Molecular changes during extended neoadjuvant letrozole treatment of breast cancer: distinguishing acquired resistance from dormant tumours

Abstract

BackgroundThe risk of recurrence for endocrine-treated breast cancer patients persists for many years or even decades following surgery and apparently successful adjuvant therapy. This period of dormancy and acquired resistance is inherently difficult to investigate, previous efforts have been limited to in vitro or in vivo approaches. In this study, sequential tumour samples from patients receiving extended neoadjuvant endocrine treatment were characterised as a novel clinical model.MethodsConsecutive tumour samples from 62 patients undergoing extended (4-45 months) neoadjuvant aromatase inhibitor, letrozole, therapy were subjected to transcriptomic and proteomic analysis, representing before (≤0), early-on (13-120 days) and long-term (>120 days) neoadjuvant letrozole treatment. Patients with at least a 40% initial reduction in tumour size by 4 months of treatment were included. Of these, 42 patients with no subsequent progression were classified as “dormant”, and the remaining 20 patients as “acquired resistant”.ResultsChanges in gene expression in dormant tumours begin early and become more pronounced at later timepoints. Therapy-induced changes in resistant tumours were common features of treatment, rather than being specific to resistant phenotype. Comparative analysis of long-term treated dormant and resistant tumours highlighted changes in epigenetics pathways including DNA methylation and histone acetylation. DNA methylation marks 5-methylcytosine and 5-hydroxymethylcytosine were significantly reduced in resistant tumours compared to dormant tissues after extended letrozole treatment.ConclusionsThis is the first patient-matched gene expression study investigating long-term aromatase inhibitor-induced dormancy and acquired resistance in breast cancer. Dormant tumours continue to change during treatment whereas acquired resistant tumours more closely resemble their diagnostic samples. Global loss of DNA methylation was observed in resistant tumours under extended treatment. Epigenetic alterations may lead to escape from dormancy and drive acquired resistance in a subset of patients supporting a potential role for therapy targeted at these epigenetic alterations in the management of endocrine resistant breast cancer.

G9a Promotes Breast Cancer Recurrence Through Repression of a Pro-inflammatory Program

“…Patient data also support the role of epigenetic 17 dysregulation in breast cancer recurrence. Global histone lysine hypoacetylation and DNA hypomethylation 18 are associated with poor prognosis in breast cancer (Elsheikh et al, 2009;Selli et al, 2019;Suzuki et al, 2009), 19 and transcriptional reprogramming is a hallmark of chemoresistant recurrent breast tumors (Yates et al, 2017). 20…”

Neoadjuvant Therapy for Breast Cancer as a Model for Translational Research

“…Using this novel clinical model, we have identified extended (>4 months) letrozole-treatment-induced changes in dormant and resistant tumours by comparing pre- and on-treatment samples. 41,42 Some of the identified pathways were dormancy-related such as cell cycle arrest and senescence with established roles in metastasis dormancy, 43 further supporting the relevance of extended neoadjuvant therapy as a clinical model.…”

“…These patients continue to receive neoadjuvant endocrine therapy for longer duration, and we have suggested that these tumours represent a unique circumstance, which can be used to study how tumours respond to extended oestrogen deprivation in situ. 41,42 Tumours that initially shrink in size and continue to respond to neoadjuvant therapy model dormancy, whereas those that subsequently begin to regrow under neoadjuvant treatment, represent acquired resistance (Figure 1C).…”

Increased Expression of Interleukin-1 Receptor Characterizes Anti-estrogen-Resistant ALDH+ Breast Cancer Stem Cells

“…Interestingly, only 10% of the non-treated ALDH + cells belonged to the quiescent population B; however, following tamoxifen and fulvestrant treatment the percentage of quiescent cells represented 44% and 19% of the total cells, respectively (Figure 4F). A recent study (Selli et al, 2019) investigated gene expression changes of dormant and acquired resistant ER + tumors treated with an AI for more than 4 months. Notably, ALDH1A1 and ALDH1A3 gene expression levels were significantly increased in dormant tumors compared with acquired resistant tumors, which supports the existence of an ALDH + dormant population after AE treatment (Figure 4G).…”