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Promoter capture Hi-C-based identification of recurrent noncoding mutations in colorectal cancer

Nature Genetics volume 50, pages 1375–1380 (2018)Cite this article

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Abstract

Efforts are being directed to systematically analyze the non-coding regions of the genome for cancer-driving mutations1,2,3,4,5,6. cis-regulatory elements (CREs) represent a highly enriched subset of the non-coding regions of the genome in which to search for such mutations. Here we use high-throughput chromosome conformation capture techniques (Hi-C) for 19,023 promoter fragments to catalog the regulatory landscape of colorectal cancer in cell lines, mapping CREs and integrating these with whole-genome sequence and expression data from The Cancer Genome Atlas7,8. We identify a recurrently mutated CRE interacting with the ETV1 promoter affecting gene expression. ETV1 expression influences cell viability and is associated with patient survival. We further refine our understanding of the regulatory effects of copy-number variations, showing that RASL11A is targeted by a previously identified enhancer amplification1. This study reveals new insights into the complex genetic alterations driving tumor development, providing a paradigm for employing chromosome conformation capture to decipher non-coding CREs relevant to cancer biology.

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Fig. 1
Fig. 2: Non-coding mutations in CREs.
Fig. 3: Mutations in CREs affect ETV1 expression.
Fig. 4: Amplification of the CRE upregulates RASL11A expression.
Fig. 5: ETV1 and RASL11A levels are associated with differential cell growth.

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Data availability

Hi-C, CHi-C and histone ChIP–seq sequencing data have been deposited in the European Genome-phenome Archive (EGA) under accession number EGAS00001001946. WGS, RNA-seq, CNV and survival data for TCGA COAD and READ samples and RNA-seq data for HT29 and LoVo lines (CCLE program) were obtained from the NCI Genomic Data Commons Data Portal (see URLs). Transcription-factor ChIP–seq data were obtained from the Gene Expression Omnibus (GEO) (GSE49402). Survival data were obtained from GEO (GSE33113, GSE39582). Replication timing data were downloaded from the UCSC Genome Browser (see URLs). GTEx data (release v.6) were obtained from the GTex portal (see URLs).

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Acknowledgements

This work was supported by grants from Cancer Research UK grant (C1298/A8362), the European Union Seventh Framework Programme (FP7/207–2013) under grant 258236 and FP7 collaborative project SYSCOL, all awarded to R.S.H. This publication is supported by COST Action BM1206. CIHR funded Epigenome Mapping Centre at McGill University (EP1-120608), awarded to T.P. We acknowledge the work of The Institute of Cancer Research Tumour Profiling Unit. The results published here are in part based on data generated by TCGA established by the NCI and NHGRI. Information about TCGA and the investigators and institutions that constitute the TCGA research network can be found at http://cancergenome.nih.gov/.

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Author notes

  1. These authors contributed equally: Giulia Orlando, Philip J. Law, Alex J. Cornish.

Authors and Affiliations

  1. Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK

    Giulia Orlando, Philip J. Law, Alex J. Cornish, Sara E. Dobbins, Daniel Chubb, Peter Broderick, Kevin Litchfield & Richard S. Houlston

  2. McGill University and Genome Quebec Innovation Centre, Department of Human Genetics, McGill University, Montreal, Quebec, Canada

    Fadi Hariri & Tomi Pastinen

  3. Center for Pediatric Genomic Medicine, Children’s Mercy, Kansas City, MO, USA

    Tomi Pastinen

  4. Department of Medical and Molecular Genetics, King’s College London, London, UK

    Cameron S. Osborne

  5. Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, and Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden

    Jussi Taipale

  6. Genome-Scale Biology Program, University of Helsinki, Biomedicum, Helsinki, Finland

    Jussi Taipale

  7. Department of Biochemistry, University of Cambridge, Cambridge, UK

    Jussi Taipale

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Contributions

G.O., P.J.L. and R.S.H. conceived and designed the study; G.O. performed Hi-C and CHi-C experiments, luciferase assays, CRISPR experiments, and cell viability and proliferation assays; G.O. and P.B. performed 3C validation; G.O., P.J.L., A.J.C., S.E.D., D.C. and K.L. performed bioinformatics; F.H. performed ChIP–seq experiments; T.P. and J.T. contributed reagents and materials for the ChIP–seq experiments; C.S.O. designed the capture baits; and G.O., P.J.L., A.J.C., S.E.D., D.C., P.B. and R.S.H wrote the manuscript with contributions from T.P., C.S.O. and J.T. All authors reviewed the final manuscript.

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Correspondence to Richard S. Houlston.

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Orlando, G., Law, P.J., Cornish, A.J. et al. Promoter capture Hi-C-based identification of recurrent noncoding mutations in colorectal cancer. Nat Genet 50, 1375–1380 (2018). https://doi.org/10.1038/s41588-018-0211-z

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