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

Nature Medicine volume 21, pages 1357–1363 (2015)Cite this article

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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.

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Figure 1: Overview of the CAUSEL pipeline.
Figure 2: Genetic and epigenetic landscape of the 6q22.1 region.
Figure 3: High-throughput sequencing pipeline and barcoding strategy.
Figure 4: Sequencing reveals allelic diversity created by genome editing.
Figure 5: Genotypic status at rs339331 causally affects RFX6 gene expression, HOXB13 binding and the H3K4me2 histone modification.
Figure 6: Genotype at rs339331 alters morphology, cellular adhesion, and transcripts that are predicted to be regulated by androgens.

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European Nucleotide Archive

Sequence Read Archive

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Acknowledgements

M.L.F. and J.K.J. were supported by US National Institutes of Health (NIH) grant no. R01 GM107427; J.K.J. was supported by a NIH Director's Pioneer Award (DP1 GM105378) and The Jim and Ann Orr Massachusetts General Hospital Research Scholar Award; M.L.F. is supported by the Prostate Cancer Foundation (Challenge Award), the US NIH grant no. R01CA193910, and the H.L. Snyder Medical Foundation. The scientific development and funding for this project were in part supported by the US National Cancer Institute GAME-ON Post-GWAS Initiative (U19CA148112 and U19CA148537). K.L. is supported by a K99/R00 grant from the National Cancer Institute (grant no. 1K99CA184415-01). I.C. is supported by grants from the Hungarian National Research, Development and Innovation Office (KMR-12-1-2012-0216) and the Hungarian National Research Fund (OTKA103244). Z.S. is supported by the Breast Cancer Research Foundation and the Széchenyi Progam, Hungary (KTIA_NAP_13-2014-0021). This project was also supported by a Program Project Development Grant from the Ovarian Cancer Research Fund (K.L. and S.A.G). We thank the Dana-Farber Cancer Institute Molecular Biology Core Facility for Sanger sequencing and Illumina high-throughput sequencing. We thank C. Nicolet at the University of Southern California Epigenome Center Core for RNA-seq services and M. Li at the University of Southern California Norris Medical Library Bioinformatics Center, who provided assistance with the analysis of RNA-seq data.

Author information

Author notes

  1. Kate Lawrenson

    Present address: Present address: Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA,

  2. Yanfang Fu

    Present address: Present address: Cell and Gene Therapy, Biogen, Cambridge, Massachusetts, USA.,

  3. Sándor Spisák, Kate Lawrenson and Yanfang Fu: These authors contributed equally to this work.

  4. Center for Cancer Prevention and Translational Genomics at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA.

Authors and Affiliations

  1. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA

    Sándor Spisák, Ji-Heui Seo, Romina Lenci, Qiyuan Li, Viktória Tisza, Matthew Chabot, Mark Pomerantz & Matthew L Freedman

  2. Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA

    Sándor Spisák, Ji-Heui Seo, Romina Lenci, Qiyuan Li & Matthew L Freedman

  3. Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA

    Kate Lawrenson, Christopher Haiman, Ying Han & Simon A Gayther

  4. Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA

    Yanfang Fu, Rebecca T Cottman & J Keith Joung

  5. Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA

    Yanfang Fu, Rebecca T Cottman & J Keith Joung

  6. Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA

    Yanfang Fu, Rebecca T Cottman & J Keith Joung

  7. Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA

    Yanfang Fu & J Keith Joung

  8. Department of Physics of Complex Systems, Eötvös Loránd University, Budapest, Hungary

    István Csabai

  9. Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts, USA

    Rebecca T Cottman & J Keith Joung

  10. Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA

    Christopher Haiman

  11. Medical College, Xiamen University, Xiamen, China

    Qiyuan Li

  12. Computational Health Informatics Program (CHIP), Boston Children's Hospital, Boston, Massachusetts, USA

    Viktória Tisza & Zoltán Szállási

  13. Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark

    Zoltán Szállási

  14. Second Department of Pathology, Semmelweis University, Budapest, Hungary

    Zoltán Szállási

  15. Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, Massachusetts, USA

    Zachery T Herbert

  16. Department of Animal Hygiene, Szent István University, Budapest, Hungary

    Norbert Solymosi

  17. The Eli and Edythe L. Broad Institute, Cambridge, Massachusetts, USA

    Simon A Gayther & Matthew L Freedman

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Consortia

The GAME-ON/ELLIPSE Consortium

Contributions

S.S., K.L. and Y.F. designed and performed experiments, J.K.J. and M.L.F. designed experiments, R.T.C., J.-H.S., R.L., V.T., M.C. and M.P. performed experiments, S.S., I.C. and M.L.F. developed the sequencing pipeline, S.S., K.L., Y.F., Y.H., Q.L., I.C., Z.T.H. and N.S. analyzed the data, S.S., K.L., I.C., J.K.J. and M.L.F. wrote the manuscript, S.S., Y.F., R.T.C., S.A.G., J.K.J. and M.L.F. revised the manuscript, C.H., Z.S., Z.T.H. and S.A.G. provided technical support and conceptual advice. The GAME-ON/ELLIPSE Consortium provided early access to fine-mapping data.

Corresponding authors

Correspondence to Simon A Gayther, J Keith Joung or Matthew L Freedman.

Ethics declarations

Competing interests

J.K.J. is a consultant for Horizon Discovery. J.K.J. has financial interests in Editas Medicine, Hera Testing Laboratories, Poseida Therapeutics, and Transposagen Biopharmaceuticals. J.K.J.'s interests were reviewed and are managed by Massachusetts General Hospital and Partners HealthCare in accordance with their conflict of interest policies.

Additional information

A complete list of all consortium members is provided in the Supplementary Note.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–10 and Supplementary Note (PDF 9987 kb)

Supplementary Table 1

The most associated markers for the 6q22.1 prostate risk locus (XLSX 20 kb)

Supplementary Table 2

Description and study design of the studies included in the meta-analysis. (XLSX 18 kb)

Supplementary Table 3

Identified allele variants (459) and their fraquencies. Deleted base represented by “x” (XLSX 16 kb)

Supplementary Table 4

Differentially expressed transcripts between rs339331 isogenic series (XLSX 13 kb)

Supplementary Table 5

Oligonucleotide seqences (XLSX 12 kb)

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Spisák, S., Lawrenson, K., Fu, Y. et al. CAUSEL: an epigenome- and genome-editing pipeline for establishing function of noncoding GWAS variants. Nat Med 21, 1357–1363 (2015). https://doi.org/10.1038/nm.3975

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