Thrasher Research Fund - Medical research grants to improve the lives of children

Project Details

Early Career

Status: Funded - Open

Cerebral Organoids as a Model to Understand Genetic and Acquired Hydrocephalus

Andrew Hale, MD, PhD

Summary

BACKGROUND: The most common indication for pediatric brain surgery across the world is for the treatment of hydrocephalus (HC), a disorder of abnormal cerebrospinal fluid (CSF) homeostasis, which has both genetic and acquired (most commonly infection) causes. There are ~400,000 new cases of HC annually across the world, but treatment is limited to suboptimal surgical treatments largely due to a rudimentary understanding of HC genetics and disease mechanisms. GAP: The field lacks a human-specific, ancestrally representative, and genetically tractable experimental system to elucidate the molecular mechanisms underlying genetic and acquired forms of HC. I believe these limitations can be overcome using induced pluripotent stem cell (iPSC) derived cerebral organoids. HYPOTHESIS: I hypothesize that cerebral organoids will recapitulate the genetic, molecular, and phenotypic alterations seen in human hydrocephalus and brain injury. METHODS: I will generate iPSC from European and Xhosa, Zulu, and Bantu ancestry patients (n= 3 per group). In European ancestry individuals, I will use CRISPR-Cas9 to generate MAEL knockout iPSC and isogenic controls. I will use single-cell (sc) RNA, assay for transposase-accessible chromatin (ATAC), and whole-genome sequencing (WGS) to determine the molecular genetic consequences of MAEL loss of function. In addition, these assays will be used to understand the global, unbiased effects of pathogen and injury exposure on cortical development in cerebral organoids across both European and African ancestries. Finally, I will compare the genetic information obtained from organoids with primary brain tissue of HC patients (spanning from the cortical surface to the ventricular wall) obtained during surgery for HC. RESULTS: To delineate the genetic basis of HC, I performed a transcriptome-wide association study (TWAS) of HC in 10 brain tissues and whole blood, identifying decreased expression of MAEL in the cortex reaching experiment-wide significance (Hale et al. Cell Reports, 2021). Additional support for MAEL was obtained through convergent and complementary functional genomics analyses. When I performed analogous human genetics studies of HC in patients of African ancestry, I identified genes converging on regulation of infection/inflammatory processes underlying HC risk (Hale et al., unpublished). Given that infection is the leading cause of HC globally, I undertook an integrative phenomics and genomics analysis of HC and infectious diseases (ID) across European and African ancestry individuals (Hale et al., medRxiv 2020). These data suggested that co-evolution of humans and pathogen-imposed selection pressures have differentially shaped the genetic etiology of HC across ancestral populations. While we know that HC is characterized by a combination of molecular genetic hallmarks (Hale et al., Science Translational Medicine, in revision), a lack of human model system has impeded progress. Here, I will generate cerebral organoid models of genetic and acquired forms of HC. IMPACT: The goal of this proposal is to elucidate the mechanistic basis of genetic and acquired HC, including antecedent neonatal brain injury. The major obstacles in HC biology are 1) mechanistic validation of HC associated genes identified by human genetic screens using human models, 2) lack of African representation in stem cell and genomics studies, and 3) limited primary analysis of human HC brain tissue. To overcome these challenges, I will develop human iPSC derived cerebral organoid models from patients with HC to understand both genetic and acquired causes of HC in both European and African peoples. All organoid models will be rigorously characterized using multi-omics sequencing methods, confirmed and complemented with biochemical, cellular, and molecular approaches. Leveraging my unique background as a neurosurgeon, I will collect primary human HC brain tissue (normally discarded during surgery) to delineate disease-induced vs disease-causing genetic changes. I hypothesize that these approaches will, at least in part, mirror the genetic architecture of human HC, aid our mechanistic understanding of HC, and enable identification of therapeutic targets. Website: https://x.com/andrewthale3

Supervising Institution:
University of Cape Town

Mentors
Mubeen Goolam

Project Location:
South Africa, United States

Award Amount:
$26,750