Interrogating ARDS Risk and Severity Utilizing Genomic and Systems Biology Approaches
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Interrogating ARDS Risk and Severity Utilizing Genomic and Systems Biology Approaches Item Type text; Electronic Dissertation Authors Lynn, Heather D. Citation Lynn, Heather D. (2020). Interrogating ARDS Risk and Severity Utilizing Genomic and Systems Biology Approaches (Doctoral dissertation, University of Arizona, Tucson, USA). Publisher The University of Arizona. Rights Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction, presentation (such as public display or performance) of protected items is prohibited except with permission of the author. Download date 07/10/2021 14:43:39 Link to Item http://hdl.handle.net/10150/650808 INTERROGATING ARDS RISK AND SEVERITY UTILIZING GENOMIC AND SYSTEMS BIOLOGY APPROACHES by Heather Lynn _________________________ Copyright © Heather Lynn 2020 A Dissertation Submitted to the Faculty of the GRADUATE INTERDISCIPLINARY PROGRAM IN PHYSIOLOGICAL SCIENCES In Partial Fulfillment of the Requirements For the Degree of DOCTOR OF PHILOSOPHY In the Graduate College THE UNIVERSITY OF ARIZONA 2020 Acknowledgements & Dedications Many people’s efforts and time besides my own went into the creation and refinement of this work. I would first like to acknowledge my mentor, Dr. Garcia, without whose support none of this would be possible. Secondly, I want to acknowledge my committee members (Drs Coletta, Karnes, Ledford, and Sun) that have contributed to both the scientific aspects of this thesis and to the personal task of mentoring and teaching me their own areas of expertise they brought to this project. Third, I would like to thank the support of the many professors and staff of the Physiological Sciences GIDP for financial, logistical, and intellectual support during graduate school. Finally, I want to thank my family and friends (first among them being my husband, Charlie) for their patience while I was navigating the work of graduate school and the final task of completing this thesis. 3 | Lynn Table of Contents List of Figures and Illustrations ............................................................. Page 9 List of Tables ............................................................................................ Page 11 Abstract ...................................................................................................... Page 12 Description of Dissertation Format ...................................................... Page 15 Chapter 1: Introduction .......................................................................... Page 16 ARDS is a Critical Care Illness .......................................................... Page 16 Endothelial Barrier Dysfunction in ARDS ........................................... Page 20 Biomarkers as a Clinically Useful Sub-Phenotyping Tool in ARDS ... Page 21 Genomics in ARDS ............................................................................ Page 24 Epigenetics in ARDS ......................................................................... Page 28 MYLK and NAMPT: Two Candidate Risk Genes in ARDS ................ Page 30 Summary and the Promise of System Biology................................... Page 32 Hypothesis ......................................................................................... Page 33 Chapter 2: Aim 1--Genomic and Genetic Approaches to Deciphering Acute Respiratory Distress Syndrome Risk and Mortality ......................... Page 35 Significance ....................................................................................... Page 35 Recent Advances and ARDS in the Clinical and Genetic Literature .. Page 37 Potential ARDS Candidate Genes Identified by Dysregulated Gene Expression .......................................................................................................... Page 41 PBMC Gene Expression in ARDS as Predictors of Mortality ............. Page 43 Pathway Analysis .............................................................................. Page 46 4 | Lynn Reactive Oxygen Species (ROS) Pathways ...................................... Page 50 Immune-linked and Inflammation-linked Pathways ............................ Page 53 Endothelial Vascular and Cellular Signaling Pathways ...................... Page 57 Other Transcription Factor and Signaling Pathways .......................... Page 61 Critical Issues .................................................................................... Page 61 ARDS Genetic Variants Identified by Genome-Wide Association Studies ................................................................ Page 62 GWAS Studies of ARDS Mortality .......................................... Page 65 ARDS Genetic Variants/Genes Identified by Candidate Gene Studies .......................................................................... Page 67 Candidate Gene Studies of ARDS Mortality ........................... Page 68 ARDS risk SNPs in African Americans ................................... Page 71 Future Directions ............................................................................... Page 74 Chapter 3: Aim 2—NAMPT Haplotypes and Plasma eNAMPT levels Predict ARDS Mortality Risk ..................................................... Page 76 Significance ....................................................................................... Page 76 Methods ............................................................................................. Page 78 Demographics of the ARDS Genotyping and Biomarker Cohort ................................................................................................ Page 78 Patient Sample Collection ....................................................... Page 79 Detection of Secreted NAMPT ................................................ Page 79 NAMPT Genotyping ................................................................ Page 80 Endothelial Cell Culture .......................................................... Page 80 5 | Lynn NAMPT Promoter Activity ....................................................... Page 81 Statistical Analysis .................................................................. Page 81 Results .............................................................................................. Page 83 NAMPT Promoter Genotypes and eNAMPT Plasma Levels in ARDS Cohorts ........................................................................ Page 83 The NAMPT Promoter SNP rs61330082 (-1535) is Significantly Associated with ARDS Mortality Risk ................. Page 86 NAMPT Promoter SNP rs61330082 (-1535) Alters LPS- and Mechanical Stress-induced NAMPT Promoter Activity .... Page 88 eNAMPT Levels are Associated with APACHE II Scores and rs61330082 Genotypes .................................................... Page 89 Optimized ARDS Mortality Prediction Model: eNAMPT Plasma Values and a rs61330082/rs59744560-based Haplotype Risk Score ................................................................................................ Page 91 Discussion ........................................................................................ Page 94 Future Directions ............................................................................... Page 98 NAMPT as a Biomarker in Other Pulmonary Diseases ........... Page 98 ARDS is an Endotype for COVID-19 ...................................... Page 102 Chapter 4: Aim 3—ARDS & Methylation........................................... Page 103 Significance ....................................................................................... Page 103 Methods ............................................................................................. Page 105 Patient Demographics and Sample Collections ...................... Page 105 Genome-wide Methylation Profiling ChIP ............................... Page 106 6 | Lynn mRNA Extraction and Genome-wide Transcription Profiling ... Page 107 Pathway Analysis .................................................................... Page 108 ARDS Combined Lung Injury Preclinical Rat Model ............... Page 108 ARDS Combo Model............................................................... Page 108 qPCR Assay ........................................................................... Page 109 Results .............................................................................................. Page 109 A Unique Methylation Profile in PBMCs is Present for Severe ARDS Outcomes ............................................................................... Page 109 c-MET Pathway is Associated with Methylation Enrichment in ARDS ................................................................................................ Page 113 GSEA Analysis Reveals an Interconnected Network of Receptor Tyrosine Kinase Signaling Genes and Transcription Factors . Page 114 Global Genome Methylation is Increased in Severe ARDS Outcomes in a Validation ARDS Cohort ................................................... Page 116 Methylation in CpG Islands in Key Transcription Factors in ARDS Show Altered Levels of Methylation in ARDS/VILI ....... .......... Page 118 Discussion ......................................................................................... Page 120 Future Directions ............................................................................... Page 125 Chapter 5: Discussion ........................................................................... Page 127 Conclusion ........................................................................................