Dissertation
Elucidating the role of DNA demethylation during thymic development and peripheral CD8 T cell differentiation
University of Iowa
Doctor of Philosophy (PhD), University of Iowa
Autumn 2024
DOI: 10.25820/etd.007738
Abstract
T lymphocytes, or T cells, undergo meticulously orchestrated epigenetic programming during their development in the thymus and during subsequent differentiation in the periphery. This epigenetic process enables the establishment of cell-type and context-specific transcriptional programs are engaged downstream of signals from the T cell receptor, thereby regulating both T cell development and immune responses to infections. DNA methylation plays a pivotal role during lineage and differentiation decisions. This epigenetic modification is predominantly controlled by two opposing forces: DNA methyltransferases, which add methyl groups to the fifth position carbon of cytosine residues, and Ten-eleven translocation (Tet) enzymes, which actively remove these methyl groups through iterative oxidative processes. The dynamic changes in DNA methylation patterns enable context and temporal regulation of gene expression which direct cell fates and functions.
During development in the thymus, Tet enzyme activity increases as T cells commit to their respective lineages from CD4+CD8+ cells. However, it remains unclear whether this activity is required for lineage specification. The family of Tet methylcytosine dioxygenases is comprised of three genes (Tet1, Tet2 and Tet3) expressed in T cells and have both overlapping and distinct functions. In this dissertation, I investigated the role of Tet1/3 in T cell development and differentiation. I found that Tet1/3 are required for regulatory T cell differentiation in the thymus by calibrating responses downstream of TCR signaling and IL-2 production. Unexpectedly, I also uncovered that Tet1/3 pre-program the epigenetic landscape of naïve CD8 T cells, which influence their cell fates during an acute viral infection. CD8 T cells that develop in the absence of Tet1/3 preferentially differentiate into short-lived effectors and effector memory cells following acute infection. Using genome-wide analyses and mice in which Tet1/3 were ablated during T cell development and in mature CD8 T cells, respectively, I established that Tet1/3 regulate cell fates by licensing the chromatin landscape and genes downstream of T cell receptor activation during thymic T cell maturation. However, in mature CD8 T cells, Tet1/3 are dispensable for effector and memory cell fates. A critical mechanism by which Tet1/3 modulate cell fates is by controlling chromatin accessibility at cis regulatory elements of genes that are engaged downstream of TCR signaling. Interestingly, many of these genes are themselves associated with regulation of the TCR-response. These findings unveil the context-specific roles of DNA demethylation, which is essential for defining pathways that contribute to CD8 memory T cell generation against infectious diseases.
Together, my work establishes that Tet1/3 are critical epigenetic regulators of genes associated with regulation of the TCR pathway during T cell ontogeny and underscore the non-redundant roles for Tet enzymes during T cell development. These findings bring into focus the importance of understanding the unique contributions of Tet enzymes in a context-dependent manner to effectively manipulate epigenetic pathways for optimal vaccination outcomes.
Details
- Title: Subtitle
- Elucidating the role of DNA demethylation during thymic development and peripheral CD8 T cell differentiation
- Creators
- Kara Marie Misel-Wuchter
- Contributors
- Priya Issuree (Advisor)Noah Butler (Committee Member)Chad Grueter (Committee Member)Jon Houtman (Committee Member)Miles Pufall (Committee Member)
- Resource Type
- Dissertation
- Degree Awarded
- Doctor of Philosophy (PhD), University of Iowa
- Degree in
- Biomedical Science (Molecular Medicine)
- Date degree season
- Autumn 2024
- DOI
- 10.25820/etd.007738
- Publisher
- University of Iowa
- Number of pages
- xxii, 162 pages
- Copyright
- Copyright 2024 Kara Marie Misel-Wuchter
- Language
- English
- Date submitted
- 07/30/2024
- Description illustrations
- color illustrations
- Description bibliographic
- Includes bibliographical references (pages 142-162).
- Public Abstract (ETD)
Epigenetic programming refers to the process by which our genes can be switched on or off by “tags” attached to our DNA, as well as proteins, to indicate packaging instructions. These tags do not change the DNA sequence itself but can influence how genes are expressed and behave. This programming is crucial because it determines how our cells function and develop, affecting everything from our growth and health, to how we respond to our environment. Understanding epigenetic programming is important as it unveils how our genes are regulated by distinct tags in regions that coordinate expression without affecting protein function. It also enables us to understand how our bodies adapt to changes in our environment and to external pathogens and can offer potential insights into new treatments and therapies.
In my thesis, I examined how a specific modification on the DNA, known as DNA methylation, regulates the identity and function of class of cells known as T cells. T cells are important guardians of the immune system and provide long-lasting cellular immunity to viruses and bacteria. I investigated how removal of DNA methylation tags when T cells develop is important for them to acquire specific identities and how these marks influence their functions during an immune response. I found that removal of DNA methylation during development is important for enabling DNA to become accessible when T cells are stimulated during an immune response. This early programming pre-determines the ability of T cells to acquire specific cellular identities and functions, which are important for viral clearance. I also found that the removal of DNA methylation was important to enable the development of a specific type of T cell important for maintaining homeostasis and prevent autoimmune disease. Together these findings illustrate the importance of epigenetic programming during T cell development, and provides new conceptual insights on how T cell responses can be pre-programmed to respond in specific ways to external pathogens.
- Academic Unit
- Biomedical Science Program; Craniofacial Anomalies Research Center
- Record Identifier
- 9984774869102771
Metrics
1 File views/ downloads
22 Record Views