Epigenetic inheritance in stem cells and in immune cell development and function
The epigenetic process safeguards cell identity through the inheritance of appropriate gene expression programs. Among the key determinants of epigenetic inheritance are histones and their post-translational modifications that shape chromatin structures to either facilitate or impede transcription (Figure 1). The overarching goal of our research is to understand the fundamental mechanisms for cell fate decisions. We use immune cell development and function to elucidate how chromatin contributes towards the delicate balance between preserving a chromatin state and cell identity while permitting changes from the environment to achieve cellular diversity. We have a number of specific projects in the lab that work towards this goal such as: 1) delineating the epigenetic mechanisms by which chromatin shapes a hematopoietic cascade and 2) identifying the molecular basis involved in constructing the heritable epigenome of immunological memory.
Figure 1. Chromatin organizational states
Investigate the epigenome regulation of hematopoietic stem cells (HSCs) in health and disease
The epigenome of hematopoietic stem cells (HSCs) confers self-renewal and differentiation functions wherein inheritance of an HSC chromatin state is persistent across cell cycles. We recently identified nucleophosmin (NPM1) as a key player in the epigenetic preservation of facultative heterochromatin, functioning with the Polycomb Repressive Complex 2 (PRC2) to sustain the post-translational modifications (PTMs) di- and tri- methylation of histone H3 at lysine 27 (H3K27me2/H3K27me3) across DNA replication in mouse embryonic stem cells [1]. NPM1 gene mutations are considered driver mutations in the pathogenesis of acute myeloid leukemia (AML), however, NPM1 function in normal hematopoiesis remains unknown. We are collaborating with Dr. Sergei Doulatov’s laboratory at the University of Washington Department of Hematology to study normal NPM biology and determine whether aberrant function in epigenetic inheritance contributes to the etiology of NPM1-driven cancer mutations (Figure 2). We are utilizing in vitro human and in vivo mouse systems to identify the molecular basis of NPM in constructing the heritable epigenome of HSCs.
Figure 2. Role of NPM1. (A) Preservation of epigenetic memory with PRC2 and NPM1. (B) The effect of NPM1 mutations on stem cell differentiation.
Discover how memory T cells form and sustain their poised epigenome.
In the memory stage of a mammalian immune response, the persistence and stability of pathogen-specific memory cells is juxtaposed with their poised state to self-renew and differentiate upon re-infection. Fundamental to the poised state of memory cells is the chromatin organization that permits the heritable gene expression program even after pathogen-stimulation has subsided, a phenomenon integral to the concept of epigenetics and gene regulation. CD8+ T cells are essential effectors for long-term immunity, as they provide protection against intracellular pathogens and cancer. Upon first encounter with an acute viral infection, naïve CD8+ T cells become activated and expand and differentiate into pathogen-specific Terminal Effector (TE) and Memory Precursors (MP) cells. TEs produce inflammatory cytokines and cytolytic molecules to eliminate infected cells while MPs give rise to memory T cells. As the pathogen is cleared, the majority of TEs die, with a small number of MPs surviving to make up a collection of memory T cells that remain poised for rapid and robust function if pathogen re-exposure occurs (Figure 3A). How can memory precursor cells and long-lived memory cells retain their gene expression programs after the initial pathogen-stimulation has subsided, and how do they remain poised for re-activation upon re-infection? Key to bypassing the de novo gene expression program of a particular cell identity are its epigenetic mechanisms, which entail the regulated inheritance of gene expression patterns previously experienced by a parental cell and maintained through DNA replication, following multiple cell divisions, and in some instances, for an entire human lifespan. Unique to memory CD8+ T cells is the repressive and permissive chromatin decorating both pro-memory and pro-effector genes, revealing its multipotency (Figure 3B). The underlying epigenetic mechanisms that guide the cell fate decisions and maintain longevity endowed to CD8+ T cells remain incompletely understood (Figure 3B, ① and ②). Our lab is creating an atlas for memory potential and utilizing this information to conduct CRISPR-Cas Biotinylation experiments to discover chromatin mechanisms unique to poised chromatin.
Figure 3. Cellular and molecular dynamics of CD8 + T cell differentiation upon pathogen exposure
Citations.
- T. M. Escobar, J.-R. Yu, S. Liu, K. Lucero, N. Vasilyev, E. Nudler, and D. Reinberg, “Inheritance of repressed chromatin domains during S phase requires the histone chaperone NPM1,” Science Advances, vol. 8, no. 17, Apr. 2022.