Abstract P1-04-04: DNA methylation landscapes of breast cancer progression to brain metastasis: A pre-clinical study
Authors: Orozco JIJ , Bustos MA , Nelson N , Hsu SC , Cheung G , Bostick PJ , Lucci A , DiNome M , Kelly DF , Hoon DSB , Marzese DM 
Published: March 2017

Due to improvements in overall survival rates, breast cancer brain metastasis (BCBM) is a major life-limiting condition with rising incidence. The molecular mechanisms involved in breast cancer (BC) progression to brain metastasis are still poorly understood. We have demonstrated that DNA methylation, a key epigenetic regulatory mechanism, is involved in BC progression to metastatic disease. Here, we characterized the BCBM DNA methylation landscapes according to their molecular subtypes. Methods: This study included 22 BCBM specimens from 19 patients (ER+/PgR+/HER2-(n=6), HER2+(n=7), and ER-/PgR-/HER2-(TNBC; n=6)) and primary BC specimens with paired molecular subtypes. After microdissection, we generated genome-wide DNA methylomes using HM450K BeadChips. Results: Multidimensional scaling revealed that DNA methylation patterns specifically clustered BCBMs according to their respective molecular subtypes. Additionally, we observed that while ER+/PgR+/HER2- BCBM showed a significant global hypermethylation, HER2+ and TNBC BCBMs presented a significant global hypomethylation compared to the respective primary BC specimens. Hypermethylation on ER+/PgR+/HER2- BCBMs mainly affected CpG islands and was significantly enriched in regions overlapping tumor-related genes, such as APC2, CREB3L1, and GLI3; and a large number of developmental genes, including HOXA9, HOXA10, HOXB13, and PAX6 (Table1). On the other hand, hypomethylation on HER2+ and TNBC BCBMs significantly overlapped with conserved intergenic cis regulatory elements. Two significantly affected regions included enhancer elements associated with NEUROD1, a neurogenic differentiation factor, and MYT1L, a Pan-neural transcription factor associated with neuronal differentiation, suggesting an acquisition of brain-like properties (Table2). Conclusions: Our study suggests a significant role of DNA methylation reprogramming during BC progression to brain metastasis and describes the existence of molecular subtype-specific DNA methylomes. Altogether, this data offers new insight into the complexity of this clinical complication.

Table1: Hypermethylated CpG sites in ER+/PgR+/HER2- BCBMChrStartGeneCpG ContextDiff. MethFDR P-val1746802888HOXB13Island0.824.6E-061656666575MT1MIsland0.813.7E-101685160569IntergenicShelf0.773.7E-17742277807GLI3Island0.738.7E-0567728888BMP6Island0.713.1E-051811149470FAM38BIsland0.703.4E-081146317577CREB3L1Shore0.705.3E-17191467979APC2Island0.693.0E-05727213984HOXA10Island0.697.5E-061131826421PAX6Island0.677.4E-06727205381HOXA9Island0.651.7E-061396204854CLDN10Island0.642.1E-042176956678HOXD13Island0.632.3E-04

Table2: Hypomethylated CpG sites in HER2+ and TNBC BCBMsChrStartGeneCpG ContextDiff. Meth.FDR P-val1746619555IntergenicShore-0.583.2E-042182543233NEUROD1OpenSea-0.566.9E-0312132900938GALNT9Island-0.562.1E-051391827042IntergenicShore-0.558.7E-051746618614IntergenicShore-0.551.4E-0522119853MYT1LOpenSea-0.532.5E-041156623074BCANOpenSea-0.532.1E-0310128275008IntergenicOpenSea-0.521.6E-04480885981ANTXR2Island-0.515.2E-037157280331IntergenicShelf-0.516.9E-032059832924CDH4Shelf-0.512.7E-0241407858IntergenicIsland-0.513.7E-03592925721NR2F1Shore-0.513.1E-08

Citation Format: Orozco JIJ, Bustos MA, Nelson N, Hsu SC, Cheung G, Bostick PJ, Lucci A, DiNome M, Kelly DF, Hoon DSB, Marzese DM. DNA methylation landscapes of breast cancer progression to brain metastasis: A pre-clinical study [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-04-04.