Research Update: ACRF Breakthrough Technologies Laboratory

In 2014, our incredible supporters’ generosity allowed us to award $2.5 million to Walter and Eliza Hall Institute. The grant established the ACRF Breakthrough Technologies Laboratory, to analyse genetic mutations at the individual cell-level.

One of the technologies supported was CRISPR (Clustered Regularly Interspaced Short Palindromic Repeat), which was awarded the 2020 Nobel Prize for Chemistry.

Highlights of Progress

In 2019, the ACRF Breakthrough Technologies Laboratory was integral to aspects of around 55 published investigations related to various types of cancers. 

Every year since 2015 approximately 67 staff and 10 students have used, accessed, or been involved in projects within the ACRF Breakthrough Technologies Laboratory.

The most significant finding so far has been the development of new chemotherapy combination strategies to target 413 genes potentially linked to colorectal cancer.

Research progress in 2019

Currently, there are two screens that are in development which will be run in parallel using the arrayed mouse whole genome CRISPR library. The first screen has been designed to identify genes that control neutrophil nuclear morphology. 

Neutrophils are the first leukocyte responders of the innate immune system, and have unique migratory and functional capabilities are largely impacted by their nuclear shape, composition and plasticity. A well defined, inducible model of neutrophil maturation will be used with high content confocal microscopy (Opera Phenix™) as the endpoint readout. 

The second screen in development is a synthetic lethal screen to identify targets that either sensitise cells or confer resistance to inhibition of the pro-survival protein MCL-1. Several potent and selective MCL-1 inhibitors are now in the clinic for the treatment of hematological malignancies and this study aims to help define improved strategies for cancer therapy. The screen design utilises the Intellicyt® iQue Screener PLUS, a high throughout, automated flow cytometer which enables analysis of suspension cell lines.

The Janus liquid handling platform continues to be used extensively to support multiple projects at WEHI. These include follow up studies from one of the first functional genomic screens performed to identify synthetic lethal combinations with standard of care therapeutics in colorectal cancer.

These studies have now been extended to include testing of patient-derived organoids. Following our discovery of BCL2 mutations as a cause of resistance to venetoclax in patients with chronic lymphcytic leukemia, we have been able to further explore resistance to Venetoclax using facilities within the ACRF Breakthrough Technologies Lab.

We have used mass cytometry (CyTOF) to make new discoveries in the mechanisms of resistance employed by blood cancers to resist treatment with targeted therapies. The in-kind support from WEHI established key reagents and analytical platforms for us to perform these experiments.

Multiple myeloma is the second most common blood cancer. Although most treatments can be effective, these almost always fail as the cancer changes to become resistant. We developed a new CyTOF approach to analyse the configuration of cell death proteins in millions of individual myeloma cells after they are exposed to cytotoxic treatments. This allowed us to visualise the “decision-making” process in these cells. We employed machine learning approaches to determine the most critical changes in predicting whether the cells live or die. We then tested these predictions using a new inhibitor of the survival protein, MCL-1, and found that it synergised potently to kill more myeloma cells than standard-of-care therapies. Indeed, myeloma cells taken directly from patients also responded better to this combination. These findings were recently published.

We have since developed our CyTOF platform for the analysis of patient samples in clinical trials. We know this approach has been effective in discovering resistance mechanisms in other blood cell cancers and are excited to apply them to multiple myeloma.

Our capacity in CyTOF analysis has also been applied to profiling immune cells in lung cancer specimens from patients. In unpublished work, we have made new insights into the types of immune cells implicated in frustrating the immune response to cancer. We are preparing these for publication and believe they will inform new treatment options to control metastasis.