Carbohydrate response element binding protein (ChREBP) is a key transcriptional regulator of de novo lipogenesis (DNL) in response to carbohydrates and in hepatic steatosis. Mechanisms underlying nutrient modulation of ChREBP are under active investigation. Here we identify host cell factor 1 (HCF-1) as a previously unknown ChREBP-interacting protein that is enriched in liver biopsies of nonalcoholic steatohepatitis (NASH) patients. Biochemical and genetic studies show that HCF-1 is O-GlcNAcylated in response to glucose as a prerequisite for its binding to ChREBP and subsequent recruitment of OGT, ChREBP O-GlcNAcylation, and activation. The HCF-1:ChREBP complex resides at lipogenic gene promoters, where HCF-1 regulates H3K4 trimethylation to prime recruitment of the Jumonji C domain-containing histone demethylase PHF2 for epigenetic activation of these promoters. Overall, these findings define HCF-1's interaction with ChREBP as a previously unappreciated mechanism whereby glucose signals are both relayed to ChREBP and transmitted for epigenetic regulation of lipogenic genes.
Immune-checkpoint-blockade (ICB)-mediated rejuvenation of exhausted T cells has emerged as a promising approach for treating various cancers and chronic infections. However, T cells that become fully exhausted during prolonged antigen exposure remain refractory to ICB-mediated rejuvenation. We report that blocking de novo DNA methylation in activated CD8 T cells allows them to retain their effector functions despite chronic stimulation during a persistent viral infection. Whole-genome bisulfite sequencing of antigen-specific murine CD8 T cells at the effector and exhaustion stages of an immune response identified progressively acquired heritable de novo methylation programs that restrict T cell expansion and clonal diversity during PD-1 blockade treatment. Moreover, these exhaustion-associated DNA-methylation programs were acquired in tumor-infiltrating PD-1hi CD8 T cells, and approaches to reverse these programs improved T cell responses and tumor control during ICB. These data establish de novo DNA-methylation programming as a regulator of T cell exhaustion and barrier of ICB-mediated T cell rejuvenation.
Mechanisms of de novo mutations. De novo mutations can arise because of static properties of the genome, such as the underlying sequence (deamination of methylated CpGs, transitions versus transversions) or due to erroneous pairing of nucleotides during DNA replication. However, de novo mutations can also occur in relation to cell-specific properties such as the chromatin state, transcriptional status, and gene expression levels. Mutational hotspots for genomic rearrangements are largely determined by the underlying genomic architecture. One such example is given for non-allelic homologous recombination (NAHR). Arrows represent the influence of each feature on the de novo mutation rate. Green arrows pointing upwards indicate elevated mutability; red arrows pointing downwards indicate lower mutability. M methyl group modifying cytosine
In this review, we first touch on the biological aspects of de novo mutations in humans, such as their origin, distribution throughout the genome, and factors related to their occurrence and timing. Later, we discuss the increasingly recognized role of de novo mutations in human disease and other translational aspects. Throughout, we will focus mostly on de novo SNVs; readers should refer to Box 2 and previous work from others for more information on the role of de novo CNVs and other structural genomic variation in human disease [36, 37].
The difference between the rate at which pre-mutagenic damage appears in DNA and the rate at which it is repaired defines the rate at which de novo mutations arise. It is often assumed that germline de novo mutations originate from errors in DNA replication during gametogenesis, particularly in sperm cells and their precursors (see section below on parental origin of de novo mutatio