Tumour mutation burden in oestrogen receptor positive breast cancer

Conor Friend McGuinness

Immune checkpoint blockade (ICB) is a cancer therapy that is based on promoting an antitumour immune response. Tumour mutation burden (TMB) is an effective biomarker for ICB response, due to the increased likelihood of immune “recognition” of high TMB tumours. Response rates to ICB are low in oestrogen receptor positive (ER+) breast cancer, potentially due to the low TMB of this subtype. Some ER+ tumours, however, exhibit a high TMB, due to the action of apolipoprotein B mRNA-editing enzyme, catalytic polypeptide (APOBEC) enzymes. This research was undertaken to investigate the feasibility of TMB as a potential biomarker for ICB response in ER+ breast cancer. Clinicians and researchers wishing to estimate TMB and perform mutation signature analysis to identify patients that are likely to respond to ICB are limited to either using whole genome sequencing methodologies, or using cancer gene panels to estimate TMB. These options may pose problems in terms of cost and accuracy, warranting investigation into alternative methodologies to estimate TMB. It was hypothesised that restriction enzyme associated DNA sequencing (RADseq), could be a cheaper, more accurate alternative for TMB estimation and mutation signature analysis. Using in silico generated libraries based on available breast cancer mutation data, it was determined that RADseq libraries provide more accurate estimates of both mutation profile recapitulation and TMB estimation compared to a widely used cancer gene panel. Using simulations of ICB trials, it was demonstrated that the use of cancer gene panels to estimate TMB may reduce the power of determining associations between TMB and ICB. It was also determined that prioritising inclusion of APOBEC hypermutated tumours in ICB trials would increase the power of such studies. The SSM3 cell line is a murine ER+ breast cancer cell line that can be injected into immunocompetent mice. Due to the lack of suitable preclinical models for high TMB ER+ breast cancer, a method to generate high TMB SSM3 clones was developed, using RADseq to evaluate the success of genomic editing in this methodology. This will allow for future researchers to examine cancer- immune interactions in high TMB ER+ breast cancer. A polymorphism that results in deletion of the APOBEC3B gene results in increased APOBEC mutagenesis in ER+ breast cancer. APOBEC3B-AS1, herein referred to as ALBEX1, was hypothesised to regulate the expression of APOBEC3 genes, and to play a role in the APOBEC deletion polymorphism association. Expression of this transcript was found in scRNAseq data derived from both pluripotent and luminal progenitor cells. A model by which APOBEC mutagenesis occurs in luminal progenitors was thus proposed. Some ER+ breast cancers have a high TMB, especially tumours in carriers of the APOBEC deletion polymorphism. The results of this thesis imply that a subset of ER+ breast cancer may derive benefit from ICB, warranting further investigation into this association. Ultimately the findings of this research may lead to improved treatment options for a subset of ER+ breast cancer patients.

Tumour mutation burden in oestrogen receptor positive breast cancer

(1)