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Using machine learning and “multi-omics” data to find new targets to treat adult brain cancers

A Toronto-based researcher will use integrative machine learning strategies try to turn the tide on a deadly brain cancer thanks to new funding provided by the Terry Fox New Investigator Award.

Dr. Jüri Reimand, a computational biologist at the Ontario Institute for Cancer Research, will receive a total of $450,000 from the Terry Fox Research Institute (TFRI) and the Canadian Institutes of Health Research (CIHR) over the next three years to develop an integrative computational platform to find potential targets for treatment in glioblastoma (GBM), a deadly brain cancer with no known cures.

“This is a terrible disease with a dismal prognosis. It is usually fatal within a year or two after diagnosis and current therapies mostly fail to halt its recurrence and progress,” says Dr. Reimand. “We are taking a data-driven approach to see if we can change the tide on this terrible disease by mapping the evolutionary history of each tumor and identifying genes and pathways that could be targeted through new or existing drugs.”

To find these candidate targets, Dr. Reimand and his team will create a robust multi-omics data set derived from samples of primary and recurrent tumours. The data set will incorporate at least three types of layered data from each sample: whole genome sequencing data, RNA sequencing data and proteomics.

The team will then devise machine-learning algorithms to effectively analyze these large data sets to gain new insights into glioblastoma and its recurrence mechanisms. The methodologies will be freely available and can be applied to study of recurrence and metastasis of other types of cancer.

“We hope that our expertise in computational biology can help shed new light on GBM recurrence by analyzing tens of thousands of genes, proteins and RNAs in complex interaction networks, and ultimately provide a small number of high-confidence targets for further experimental work and therapy development,” said Dr. Reimand.

As part of the Terry Fox New Investigator Award, Dr. Reimand will be mentored by a TFRI-funded New Frontiers Program Project Grant led by Dr. Sheila Singh, a clinician-scientist at McMaster University in Hamilton.

"In our New Frontiers PPG, we are routinely generating large amounts of complementary data utilizing different platforms that are difficult to compare,” says Dr. Singh. “This is why we are so excited to collaborate with Dr. Reimand to decipher GBM recurrence, as he brings invaluable expertise in computational biology, bioinformatics and machine learning. Dr. Reimand's multi-omics integrative analysis will deliver our PPG with target genes, pathways and drug interactions that will help us to identify new therapies and understand the complex mechanisms of GBM recurrence."

Read more about all the 2020 Terry Fox New Investigator Award recipients here.

Mentoring program: Targeting clonal heterogeneity in treatment-refractory glioblastoma with novel and empiric immunotherapies

Mentor: Dr. Sheila Singh