Genetics and Genomics Commons^™

Regulation Of De Novo And Maintenance Dna Methylation By Dnmt3a And Dnmt3b, Yang Zeng

Dissertations and Theses (Open Access)

DNA methylation (5-methylcytosine, 5mC) is essential for the regulation of gene expression and integrity of the mammalian genome. It occurs predominantly in the context of CpG dinucleotides to form a symmetrical pattern on both DNA strands, which allows DNA methylation patterns to be semi-conservatively maintained during DNA replication. There are two classes of DNA methyltransferases (DNMTs): DNMT3A and DNMT3B function primarily as de novo methyltransferases that establish DNA methylation patterns, whereas DNMT1 is the major enzyme responsible for maintaining DNA methylation patterns by converting hemi-methylated CpGs to fully methylated CpGs during DNA replication. Two accessory factors also play critical regulatory …

Prenatal Screening Decision-Making Facilitated Through An Online Patient Education Module, Erin Atkinson

Dissertations and Theses (Open Access)

As recommendations for prenatal genetic screening are expanded to include patients with pregnancies at low risk for aneuploidy, there is a need to develop accessible mechanisms to promote informed decision-making about genetic screening. The use of patient decision aids has been shown to promote informed decision-making. UTHealth Houston has developed and implemented an online module for pre-test triage for genetic counseling and education of low-risk pregnant patients about genetic screening, called the Prenatal Genetic Education Program (PGEP).

Here, through a retrospective chart review, we characterize the use of PGEP to triage previously presumed low-risk patients to genetic counseling, and whether …

The Need For Racial And Ethnic Health Disparity Curriculum In Genetic Counseling Programs, Yusra Aziz

Dissertations and Theses (Open Access)

Racial and ethnic health disparities (REHD) exist across all organized medicine, including the spectrum of genetic counseling, particularly in genomic testing and access to care. While cultural competency and health disparities have been included as a part of the Standards of Accreditation for Genetic Counseling, there have not been previous efforts to define what topics related to REHD are most important to include in graduate program curriculum. Therefore, this study aimed to determine what topics related to REHD should be taught in genetic counseling program curriculum by assessing what topics genetic counselors (GCs) learned about and in what settings, …

Genetic Regulation Of Müllerian Duct Regression, Malcolm Moses

Dissertations and Theses (Open Access)

Mammals, including humans, develop progenitor tissues for both male and female reproductive tract organs before they fully differentiate into a male or female tract. The progenitor tissue for the male reproductive tract is known as the Wolffian duct (WD), and the progenitor tissue for the female reproductive tract is the Müllerian duct (MD). The WD further differentiates into the vas deferens, epididymis, and seminal vesicle, while the MD differentiates into the oviduct, uterus and upper vagina. An essential step in sex differentiation for males is the regression of the MD. This regression initiates with anti-Müllerian hormone (Amh) transcription …

Functions Of The Trna Splicing Endonuclease And Other Adventures In Rna Processing, Jennifer Hurtig, Ambro Van Hoof

Dissertations and Theses (Open Access)

The tRNA splicing endonuclease (TSEN), has been studied for over three decades for its function in tRNA splicing. However, this enzyme has other functions that are just beginning to be characterized. Mutations in TSEN cause the neuronal disease pontocerebellar hypoplasia (PCH) that is characterized by atrophy of the cerebellum and pons, overall developmental failure, and usually results in death before adolescence. How mutations in TSEN cause these neuronal defects and disease is not understood. In yeast, TSEN has another essential function that is independent of tRNA splicing and is still unknown. In this thesis I strived to understand the other …

Med12 Is A Critical Regulator Of Neural Crest Lineage And Nervous System Myelination, Fatma Betul Aksoy Yasar

Dissertations and Theses (Open Access)

The Mediator complex (MED) is a multi-subunit protein complex integral to the eukaryotic transcription machinery. MED12 is a Cdk8- regulatory kinase module subunit directly implicated in human disease and is genetically altered in neurological disease and cancer. Numerous attempts at generating an in vivo system to study the role of Med12 failed due to embryonic lethality associated with germline or developmental disruption of Med12 gene. To understand the cellular and molecular processes associated with its role in disease, we generated multiple mouse models with targeted depletion of MED12 in distinct cellular lineages. Our genetically engineered models with induced and conditional …

Redox Sensing By Yeast Hsp70 Facilitates Modulation Of Protein Quality Control And The Cytoprotective Response, Alec Santiago

Dissertations and Theses (Open Access)

Neurodegenerative disease affects millions of Americans every year, through diagnoses such as Alzheimer’s, Parkinson’s, and Huntington’s diseases. One factor linked to formation of these aggregates is damage sustained to proteins by oxidative stress. Cellular protein homeostasis (proteostasis) relies on the ubiquitous Hsp70 chaperone family. Hsp70 activity has been previously shown to be modulated by modification of two key cysteines in the ATPase domain by oxidizing or thiol-modifying compounds. To investigate the biological consequences of cysteine modification on the Hsp70 Ssa1 in budding yeast, I generated cysteine null (cysteine to serine) and oxidomimetic (cysteine to aspartic acid) mutant variants of both …

Genetic Analysis Of Rna Exosome Complex Cofactors, Luisa Orlando

Dissertations and Theses (Open Access)

The RNA exosome complex is known to process and/or degrade many classes of RNA, including mRNA, rRNA, tRNA and snRNA, through its 3’-to-5’ exoribonuclease catalytic activity. The RNA exosome complex comprises a 9-unit core (exo-9), with six proteins making up a PH-Ring barrel and three proteins making up a S1-KH cap. The RNA exosome complex exo-9 core is inactive by itself and requires different cofactors in the nucleus and cytoplasm to perform different localized functions. This exo-9 core can associate with one or two catalytic subunits, including Rrp44/Dis3 and Rrp6 in yeast and DIS3 or DIS3L and RRP6/EXOSC10 in humans. …

Haplotype-Informed Allelic Imbalance Detection From Rna In Cancer, Zuhal Ozcan

Dissertations and Theses (Open Access)

Comprehensive genomic and transcriptomic characterization of tumors has uncovered enrichment for distinct aneuploidy and expression patterns, demonstrating the utility of molecular based classification of cancers and their subtypes. Existing cohorts with transcriptomic profiling from next-generation sequencing contain an untapped potential to also relate genomics with rich clinical phenotypes. Yet, derivation of somatic copy number and expression profiles from analyses of RNA has remained elusive. Further, DNA analysis in these cohorts is not always feasible due to limited tissue availability or financial constraints. Here, we present a statistical approach that overcomes these challenges using haplotype information to aid detection of somatic …

Decoding The Tumor And Immune Microenvironment In Pdac And Breast Cancer By Single Cell Sequencing., Aislyn Schalck

Dissertations and Theses (Open Access)

This work utilizes single cell RNA sequencing to identify transcriptional populations and gene changes for the purpose of immune-related cancer therapies. First we have characterized the T cell populations of the normal and malignant human pancreas. Furthermore, we utilized single cell TCR sequencing to track transcriptional states of T cell clones from human PDACs into a T cell culture product for adoptive cell therapy. Second, we examined the potential role of radiotherapy in inducing an immune response in hormone receptor positive breast tumors.

Decoding Copy Number Substructure And Evolution From Single Cell Genomics, Darlan Conterno Minussi

Dissertations and Theses (Open Access)

Aneuploidy is a prominent feature in Triple-Negative Breast Cancers (TNBC), however, the evolution of genotypes during tumor expansion remains poorly understood. The prevalent model of TNBC evolution is the Punctuated Copy Number Evolution (PCNE), in which tumors undergo a period of elevated genomic instability, acquiring complex genomic rearrangements within a short timeframe followed by clonal stasis. However, these observations rely on limited cell numbers and inherent experimental bias from first-generation single cell technologies. Therefore, the evolutionary trajectory after the punctuated burst remains unknown. To address this question, we sequenced 9,765 cells from 8 primary TNBCs and 6,413 cells from 4 …

Development Of Graphical Models And Statistical Physics Motivated Approaches To Genomic Investigations, Yashwanth Lagisetty

Dissertations and Theses (Open Access)

Identifying genes involved in disease pathology has been a goal of genomic research since the early days of the field. However, as technology improves and the body of research grows, we are faced with more questions than answers. Among these is the pressing matter of our incomplete understanding of the genetic underpinnings of complex diseases. Many hypotheses offer explanations as to why direct and independent analyses of variants, as done in genome-wide association studies (GWAS), may not fully elucidate disease genetics. These range from pointing out flaws in statistical testing to invoking the complex dynamics of epigenetic processes. In the …

Genomewide Crispr/Cas9 Screen Identifies Network Of Protein Complexes That Regulate Trim24, Lalit Patel

Dissertations and Theses (Open Access)

TRIM24 is an oncogenic chromatin reader that is frequently overexpressed in human tumors and associated with poor prognosis. However, TRIM24 is rarely mutated, duplicated, or rearranged in cancer. This raises questions about how TRIM24 is regulated and whether changes in its regulation are responsible for its activity in cancer.

To investigate this possibility, I performed a genomewide CRISPR/Cas9 screen library using fluorescence activated cell sorting (FACS) to identify regulators of TRIM24. The screen was enabled by two innovations. I engineered cells with an in-frame knock-in of mClover3 to the endogenous copy of TRIM24 to allow fluorescent monitoring of TRIM24 expression …

Yap And Taz Are Required For Neural Crest-Derived Cardiovascular Development, Shannon Erhardt

Dissertations and Theses (Open Access)

Congenital heart defects (CHDs) are the most common human birth defect, occurring in ~1/100 newborns, and are a leading cause of early infant death. Cardiac neural crest cells (NCCs) are a migratory and multipotent cell population known to aid in the development of the cardiac outflow tract (OFT), valves, and interventricular septum, during embryogenesis. Yap and Taz are downstream effectors of the fundamental Hippo signaling pathway and are vital for proper organ and tissue development, yet their role in neural crest (NC)-derived heart formation is still largely unknown. We generated Yap and Taz conditional knockout (CKO) mice using a Cre-lox …

The Role Of The Hypoxia-Inducible Factor 2 In Pancreatic Cancer: Mechanisms Of Tumor Immunosuppression And Intestinal Radioprotection, Carolina Garcia Garcia

Dissertations and Theses (Open Access)

Pancreatic ductal adenocarcinoma (PDAC) is a devastating disease with dismal prognosis. The only curative option for patients is surgery, but over 80% of patients are not surgical candidates. Unfortunately, PDAC is resistant to the three remaining options. PDAC is characterized by a profoundly hypoxic and immunosuppressive stroma, which contributes to its therapeutic recalcitrance. Alpha-smooth muscle actin+ (αSMA+) cancer-associated fibroblasts (CAFs) are the most abundant stromal component, as well as mediators of stromal deposition. The hypoxia-inducible factors (HIF1 and HIF2) coordinate responses to hypoxia, yet, despite their known association to poor patient outcomes, their functions within the PDAC tumor microenvironment (TME) …

Roles Of Oxidative Stress And Dna Methylation In Cigarette Smoking-Induced Accelerated Acute Myeloid Leukemia Progression, Mary Figueroa

Dissertations and Theses (Open Access)

Acute myeloid leukemia (AML) is a commonly diagnosed cancer in smokers. When current or former smokers have AML, they have worse survival compared to never smoking patients. This has been observed clinically for decades, but then it is unknown how smoking leads to worsened AML survival. Smoking causes oxidative stress and altered DNA methylation that persists for decades in peripheral blood mononuclear cells, but these changes from smoking have not been evaluated in the context of AML. We hypothesize that smoking-induced molecular changes, including altered DNA methylation associated with poor AML prognosis, promote AML. We developed a novel model to …

Novel Regulators Of Cellular Secretion Alter The Tumor Microenvironment To Drive Metastasis, Rakhee Bajaj

Dissertations and Theses (Open Access)

Lung cancer is a highly aggressive disease responsible for ~25% of all cancer-related deaths, due in part to its proclivity to metastasize. Treating metastasis holds potential for improving patient survival but requires a deeper investigation into the underlying mechanisms. Some of these processes that can regulate metastasis are: (1) Oncogenic targets of epithelial micro-RNAs (miRNAs) are epigenetically de-repressed upon loss of the miRNAs during epithelial-to-mesenchymal transition (EMT) and in cancer. EMT confers plasticity and fitness to cancer cells promoting their survival through the metastatic cascade. This cascade and EMT are initiated by loss of the miRNA200 family (miR-200) and the …

Parental Stress In Tuberous Sclerosis Complex, Jenny Do

Dissertations and Theses (Open Access)

Tuberous Sclerosis Complex (TSC) is a multi-systemic genetic disorder with great clinical variability. As the needs of one child with TSC may vastly differ from another, parenting demands may similarly differ. Characterizing parental stress, or emotional maladaptation arising from parenting duties, can enable healthcare providers to assist parents of children most efficiently with TSC-related symptoms and improve both parent and child health outcomes. This study surveyed 269 parents of children (aged 0-12 years) with TSC and received the following information: children’s TSC clinical features, parent demographics, and a Parent Stress Index (PSI) score. Parents reported higher stress levels for children …

Prenatal Testing Decisions And Motivations In Pregnancies Conceived Via In Vitro Fertilization, Michelle Appel

Dissertations and Theses (Open Access)

Currently, there is limited information about how conceiving through in vitro fertilization (IVF) and preimplantation genetic testing for aneuploidy (PGT-A) impact the decisions individuals make about prenatal genetic testing. This quantitative study aimed to examine the prenatal testing decisions made by pregnant individuals who conceived via IVF as well as to compare the prenatal testing decisions and motivations between those who had PGT-A and those who did not. An anonymous survey was distributed through online support forums and in clinical settings to eligible individuals. Overall, 230 complete responses were collected with 203 participants far enough along in pregnancy to make …

Development Of The Ark Assay For Quantitating Dna- Protein Crosslink Accumulation And Fanconi Anemia Pathway Involvement In The Repair Process, Naeh Klages-Mundt

Dissertations and Theses (Open Access)

DNA-protein crosslinks (DPCs) are a common DNA lesion naturally arising in cells, wherein protein becomes covalently and irreversibly bound to the DNA. Given their excessive size, these adducts present a significant challenge to replication and transcription, thus requiring timely and efficient repair. However, the precise mechanisms involved with processing DPC removal remain unclear. Moreover, current methodologies to quantitate DPC accumulation and removal are restrained by a range of limitations. Here, we describe and discuss a new DPC detection assay – the ARK assay – capable of overcoming the limitations incurred by prior assays. The design, which uses dual chaotropic lysis …

Investigating The Ecology And Evolution Of Normal Breast Tissues And Breast Cancer With Single Cell Genomics, Tapsi Kumar, Tapsi Kumar

Dissertations and Theses (Open Access)

There is vast cellular heterogeneity in human breast tissues, with different transcriptional programs in the stromal, epithelial, and immune components, however, it remains unclear how their reprogramming and interplay leads to the progression of invasive phenotypes such as Triple- Negative Breast cancer (TNBC). To do define the microenvironmental alterations that occur during cancer, we first established a human breast cell atlas, a reference of normal breast cell types from disease free women. We profiled 535,941 cells from 62 women and 124,024 nuclei from 20 women revealing 11 major cell types and 52 cell states that reflect different biological functions that …

Exploiting Chemogenetic And Genetic Interactions In Human Cells As An Avenue For New Therapeutic Opportunities, Medina Colic

Dissertations and Theses (Open Access)

The advent of CRISPR technology and its adaptation to the mammalian genome made whole-genome knockout screens possible directly in human cells. Gene knockout answers how essential that gene is for cell fitness and proliferation. Genes showing moderate to severe fitness defects are called essential genes and provide insights into disease-specific candidate therapeutic targets. Additionally, CRISPR offers other applications for genome editing. Two applications this dissertation is based on are 1) combination of gene knockout and drug treatment, which enables the identification of chemogenetic interactions, or gene mutations that enhance or suppress the activity of a drug, and 2) combinatorial editing, …

An Investigation Of Epigenetic Mechanisms Driving The Biology Of Head And Neck Squamous Cell Carcinoma, Scot Carson Callahan

Dissertations and Theses (Open Access)

Head and neck squamous cell carcinoma (HNSCC) is the 6th most common cancer worldwide and is associated with significant morbidity and mortality. To date, the majority of work in the field has focused on genomic alterations such as mutations and copy number alterations. However, the clinical success of targeted therapies that exploit known genomic alterations, such as EGFR mutations, has remained mixed. Over the past decade, the importance of epigenetic regulators has come to the forefront, with the realization that many of these genes are mutated in cancer. Despite this realization, the role of epigenetics in regulating tumorigenesis, progression and …

Experiences Of Racial And Ethnic Minority Patients With Genetic Counseling, Emile Moura Coelho Da Silva

Dissertations and Theses (Open Access)

Racial and ethnic minority patients in the United States undoubtedly suffer from inequalities in healthcare. While some studies have explored these inequalities in the field of genetic counseling specifically, research relating to genetic counseling outcomes in diverse patient populations is still limited. With the number of non-Hispanic White individuals in the United States projected to decrease by 20 million by 2060, it becomes imperative to better understand the experiences of racial and ethnic minority patients to meet their needs. Therefore, this study aimed to further describe the experiences of racial and ethnic minority patients who received genetic counseling services. In …

Invisible Disabilities, Academic Capital And Competitiveness Of Genetic Counseling Applicants, Natalie E. Stoner, Meagan Choates, Carla Mcgruder, Debra Murray, Theresa Wittman, Sara Wofford, Claire N. Singletary

Dissertations and Theses (Open Access)

The field of genetic counseling has historically lacked diversity. Recent research has begun to explore how visible diversity may present barriers to a genetic counseling applicant becoming competitive, but has not yet characterized potential barriers with invisible diversities, such as being a first-generation college student, or a part of the LBGTQ+ community. Therefore, this study aimed to address this gap among those with invisible diversities, as well as explore their academic capital (AC), a theoretical framework used to identify factors that make students more likely to succeed in post-secondary work including supportive networks, trustworthy information, family uplift, college knowledge, overcoming …

Computational Approaches To Understand Chemoresistance & Tumor Evolution Using Longitudinal Clinical Data And Lineage Tracing, Sahil Seth

Dissertations and Theses (Open Access)

Tumors are highly heterogeneous and dynamic, continually adapting and evolving in response to their microenvironment as well as external perturbations. Multi-region (spatial) and single cell sequencing has enabled us to anatomize the heterogeneity further and provide evidence of its association with chemo and drug resistance. To investigate this further we took two different approaches to understand the chemo-resistance, and functional heterogeneity in Triple negative breast cancer (TNBC) and Pancreatic ductal carcinoma in situ (PDAC) from an evolutionary perspective.

The first approach was to leverage tumor profiling from an ongoing randomized clinical trial in triple-negative breast cancer (ARTEMIS) to assess mechanisms …

Mutant Kras Alters Extracellular Vesicle Microrna Sorting In Pancreatic Cystic Neoplasms, Rachel L. Dittmar

Dissertations and Theses (Open Access)

Pancreatic ductal adenocarcinoma (PDAC) is among the deadliest cancers by organ site with a 5-year survival rate of just 10.8%. This is largely because most patients do not experience symptoms until the disease has already metastasized. The best hope to cure PDAC is surgery, which can only be done with a curative intent at an early stage when the disease is localized. There are no reliable circulating, body-fluid-based biomarkers to detect early stage PDAC or its precursor lesions in a timely manner for effective surgical intervention. When potential PDAC precursor lesions, such as mucinous pancreatic cysts are found, there are …

Deciphering The Role Of Hsp110 Chaperones In Diseases Of Protein Misfolding, Unekwu M. Yakubu

Dissertations and Theses (Open Access)

Molecular chaperones maintain protein homeostasis (proteostasis) by ensuring the proper folding of polypeptides. Loss of proteostasis has been linked to the onset of numerous neurodegenerative disorders including Alzheimer’s, Parkinson’s, and Huntington’s disease. Hsp110 is a member of the Hsp70 class of molecular chaperones and acts as a nucleotide exchange factor (NEF) for Hsp70, the preeminent Hsp70-family protein folding chaperone. Hsp110 promotes rapid cycling of ADP for ATP, allowing Hsp70 to properly fold nascent or unfolded polypeptides in iterative cycles. In addition to its NEF activity, Hsp110 possesses an Hsp70-like substrate binding domain (SBD) whose biological roles are undefined. Previous work …

Epithelial Memory Of Resolved Inflammation Limits Tissue Damage While Promoting Pancreatic Tumorigenesis, I-Lin Ho

Dissertations and Theses (Open Access)

Inflammation is a major risk factor for pancreatic ductal adenocarcinoma. When occurring in the context of pancreatitis, mutations of KRAS accelerate tumor development. We discovered that long after its complete resolution, a transient inflammatory event primes pancreatic epithelial cells to subsequent transformation by oncogenic KRAS. Upon recovery from acute inflammation, epithelial cells of the pancreas display an enduring adaptive response associated with sustained transcriptional and epigenetic reprogramming. Such adaptation enables the prompt reactivation of acinar-to-ductal metaplasia (ADM) upon subsequent inflammatory events, thus efficiently limiting tissue damage via rapid decrease of zymogen production. We propose that since activating mutations of KRAS …

Npsd4: A New Player In Sumo-Dependent Dna Repair, Erin Atkinson

Dissertations and Theses (Open Access)

The human genome is under constant threat from sources of damage and stress. Improper resolution of DNA damage lesions can lead to mutations, oncogene activation, and genomic instability. Difficult-to-replicate-loci present barriers to DNA replication that, when not properly resolved, lead to replication fork stalling and collapse and genomic instability.

DNA damage and replication stress trigger signaling cascades potentiated by multiple types of post-translational modifications, including SUMOylation. Through proteomic analysis of proteins involved in SUMOylation following DNA damage, our lab identified an uncharacterized protein that we named New Player in SUMO-dependent DNA damage repair 4 (NPSD4). Through an additional proteomic screen, …