Aberrant interferon signaling may predict acquired resistance to CDK4/6 inhibitors in women with estrogen-receptor positive/HER2-negative and early breast cancers, according to the results of a gene expression study presented at the 2019 San Antonio Breast Cancer Symposium.

In particular, the researchers observed a correlation with palbociclib treatment and activation of the interferon pathway, suggesting a link to resistance.

Photo by © MedMeetingImages/Todd Buchanan 2018

Palbociclib, ribociclib and abemaciclib are frequently used to treat estrogen receptor-positive, HER2-negative breast cancers, and are currently under investigation for the treatment of early-stage breast cancers. However, de novo and acquired resistance to these CDK4/6 inhibitors can commonly occur.

To better understand the molecular underpinnings of resistance and to identify biomarkers, the researchers studied gene expression data from the Cancer Dependency Map and baseline tumor samples from neoadjuvant clinical trials.

Parental breast cancer cells (MCF7, T47D and ZR75-1) and their derivatives were made resistant to tamoxifen, estrogen deprivation and fulvestrant, then exposed to palbociclib to generate acquired resistance.

“IC50s were determined by exposing MCF7, T47D, and ZR75-1 P and EndoR lines (n=12) to increasing concentrations of [palbociclib],” the researchers noted. “Cell growth was assessed by methylene blue staining, and changes in the mRNA and protein levels of key cell cycle molecules were assessed by RT-PCR and Western blot, respectively.”

Results showed that treatment with palbociclib initiated a dose-dependent inhibition of growth in parental and endocrine-resistant breast cancer cell lines, with variable sensitivity. A comparison of the least sensitive and most sensitive cell lines (IC50>350nM vs. IC50>100) found that interferon gamma response and interferon alpha response were the top-ranked enriched signatures.

An analysis of 11 breast cancer cell lines further showed that cells with low CDK4 dependency had high interferon signaling.

Based on these data, the researchers created a 35-gene signature (interferon-related, palbociclib resistance signature; IRPS) made up of interferon gamma and interferon alpha genes that showed a positive correlation with palbociclib IC50 values.

A further investigation of two early breast cancer trials found that interferon alpha, interferon gamma and IRPS signatures were highly enriched in CDK4/6-resistance tumors. Based on these findings, the researchers investigated molecular changes to resistant cell lines.

“Compared to the untreated cells, the [resistance] models commonly displayed alterations in several components of the cyclin D-CDK4/6-Rb axis, including elevated expression of cyclin-D1, -E1, and CDK6, and reduced levels of Rb,” they noted. “Notably, the [resistance] derivatives commonly displayed a dramatic activation of interferon/STAT1-signaling compared to their short-term treated or untreated counterparts.”

The researchers observed higher IRPS scores in women with luminal B subtypes, when compared with luminal A subtypes, as well as correlations with increased expression of immune checkpoints, endocrine resistance and worsened prognosis.

“Future studies are warranted to provide mechanistic insights into the association of interferon-signaling with response to CDK4/6 inhibitors,” the researchers concluded.