Higher Degree by Research Candidate
School of Biomedicine
Faculty of Health and Medical Sciences
Jayshen is a Doctor of Philosophy student at the South Australian Health and Medical Research Institute (SAHMRI) in the Genome Editing Lab, under the Precision Medicine theme. He is currently supervised by Professor Paul Thomas and Dr. Fatwa Adikusuma. The primary focus of his research is to develop a novel high efficiency genome editing strategy for Duchenne Muscular Dystrophy (DMD) through harnessing CRISPR-Cas9.
Duchenne Muscular Dystrophy:
This inherited X-linked genetic disorder is caused by mutations in the Dmd gene encoding dystrophin protein on the X-chromosome. The structural implications of dysfunctional dystrophin are severe, with approx. 1 in 35,000 male births burdened with this progressive muscle weakness and shortened life span. This cytoskeletal protein is integral for the structural maintenance of the muscle cell membrane (sarcolemma) integrity in cardiac, respiratory and skeletal muscle tissue. This 'shock absorber-like' protein works in tandem with the dystrophin-glycoprotein complex (DGC).
CRISPR-Cas9 as a technological forefront can be manipulated from its biological purpose (bacterial adaptive immunity) to be used to induce targeted double-stranded breaks (DSBs) at crucial sites in the genome, where the error-prone non-homologous end joining (NHEJ) is the primary repair pathway in absence of a homologous template sequence. All we need is a single gRNA (made from covalently linked crRNA + tracrRNA) and a Cas9 nuclease to let it cut! Microhomology-mediated end joining (MMEJ) is an alternative repair outcome that can also play a role in generation of large deletions:
1) Enable specific insertion of gene-edited sequence through 5'-3' resection on coding and non-coding strands, where microhomologous sequences (25bp) on either ends can function to allow deletion after annealing.
Theory and Experimental Plan:
The Dmd gene spans 79 exons of around 2500kb, where there are over 4000 characterised mutations in the vicinity of critical coding residues of exon 45-55 amenable to the majority of those diagnosed. We aim to utilise the innovative CRISPR-Cas9 as a gene therapy in targeting Exons 51 - 55 of the Dmd gene for the purpose of re-framing changes made from the single exon deletion and restoring the correct reading frame as a viable outcome of gene therapy. Through the testing of multiple re-framing strategies across an exon deletion model, the most efficient sgRNA candidates that induce favourable re-framing mutations can be discovered and tested in vitro and in a mouse disease model. Thus, there can be advancement of this proof-of-concept towards clinical viability.
- Aran and colleagues (2019) have developed CRISPR-CHIP - a graphene-based field effect transistor that can be used as a dCas9-guided biosensor. This can allow through screening clinical samples for the DMD-edited alleles without the need for isolation and PCR-amplification.
- David Liu and his lab (2019) have developed an efficient PRIME Editing system consisting of a Cas9 H840A Nickase fused to a Reverse Transcriptase, in combination with an elongated gRNA to introduce desired mutations in human cells without the need for DSBs!
The PQT Lab
Awards and Achievements
Date Type Title Institution Name Country Amount 2019 Scholarship Master of Philosophy (No Honours) Scholarship University of Adelaide Australia — 2018 Award Outstanding Academic Achievement 2018 The University of Adelaide Australia — 2017 Award Outstanding Academic Achievement 2017 The University of Adelaide Australia — 2017 Scholarship Summer Research Scholarship The University of Adelaide Australia — 2016 Award Outstanding Academic Achievement 2016 The University of Adelaide Australia —
Language Competency English Can read, write, speak, understand spoken and peer review Malay Can read, write, speak and understand spoken
Date Institution name Country Title 2020 South Australian Health and Medical Research Institute Australia PhD (Medicine) 2019 - 2020 South Australian Health and Medical Research Institute Australia Master of Philosophy (Medical Science) 2016 - 2018 University of Adelaide Australia Bachelor of Science (Biomedical Science)
Year Citation 2021 Adikusuma, F., Lushington, C., Arudkumar, J., Godahewa, G. I., Chey, Y. C. J., Gierus, L., . . . Thomas, P. Q. (2021). Optimized nickase- and nuclease-based prime editing in human and mouse cells. Nucleic Acids Research, 49(18), 10785-10795.
DOI Scopus5 WoS5 Europe PMC3
— Adikusuma, F., Lushington, C., Arudkumar, J., Godahewa, G. I., Chey, Y. C. J., Gierus, L., . . . Thomas, P. Q. (n.d.). Optimized nickase- and nuclease-based prime editing in human and mouse cells.
- 2020-2021: Supervised an undergraduate Summer Research Scholar for their 6-week laboratory placement at SAHMRI.
Date Role Committee Institution Country 2021 - 2023 Member Australia and New Zealand Society for Cell and Developmental Biology University of South Australia Australia 2020 - ongoing Member Australian Society for Biochemistry and Molecular Biology ASBMB Australia 2020 - ongoing Member Australian Society of Medical Research ASMR Australia
Date Topic Presented at Institution Country 2020 - 2020 Exploring strategies for a highly efficient CRISPR-Cas9 gene therapy toward precise restoration of dystrophin in Duchenne Muscular Dystrophy (DMD) EMBL Australian Postgraduate Symposium SAHMRI Australia 2020 - 2020 Exploring Strategies for a highly efficient CRISPR-Cas9 gene therapy toward precise restoration of dystrophin in Duchenne Muscular Dystrophy (DMD) Australian Society for Medical Research SAHMRI Australia
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