Genome-wide methylation analyses identifies Non-coding RNA genes dysregulated in breast tumours that metastasise to the brain

Abstract

Brain metastases comprise 40% of all metastatic tumours and breast tumours are among the tumours that most commonly metastasise to the brain, the role that epigenetic gene dysregulation plays in this process is not well understood. We carried out 450 K methylation array analysis to investigate epigenetically dysregulated genes in breast to brain metastases (BBM) compared to normal breast tissues (BN) and primary breast tumours (BP). For this, we referenced 450 K methylation data for BBM tumours prepared in our laboratory with BN and BP from The Cancer Genome Atlas. Experimental validation on our initially identified genes, in an independent cohort of BP and in BBM and their originating primary breast tumours using Combined Bisulphite and Restriction Analysis (CoBRA) and Methylation Specific PCR identified three genes (RP11-713P17.4, MIR124-2, NUS1P3) that are hypermethylated and three genes (MIR3193, CTD-2023M8.1 and MTND6P4) that are hypomethylated in breast to brain metastases. In addition, methylation differences in candidate genes between BBM tumours and originating primary tumours shows dysregulation of DNA methylation occurs either at an early stage of tumour evolution (in the primary tumour) or at a later evolutionary stage (where the epigenetic change is only observed in the brain metastasis). Epigentic changes identified could also be found when analysing tumour free circulating DNA (tfcDNA) in patient’s serum taken during BBM biopsies. Epigenetic dysregulation of RP11-713P17.4, MIR3193, MTND6P4 are early events suggesting a potential use for these genes as prognostic markers.

Advances in Brain Metastases Diagnosis: Non-coding RNAs As Potential Biomarkers

“…This suggests using these microRNAs as possible biomarkers to differentiate between primary brain tumors and brain metastases [ 16 ]. Another study by Pangeni et al found that many deregulated non-protein-coding genes are associated with brain metastases [ 17 ]. They found three of these genes are hypermethylated (MIR124-2, RP11-713P17.4, NUS1P3), while the other three genes, including CTD-2023M8.1, MIR3193, and MTND6P4, are found to be hypomethylated in brain metastases compared to primary brain tumors [ 17 ].…”

“…Another study by Pangeni et al found that many deregulated non-protein-coding genes are associated with brain metastases [ 17 ]. They found three of these genes are hypermethylated (MIR124-2, RP11-713P17.4, NUS1P3), while the other three genes, including CTD-2023M8.1, MIR3193, and MTND6P4, are found to be hypomethylated in brain metastases compared to primary brain tumors [ 17 ]. This suggests that epigenetic regulation of the genes coding for ncRNAs can affect their expression, leading to altered levels and inducing tumor cell invasion, proliferation, and migration.…”

Liquid biopsies to occult brain metastasis

“…There was 100% concordance with the tissue status in miR124-2 and CTD-2028 M8 . However, CCDC8 showed 80%, and miR3193 had a 50% similar status [ 42 ]. Out of these genes miR124-2, CCDC8 were found to be hypermethylated, whereas miR3193 was hypomethylated.…”