Molecular model of the drug cisplatin.

© Science Photo Library/Alamy

Poised for survival

16 Apr 2019

State-of-the-art single-cell RNA sequencing technologies shed light on the mechanisms through which cancer cells become resistant to tumor-treating drugs

Exploring the survival strategies adopted by tumor cells when exposed to a cancer-treating drug, researchers in Singapore have identified mechanisms of drug-resistance only triggered when cancer cells experience the drug’s selection pressure.

A study led by Ramanuj DasGupta at the A*STAR Genome Institute of Singapore, in collaboration with N. Gopalakrishna Iyer at the National Cancer Centre Singapore, have uncovered one mechanism used by cells when exposed to the chemotherapeutic drug, cisplatin.

Drug resistance is a leading cause of cancer-associated deaths.  Although many types of cancers initially succumb to chemotherapy, over time, a small subpopulation of cells stop responding to treatment and continue to proliferate and metastasize.

Proposed model for drug-induced cell-state transition and activation of resistance genes.

© 2019 A*STAR Genome Institute of Singapore

Tumors are comprised of a diverse collection of cells with distinct molecular signatures and different sensitivity to treatment. In these heterogeneous tumors, chemotherapeutics exert a selective pressure that favors the expansion of a small number of pre-existing, genetically drug-resistant cells.

Tumors that harbor less diverse cancer cell populations are thought to be more sensitive to drug treatment. However, homogeneous tumors are also able to adapt and develop resistance through epigenetic mechanisms that regulate gene expression without changing the underlying DNA sequence.

DasGupta and colleagues have taken advantage of recent advances in single cell transcriptomics to explore how changes in gene expression in individual, patient-derived primary cells contribute to drug resistance. They analyzed the RNA sequences of oral squamous carcinoma cells before and after exposure to cisplatin.

The molecular profiles of drug-treated cells grown in the laboratory were remarkably similar to those of tumor cells in the same patient’s body. As DasGupta explains, “by mimicking the clinical conditions and tracking the behavior of individual cancer cells, we are able to precisely predict and identify mechanisms of tumor evolution in the clinic”.

They found that upon drug treatment, some cancer cells continue to proliferate even when treated with high doses and start to express genes associated with drug resistance and metastasis.

As anticipated, in a patient-derived primary cell line that was representative of a heterogeneous tumor, exposure to cisplatin led to the selection of pre-existing drug-resistant cells. However, in a patient-derived primary cell line that was representative of a homogeneous tumor (HN120Pri), drug-exposure induced a cell-state transition as some epithelial cells adopt a mesenchymal-like fate. These results highlighted the mechanisms of drug-resistance prompted when cells experience the drug’s selection pressure.

The authors found that HN120Pri cells contained transcription-regulating chromatin marks on resistance-associated genes, indicating that they are epigenetically poised for changing fate. Drug exposure increased the addition of acetyl groups to Lysine 27 of the DNA-packing protein histone H3 (H3K27ac), which allows the recruitment of transcription factors to otherwise inaccessible sites.

There was another surprise for the research team when they identified that drug-induced resistant cells are characterized by the loss of stem-cell factor Sox2 and a gain of Sox9 expression. The specific enrichment of Sox9 at H3K27ac sites underscores the role of this factor in the epigenetic reprogramming that drives drug-induced cancer resistance in homogeneous tumors.

“The switch from one stem-cell factor to another was completely unexpected,” said Ankur Sharma, the study’s first author. “It provides a unique opportunity to predict drug-response in patients and target tumor evolution itself”.

Inhibiting the histone acetyltransferase BRD4 with the small molecule epigenetic drug JQ1 reduced H3K27ac and the cisplatin-induced cell-fate switching, reversing drug-resistance. This result highlights the exciting possibility of using epigenetic inhibitors along with targeted therapies to prevent or delay the emergence of drug resistance.

“Our next steps will involve looking at the evolution of different cancers under a variety of selective stresses and at the cell-cell interactions within the tumor to determine how they influence the evolution of different cell types” concludes DasGupta.

The A*STAR-affiliated researchers contributing to this research are from the A*STAR Genome Institute of Singapore.  For more information about the team’s research, please visit the DasGupta webpage.

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Sharma, A., Cao, E. Y., Kumar, V., Zhang, X, Leong, H. S., et al. Longitudinal single-cell RNA sequencing of patient-derived primary cells reveals drug-induced infidelity in stem cell hierarchy. Nature Communications 9, 4931 (2018). | article

About the Researcher

Ramanuj DasGupta

Group Leader

Genome Institute of Singapore
Dr. Dasgupta leads the DasGupta lab at A*STAR's Genome Institute of Singapore. The group's overall aim is to implement the next-generation functional genomic technologies on individualized patient-derived models to query novel genetic and therapeutic vulnerabilities in solid cancers. The major research focus is to establish novel 'Precision Oncology' platforms (such as patient-derived tumor organoids and primary cancer cell lines) that can be used to a) study the impact of tumor heterogeneity on the evolutionary mechanisms of tumour metastasis and treatment-resistance; b) identify novel transcriptomic/ epigenetic biomarkers of treatment response and tumor progression; c) identify novel therapeutic targets and drug candidates for the precision targeting of specific oncogenic pathways and immune-modulatory response; d) dissect the function of the tumor microenvironment in modulating response to chemo/targeted therapies and immune-oncology drugs.

This article was made for A*STAR Research by Nature Research Custom Media, part of Springer Nature