Breast cancer is the second most common cancer in Australia. Over the past several decades the implementation of population-based screening, identifying risk factors and new treatments has improved outcomes for patients. Nevertheless, incidence is increasing, especially for pre-cancerous lesions such as Ductal carcinoma in situ (DCIS) or Atypical Ductal Hyperplasia (ADH). However, increased detection and treatment of these putative precursor lesions has not resulted in decreased rates of invasive cancer. This suggests not all precursor lesions would progress and highlights the limitations in our knowledge of early stages of breast cancer progression.
Whilst limited molecular profiling exists, the precursor lesions have been shown to already harbour oncogenic driver mutations and similar transcriptional profiles to more advanced disease. This indicates an potential role for the local tumour microenvironment in cancer development and progression. To determine if this is the case our study comprehensively analyses and correlates the genomic, transcriptomic and immune-spatial profile of early lesions. We hypothesise that there are genomic and transcriptomic changes that occur within early breast lesions and that drive cancer initiation and influence the local immune microenvironment.
We have established a cohort of formalin-fixed paraffin-embedded samples from human normal breast (reduction mammoplasties) and several pre-cancerous lesions (ADH, low, and high nuclear-grade DCIS). For each sample two OPAL multiplex immunohistochemistry panels are run on sequential sections identifying lymphoid (CD3, CD4, CD8 and CD20), and myeloid (CD68, CD163, CD206, CD11c) populations. These were integrated and analysed using the HALO AI platform and R package SPIAT to investigate the proportion, distribution and spatial relationships of different immune cell populations. To define the molecular changes in the early lesions we manually dissected the epithelial lesions and surrounding stroma, extracted nucleic acids and performed RNAseq and Whole Genome Sequencing.
With our integrated analysis we are beginning to produce a detailed portrait of the molecular underpinnings of breast cancer initiation and its relationship with the local microenvironment. Our work will inform how the developing breast lesions interact with their microenvironment and may help to identify prognostic biomarkers of more aggressive lesions to aid in clinical detection and management.