Alternative splicing perturbation landscape identifies RNA binding proteins as potential therapeutic targets in cancer

The p53-induced RNA-binding protein ZMAT3 is a splicing regulator that inhibits the splicing of oncogenic CD44 variants in colorectal carcinoma

(2021) Bruna R. Muys et al.   GENES & DEVELOPMENT

Clinical, surgical, pathological and follow-up features of kidney cancer patients with Von Hippel-Lindau syndrome: novel insights from a large consortium

(2021) Umberto Capitanio et al.   WORLD JOURNAL OF UROLOGY

RBP EIF2S2 Promotes Tumorigenesis and Progression by Regulating MYC-Mediated Inhibition via FHIT-Related Enhancers

(2020) Jiwei Zhang et al.   MOLECULAR THERAPY

Complex impact of DNA methylation on transcriptional dysregulation across 22 human cancer types

(2020) Zishan Wang et al.   NUCLEIC ACIDS RESEARCH

Arid5a, an RNA-Binding Protein in Immune Regulation: RNA Stability, Inflammation, and Autoimmunity

(2020) Kishan Kumar Nyati et al.   TRENDS IN IMMUNOLOGY

Pan-cancer characterization of immune-related lncRNAs identifies potential oncogenic biomarkers

(2020) Yongsheng Li et al.   Nature Communications

A pan-cancer analysis of PBAF complex mutations and their association with immunotherapy response

(2020) A. Ari Hakimi et al.   Nature Communications

Metastasis Suppressors NME1 and NME2 Promote Dynamin 2 Oligomerization and Regulate Tumor Cell Endocytosis, Motility and Metastasis.

(2019) Imran Khan et al.   CANCER RESEARCH

Vitamin D differentially regulates colon stem cells in patient‐derived normal and tumor organoids

(2019) Asunción Fernández‐Barral et al.   FEBS Journal

Cancer the‘RBP’eutics–RNA-binding proteins as therapeutic targets for cancer

(2019) Shakur Mohibi et al.   PHARMACOLOGY & THERAPEUTICS

Molecular characterization and clinical relevance of m6A regulators across 33 cancer types

(2019) Yongsheng Li et al.   Molecular Cancer

C6orf203 is an RNA-binding protein involved in mitochondrial protein synthesis

(2019) Shreekara Gopalakrishna et al.   NUCLEIC ACIDS RESEARCH

Pan-cancer analysis of clinical relevance of alternative splicing events in 31 human cancers

(2019) Yangjun Zhang et al.   ONCOGENE

RNA-binding protein isoforms ZAP-S and ZAP-L have distinct antiviral and immune resolution functions

(2019) Johannes Schwerk et al.   NATURE IMMUNOLOGY

The RNA-Binding Protein A1CF Regulates Hepatic Fructose and Glycerol Metabolism via Alternative RNA Splicing

(2019) Kostas C. Nikolaou et al.   Cell Reports

Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer

(2018) Katherine A. Hoadley et al.   CELL

Cancer-Cell-Intrinsic Mechanisms Shaping the Tumor Immune Landscape

(2018) Max D. Wellenstein et al.   IMMUNITY

The RNA-binding protein PTBP1 is necessary for B cell selection in germinal centers

(2018) Elisa Monzón-Casanova et al.   NATURE IMMUNOLOGY

APOBEC3B and APOBEC mutational signature as potential predictive markers for immunotherapy response in non-small cell lung cancer

(2018) Shixiang Wang et al.   ONCOGENE

Gene Regulatory Network Perturbation by Genetic and Epigenetic Variation

(2018) Yongsheng Li et al.   TRENDS IN BIOCHEMICAL SCIENCES

Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients

(2018) André Kahles et al.   CANCER CELL

Translation acrobatics: how cancer cells exploit alternate modes of translational initiation

(2018) Ashwin Sriram et al.   EMBO REPORTS

AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors

(2018) Hui Hu et al.   NUCLEIC ACIDS RESEARCH

Systematic Analysis of Survival-Associated Alternative Splicing Signatures in Gastrointestinal Pan-Adenocarcinomas

(2018) Peng Lin et al.   EBioMedicine

RNA binding protein RALY promotes Protein Arginine Methyltransferase 1 alternatively spliced isoform v2 relative expression and metastatic potential in breast cancer cells

(2017) Emma Bondy-Chorney et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Multilayered Control of Alternative Splicing Regulatory Networks by Transcription Factors

(2017) Hong Han et al.   MOLECULAR CELL

Alternative splicing: A thermometer controlling gene expression

(2017) Linda Koch   NATURE REVIEWS GENETICS

Systematic Analysis of the Expression of the Mitochondrial ATP Synthase (Complex V) Subunits in Clear Cell Renal Cell Carcinoma

(2017) Maria Brüggemann et al.   Translational Oncology

The Relationship between Alternative Splicing and Proteomic Complexity

(2017) Benjamin J. Blencowe   TRENDS IN BIOCHEMICAL SCIENCES

Alternative splicing discriminates molecular subtypes and has prognostic impact in diffuse large B-cell lymphoma

(2017) S-K Leivonen et al.   Blood Cancer Journal

Revealing the Determinants of Widespread Alternative Splicing Perturbation in Cancer

(2017) Yongsheng Li et al.   Cell Reports

The Functional Impact of Alternative Splicing in Cancer

(2017) Héctor Climente-González et al.   Cell Reports

Robust stratification of breast cancer subtypes using differential patterns of transcript isoform expression

(2017) Thomas P. Stricker et al.   PLoS Genetics

Large-scale analysis of genome and transcriptome alterations in multiple tumors unveils novel cancer-relevant splicing networks

(2016) Endre Sebestyén et al.   GENOME RESEARCH

Resources for the Comprehensive Discovery of Functional RNA Elements

(2016) Balaji Sundararaman et al.   MOLECULAR CELL

ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data

(2016) Ke-Ren Zhou et al.   NUCLEIC ACIDS RESEARCH

CD44 high CD24 low molecular signature determines the Cancer Stem Cell and EMT phenotype in Oral Squamous Cell Carcinoma

(2016) Sangeeta Ghuwalewala et al.   Stem Cell Research

Oncogenic Deregulation of EZH2 as an Opportunity for Targeted Therapy in Lung Cancer

(2016) H. Zhang et al.   Cancer Discovery

The Cardiomyocyte RNA-Binding Proteome: Links to Intermediary Metabolism and Heart Disease

(2016) Yalin Liao et al.   Cell Reports

Pelitinib (EKB-569) targets the up-regulation of ABCB1 and ABCG2 induced by hyperthermia to eradicate lung cancer

(2015) Kenneth K W To et al.   BRITISH JOURNAL OF PHARMACOLOGY

Intron retention is a widespread mechanism of tumor-suppressor inactivation

(2015) Hyunchul Jung et al.   NATURE GENETICS

Detection of recurrent alternative splicing switches in tumor samples reveals novel signatures of cancer

(2015) Endre Sebestyén et al.   NUCLEIC ACIDS RESEARCH

TCGASpliceSeq a compendium of alternative mRNA splicing in cancer

(2015) Michael Ryan et al.   NUCLEIC ACIDS RESEARCH

TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data

(2015) Antonio Colaprico et al.   NUCLEIC ACIDS RESEARCH

A Gene Gravity Model for the Evolution of Cancer Genomes: A Study of 3,000 Cancer Genomes across 9 Cancer Types

(2015) Feixiong Cheng et al.   PLoS Computational Biology

Complement Receptor 1 Genetic Variants Contribute to the Susceptibility to Gastric Cancer in Chinese Population

(2015) Lina Zhao et al.   Journal of Cancer

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

Dissecting the expression landscape of RNA-binding proteins in human cancers

(2014) Bobak Kechavarzi et al.   GENOME BIOLOGY

GSVA: gene set variation analysis for microarray and RNA-Seq data

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

Control of alternative splicing in immune responses: many regulators, many predictions, much still to learn

(2013) Nicole M. Martinez et al.   IMMUNOLOGICAL REVIEWS

RBM5, 6, and 10 Differentially Regulate NUMB Alternative Splicing to Control Cancer Cell Proliferation

(2013) Elias G. Bechara et al.   MOLECULAR CELL

Evidence for APOBEC3B mutagenesis in multiple human cancers

(2013) Michael B Burns et al.   NATURE GENETICS

SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts

(2012) Michael C. Ryan et al.   BIOINFORMATICS

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

(2012) Wanjuan Yang et al.   NUCLEIC ACIDS RESEARCH

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

Deciphering the role of RNA-binding proteins in the post-transcriptional control of gene expression

(2011) S. Kishore et al.   Briefings in Functional Genomics

Extensive relationship between antisense transcription and alternative splicing in the human genome

(2011) A. Sorana Morrissy et al.   GENOME RESEARCH

ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking

(2010) Matthew D. Wilkerson et al.   BIOINFORMATICS

Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP

(2010) Markus Hafner et al.   CELL

Splicing factors PTBP1 and PTBP2 promote proliferation and migration of glioma cell lines

(2009) Hannah C. Cheung et al.   BRAIN

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

(2008) Qun Pan et al.   NATURE GENETICS

Modulation of the antitumor immune response by complement

(2008) Maciej M Markiewski et al.   NATURE IMMUNOLOGY