Vincent Peng


Date of Award

Spring 5-15-2023

Author's School

Graduate School of Arts and Sciences

Author's Department

Biology & Biomedical Sciences (Immunology)

Degree Name

Doctor of Philosophy (PhD)

Degree Type



The defining hallmark of adaptive immunity is the expression of somatically rearranged antigen receptors, which impart the exquisite diversity and specificity of T and B lymphocytes. For almost half a century, immunologists have described cellswhich possess lymphoid characteristics yet lack such antigen-specific receptors. These cells are collectively referred to as innate lymphoid cells (ILC). ILC are composed of natural killer (NK) cells, lymphoid tissue-inducing cells (LTi), group 1 ILC (ILC1), group 2 ILC (ILC2), and group 3 ILC (ILC3). Despite the absence of a unique antigen receptor, ILC effector programs and phenotypic features resemble those employed by adaptive immune cells. NK cells parallel CD8 T cells in terms of their cytotoxic function, whereas ILC1, ILC2, and ILC3 mirror TH1, TH2, and TH17 cells, respectively, in the hallmark cytokines they produce. However, while T cells require several days to undergo clonal proliferation and acquire effector functions, ILC are fully differentiated and capable of responding immediately to stimuli. Additionally, ILC1, ILC2, and ILC3 are largely tissue-resident and are enriched at mucosal barrier tissues. These unique features establish a critical position for ILC at the interface between innate and adaptive immunity, where they play important roles in both the initiation and amplification of the immune response. The regulation of ILC identity and function remains an open and important question. In this thesis, I will outline three approaches we have taken to understand how ILC are regulated through DNA methylation, phosphoinositide signaling, and polyamine metabolism. DNA methylation is an essential mechanism for maintaining epigenetic fidelity and fate commitment. The relevance and importance of this epigenetic mechanism is unknown in ILC. We have performed a novel genome-wide profiling of DNA methylation and hydroxymethylation in three hallmark ILC subsets: natural killer (NK) cells, group 2 ILC (ILC2), and group 3 ILC (ILC3). We integrate these analyses with transcriptomic, chromatin accessibility, and histone modification information to define distinct regulatory paradigms controlling lineage-defining transcription factors (Rorc, Gata3, Tbx21) and hallmark effector molecules (Il22, Il13, Ifng). To complement our DNA methylation profiling, we define a causal role for Tet2-dependent hydroxy-methylation in regulating the effector function and plasticity of ILC. This chapter defines the landscape and function of DNA methylation in ILC and furthers our understanding of the regulatory code that dictates ILC fate and function. While they share many phenotypic markers, NK cells and ILC1 display striking differences in ontogeny and regulation of effector functions. In contrast to NK cells which are constantly produced in the bone marrow and circulate throughout the body, ILC1 are largely tissue-resident where they self-renew in situ. Through bulk and single-cell transcriptomics, we identified the inositol phosphatase Inpp4b as a striking feature of ILC1. Furthermore, we demonstrate that imprinting by TGF-β family factors induces Inpp4b expression. Through conditional deletion of Inpp4b, we demonstrate that Inpp4b is necessary for the maintenance and maturation of tissue-resident ILC1 whereas NK are relatively spared. Additionally, we find an unexpected role for Inpp4b in promoting NK survival during antiviral and antitumor responses in vivo. As a result, Inpp4b deficiency leads to impaired NK-mediated antitumor immunity. This chapter defines a novel role for Inpp4b in the immune system and further elucidates the regulatory modules that drive ILC1 and tissue-resident NK formation. Metabolism is a critical and consequential regulator of immune cell identity and effector function. While the immunometabolic requirements of adaptive lymphocytes have been well-studied, similar circuits have not been investigated in ILC. Through an integrative approach using single-cell transcriptomics and untargeted mass spectrometry-based metabolomics, we have identified the polyamine biosynthetic pathway to be enriched in ILC3. Using a conditional loss-of-function model ablating ILC3-intrinsic polyamine biosynthesis, we have shown that this metabolic pathway is required for effective defense against enteric pathogens. Mechanistically, we demonstrate that polyamines have a selective role in augmenting ILC3 production of IL-22 and IL-17a, which play vital roles in maintaining mucosal barrier integrity. This chapter establishes a novel regulatory axis between polyamine metabolism and ILC3 effector functions which may be therapeutically manipulated for the treatment of GI pathology.


English (en)

Chair and Committee

Marco Colonna

Committee Members

Todd Fehniger, Haina Shin, Steven Van Dyken, Ting Wang,

Available for download on Wednesday, May 10, 2028