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Table 1 Genes frequently methylated in breast to brain metastases. Twenty-one genes are frequently methylated in brain metastases (n = 15) of which 18 genes are also frequently methylated in primary breast tumours (n = 20). Three genes, CCDC8, BNC1 and GALNT9 (highlighted in grey), are infrequently methylated in primary breast tumours. These genes were further analysed in 20 primary breast samples (n = 40 in total) and 15 breast to brain metastases (n = 30 in total)

From: The GALNT9, BNC1 and CCDC8 genes are frequently epigenetically dysregulated in breast tumours that metastasise to the brain

Gene symbol Accession Gene name % of metastatic tumours methylated Function
CLDN18 NM_016369.3 Claudin 18 100 Intercellular adhesion molecule responsible for tight junction strand formation [77]
KRT85 NM_002283.3 Keratin 85 100 Component of intermediate filament in epithelial cells contributing to cell-cell adhesion [7880]
MIR127 NR_029696.1 microRNA 127 100 Regulator of cell proliferation and senescence [81]
MIR433 NR_029966.1 microRNA 433 100 Deregulated in gastric cancer, regulator of cell migration and drug response [82, 83]
HOXD3 NM_006898.4 HomeoboxD3 100 Proangiogenic transcription factor [84]
MIR23B NR_029664.1 microRNA 23b 92 Involved in cytoskeleton modelling, motility and metastasis [8588]
CCDC8 NM_032040.4 Coil coiled domain containing 8 73 Mutated in patients with 3 M syndrome [70]. Loss is associated with genomic instability and aneuploidy [75].
KRT83 NM_002282.3 Keratin 83 84 Component of intermediate filament, contributes to cell to cell adhesion [78, 80]
HOXB13 NM_006361.5 Homeobox B13 80 TSG for prostate cancer, inhibits androgen mediated signalling [89]
ABCB1 NM_000927.4 ATP-binding cassette sub-family B member 1 80 Controls efflux of substances across plasma membranes, associated with multidrug resistance [90]
PENK NM_006211.3 Proenkephalin 80 Promotes RNA splicing in osteoblasts and neural cells, plays role in bone development [91]
MST1R NM_002447.2 Macrophage stimulating 1 receptor 78 Involved in intracellular signalling cascades leading to cellular growth, motility and invasion [92]
BNC1 NM_001717.3 Basonuclin 1 71 Zink finger transcription factor, regulator of EMT [68]
PCDH8 NM_002590.3 Procadhern 8 73 Helps in cell to cell adhesion [93]
STAT3 NM_139276.2 Signal transducer and activator of transcription 3 67 Involved in embryonic stem cell regulation, somatic cell growth [9496]
BVES NM_007073.4 Blood vessel epicardial substance 64 Involved in inter-cellular interaction and cell adhesion [97]
TNFRSF10D NM_003840.4 Tumour Necrosis Factor receptor superfamily 10 D 60 Member of TNF (Tumour Necrosis Factor) receptor superfamily, promotes apoptosis in cancer cells [98]
CLDN6 NM_021195.4 Claudin 6 55 Intercellular adhesion molecules responsible for tight junction strand formation, its epigenetic silencing is associated with migration and invasiveness of breast cancer [77, 99]
HOXD10 NM_002148.3 Homeobox D10 55 Maintain epithelial cell plasticity and contributes to stability of extracellular matrix [100]
GALNT9 NM_001122636.1 N-acetyl galactosaminyl transferase 9 55 Catalyzes O-glycosylation [53, 101]
WIF1 NM_007191.4 Wnt inhibitory factor-1 gene 53 Inhibitor of Wnt-signalling [102, 103]