Abstract PD15-03: Overlapping molecular features (proliferation, immune signatures andTP53mutations) associated with palbociclib resistance inER+HER2- primary breast cancer
Authors: Schuster Eugene F , Xiao Hui , Cheang Maggie , Lopez-Knowles Elena , Kilburn Lucy , Korchina Viktoriya , Salvi Sejal , Jacobs Samuel A , Finnigan Melanie , Wheeler David A , Puhalla Shannon , Muzny Donna , Doddapaneni Harsha , Pogue-Geile Katherine , Liu Yuan , Bliss Judith , Johnston Stephen , Dowsett Mitch , Rimawi Mothaffar ,   On behalf of the PALLET Trialists
Published: March 2022

Abstract
Background: Cyclin-dependent kinase 4/6 (CDK4/6) inhibitors in combination with anti-hormone therapy are highly effective treatments for oestrogen receptor positive (ER+) and HER2 negative (HER2-) advanced breast cancer. Pre-clinical and clinical studies have reported mechanisms of resistance to CDK4/6 inhibitors to include interferon signalling, high CCNE1 expression and loss of RB1 expression. The PALLET phase II randomized neoadjuvant trial of letrozole (LET) ± palbociclib (PALBO) in postmenopausal ER+HER2- primary breast cancer showed that suppression of proliferation as measured by Ki67 was significantly greater with addition of PALBO to LET but did not result in all patients achieving complete cell-cycle arrest, indicating intrinsic resistance in some patients. We report phenotypes/genotypes associated with that resistance. Methods: In the PALLET trial, 307 patients were randomized to LET+PALBO (n=204) or LET (n=103) for 14wks. For the first 2wks of LET+PALBO patients were randomised to LET, PALBO or LET+PALBO. RNA-seq of baseline samples from consented patients was performed on fresh frozen biopsies for 224 patients (LET-only n=77; LET+PALBO n=147); whole exome sequencing was performed on 188 tumors and matched blood samples (LET-only n=61; LET+PALBO n=127). After 14wks of treatment, those patients with Ki67% &lt; 2.7% were classified as having complete cell-cycle arrest (CCCA). Differentially expressed genes (DEGs) were identified between patients sensitive (CCCA) and resistant (non-CCCA) to treatments with or without PALBO at 14wks by DESeq2. Mutect2 and VarScan was used to identify somatic mutations and CNVkit was used to identify copy number alterations in whole exome sequencing (WES). Results: In LET+PALBO treated patients, higher expression of E2F targets, interferon gamma response and mTORC1 signalling genes were observed in baseline gene expression of non-CCCA patients at 14wks (FDR&lt;0.05, GSEA). Similar results were also observed if using 2wk Ki67 data. In LET-only non-CCCA patients, higher expression of mTORC1 signalling and lower expression of oestrogen response genes (FDR&lt;0.05, GSEA) were observed. Additional analysis of baseline gene expression for non-CCCA at 14wks LET+PALBO patients showed higher expression of immune checkpoint inhibition associated genes including IFNG, IDO1, PD-L1 (FDR&lt;0.05, DESeq2), higher expression of genes expressed only in immune cells and two gene signatures related to interferon signalling and immune checkpoint blockade (FDR&lt;0.05, GSEA). Somatic mutation analysis showed a trend for enrichment of mutations in TP53 for both LET-only and LET+PALBO non-CCCA patients (p=0.02 and p=0.06, respectively, Fisher-exact) and significant enrichment of MAP3K1 mutations in LET-only CCCA patients (p&lt;0.05, Fisher-exact). TP53 mutations were also associated with higher proliferation, mTORC1 and immune related signatures (all p&lt;0.01, Mann-Whitney). Change at 14wks Ki67 was significantly different (p=0.02, Mann-Whitney) between TP53wt and TP53MUT for LET-only patients (median WT = -92%, MUT = -66%, p=0.02, Mann-Whitney ) but not for LET+PALBO (median WT = -99% MUT = -95%, p=0.13, Mann-Whitney). No copy number alterations were significantly enriched in LET+PALBO non-CCCA patients. Conclusion: We observe, confirming previous studies, an association of CDK4/6 inhibitor resistance, high expression of CCNE1 and genes related to interferon gamma signalling. We show that there is an overlap between resistance mechanisms and TP53 mutations. However, ER+HER2- patients with TP53 mutations may still benefit from PALBO adding to suppression of proliferation compared to LET-only treatment.
Citation Format: Eugene F Schuster, Hui Xiao, Maggie Cheang, Elena Lopez-Knowles, Lucy Kilburn, Viktoriya Korchina, Sejal Salvi, Samuel A Jacobs, Melanie Finnigan, David A Wheeler, Shannon Puhalla, Donna Muzny, Harsha Doddapaneni, Katherine Pogue-Geile, Yuan Liu, Judith Bliss, Stephen Johnston, Mitch Dowsett, Mothaffar Rimawi, On behalf of the PALLET Trialists. Overlapping molecular features (proliferation, immune signatures andTP53mutations) associated with palbociclib resistance inER+HER2- primary breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr PD15-03.