A very techie Christmas

28 Nov 2017

We’ve already started opening our presents. Christmas has come early as new technologies take their place in our labs, promising to speed up childhood cancer research.

New to our labs this Christmas are some new technologies that will boost our research – a single cell sequencer, micro-CT imager and a robotic dispenser that measures out liquid samples in billionths of a litre. The first of these has already arrived in the lab.

The single cell sequencer, roughly the size of shoe-box, will help us understand cancer cells’ diversity to find new childhood cancer treatments. Because not only is every cancer and every cancer patient different, cancer cells within a tumour are genetically different.

Single cell sequencing is a new technology that’s beginning to transform cancer research. It’s making what was once the domain of only specialised labs more widely accessible and allowing researchers to ‘understand biology at the unitary resolution of life’ – the cell. The journal Nature named it their ‘Method of the Year 2013’.

It’s cancer cells’ complexity and diversity, their ‘heterogeneity’, that helps them evade treatment. Getting a handle on just how different cancer cells are within a tumour will be aided by the new single cell sequencer which barcodes individual cancer cells, then, within 24-48 hours, reports back the nucleotide sequence of the cells’ genome (DNA) or transcriptome (RNA).

Single cell sequencer with minders Janith Seneviratne and Dr Dan Carter

Researchers can then use bioinformatics to characterise the cells’ mutations and see how much they vary. Project Leader in our Molecular Carcinogenesis program, Dr Dan Carter says this is important because some cancer cell sub-populations have genes that help them resist chemotherapy treatment.

“These are the cells that cause a patient to relapse, making it harder to treat.

“Finding ways to not only predict relapse but to also aid targeted therapy selection is a really important area of research.

“If we can find out what’s genetically unique about these cells and how they evade treatment, we can potentially find new treatments that address that,” he said.

Dan and PhD student Janith Seneviratne will analyse individual tumour cells to explore neuroblastoma tumour heterogeneity and develop ways to improve personalised medicine approaches.

Janith says single cell sequencing gives a much more detailed picture of cancer.

“Like blending a fruit salad into a smoothie, when you sequence tumour cells the traditional way, you sequence a lot of cells together and get an overall picture of their gene sequences.”

“The single cell sequencer gives us individual sequences for individual cells, the equivalent of picking out the strawberries or mango pieces from the fruit salad,” he said.

Just like the fruit in a fruit salad, cells in the same place can be different

Unboxing our new acoustic workstation

Maybe you’ve seen unboxing videos on YouTube, like this video of Google Home being taken out of its packaging.

In a few weeks, some very big boxes, much much bigger than a shoebox, will arrive at our labs. When unpacked and assembled, they will make a workstation, the ECHO acoustic workstation, that looks like this.

Schematic of ECHO workstation which will use sound to automatically dispense tiny volumes of fluid

This $1M automated acoustic liquid dispensing system uses robotics and was co-funded by Cancer Institute NSW’s research equipment grants and the University of NSW. It will increase the capacity to screen drugs and drug combinations as much as tenfold. Our Executive Director, Professor Michelle Haber AM said it will help find effective anti-cancer drug combinations and individualised treatments for children and adults with cancer.

“It will enhance our ability to deliver personalised treatments for children in NSW and throughout Australia with the most aggressive cancers,” Professor Haber says.

Over the next three years around 400 children in the Zero Childhood Cancer program, led by us and The Kids Cancer Centre at Sydney Children’s Hospital, Randwick, will have their tumour samples, often very small biopsies, analysed in detail to see which anti-cancer drugs work best against their individual cancer.

“This will give us the opportunity to do much more comprehensive testing than before, on much smaller tumour samples.

“It will increase the likelihood of pinpointing an effective treatment for each child and giving their families hope,” Professor Haber explained.

“The automated acoustic liquid dispensing system will use intense bursts of sound energy to precisely measure out as little as 2.5 nanolitres, 2.5 billionths of a litre, of each sample.”

The cutting edge system will be established at the Australian Cancer Research Foundation’s Drug Discovery Centre in December and begin processing samples for the Zero Childhood Cancer program in 2018.

MicroCT to help researchers image tiny tumours

Advanced imaging tools such as magnetic resonance imaging (MRI), positron emission tomography (PET) and microCT are powerful ways of assessing research results in animal models, an important step in taking potential treatments from lab bench to a child’s bedside in the clinic.

An advanced microCT scanner, funded by a generous Cancer Institute NSW grant announced this month, will help researchers at the Institute and other medical research centres analyse tumours and blood vessel features in preclinical research. It will complement existing imaging instrumentation at UNSW.

The system gives researchers access to ultra-high resolution imaging to allow them to see specific features in laboratory animals that may be one thousandth the size of comparable features in humans. This incredibly detailed imaging allows anatomical structures and administered nanoparticles to be detected, measured and monitored over time, quickly and accurately.

Data for Christmas

These new technologies will speed the development of future childhood cancer treatments, generating more data and more kinds of data than before, driving our research forward. Now that’s a great Christmas present to have.

Read about the robotics in our Drug Discovery Centre, where the new ECHO workstation will ultimately reside.

Top image: The new single cell sequencer in the lab where it will aid research in tumour cell diversity.