How Bioinformatics Could Find The Next Breakthrough Cancer Drug
Immunotherapy is being hailed as the future of cancer treatment. Harnessing the body’s own immune system to attack and kill cancer cells, immunotherapy is a burgeoning field of medicine that offers a more nuanced way to treat cancer than traditional chemotherapy, which works by delivering a broad punch – often with severe side effects.
Some cancer immunotherapies have already shown standout results in clinical trials, including partial and complete responses in patients with advanced cancer. But while interest in immunotherapy is surging in the biotech and pharmaceutical space, the drugs don’t work for every cancer patient. Researchers are trying to change that by identifying more high-performing immune cells that could be used to develop new immunotherapies.
Engineers from the University of Houston, working with physicians from the University of Texas M.D. Anderson Cancer Center, have invented new software that can pinpoint tens of thousands – and even hundreds of thousands – of these cells. They’re particularly interested in how various types of T-cells – white blood cells that play a key role in the immune system – can kill cancer cells.
The researchers have dubbed the software TIMING, which stands for Time-lapse Imaging Microscopy in Nanowell Grids, and detail the technology in a new paper appearing in the Aug. 15 issue of the journal Bioinformatics. The field of bioinformatics combines elements of computer science and biology and has arisen from the flood of data being generated by newly available genomic sequencing tests.
“There is a huge need to develop tools and techniques to unravel the interactions between the immune cells and the tumor cells. For example, you don’t want the immune cells to kill other cells,” Badri Roysam, chairman of the University of Houston Department of Electrical and Computer Engineering and lead author of the Bioinformatics paper, told me in an interview.
Conventional analysis of these cells is done manually, by assessing between 10 and 100 samples of cells at a time.
TIMING tracks individual cell-to-cell interactions by using a time-lapse video recording to look at isolated samples of immune cells and cancer cells though an expandable structure called a nanowell grid. Essentially, the software combines the power of a supermicroscope and a supercomputer to look at cell-to-cell interactions on a large scale. (Watch a video of some of the cell-to-cell interactions the researchers captured here.)
Roysam and his colleagues used TIMING to analyze samples of leukemia and melanoma tumor tissue and were able to observe, at a single-cell level, how different types of T-cells function against cancer cells.
And all cancer cells are not created equal. They all have subtle variations of surface molecules – called cancer antigens – that can be detected by the immune system. Immunotherapies incite the immune system into attacking tumor cells by using these antigens as targets.
“We have to be able to cope with heterogeneity in cancer,” Roysam said. “Every patient is different, which means we have to make immunotherapy adaptable to different patients.”
The technology is in early stages though, and Roysam said there are still improvements to be made. For one, he wants the software to be faster – 100-fold faster. Right now, analysis takes several hours, or even days, to complete. He wants to speed that up to a matter of minutes. Eventually, his team hopes to make the technology available to research laboratories and pharmaceutical companies.
Meanwhile, the European Union is also turning to bioinformatics to find new immunotherapies. Leading the charge is the Medical University of Innsbruck in Austria with help from collaborators in the Czech Republic, France, Germany, Spain and the Netherlands. Industry partners Definiens AG and AptaIT, both German companies, and Austria’s Cemit will also be involved in the effort.
The project received an initial €3 million in grant funding from the European Union.
Dr. Zlatko Trajanoski, director of the Innsbruck Division of Bioinformatics, is coordinating the initiative, dubbed the Advanced Bioinformatics Platform for Personalized Cancer Immunotherapy, or APERIM for short. “We are creating the conditions needed to better treat cancer with state-of-the-art precision medicine in [the] future,” Trajanoski said in a university-issued statement.
Source: Forbes
