Abstract P4-06-05: Heterogeneity of DCIS does not appear to be a biomarker for development of subsequent invasive cancer
Authors: Anargyros Megalios, Vandna Shah, Rana Shami, Salpie Nowinski, Jelmar Quist, Mathini Sridharan, Carolina Salinas de Souza, Karen Clements, Anita Grigoriadis, Sarah Pinder, Alastair Thompson, Elinor Sawyer
Journal: Cancer Research (2020)

Abstract Genomic instability is a key feature of carcinogenesis, giving rise to tumour promoting aberrations. The inherent unpredictability of these processes leads to a high degree of intratumour heterogeneity, previously shown to be advantageous for cancer progression in a series of cancer types. We sought to explore the role of genomic instability and intratumour heterogeneity in the progression of ductal carcinoma in situ (DCIS) to invasive disease, in a cohort of 49 women with pure DCIS that developed subsequent ipsilateral invasive disease and 90 women with pure DCIS with no evidence of recurrence with a median follow up of 5.4 years. All samples were identified from within the Sloane project, a prospective national cohort study of DCIS within the UK National Health Service Breast Screening Programme. DNA extracted from bulk tissue samples was processed on the HumanCytoSNP array, and allele-specific copy number aberration (CNA) data was obtained from ASCAT. We measured genomic instability using Scores Of Chromosomal Instability Scarring (SCINS), as well as by calculating the Shannon diversity index for the different copy number states occurring in the tumour genome. We also attempted to deconvolute the clonal structure of the tumours by applying the Shannon diversity index on the raw copy number estimates provided by ASCAT. Non-integer copy number states were interpreted as indicative of the presence of subclonal CNAs. As a positive control, we compared ER+ and ER- DCIS in a larger cohort of 173 DCIS samples (129 ER+ and 44 ER-), using the same methods. We expect ER- tumours to be more genomically unstable, and consequentially more clonally diverse. Measured using SCINS, both copy-neutral loss of heterozygosity (≥ 4 Mbp) and allelic-imbalanced CNAs (≥ 8 Mbp) were shown to be higher in ER- tumours (Fisher’s exact test, p = 0.014 and p = 0.034, respectively). Overall genomic instability was also shown to be higher in ER- tumours using the Shannon diversity index (Fisher’s exact test, p = 0.0085). Our attempt at clonal structure deconvolution also indicates increased heterogeneity in ER- tumours (Fisher’s exact test, p = 0.027). However, no significant difference was identified in the genomic instability or heterogeneity of DCIS that developed subsequent invasive disease compared to that of indolent DCIS, using any of the aforementioned measures. We were therefore unable to identify evidence of a direct link between DCIS heterogeneity and progression to invasive cancer. Our methods did, however, demonstrate that DCIS in general is highly genomically diverse, with ER- tumours exhibiting increased diversity compared to ER+ ones. We aim to validate these findings using spatial sampling data from our cohort, as well as integrating mutation data to allow the use of established clonal heterogeneity deconvolution pipelines. Citation Format: Anargyros Megalios, Vandna Shah, Rana Shami, Salpie Nowinski, Jelmar Quist, Mathini Sridharan, Carolina Salinas de Souza, Karen Clements, Anita Grigoriadis, Sarah Pinder, Alastair Thompson, Elinor Sawyer. Heterogeneity of DCIS does not appear to be a biomarker for development of subsequent invasive cancer [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P4-06-05.