m6A-driven SF3B1 translation control steers splicing to direct genome integrity and leukemogenesis

Transcriptome-wide profiling and quantification of N6-methyladenosine by enzyme-assisted adenosine deamination

(2023) Yu-Lan Xiao et al.   NATURE BIOTECHNOLOGY

CANCER-ASSOCIATED SF3B1 MUTATIONS CONFER A BRCA-LIKE CELLULAR PHENOTYPE AND SYNTHETIC LETHALITY TO PARP INHIBITORS

(2022) Katrina M Lappin et al.   CANCER RESEARCH

SF3B1 homeostasis is critical for survival and therapeutic response in T cell leukemia

(2022) Cuijuan Han et al.   Science Advances

m6A RNA modifications are measured at single-base resolution across the mammalian transcriptome

(2022) Lulu Hu et al.   NATURE BIOTECHNOLOGY

Pseudouridine-modified tRNA fragments repress aberrant protein synthesis and predict leukaemic progression in myelodysplastic syndrome

(2022) Nicola Guzzi et al.   NATURE CELL BIOLOGY

Detection of m6A from direct RNA sequencing using a multiple instance learning framework

(2022) Christopher Hendra et al.   NATURE METHODS

Genetic and epigenetic defects of the RNA modification machinery in cancer

(2022) Ines Orsolic et al.   TRENDS IN GENETICS

Oncogenic translation directs spliceosome dynamics revealing an integral role for SF3A3 in breast cancer

(2021) Maciej Cieśla et al.   MOLECULAR CELL

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

Splicing factor mutations in hematologic malignancies

(2021) Sisi Chen et al.   BLOOD

Differential m6A RNA landscapes across hematopoiesis reveal a role for IGF2BP2 in preserving hematopoietic stem cell function

(2021) Rong Yin et al.   Cell Stem Cell

MYC overexpression is associated with an early disease progression from MDS to AML

(2021) David Gajzer et al.   LEUKEMIA RESEARCH

SF3B1 mutations induce R-loop accumulation and DNA damage in MDS and leukemia cells with therapeutic implications

(2020) Shalini Singh et al.   LEUKEMIA

Leukemogenic Chromatin Alterations Promote AML Leukemia Stem Cells via a KDM4C-ALKBH5-AXL Signaling Axis

(2020) Jiazhen Wang et al.   Cell Stem Cell

RNA Demethylase ALKBH5 Selectively Promotes Tumorigenesis and Cancer Stem Cell Self-Renewal in Acute Myeloid Leukemia

(2020) Chao Shen et al.   Cell Stem Cell

Translation control of the immune checkpoint in cancer and its therapeutic targeting

(2019) Yichen Xu et al.   NATURE MEDICINE

Targeting the RNA m6A Reader YTHDF2 Selectively Compromises Cancer Stem Cells in Acute Myeloid Leukemia

(2019) Jasmin Paris et al.   Cell Stem Cell

c-MYC regulates mRNA translation efficiency and start-site selection in lymphoma

(2019) Kamini Singh et al.   JOURNAL OF EXPERIMENTAL MEDICINE

In vivo analysis of influenza A mRNA secondary structures identifies critical regulatory motifs

(2019) Lisa Marie Simon et al.   NUCLEIC ACIDS RESEARCH

Programmable RNA N6-methyladenosine editing by CRISPR-Cas9 conjugates

(2019) Xiao-Min Liu et al.   Nature Chemical Biology

Reading, writing and erasing mRNA methylation

(2019) Sara Zaccara et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Altered m6A Modification of Specific Cellular Transcripts Affects Flaviviridae Infection

(2019) Nandan S. Gokhale et al.   MOLECULAR CELL

Matt: Unix tools for alternative splicing analysis

(2018) André Gohr et al.   BIOINFORMATICS

Impact of spliceosome mutations on RNA splicing in myelodysplasia: dysregulated genes/pathways and clinical associations

(2018) Andrea Pellagatti et al.   BLOOD

Pseudouridylation of tRNA-Derived Fragments Steers Translational Control in Stem Cells

(2018) Nicola Guzzi et al.   CELL

N 6 -Methyladenosine Guides mRNA Alternative Translation during Integrated Stress Response

(2018) Jun Zhou et al.   MOLECULAR CELL

RNA Framework: an all-in-one toolkit for the analysis of RNA structures and post-transcriptional modifications

(2018) Danny Incarnato et al.   NUCLEIC ACIDS RESEARCH

Inhibition of SF3B1 by molecules targeting the spliceosome results in massive aberrant exon skipping

(2018) Gang Wu et al.   RNA

Translational Control in Cancer

(2018) Nathaniel Robichaud et al.   Cold Spring Harbor Perspectives in Biology

Synthetic Lethal and Convergent Biological Effects of Cancer-Associated Spliceosomal Gene Mutations

(2018) Stanley Chun-Wei Lee et al.   CANCER CELL

The Role of m6A/m-RNA Methylation in Stress Response Regulation

(2018) Mareen Engel et al.   NEURON

Characterization and targeting of malignant stem cells in patients with advanced myelodysplastic syndromes

(2018) Brett M. Stevens et al.   Nature Communications

Aberrant splicing and defective mRNA production induced by somatic spliceosome mutations in myelodysplasia

(2018) Yusuke Shiozawa et al.   Nature Communications

Single sample scoring of molecular phenotypes

(2018) Momeneh Foroutan et al.   BMC BIOINFORMATICS

State-of-the-art strategies for targeting the DNA damage response in cancer

(2018) Patrick G. Pilié et al.   Nature Reviews Clinical Oncology

DNA damage response and hematological malignancy

(2017) Masatoshi Takagi   INTERNATIONAL JOURNAL OF HEMATOLOGY

Simplified CRISPR tools for efficient genome editing and streamlined protocols for their delivery into mammalian cells and mouse zygotes

(2017) Ashley M. Jacobi et al.   METHODS

Translation from unconventional 5′ start sites drives tumour initiation

(2017) Ataman Sendoel et al.   NATURE

The N6-methyladenosine (m6A)-forming enzyme METTL3 controls myeloid differentiation of normal hematopoietic and leukemia cells

(2017) Ly P Vu et al.   NATURE MEDICINE

Copy-number and gene dependency analysis reveals partial copy loss of wild-type SF3B1 as a novel cancer vulnerability

(2017) Brenton R Paolella et al.   eLife

The 2016 revision to the World Health Organization classification of myeloid neoplasms and acute leukemia

(2016) D. A. Arber et al.   BLOOD

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

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

RNA Splicing Modulation Selectively Impairs Leukemia Stem Cell Maintenance in Secondary Human AML

(2016) Leslie A. Crews et al.   Cell Stem Cell

Progression in patients with low- and intermediate-1-risk del(5q) myelodysplastic syndromes is predicted by a limited subset of mutations

(2016) Christian Scharenberg et al.   HAEMATOLOGICA

DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo

(2016) Meghan Zubradt et al.   NATURE METHODS

The lncRNA SLNCR1 Mediates Melanoma Invasion through a Conserved SRA1-like Region

(2016) Karyn Schmidt et al.   Cell Reports

Progression in patients with low- and intermediate-1-risk del(5q) myelodysplastic syndromes is predicted by a limited subset of mutations

(2016) Christian Scharenberg et al.   HAEMATOLOGICA

Functional Splicing Network Reveals Extensive Regulatory Potential of the Core Spliceosomal Machinery

(2015) Panagiotis Papasaikas et al.   MOLECULAR CELL

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

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

DNA damage accumulation and repair defects in acute myeloid leukemia: implications for pathogenesis, disease progression, and chemotherapy resistance

(2014) Maria Teresa Esposito et al.   CHROMOSOMA

Identification of a BRCA1-mRNA Splicing Complex Required for Efficient DNA Repair and Maintenance of Genomic Stability

(2014) Kienan I. Savage et al.   MOLECULAR CELL

rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data

(2014) Shihao Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ezh2 loss promotes development of myelodysplastic syndrome but attenuates its predisposition to leukaemic transformation

(2014) Goro Sashida et al.   Nature Communications

Splicing factor mutations and cancer

(2014) Kenichi Yoshida et al.   Wiley Interdisciplinary Reviews-RNA

SF3B1 mutations in chronic lymphocytic leukemia

(2013) Y. Wan et al.   BLOOD

Clinical and biological implications of driver mutations in myelodysplastic syndromes

(2013) E. Papaemmanuil et al.   BLOOD

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

Myc and mTOR converge on a common node in protein synthesis control that confers synthetic lethality in Myc-driven cancers

(2013) M. Pourdehnad et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hematopoietic stem cell and progenitor cell mechanisms in myelodysplastic syndromes

(2013) W. W. Pang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Revised International Prognostic Scoring System for Myelodysplastic Syndromes

(2012) P. L. Greenberg et al.   BLOOD

Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq

(2012) Dan Dominissini et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

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

The spliceosome as a target of novel antitumour drugs

(2012) Sophie Bonnal et al.   NATURE REVIEWS DRUG DISCOVERY

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Polycomb protein EZH2 regulates cancer cell fate decision in response to DNA damage

(2011) Z Wu et al.   CELL DEATH AND DIFFERENTIATION

Functional consequences of developmentally regulated alternative splicing

(2011) Auinash Kalsotra et al.   NATURE REVIEWS GENETICS

SomaticSF3B1Mutation in Myelodysplasia with Ring Sideroblasts

(2011) E. Papaemmanuil et al.   NEW ENGLAND JOURNAL OF MEDICINE

Genetic Dissection of the Oncogenic mTOR Pathway Reveals Druggable Addiction to Translational Control via 4EBP-eIF4E

(2010) Andrew C. Hsieh et al.   CANCER CELL

Deregulation of oncogene-induced senescence and p53 translational control in X-linked dyskeratosis congenita

(2010) Cristian Bellodi et al.   EMBO JOURNAL

Spliceosome Structure and Function

(2010) C. L. Will et al.   Cold Spring Harbor Perspectives in Biology

Microarray-based classifiers and prognosis models identify subgroups with distinct clinical outcomes and high risk of AML transformation of myelodysplastic syndrome

(2009) K. I. Mills et al.   BLOOD

The Spliceosome: Design Principles of a Dynamic RNP Machine

(2009) Markus C. Wahl et al.   CELL

Suppression of the DNA damage response in acute myeloid leukemia versus myelodysplastic syndrome

(2009) S Boehrer et al.   ONCOGENE

Transplantation of a myelodysplastic syndrome by a long-term repopulating hematopoietic cell

(2008) Y. J. Chung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA