Medicine and Health Sciences Commons^™

Rare Variant Association Studies In Crohn’S Disease And Colorectal Cancer: Methods And Applications, Jiun-Sheng Chen

Dissertations and Theses (Open Access)

Genetic factors account for a substantial portion of Crohn’s disease and colorectal cancer (CRC) risk. Patients with Crohn’s disease, a condition that causes chronic inflammation of the gastrointestinal tract, are at increased risk of colorectal cancer morbidity and mortality. Genome-wide association studies using single marker approaches have identified loci responsible for these diseases, but disease susceptibility from rare variants is incompletely understood. This dissertation includes three chapters, two association studies for Crohn’s disease and CRC, and a statistical method to improve the power of statistical tests.

For Crohn’s disease, we performed targeted sequencing of 101 genes in 205 children with …

Spectrum And Incidence Of Primary And Therapy-Related Hematologic Malignancies In Individuals With Brca1 And Brca2 Pathogenic Variants, Rosemary Rogers, Rosemary Rogers

Dissertations and Theses (Open Access)

Therapy-related myeloid neoplasms (t-MN) are rare and deadly hematologic malignancies that develop following exposure to cytotoxic therapies such as radiation, chemotherapy, and poly (adenosine diphosphate-ribose)-ADP polymerase (PARP) inhibitors. Preliminary evidence suggests that germline BRCA1 and BRCA2 pathogenic and likely pathogenic (P/LP) variants may increase susceptibility to t-MNs due to the genes’ established role in DNA damage response. There is also evidence that individuals with BRCA1/2 P/LP variants may be more susceptible to developing primary hematologic malignancies. We reviewed medical records of 706 individuals with BRCA1/2 P/LP variants to assess hematologic malignancy diagnoses and t-MN development. Our study population was 5.1% …

Cortical Dynamics Of Language, Kiefer Forseth

Dissertations and Theses (Open Access)

The human capability for fluent speech profoundly directs inter-personal communication and, by extension, self-expression. Language is lost in millions of people each year due to trauma, stroke, neurodegeneration, and neoplasms with devastating impact to social interaction and quality of life. The following investigations were designed to elucidate the neurobiological foundation of speech production, building towards a universal cognitive model of language in the brain. Understanding the dynamical mechanisms supporting cortical network behavior will significantly advance the understanding of how both focal and disconnection injuries yield neurological deficits, informing the development of therapeutic approaches.

Genetic Testing In Pregnancies With Ultrasound Anomalies: Exploration Of Factors That Influence Uptake, Lukas D. Kruidenier

Dissertations and Theses (Open Access)

Prenatal genetic diagnostic and screening tests have been rapidly evolving over the past decade with the introduction and expansion of cell free DNA screening (cfDNA) and the use of chromosomal microarray (CMA) as a first-line test for evaluation of fetal anomalies. Understanding patient motivations for or against expanded genetic testing options is paramount, therefore this study aimed to ascertain the patient perspective. Ninety-nine patients with an ultrasound anomaly participated in an anonymous, cross-sectional, research survey assessing coping strategies, factors influencing the genetic testing decision, and demographic variables. After multivariable analysis, the desire for directive counseling regarding testing was correlated with …

The Functional Contribution Of Adaptive Immunity In The Biology Of Pancreatic Cancer And Therapeutic Targeting Of Oncogenic Kras, Krishnan Mahadevan

Dissertations and Theses (Open Access)

The Functional Contribution Of Adaptive Immunity In The Biology Of Pancreatic Cancer And Therapeutic Targeting Of Oncogenic Kras

Krishnan K. Mahadevan M.B.B.S*

Advisory professor: Dr. Raghu Kalluri

Pancreatic ductal adenocarcinoma (PDAC) is the third leading cause of cancer related deaths in the USA(https://seer.cancer.gov/statfacts/html/pancreas.html), whereby survival remains poor despite advances in surgical technique and new combination chemotherapies. Immune checkpoint blockade has revolutionized the treatment of cancers such as melanoma, bladder cancer and non-small cell lung carcinomas. Unfortunately, PDAC is among the tumor types that remain refractory to checkpoint immunotherapy(Royal et al., 2010, Le et al., 2013), with no survival benefits in …

Improving Treatment Of Local Liver Ablation Therapy With Deep Learning And Biomechanical Modeling, Brian Anderson, Kristy Brock, Laurence Court, Carlos Eduardo Cardenas, Erik Cressman, Ankit Patel

Dissertations and Theses (Open Access)

In the United States, colorectal cancer is the third most diagnosed cancer, and 60-70% of patients will develop liver metastasis. While surgical liver resection of metastasis is the standard of care for treatment with curative intent, it is only avai lable to about 20% of patients. For patients who are not surgical candidates, local percutaneous ablation therapy (PTA) has been shown to have a similar 5-year overall survival rate. However, PTA can be a challenging procedure, largely due to spatial uncertainties in the localization of the ablation probe, and in measuring the delivered ablation margin.

For this work, we hypothesized …

Genetics In The Nicu: Nurses’ Perceived Knowledge And Desired Education, Kathleen Shields

Dissertations and Theses (Open Access)

A large proportion of infants admitted to neonatal intensive care units (NICUs) have genetic conditions. NICU nurses play an important role in providing comprehensive care to these patients and their families. Previous research has demonstrated gaps exist in the genetics knowledge of nurses and that they lack comfort applying genetics information to clinical practice, but no research has been done assessing the knowledge of or comfort with genetics of NICU nurses specifically. NICU nurses (n=122) completed an online survey assessing their perceived knowledge of genetics, comfort with clinical scenarios involving genetics, and desired genetics education. Participants reported the highest levels …

Investigating Diffusion Tensor Imaging Correlates Of Cognitive Impairment In Idiopathic Normal Pressure Hydrocephalus And Alzheimer's Disease, Omar Hasan, Omar Hasan

Dissertations and Theses (Open Access)

Modest expansion of the human brain cerebrospinal fluid (CSF)-filled ventricles is normal with aging, and because of this, it can be difficult for physicians to accurately diagnose and treat enlarged ventricles (ventriculomegaly), called hydrocephalus¹ (fluid or water in the brain) Ventriculomegaly occurs due to an obstruction (such as a blood clot or tumor), or a change in CSF absorption². Primary hydrocephalus, also called idiopathic normal pressure hydrocephalus (iNPH), is non-obstructive and may be comorbid with other neurodegenerative diseases such as Alzheimer’s disease (AD) or frontotemporal dementia (FTD). Clinically, it can be difficult to tell whether the pathophysiological …

Characterization Of A Novel Oncogenic Mirna Inhibitor In Cancer Therapy, Iman Sahnoune

Dissertations and Theses (Open Access)

As cancer research continues to move towards more personalized methods, targeted inhibitors of oncogenic drivers of cancer are found to be an innovative and promising therapeutic approach. Previously thought to be undruggable regions of the genome, RNA has become an area of increasing interest in cancer due to the identification of more targetable regions and their relationship to tumor growth and progression. This work reports on the development of IACS-13743, a novel small molecule found to directly bind and inhibit microRNA-10b. Oncogenic miR-10b has been found to be overexpressed in several malignant cancer types, making it an attractive biomarker for …

Mixture Model Approaches To Integrative Analysis Of Multi-Omics Data And Spatially Correlated Genomic Data, Ziqiao Wang

Dissertations and Theses (Open Access)

Integrative genomic data analysis is a powerful tool to study the complex biological processes behind a disease. Statistical methods can model the interrelationships of the involved gene activities through jointly analyzing multiple types of genomic data from different platforms (vertical integration), or improve the power of a study through aggregating the same type of genomic data across studies (horizontal integration). In this dissertation, we propose statistical methods and strategies for integrative multi-omics data in association analysis of disease phenotypes, with an emphasis on cancer applications.

We develop a new strategy based on horizontal integration by leveraging publicly available datasets into …

Survival Analysis Of Colorectal Cancer Patients With Liver Metastasis, Brandon O’Grady

Dissertations and Theses (Open Access)

Background- Colorectal cancer is the third most common cancer in the world. I investigated the survival rates among colorectal cancer patients diagnosed with hepatic metastasis to see if any variables are associated colorectal risk and survival. Methods- Patients were diagnosed from 2000-2019 and collected through MD Anderson’s database. A descriptive analysis, univariate analysis, Kaplan-Meier with Mantel log-rank test, Cox proportion hazard regression and a Stratified Cox Model was performed to investigate death. A competing risk regression was implemented to investigate liver recurrence. Results- There was a clear difference in the survival outcome between liver surgery patients and non-liver surgery patients …

Applications Of Statistical Methods Studying The Impact Of Mobilization Regimes On The Total Collection Yield Of Hematologic Stem Cell, Mengchen Ding

Dissertations and Theses (Open Access)

Hematologic malignancies are cancers that develop in the blood, bone marrow, and lymph nodes. Hematopoietic stem cell transplantation (HSCT) is a critical therapeutic approach that contributes to offer a potential cure for hematologic cancers and other hematologic disorders by replacing abnormal bone marrow with healthy bone marrow components to help bone marrow function recovery. Peripheral blood is the primary resource for collecting hematopoietic stem cells (HSCs). The collection yield of HSCs is critical for successful transplantation. Few articles have discussed this topic that the collection of stem cells not only from healthy donors but also from donors with a hematologic …

The Comparative Effect Of Automated Reminders/Recalls Interventions On The Appointments Rate Of Adolescent Wellness Care Visit, Biai Dominique Elmir Digbeu

Dissertations and Theses (Open Access)

An Adolescent Wellness Care (AWC) visit is an annual preventive doctor visit predestined to assess the overall health of adolescents aged between 12 and 21 years old. Compared to their younger counterparts, adolescents who are using public insurance are at risk of not completing AWC visits due to several factors related to age or providers disparities in their living environment. This research was a quasiexperimental study aiming to compare two methods of automated Reminders/Recalls (RR) interventions, ‘phone-only’ versus ‘phone-and-text’, in order to evaluate which method is more effective in helping parents/guardians or young adults to schedule an AWC visit. A …

Characterization Of Age-Associated Copd Progression In The Copd Gene Cohort, Lauryn A. Winter

Dissertations and Theses (Open Access)

Chronic obstructive pulmonary disease (COPD) is a progressive and debilitating lung disease affecting primarily older adults. Incidence, morbidity and mortality from COPD are increasing worldwide. The purpose of this study was to determine the associations between age at baseline and markers of disease progression in COPD patients using data generated by the Genetic Epidemiology of COPD (COPD Gene) study. Participants with COPD were stratified by age (younger: age <65 years, elderly: age ≥ 65 years) and disease characteristics (lung function, exercise tolerance, exacerbation history, and comorbidity burden) at baseline and five-year follow up were compared between groups. Associations between age group and changes in these measures were also assessed. Disease characteristics differed significantly between elderly and younger COPD patients at both study visits. Elderly COPD patients had worse lung function and more comorbidities than younger COPD patients, while younger COPD patients reported more dyspnea and more frequent and severe exacerbations than elderly COPD patients. Following covariate adjustment, elderly participants were less likely than younger participants to develop new frequent exacerbations over the study period (relative risk ratio (95% confidence interval): 0.42 (0.20, 0.87)). There were no other significant associations between age group and markers of disease progression. These results suggest that although elderly COPD patients exhibit evidence of more severe lung function impairment than younger COPD patients, the rate of disease progression is similar between elderly and younger patients. However, further exploration is needed to understand the possible contribution of survivorship bias to this finding. Nevertheless, this study supports the importance of early detection and early intervention to slow disease progression and maximize both life expectancy and quality of life for COPD patients.

Asthma-Copd Overlap Syndrome And Disease Progression In The Copdgene Cohort Study, Caitlyn Winter

Dissertations and Theses (Open Access)

Chronic Obstructive Pulmonary Disease (COPD) is a debilitating and degenerative lung disease characterized by progressive airway obstruction and alveolar destruction. When asthma and COPD co-occur and interact, with asthma having been diagnosed first, the resulting respiratory disease is called Asthma-COPD Overlap Syndrome (ACOS). Current research suggests that persons with ACOS may have more severe respiratory disease and lifestyle limitations than those with either disease alone. The purpose of the current study was to determine if and how disease progression differs in patients with ACOS versus COPD only, using data collected during the COPDGene cohort study. Demographic characteristics and disease outcome …

Breastfeeding Duration And Reasons Given For Early Cessation Of Breastfeeding Among Wic Mothers, Amy Willa

Dissertations and Theses (Open Access)

The Breastfeeding Duration and Reasons for Early Cessation of Breastfeeding Among WIC Mothers study was conducted to describe the duration of and factors associated with early breastfeeding cessation among the Women, Infants, and Children (WIC) population. We collected data from a random sample of WIC medical records, sampling medical records belonging to mothers who initiated breastfeeding an infant but did not breastfeed to 52 weeks. Data were analyzed to answer the questions: How long do WIC mothers breastfeed? What reasons are given during counseling sessions at WIC for early cessation of breastfeeding? Do socio-economic, demographic, or medical factors influence the …

Disruption Of Dna Polymerase Zeta Promotes An Innate Immune Response, Sara Martin

Dissertations and Theses (Open Access)

DNA polymerase ζ (pol ζ) is a specialized polymerase that protects cells from the consequences of DNA damage and stress. Without pol ζ function mammalian cells and yeast are exquisitely sensitive to genotoxic stresses including ultraviolet irradiation and platinum compounds such as the chemotherapeutic agent cisplatin. This elevated sensitivity arises from the central role of pol ζ in lesion bypass. Pol ζ is also required to protect cells from endogenous genomic damage or stress. In primary mammalian cells, the function of pol ζ is required for genome protection and normal proliferation. Immortalized Rev3lknockout (KO) MEFs are under considerable constitutive …

Inducible Epithelial Resistance Against Acute Viral Pneumonia And Chronic Asthma, Shradha Wali

Dissertations and Theses (Open Access)

Viral pneumonia remains a global health threat despite worldwide vaccination and therapeutic programs. The influenza pandemic of 1918 and SARS-CoV2 pandemic of 2019-2020 are cautionary reminders demanding the need for novel treatment strategies. Moreover, in addition to causing acute disease, respiratory virus infections are often complicated by chronic lung pathologies, such as asthma induction, progression, and exacerbation. We have reported that mice treated with a combination of inhaled Toll-like receptor (TLR) 2/6 and TLR 9 agonists (Pam2-ODN) to stimulate innate immunity are broadly protected against respiratory pathogens, but the mechanisms underlying this protection remain incompletely elucidated. Here, we show in …

Hyperpolarized Carbon-13 Magnetic Resonance Measurements Of Tissue Perfusion And Metabolism, Keith Michel

Dissertations and Theses (Open Access)

Hyperpolarized Magnetic Resonance Imaging (HP MRI) is an emerging modality that enables non-invasive interrogation of cells and tissues with unprecedented biochemical detail. This technology provides rapid imaging measurements of the activity of a small quantity of molecules with a strongly polarized nuclear magnetic moment. This polarization is created in a polarizer separate from the imaging magnet, and decays continuously towards a non-detectable thermal equilibrium once the imaging agent is removed from the polarizer and administered by intravenous injection. Specialized imaging strategies are therefore needed to extract as much information as possible from the HP signal during its limited lifetime.

In …

Subclonal Evolution Of Chronic Lymphocytic Leukemia After Allogeneic T Cell Therapies, Haven Garber

Dissertations and Theses (Open Access)

Subclonal evolution of chronic lymphocytic leukemia after allogeneic T-cell therapies

Haven Garber, MD

Advisory Professor: Jeffrey Molldrem, MD

Intratumoral genetic heterogeneity describes the molecular differences among subclones within a tumor and is a major barrier to effective therapy in many solid and liquid cancers, including chronic lymphocytic leukemia (CLL). Rare, treatment-resistant subclones can expand to compose relapsed disease during tumor evolution. Examination of malignant evolution in the context of specific treatment provides insight into the molecular lesions that mediate therapeutic response and resistance. Both chemotherapy and targeted therapy were shown to precipitate CLL subclonal evolution. We hypothesized that allogeneic T-cell …

Genetic And Clinical Determinants Of Racial/Ethnic Differences In Multiple Myeloma Susceptibility And Outcomes Focusing On Hispanics, Alem Belachew

Dissertations and Theses (Open Access)

Multiple Myeloma (MM) constitutes 10% of diagnosed hematologic malignancies in the US, with over 12,000 deaths recorded each year. Race/ethnicity is a well-known MM risk factor, where individuals of African descent have over 2- to 3-fold increased risk of incidence compared to those of European descent. Additionally, Hispanics are diagnosed approximately three years younger than white American counterparts, for unknown reasons. Differences in clinical phenotype are also present for MM patients by ancestry, including varying rates of common initiation mutations such as IgH translocations and TP53 mutation between patients of European and African descent. Studies have begun to interrogate the …

Reversal Of Neurodegeneration By Engineered Monocytes In Alzheimer’S Disease, Chao-Hsien Chen

Dissertations and Theses (Open Access)

The health challenges posed by Alzheimer’s disease (AD) continue to grow as societies age worldwide. Accumulation of Tau-associated pathology correlates with clinical cognitive deterioration in AD. Resident myeloid cells within the central nervous system (CNS) have a limited capacity to uptake and degrade Tau; however, the resulting secretion of proinflammatory cytokines only acts to accelerate neurodegeneration. Therapeutic antibodies can reduce the neurotoxic oligomeric form of Tau (o-Tau), but in doing so they also aggravate inflammation. Attenuating mutation of the antibody Fc region can silence inflammation but also eliminates its capacity to mediate o-Tau clearance by CNS myeloid cells. Thus, there …

A Context-Forward In Vivo Functional Genomics Platform For Target Discovery And Establishing Vulnerability Context In Pancreatic Cancer, Johnathon Rose, Johnathon Lynn Rose

Dissertations and Theses (Open Access)

Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy with a very poor patient prognosis (5-year survival of ≤ 7%). While transcriptional profiling has aided in the classification of this disease into at least two broader subtypes, this alone has so far been insufficient to inform on more nuanced patterns of oncogenic dependency. We hypothesized that a more comprehensive and granular characterization of PDAC disease diversity is required to establish relevant context for targeted therapy. To this end, we sought to establish an integrated platform to: i) more comprehensively characterize differential oncogenic signaling across our tumor models, and ii) establish …

Influence Of Genetic Counselor Personal Or Family Medical History On Genetic Counseling Specialization And Practice, Kaitlyn K. Amos Ms

Dissertations and Theses (Open Access)

A personal or family medical history inherently becomes part of a genetic counselor’s life story. Yet the degree to which a counselor’s experience influences his or her specialty choice and their psychosocial practice is unexplored. A medical diagnosis may foster a counselor’s capacity for greater empathy, understanding and rapport-building self-disclosure. Conversely, it could lead to interruptive countertransference, compassion fatigue, and eventually burnout. However, research has not specifically investigated this intersection. Therefore, the aim of this study was to explore the impact of a genetic counselor’s personal or family medical history on his or her choice of practice area, as well …

P53 Drives A Transcriptional Program That Elicits A Non-Cell-Autonomous Response And Alters Cell State In Vivo, Sydney Moyer

Dissertations and Theses (Open Access)

Cell stress and DNA damage activate the tumor suppressor p53, triggering transcriptional activation of a myriad of target genes. The molecular, morphological, and physiological consequences of this activation remain poorly understood in vivo. We activated a p53 transcriptional program in mice by deletion of Mdm2, a gene which encodes the major p53 inhibitor. By overlaying tissue-specific RNA-sequencing data from pancreas, small intestine, ovary, kidney, and heart with existing p53 ChIP-sequencing, we identified a large repertoire of tissue-specific p53 genes and a common p53 transcriptional signature of seven genes which included Mdm2 but not p21. Global p53 activation …

Development Of Computational To Ols To Target Microrna, Luo Song

Dissertations and Theses (Open Access)

MicroRNAs (a.k.a, miRNAs) play an important role in disease development. However, few of their structures have been determined and structure-based computational methods remain challenging in accurately predicting their interactions with small molecules. To address this issue, my thesis is to develop integrated approaches to screening for novel inhibitors by targeting specific structure motifs in miRNAs. The project starts with implementing a tool to find potential miRNA targets with desired motifs. I combined both sequence information of miRNAs and known RNA structure data from Protein Data Bank (PDB) to predict the miRNA structure and identify the motif to target, then I …

Sine Oculis Homeobox Homolog 1 (Six1) Plays A Critical Role In The Progression Of Pulmonary Fibrosis., Cory Wilson

Dissertations and Theses (Open Access)

Idiopathic pulmonary fibrosis (IPF) is the most common idiopathic interstitial pneumonia with a median survival time of 2-4 years after diagnosis. The alarming mortality rate is due to the lack of effective treatments. IPF is a chronic disease that is characterized by alveolar destruction due to increasing extracellular matrix deposition that leads to poor lung compliance, impaired gas exchange, and ultimately respiratory failure. Repetitive alveolar epithelial injury is a central process to the underlying pathology with injury to the type II alveolar epithelial cells (AT2) specifically being a key player in the pathogenesis of IPF. Recent studies have shown that …

Investigation Of The Functional Impact Of Anti-Pd-1 On Tumor-Infiltrating Lymphocytes (Til) And Mapping Of Tumor Genomic Features Relevant For Response To Til Therapy, Caitlin Creasy

Dissertations and Theses (Open Access)

With the growing use of both cellular and antibody-based immunotherapies, it has become more important to uncover biomarkers to predict patient response to therapy and ideally aid in patient selection for specific therapeutics, thereby enhancing treatment outcome. At MD Anderson, we have a 43% response rate to therapy when treating metastatic melanoma patients with adoptive cell therapy (ACT) of tumor-infiltrating lymphocytes (TIL), but it is unknown what makes the other 57% of patients not respond to therapy. It is further unknown how particularly early doses of checkpoint inhibitors, like anti-PD-1, attribute to TIL functionality, adding another confounding factor in determining …

Elucidating The Roles Of Il-15 In The Tumor Microenvironment, Rosa Maria Santana Carrero

Dissertations and Theses (Open Access)

ELUCIDATING THE ROLES OF IL-15 IN THE TUMOR MICROENVIRONMENT

Rosa M. Santana Carrero, B.S.

Advisory Professors: Shao-Cong Sun, Ph.D. & Kimberly S. Schluns, Ph.D.

Interleukin-15 (IL-15) is a factor that promotes activation, proliferation, cytotoxicity, and survival of CD8 T cells and NK cells, and has been shown to have anti-tumor effects. Moreover, loss of IL-15 expression in human colorectal tumors correlates with increased risk of relapse, diminished survival, decreased density and proliferation of T cells. All together these findings suggest that IL-15 expressed locally in the tumor microenvironment (TME) is an important mediator of anti-tumor responses by tumor infiltrating lymphocytes …

The Role Of Daam1 In Kidney Development, Vanja Krneta-Stankic

Dissertations and Theses (Open Access)

Kidneys, like most organs in our bodies, consist of a network of epithelial tubules. Kidney tubules are called nephrons, and their morphology is important for kidney function. Nephrons develop from mesodermally derived aggregates of progenitor cells. The nephric progenitors organize into nephric tubules lined with hair-like sensory projections called cilia. Many diseases of the kidney are characterized by abnormal nephron morphology with current treatment aimed at symptom control. To understand the mechanisms underlying kidney diseases and achieve the development of novel therapies, a better understanding of how nephrons develop is needed. Although the actin cytoskeleton is critical for cell behaviors …