Elucidating the impact of micro-exon splicing defects in epilepsy with human iPSC-derived brain organoids

About this project

Project description

Alternative splicing strongly contributes to the transcriptome complexity of the brain. A highly conserved alternative splicing program of 3–27 nucleotide long microexons in several hundred genes displays conspicuous switch-like behavior during neuronal differentiation, and defects in this program have been linked to the development of epilepsy. However, to date it remains unclear which cell types display what type of micro-exon splicing. Nor is it clear when this occurs and how defects in this process cause defective brain development that leads to epilepsy. To investigate this we propose to generate brain organoids from control and epilepsy patient iPSC we generated and use a combination of BLADE-enabled linage tracing, single cell bar-coding, and Nanopore sequencing to map alternative micro-exon splicing at a single cell level during sequential stages of early human brain development. Using CRISPRa/i enabled manipulation of splicing factor expression we next intend to elucidate the functional impact of altered micro-exon splicing on early human brain development. These advances will be critical for developing and testing of therapeutics (such as anti-sense oligonucleotides) for patients with specific forms of epilepsy.



  • Novel insight into the extent and nature of micro-exon splicing events in individual cell types during sequential stages of early human brain development, and how this differs in epilepsy patients.
    Novel insight as to how manipulation of the expression of splicing factors implicated in epilepsy results in abnormal brain development, neuronal connectivity and abnormal activity.


  • Development of expertise in Nanopore sequencing and analysis of splicing alterations.
  • Acquisition of expertise in human pluripotent stem cell culture and organoid generation.
  • The ability to use and further develop cutting edge lineage tracing and CRISPRa/I technology in human stem cell brain organoid models.


  • High impact papers and presentation of results at leading international conferences.

Information for applicants

Essential capabilities

experience with cell culture and molecular biology

Desireable capabilities


Expected qualifications (Course/Degrees etc.)

First class or H2a honours in Science, Medicine, Molecular biology or related fields

Project supervisors

Principal supervisors

UQ Supervisor

Professor Ernst Wolvetang

Australian Institute for Bioengineering and Nanotechnology (AIBN)
IITD Supervisor

Assistant professor Ishaan Gupta

Department of Biochemical Engineering and Biotechnology