Resistance to CDK4/6 inhibitors is likely due to expansion of pre-existing resistant clones

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 largely unknown, as well as if the mechanisms of resistance to different CDK4/6 inhibitors are disparate.

To get more insight, Dr Cristina Guarducci (Dana-Farber Cancer Institute, MA, USA) studied the clonal dynamics and mechanisms of resistance in vitro using a DNA barcoded, doxycycline-inducible ERS1-mutant MCF7 cell line [2]. These cells express the Y537S ERS1-mutated oestrogen receptor (on top of the wildtype 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 oestrogen 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 was associated with the selection of pre-existing subclones. In addition, expression of the mutant oestrogen receptor was associated with the selection of different palbociclib-resistant subclones. ESR1 mutation was also associated with an earlier and more heterogeneous clonal selection compared with the wildtype receptor. Resistance to abemaciclib was also associated with the selection of pre-existing subclones. However, in abemaciclib-resistant cells, oestrogen-receptor wildtype cells and oestrogen-receptor mutant cells had a high number of overlapping selected clones. Again, ESR1 mutation was associated with an earlier – but not more heterogenous – selection of subclones.

The barcodes enriched in palbociclib-resistant and abemaciclib-resistant cells were different. This difference was more pronounced in the setting of oestrogen-receptor wildtype cells compared with oestrogen-receptor mutated cells. Functional studies showed that palbociclib-resistant cells retained sensitivity to abemaciclib, while abemaciclib-resistant cells were 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 2 CDK4/6 inhibitors,” concluded Dr Guarducci.

1. Álvarez-Fernández M, Malumbres M. Cancer Cell. 2020;37:514–529.
2. Guarducci C, et al. Clonal evolution and mechanisms of acquired resistance to CDK4/6 inhibitors in ER-WT and ER-Mutant breast cancer. Abstract GS3-07, SABCS 2022, 06–10 December, San Antonio, TX, USA.
3. Kebschull JM, Zador AM. Nat Methods. 2018;15:871–879.

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Posted on 1 February 2023