Genetic and epigenetic regulation of PD-1 Open Access

Bally, Lex (2017)

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The receptor PD-1 drives immune cell inhibition and exhaustion upon up-regulation. Blockade of this receptor has been shown to be an effective way to restore the function of cells during chronic inflammation, and has been employed therapeutically to that end in cancer patients. Here, systems and regulomes that drive PD-1 expression were studied across multiple cell types and in response to various immune stimuli. A novel driver of PD-1 expression (NF-kB) was identified as the primary driver of PD-1 expression in macrophages. This transcription factor, similarly to the previously identified NFATc1 and STAT3 activators and the repressor FoxO1, binds to the CR-C region of the Pdcd1 locus. The function of this cis-element was found to be involved in driving early changes to PD-1 expression, but not necessary for the prolonged expression of PD-1 during chronic inflammation. Abrogating early PD-1 expression through deletion of CR-C, without altering later modalities of expression, resulted in a shift away from effector cell formation towards a stronger memory cell formation. Furthermore, the histone modifier LSD1 was shown to bind to and regulate the PD-1 locus on an epigenetic level, enforcing a silenced profile following the transient expression seen in the late stages of an acute infection. This partially accounts for the differential expression of PD-1 seen in acute compared to chronic inflammatory settings. In further analysis of the epigenetics of immune responses, distinct chromatin accessibility profiles were identified for naïve, effector, exhausted, and memory T cells during viral infection, and correlated with changes in mRNA expression. Specifically, a set of loci that remains accessible during the effector to memory transition identifies drivers of improved memory functionality compared to naïve cells. In addition to providing an understanding of which active immune environments may induce and be affected by PD-1's function, knowledge of both the molecular mechanisms regulating PD-1, as well as the dynamic epigenetics of the immune response, may help tailor future immunotherapies for fighting cancer, chronic HIV and HCV infections, or prevention of allergic responses, transplant rejection, and autoimmunity as well as improving durable responses to vaccines.

Table of Contents

Table of Contents

Chapter 1: the PD-1 Regulome 1

Programmed Death 1 2

Models for Studying PD-1 Regulation 3

Identifying cis regulatory elements of the Pdcd1 gene 5

Transcription factors inducing acute PD-1 expression 6

Inhibitors of PD-1 expression 7

Chronic regulators of PD-1 and factors in other cell types 9

Epigenetic regulation of Pdcd1 11

DNA methylation of Pdcd1 11

The histone landscape of PD-1 13

Lysine-specific Demethylase 1 and its effects on the immune system 14

PD-1, immune memory, and programming T cell fate 15

Novel technologies for studying T cells 16

Chapter 2: Regulation of PD-1 in B cells, CD4 T cells, and Macrophages 19

Introduction 20

Methods 23

Results 27

Discussion 36

Chapter 3: the role of CR-C on PD-1 expression and memory 48

Introduction 49

Methods 52

Results 57

Discussion 67

Chapter 4: LSD1 and its effects on PD-1 through epigenetic programming 84

Introduction 85

Methods 87

Results 89

Discussion 93

Chapter 5: Genome-wide chromatin accessibility during viral infection 100

Introduction 101

Methods 102

Results 104

Discussion 111

Chapter 6: Discussion 121

Summary 122

PD-1 expression on multiple immune cell types 122

PD-1 outside of T cell exhaustion 124

PD-1 and memory formation 125

Epigenetics of the antiviral immune response 127

The future of immune checkpoint therapies 128

Works Cited 130

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