Epigenetic signatures in cancer: proper controls, current challenges and the potential for clinical translation

Integrative analysis defines distinct prognostic subgroups of intrahepatic cholangiocarcinoma

(2019) Benjamin Goeppert et al.   HEPATOLOGY

Epigenetic Enzyme Mutations: Role in Tumorigenesis and Molecular Inhibitors

(2019) Mei Han et al.   Frontiers in Oncology

Osteogenesis depends on commissioning of a network of stem cell transcription factors that act as repressors of adipogenesis

(2019) Alexander Rauch et al.   NATURE GENETICS

EZH2 oncogenic mutations drive epigenetic, transcriptional, and structural changes within chromatin domains

(2019) Maria C. Donaldson-Collier et al.   NATURE GENETICS

The expanding landscape of ‘oncohistone’ mutations in human cancers

(2019) Benjamin A. Nacev et al.   NATURE

DNA Hypermethylation Encroachment at CpG Island Borders in Cancer Is Predisposed by H3K4 Monomethylation Patterns

(2019) Ksenia Skvortsova et al.   CANCER CELL

Aging-like Spontaneous Epigenetic Silencing Facilitates Wnt Activation, Stemness, and BrafV600E-Induced Tumorigenesis

(2019) Yong Tao et al.   CANCER CELL

Aging Human Hematopoietic Stem Cells Manifest Profound Epigenetic Reprogramming of Enhancers That May Predispose to Leukemia

(2019) Emmalee R Adelman et al.   Cancer Discovery

Cell-type-specific resolution epigenetics without the need for cell sorting or single-cell biology

(2019) Elior Rahmani et al.   Nature Communications

Machine learning analysis of DNA methylation profiles distinguishes primary lung squamous cell carcinomas from head and neck metastases

(2019) Philipp Jurmeister et al.   Science Translational Medicine

DNA Methylation Patterns Separate Senescence from Transformation Potential and Indicate Cancer Risk

(2018) Wenbing Xie et al.   CANCER CELL

LSD1 Ablation Stimulates Anti-tumor Immunity and Enables Checkpoint Blockade

(2018) Wanqiang Sheng et al.   CELL

Single-Cell Chromatin Modification Profiling Reveals Increased Epigenetic Variations with Aging

(2018) Peggie Cheung et al.   CELL

An atlas of chromatin accessibility in the adult human brain

(2018) John F. Fullard et al.   GENOME RESEARCH

Diagnostic utility of histone H3.3 G34W, G34R, and G34V mutant-specific antibodies for giant cell tumors of bone

(2018) Hidetaka Yamamoto et al.   HUMAN PATHOLOGY

Histone H3.3 G34 Mutations Alter Histone H3K36 and H3K27 Methylation In Cis

(2018) Leilei Shi et al.   JOURNAL OF MOLECULAR BIOLOGY

DNA methylation-based classification of central nervous system tumours

(2018) David Capper et al.   NATURE

DNA methylation loss in late-replicating domains is linked to mitotic cell division

(2018) Wanding Zhou et al.   NATURE GENETICS

Potent antitumor efficacy of anti-GD2 CAR T cells in H3-K27M+ diffuse midline gliomas

(2018) Christopher W. Mount et al.   NATURE MEDICINE

Analysis of DNA methylation in cancer: location revisited

(2018) Alexander Koch et al.   Nature Reviews Clinical Oncology

Cell-of-Origin DNA Methylation Signatures Are Maintained during Colorectal Carcinogenesis

(2018) Felix Bormann et al.   Cell Reports

Cross-talk between Lysine-Modifying Enzymes Controls Site-Specific DNA Amplifications

(2018) Sweta Mishra et al.   CELL

Targeting Epigenetic Crosstalk as a Therapeutic Strategy for EZH2-Aberrant Solid Tumors

(2018) Xun Huang et al.   CELL

Ivosidenib: First Global Approval

(2018) Sohita Dhillon   DRUGS

The DNA methylation landscape of glioblastoma disease progression shows extensive heterogeneity in time and space

(2018) Johanna Klughammer et al.   NATURE MEDICINE

Inhibition of a K9/K36 demethylase by an H3.3 point mutation found in paediatric glioblastoma

(2018) Hsiao P. J. Voon et al.   Nature Communications

Genetic and Epigenetic Perturbations by DNMT3A-R882 Mutants Impaired Apoptosis through Augmentation of PRDX2 in Myeloid Leukemia Cells

(2018) Rabindranath Bera et al.   NEOPLASIA

Histone H3.3 K27M Accelerates Spontaneous Brainstem Glioma and Drives Restricted Changes in Bivalent Gene Expression

(2018) Jon D. Larson et al.   CANCER CELL

Predictable and precise template-free CRISPR editing of pathogenic variants

(2018) Max W. Shen et al.   NATURE

Discovery of methylated circulating DNA biomarkers for comprehensive non-invasive monitoring of treatment response in metastatic colorectal cancer

(2017) Ludovic Barault et al.   GUT

Cell-type deconvolution from DNA methylation: a review of recent applications

(2017) Alexander J. Titus et al.   HUMAN MOLECULAR GENETICS

The chromatin accessibility signature of human immune aging stems from CD8+T cells

(2017) Duygu Ucar et al.   JOURNAL OF EXPERIMENTAL MEDICINE

DNA methylation-based classification and grading system for meningioma: a multicentre, retrospective analysis

(2017) Felix Sahm et al.   LANCET ONCOLOGY

Histone H3.3K27M Represses p16 to Accelerate Gliomagenesis in a Murine Model of DIPG

(2017) Francisco J. Cordero et al.   MOLECULAR CANCER RESEARCH

BCAT1 restricts αKG levels in AML stem cells leading to IDHmut-like DNA hypermethylation

(2017) Simon Raffel et al.   NATURE

DNMT and HDAC inhibitors induce cryptic transcription start sites encoded in long terminal repeats

(2017) David Brocks et al.   NATURE GENETICS

The interplay of epigenetic marks during stem cell differentiation and development

(2017) Yaser Atlasi et al.   NATURE REVIEWS GENETICS

The Encyclopedia of DNA elements (ENCODE): data portal update

(2017) Carrie A Davis et al.   NUCLEIC ACIDS RESEARCH

DNA-hypomethylating agents as epigenetic therapy before and after allogeneic hematopoietic stem cell transplantation in myelodysplastic syndromes and juvenile myelomonocytic leukemia

(2017) Christian Flotho et al.   SEMINARS IN CANCER BIOLOGY

RAS-pathway mutation patterns define epigenetic subclasses in juvenile myelomonocytic leukemia

(2017) Daniel B. Lipka et al.   Nature Communications

Epigenome-wide discovery and evaluation of leukocyte DNA methylation markers for the detection of colorectal cancer in a screening setting

(2017) Jonathan Alexander Heiss et al.   Clinical Epigenetics

K27M-mutant histone-3 as a novel target for glioma immunotherapy

(2017) Katharina Ochs et al.   OncoImmunology

Reference-free deconvolution of DNA methylation data and mediation by cell composition effects

(2016) E. Andres Houseman et al.   BMC BIOINFORMATICS

Atypical Teratoid/Rhabdoid Tumors Are Comprised of Three Epigenetic Subgroups with Distinct Enhancer Landscapes

(2016) Pascal D. Johann et al.   CANCER CELL

Combination Epigenetic Therapy in Advanced Breast Cancer with 5-Azacitidine and Entinostat: A Phase II National Cancer Institute/Stand Up to Cancer Study

(2016) Roisin M. Connolly et al.   CLINICAL CANCER RESEARCH

TAD disruption as oncogenic driver

(2016) Anne-Laure Valton et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Epigenetic Homogeneity Within Colorectal Tumors Predicts Shorter Relapse-Free and Overall Survival Times for Patients With Locoregional Cancer

(2016) Anna Martínez-Cardús et al.   GASTROENTEROLOGY

Epigenetic profiling to classify cancer of unknown primary: a multicentre, retrospective analysis

(2016) Sebastian Moran et al.   LANCET ONCOLOGY

Tumour hypoxia causes DNA hypermethylation by reducing TET activity

(2016) Bernard Thienpont et al.   NATURE

DNA methylation dynamics during B cell maturation underlie a continuum of disease phenotypes in chronic lymphocytic leukemia

(2016) Christopher C Oakes et al.   NATURE GENETICS

The molecular hallmarks of epigenetic control

(2016) C. David Allis et al.   NATURE REVIEWS GENETICS

Mutational landscape of uterine and ovarian carcinosarcomas implicates histone genes in epithelial–mesenchymal transition

(2016) Siming Zhao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Histone H3K36 mutations promote sarcomagenesis through altered histone methylation landscape

(2016) C. Lu et al.   SCIENCE

The histone H3.3K36M mutation reprograms the epigenome of chondroblastomas

(2016) D. Fang et al.   SCIENCE

Epigenetic Determinants of Cancer

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

Spatial and temporal homogeneity of driver mutations in diffuse intrinsic pontine glioma

(2016) Hamid Nikbakht et al.   Nature Communications

HDACs and HDAC Inhibitors in Cancer Development and Therapy

(2016) Yixuan Li et al.   Cold Spring Harbor Perspectives in Medicine

The International Human Epigenome Consortium Data Portal

(2016) David Bujold et al.   Cell Systems

Histone Methylation Marks on Circulating Nucleosomes as Novel Blood-Based Biomarker in Colorectal Cancer

(2015) Ugur Gezer et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Whole-genome fingerprint of the DNA methylome during human B cell differentiation

(2015) Marta Kulis et al.   NATURE GENETICS

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

(2015) D. A. Cusanovich et al.   SCIENCE

TET proteins and the control of cytosine demethylation in cancer

(2015) Laurianne Scourzic et al.   Genome Medicine

Prognostic value of neutrophil-to-lymphocyte ratio in breast cancer

(2015) Jie Chen et al.   FEBS Open Bio

Integrated DNA methylation and copy-number profiling identify three clinically and biologically relevant groups of anaplastic glioma

(2014) Benedikt Wiestler et al.   ACTA NEUROPATHOLOGICA

The R882H DNMT3A Mutation Associated with AML Dominantly Inhibits Wild-Type DNMT3A by Blocking Its Ability to Form Active Tetramers

(2014) David A. Russler-Germain et al.   CANCER CELL

Identification of DNA methylation changes atcis-regulatory elements during early steps of HSC differentiation using tagmentation-based whole genome bisulfite sequencing

(2014) Daniel B Lipka et al.   CELL CYCLE

Epigenomic Profiling of Young and Aged HSCs Reveals Concerted Changes during Aging that Reinforce Self-Renewal

(2014) Deqiang Sun et al.   Cell Stem Cell

Histone Methylation Patterns Are Cell-Type Specific in Human Monocytes and Lymphocytes and Well Maintained at Core Genes

(2014) F. Miao et al.   JOURNAL OF IMMUNOLOGY

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity

(2014) Sébastien A Smallwood et al.   NATURE METHODS

Accounting for cellular heterogeneity is critical in epigenome-wide association studies

(2014) Andrew E Jaffe et al.   GENOME BIOLOGY

Differential expression and methylation of brain developmental genes define location-specific subsets of pilocytic astrocytoma

(2013) Sally R. Lambert et al.   ACTA NEUROPATHOLOGICA

Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing

(2013) H. Guo et al.   GENOME RESEARCH

Succinate dehydrogenase deficiency is associated with decreased 5-hydroxymethylcytosine production in gastrointestinal stromal tumors: implications for mechanisms of tumorigenesis

(2013) Emily F Mason et al.   MODERN PATHOLOGY

Mutations in regulators of the epigenome and their connections to global chromatin patterns in cancer

(2013) Christoph Plass et al.   NATURE REVIEWS GENETICS

Improved PCR Performance Using Template DNA from Formalin-Fixed and Paraffin-Embedded Tissues by Overcoming PCR Inhibition

(2013) Dimo Dietrich 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

DNA methylation arrays as surrogate measures of cell mixture distribution

(2012) Eugene Houseman et al.   BMC BIOINFORMATICS

A DNA hypermethylation module for the stem/progenitor cell signature of cancer

(2012) H. Easwaran et al.   GENOME RESEARCH

Quantitative DNA Methylation Analysis Identifies a Single CpG Dinucleotide Important for ZAP-70 Expression and Predictive of Prognosis in Chronic Lymphocytic Leukemia

(2012) Rainer Claus et al.   JOURNAL OF CLINICAL ONCOLOGY

IDH1 mutation is sufficient to establish the glioma hypermethylator phenotype

(2012) Sevin Turcan et al.   NATURE

Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma

(2012) Jeremy Schwartzentruber et al.   NATURE

Somatic histone H3 alterations in pediatric diffuse intrinsic pontine gliomas and non-brainstem glioblastomas

(2012) Gang Wu et al.   NATURE GENETICS

Widespread Hypomethylation Occurs Early and Synergizes with Gene Amplification during Esophageal Carcinogenesis

(2011) Hector Alvarez et al.   PLoS Genetics

Interobserver variation of the histopathological diagnosis in clinical trials on glioma: a clinician’s perspective

(2010) Martin J. van den Bent   ACTA NEUROPATHOLOGICA

Distinct Epigenomic Landscapes of Pluripotent and Lineage-Committed Human Cells

(2010) R. David Hawkins et al.   Cell Stem Cell