Our proposal is focused on understanding how injury to blood vessels cells contributes to organ damage in children with sepsis–a life-threatening condition caused by an infection. By detailed study of free-floating blood vessel cells in children with sepsis and by treating miniature blood vessel organs with the serum of children with sepsis, we seek to identify genes that lead to heart, lung, liver, and kidney damage. Our studies may lead to the discovery of new medicines that can prevent organ damage and help save the lives of very sick children with sepsis.

In our cells, proteins bind DNA to regulate gene activity, to replicate the genome, and to repair DNA mutations, while abnormal protein-DNA binding causes many diseases including cancers and developmental disorders. This project aims to develop a new technique (called MACHA) to detect protein-DNA binding in every cell in a specimen. If successful, MACHA will help elucidate how individual cells work within organs and allow us to pinpoint disease-causing abnormal cells within a specimen. This project is a collaboration between Kohta Ikegami, Assistant Professor at the Division of Molecular Cardiovascular Biology and the Heart Institute at Cincinnati Children's Hospital Medical Center, and Sebastian Pott, Research Associate Professor at the University of Chicago.

Gene regulation is largely defined by the interactions between different epigenetic marks under the genetic context within the cells. To understand gene regulation in prestigious tissues, we propose to develop a single-molecule and single-nuclei multiomics assay with the requirement of a small number of starting materials. The methods proposed to develop here will allow us to understand the gene regulation from genetic variations to molecular phenotypic variations during the early development, which will eventually pave the road for discovering molecular mechanisms, drug targets, and early intervention strategies for different complex diseases.

Transcription factors read the genome, fundamentally connecting DNA sequence to gene expression across diverse cell types. Determining how, where, and when transcription factors bind chromatin will advance our understanding of gene regulatory networks and genetics. This project builds computational models to predict transcription factors binding sites in any human cell type from minimal datatypes, selected for feasibility in scarce cell types and clinical specimens.

Antidepressant and antipsychotic medications are commonly prescribed to pediatric patients, but how genetic variants influence response and side effects of these medications has primarily been evaluated in adults with European ancestry. The impact of variants found primarily in people with African ancestry, especially children, is not understood well. This proposal aims to study how genetic variants in two drug metabolizing enzymes impact response to medications used for mental health disorders in pediatric patients with African ancestry. This project will improve dosing recommendations for Cincinnati Children's genetic pharmacology service for these medications and could influence the prescribing of these medications in patients with African ancestry around the world.

Isolated infantile nystagmus syndrome (INS) is a constant rhythmic “eye shaking” that presents in the first two to three months of life and results in the development of life-long subnormal vision. The biologic mechanisms that underlie the development of isolated INS are poorly understood. The goals of this project are to perform an innovative and ground-breaking analysis (1) to identify causative candidate genes associated with isolated INS, and (2) to understand the molecular physiology of the extraocular muscles of this condition, which act as the end-stage effector contributing to these abnormal eye movements. The findings from this proposed research will provide both critical new insights into EOMs development and INS as well as identify new molecular targets to treat not only isolated INS, but all nystagmus as well.

By using our newly developed human mini-brain organoid model, we aim to study how neuronopathic Gaucher disease impacts the brain transcriptome at a single cell level. This model will also allow us to understand the profiles of organoid-released exosomes that could be affected by this disease. These studies may lead to the development of new effective treatments and improve the survival rate in this devastating disease.

Natural killer cells are a type of immune cell critical for protection against cancer, yet occasionally these cells become tumors themselves, resulting in an aggressive and hard to treat type of lymphoma. An improved understanding of the dysfunctions that lead these cells to turn into tumors will be critical to developing better therapies to treat this disease. In this project, we will investigate synergy between mutations in an RNA helicase DDX3X and gene products of Epstein-Barr virus in promoting tumorigenesis of natural killer cells.