Down syndrome
The current view of the field is that inter-connected gene regulatory networks with many minor genetic variants collectively contribute to Alzheimer's disease initiation. Identification of these genome wide networks and testing their contribution to Alzheimer’s pathogenesis is likely to provide novel therapeutic targets. Induced pluripotent stem cells from Down syndrome individuals provide an opportunity to achieve this. All individuals with Down syndrome (DS, trisomy 21) will develop brain changes characteristic of Alzheimer’s disease (AD). While this shows that chromosome 21 genes are major drivers of the disease, the genes or combinations of genes on chromosome 21 responsible have thus far remained unclear. We have established a unique resource of Down syndrome induced pluripotent stem cells and are able to show that neurons and astrocytes derived from these cells display typical hallmarks of Alzheimer’s disease in vitro. We next performed the most comprehensive gene expression analysis of Down syndrome neurons to date to reveal altered gene regulatory pathways that are both linked to chromosome 21 and Alzheimer’s pathogenesis (In collaboration with the RIKEN and Prof Christine Wells (AIBN). By sequentially deleting single genes and small gene cohorts from chromosome 21 using TALEN technology and over-expressing them in control cells we will be able to systematically unravel the interacting gene regulatory networks that underlie early Alzheimer’s pathology in Down syndrome neurons and astrocytes, thereby providing novel therapeutic targets for treating sporadic Alzheimer’s disease. These genome- edited Down syndrome iPSC are further used to model myeloproliferative disease and leukemia (in collaboration with Prof Ma, UNSW).
 
Ataxia-telangiectasia
Ataxia-telangiectasia (A-T) is a rare autosomal recessive genetic disorder characterized by chromosomal instability, progressive neurodegeneration, a high risk of cancer and immunodeficiency. ATM, the gene defective in A-T is a Ser/Thr protein kinase and a member of the phosphoinositide-3-kinase (P13K) – related protein kinase (PIKK) family which is activated following DNA damage response proteins and phosphorylates as many as 700 substrates involved in DNA repair and cell cycle checkpoint activation. To understand the progressive neurodegeneration in A-T we have as a world-first generated A-T iPSC and identified mitochondrial gene expression changes as an early A-T associated phenotype. We subsequently generated cortical neuronal cultures and neuronal cells from the cerebellum that reveal novel aspects of A-T pathogenesis. TALEN-based gene correction of A-T iPSC to gene correct patient stem cells provides a potential avenue for cell based therapies in the future while RNA-seq comparisons of A-T patient and control iPSc derived neuronal cells is used to identify A-T specific gene regulatory newtworks and potential drug targets. This project is performed in collaboration with Prof martin lavin (QIMR).
 
Prader –willi syndrome
Prader-Willi syndrome (PWS) is a devastating developmental disorder resulting in intellectual disability, hypogonadism, obesity and hyperphagia that stems from the loss, or improper imprinting, of up to 13 genes and more than 100 snoRNAs on 15q11.2-q13. This has been linked with the deletion of the uncharacterized SNORD116 cluster. Particularly in the brain these snoRNAs can be processed into regulatory sno-derived small RNAs (sdRNAs). Taking advantage of our ability to perform TALEN based genome editing in human iPSC we investigate in this project the role of PWS sdRNAs in small RNA-mediated epigenetic and neurological regulatory loops with the aim to increase our understanding of the link between non-protein-coding RNAs and disease and PWS pathogenesis specifically. This project is performed in close collaboration with Prof Ryan Taft (IMB).
 
Beta-thalassemia
In this study we use non-integrative approach to derive iPSCs from two different types of donor cells, peripheral blood mononuclear cells (PBMNCs) and fibroblast cells from Saudi-Arabian patients with homozygous beta thalassemia and healthy controls, comparing the effect of the epigenetic make-up of the donor cells on in vitro functionality of hematopoietic progenitors. TALEN based gene correction of the beta thalassemia iPSC with homozygous IVII-1 (G-A) mutations is pursued as a potential therapy for this disease. This project is performed in collaboration with Prof Ali from the university of Dammam (Saudi Arabia).
 
 
 
Differentiation, reprogramming and drug screening in microfluidic bioreactors
In collaboration with Prof Cooper-White (AIBN) we are leveraging a high through-put combinatorial microfluidic bioreactor platform to both optimise and innovate cell reprogramming and differentiation technologies and to perform drug screening on iPSc derived cell types, such as cardiomyocytes. Together with Prof Little (IMB) we are further exploring kidney differentiation and direct kidney reprogramming strategies.

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