RNA Expression States Affect Cancer Cells’ Susceptibility to Different Treatments

pancreatic cancer cells
[Source: Stocktrek Images / Getty Images]

A team of investigators led by scientists at the Dana Farber Cancer Institute has identified three prototypical RNA-expression states and uncovered differences in their susceptibility to various cancer drugs, according to research published in Cell. The study, which used pancreatic cancer cells, also discovered that altering the tumor microenvironment can drive tumor cells from one state to another, potentially offering a way to make them more susceptible to a particular drug.

Findings from the new study—published recently in Cell through an article titled, “Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer“— examines whether a cell trait-like RNA expression patterns influence drug responses and can be used to identify treatments for a tumor might be susceptible to.

“What we show in this paper is that cancer cell state is plastic in response to the microenvironment and has a dramatic impact on drug sensitivity. This opens new frontiers for thinking about drug development and how to select drugs for individual patients,” noted co-senior study investigator Alex Shalek, PhD, a core member of the Institute for Medical Engineering and Science (IMES) at MIT, an associate professor of chemistry, and an extramural member of MIT’s Koch Institute for Integrative Cancer Research.

Sequencing a cell’s genome can reveal cancer-linked mutations, but identifying these mutations doesn’t always provide information that can be acted upon to treat a particular tumor. To generate additional data that could be used to help choose more targeted treatments, Shalek, and other researchers have turned to single-cell RNA-sequencing, which reveals the genes that are being expressed by each cell at a moment in time.

“There are plenty of situations where the genetics are incredibly important, where you can develop these very precise drugs that target mutations or translocations,” explained study co-author Andrew Navia, a graduate student at MIT. “But in many instances, mutations alone don’t give you an effective way to target cancer cells relative to healthy ones.”

The researchers analyzed cells from pancreatic ductal adenocarcinoma (PDAC) in this study. There are very few targeted drugs available to treat pancreatic tumors, so most patients receive chemotherapy drugs that may be effective initially but often stop working as tumors become resistant. Using single-cell RNA-sequencing, the researchers analyzed about 25 metastatic tumor samples from pancreatic cancer patients.

Previous analyses of pancreatic tumor cell RNA have revealed two broad categories of cell states: basal-like, a more aggressive state, and classical. The researchers identified a third state that appears to be an intermediate between those two in the new study. The researchers say that cancer cells may pass through this state as they transition from classical to basal-like.

The researchers also found that the environment in which cancer cells are grown plays a key role in determining their state. This study grew matched “organoids,” or tiny cancer aggregates from each patient’s biopsy. Such organoids are often used in precision medicine pipelines to model tumors from individual patients, to help identify drugs that might be useful for those individuals.

When comparing each in vivo single-cell profile to the matched ex vivo organoid model, the researchers found that the organoids often exist in a different RNA state than cancer cells examined directly from the same patient. “We see the same DNA mutations in the original tumor and its model, but when we start to examine what they look like at the RNA level, we find that they’re very, very different,” Shalek remarked.

That suggests that the state of a tumor can be influenced by the conditions in which it’s grown rather than its genetics alone, he says. The researchers also found that they could drive cancer cells, even long-established cell line models, to switch between different states by changing their growth conditions. Treating cells with TGF-beta, for example, drives them to a more aggressive, basal-like state, while taking TGF-beta away leads the cells to revert to the classical state in a dish.

Cells in each of those states depend on different cell-signaling pathways to survive, so knowing the cell state is critical to selecting the right kind of drug to treat a particular tumor, the researchers say.

“When we started looking at drug sensitivity, it became evident that the same model pushed into a different state would respond very differently to a drug,” Navia stated. “These state-specific sensitivities become critical as we think about selecting drugs and avoiding resistance. If you don’t know the right state, you could pick the entirely wrong compound and try to target the wrong pathways. For example, if you don’t consider plasticity, the cancer may only respond temporarily until its cells change state.”

The findings suggest that further analyzing the interplay of genetics, cell state, and the tumor microenvironment could help researchers to develop new drugs that would effectively target individual patients’ tumors.

“We’re not erasing decades of understanding cancer as a genetic disease, but we’re certainly saying that we need to much better understand the intersection between genetics and state,” concluded study co-author Peter Winter, PhD, a postdoc at MIT. “Cell state absolutely has ties to the underlying sensitivity of certain models, and therefore patients and to specific drugs.”

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