Multi-level functional genomics reveals molecular and cellular oncogenicity of patient-based 3′ untranslated region mutations

Cancer statistics, 2022

(2022) Rebecca L. Siegel et al.   CA-A CANCER JOURNAL FOR CLINICIANS

FXR1 can bind with the CFIm25/CFIm68 complex and promote the progression of urothelial carcinoma of the bladder by stabilizing TRAF1 mRNA

(2022) Minhua Deng et al.   Cell Death & Disease

ASCL1 activates neuronal stem cell-like lineage programming through remodeling of the chromatin landscape in prostate cancer

(2022) Shaghayegh Nouruzi et al.   Nature Communications

Fibroblast-derived LPP as a biomarker for treatment response and therapeutic target in gastric cancer

(2022) Hao Wang et al.   Molecular Therapy-Oncolytics

FOXA1 regulates alternative splicing in prostate cancer

(2022) Marco Del Giudice et al.   Cell Reports

In Vivo Application of CRISPR/Cas9 Revealed Implication of Foxa1 and Foxp1 in Prostate Cancer Proliferation and Epithelial Plasticity

(2022) Huiqiang Cai et al.   Cancers

Silencing of KNTC1 inhibits hepatocellular carcinoma cells progression via suppressing PI3K/Akt pathway

(2022) Hui Tong et al.   CELLULAR SIGNALLING

Myeloid-derived suppressor cells promote lung cancer metastasis by CCL11 to activate ERK and AKT signaling and induce epithelial-mesenchymal transition in tumor cells

(2021) Shouheng Lin et al.   ONCOGENE

Massively parallel assessment of human variants with base editor screens

(2021) Ruth E. Hanna et al.   CELL

Functional interrogation of DNA damage response variants with base editing screens

(2021) Raquel Cuella-Martin et al.   CELL

Musashi 2 influences chronic lymphocytic leukemia cell survival and growth making it a potential therapeutic target

(2021) Florencia Palacios et al.   LEUKEMIA

Regulatory genomic circuitry of human disease loci by integrative epigenomics

(2021) Carles A. Boix et al.   NATURE

Small-molecule inhibitors of histone deacetylase improve CRISPR-based adenine base editing

(2021) Ha Rim Shin et al.   NUCLEIC ACIDS RESEARCH

Genome-wide functional screen of 3′UTR variants uncovers causal variants for human disease and evolution

(2021) Dustin Griesemer et al.   CELL

Genome-wide interrogation of gene functions through base editor screens empowered by barcoded sgRNAs

(2021) Ping Xu et al.   NATURE BIOTECHNOLOGY

Zwint facilitates melanoma progression by promoting c‑Myc expression

(2021) Kuanhou Mou et al.   Experimental and Therapeutic Medicine

Multiplexed functional genomic analysis of 5’ untranslated region mutations across the spectrum of prostate cancer

(2021) Yiting Lim et al.   Nature Communications

MicroRNA-21 deficiency suppresses prostate cancer progression through downregulation of the IRS1-SREBP-1 signaling pathway

(2021) Thanigaivelan Kanagasabai et al.   CANCER LETTERS

RNA-binding protein FXR1 drives cMYC translation by recruiting eIF4F complex to the translation start site

(2021) Jasmine George et al.   Cell Reports

Loss of MBD2 attenuates MLL-AF9-driven leukemogenesis by suppressing the leukemic cell cycle via CDKN1C

(2021) Kuangguo Zhou et al.   Oncogenesis

Phage-assisted evolution of an adenine base editor with improved Cas domain compatibility and activity

(2020) Michelle F. Richter et al.   NATURE BIOTECHNOLOGY

Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors

(2020) Andrew V. Anzalone et al.   NATURE BIOTECHNOLOGY

mRNAs, proteins and the emerging principles of gene expression control

(2020) Christopher Buccitelli et al.   NATURE REVIEWS GENETICS

The role of SOX family members in solid tumours and metastasis

(2019) Daniela Grimm et al.   SEMINARS IN CANCER BIOLOGY

Genomic correlates of clinical outcome in advanced prostate cancer

(2019) Wassim Abida et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A massively parallel 3′ UTR reporter assay reveals relationships between nucleotide content, sequence conservation, and mRNA destabilization

(2019) Adam J. Litterman et al.   GENOME RESEARCH

Modeling RNA-Binding Protein Specificity In Vivo by Precisely Registering Protein-RNA Crosslink Sites

(2019) Huijuan Feng et al.   MOLECULAR CELL

Continuous evolution of base editors with expanded target compatibility and improved activity

(2019) Benjamin W. Thuronyi et al.   NATURE BIOTECHNOLOGY

Small-molecule targeting of MUSASHI RNA-binding activity in acute myeloid leukemia

(2019) Gerard Minuesa et al.   Nature Communications

Molecular profiling stratifies diverse phenotypes of treatment-refractory metastatic castration-resistant prostate cancer

(2019) Mark P. Labrecque et al.   JOURNAL OF CLINICAL INVESTIGATION

Rational discovery of antimetastatic agents targeting the intrinsically disordered region of MBD2

(2019) Min Young Kim et al.   Science Advances

Genomic Alteration Burden in Advanced Prostate Cancer and Therapeutic Implications

(2019) Matthew J. Ryan et al.   Frontiers in Oncology

RNA‐binding protein Musashi2 stabilizing androgen receptor drives prostate cancer progression

(2019) Jing Zhao et al.   CANCER SCIENCE

GenomicScores: seamless access to genomewide position-specific scores from R and Bioconductor

(2018) Pau Puigdevall et al.   BIOINFORMATICS

Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer

(2018) David A. Quigley et al.   CELL

Proteomic Analysis of Charcoal-Stripped Fetal Bovine Serum Reveals Changes in the Insulin-Like Growth Factor Signaling Pathway

(2018) Chengjian Tu et al.   JOURNAL OF PROTEOME RESEARCH

Strelka2: fast and accurate calling of germline and somatic variants

(2018) Sangtae Kim et al.   NATURE METHODS

Cellular plasticity and the neuroendocrine phenotype in prostate cancer

(2018) Alastair H. Davies et al.   Nature Reviews Urology

PTRE-seq reveals mechanism and interactions of RNA binding proteins and miRNAs

(2018) Kyle A. Cottrell et al.   Nature Communications

XenofilteR: computational deconvolution of mouse and human reads in tumor xenograft sequence data

(2018) Roelof J. C. Kluin et al.   BMC BIOINFORMATICS

Base editing: precision chemistry on the genome and transcriptome of living cells

(2018) Holly A. Rees et al.   NATURE REVIEWS GENETICS

miRBase: from microRNA sequences to function

(2018) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

COSMIC: the Catalogue Of Somatic Mutations In Cancer

(2018) John G Tate et al.   NUCLEIC ACIDS RESEARCH

The risk variant rs884225 within EGFR impairs miR-103a-3p’s anti-tumourigenic function in non-small cell lung cancer

(2018) Zhongyi Fan et al.   ONCOGENE

Genome-Wide CRISPR Screen Identifies Regulators of Mitogen-Activated Protein Kinase as Suppressors of Liver Tumors in Mice

(2017) Chun-Qing Song et al.   GASTROENTEROLOGY

Cancer-associated fibroblasts regulate endothelial adhesion protein LPP to promote ovarian cancer chemoresistance

(2017) Cecilia S. Leung et al.   JOURNAL OF CLINICAL INVESTIGATION

A Massively Parallel Reporter Assay of 3′ UTR Sequences Identifies In Vivo Rules for mRNA Degradation

(2017) Michal Rabani et al.   MOLECULAR CELL

m6A modulates haematopoietic stem and progenitor cell specification

(2017) Chunxia Zhang et al.   NATURE

Genomic hallmarks of localized, non-indolent prostate cancer

(2017) Michael Fraser et al.   NATURE

LPP is a Src substrate required for invadopodia formation and efficient breast cancer lung metastasis

(2017) Elaine Ngan et al.   Nature Communications

Epigenetically regulated Fibronectin leucine rich transmembrane protein 2 (FLRT2) shows tumor suppressor activity in breast cancer cells

(2017) Hansol Bae et al.   Scientific Reports

High-throughput discovery of post-transcriptional cis-regulatory elements

(2016) Erin M. Wissink et al.   BMC GENOMICS

GLI pathogenesis-related 1 functions as a tumor-suppressor in lung cancer

(2016) Xiumei Sheng et al.   Molecular Cancer

Genome-wide assessment of differential translations with ribosome profiling data

(2016) Zhengtao Xiao et al.   Nature Communications

Integrative Clinical Genomics of Advanced Prostate Cancer

(2015) Dan Robinson et al.   CELL

The Molecular Taxonomy of Primary Prostate Cancer

(2015) Adam Abeshouse et al.   CELL

LPP inhibits collective cell migration during lung cancer dissemination

(2015) S Kuriyama et al.   ONCOGENE

Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data

(2014) F. Favero et al.   ANNALS OF ONCOLOGY

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Insulin-like growth factor receptor-1 (IGF-IR) as a target for prostate cancer therapy

(2014) Jennifer Wu et al.   CANCER AND METASTASIS REVIEWS

Downregulation of BRCA1 protein in BCR-ABL1 leukemia cells depends on stress-triggered TIAR-mediated suppression of translation

(2014) Paulina Podszywalow-Bartnicka et al.   CELL CYCLE

RNA Bind-n-Seq: Quantitative Assessment of the Sequence and Structural Binding Specificity of RNA Binding Proteins

(2014) Nicole Lambert et al.   MOLECULAR CELL

Massively parallel functional annotation of 3′ untranslated regions

(2014) Wenxue Zhao et al.   NATURE BIOTECHNOLOGY

PyClone: statistical inference of clonal population structure in cancer

(2014) Andrew Roth et al.   NATURE METHODS

Systematic Identification of Regulatory Elements in Conserved 3′ UTRs of Human Transcripts

(2014) Panos Oikonomou et al.   Cell Reports

Physiological networks and disease functions of RNA-binding protein AUF1

(2014) Ashleigh E. Moore et al.   Wiley Interdisciplinary Reviews-RNA

Insulin-like growth factor-1 receptor (IGF1R) as a novel target in chronic lymphocytic leukemia

(2013) N. Yaktapour et al.   BLOOD

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

(2013) Edward Y Chen et al.   BMC BIOINFORMATICS

IGF1R-directed targeted therapy enhances the cytotoxic effect of chemotherapy in endometrial cancer

(2013) Connie Bitelman et al.   CANCER LETTERS

Systemic GLIPR1-ΔTM protein as a novel therapeutic approach for prostate cancer

(2013) Theodoros Karantanos et al.   INTERNATIONAL JOURNAL OF CANCER

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells

(2013) Yanfang Fu et al.   NATURE BIOTECHNOLOGY

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

GLIPR1 Suppresses Prostate Cancer Development through Targeted Oncoprotein Destruction

(2011) L. Li et al.   CANCER RESEARCH

Interleukin-1 Activates Synthesis of Interleukin-6 by Interfering with a KH-type Splicing Regulatory Protein (KSRP)-dependent Translational Silencing Mechanism

(2011) Sonam Dhamija et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Integrative Genomic Profiling of Human Prostate Cancer

(2010) Barry S. Taylor et al.   CANCER CELL

Rapid-Response Splicing Reporter Screens Identify Differential Regulators of Constitutive and Alternative Splicing

(2010) I. Younis et al.   MOLECULAR AND CELLULAR BIOLOGY

Post-transcriptional regulation of androgen receptor mRNA by an ErbB3 binding protein 1 in prostate cancer

(2010) Hua Zhou et al.   NUCLEIC ACIDS RESEARCH

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

SSBP2 is an in vivo tumor suppressor and regulator of LDB1 stability

(2010) Y Wang et al.   ONCOGENE

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

An A13 Repeat within the 3'-Untranslated Region of Epidermal Growth Factor Receptor (EGFR) Is Frequently Mutated in Microsatellite Instability Colon Cancers and Is Associated with Increased EGFR Expression

(2009) Z. Yuan et al.   CANCER RESEARCH

miR-21: An Androgen Receptor-Regulated MicroRNA that Promotes Hormone-Dependent and Hormone-Independent Prostate Cancer Growth

(2009) J. Ribas et al.   CANCER RESEARCH

Role of Eotaxin-1 Signaling in Ovarian Cancer

(2009) V. Levina et al.   CLINICAL CANCER RESEARCH

Igf1r as a therapeutic target in a mouse model of basal-like breast cancer

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

ssDNA-Binding Protein 2 Is Frequently Hypermethylated and Suppresses Cell Growth in Human Prostate Cancer

(2008) J.-W. Liu et al.   CLINICAL CANCER RESEARCH

EBP1, an ErbB3-binding protein, is decreased in prostate cancer and implicated in hormone resistance

(2008) Yuexing Zhang et al.   MOLECULAR CANCER THERAPEUTICS

The Vienna RNA Websuite

(2008) A. R. Gruber et al.   NUCLEIC ACIDS RESEARCH