1. Genetics and Genomics
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Determining the genetic basis of anthracycline-cardiotoxicity by response QTL mapping in induced cardiomyocytes

  1. David A Knowles  Is a corresponding author
  2. Courtney K Burrows
  3. John D Blischak
  4. Kristen M Patterson
  5. Daniel J Serie
  6. Nadine Norton
  7. Carole Ober
  8. Jonathan K Pritchard
  9. Yoav Gilad
  1. Stanford University, United States
  2. University of Chicago, United States
  3. Mayo Clinic, United States
Research Article
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Cite this article as: eLife 2018;7:e33480 doi: 10.7554/eLife.33480

Abstract

Anthracycline-induced cardiotoxicity (ACT) is a key limiting factor in setting optimal chemotherapy regimes, with almost half of patients expected to develop congestive heart failure given high doses. However, the genetic basis of sensitivity to anthracyclines remains unclear. We created a panel of iPSC-derived cardiomyocytes from 45 individuals and performed RNA-seq after 24h exposure to varying doxorubicin dosages. The transcriptomic response is substantial: the majority of genes are differentially expressed and over 6000 genes show evidence of differential splicing, the later driven by reduced splicing fidelity in the presence of doxorubicin. We show that inter-individual variation in transcriptional response is predictive of in vitro cell damage, which in turn is associated with in vivo ACT risk. We detect 447 response-expression QTLs and 42 response-splicing QTLs, which are enriched in lower ACT GWAS p-values, supporting the in vivo relevance of our map of genetic regulation of cellular response to anthracyclines.

Data availability

All the custom analysis scripts used for this project are available at https://github.com/davidaknowles/dox (Knowles and Blischak, 2017). The suez response eQTL mapping R package is available at https://github.com/davidaknowles/suez (Knowles, 2017). The following data are available as Supplementary Data: 1) differential expression cluster assignments, 2) significant (5% FDR) eQTLs and sQTLs, 3) differential splicing results, 4) levels of cardiac troponin and the predicted transcriptomic response. In addition to the Supplementary Data included with this paper, further results are hosted at Dryad (doi:10.5061/dryad.r5t8d04) including 1) gene-by-sample matrix of RNA-seq quantification (log counts per million), 2) LeafCutter intron excision quantification 3) p-values for all tested eQTLs, reQTLs, sQTLs, and rsQTLs, 4) RARG variant response and marginal trans-eQTLs, 5) RIN, RNA concentration and other technical covariates, 6) embryoid body imaging for all iPSC lines. The RNA-seq FASTQ files will be added to the dbGaP database (Tryka et al., 2014) under dbGaP accession phs000185 (https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000185). The genotype data files cannot be shared because releasing genotype data from a subset of individuals in the pedigree would enable the reconstruction of genotypes of other members of the pedigree, which would violate the original protocol approved by the research ethics board (Livne et al., 2015). The summary statistics for the ACT GWAS were given to us by the authors of the study (Schneider et al., 2016; Serie et al. 2017).

The following data sets were generated
    1. Knowles DA
    (2018) Expression and splicing quantification, eQTLs and sQTLs
    Available at Dryad Digital Repository under a CC0 Public Domain Dedication.

Article and author information

Author details

  1. David A Knowles

    Department of Genetics, Stanford University, Stanford, United States
    For correspondence
    knowles84@gmail.com
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7408-146X
  2. Courtney K Burrows

    Department of Human Genetics, University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. John D Blischak

    Department of Human Genetics, University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2634-9879
  4. Kristen M Patterson

    Department of Human Genetics, University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Daniel J Serie

    Department of Health Sciences Research, Mayo Clinic, Jacksonville, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Nadine Norton

    Department of Cancer Biology, Mayo Clinic, Jacksonville, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Carole Ober

    Department of Human Genetics, University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Jonathan K Pritchard

    Department of Genetics, Stanford University, Stanford, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8828-5236
  9. Yoav Gilad

    Department of Human Genetics, University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8284-8926

Funding

NIH Office of the Director (HL092206)

  • Yoav Gilad

Howard Hughes Medical Institute

  • Jonathan K Pritchard

NIH Office of the Director (HG008140)

  • Jonathan K Pritchard

NIH Office of the Director (HG009431)

  • Jonathan K Pritchard

NIH Office of the Director (TL1 TR 432-7)

  • Courtney K Burrows

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Human subjects: Human Subjects work was approved by the University of Chicago IRB (protocol 10-416-B). Written informed consent was obtained from all participants.

Reviewing Editor

  1. Gilean McVean, Oxford University, United Kingdom

Publication history

  1. Received: November 11, 2017
  2. Accepted: April 30, 2018
  3. Accepted Manuscript published: May 8, 2018 (version 1)
  4. Version of Record published: June 15, 2018 (version 2)

Copyright

© 2018, Knowles et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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