Epigenetic Memories in Hematopoietic Stem and Progenitor Cells

Abstract

The recent development of next-generation sequencing (NGS) technologies has contributed to research into various biological processes. These novel NGS technologies have revealed the involvement of epigenetic memories in trained immunity, which are responses to transient stimulation and result in better responses to secondary challenges. Not only innate system cells, such as macrophages, monocytes, and natural killer cells, but also bone marrow hematopoietic stem cells (HSCs) have been found to gain memories upon transient stimulation, leading to the enhancement of responses to secondary challenges. Various stimuli, including microbial infection, can induce the epigenetic reprogramming of innate immune cells and HSCs, which can result in an augmented response to secondary stimulation. In this review, we introduce novel NGS technologies and their application to unraveling epigenetic memories that are key in trained immunity and summarize the recent findings in trained immunity. We also discuss our most recent finding regarding epigenetic memory in aged HSCs, which may be associated with the exposure of HSCs to aging-related stresses.

Keywords: chromatin accessibility; epigenetic memory; epigenome; hematopoietic progenitor cells; hematopoietic stem cells; innate immune cells; next-generation sequencing.

Figure 1

Overview of NGS analyses. (A) In (bulk) RNA-seq, poly-A-selected total RNA undergoes cDNA synthesis and adapter ligation, followed by PCR amplification. The resulting library is subjected to sequencing and mapping to the genome. (B) In scRNA-seq with 10× Genomics Next GEM Technology, barcoded Gel Beads mixed with the cells, reagents, and partitioning oil within chromium instrument form GEMs (Gel Bead-in-emulsion) that contain a single cell. cDNAs are synthesized and barcoded in each GEM, then pooled to generate library for sequencing. (C) In ATAC-seq with a Tn5 transposase-based method, Tn5 transposases bind open chromatin regions and cut and ligate adaptors. After purification, PCR amplification, and sequencing, ligated adaptors are mapped to the genome. (D) In Hi-C analysis, formaldehyde generates cross-links between spatially adjacent DNA. After digestion with a restriction enzyme, the sticky ends are filled, marked with biotin, and ligated. The resulting DNA is purified, sheared, followed by isolation for biotin-marked DNA. Isolated DNA is subjected to sequencing and mapping to the genome [54].

Figure 3

Histone marks and enhancer activity. The histone modifications, H3K4me1, H3K27me3, and H3K27ac, and chromatin accessibility are associated with enhancer activity. Inactive, poised, primed, and active enhancers are defined as H3K4me1+/H3K27me3+/H3K27ac−, H3K4me1+/H3K27me3−/H3K27ac−, and H3K4me1+/H3K27me3−/H3K27ac+ open chromatin regions, respectively [59,62,63].

Figure 2

Trained immunity. Initial stimulations can trigger innate immune responses and establish long-term memories via epigenetic and metabolic alterations. Secondary stimulations induce enhanced innate immune responses, leading to better resistance to diseases [4,5].

Figure 4

Signaling pathways that induce trained immunity through epigenetic reorganization. Novel technologies, such as scRNA-seq and ATAC-seq, have unveiled signaling pathways for trained immunity through epigenetic reorganization [68]. (A) Bacillus Calmette–Guérin (BCG)-induced trained immunity involves type II IFN-mediated alterations in transcription, H3K27ac, and H3K4me1 [69]. (B) Mycobacterium tuberculosis (Mtb)-induced trained immunity involves type I IFN-mediated alterations in transcription [70]. (C) Lipopolysaccharide (LPS)-induced trained immunity involves TRL4-mediated alterations in chromatin accessibility that is dependent on C/EBPβ [71]. (D) β-glucan-induced trained immunity involves type I IFN-mediated alterations in chromatin accessibility [72]. (E) Inflammation-induced trained immunity involves alterations in chromatin accessibility, H3K27ac, and H3K4me1 in epidermal stem cells (EpSCs) [73].

Figure 5

Epigenetic memory established by aging. (A) Aging stress-induced epigenetic memory inscribed in chromatin accessibility and histone modifications (H3K4me1 and H3K27ac). The transcription factors, the binding sites of which were enriched in DARs, are depicted. (B) Differences in transcriptional responses of open DAR-linked genes between young and aged HSCs [102].