Targeting KDM4 for treating PAX3-FOXO1–driven alveolar rhabdomyosarcoma

Advances in histone demethylase KDM4 as cancer therapeutic targets

(2020) Dong Hoon Lee et al.   FASEB JOURNAL

17-DMAG dually inhibits Hsp90 and histone lysine demethylases in alveolar rhabdomyosarcoma

(2020) Shivendra Singh et al.   iScience

Rhabdomyosarcoma

(2019) Stephen X. Skapek et al.   Nature Reviews Disease Primers

Targeting epigenetic modifications in cancer therapy: erasing the roadmap to cancer

(2019) Helai P. Mohammad et al.   NATURE MEDICINE

Twist2 amplification in rhabdomyosarcoma represses myogenesis and promotes oncogenesis by redirecting MyoD DNA binding

(2019) Stephen Li et al.   GENES & DEVELOPMENT

Preclinical rationale for entinostat in embryonal rhabdomyosarcoma

(2019) Narendra Bharathy et al.   Skeletal Muscle

Insights into pediatric rhabdomyosarcoma research: Challenges and goals

(2019) Marielle E. Yohe et al.   PEDIATRIC BLOOD & CANCER

Chemical genomics reveals histone deacetylases are required for core regulatory transcription

(2019) Berkley E. Gryder et al.   Nature Communications

ChIPseqSpikeInFree: A ChIP-seq normalization approach to reveal global changes in histone modifications without spike-in

(2019) Hongjian Jin et al.   BIOINFORMATICS

First-in-Human Study of Mivebresib (ABBV-075), an Oral Pan-Inhibitor of Bromodomain and Extra Terminal Proteins, in Patients with Relapsed/Refractory Solid Tumors

(2019) Sarina A. Piha-Paul et al.   CLINICAL CANCER RESEARCH

Insight into ponatinib resistance mechanisms in rhabdomyosarcoma caused by the mutations in FGFR4 tyrosine kinase using molecular modeling strategies

(2019) Chao Wu et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

Histone hyperacetylation disrupts core gene regulatory architecture in rhabdomyosarcoma

(2019) Berkley E. Gryder et al.   NATURE GENETICS

ASCL1 is a MYCN- and LMO1-dependent member of the adrenergic neuroblastoma core regulatory circuitry

(2019) Lu Wang et al.   Nature Communications

Targeting ALK in pediatric RMS does not induce antitumor activity in vivo

(2018) Monika Wierdl et al.   CANCER CHEMOTHERAPY AND PHARMACOLOGY

Detecting Differential Transcription Factor Activity from ATAC-Seq Data

(2018) Ignacio Tripodi et al.   MOLECULES

Targeted in situ genome-wide profiling with high efficiency for low cell numbers

(2018) Peter J Skene et al.   Nature Protocols

Functional screening of FGFR4-driven tumorigenesis identifies PI3K/mTOR inhibition as a therapeutic strategy in rhabdomyosarcoma

(2018) Timothy McKinnon et al.   ONCOGENE

PAX3-FOXO1 transgenic zebrafish models identify HES3 as a mediator of rhabdomyosarcoma tumorigenesis

(2018) Genevieve C Kendall et al.   eLife

The SS18-SSX Oncoprotein Hijacks KDM2B-PRC1.1 to Drive Synovial Sarcoma

(2018) Ana Banito et al.   CANCER CELL

Identification of Therapeutic Targets in Rhabdomyosarcoma through Integrated Genomic, Epigenomic, and Proteomic Analyses

(2018) Elizabeth Stewart et al.   CANCER CELL

Loss of MST/Hippo signaling in a genetically engineered mouse model of fusion-positive rhabdomyosarcoma accelerates tumorigenesis

(2018) Kristianne M. Oristian et al.   CANCER RESEARCH

Selective gene dependencies in MYCN-amplified neuroblastoma include the core transcriptional regulatory circuitry

(2018) Adam D. Durbin et al.   NATURE GENETICS

The addition of cixutumumab or temozolomide to intensive multiagent chemotherapy is feasible but does not improve outcome for patients with metastatic rhabdomyosarcoma

(2018) Suman Malempati et al.   CANCER

Enhancer Architecture and Essential Core Regulatory Circuitry of Chronic Lymphocytic Leukemia

(2018) Christopher J. Ott et al.   CANCER CELL

Therapeutic Approaches Targeting PAX3-FOXO1 and Its Regulatory and Transcriptional Pathways in Rhabdomyosarcoma

(2018) Thanh Hung Nguyen et al.   MOLECULES

FusionGDB: fusion gene annotation DataBase

(2018) Pora Kim et al.   NUCLEIC ACIDS RESEARCH

The HDAC3–SMARCA4–miR-27a axis promotes expression of the PAX3:FOXO1 fusion oncogene in rhabdomyosarcoma

(2018) Narendra Bharathy et al.   Science Signaling

TBX2 is a neuroblastoma core regulatory circuitry component enhancing MYCN/FOXM1 reactivation of DREAM targets

(2018) Bieke Decaesteker et al.   Nature Communications

PAX3-FOXO1 is essential for tumour initiation and maintenance but not recurrence in a human myoblast model of rhabdomyosarcoma

(2017) Puspa R Pandey et al.   JOURNAL OF PATHOLOGY

HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis

(2017) Ivan V Kulakovskiy et al.   NUCLEIC ACIDS RESEARCH

Histology, fusion status, and outcome in metastatic rhabdomyosarcoma: A report from the Children's Oncology Group

(2017) Erin R. Rudzinski et al.   PEDIATRIC BLOOD & CANCER

Design of KDM4 Inhibitors with Antiproliferative Effects in Cancer Models

(2017) Young K. Chen et al.   ACS Medicinal Chemistry Letters

FOXF1 Defines the Core-Regulatory Circuitry in Gastrointestinal Stromal Tumor

(2017) Leili Ran et al.   Cancer Discovery

PAX3–FOXO1 Establishes Myogenic Super Enhancers and Confers BET Bromodomain Vulnerability

(2017) Berkley E. Gryder et al.   Cancer Discovery

Myogenic regulatory transcription factors regulate growth in rhabdomyosarcoma

(2017) Inês M Tenente et al.   eLife

An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites

(2017) Peter J Skene et al.   eLife

Targeting Aberrant Epigenetic Networks Mediated by PRMT1 and KDM4C in Acute Myeloid Leukemia

(2016) Ngai Cheung et al.   CANCER CELL

Targeting MET Receptor in Rhabdomyosarcoma: Rationale and Progress

(2016) Barbara Szewczyk et al.   CURRENT DRUG TARGETS

Jmjd2/Kdm4 demethylases are required for expression ofIl3raand survival of acute myeloid leukemia cells

(2016) Karl Agger et al.   GENES & DEVELOPMENT

Models of human core transcriptional regulatory circuitries

(2016) Violaine Saint-André et al.   GENOME RESEARCH

Helicase CHD4 is an epigenetic coregulator of PAX3-FOXO1 in alveolar rhabdomyosarcoma

(2016) Maria Böhm et al.   JOURNAL OF CLINICAL INVESTIGATION

Erratum: Mechanism and relevance of EWS/FLI-mediated transcriptional repression in Ewing sarcoma

(2016) S Sankar et al.   ONCOGENE

Epigenetic Determinants of Cancer

(2016) Stephen B. Baylin et al.   Cold Spring Harbor Perspectives in Biology

Clinical Response of Carcinomas Harboring the BRD4-NUT Oncoprotein to the Targeted Bromodomain Inhibitor OTX015/MK-8628

(2016) A. Stathis et al.   Cancer Discovery

Bromodomain inhibitor OTX015 in patients with lymphoma or multiple myeloma: a dose-escalation, open-label, pharmacokinetic, phase 1 study

(2016) Sandy Amorim et al.   Lancet Haematology

The histone demethylase KDM4B interacts with MyoD to regulate myogenic differentiation in C2C12 myoblast cells

(2015) Jang Hyun Choi et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

The Role of Histone Demethylase KDM4B in Myc Signaling in Neuroblastoma

(2015) Jun Yang et al.   JNCI-Journal of the National Cancer Institute

The Role of Histone Demethylase KDM4B in Myc Signaling in Neuroblastoma

(2015) Jun Yang et al.   JNCI-Journal of the National Cancer Institute

A phase 2 trial of R1507, a monoclonal antibody to the insulin-like growth factor-1 receptor (IGF-1R), in patients with recurrent or refractory rhabdomyosarcoma, osteosarcoma, synovial sarcoma, and other soft tissue sarcomas: Results of a Sarcoma Alliance

(2014) Alberto S. Pappo et al.   CANCER

Lineage of origin in rhabdomyosarcoma informs pharmacological response

(2014) J. Abraham et al.   GENES & DEVELOPMENT

RecurrentMYOD1mutations in pediatric and adult sclerosing and spindle cell rhabdomyosarcomas: Evidence for a common pathogenesis

(2014) Narasimhan P. Agaram et al.   GENES CHROMOSOMES & CANCER

A recurrent neomorphic mutation in MYOD1 defines a clinically aggressive subset of embryonal rhabdomyosarcoma associated with PI3K-AKT pathway mutations

(2014) Shinji Kohsaka et al.   NATURE GENETICS

PARP1-dependent recruitment of KDM4D histone demethylase to DNA damage sites promotes double-strand break repair

(2014) H. Khoury-Haddad et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A MYOD1 Mutation Cooperates with PI3K Pathway Activation in ERMS

(2014)   Cancer Discovery

Comprehensive Genomic Analysis of Rhabdomyosarcoma Reveals a Landscape of Alterations Affecting a Common Genetic Axis in Fusion-Positive and Fusion-Negative Tumors

(2014) J. F. Shern et al.   Cancer Discovery

Rhabdomyosarcoma: Current Challenges and Their Implications for Developing Therapies

(2014) S. Hettmer et al.   Cold Spring Harbor Perspectives in Medicine

Oral ciclopirox olamine displays biological activity in a phase I study in patients with advanced hematologic malignancies

(2013) Mark D. Minden et al.   AMERICAN JOURNAL OF HEMATOLOGY

Targeting Oxidative Stress in Embryonal Rhabdomyosarcoma

(2013) Xiang Chen et al.   CANCER CELL

Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

(2013) Jakob Lovén et al.   CELL

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Kdm4b Histone Demethylase Is a DNA Damage Response Protein and Confers a Survival Advantage following γ-Irradiation

(2013) Leah C. Young et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Alveolar rhabdomyosarcoma–associated PAX3-FOXO1 promotes tumorigenesis via Hippo pathway suppression

(2013) Lisa E.S. Crose et al.   JOURNAL OF CLINICAL INVESTIGATION

Transactivating mutation of theMYOD1gene is a frequent event in adult spindle cell rhabdomyosarcoma

(2013) Karoly Szuhai et al.   JOURNAL OF PATHOLOGY

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

The lysine demethylase, KDM4B, is a key molecule in androgen receptor signalling and turnover

(2013) Kelly Coffey et al.   NUCLEIC ACIDS RESEARCH

PAX-FOXO1fusion status drives unfavorable outcome for children with rhabdomyosarcoma: A children's oncology group report

(2013) Stephen X. Skapek et al.   PEDIATRIC BLOOD & CANCER

Targeting Wild-Type and Mutationally Activated FGFR4 in Rhabdomyosarcoma with the Inhibitor Ponatinib (AP24534)

(2013) Samuel Q. Li et al.   PLoS One

Inhibition of PRC2 Activity by a Gain-of-Function H3 Mutation Found in Pediatric Glioblastoma

(2013) P. W. Lewis et al.   SCIENCE

Towards automated crystallographic structure refinement withphenix.refine

(2012) Pavel V. Afonine et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

The Histone Demethylase KDM1A Sustains the Oncogenic Potential of MLL-AF9 Leukemia Stem Cells

(2012) William J. Harris et al.   CANCER CELL

Core Transcriptional Regulatory Circuit Controlled by the TAL1 Complex in Human T Cell Acute Lymphoblastic Leukemia

(2012) Takaomi Sanda et al.   CANCER CELL

Circuitry and Dynamics of Human Transcription Factor Regulatory Networks

(2012) Shane Neph et al.   CELL

FGFR4 Blockade Exerts Distinct Antitumorigenic Effects in Human Embryonal versus Alveolar Rhabdomyosarcoma

(2012) L. E. S. Crose et al.   CLINICAL CANCER RESEARCH

A selective jumonji H3K27 demethylase inhibitor modulates the proinflammatory macrophage response

(2012) Laurens Kruidenier et al.   NATURE

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Histone Demethylase JMJD2B Functions as a Co-Factor of Estrogen Receptor in Breast Cancer Proliferation and Mammary Gland Development

(2011) Masahito Kawazu et al.   PLoS One

Withaferin A-Induced Apoptosis in Human Breast Cancer Cells Is Mediated by Reactive Oxygen Species

(2011) Eun-Ryeong Hahm et al.   PLoS One

Histone demethylase JMJD2B coordinates H3K4/H3K9 methylation and promotes hormonally responsive breast carcinogenesis

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

Features and development ofCoot

(2010) P. Emsley et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Genome-Wide Identification of PAX3-FKHR Binding Sites in Rhabdomyosarcoma Reveals Candidate Target Genes Important for Development and Cancer

(2010) L. Cao et al.   CANCER RESEARCH

The Histone Demethylase JMJD2B Is Regulated by Estrogen Receptor   and Hypoxia, and Is a Key Mediator of Estrogen Induced Growth

(2010) J. Yang et al.   CANCER RESEARCH

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Role of Hypoxia-Inducible Factors in Epigenetic Regulation via Histone Demethylases

(2009) Jun Yang et al.   Annals of the New York Academy of Sciences

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Credentialing a Preclinical Mouse Model of Alveolar Rhabdomyosarcoma

(2009) K. Nishijo et al.   CANCER RESEARCH

PAX3–FOXO1 fusion gene in rhabdomyosarcoma

(2008) Corinne M. Linardic   CANCER LETTERS

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL

Identification of PAX3-FKHR-regulated genes differentially expressed between alveolar and embryonal rhabdomyosarcoma: Focus onMYCN as a biologically relevant target

(2008) Gabriela E. Mercado et al.   GENES CHROMOSOMES & CANCER

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY