4.8 Article

The 5-Hydroxymethylcytosine Landscape of Prostate Cancer

Related references

Note: Only part of the references are listed.
Article Oncology

BRCA2, ATM, and CDK12 Defects Differentially Shape Prostate Tumor Driver Genomics and Clinical Aggression

Evan Warner et al.

Summary: The study identifies BRCA2, ATM, and CDK12 as the most frequently disrupted DDR genes in ctDNA of metastatic prostate cancer patients, collectively mutated in 15% of cases. ATM defects and TP53 mutations were rare, with most patients showing biallelic gene disruption. Loss of BRCA2 and CDK12, but not ATM, was associated with poor clinical outcomes.

CLINICAL CANCER RESEARCH (2021)

Review Biochemistry & Molecular Biology

Loss and revival of androgen receptor signaling in advanced prostate cancer

Nicolo Formaggio et al.

Summary: Targeting the androgen receptor signaling axis has long been the main strategy for prostate cancer therapy, but stronger inhibition has led to a subset of cancers becoming AR-negative, with a poorer prognosis.

ONCOGENE (2021)

Article Multidisciplinary Sciences

Dynamic prostate cancer transcriptome analysis delineates the trajectory to disease progression

Marco Bolis et al.

Summary: The study integrates a transcriptomics atlas of prostate cancer and validates it with preclinical models and single-cell RNA-seq, revealing the role of EZH2 and macrophage polarization in tumour progression.

NATURE COMMUNICATIONS (2021)

Article Oncology

Increased Pathway Complexity Is a Prognostic Biomarker in Metastatic Castration-Resistant Prostate Cancer

Bram De Laere et al.

Summary: Circulating tumour DNA profiling can efficiently accelerate biomarker discovery in oncology trials. In metastatic castration-resistant prostate cancer, the complex genomic landscape with rare driver gene alterations complicates biomarker identification, requiring large sample sizes for evaluation. Grouping genomic alterations within the same cellular pathways may provide increased precision for biomarker discovery, highlighting the importance of comprehensive genomic profiling for prognosis and treatment outcomes.

CANCERS (2021)

Article Multidisciplinary Sciences

Tissue-specific 5-hydroxymethylcytosine landscape of the human genome

Bo He et al.

Summary: 5hmC in human tissues shows tissue-specific patterns that may affect tissue-specific gene expression networks and are associated with specific single-nucleotide polymorphisms and diseases.

NATURE COMMUNICATIONS (2021)

Article Medicine, Research & Experimental

Circulating tumor DNA profile recognizes transformation to castration-resistant neuroendocrine prostate cancer

Himisha Beltran et al.

JOURNAL OF CLINICAL INVESTIGATION (2020)

Article Multidisciplinary Sciences

Noncoding mutations target cis-regulatory elements of the FOXA1 plexus in prostate cancer

Stanley Zhou et al.

NATURE COMMUNICATIONS (2020)

Article Urology & Nephrology

Activating AKT1 and PIK3CA Mutations in Metastatic Castration-Resistant Prostate Cancer

Cameron Herberts et al.

EUROPEAN UROLOGY (2020)

Article Medicine, Research & Experimental

Genome-wide plasma DNA methylation features of metastatic prostate cancer

Anjui Wu et al.

JOURNAL OF CLINICAL INVESTIGATION (2020)

Article Multidisciplinary Sciences

A genomic and epigenomic atlas of prostate cancer in Asian populations

Jing Li et al.

NATURE (2020)

Article Genetics & Heredity

Prostate cancer reactivates developmental epigenomic programs during metastatic progression

Mark M. Pomerantz et al.

NATURE GENETICS (2020)

Article Genetics & Heredity

The DNA methylation landscape of advanced prostate cancer

Shuang G. Zhao et al.

NATURE GENETICS (2020)

Article Multidisciplinary Sciences

Detection of early stage pancreatic cancer using 5-hydroxymethylcytosine signatures in circulating cell free DNA

Gulfem D. Guler et al.

NATURE COMMUNICATIONS (2020)

Article Multidisciplinary Sciences

Role of specialized composition of SWI/SNF complexes in prostate cancer lineage plasticity

Joanna Cyrta et al.

NATURE COMMUNICATIONS (2020)

Article Oncology

The Role of Lineage Plasticity in Prostate Cancer Therapy Resistance

Himisha Beltran et al.

CLINICAL CANCER RESEARCH (2019)

Article Multidisciplinary Sciences

Distinct structural classes of activating FOXA1 alterations in advanced prostate cancer

Abhijit Parolia et al.

NATURE (2019)

Article Biochemistry & Molecular Biology

Genome-wide germline correlates of the epigenetic landscape of prostate cancer

Kathleen E. Houlahan et al.

NATURE MEDICINE (2019)

Review Biochemistry & Molecular Biology

The DNA methylation landscape in cancer

Ksenia Skvortsova et al.

DNA METHYLATION (2019)

Article Oncology

Concordance of Circulating Tumor DNA and Matched Metastatic Tissue Biopsy in Prostate Cancer

Alexander W. Wyatt et al.

JNCI-JOURNAL OF THE NATIONAL CANCER INSTITUTE (2018)

Article Oncology

Concordance of Circulating Tumor DNA and Matched Metastatic Tissue Biopsy in Prostate Cancer

Alexander W. Wyatt et al.

JNCI-JOURNAL OF THE NATIONAL CANCER INSTITUTE (2018)

Article Biochemistry & Molecular Biology

Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer

David A. Quigley et al.

Article Biochemistry & Molecular Biology

The ExAC browser: displaying reference data information from over 60 000 exomes

Konrad J. Karczewski et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemistry & Molecular Biology

Altered hydroxymethylation is seen at regulatory regions in pancreatic cancer and regulates oncogenic pathways

Sanchari Bhattacharyya et al.

GENOME RESEARCH (2017)

Article Multidisciplinary Sciences

Genomic hallmarks of localized, non-indolent prostate cancer

Michael Fraser et al.

NATURE (2017)

Article Multidisciplinary Sciences

5-hydroxymethylcytosine accumulation in postmitotic neurons results in functional demethylation of expressed genes

Marian Mellen et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)

Article Oncology

TOP2A and EZH2 Provide Early Detection of an Aggressive Prostate Cancer Subgroup

David P. Labbe et al.

CLINICAL CANCER RESEARCH (2017)

Article Biochemistry & Molecular Biology

Whole-genome analysis of the methylome and hydroxymethylome in normal and malignant lung and liver

Xin Li et al.

GENOME RESEARCH (2016)

Article Biochemistry & Molecular Biology

Divergent clonal evolution of castration-resistant neuroendocrine prostate cancer

Himisha Beltran et al.

NATURE MEDICINE (2016)

Article Multidisciplinary Sciences

Stem cell and neurogenic gene-expression profiles link prostate basal cells to aggressive prostate cancer

Dingxiao Zhang et al.

NATURE COMMUNICATIONS (2016)

Article Multidisciplinary Sciences

5-Hydroxymethylcytosine localizes to enhancer elements and is associated with survival in glioblastoma patients

Kevin C. Johnson et al.

NATURE COMMUNICATIONS (2016)

Article Biochemical Research Methods

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

Guangchuang Yu et al.

BIOINFORMATICS (2015)

Article Biochemistry & Molecular Biology

Using informative Multinomial-Dirichlet prior in a t-mixture with reversible jump estimation of nucleosome positions for genome-wide profiling

Rawane Samb et al.

STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY (2015)

Article Biochemistry & Molecular Biology

Using informative Multinomial-Dirichlet prior in a t-mixture with reversible jump estimation of nucleosome positions for genome-wide profiling

Rawane Samb et al.

STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY (2015)

Article Biochemistry & Molecular Biology

The Molecular Signatures Database Hallmark Gene Set Collection

Arthur Liberzon et al.

CELL SYSTEMS (2015)

Article Chemistry, Multidisciplinary

5-Hydroxymethylcytosine is a predominantly stable DNA modification

Martin Bachman et al.

NATURE CHEMISTRY (2014)

Article Biotechnology & Applied Microbiology

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Michael I. Love et al.

GENOME BIOLOGY (2014)

Article Multidisciplinary Sciences

Global Epigenomic Reconfiguration During Mammalian Brain Development

Ryan Lister et al.

SCIENCE (2013)

Article Biochemistry & Molecular Biology

Tissue type is a major modifier of the 5-hydroxymethylcytosine content of human genes

Colm E. Nestor et al.

GENOME RESEARCH (2012)

Article Multidisciplinary Sciences

Differential oestrogen receptor binding is associated with clinical outcome in breast cancer

Caryn S. Ross-Innes et al.

NATURE (2012)

Article Biochemical Research Methods

Kaviar: an accessible system for testing SNV novelty

Gustavo Glusman et al.

BIOINFORMATICS (2011)

Article Multidisciplinary Sciences

Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells

William A. Pastor et al.

NATURE (2011)

Article Biotechnology & Applied Microbiology

Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine

Chun-Xiao Song et al.

NATURE BIOTECHNOLOGY (2011)

Article Biotechnology & Applied Microbiology

5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells

Hume Stroud et al.

GENOME BIOLOGY (2011)

Article Biotechnology & Applied Microbiology

GREAT improves functional interpretation of cis-regulatory regions

Cory Y. McLean et al.

NATURE BIOTECHNOLOGY (2010)

Article Biochemistry & Molecular Biology

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

Kai Wang et al.

NUCLEIC ACIDS RESEARCH (2010)

Article Multidisciplinary Sciences

A causal role for ERG in neoplastic transformation of prostate epithelium

Olga Klezovitch et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Biotechnology & Applied Microbiology

Model-based Analysis of ChIP-Seq (MACS)

Yong Zhang et al.

GENOME BIOLOGY (2008)

Review Oncology

Recurrent gene fusions in prostate cancer

Chandan Kumar-Sinha et al.

NATURE REVIEWS CANCER (2008)