Genetics and Genomics Commons^™

Integrating Genetic Modifier Genotype With Serum Proteomics In Duchenne Muscular Dystrophy Clinical Trials Links Ltbp4 Genetic Modifier To Il-23/Cd93 Pathways In Muscle, Utkarsh J. Dang, Yuan Fang, Daniele Sabbatini, Elena Pegoraro, Luca Bello, Paula R. Clemens, Michela Guglieri, John Van Den Anker, Jesse Damsker, Laura Hagerty, Yetrib Hathout, Michael Ziemba, Lauren Morgenroth, Surajit Bhattacharya, Kanneboyina Nagaraju, Jyoti K. Jaiswal, Eric P. Hoffman

Mathematics & Statistics Faculty Publications

Genetic modifiers of Duchenne muscular dystrophy (DMD) that alter disease severity or response to therapy have been reported using natural history or registry data sets of older corticosteroid-treated patients. We tested associations of genetic modifiers on motor function outcomes in young (4 to <  7 years) steroid naïve clinical trial participants. Participants in clinical trials (VBP15-002/003 [n = 48]; VBP15-004 [n = 121]; DNA available for n = 110) were genotyped for eight published genetic modifier loci, and associations of genotypes with baseline motor function defined via an age-adjusted linear model. Corticosteroid drug response was modeled by genotype-stratified placebo vs. steroid treatment at 12- and 24-weeks posttreatment (mixed model for repeated measures). …

The Yeast Checkpoint Kinase Mec1p Functions In Transcription Termination By Facilitating Recruitment Of Pcf11p And Regulating The Torpedo Exonuclease Rat1p, Riddhi Patel

Theses and Dissertations

My dissertation includes two projects, centered on transcription regulation by checkpoint kinases of the DNA damage response (DDR). The first project focused on the role of checkpoint kinase Mec1p in transcription termination and regulation of the torpedo exonuclease Rat1p. Termination, closely linked with pre-mRNA 3’ processing, dissociates RNA polymerase II (RNAPII) from DNA and releases the nascent RNA transcript. Efficient termination is required for maintaining a pool of RNAPII that is available for re-entry into new transcription cycle. Previous results showed that inactivation of Mec1p in the absence of exogenous genotoxic stress downregulates the efficiency of transcription termination. This study …

Identifying Relevant Covariates In Rna-Seq Analysis By Pseudo-Variable Augmentation, Yet Nguyen, Dan Nettleton

Mathematics & Statistics Faculty Publications

RNA-sequencing (RNA-seq) technology allows for the identification of differentially expressed genes, which are genes whose mean transcript abundance levels vary across conditions. In practice, RNA-seq datasets often include covariates that are of primary interest in addition to a set of covariates that are subject to selection. Some of these covariates may be relevant to gene expression levels, while others may be irrelevant. Ignoring relevant covariates or attempting to adjust for the effect of irrelevant covariates can compromise the identification of differentially expressed genes. To address this issue, we propose a variable selection method that uses pseudo-variables to control the expected …

Accelerating The Discovery Of The Genetic And Molecular Bases Of Neurodevelopmental Disorders In Vivo Using Breasi-Crispr, Claire Mae Kittock

Dissertations and Theses

Many neurodevelopmental disorders occur due to perturbations in prenatal brain development. More genetic variants associated with neurodevelopmental disorders are continuously being identified. However, there is a lack of understanding of the pathogenic mechanisms. Here, we describe a novel application of the technique Breasi-CRISPR in modeling specific patient variants in the embryonic mouse brain. Breasi-CRISPR is a highly efficient system combining in utero electroporation with CRISPR-CAS9 genome editing. We hypothesized that Breasi-CRISPR would be sufficient at inserting patient analogous variants into endogenous loci to be used as a new paradigm for modeling neurodevelopmental disorders. We aimed to test if Breasi-CRISPR could …

Crispr-Cas9: Transforming Biomedical Technology Through Gene Editing, Zaina Issa

A with Honors Projects

The research paper describe the gene editing technique CRISPR-Cas9 and the implications of its use in different fields, including medicine and agriculture.

Fluorescent Protein Imaging Approaches Uncover Dynamic Subcellular Distribution Of Core Clock Proteins In Neurospora Crassa, Ziyan Wang

Dartmouth College Ph.D Dissertations

Circadian clocks are endogenous self-sustained timekeeping systems that allow organisms to anticipate and adapt to daily environmental cycles. Found in diverse forms of life, these molecular clocks regulate the expression of ~ 40% of the genome in animals, fungi, and plants. In animals and fungi, circadian oscillators are built on transcription-translation feedback loops (TTFLs), in which positive regulators drive the expression of negative regulators which, once synthesized and imported into the nucleus, inhibit their own activators. This precisely regulated negative feedback incorporates multiple steps of delays that are essential for generating ~24-hour rhythms. Through these mechanisms, circadian clocks temporally coordinate …

Genomic Determinants Of Appetite Regulation And Their Role In Obesity Risk, Timothy J. Renier

Dartmouth College Ph.D Dissertations

Over 40% of US adults and 20% of children live with obesity. It is related to increased risks of diseases including type II diabetes and cancer, is a source of harmful stigma, and impairs child development. Appetitive traits describing patterns of food approach and avoidance behaviors may serve as windows into the underlying pathophysiology of obesity. As both obesity and appetitive traits are heritable, common genetic drivers of obesity may lead to phenotypic obesity through appetitive traits as a disease mechanism. Additionally, GLP-1 receptor agonists (GLP-1RAs) have been shown to exert their profound clinical effects in part by modulating appetite. …

Metabolic Reprogramming Following Mitochondrial Transfer Between Idh2-Mutant Chondrosarcoma Cells And A Normal B-Cell Line, Caleb Wyckoff, Christopher Osgood, Ellen Jing, Michael Stacey

Bioelectrics Publications

Background/Objectives: Chondrosarcoma, glioblastoma, acute myeloid leukemia, chronic lymphocytic leukemia, and cholangiocarcinoma cancers all contain mutations in the gene isocitrate dehydrogenase 2 (IDH2). The mutant IDH2 enzyme metabolizes alpha-ketoglutarate (αKG) into the potent oncometabolite D-2-hydroxyglutarate (D2HG) in the mitochondria of these cancers, leading to altered cellular metabolism. Emerging evidence suggests that mitochondrial transfer between cancer and recipient cells represents an important form of intercellular communication that may influence cellular metabolism. The presence of intercellular TNTs between IDH2-mutant chondrosarcoma cells motivated an investigation into mitochondria-associated physiological changes occurring during an intercellular exchange with immune cells. A mitochondrial transfer is a two-way …

Nutrient-Driven Transcription Factor-Dna Interactions And Their Signaling Mechanisms In Metabolic Disease, Evelyn A. Bates

Theses and Dissertations--Nutritional Sciences

Metabolic homeostasis is maintained through tightly coordinated signaling networks that integrate diverse physiological inputs. Central to this regulation are transcription factors, which sense nutrient, hormonal, and vitamin-derived signals and translate them into coordinated gene expression programs. Transcription factor activity is governed by DNA binding, recruitment of coregulatory proteins, and interactions with specific response elements in gene promoters, which allows them to selectively modulate diverse metabolic pathways. Owing to their multifactorial and tunable nature, transcription factors have emerged as promising targets for the treatment and diagnosis of metabolic diseases, including metabolic dysfunction-associated steatotic liver disease (MASLD). This dissertation explores the molecular …

Genomic Signatures Of Decline And Recovery In An Endangered Bat, Myotis Grisescens, Marxe Altman-Orbach

Graduate Theses/Dissertations

Tremendous population declines may result in the loss of genetic diversity, which can, in turn, lead to reduced adaptive potential, overexpression of deleterious phenotypes, and further population declines. In this way, genetic drift from a severe demographic decline may ultimately lead to an extinction vortex. However, populations that avoid the loss of genetic diversity may remain viable, despite demographic crashes. Therefore, understanding genetic diversity is vital for assessing the conservation status of species that have undergone declines, and can even reflect the effectiveness of management actions. I investigated signatures of genetic bottlenecks in the gray bat (Myotis grisescens), …

Chronic Alcohol Consumption Enhances The Differentiation Capacity Of Hematopoietic Stem And Progenitor Cells Into Osteoclast Precursors, Hami Hemati, Madison B. Blanton, Jude Koura, Rupak Khadka, Kathleen A. Grant, Ilhem Messaoudi

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Chronic alcohol consumption (CAC) is associated with an enhanced risk of bone fracture, reduced bone density, and osteoporosis. In a rhesus macaque model of voluntary ethanol consumption, CAC induces functional, transcriptomic, and epigenomic changes in hematopoietic stem and progenitor cells (HSPCs) and their resultant monocytes/macrophages, skewing them toward a hyper-inflammatory response. In the present study, those studies were extended to investigate alterations in osteoclast development, which, in postnatal life, differentiate from HSPCs and play a critical role in maintaining bone homeostasis. Spectral flow cytometry revealed a skewing of HSPCs toward granulocyte-monocyte progenitors in the CAC group, consistent with an increased …

Chronic Alcohol Consumption Reprograms Osteoclast Lineage Communications To Promote Osteoclastogenesis, Hami Hemati, Brianna M. Doratt, Ilhem Messaoudi

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Chronic alcohol consumption increases the risk of osteoporosis and fracture by disrupting bone remodeling, in part by enhancing osteoclastogenesis. However, the cellular mechanisms underlying this process remain incompletely defined. We analyzed scRNA-seq data from osteoclasts differentiated in vitro from bone marrow mononuclear cells obtained from macaques following 12 months of chronic ethanol or isocaloric control solution consumption. Module scoring, trajectory inference with generalized additive modeling (tradeSeq), and CellChat-based analyses of intercellular communication were applied to uncover ethanol-induced changes in metabolic reprogramming, lineage progression, and signaling network dynamics. Module scoring indicated metabolic reprogramming toward oxidative phosphorylation, with reduced glycolytic, migratory, and …

Alcohol Consumption Exacerbates High-Fat Diet- Mediated Disruptions In Myelopoiesis And Osteoclastogenesis In Mouse Models Of Metabolic Dysfunction-Associated Liver Diseases, Hami Hemati, Madison B. Blanton, Lauren Rutt, Nicholas Keiran, Rebecca Geron, Florence Lima, Rebecca L. Mccullough, Ilhem Messaoudi

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Objective: Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD) and Metabolic Dysfunction-Associated Alcohol-related Liver Disease (MetALD) exhibit systemic immune abnormalities. Given that such immune dysregulation is closely linked to the skeletal complications frequently observed in MASLD and MetALD, we sought to comprehensively characterize the bone marrow hematopoietic compartment and its link to osteoclastogenesis.

Methods: We utilized bone marrow from mouse models of MASLD (high-fat diet, HFD) and MetALD (high-fat diet plus ethanol, HFD+EtOH), followed by flow cytometric analysis to phenotype hematopoietic stem and progenitor cells (HSPCs), as well as in vitro and in vivo assays to evaluate osteoclastogenesis.

Results: We found that …

Bpa: Effects Of The "Plastic Era", Bianca G. Pietrangeli

Student Work

Infographic review of sources of BPA and its impacts on human health with a focus on osteoporosis.

Transcriptional Signatures Of Rapid Protection From Sudan Virus Infection By A Single Dose Of A Vesicular Stomatitis Virus-Based Vaccine, Brianna M. Doratt, Sheridan B. Wagner, Delphine C. Malherbe, Gregory T. Smith, Andrea Marzi, Ilhem Messaoudi

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Sudan virus (SUDV) has caused multiple outbreaks of human disease with case fatality rates ranging from 41 to 100%. We have previously shown that a single vaccination with a recombinant vesicular stomatitis virus-based vaccine expressing the SUDV-Gulu glycoprotein (VSV-SUDV) prevented clinical and fatal disease from lethal SUDV challenge in cynomolgus macaques. With the high probability of future outbreaks, it is critical to determine the molecular mechanisms of VSV-SUDV-mediated protection and the ability to impart rapid protection against SUDV infection. In this study, RNA from whole blood samples obtained from nine cynomolgus macaques that were challenged with SUDV-Gulu post-vaccination with either …

Characterizing Immune Perturbations In Peripheral Blood Following The East Palestine, Ohio Train Derailment, Sheridan B. Wagner, Hami Hemati, Siva Gandhapudi, Timothy J. Hilbert, Candace J. Brancato, Erin N. Haynes, Ilhem Messaoudi

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Background: The East Palestine, Ohio, train derailment on February 3rd, 2023, resulted in the exposure of residents and the surrounding area to numerous hazardous chemicals, which included known acute irritants and human carcinogens. Despite evacuation and cleanup, both residents and responders reported high occurrences of symptoms associated with exposure in the months following, such as eye, skin, and respiratory irritation, headaches, and fatigue. The long-term health consequences for residents remain uncertain.

Objective: To assess the potential for immune perturbations resulting from the exposure, we performed a broad investigation of circulating immune cells and mediators from residents of East Palestine, OH, …

Combinatorial Immunotherapy Drives Exhaustion In Tumor Antigen–Specific Cd8+ T Cells Within The Mouse Renal Tumor Microenvironment, Holly R. Stephens, Elizabeth Elkins, Jing Li, Zoey N. Swalley, Henry Nnaemeka Ogbonna, Pia Muri, Zachary Roberts, Francesca R. Dempsey, Md Akkas Ali, Md Hasanul Banna Siam, Richard Kirkman, Jianqing Zhang, Sunil Sudarshan, Daniel J. Tyrrell, Hubert M. Tse, Daniel L. Smith Jr, Lyse A. Norian

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Immunotherapies have greatly improved outcomes for patients with renal cell carcinoma (RCC), yet response rates remain suboptimal and the factors promoting therapy resistance versus sensitivity are incompletely understood. Currently, no preclinical model of orthotopic renal cancer exists that permits evaluation of tumor antigen–specific (TAS) CD8⁺ tumor-infiltrating lymphocytes (TILs). To address this deficiency, we developed a mouse renal cancer model that permits tracking of adoptively transferred TAS CD8⁺ T cells. Renca-LUC tumor cells were transduced to express tumor ERK (tERK), a model antigen expressing a one-amino-acid change from wild-type ERK, resulting in recognition by tERK/H-2K^d-specific DUC Thy1.1 …

A Trajectory Of Zostera Marina (Eelgrass) Ecosystem Recovery: Pre- And Post-Hurricane Sandy Degradation In Barnegat Bay, New Jersey, Edgar A. Medina

Theses, Dissertations and Culminating Projects

Hurricane Sandy struck Barnegat Bay, New Jersey in 2012 and obliterated the benthic marine ecosystem with extensive damage to Zostera marina meadows. Previous genetic assessments of Barnegat Bay Z. marina in 2008 revealed low heterozygosity and low connectivity between populations. The great disruption caused by Hurricane Sandy motivated us to investigate the long-term effects of the storm on the genetic condition of the eelgrass populations in the year 2021. The investigation revealed improvements in heterozygosity, inbreeding, and connectivity. These findings drove us to investigate the genetics of Barnegat Bay eelgrass populations in the intervening years of 2013 and 2017 with …

Toward Interpretable Multi-Omics Multimodal Biomedical Artificial Intelligence, Yanjun Lyu

Computer Science and Engineering Dissertations

The complexity of human disease arises from biological processes that unfold across multiple scales, from molecular variation through cellular function, tissue organisation, brain phenotypes, each of which is associated with distinct measurement modalities, regularities, and characteristic. Contemporary biomedical artificial intelligence has brought the opportunity to reveal the complexity with in; however, its methodological default, in which models are trained on most readily available modality, does not adequately engage with the multi-scale connected structure by which biological meaning is constituted. The research area of multi-omics and multi-modal AI for biomedicine remains at an early exploratory stage, and the work presented in …

Rna-Sequence-Driven Identification Of Differentially Expressed Genes In Α-Crystallin-Deficient Zebrafish, Kehlie Hopper

SPARK Symposium Presentations

Fetal Alcohol Syndrome (FAS) is a condition that develops in infants when exposed to alcohol in utero, leading to physical impairments such as reduced eye size and disrupted retinal function. Alpha-crystallin A is a key structural protein required for proper lens development and maintenance of transparency, while Alpha-crystallin B plays a protective role against cellular stress during eye development. In this study, I compared AB wild-type (ABWT), αA-crystallin knockout (cryaa), and αB-crystallin knockout (cryaba) zebrafish to investigate how the loss of these proteins influences eye development under ethanol exposure. The cryaa mutants exhibited reduced eye size even under control conditions, …