DNA methylation analyses of urothelial carcinoma reveal distinct epigenetic subtypes and an association between gene copy number and methylation status.
We assessed DNA methylation and copy number status of 27,000 CpGs in 149 urothelial carcinomas and integrated the findings with gene expression and mutation data. Methylation was associated with gene expression for 1,332 CpGs, of which 26% showed positive correlation with expression, i.e., high methylation and high gene expression levels. These positively correlated CpGs were part of specific transcription factor binding sites, such as sites for MYC and CREBP1, or located in gene bodies. Furthermore, we found genes with copy number gains, low expression and high methylation levels, revealing an association between methylation and copy number levels. This phenomenon was typically observed for developmental genes, such as HOX genes, and tumor suppressor genes. In contrast, we also identified genes with copy number gains, high expression and low methylation levels. This was for instance observed for some keratin genes. Tumor cases could be grouped into four subgroups, termed epitypes, by their DNA methylation profiles. One epitype was influenced by the presence of infiltrating immune cells, two epitypes were mainly composed of non-muscle invasive tumors, and the remaining epitype of muscle invasive tumors. The polycomb complex protein EZH2 that blocks differentiation in embryonic stem cells showed increased expression both at the mRNA and protein levels in the muscle invasive epitype, together with methylation of polycomb target genes and HOX genes. Our data highlights HOX gene silencing and EZH2 expression as mechanisms to promote a more undifferentiated and aggressive state in UC.
Department of Oncology, Clinical Sciences, Skåne University Hospital, Lund University, Lund, Sweden.
Martin
M
Lauss
Mattias
M
Aine
Gottfrid
G
Sjödahl
Srinivas
S
Veerla
Oliver
O
Patschan
Sigurdur
S
Gudjonsson
Gunilla
G
Chebil
Kristina
K
Lövgren
Mårten
M
Fernö
Wiking
W
Månsson
Fredrik
F
Liedberg
Markus
M
Ringnér
David
D
Lindgren
Mattias
M
Höglund
D051698:Activating Transcription Factor 2 / Q000235:genetics; D002277:Carcinoma / Q000235:genetics*; D018899:CpG Islands; D019175:DNA Methylation; D000071221:Enhancer of Zeste Homolog 2 Protein; D044127:Epigenesis, Genetic; D018628:Gene Dosage; D005801:Genes, Homeobox; D016147:Genes, Tumor Suppressor; D016259:Genes, myc; D006801:Humans; D063151:Polycomb Repressive Complex 2 / Q000235:genetics; D001749:Urinary Bladder Neoplasms / Q000235:genetics*; D019459:Urothelium
C497105:ATF2 protein, human; D051698:Activating Transcription Factor 2; C498409:EZH2 protein, human; D000071221:Enhancer of Zeste Homolog 2 Protein; D063151:Polycomb Repressive Complex 2