Loss of SYNCRIP unleashes APOBEC-driven mutagenesis, tumor heterogeneity, and AR-targeted therapy resistance in prostate cancer

RNA binding protein SYNCRIP maintains proteostasis and self-renewal of hematopoietic stem and progenitor cells

(2023) Florisela Herrejon Chavez et al.   Nature Communications

Chromatin profiles classify castration-resistant prostate cancers suggesting therapeutic targets

(2022) Fanying Tang et al.   SCIENCE

Mechanisms of APOBEC3 mutagenesis in human cancer cells

(2022) Mia Petljak et al.   NATURE

Identification of therapeutic targets and prognostic biomarkers from the hnRNP family in invasive breast carcinoma

(2021) Jiawei Zhou et al.   Aging-US

HDAC5 loss impairs RB repression of pro-oncogenic genes and confers CDK4/6 inhibitor resistance in cancer

(2021) Yingke Zhou et al.   CANCER RESEARCH

Targeting p300/CBP axis in lethal prostate cancer

(2021) Jonathan Welti et al.   Cancer Discovery

MYC-mediated ribosomal gene expression sensitizes enzalutamide-resistant prostate cancer cells to EP300/CREBBP inhibitors

(2021) Tobias Furlan et al.   AMERICAN JOURNAL OF PATHOLOGY

An extended APOBEC3A mutation signature in cancer

(2021) Adam Langenbucher et al.   Nature Communications

Posttranslational regulation of FOXA1 by Polycomb and BUB3/USP7 deubiquitin complex in prostate cancer

(2021) Su H. Park et al.   Science Advances

Loss of polycomb repressive complex 1 activity and chromosomal instability drive uveal melanoma progression

(2021) Mathieu F. Bakhoum et al.   Nature Communications

p300 is upregulated by docetaxel and is a target in chemoresistant prostate cancer

(2020) Martina Gruber et al.   ENDOCRINE-RELATED CANCER

Syncrip/hnRNP Q is required for activity-induced Msp300/Nesprin-1 expression and new synapse formation

(2020) Joshua Titlow et al.   JOURNAL OF CELL BIOLOGY

The repertoire of mutational signatures in human cancer

(2020) Ludmil B. Alexandrov et al.   NATURE

Tumor neoantigenicity assessment with CSiN score incorporates clonality and immunogenicity to predict immunotherapy outcomes

(2020) Tianshi Lu et al.   Science Immunology

Androgen-induced Epigenetic Profiles of Polycomb and Trithorax Genes in Prostate Cancer Cells

(2020) SONGPING WANG et al.   ANTICANCER RESEARCH

Loss of CHD1 Promotes Heterogeneous Mechanisms of Resistance to AR-Targeted Therapy via Chromatin Dysregulation

(2020) Zeda Zhang et al.   CANCER CELL

Intratumor Heterogeneity: The Rosetta Stone of Therapy Resistance

(2020) Andriy Marusyk et al.   CANCER CELL

A genomic and epigenomic atlas of prostate cancer in Asian populations

(2020) Jing Li et al.   NATURE

A novel antisense lncRNA NT5E promotes progression by modulating the expression of SYNCRIP and predicts a poor prognosis in pancreatic cancer

(2020) Pengbo Zhang et al.   JOURNAL OF CELLULAR AND MOLECULAR MEDICINE

Targeting both BET and CBP/EP300 proteins with the novel dual inhibitors NEO2734 and NEO1132 leads to anti‐tumor activity in multiple myeloma

(2020) Katie R. Ryan et al.   EUROPEAN JOURNAL OF HAEMATOLOGY

Chromatin binding of FOXA1 is promoted by LSD1-mediated demethylation in prostate cancer

(2020) Shuai Gao et al.   NATURE GENETICS

Identification of a Twelve-Gene Signature and Establishment of a Prognostic Nomogram Predicting Overall Survival for Medulloblastoma

(2020) Sihan Zhu et al.   Frontiers in Genetics

SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data

(2020) Matthew D Young et al.   GigaScience

Nucleotide Weight Matrices Reveal Ubiquitous Mutational Footprints of AID/APOBEC Deaminases in Human Cancer Genomes

(2019) Igor Rogozin et al.   Cancers

APOBEC Mutagenesis and Copy-Number Alterations Are Drivers of Proteogenomic Tumor Evolution and Heterogeneity in Metastatic Thoracic Tumors

(2019) Nitin Roper et al.   Cell Reports

Principles of Resistance to Targeted Cancer Therapy: Lessons from Basic and Translational Cancer Biology

(2019) Amit J. Sabnis et al.   TRENDS IN MOLECULAR MEDICINE

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

Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data

(2019) Samuel L. Wolock et al.   Cell Systems

Forkhead domain mutations in FOXA1 drive prostate cancer progression

(2019) Shuai Gao et al.   CELL RESEARCH

The DNA deaminase APOBEC3B interacts with the cell cycle protein CDK4 and disrupts CDK4-mediated nuclear import of Cyclin D1

(2019) Jennifer M. McCann et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

FOXA1 mutations alter pioneering activity, differentiation and prostate cancer phenotypes

(2019) Elizabeth J. Adams et al.   NATURE

Distinct structural classes of activating FOXA1 alterations in advanced prostate cancer

(2019) Abhijit Parolia et al.   NATURE

Somatic mutations and cell identity linked by Genotyping of Transcriptomes

(2019) Anna S. Nam et al.   NATURE

The deaminase APOBEC3B triggers the death of cells lacking uracil DNA glycosylase

(2019) Artur A. Serebrenik et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A general approach for detecting expressed mutations in AML cells using single cell RNA-sequencing

(2019) Allegra A. Petti et al.   Nature Communications

CONICS integrates scRNA-seq with DNA sequencing to map gene expression to tumor sub-clones

(2018) Sören Müller et al.   BIOINFORMATICS

Pancancer analysis identifies prognostic high-APOBEC1 expression level implicated in cancer in-frame insertions and deletions

(2018) Ahmadreza Niavarani et al.   CARCINOGENESIS

Chemoresistance Evolution in Triple-Negative Breast Cancer Delineated by Single-Cell Sequencing

(2018) Charissa Kim et al.   CELL

Whole-genome and Transcriptome Sequencing of Prostate Cancer Identify New Genetic Alterations Driving Disease Progression

(2018) Shancheng Ren et al.   EUROPEAN UROLOGY

Detecting Differential Transcription Factor Activity from ATAC-Seq Data

(2018) Ignacio Tripodi et al.   MOLECULES

The long tail of oncogenic drivers in prostate cancer

(2018) Joshua Armenia et al.   NATURE GENETICS

Strelka2: fast and accurate calling of germline and somatic variants

(2018) Sangtae Kim et al.   NATURE METHODS

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

(2018) Shixiang Wang et al.   ONCOGENE

A cryptic RNA-binding domain mediates Syncrip recognition and exosomal partitioning of miRNA targets

(2018) Fruzsina Hobor et al.   Nature Communications

Deletion 6q drives T-cell leukemia progression by ribosome modulation

(2018) Stéphanie Gachet et al.   Cancer Discovery

Key role of SMN/SYNCRIP and RNA-Motif 7 in spinal muscular atrophy: RNA-Seq and motif analysis of human motor neurons

(2018) Federica Rizzo et al.   BRAIN

Targeting FOXA1-mediated repression of TGF-β signaling suppresses castration-resistant prostate cancer progression

(2018) Bing Song et al.   JOURNAL OF CLINICAL INVESTIGATION

Functional screen of MSI2 interactors identifies an essential role for SYNCRIP in myeloid leukemia stem cells

(2017) Ly P Vu et al.   NATURE GENETICS

Single-cell transcriptomics uncovers distinct molecular signatures of stem cells in chronic myeloid leukemia

(2017) Alice Giustacchini et al.   NATURE MEDICINE

Tumour heterogeneity and resistance to cancer therapies

(2017) Ibiayi Dagogo-Jack et al.   Nature Reviews Clinical Oncology

SOX2 promotes lineage plasticity and antiandrogen resistance in TP53 - and RB1 -deficient prostate cancer

(2017) Ping Mu et al.   SCIENCE

Translational upregulation of Aurora-A by hnRNP Q1 contributes to cell proliferation and tumorigenesis in colorectal cancer

(2017) Chien-Hsien Lai et al.   Cell Death & Disease

Estrogen receptor coregulator binding modulators (ERXs) effectively target estrogen receptor positive human breast cancers

(2017) Ganesh V Raj et al.   eLife

Single‐cell sequencing maps gene expression to mutational phylogenies in PDGF‐ and EGF‐driven gliomas

(2016) Sören Müller et al.   Molecular Systems Biology

Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma

(2016) Itay Tirosh et al.   NATURE

Landscape of somatic mutations in 560 breast cancer whole-genome sequences

(2016) Serena Nik-Zainal et al.   NATURE

Substantial interindividual and limited intraindividual genomic diversity among tumors from men with metastatic prostate cancer

(2016) Akash Kumar et al.   NATURE MEDICINE

Divergent clonal evolution of castration-resistant neuroendocrine prostate cancer

(2016) Himisha Beltran et al.   NATURE MEDICINE

Single-cell multimodal profiling reveals cellular epigenetic heterogeneity

(2016) Lih Feng Cheow et al.   NATURE METHODS

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements

(2016) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

The APOBEC Protein Family: United by Structure, Divergent in Function

(2016) Jason D. Salter et al.   TRENDS IN BIOCHEMICAL SCIENCES

The DNA cytosine deaminase APOBEC3H haplotype I likely contributes to breast and lung cancer mutagenesis

(2016) Gabriel J. Starrett et al.   Nature Communications

Cross-validation of survival associated biomarkers in gastric cancer using transcriptomic data of 1,065 patients

(2016) A. Marcell Szász et al.   Oncotarget

The RNA-Binding Protein SYNCRIP Is a Component of the Hepatocyte Exosomal Machinery Controlling MicroRNA Sorting

(2016) Laura Santangelo et al.   Cell Reports

Sambamba: fast processing of NGS alignment formats

(2015) Artem Tarasov et al.   BIOINFORMATICS

IBS: an illustrator for the presentation and visualization of biological sequences: Fig. 1.

(2015) Wenzhong Liu et al.   BIOINFORMATICS

Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications

(2015) Xiaoyu Chen et al.   BIOINFORMATICS

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

Progesterone receptor modulates ERα action in breast cancer

(2015) Hisham Mohammed et al.   NATURE

An APOBEC3A hypermutation signature is distinguishable from the signature of background mutagenesis by APOBEC3B in human cancers

(2015) Kin Chan et al.   NATURE GENETICS

Clock-like mutational processes in human somatic cells

(2015) Ludmil B Alexandrov et al.   NATURE GENETICS

SpeedSeq: ultra-fast personal genome analysis and interpretation

(2015) Colby Chiang et al.   NATURE METHODS

The MEME Suite

(2015) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

APOBEC Enzymes: Mutagenic Fuel for Cancer Evolution and Heterogeneity

(2015) C. Swanton et al.   Cancer Discovery

Polycomb-mediated silencing in neuroendocrine prostate cancer

(2015) Pier-Luc Clermont et al.   Clinical Epigenetics

Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells

(2015) Kyu-Tae Kim et al.   GENOME BIOLOGY

fastcluster: Fast Hierarchical, Agglomerative Clustering Routines forRandPython

(2015) Daniel Müllner   Journal of Statistical Software

Organoid Cultures Derived from Patients with Advanced Prostate Cancer

(2014) Dong Gao et al.   CELL

Single-cell analyses of transcriptional heterogeneity during drug tolerance transition in cancer cells by RNA sequencing

(2014) M.-C. W. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DrosophilaSyncrip modulates the expression of mRNAs encoding key synaptic proteins required for morphology at the neuromuscular junction

(2014) Suzanne M. McDermott et al.   RNA

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

(2014) A. P. Patel et al.   SCIENCE

Syncrip/hnRNP Q influences synaptic transmission and regulates BMP signaling at the Drosophila neuromuscular synapse

(2014) J. M. Halstead et al.   Biology Open

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

(2013) Y. Liao et al.   BIOINFORMATICS

Shimmer: detection of genetic alterations in tumors using next-generation sequence data

(2013) Nancy F. Hansen et al.   BIOINFORMATICS

A novel histone deacetylase (HDAC) inhibitor MHY219 induces apoptosis via up-regulation of androgen receptor expression in human prostate cancer cells

(2013) Nabanita Patra et al.   BIOMEDICINE & PHARMACOTHERAPY

Punctuated Evolution of Prostate Cancer Genomes

(2013) Sylvan C. Baca et al.   CELL

APOBEC3B is an enzymatic source of mutation in breast cancer

(2013) Michael B. Burns et al.   NATURE

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers

(2013) Steven A Roberts et al.   NATURE GENETICS

Online Survival Analysis Software to Assess the Prognostic Value of Biomarkers Using Transcriptomic Data in Non-Small-Cell Lung Cancer

(2013) Balázs Győrffy et al.   PLoS One

Mutational landscape of gingivo-buccal oral squamous cell carcinoma reveals new recurrently-mutated genes and molecular subgroups

(2013)   Nature Communications

An Optimized microRNA Backbone for Effective Single-Copy RNAi

(2013) Christof Fellmann et al.   Cell Reports

Control of Translation and miRNA-Dependent Repression by a Novel Poly(A) Binding Protein, hnRNP-Q

(2013) Yuri V. Svitkin et al.   PLOS BIOLOGY

DNA deaminases induce break-associated mutation showers with implication of APOBEC3B and 3A in breast cancer kataegis

(2013) Benjamin JM Taylor et al.   eLife

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Mutational Processes Molding the Genomes of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

hnRNP Q regulates translation of p53 in normal and stress conditions

(2012) D-Y Kim et al.   CELL DEATH AND DIFFERENTIATION

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

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

hnRNP Q Regulates Cdc42-Mediated Neuronal Morphogenesis

(2012) H.-H. Chen et al.   MOLECULAR AND CELLULAR BIOLOGY

The mutational landscape of lethal castration-resistant prostate cancer

(2012) Catherine S. Grasso et al.   NATURE

Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer

(2012) Christopher E Barbieri et al.   NATURE GENETICS

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Identifying ChIP-seq enrichment using MACS

(2012) Jianxing Feng et al.   Nature Protocols

Increased Survival with Enzalutamide in Prostate Cancer after Chemotherapy

(2012) Howard I. Scher et al.   NEW ENGLAND JOURNAL OF MEDICINE

Cell Autonomous and Nonautonomous Mechanisms Drive Hematopoietic Stem/progenitor Cell Loss in the Absence of DNA Repair

(2012) Joon Seok Cho et al.   STEM CELLS

APOBEC3B can impair genomic stability by inducing base substitutions in genomic DNA in human cells

(2012) Masanobu Shinohara et al.   Scientific Reports

Green tea polyphenols causes cell cycle arrest and apoptosis in prostate cancer cells by suppressing class I histone deacetylases

(2011) V. S. Thakur et al.   CARCINOGENESIS

APOBEC3A can activate the DNA damage response and cause cell-cycle arrest

(2011) Sébastien Landry et al.   EMBO REPORTS

Selective Roles for cAMP Response Element-binding Protein Binding Protein and p300 Protein as Coregulators for Androgen-regulated Gene Expression in Advanced Prostate Cancer Cells

(2011) Irina Ianculescu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Inhibition of the Acetyltransferases p300 and CBP Reveals a Targetable Function for p300 in the Survival and Invasion Pathways of Prostate Cancer Cell Lines

(2011) F. R. Santer et al.   MOLECULAR CANCER THERAPEUTICS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Somatic hypermutation of human mitochondrial and nuclear DNA by APOBEC3 cytidine deaminases, a pathway for DNA catabolism

(2011) R. Suspene et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functions and regulation of the APOBEC family of proteins

(2011) Harold C. Smith et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

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

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Antitumour activity of MDV3100 in castration-resistant prostate cancer: a phase 1–2 study

(2010) Howard I Scher et al.   LANCET

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

Genomic instability — an evolving hallmark of cancer

(2010) Simona Negrini et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

APOBEC3 proteins mediate the clearance of foreign DNA from human cells

(2010) Mark D Stenglein et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Development of a Second-Generation Antiandrogen for Treatment of Advanced Prostate Cancer

(2009) C. Tran et al.   SCIENCE

SYNCRIP, a component of dendritically localized mRNPs, binds to the translation regulator BC200 RNA

(2008) Kerstin Duning et al.   JOURNAL OF NEUROCHEMISTRY

The RNA Binding Protein hnRNP Q Modulates the Utilization of Exon 7 in the Survival Motor Neuron 2 (SMN2) Gene

(2008) H.-H. Chen et al.   MOLECULAR AND CELLULAR BIOLOGY

p300 (histone acetyltransferase) biomarker predicts prostate cancer biochemical recurrence and correlates with changes in epithelia nuclear size and shape

(2008) Sumit Isharwal et al.   PROSTATE

Evidence for Editing of Human Papillomavirus DNA by APOBEC3 in Benign and Precancerous Lesions

(2008) J.-P. Vartanian et al.   SCIENCE