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Intron retention is a source of neoepitopes in cancer

Nature Biotechnology volume 36, pages 10561058 (2018) | Download Citation

Abstract

We present an in silico approach to identifying neoepitopes derived from intron retention events in tumor transcriptomes. Using mass spectrometry immunopeptidome analysis, we show that retained intron neoepitopes are processed and presented on MHC I on the surface of cancer cell lines. RNA-derived neoepitopes should be considered for prospective personalized cancer vaccine development.

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Acknowledgements

We are grateful to D. Neri for fruitful discussions, D. Ritz for the purification of HLA peptides from cell lines, and M. Ghandi for assistance in coordinating access to cell line transcriptome data. This work was supported by the BroadNext10, NIH K08 CA188615, NIH R01 CA227388 and a Prostate Cancer Foundation–V Foundation Challenge Award.

Author information

Author notes

    • Alicia C Smart
    •  & Claire A Margolis

    These authors contributed equally to this work.

Affiliations

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

    • Alicia C Smart
    • , Claire A Margolis
    • , Meng Xiao He
    • , Diana Miao
    • , Dennis Adeegbe
    • , Kwok-Kin Wong
    •  & Eliezer M Van Allen
  2. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.

    • Alicia C Smart
    • , Claire A Margolis
    • , Meng Xiao He
    • , Diana Miao
    •  & Eliezer M Van Allen
  3. Department of Genetics and Biology, Stanford University, Stanford, California, USA.

    • Harold Pimentel
  4. Perlmutter Cancer Center at NYU Langone Medical Center, New York, New York, USA.

    • Dennis Adeegbe
    •  & Kwok-Kin Wong
  5. Philochem AG, Otelfingen, Switzerland.

    • Tim Fugmann

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Contributions

Conception and design: A.C.S., C.A.M., E.M.V.A. Development of methodology: C.A.M., A.C.S., H.P., M.X.H., T.F., D.M., K.-K.W., E.M.V.A. Analysis and interpretation of data (for example, pipeline development, statistical analysis, computational analysis): C.A.M., A.C.S., D.A. Writing, review and/or revision of the manuscript: C.A.M., A.C.S., H.P., M.X.H., D.M., D.A., T.F., K.-K.W., E.M.V.A. Study supervision: E.M.V.A.

Competing interests

E.M.V.A. holds consulting roles with Tango Therapeutics, Invitae and Genome Medical and receives research support from Bristol-Myers Squibb and Novartis. T.F. is an employee of Philochem AG.

Corresponding author

Correspondence to Eliezer M Van Allen.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–9, Supplementary Table 4, Supplementary Table Legends and Supplementary Code

  2. 2.

    Life Sciences Reporting Summary

Excel files

  1. 1.

    Supplementary Table 1: Clinical and molecular summary features from Hugo (n = 27) and Snyder (n = 21) patient cohorts.

    Clinical characteristics included for each patient: cohort, immunotherapy response status, type of immunotherapy. These characteristics were obtained directly from original publications for each cohort. Molecular characteristics included for each patient: total retained intron (RI) load, neoepitope-yielding RI load, RI neoepitope load, mean number of RI neoepitopes yielded by each RI, somatic neoepitope load.

  2. 2.

    Supplementary Table 3: Cancer cell line RI neoepitopes that were both predicted computationally and discovered experimentally bound to MHC Class I molecules via mass spectrometry.

    Table contains one cell line neoepitope (unique peptide, HLA allele combination) per row. Rows colored by cell line. Fields included: Cell line, Peptide, Intron ID (genomic coordinates of RI yielding neoepitope), Gene, Strand (positive or negative genomic strand), Allele (HLA Class I allele), 1-log50k (NetMHCpan prediction score), nM (NetMHCpan predicted binding affinity, measured in nM), rank (NetMHCpan rank of predicted affinity compared to a set of random natural peptides), Expression (neoepitope expression level, measured in transcripts per million).

  3. 3.

    Supplementary Table 5: Gene set enrichment analysis results for Hallmark and corresponding Founders gene sets comparing both top quartile vs. bottom quartile RI neoepitope load patients and immunotherapy responders vs. nonresponders.

    File contains raw Gene Set Enrichment Analysis (GSEA) results, with four tabs corresponding to Tables S4A-D. A: Hallmark gene sets, top quartile vs. bottom quartile RI neoepitope load. B: Hallmark gene sets, immunotherapy responders vs. nonresponders. C: Founders gene sets, top quartile vs. bottom quartile RI neoepitope load. D: Founders gene sets, immunotherapy responders vs. nonresponders. Founders results reported for all significantly enriched Hallmark gene sets.

  4. 4.

    Supplementary Table 6: Retained introns filtered from RI neoepitope analysis due to either (a) presence in normal skin tissue yielding likely immune tolerance or (b) determination of false-positive nature upon manual review.

    File contains two tabs corresponding to Tables S5A-B. A: Introns retained in Human Protein Atlas (HPA) normal skin tissue that were filtered from RI neoepitope analysis of patient tumors due to likely host immune competence (n = 7,050). B: Introns filtered from analysis of patient tumors after manual review (n = 63).

Text files

  1. 1.

    Supplementary Table 2: All RI neoepitopes predicted for each patient in Hugo (n = 27) and Snyder (n = 21) cohorts.

    Table contains one patient neoepitope (unique peptide, HLA allele combination) per row. Fields included: Pos (position in original retained intron peptide sequence), Peptide, Intron_ID (genomic coordinates of RI yielding neoepitope), Allele (HLA Class I allele), 1-log50k (NetMHCpan prediction score), nM (NetMHCpan predicted binding affinity, measured in nM), Rank (NetMHCpan rank of predicted affinity compared to a set of random natural peptides), TPM (neoepitope expression level, measured in transcripts per million), SampleID, Gene, Strand (positive or negative genomic strand).

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DOI

https://doi.org/10.1038/nbt.4239