Royal College of Surgeons in Ireland
Thesis Michael Flanagan revised.pdf (5.21 MB)

Alterations in ER Signalling and DNA Methylation Following Neoadjuvant Treatment in HER2 Positive Breast Cancer

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posted on 2022-07-22, 15:03 authored by Michael FlanaganMichael Flanagan

Up to 40% of patients with oestrogen receptor-positive (ER+) breast cancer develop resistance to endocrine treatment, leading to progression of disease. Altered receptor status occurs throughout tumour progression and may be influenced by adjuvant and neoadjuvant therapies. Therapeutic pressure functionally affects oncogenes and related signalling pathways through transcriptional and epigenetic alterations. Previous work from our group observed loss of ESR1 gene expression and corresponding gain in tyrosine kinase signalling from gene expression profiling of 21 primary breast tumours with matched metastases. We hypothesise that oestrogen/ER signalling in primary breast cancer regulates differential gene expression through coordinated inhibition of DNA methylation and that in the setting of tyrosine kinase inhibition, an increase in ER signalling is observed. Our aim is to elucidate the mechanism by which oestrogen/ER regulates gene expression and evaluate changes in the DNA methylation landscape following tyrosine kinase inhibition.

We investigated ESR1 expression in response to oestrogen treatment and HER2 inhibition using trastuzumab in an ER+ and ER- breast cancer cells and in ER+ breast cancer brain metastatic cells. Patients enrolled on clinical trial NCT01840293 with histologically confirmed HER2-overexpressing or HER2 amplified, invasive breast cancer who received neoadjuvant trastuzumab, either alone or in combination with neoadjuvant systemic chemotherapy were identified. Using the Illumina Infinium Human MethylationEPIC BeadChip Array, we performed a genome-wide analysis of DNA methylation in a cohort of nine neo-adjuvant treated patients.

In endocrine sensitive and endocrine resistant cells lines ESR1 expression increased in response to HER2 inhibition, although this response did not reach statistical significance. A gain in mean ER staining percentage positivity was observed in the residual disease post neoadjuvant trastuzumab compared to diagnostic biopsy. This was associated with a corresponding hypomethylation of ESR1. Hypomethylation of ESR1 and clinical gain in ER positivity were observed following tyrosine kinase inhibition. An inverse correlation was observed with loss of HER2 positivity. The mechanism of ER/HER2 crosstalk may in part be regulated through DNA methylation.


RCSI (via Star MD program)


First Supervisor

Prof. L Young

Second Supervisor

Prof. A Hill


Submitted for the degree of Doctor of Medicine to the Royal College of Surgeons in Ireland, 2022

Published Citation

Flanagan M,. Alterations in ER Signalling and DNA Methylation Following Neoadjuvant Treatment in HER2 Positive Breast Cancer [MD Thesis] Dublin: Royal College of Surgeons in Ireland; 2022

Degree Name

  • Doctor of Medicine (MD)

Date of award



  • Doctor of Medicine (MD)

Research Area

  • Cancer

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