WEHI Bioinformatics & Computational Biology Special Seminar hosted by Drs James Fu, Mengbo Li & Nadia Davidson

Dr Jovana Maksimovic

Senior Research Associate – Oshlack Laboratory, Bioinformatics and Computational Biology – Peter MacCallum Cancer Centre

Back to the future! Using custom probes to detect cancer fusion transcripts in 10X Flex single-cell

Davis Auditorium

Join via ZOOM

Including Q&A session

Gene fusions are caused by chromosomal rearrangements such as translocations and can drive tumor initiation, progression, and resistance to therapy. It is estimated that they drive approximately 16.5% of all cancers, and are particularly prevalent in haematological malignancies.  

 Bulk RNA sequencing (RNA-seq) is a powerful tool for identifying fusion transcripts that can be used clinically to guide diagnosis and treatment. However, it cannot determine which cell types express gene fusions or how their expression profiles differ from other cells. Detecting fusions at the single-cell level is of growing interest, but high noise, technical artifacts, cost and throughput are limiting factors in current fusion detection approaches that require full-length transcript protocols, such as Smart-seq or long-reads.

 Here, we develop an approach using the 10X Flex single-cell RNA-seq protocol to detect fusion expression at single-cell resolution. 10X Flex uses a probes to detect the expression of >18,000 protein-coding genes and allows for the design of custom probes to detect expression of features of interest. Our fusion detection approach leverages the sensitivity of bulk RNA-seq for the design of custom probes that target the fusion transcript breakpoint allowing their detection along with the transcriptome. 

 We show detection of fusion transcripts in MCF7 cells and 11 B-ALL bone marrow samples and demonstrate biological insights that can be gained using the fusion data.

 Dr. Jovana Maksimovic is a Senior Research Associate in bioinformatics and computational biology in the Oshlack Lab at the Peter MacCallum Cancer Centre. Her research has focused on epigenetics and transcriptomics data analysis, with a strong influence in methylation array analysis as the co-creator of the widely used missMethyl Bioconductor package. She was a Co-PI on a Chan Zuckerberg Initiative Paediatric Cell Atlas Network Grant focused on the development of a globally accessible cell atlas of the healthy paediatric airway. Currently, she holds an NHMRC EL2 Investigator Grant and is developing analytical approaches for multi-sample, multi-condition single-cell transcriptomics experiments.

All welcome!