Single-Molecule DNA Methylation Reveals Unique Epigenetic Identity Profiles of T Helper Cells.
Chloe D GoldsmithValentin ThevinOlivier FesneauMaria I MatiasJulie PerraultAli Hani AbidNaomi TaylorValérie DardalhonJulien C MarieHéctor Hernández-VargasPublished in: Journal of immunology (Baltimore, Md. : 1950) (2024)
Both identity and plasticity of CD4 T helper (Th) cells are regulated in part by epigenetic mechanisms. However, a method that reliably and readily profiles DNA base modifications is still needed to finely study Th cell differentiation. Cytosine methylation in CpG context (5mCpG) and cytosine hydroxymethylation (5hmCpG) are DNA modifications that identify stable cell phenotypes, but their potential to characterize intermediate cell transitions has not yet been evaluated. To assess transition states in Th cells, we developed a method to profile Th cell identity using Cas9-targeted single-molecule nanopore sequencing. Targeting as few as 10 selected genomic loci, we were able to distinguish major in vitro polarized murine T cell subtypes, as well as intermediate phenotypes, by their native DNA 5mCpG patterns. Moreover, by using off-target sequences, we were able to infer transcription factor activities relevant to each cell subtype. Detection of 5mCpG and 5hmCpG was validated on intestinal Th17 cells escaping transforming growth factor β control, using single-molecule adaptive sampling. A total of 21 differentially methylated regions mapping to the 10-gene panel were identified in pathogenic Th17 cells relative to their nonpathogenic counterpart. Hence, our data highlight the potential to exploit native DNA methylation profiling to study physiological and pathological transition states of Th cells.
Keyphrases
- transforming growth factor
- single molecule
- epithelial mesenchymal transition
- induced apoptosis
- dna methylation
- cell cycle arrest
- single cell
- gene expression
- genome wide
- transcription factor
- living cells
- endoplasmic reticulum stress
- cell therapy
- atomic force microscopy
- machine learning
- circulating tumor
- cell free
- dendritic cells
- stem cells
- pi k akt
- climate change
- risk assessment
- electronic health record
- immune response
- crispr cas
- regulatory t cells
- mass spectrometry
- copy number
- cell proliferation
- bone marrow
- deep learning
- quantum dots
- human health
- fluorescent probe