Biomarkers associated with resistance or response to CDK46 treatment in patients with metastatic hormone‐receptive positive breast cancer


Janice Mullins, AminaChaudhry, Kelsey Poorman Harsha Ranganath, Julie Ryder, AmitJain, Felicia Hare, Poojitha Valasareddy, Michelle Saul, Gregory Vidal


CDK4/6 inhibitor (CDKi) drugs are the current standard of care for treatment of first and second‐line hormone‐receptor positive/HER2 negative (HR+/HER2‐) metastatic breast cancers. To date, no biomarker of response has been identified. Treatment induced RB1 mutations were noted as mechanism of resistance to palbociclib and fulvestrant in about 5% of patients treated on PALOMA3 trials, whereas PI3K and ESR1 mutations emerged as potential resistance to the anti‐hormonal backbone1. Additionally, FGFR1 amplification has been suggested as a resistance pathway to fulvestrant and ribociclib2. Utilizing next‐gen sequencing (NGS), chromogenic in situ hybridization (CISH) and immunohistochemistry (IHC) (Caris Life Sciences, Phoenix, AZ) data from n=155 HR+/HER2‐ patients treated at the University of Tennessee West Cancer Center, we attempted to retrospectively identify a molecular signature of resistance or response as measured by PFS.


Specimens were profiled using massively parallel NGS sequencing using either a 45‐gene TruSeq Amplicon panel (n=) or a 592‐gene SureSelect XT panel (Agilent, Santa Clara, CA). Sequencing was performed on an Illumina MiSeq or NextSeq instrument for the 45‐ and 592‐gene panels respectively (Illumina, San Diego, CA). Only alterations with known pathogenic potential were considered aberrant. Copy number alterations (CNA) were also explored on samples profiled with the 592‐gene NGS panel. Gains ≥6 copies were considered amplified.

All IHC stains were performed using automated platforms (Benchmark, Ventana Medical Systems and DAKO Autostainer, Agilent) at CLIA/CAP/ISO15189/NYSDOH certified clinical laboratory (Caris Life Sciences, Phoenix, AZ). PD‐L1 expression was evaluated in the tumor cells (TC) using SP142 (Ventana).


  • NSD3 gene amplification appears to be the only alteration that may significantly affect tumor CDK4/6 response. NSD3 gene is a member of DNA‐methyltransferase pathway and highly correlated with ESR1 and ER.
  • Three biomarkers, RB1, CDH1, TML>17 mutations are significantly more frequent in post‐palbociclib biopsies.
  • FGFR1 does not appear to play a clinical role in our population.
  • RB1 mutations are present post treatment, but are infrequent.
  • ESR1, PI3K, ARID1A are numerically more frequently seen in post treatment biopsies.
  • TP53 mutation represents poor prognosis regardless of line of therapy or treatment option.
  • This study is limited by its retrospective nature and relatively small numbers. Further testing will be required to confirm the relationships observed.

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