Oral Presentation NSW State Cancer Conference 2023

Identification of differential DNA methylation in phyllodes tumours establishes a signature of malignancy and delineates from metaplastic breast carcinoma (#34)

Braydon Meyer 1 2 , Clare Stirzaker 1 2 , Sonny Ramkomuth 1 , Kate Harvey 1 , Alex Swarbrick 1 2 , Susan J. Clark 1 2 , Sandra O'Toole 1 2 3 , Ruth Pidsley 1 2
  1. Garvan Institute of Medical Research, Sydney, NSW, Australia
  2. St Vincent's Clinical School, UNSW, Sydney, NSW, Australia
  3. Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia

Background: Phyllodes tumours (PTs) are rare, fibroepithelial lesions that account for less than 1% of all breast cancers. The Singapore General Hospital classifies PTs as benign, borderline, or malignant, based on histopathological features such as increased cellularity, atypia, mitotic activity and metastatic potential. Majority of patients present with the easily treatable benign PT, however ~25% of patients present with a malignant PT which have poor long-term prognosis[1]. However, a lack of understanding of PT biology makes it difficult to accurately categorise PTs, particularly when differentiating between borderline and malignant, presenting a clinical problem regarding how to accurately treat these patients. PTs also present other clinical challenges, with benign PTs being misdiagnosed as fibroadenoma[2], while malignant PTs are difficult to distinguish from spindle-cell metaplastic breast cancer. Given that epigenetic alterations – specifically DNA methylation – is initiated early in tumorigenesis and has been recognised as a hallmark of cancer, methylation profiling in phyllodes tumours could potentially aid in answering these clinical challenges.

Aims: We aim to characterise the DNA methylation landscape of PTs and identify biomarkers that can improve classification of PT disease risk as well as delineate fibroadenoma and metaplastic breast cancer from phyllodes tumours.

Methods: We performed methylome profiling using the MethylationEPIC array on primary PT patient biopsies (n=29). We compared a combined group of benign and borderline PT samples against malignant samples to find malignant-associated differentially methylated regions (DMRs). Samples were also compared to multiple related cancer types (n=529) to better define the methylation landscape of PTs and matched sample scRNA-seq was performed to interrogate functional significance of these methylation changes.

Results: We discovered differential methylation that defines PTs from other cancers such as breast cancer and sarcoma. We also identified loci that distinguish benign PTs from fibroadenomas, and malignant PTs from metaplastic breast cancer, and use this to distinguish misdiagnosed PTs in the TCGA breast cancer dataset. Finally, we identified DMRs (adj.P<0.05) delineating malignant PTs from non-malignant samples and validated these findings in an independent cohort.

Conclusion: Our study is the first detailed characterisation of the PT methylome. We have identified methylation signatures associated with aetiology, risk stratification, and misdiagnosis; all of which have potential to better inform clinical decision making.

  1. 1. Chng TW, Gudi M, Lim SH, Li H, Tan PH. Validation of the Singapore nomogram for outcome prediction in breast phyllodes tumours in a large patient cohort. J Clin Pathol. 2018;71(2):125-8.
  2. 2. Huang KT, Dobrovic A, Yan M, Karim RZ, Lee CS, Lakhani SR, et al. DNA methylation profiling of phyllodes and fibroadenoma tumours of the breast. Breast cancer research and treatment. 2010;124(2):555-65.