Continuously evolving cells help pancreatic cancer evade treatment and spread

An analysis of nearly half a million cells from dozens of patients’ tumors reveals how cancer cells continuously reshape their genetic makeup over time, enabling them to evade treatment for one of the deadliest forms of cancer.

Led by researchers at NYU Langone Health and its Perlmutter Cancer Center, the study focused on pancreatic ductal adenocarcinoma, an often difficult-to-treat disease known to kill nearly 85% of people within five years of diagnosis.

While more than half a dozen genes have been implicated in the complex disease, the analysis of single tumor cells provided new insights into how subpopulations of pancreatic cancer cells reconfigure their DNA within tumors over time.

Genetic shifts drive tumor evolution

The team’s analysis revealed a diverse set of clones, or clusters of tumor cells that have a similar genetic makeup. These clones showed striking differences in behavior, with some evolving to resist therapy and others acquiring the ability to spread rapidly. The findings suggest that ongoing reshaping of the cancer cells’ DNA fuels both treatment resistance and metastasis.

Past research analyzing bulk groups of pancreatic cancer cells had focused on separating them into two subtypes—classical (less aggressive) and basal (more aggressive). However, the research could not explain how cancer cells shift between these subtypes. The new findings show that genetic reconfiguration within a tumor enables cancer cells to transition between subtypes.

Blocking MYC changes cancer cell behavior

Published online Oct. 13 in the journal Nature Genetics, the new study identified specific genetic changes that emerge during tumor evolution, including increased activity of the MYC gene in aggressive tumor cell populations.

Further experiments with pancreatic basal tumor cells showed that blocking MYC activity reverted the cells to the less aggressive classical form and exposed them to more immune cells, potentially making them more vulnerable to immune attack.

“Our study provides the most granular view to date of pancreatic ductal adenocarcinoma, revealing how ongoing genetic reshaping drives tumor evolution over the course of disease,” said study lead investigator Despoina Kalfakakou, Ph.D., a postdoctoral research fellow at NYU Grossman School of Medicine and Perlmutter Cancer Center. “These findings suggest that targeting the mechanisms underlying tumor evolution, including MYC, may help restrain the cancer’s rapid progression.”

“Our research also suggests that single-cell clonal analysis offers a better approach to understanding complex cancers, like pancreatic ductal adenocarcinoma, as they develop over time, by mapping how tumors evolve and adapt at each stage of disease progression,” said study co-senior investigator Aristotelis Tsirigos, Ph.D., a professor in the departments of medicine and pathology at NYU Grossman School of Medicine and a member of Perlmutter Cancer Center.

“More broadly, our study results highlight the critical role of clonal diversity, genetic plasticity and interactions with the tumor’s microenvironment in shaping human pancreatic ductal adenocarcinoma biology,” said Tsirigos, who also serves as co-director of the Division of Precision Medicine and director of NYU Langone’s Applied Bioinformatics Laboratories.

Clones reveal routes around immune defenses

Among the study’s other key findings was how cell clones influenced the tumor’s ability to evade immune detection, possibly explaining why pancreatic ductal carcinoma resists immune therapy.

The researchers found that in some clones, the TIGIT gene was also more active, producing proteins that help cancer evade immune detection. In the same clonal cells, activity of the PD1 gene was found to be suppressed, which may help explain why some immunotherapies that target PD1 are rarely effective.

Tsirigos said that clinical trials using MYC inhibitors or TIGIT inhibitors for pancreatic ductal carcinoma and other cancers are underway, and that his team’s latest findings should encourage larger investigations into different cancer cell states and how to target treatment toward them.

Tracing clones across 62 tumors

For the study, researchers analyzed the genetic activity (using transcriptomics) in clones of 443,451 single cells taken from 62 tumors in 56 men and women with pancreatic ductal adenocarcinoma. Six patients provided tumor samples before and after chemotherapy. Traditionally, cells have been analyzed in bulk for increases and decreases in gene activity, and not individually, as in the latest analysis.

Single-cell analysis showed that individual tumors contained, on average, between two and 11 mixes, or clones, of basal and classical tumor cells. When the researchers traced the clones’ genetic origins, based on gene activity, they were able to link cell copy variations to the cell composition of tumors. This was then used to find which genes, such as MYC and TIGIT, were most active at different stages of disease progression.

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