In vitro studies using DNA barcoded cell lines demonstrated that resistance to CDK4/6 inhibitors is likely due to the expansion of pre-existing resistant clones, suggesting that targeting resistance upfront could delay the acquisition of clinical resistance.


Multiple mechanisms of acquired resistance to CDK4/6 inhibitors have been identified in clinical and pre-clinical studies.1 It remains unknown if these mechanisms are pre-existing or acquired during treatment. In addition, the role of ESR1 mutations in resistance to CDK4/6 inhibitors (plus endocrine therapy) is unknown, as is whether the mechanism of resistance to different CDK4/6 inhibitors is disparate.

To get more insight, Dr. Cristina Guarducci (Dana-Farber Cancer Institute) studied the clonal dynamics and mechanisms of resistance in vitro using a DNA-barcoded, doxycycline-inducible ERS1-mutant MCF7 cell line.2 She presented the results at the 2022 San Antonio Breast Cancer Symposium. These cells express the Y537S ERS1-mutated estrogen receptor (on top of the wild-type receptor) when treated with doxycycline. Cellular barcoding is a technique in which individual cells are labelled with unique nucleic acid sequences, termed barcodes, so that they can be tracked through space and time.3

Cells with or without a mutated estrogen receptor were treated—in triplicates—with escalating doses of palbociclib or abemaciclib until resistance. Clustering of identical barcodes in the resistant cells indicated that resistance to palbociclib is the result of the selection of pre-existing subclones. In addition, expression of the mutant estrogen receptor resulted in the selection of different palbociclib-resistant subclones. ESR1-mutation also resulted in an earlier and more heterogeneous clonal selection compared with the wild-type receptor. Resistance to abemaciclib is also the result of the selection of pre-existing subclones. However, in abemaciclib-resistant cells, estrogen-receptor wild-type cells and estrogen-receptor mutant cells have a high number of overlapping selected clones. Again, ESR1 mutation resulted in an earlier—but not more heterogenous—selection of subclones.

The barcodes enriched in palbociclib-resistant and abemaciclib-resistant cells are different. This difference is more pronounced in the setting of estrogen-receptor, wild-type cells compared with estrogen-receptor mutated cells. Functional studies showed that palbociclib-resistant cells retain sensitivity to abemaciclib, while abemaciclib-resistant cells are cross-resistant to palbociclib.

“Resistance to CDK4/6 inhibitors is likely due to the expansion of pre-existing resistant clones, suggesting that targeting resistance upfront could delay the acquisition of clinical resistance. The clonal selection during the acquisition of resistance to palbociclib and abemaciclib is different, highlighting the differences between these two CDK4/6 inhibitors,” concluded Dr. Guardicci.

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