When Computers Meet Cancer




Beast of Many Shapes

If you are lucky enough to not have any personal experience with cancer, then you may not know how many flavors it comes in. Cancer is a general description of a disease type that can get very specific the closer you look. Each tissue type is affected differently, each tumor set has its own characteristics, and each patient responds differently to treatments. One of the most progressive ideas in cancer research right now is the concept of individualized medicinal treatment. Basically, scientists and doctors use cutting-edge technology to examine the unique characteristics of the tumor plaguing the patient then analyze exactly the best strategy of attack. This tactic has been predicted to have more disease disruption, less recurrence of tumor growth, and more positive patient outcomes.

The lab of Dr. Traver Hart at MD Anderson Cancer Center is currently using advanced techniques to look specifically at the interactions between the mutations in specific cancer cell lines and their effects on sensitivity to treatment drugs. The team has recently created a program to investigate large scale data from a technique called CRISPR. Their analysis may help to identify holes in cancers’ armor caused by mutations that allow doctors to prescribe treatment drugs known to attack these specific holes, as well as to avoid prescribing those known not to work.



What a Quantitative Researcher Sees


Cancer as An Individual

To really understand how cancers can be individually treated, we must understand how different cancers are from each other. We tend to think of cancers as being grouped into the organ that they arise in, but this is oversimplified. For example, ‘pancreatic cancer’ is an umbrella term that describes 20 known tumor types that can inhabit the pancreas, all with their own diagnosis, prognosis, and treatment. To add onto that, a person’s individual tumor may have genetic differences, either in the form of mutations or modifications, that are specific to that tumor. We can think of genes as a set of instructions for the cell, instructions that can be turned on and off with switches, made to work faster or slower, as well as copied or deleted. Some of these genes in cancer cells have effects on whether the treatment drugs are going to be effective, or if the tumor is resistant and able to overcome them.

For example, imagine a patient that had an aggressive form of cancer that did not respond to any treatments prescribed so far. Researchers may examine the tumor cells, looking for specific genetic alterations. “Look!” cries one scientist. “Gene h453 is different than it normally is! Usually gene h453 protects the cell from the drug CancerAway, but this change may allow us to use it!”

The technique put together by the Hart lab is the first step in how a doctor would know that this genetic change resulted in the tumor having a different response to CancerAway. What the Hart lab is currently working on is a system for analyzing the huge amounts of data that can come from monitoring these cancer/drug interactions. They are able to look a little closer at what’s going on when these cancer cells are treated with drugs, to really see which genes are affected, and to describe the best method of attack.



The Hart Lab


A Sensitive Subject

Heightened sensitivity to small changes is the biggest asset of the Hart lab’s technique. They use binoculars when everyone else just makes circles over their eyes with their hands. Another hot topic in biology right now is the advent of CRISPR, which is a technique for editing the genome of living cells. The power of CRISPR lies in its widespread applicability, relative ease of use, and the specificity of changes that can be made. Single nucleotides can be changed in a gene, allowing the most minute of variations to be studied. One other advantage to CRISPR is that when analyzing the data outputs, genes who only have small fluctuations can still be detected. However, in the uber-complex machine that is a human cell, these tiny genetic waves can result in systemic hurricanes in the body, causing large downstream shifts.

Previously, scientists haven’t had the computer power to pick apart these miniscule signals sent off by cells interacting with treatments and have had to rely on larger ones and alternative monitoring techniques to try to explain tumor cell adaptations. Luckily, in an upcoming publication, the Hart lab has married the world of biological engineering with CRISPR to the innovations of computer modeling. This work will allow researchers to tease apart the details of how these cells are responding to the treatment drugs, along with how they are able to adapt and overcome them. With this knowledge in hand, they can potentially treat patients with a much more personalized mindset that may lead to dramatic reductions in cancer deaths, as well as understand why these cells become resistant to drugs in the first place, and possibly even resuscitate treatment drugs thought to be obsolete by giving them new purposes. The power of quantitative technology is working hand in hand with live biologic research to change the face of research and help MD Anderson Cancer Center and Dr. Hart to wipe out cancer as we know it.

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