in cancer cells

Wanjuan Yang et al.

NUCLEIC ACIDS RESEARCH (2013)