Journal article
CAUSEL: an epigenome- and genome-editing pipeline for establishing function of noncoding GWAS variants
Dana-Farber Cancer Institute1
Hungarian University of Agriculture and Life Sciences2
University of Southern California3
Massachusetts General Hospital4
Eotvos Lorand University5
Xiamen University6
Boston Children's Hospital7
Department of Systems Biology, Technical University of Denmark8
Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark9
Cancer Systems Biology, Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark10
...and 0 moreThe vast majority of disease-associated single-nucleotide polymorphisms (SNPs) mapped by genome-wide association studies (GWASs) are located in the non-protein-coding genome, but establishing the functional and mechanistic roles of these sequence variants has proven challenging. Here we describe a general pipeline in which candidate functional SNPs are first evaluated by fine mapping, epigenomic profiling, and epigenome editing, and then interrogated for causal function by using genome editing to create isogenic cell lines followed by phenotypic characterization.
To validate this approach, we analyzed the 6q22.1 prostate cancer risk locus and identified rs339331 as the top-scoring SNP. Epigenome editing confirmed that the rs339331 region possessed regulatory potential. By using transcription activator-like effector nuclease (TALEN)-mediated genome editing, we created a panel of isogenic 22Rv1 prostate cancer cell lines representing all three genotypes (TT, TC, CC) at rs339331.
Introduction of the 'T' risk allele increased transcription of the regulatory factor 6 (RFX6) gene, increased homeobox B13 (HOXB13) binding at the rs339331 region, and increased deposition of the enhancer-associated H3K4me2 histone mark at the rs339331 region compared to lines homozygous for the 'C' protective allele.
The cell lines also differed in cellular morphology and adhesion, and pathway analysis of differentially expressed genes suggested an influence of androgens. In summary, we have developed and validated a widely accessible approach that can be used to establish functional causality for noncoding sequence variants identified by GWASs.
Language: | English |
---|---|
Publisher: | Nature Publishing Group US |
Year: | 2015 |
Pages: | 1357-1363 |
ISSN: | 1546170x and 10788956 |
Types: | Journal article |
DOI: | 10.1038/nm.3975 |
ORCIDs: | 0000-0003-1783-2041 |
Alleles Cell Line, Tumor Chromosome Mapping Chromosomes, Human, Pair 6 DNA-Binding Proteins Gene Expression Regulation, Neoplastic Genetic Predisposition to Disease Genome-Wide Association Study HOXB13 protein, human Histone Code Histones Homeodomain Proteins Humans Male Polymorphism, Single Nucleotide Prostatic Neoplasms RNA, Messenger Regulatory Factor X Transcription Factors Reverse Transcriptase Polymerase Chain Reaction Rfx6 protein, human Transcription Factors