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EVALUATING THE EFFECTS OF PARTICLE-DELIVERED COMBINATION ADJUVANTS ON ANTIGEN-PRESENTING CELLS A Dissertation Presented to The Academic Faculty by Alexandra Maria Atalis In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University May 2021 COPYRIGHT © 2021 BY ALEXANDRA MARIA ATALIS EVALUATING THE EFFECTS OF PARTICLE-DELIVERED COMBINATION ADJUVANTS ON ANTIGEN-PRESENTING CELLS Approved by: Dr. Krishnendu Roy, Advisor Dr. Philip Santangelo School of Biomedical Engineering School of Biomedical Engineering Georgia Institute of Technology Georgia Institute of Technology Dr. J. Brandon Dixon, Co-Advisor Dr. Manmohan Singh School of Mechanical Engineering Senior VP, Pharmaceutical Sciences Georgia Institute of Technology and Delivery Technologies Beam Therapeutics Dr. Susan Thomas School of Mechanical Engineering Georgia Institute of Technology Date Approved: February 12, 2021 To my mom, Elaine Atalis, in loving memory ACKNOWLEDGEMENTS I would like to acknowledge all current and previous labmates who helped me throughout my Ph.D. journey. Dr. Jardin Leleux, Dr. Pallab Pradhan, Dr. Randall Toy, and Dr. Timothy Kassis taught me the basics of experimental design and foundational lab techniques and provided much-needed encouragement and motivation. Dr. Bhawana Pandey helped tremendously by preparing particle formulations for most experiments in Aim 2 and provided many chemistry-related experimental tips. When times were tough, she reminded me to stay positive. Cole Keenum and Alexander Beach were a big part of the COVID-19 research team. Alex collected BMDC cytokine and serological antibody titer data from ELISA and Luminex assays. Cole helped with preparing particle formulations, ELISA assays, and staining samples for flow cytometry. Paramita Chatterjee and Angela Jimenez performed RT-PCR experiments and data analysis. Paramita Chatterjee and Cole Keenum provided the single-cell mRNA and protein expression data analyzed in SEURAT. A big team worked on the COVID-19 intranasal vaccination study: Bhawana Pandey, Pallab Pradhan, Alexander Beach, Cole Keenum, Ritika Jain, Casey Vantucci, and Justin Hosten. Thank you to my advisors, Dr. Roy and Dr. Dixon, for all of their guidance and support, especially when I had to take a personal hiatus to spend time with family. To Dr. Dixon: I will never forget when attended the Lymphatics Gordon Research Conference in Italy with LLBB. Thank you for allowing me that opportunity. To Dr. Roy: it is hard to believe I have known you for over 10 years since I was a sophomore at UT Austin. I remember sitting in the lobby of the Biomedical Engineering Building wondering what I would do after college, and you encouraged me to apply to graduate school. Finally, thank you to my friends and family who have supported me through the iv ups and downs. My roommate and friend, Dr. Roxanne Glazier, and I had many late-night talks about life and research that I will never forget. My close friend and confidante, Michelle Humphrey, was always a phone call away when times were tough (and thank you for the box of snacks to help me get through writing this dissertation). My godfather, Dr. John Pappadas has been my #1 fan since Day 1 of starting this program. He supported me through my anxiety and encouraged me to stick with it. Thank you to my brothers, Sam and John, and to cousins, aunts, uncles, and Yiayias who provided much love and prayer. Thank you to my Dad, Andy Atalis, who was always there to talk me through the tough moments and has encouraged me to be my best self. Thank you to my husband-to-be Nick Grivas, who is my rock. I look forward to our marriage and life together. Finally, I want to acknowledge my mother, Elaine Atalis, who passed away in 2017. Her strength continually inspires me to persevere through difficult moments. She is with me in spirit every step of the way. v TABLE OF CONTENTS ACKNOWLEDGEMENTS iv LIST OF TABLES ix LIST OF FIGURES x LIST OF SYMBOLS AND ABBREVIATIONS xiii SUMMARY xv Chapter 1: Introduction and Aims 1 1.1 Introduction 1 1.2 Specific Aims 7 1.2.1 Hypothesis 7 1.2.2 Aim 1: Characterizing Immune Responses to Combined MPLA and CpG 8 1.2.3 Aim 2: Characterizing Immune Responses to Combined RLR and TLR Agonists 9 Chapter 2: Background 12 2.1 APCs: Linking Innate and Adaptive Immunity 12 2.2 Pathogen Recognition Receptors 19 2.2.1 Toll-like Receptors 19 2.2.2 RIG-I-like Receptors 24 2.3 APC Subsets and their Functions 25 2.3.1 Conventional DCs 26 2.3.2 Monocyte-derived DCs 28 2.3.3 Plasmacytoid DCs 29 2.3.4 Macrophages 30 2.3.5 B Cells 32 2.3.6 In Vitro Models of APCs 33 2.4 PRR Agonists as Vaccine Adjuvants 33 2.4.1 Monophosphoryl Lipid A (TLR4) 35 2.4.2 Imiquimod and Resiquimod (TLR7/8) 35 2.4.3 CpG Oligodeoxynucleotides (TLR9) 36 2.4.4 RIG-I-Like Receptor Ligands 37 2.4.5 Combination Adjuvants 38 2.5 Vaccine Delivery to Lymph Nodes 39 2.5.1 Particle-Based Vaccine Delivery 39 2.5.2 Dendritic Cell Migration Through Lymphatic Vessels 40 2.6 Adjuvants in SARS-CoV-2 Vaccines 41 Chapter 3: Aim 1.1. Investigating How Soluble and Particle-based Delivery of MPLA and CpG Differentially Modulate 3D Chemotaxis of Bone Marrow-Derived Dendritic Cells 44 vi 3.1 Materials and Methods 45 3.1.1 Bone marrow-derived cells (BMDCs) 45 3.1.2 Synthesis of PLGA Microparticles 46 3.1.3 Flow Cytometry Experiments 46 3.1.4 Microfluidic Device Setup 49 3.1.5 Cell Tracking 50 3.1.6 Statistical Analysis 50 3.2 Results 52 3.2.1 Synthesis of PLGA Microparticles for Dual Adjuvant Delivery 52 3.2.2 Generation of Heterogenous Cell Populations in BMDC Culture 53 3.2.3 Logistic Regression Model Filters Data for Migratory Cell Tracks 56 3.2.4 Addition of IL-4 to BMDC Culture Increases CCR7 Expression and Chemotaxis 59 3.2.5 Soluble MPLA Increases While Soluble CpG Decreases Chemotaxis 62 3.2.6 CpG Delivered on PLGA MP Increases Cell Chemotaxis 64 3.3 Discussion 66 Chapter 4: Aim 1.2. Assessing How MPLA and CpG Regulate Immune Cell Populations and Particle Transport to Draining Lymph Nodes In Vivo 73 4.1 Materials and Methods 73 4.1.1 Synthesis of Fluorescent Nanoparticles 73 4.1.2 Intramuscular Injections 75 4.1.3 NIR Imaging of Lymph Nodes 75 4.1.4 Tissue Preparation and Staining for Flow Cytometry 76 4.1.5 Statistical Analysis 78 4.2 Results 78 4.2.1 Fluorescence of IR700-Conjugated CpG and Control ODN Loaded on PLGA PEI NP Peaks at 24 Hours and Decreases at 48 Hours in Muscle-Draining Lymph Nodes 78 4.2.2 Particle-Delivered MPLA and CpG ODN Differentially Regulate Innate Immune Cell Populations and Maturation in the Muscle 82 4.2.3 MPLA and CpG ODN Loaded on PLGA PEI NP Differentially Regulate APC Populations and CD86 Expression in Muscle-Draining Lymph Nodes 86 Chapter 5: Aim 2.1. Evaluating How RLR- and TLR-Tarteting PLGA Nanoparticles Direct Bone Marrow-Derived DC Cytokine Secretion and T cell Activation In Vitro 88 4.3 Motivation 88 4.4 Materials and Methods 88 4.4.1 Synthesis of PUUC RNA 88 4.4.2 Preparation of PLGA-PEI Nanoparticles and Loading of Adjuvants 89 4.4.3 Bone-marrow derived Dendritic Cell (BMDC) Culture 90 4.4.4 Characterizing APC Subsets in BMDC Culture with Flow Cytometry 90 4.4.5 Iso-Mixed Lymphocyte Reaction 91 4.4.6 Analysis of BMDC Cytokine Secretion 92 4.5 Results 93 vii 4.5.1 FLT3L and GM-CSF Bone Marrow-Derived Dendritic Cell Cultures are Comprised of Different APC Subsets 93 4.5.2 GM-CSF and FLT3L BMDC Secrete Distinct Cytokine Patterns in Response to Combination Adjuvants 93 4.5.3 GM-CSF and FLT3L BMDCs Selectively Respond to PRR-Targeted Adjuvants to Induce CD8+ T Cell Proliferation and T Cell Death in Iso-MLR Assay 100 Chapter 6: Aim 2.2. Characterizing Innate and Adaptive Immune Responses to Intranasal Vaccination with Co-Delivered RLR and TLR agonists on PLGA Nanoparticles 103 5.1 Materials and Methods 103 5.1.1 Intranasal Administration of PLPs 103 5.1.2 Lung Gene Expression Analysis with RT-PCR 103 5.1.3 Single-Cell Gene and Protein Expression Analysis with CITE-Seq 105 5.1.4 SARS-CoV-2 Vaccination Groups 106 5.1.5 Preparation of Spike Protein-Conjugated PLGA PEI NPs 107 5.1.6 Vaccination Timeline and Tissue Collection 108 5.1.7 IgG and IgA ELISA Assays 108 5.1.8 Ex Vivo Lung Cell Stimulation Assays 109 5.1.9 Intracellular Cytokine Staining 110 5.2 Results 111 5.2.1 PUUC-TLR Agonist Combinations Differentially Regulate Inflammatory Gene Expression in Mouse Lungs after Intranasal Administration 111 5.2.2 CITE-Seq Analysis Reveals Changes in Lung Cell Populations and Genetic Expression in Response to PUUC and MPLA-PUUC PLGA NPs 116 5.2.3 MPLA-PUUC NP Increase CD4+ and CD103+CD69+ T Cell Responses to Restimulation with SARS-CoV-2 Spike Peptide Pools 119 Chapter 7: Conclusions and Future Work 123 6.1 Conclusions 123 6.1.1 APC-Mediated Immune Responses to Combination Adjuvants In Vitro are Dependent on the Type of APC Culture 123 6.1.2 APC-mediated Immune Responses to Combination Adjuvants and Antigens are Dependent on Vaccine Delivery Systems 125 6.1.3 Route of Administration Determines Success for Combination Adjuvants 126 6.2 Future Work 129 Appendix A: Supplementary Figures and Methods 132 8.1 Aim 1.1 Supporting Information 132 8.1.1 Supplemental Experimental Methods 132 8.1.2 Circular Statistical Methods 133 8.1.3 Supplemental Figures 138 8.2 Aim 1.2 Supporting Information 144 8.3 Aim 2.1 Supporting Information 146 8.4 Aim 2.2 Supporting Information 149 References 156 viii LIST OF TABLES Table 1 Single and combination adjuvant loading on PLGA NP and doses for 92 BMDC culture.