Spliceosome-targeted therapies trigger an antiviral immune response in triple-negative breast cancer

Epigenetic therapy induces transcription of inverted SINEs and ADAR1 dependency

(2020) Parinaz Mehdipour et al.   NATURE

Sensitivity to splicing modulation of BCL2 family genes defines cancer therapeutic strategies for splicing modulators

(2019) Daniel Aird et al.   Nature Communications

RNA structure maps across mammalian cellular compartments

(2019) Lei Sun et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Metascape provides a biologist-oriented resource for the analysis of systems-level datasets

(2019) Yingyao Zhou et al.   Nature Communications

Using meshes for MeSH term enrichment and semantic analyses

(2018) Guangchuang Yu   BIOINFORMATICS

The MYC oncogene is a global regulator of the immune response

(2018) Stephanie C. Casey et al.   BLOOD

The dTAG system for immediate and target-specific protein degradation

(2018) Behnam Nabet et al.   Nature Chemical Biology

H3B-8800, an orally available small-molecule splicing modulator, induces lethality in spliceosome-mutant cancers

(2018) Michael Seiler et al.   NATURE MEDICINE

DNA methyltransferase inhibition upregulates MHC-I to potentiate cytotoxic T lymphocyte responses in breast cancer

(2018) Na Luo et al.   Nature Communications

Somatic Mutational Landscape of Splicing Factor Genes and Their Functional Consequences across 33 Cancer Types

(2018) Michael Seiler et al.   Cell Reports

A minimal RNA ligand for potent RIG-I activation in living mice

(2018) Melissa M. Linehan et al.   Science Advances

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

(2018) André Kahles et al.   CANCER CELL

Therapeutically active RIG-I agonist induces immunogenic tumor cell killing in breast cancers

(2018) David L Elion et al.   CANCER RESEARCH

A druggable genome screen identifies modifiers of α-synuclein levels via a tiered cross-species validation approach

(2018) Maxime W.C. Rousseaux et al.   JOURNAL OF NEUROSCIENCE

Intron retention is a source of neoepitopes in cancer

(2018) Alicia C Smart et al.   NATURE BIOTECHNOLOGY

Integrative transcriptome analyses of the aging brain implicate altered splicing in Alzheimer’s disease susceptibility

(2018) Towfique Raj et al.   NATURE GENETICS

Loss of ADAR1 in tumours overcomes resistance to immune checkpoint blockade

(2018) Jeffrey J. Ishizuka et al.   NATURE

Tumor-derived IFN triggers chronic pathway agonism and sensitivity to ADAR loss

(2018) Huayang Liu et al.   NATURE MEDICINE

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Pan-tumor genomic biomarkers for PD-1 checkpoint blockade–based immunotherapy

(2018) Razvan Cristescu et al.   SCIENCE

Identification of ADAR1 adenosine deaminase dependency in a subset of cancer cells

(2018) Hugh S. Gannon et al.   Nature Communications

USP1–UAF1 deubiquitinase complex stabilizes TBK1 and enhances antiviral responses

(2017) Zhongxia Yu et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Basal-A Triple-Negative Breast Cancer Cells Selectively Rely on RNA Splicing for Survival

(2017) Stefanie Chan et al.   MOLECULAR CANCER THERAPEUTICS

Tumor Mutational Burden as an Independent Predictor of Response to Immunotherapy in Diverse Cancers

(2017) Aaron M. Goodman et al.   MOLECULAR CANCER THERAPEUTICS

Selective degradation of splicing factor CAPERα by anticancer sulfonamides

(2017) Taisuke Uehara et al.   Nature Chemical Biology

Tumor Mutational Burden and Response Rate to PD-1 Inhibition

(2017) Mark Yarchoan et al.   NEW ENGLAND JOURNAL OF MEDICINE

Epigenetic therapy activates type I interferon signaling in murine ovarian cancer to reduce immunosuppression and tumor burden

(2017) Meredith L. Stone et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Anticancer sulfonamides target splicing by inducing RBM39 degradation via recruitment to DCAF15

(2017) Ting Han et al.   SCIENCE

MYC: Master Regulator of Immune Privilege

(2017) Stephanie C. Casey et al.   TRENDS IN IMMUNOLOGY

Mutant U2AF1-expressing cells are sensitive to pharmacological modulation of the spliceosome

(2017) Cara Lunn Shirai et al.   Nature Communications

Identification of a small molecule inhibitor that stalls splicing at an early step of spliceosome activation

(2017) Anzhalika Sidarovich et al.   eLife

Transcriptomic Characterization of SF3B1 Mutation Reveals Its Pleiotropic Effects in Chronic Lymphocytic Leukemia

(2016) Lili Wang et al.   CANCER CELL

Physiologic Expression of Sf3b1 K700E Causes Impaired Erythropoiesis, Aberrant Splicing, and Sensitivity to Therapeutic Spliceosome Modulation

(2016) Esther A. Obeng et al.   CANCER CELL

Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma

(2016) Willy Hugo et al.   CELL

E3 ubiquitin ligase RNF128 promotes innate antiviral immunity through K63-linked ubiquitination of TBK1

(2016) Guanhua Song et al.   NATURE IMMUNOLOGY

Modulation of splicing catalysis for therapeutic targeting of leukemia with mutations in genes encoding spliceosomal proteins

(2016) Stanley Chun-Wei Lee et al.   NATURE MEDICINE

Global analysis of pre-mRNA subcellular localization following splicing inhibition by spliceostatin A

(2016) Rei Yoshimoto et al.   RNA

MYC regulates the antitumor immune response through CD47 and PD-L1

(2016) S. C. Casey et al.   SCIENCE

Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade

(2016) N. McGranahan et al.   SCIENCE

A new view of transcriptome complexity and regulation through the lens of local splicing variations

(2016) Jorge Vaquero-Garcia et al.   eLife

Tyrosine Phosphorylation of Caspase-8 Abrogates Its Apoptotic Activity and Promotes Activation of c-Src

(2016) Jennifer LY Tsang et al.   PLoS One

F-box protein Fbxo3 targets Smurf1 ubiquitin ligase for ubiquitination and degradation

(2015) Dongnian Li et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

SRSF2 Mutations Contribute to Myelodysplasia by Mutant-Specific Effects on Exon Recognition

(2015) Eunhee Kim et al.   CANCER CELL

Molecular and Genetic Properties of Tumors Associated with Local Immune Cytolytic Activity

(2015) Michael S. Rooney et al.   CELL

DNA-Demethylating Agents Target Colorectal Cancer Cells by Inducing Viral Mimicry by Endogenous Transcripts

(2015) David Roulois et al.   CELL

Inhibiting DNA Methylation Causes an Interferon Response in Cancer via dsRNA Including Endogenous Retroviruses

(2015) Katherine B. Chiappinelli et al.   CELL

The SF3B1 inhibitor spliceostatin A (SSA) elicits apoptosis in chronic lymphocytic leukaemia cells through downregulation of Mcl-1

(2015) M Larrayoz et al.   LEUKEMIA

The spliceosome is a therapeutic vulnerability in MYC-driven cancer

(2015) Tiffany Y.-T. Hsu et al.   NATURE

MYC regulates the core pre-mRNA splicing machinery as an essential step in lymphomagenesis

(2015) Cheryl M. Koh et al.   NATURE

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

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

(2015) Antonio Colaprico et al.   NUCLEIC ACIDS RESEARCH

Disease-associated mutation inSRSF2misregulates splicing by altering RNA-binding affinities

(2015) Jian Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer

(2015) N. A. Rizvi et al.   SCIENCE

Cancer-Associated SF3B1 Hotspot Mutations Induce Cryptic 3′ Splice Site Selection through Use of a Different Branch Point

(2015) Rachel B. Darman et al.   Cell Reports

Widespread intron retention diversifies most cancer transcriptomes

(2015) Heidi Dvinge et al.   Genome Medicine

Transcriptome Sequencing Reveals Potential Mechanism of Cryptic 3’ Splice Site Selection in SF3B1-mutated Cancers

(2015) Christopher DeBoever et al.   PLoS Computational Biology

TDP‐1, theCaenorhabditis elegansortholog of TDP‐43, limits the accumulation of double‐stranded RNA

(2014) Tassa K Saldi et al.   EMBO JOURNAL

Widespread intron retention in mammals functionally tunes transcriptomes

(2014) Ulrich Braunschweig et al.   GENOME RESEARCH

Identification of Small Molecule Inhibitors of Pre-mRNA Splicing

(2014) Andrea Pawellek et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A Novel Mitochondrial MAVS/Caspase-8 Platform Links RNA Virus-Induced Innate Antiviral Signaling to Bax/Bak-Independent Apoptosis

(2014) S. El Maadidi et al.   JOURNAL OF IMMUNOLOGY

Antiviral immunity via RIG-I-mediated recognition of RNA bearing 5′-diphosphates

(2014) Delphine Goubau et al.   NATURE

Genetic Basis for Clinical Response to CTLA-4 Blockade in Melanoma

(2014) Alexandra Snyder et al.   NEW ENGLAND JOURNAL OF MEDICINE

Organizing Principles of Mammalian Nonsense-Mediated mRNA Decay

(2013) Maximilian Wei-Lin Popp et al.   Annual Review of Genetics

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Orchestrated Intron Retention Regulates Normal Granulocyte Differentiation

(2013) Justin J.-L. Wong et al.   CELL

The interaction between the helicase DHX33 and IPS-1 as a novel pathway to sense double-stranded RNA and RNA viruses in myeloid dendritic cells

(2013) Ying Liu et al.   Cellular & Molecular Immunology

Genome-wide RNAi screens in human brain tumor isolates reveal a novel viability requirement for PHF5A

(2013) C. G. Hubert et al.   GENES & DEVELOPMENT

Regulation of constitutive and alternative splicing by PRMT5 reveals a role for Mdm4 pre-mRNA in sensing defects in the spliceosomal machinery

(2013) M. Bezzi et al.   GENES & DEVELOPMENT

Spatiotemporal Dynamics of Intratumoral Immune Cells Reveal the Immune Landscape in Human Cancer

(2013) Gabriela Bindea et al.   IMMUNITY

Targeting F Box Protein Fbxo3 To Control Cytokine-Driven Inflammation

(2013) R. K. Mallampalli et al.   JOURNAL OF IMMUNOLOGY

Optimization of Antitumor Modulators of Pre-mRNA Splicing

(2013) Chandraiah Lagisetti et al.   JOURNAL OF MEDICINAL CHEMISTRY

U1 small nuclear ribonucleoprotein complex and RNA splicing alterations in Alzheimer's disease

(2013) B. Bai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic Screens in Human Cells Using the CRISPR-Cas9 System

(2013) Tim Wang et al.   SCIENCE

Misregulation of Pre-mRNA Alternative Splicing in Cancer

(2013) J. Zhang et al.   Cancer Discovery

Cytoplasmic intron retention, function, splicing, and the sentinel RNA hypothesis

(2013) Peter T. Buckley et al.   Wiley Interdisciplinary Reviews-RNA

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Transcriptional Amplification in Tumor Cells with Elevated c-Myc

(2012) Charles Y. Lin et al.   CELL

A Quantitative High-Throughput In Vitro Splicing Assay Identifies Inhibitors of Spliceosome Catalysis

(2012) M. G. Berg et al.   MOLECULAR AND CELLULAR BIOLOGY

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Oncogenic Splicing Factor SRSF1 Is a Critical Transcriptional Target of MYC

(2012) Shipra Das et al.   Cell Reports

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

MAVS Forms Functional Prion-like Aggregates to Activate and Propagate Antiviral Innate Immune Response

(2011) Fajian Hou et al.   CELL

Biological validation that SF3b is a target of the antitumor macrolide pladienolide

(2011) Akira Yokoi et al.   FEBS Journal

DDX1, DDX21, and DHX36 Helicases Form a Complex with the Adaptor Molecule TRIF to Sense dsRNA in Dendritic Cells

(2011) Zhiqiang Zhang et al.   IMMUNITY

Caspase-8-mediated Cleavage Inhibits IRF-3 Protein by Facilitating Its Proteasome-mediated Degradation

(2011) Nathaniel Sears et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

DHX9 Pairs with IPS-1 To Sense Double-Stranded RNA in Myeloid Dendritic Cells

(2011) Z. Zhang et al.   JOURNAL OF IMMUNOLOGY

Recurrent mutations in the U2AF1 splicing factor in myelodysplastic syndromes

(2011) Timothy A Graubert et al.   NATURE GENETICS

The pINDUCER lentiviral toolkit for inducible RNA interference in vitro and in vivo

(2011) Kristen L. Meerbrey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A SUMOylation-Dependent Transcriptional Subprogram Is Required for Myc-Driven Tumorigenesis

(2011) J. D. Kessler et al.   SCIENCE

An Alternative Splicing Network Links Cell-Cycle Control to Apoptosis

(2010) Michael J. Moore et al.   CELL

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Key Role of Ubc5 and Lysine-63 Polyubiquitination in Viral Activation of IRF3

(2009) Wenwen Zeng et al.   MOLECULAR CELL

Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1

(2009) David A. Barbie et al.   NATURE

HnRNP proteins controlled by c-Myc deregulate pyruvate kinase mRNA splicing in cancer

(2009) Charles J. David et al.   NATURE

MAVS-Mediated Apoptosis and Its Inhibition by Viral Proteins

(2009) Yu Lei et al.   PLoS One

5'-triphosphate RNA requires base-paired structures to activate antiviral signaling via RIG-I

(2009) A. Schmidt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Length-dependent recognition of double-stranded ribonucleic acids by retinoic acid–inducible gene-I and melanoma differentiation–associated gene 5

(2008) Hiroki Kato et al.   JOURNAL OF EXPERIMENTAL MEDICINE