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Project title
Application of ‘omic’ technology and AI/machine learning to elucidate poorly understood disease mechanisms in lysosomal storage disorders
Supervisors names
Dr Wendy Heywood
Dr Jenny Hallqvist
Background:
Fabry disease (FD) is an X-linked lysosomal storage disorder caused by mutations in the alpha-galactosidase A (GLA) gene and leads to deficiency of α-galactosidase A (α-GAL) activity. GLA mutations result in the progressive intracellular accumulation of the glycosphingolipid, globotriaosylceramide (Gb3). This contributes to a wide variety of clinical symptoms including peripheral pain, renal, cerebral and cardiovascular complications.
Curiously, Gb3 seems to be less toxic than an intermediate caused by a side reaction that occurs when accumulated Gb3 has a fatty acid removed to create a lipid called lyso-Gb3. Lyso-Gb3 is not a naturally occurring lipid and has greater association with disease progression than Gb3 [1]. Its is hypothesised that it is lyso-Gb3 that causes many of the symptoms in FD through unknown toxic mechanisms. Previous work in our laboratory shows that lyso-Gb3 interferes with microtubule dynamics, phospholipid metabolism and protein folding in neuronal cells [2] thereby affecting many pathways that could lead to peripheral pain. However, we do not know if these effects are the same in other cell types and if further tissue specific mechanisms are affected in other organs relevant in FD such as kidney and endothelial systems. Some of these affected pathways could potentially be alleviated by re-purposed drugs.
Aims/Objectives:
The aim of this project will be to elucidate the toxicological mechanisms of lyso-Gb3 on different organ systems in Fabry disease and identify disease modifying drugs that interfere with lyso-Gb3 toxicity.
Methods:
In collaboration with Dr Derralynn Hughes at the Royal Free hospital, the effect of administered and endogenous derived lyso-Gb3 will be studied using wild type and FD cell lines. These will include kidney and endothelial derived lines. Glucosylsphingosine, which is the lyso-lipid that accumulates in Gaucher disease causing a very different disease phenotype (no cardiac or renal features), will be used as a disease control. Cells will be subject to stable isotope tracer analyses (SILK) followed by deep phenotyping proteomics analysis to identify tissue specific affected pathways. This will give the student hands-on experience in the much sought after techniques of proteomics, lipidomics, flux analyses and state-of-the-art mass spectrometry. Additionally, the student will confirm findings with functional analyses and gain significant experience in targeted small molecule mass spectrometry and enzymology. To identify possible therapeutic compounds for FD the student will test microtubule modulating drugs on the cell lines to see if the toxic effect of lyso-Gb3 can be reduced. Data will be analysed using bioinformatics tools that the student will learn including AI and machine learning techniques. In summary, this is a great opportunity for a student to use cutting edge technology to elucidate the cellular mechanisms resulting in Fabry disease.
Timeline (Months ):
- 0-6 – cell culture and mass spec training.
- 3-8 First cell line experiment and proteomics analysis
- 6-12 Second cell line experiment and proteomics analysis
- 10-24 Functional analysis to confirm affected pathways
- 24-33 Drug treatment experiments
- 30-36 Thesis writing
References:
1. Nowak A, et al. Mol Genet Metab. 2018 Feb;123(2):148-153.
2. Nikoleanko V et al. Hum Mol Genet. 2023 Jul 20;32(15):2464-2472.
Contact
Dr Wendy Heywood (wendy.heywood@ucl.ac.uk)