The technique known as RNA sequencing lets researchers discover which genes are turned on and off in a sample of tissue. In cancer, RNA-seq (as it’s known) is used to find the faulty genes driving the disease. But not all cells within a tumor are the same. Some may have one set of genetic drivers, while other, next-door cancer cells depend on completely different genetic changes. Even the types of cells within tumor tissue may differ, with cancer stem cells intermixed with regular cancer cells intermixed with healthy cells and immune system cells. What this means is that RNA-seq has traditionally been like taking a picture of the rainforest from 10,000 feet: You see a lot of green trees, but many things remain hidden beneath the canopy.
Now an award from the Alex’s Lemonade Stand Foundation will help University of Colorado Cancer Center researchers look inside overall tumor genetics to the makeup of individual cells. Specifically, researchers will use an updated version of RNA-seq called single-cell RNA-seq to detail the genetic landscape of cells within the brain cancers known as pediatric low- and high-grade gliomas.
“The cool thing about single-cell RNA-seq is it gives us understanding of different populations of cells that make up these tumors. We plan to study different genetic subtypes of pediatric gliomas and learn more about how these tumors arise and how they evolve over time,” says Adam Green, MD, investigator at the University of Colorado Cancer Center and pediatric oncologist at Children’s Hospital Colorado. Green was awarded the grant along with Jean Mulcahy Levy, MD, with the help of laboratory members including Andy Donson, John DeSisto, and Shadi Zahedi.
If it’s been a while since your high school biology class, here’s a quick refresher: Your chromosomes and the genes on your chromosomes are made of DNA – it’s like a blueprint. But not everything in the blueprint is actually manufactured. Your DNA includes a bunch of nonsensical sequences and silent genes that don’t do anything in the adult body. RNA lies down next to DNA, reads the code, and transports the information of DNA to the cell’s little manufacturing centers. So by analyzing RNA, researchers look inside DNA to see what’s meaningful; and with single-cell RNA-seq, researchers look inside the bulk of a tumor to see what’s meaningful for each cell.
For example, Green and colleagues hope to discover the genetic features of cancer stem cells that give rise to the bulk of glioma tumor tissue. In this case, a genetic difference could provide a target allowing the group to attack cancer stem cells with genetically targeted treatments.
Or, “Other cells around the tumor can give us an understanding of the immune response to the tumor, and how that differs across tumor subtypes,” Green says. This understanding of how a tumor interacts with the immune system could help the group target tumors with anti-cancer immunotherapies, or know which gliomas are likely to respond to existing immunotherapies.
Additionally, because the group has multiple glioma samples from individual patients collected at different points during treatment, single-cell RNA-seq can help the researchers understand how tumors evolve over time in response to therapy – maybe as cells evolve to resist chemotherapy, they end up with new susceptibilities to other types of treatments.
“We hope this understanding will eventually lead to new treatments against pediatric gliomas, personalized based on the genetic characteristics of cells driving these cancers,” Green says.