Epigenetics as a mediator of plasticity in cancer

AP Feinberg, A Levchenko - Science, 2023 - science.org
The concept of an epigenetic landscape describing potential cellular fates arising from
pluripotent cells, first advanced by Conrad Waddington, has evolved in light of experiments …

Epigenetics, fragmentomics, and topology of cell-free DNA in liquid biopsies

YMD Lo, DSC Han, P Jiang, RWK Chiu - Science, 2021 - science.org
BACKGROUND Liquid biopsies that are based on analysis of cell-free DNA from plasma
offer diagnostic information that is otherwise accessible conventionally through invasive …

Integrating genetic and non-genetic determinants of cancer evolution by single-cell multi-omics

AS Nam, R Chaligne, DA Landau - Nature Reviews Genetics, 2021 - nature.com
Cancer represents an evolutionary process through which growing malignant populations
genetically diversify, leading to tumour progression, relapse and resistance to therapy. In …

Epigenetic encoding, heritability and plasticity of glioma transcriptional cell states

R Chaligne, F Gaiti, D Silverbush, JS Schiffman… - Nature …, 2021 - nature.com
Single-cell RNA sequencing has revealed extensive transcriptional cell state diversity in
cancer, often observed independently of genetic heterogeneity, raising the central question …

DNA methylation in mammalian development and disease

ZD Smith, S Hetzel, A Meissner - Nature Reviews Genetics, 2024 - nature.com
The DNA methylation field has matured from a phase of discovery and genomic
characterization to one seeking deeper functional understanding of how this modification …

Detecting DNA cytosine methylation using nanopore sequencing

JT Simpson, RE Workman, PC Zuzarte, M David… - Nature …, 2017 - nature.com
In nanopore sequencing devices, electrolytic current signals are sensitive to base
modifications, such as 5-methylcytosine (5-mC). Here we quantified the strength of this effect …

Single-cell multimodal glioma analyses identify epigenetic regulators of cellular plasticity and environmental stress response

KC Johnson, KJ Anderson, ET Courtois, AD Gujar… - Nature …, 2021 - nature.com
Glioma intratumoral heterogeneity enables adaptation to challenging microenvironments
and contributes to therapeutic resistance. We integrated 914 single-cell DNA methylomes …

Interplay between chromatin marks in development and disease

SM Janssen, MC Lorincz - Nature Reviews Genetics, 2022 - nature.com
DNA methylation (DNAme) and histone post-translational modifications (PTMs) have
important roles in transcriptional regulation. Although many reports have characterized the …

Genomic and epigenomic insights into the origin, pathogenesis, and clinical behavior of mantle cell lymphoma subtypes

F Nadeu, D Martin-Garcia, G Clot… - Blood, The Journal …, 2020 - ashpublications.org
Mantle cell lymphoma (MCL) is a mature B-cell neoplasm initially driven by CCND1
rearrangement with 2 molecular subtypes, conventional MCL (cMCL) and leukemic non …

Revealing the vectors of cellular identity with single-cell genomics

A Wagner, A Regev, N Yosef - Nature biotechnology, 2016 - nature.com
Single-cell genomics has now made it possible to create a comprehensive atlas of human
cells. At the same time, it has reopened definitions of a cell's identity and of the ways in …