NCBS Researchers Develop Method to Identify Cancer Cells That May Resist Treatment
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Bengaluru, August 25 : Researchers at the National Centre for Biological Sciences (NCBS) have developed a new computational method that could help identify cancer cells capable of surviving anti-cancer treatment.
The study, published in Cell Systems, was conducted by NCBS researchers Suvranil Ghosh, Shaon Chakrabarti and Archishman Raju. The team developed Power-Seek, an algorithm that can identify “memory genes” in cancer cells using single-cell RNA sequencing data from a single snapshot.
Cancer treatment kills most cancer cells, but a small fraction can survive despite having the same DNA as cells that die. Researchers say this survival can sometimes be linked to differences in which genes are switched on or off, rather than new genetic mutations.
Some of these gene-expression patterns can persist as cells divide, creating a form of cellular memory that may help cancer cells tolerate treatment.
Until now, identifying such memory genes generally required researchers to track the ancestry of cells over time, a technically demanding process that is especially difficult in patient tumour samples.
Power-Seek addresses this challenge by analysing gene-expression patterns across thousands of individual cells and detecting traces of shared cellular history, even when the relationships between individual cells are unknown.
The researchers first tested the method using previously published melanoma data, where memory genes had been identified through detailed lineage-tracking experiments. Power-Seek was able to recover many of the same genes using only a single-cell snapshot.
The team also applied the method to a clinical breast cancer sample and identified memory genes that had previously been detected through more laborious approaches. The researchers found that memory genes in melanoma and breast cancer share several common functions.
“Since memory genes are switched on even before drugs are added, our method can potentially detect future causes of drug tolerance and provide early intervention strategies,” said Shaon Chakrabarti, assistant professor at NCBS.
Archishman Raju, assistant professor at NCBS, said the approach could eventually make it possible to identify memory genes directly from clinical samples and help researchers find signatures that could be used to target treatment-tolerant cancer cells.
The researchers plan to further refine Power-Seek and study how these memory genes interact with one another to create treatment-resistant cell states.
Study: Cell Systems
Researchers: Suvranil Ghosh, Shaon Chakrabarti and Archishman Raju, NCBS
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