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Nat Med. 2015 Nov;21(11):1357-63. doi: 10.1038/nm.3975. Epub 2015 Sep 23.

CAUSEL: an epigenome- and genome-editing pipeline for establishing function of noncoding GWAS variants.

Author information

1
Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.
2
Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.
3
Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA.
4
Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA.
5
Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA.
6
Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA.
7
Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA.
8
Department of Physics of Complex Systems, Eötvös Loránd University, Budapest, Hungary.
9
Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts, USA.
10
Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA.
11
Medical College, Xiamen University, Xiamen, China.
12
Computational Health Informatics Program (CHIP), Boston Children's Hospital, Boston, Massachusetts, USA.
13
Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.
14
Second Department of Pathology, Semmelweis University, Budapest, Hungary.
15
Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, Massachusetts, USA.
16
Department of Animal Hygiene, Szent István University, Budapest, Hungary.
17
The Eli and Edythe L. Broad Institute, Cambridge, Massachusetts, USA.

Abstract

The 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.

PMID:
26398868
PMCID:
PMC4746056
DOI:
10.1038/nm.3975
[Indexed for MEDLINE]
Free PMC Article

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