Abstract P3-07-04: Molecular characterization of mucinous breast cancers
Authors: Desmedt C , Veys I , Nguyen B , Leduc S , Bareche Y , Majjaj S , Boeckx B , Lambrechts D , Sotiriou C 
Published: May 2019

Abstract
Introduction
Mucinous carcinoma, a special histological subtype of breast cancer (BC) which accounts for ˜2% of all invasive breast tumors, is characterized by the presence of extracellular mucin, typically expresses the estrogen receptor (ER), and lacks HER2 amplification. The majority of patients with mucinous BC are older at diagnosis, rarely present axillary lymph node metastases, and are associated with a better prognosis as compared to invasive ductal cancer patients (IDC, formally referred to as “breast cancer of no special type”). So far, it is unknown what is driving the mucinous phenotype of these tumors. Here we interrogated the genomics, transcriptomics, immune infiltration and epigenetics profiles of these tumors, using a retrospective institutional series and a publicly available dataset.
Patients and methods
After central pathology review and DNA extraction, a total of 31 pure mucinous cases from Institut J. Bordet Biobank were included (referred to as IJB cohort). Tumor infiltrating lymphocytes (TILs) were assessed on hematoxylin and eosin (H&E). Low pass whole genome sequencing was conducted to assess ploidy and to detect copy number aberrations (CNAs). A second cohort was analyzed from a publicly available dataset (referred to as BRCA560 cohort), with available centrally reviewed histology subtyping and DNA methylation profiles (Nik-Zainal et al. Nature 2016). 207 ER+ primary BC, 14 of which were mucinous, had HumanMethylation450K methylation profiles. RNAseq was available for a subset of 145 cancers, 13 of which were mucinous. DNA methylation data was processed in R using the minfi package. Beta-values were normalized (preprocessQuantile) and dmpFinder was used to identify differentially methylated positions.
Results
In the IJB cohort, whole genome sequencing revealed that all but two tumors were diploid. The most frequently deleted cancer genes were RB1 (38,1%), CDH1 (23,8%), BRCA2 (38,1%),TP53 (23,8%), MAP2K4 (23,8%), EGFR (28,6%) and PGR (23,8%). In terms of amplifications, only ZNF217 (19,4%) and FGFR1/ZNF703 (9,5%) were observed. These mucinous tumors generally displayed low TIL levels (median=5%). In the BRCA560 cohort, there was no significant difference in the clinico-pathological features of ER+ IDC vs mucinous subtypes. At the genomic level, we identified a lower frequency of PIK3CA mutations as compared to ER+ IDC from the same cohort. At the DNA methylation level, we identified 8013 differentially methylated CpGs (q-val &lt; .05) between IDC and mucinous tumors. The top differentially methylated CpG mapped to MUC2, an extracellular mucin. MUC2 was significantly demethylated in mucinous tumors as compared to IDC (q-val &lt;.001). There was a negative association between methylation level of this CpG and MUC2 expression (rho = - 0.27, p&lt; .001). Finally, MUC2 expression was significantly increased in mucinous tumors as compared to IDC (p&lt; .001).
Conclusion
To the best of our knowledge, this study is the first to report hypomethylation of MUC2 in mucinous carcinoma of the breast, as a possible mechanism of extracellular production of mucin in these tumors. Furthermore, it highlights the minor immune infiltration of these cancers, possibly prevented by the mucin, and sheds light on the few genomic alterations present in these overall stable cancer genomes.
Citation Format: Desmedt C, Veys I, Nguyen B, Leduc S, Bareche Y, Majjaj S, Boeckx B, Lambrechts D, Sotiriou C. Molecular characterization of mucinous breast cancers [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-07-04.