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Copyright by Alfire Sidik 2019 Copyright by Alfire Sidik 2019 The Dissertation Committee for Alfire Sidik Certifies that this is the approved version of the following Dissertation: Genetic and Bioinformatic Approaches to Characterize Ethanol Teratogenesis. Committee: Johann K. Eberhart, Supervisor R. Adron Harris Vishwanath R. Iyer Christopher S. Sullivan John B. Wallingford Genetic and Bioinformatic Approaches to Characterize Ethanol Teratogenesis. by Alfire Sidik Dissertation Presented to the Faculty of the Graduate School of The University of Texas at Austin in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy The University of Texas at Austin August 2019 Acknowledgements I first and foremost want to extend my deepest gratitude to my mentor, Dr. Johann K. Eberhart, without whom this dissertation would not be possible. Johann, thank you for your invaluable insight, patience, guidance, and unwavering encouragement. I am also extremely grateful to Mary Swartz. Mary, you truly are the glue that holds the lab together. I joined the lab with little-to-no wet lab and embryology experience and attribute a lot of what I learned to you. Thank you for always being receptive to my questions and for your valuable scientific advice. I would like to express my appreciation to all of my committee members for their constructive advice, suggestions, and professional guidance. I would especially like to thank Dr. Adron Harris. Adron, thank you for your compassion and support of me throughout the years. I’d like to thank all members of the lab, both past and present, who I’ve had the pleasure of working with. Thank you Neil McCarthy, Patrick McGurk, Ben Lovely, Anna Percy, Angie Martinez, Tim Kuka, Ranjeet Kar, Desire Buckley, Yohaan Fernandes, Scott Tucker, and Josh Everson. To my undergraduate and high school mentees, Elaine Avshman, Jenna Beam, Jennyly Nguyen, Hannah Kirby, Sruthi Ramaswamy, Maitreyi Ramaswamy, and Natasha Paul. Thank you for making the mentorship experience so enjoyable. I’d also like to thank all of my graduate school friends for their constant support and encouragement. Many thanks to Groves Dixon for his bioinformatic expertise and contributions to the project. Lastly, I want to extend my deepest appreciation to my parents and sister, Almire Sidik. I would not be where I am today if it weren’t for your unconditional love and support. iv Abstract Genetic and Bioinformatic Approaches to Characterize Ethanol Teratogenesis. Alfire Sidik, PhD The University of Texas at Austin, 2019 Supervisor: Johann K. Eberhart Alcohol consumption during pregnancy is the most preventable cause of birth defects, yet approximately 2-5% of children are afflicted with Fetal Alcohol Spectrum Disorders (FASD). FASD describes the complex and highly variable deleterious phenotypes caused by prenatal alcohol exposure. Twin studies suggest a genetic predisposition, contributing to the variation in risk for FASD. Despite this, we lack a basic understanding of 1) the factors that protect or predispose an individual to FASD and 2) how these genetic factors interact in ethanol teratogenesis. Results from a genetic “shelf” screen revealed vangl2, a member of the Wnt/planar cell polarity (PCP) pathway that mediates convergent extension movements that narrow and elongate the body axis, as an ethanol-sensitive genetic locus. Untreated vangl2 mutants displayed a relatively intact craniofacial skeleton. Ethanol-exposed vangl2 heterozygotes and mutants, displayed cyclopean and midfacial defects. To assess the relative level of variation of the transcriptional response to ethanol, I performed single embryo RNA-seq during early embryonic stages. Individual zebrafish v embryos were exposed to a subteratogenic dose of 1% ethanol in embryo media. My data suggests that the effect of ethanol is subtle; time is the most important variable driving variation in fold coverage across all samples. Despite this, I find a number of differentially expressed genes in response to ethanol. Transcriptional changes due to ethanol are indicative of increased oxidative stress and ion transport and reduced DNA replication and cell division. Using a bioinformatic approach, I find cyclopamine, a Hedgehog pathway inhibitor, interacts with ethanol. Further genetic analyses shows that ethanol disrupts convergent extension of the mesoderm, which in turn disrupts localization of shh in the axial mesoderm, a signal necessary to separate the eye field. I find this effect to be further exacerbated in the vangl2 mutant background. Together these data yield important insight necessary to advance understanding and treatment for FASD. vi Table of Contents List of Tables ..................................................................................................................... xi List of Figures ................................................................................................................... xii Chapter 1: General Introduction and Significance ..............................................................1 1.1. Fetal Alcohol Spectrum Disorders (FASD) .........................................................2 1.1.1. Holoprosencephaly ...............................................................................4 1.2 Gene-Ethanol Interactions ....................................................................................5 I.2.1. The vangl2-ethanol interaction ..............................................................6 I.2.2. The hedgehog signaling pathway ..........................................................7 1.3 Gastrulation ...........................................................................................................8 I.3.1. Germ layer formation in humans ...........................................................8 I.3.2. Germ layer formation in zebrafish .........................................................9 1.4 Eye Field Formation ...........................................................................................10 I.4.1. Optic vesicle morphogenesis ...............................................................11 I.4.2. Transcription factors specify the eye field ..........................................11 I.4.3. The Wnt signaling pathway in forebrain patterning ............................12 1.5 The Wnt Signaling Pathway ...............................................................................12 1.5.1. The non-canonical Wnt/PCP pathway ................................................13 1.5.2. Convergent extension ..........................................................................15 Chapter 2: Convergent extension defects underlie susceptibility to midfacial hypoplasia in an ethanol-sensitive mutant, vangl2. .....................................................16 2.1. Abstract ..............................................................................................................16 2.2. Introduction ........................................................................................................17 vii 2.3. Results ................................................................................................................19 2.3.1. vangl2 mutants and heterozygotes are sensitive to 1% ethanol during early embryogenesis ....................................................................19 2.3.2 The effect of ethanol on the early zebrafish transcriptome is subtle relative to developmental time ................................................................20 2.3.3. Ethanol has effects on transcription that are largely distinct between different developmental timepoints ..........................................21 2.3.4. Ethanol does not affect the Wnt/PCP pathway at the transcriptional level .................................................................................22 2.3.5. Transcriptional changes due to ethanol are indicative of increased oxidative stress and ion transport and reduced DNA replication and cell division .............................................................................................22 2.3.6. Modules of co-regulated genes related to ethanol exposure ...............23 2.3.7. Cyclopamine is predicted to mimic the effects of ethanol ..................24 2.3.8. Ethanol indirectly attenuates Shh signaling ........................................26 2.3.9. Ethanol disrupts convergent extension ...............................................27 2.3.10. Ethanol alters six3 and rx3 expression in the eye field .....................29 2.3.11. Mutation in gpc4 enhances cyclopia in a dose-dependent manner ...29 2.4. Discussion ..........................................................................................................30 2.5. Materials and Methods .......................................................................................32 2.5.1. Zebrafish (Danio rerio) Care and Use ................................................32 2.5.2. Sample collection and RNA extraction ...............................................33 2.5.3. RNA-seq data processing ....................................................................33 2.5.4. Differential expression analysis ..........................................................34 2.5.5. GO enrichment ....................................................................................35 2.5.6. Weighted Gene Correlation Network Analysis (WGCNA) ................35 viii 2.5.7. Quantitative Real-Time qRT-PCR (qRT-PCR) ..................................36 2.5.8. Cartilage and Bone Staining and Measurements ................................36
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