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Supervisor: Paula Alexandre, Nicholas Greene
Project Description:
Background
Down syndrome (DS) is one of the most common chromosomal abnormalities caused by three free copies of chromosome 21. It is characterised by a wide range of metabolic and neurological defects that include Hindbrain hypoplasia. The underlying cause of this phenotype remains unknown. The hindbrain is a vital brain structure that regulates breathing and heartbeat and plays a central role in motor coordination and cognition.
Our previous work has identified several critical differences between human and mouse hindbrain development, including the presence of expanded proliferative zones with human-specific neural progenitor types (Haldipur et al., 2019). In human hindbrain organoids from DS-derived induced Pluripotent Stem Cells (iPSC), we observed alterations in the proliferation and cellular composition of proliferative zones (unpublished data and Guidi et al. 2011). Our transcriptomic data show a significant upregulation of genes in various metabolic pathways, including mitochondrial, lipid and folate metabolism (unpublished data). These pathways are known to be involved in cell proliferation and cell fate decision.
This project aims to investigate whether the hindbrain hypoplasia observed in DS results from metabolic defects and consequent disruption of proliferative zones. We will initially focus on the folate-related gene DHFR, which is found to be upregulated in DS-derived organoids and is involved in DNA replication and cell proliferation.
Aims/Objectives
1. Determine the changes in cellular composition in proliferative zones in DS.
2. Identify global metabolic alterations occurring in DS.
3. Test whether folate-related genes are responsible for changes in cell proliferation observed in DS.
This work uses state-of-the-art approaches. It also test an original hypothesis, whether genes and metabolites implicated in folate metabolism and other metabolic pathways are responsible for the proliferative defects and cell lineage shifts observed in DS. This will allow the PhD candidate to develop translational lines of research that may rescue hindbrain hypoplasia in DS.
Methods
This project will produce three-dimensional human hindbrain organoids derived from healthy control and DS iPSCs. Hindbrain organoids can generate human-specific progenitor types (unpublished data & Silva et al. 2020) and are amenable to testing potential therapeutic interventions. Aim 1, involves histological and transcriptomic analyses to identify cell types and potential lineage shifts in DS compared to healthy controls. Aim 2 uses unbiased metabolome analysis to determine global metabolic alterations between healthy and DS samples. Aim3 tests whether the inhibition of DHFR function (e.g., methotrexate treatment) can rescue DS proliferative phenotype. This study will be expanded to other pathways identified by the metabolome analysis.
The supervisory team has strong complementary expertise in all the proposed approaches. P. Alexandre has expertise in human brain development and live-imaging approaches. T. Silva is an expert in human iPSC cell models. N. Greene is an expert in metabolism and brain metabolic disorders.
Timeline
Aim 1: Month 1-10
Aim 2: Month 6-18
Aim 3: Month 12-36
Thesis write up: Month 30-36
Prepare manuscript: Months 24-33
References
Guidi, S. et al. Brain Pathol. 21, 361–373 (2011). Haldipur, P. et al. Science 366, 454-460 (2019). Silva, T.P. et al. J. Vis. Exp. (2020b).
Contact Information:
p.alexandre@ucl.ac.uk