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Multi-omic features of oesophageal adenocarcinoma in patients treated with preoperative neoadjuvant therapy

Author

Listed:
  • Marjan M. Naeini

    (QIMR Berghofer Medical Research Institute)

  • Felicity Newell

    (QIMR Berghofer Medical Research Institute)

  • Lauren G. Aoude

    (The University of Queensland)

  • Vanessa F. Bonazzi

    (The University of Queensland)

  • Kalpana Patel

    (The University of Queensland)

  • Guy Lampe

    (Princess Alexandra Hospital)

  • Lambros T. Koufariotis

    (QIMR Berghofer Medical Research Institute)

  • Vanessa Lakis

    (QIMR Berghofer Medical Research Institute)

  • Venkateswar Addala

    (QIMR Berghofer Medical Research Institute)

  • Olga Kondrashova

    (QIMR Berghofer Medical Research Institute)

  • Rebecca L. Johnston

    (QIMR Berghofer Medical Research Institute)

  • Sowmya Sharma

    (QIMR Berghofer Medical Research Institute
    University of Queensland
    Australian Clinical Labs)

  • Sandra Brosda

    (The University of Queensland)

  • Oliver Holmes

    (QIMR Berghofer Medical Research Institute)

  • Conrad Leonard

    (QIMR Berghofer Medical Research Institute)

  • Scott Wood

    (QIMR Berghofer Medical Research Institute)

  • Qinying Xu

    (QIMR Berghofer Medical Research Institute)

  • Janine Thomas

    (Princess Alexandra Hospital
    Mater Misericordiae)

  • Euan Walpole

    (Princess Alexandra Hospital)

  • G. Tao Mai

    (Princess Alexandra Hospital)

  • Stephen P. Ackland

    (Calvary Mater Newcastle)

  • Jarad Martin

    (Calvary Mater Newcastle)

  • Matthew Burge

    (Royal Brisbane and Women’s Hospital)

  • Robert Finch

    (Royal Brisbane and Women’s Hospital)

  • Christos S. Karapetis

    (Flinders University Department of Medical Oncology, Flinders Medical Centre)

  • Jenny Shannon

    (Nepean Hospital)

  • Louise Nott

    (Royal Hobart Hospital)

  • Robert Bohmer

    (Royal Hobart Hospital)

  • Kate Wilson

    (University of Sydney)

  • Elizabeth Barnes

    (University of Sydney)

  • John R. Zalcberg

    (Monash University)

  • B. Mark Smithers

    (Princess Alexandra Hospital
    University of Queensland)

  • John Simes

    (University of Sydney)

  • Timothy Price

    (The Queen Elizabeth Hospital and University of Adelaide)

  • Val Gebski

    (University of Sydney)

  • Katia Nones

    (QIMR Berghofer Medical Research Institute)

  • David I. Watson

    (Flinders University Discipline of Surgery, Flinders Medical Centre)

  • John V. Pearson

    (QIMR Berghofer Medical Research Institute)

  • Andrew P. Barbour

    (The University of Queensland
    Princess Alexandra Hospital)

  • Nicola Waddell

    (QIMR Berghofer Medical Research Institute)

Abstract

Oesophageal adenocarcinoma is a poor prognosis cancer and the molecular features underpinning response to treatment remain unclear. We investigate whole genome, transcriptomic and methylation data from 115 oesophageal adenocarcinoma patients mostly from the DOCTOR phase II clinical trial (Australian New Zealand Clinical Trials Registry-ACTRN12609000665235), with exploratory analysis pre-specified in the study protocol of the trial. We report genomic features associated with poorer overall survival, such as the APOBEC mutational and RS3-like rearrangement signatures. We also show that positron emission tomography non-responders have more sub-clonal genomic copy number alterations. Transcriptomic analysis categorises patients into four immune clusters correlated with survival. The immune suppressed cluster is associated with worse survival, enriched with myeloid-derived cells, and an epithelial-mesenchymal transition signature. The immune hot cluster is associated with better survival, enriched with lymphocytes, myeloid-derived cells, and an immune signature including CCL5, CD8A, and NKG7. The immune clusters highlight patients who may respond to immunotherapy and thus may guide future clinical trials.

Suggested Citation

  • Marjan M. Naeini & Felicity Newell & Lauren G. Aoude & Vanessa F. Bonazzi & Kalpana Patel & Guy Lampe & Lambros T. Koufariotis & Vanessa Lakis & Venkateswar Addala & Olga Kondrashova & Rebecca L. John, 2023. "Multi-omic features of oesophageal adenocarcinoma in patients treated with preoperative neoadjuvant therapy," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-38891-x
    DOI: 10.1038/s41467-023-38891-x
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    References listed on IDEAS

    as
    1. Xiaodun Li & Hayley E. Francies & Maria Secrier & Juliane Perner & Ahmad Miremadi & Núria Galeano-Dalmau & William J. Barendt & Laura Letchford & Genevieve M. Leyden & Emma K. Goffin & Andrew Barthorp, 2018. "Organoid cultures recapitulate esophageal adenocarcinoma heterogeneity providing a model for clonality studies and precision therapeutics," Nature Communications, Nature, vol. 9(1), pages 1-13, December.
    2. Aldo Scarpa & David K. Chang & Katia Nones & Vincenzo Corbo & Ann-Marie Patch & Peter Bailey & Rita T. Lawlor & Amber L. Johns & David K. Miller & Andrea Mafficini & Borislav Rusev & Maria Scardoni & , 2017. "Whole-genome landscape of pancreatic neuroendocrine tumours," Nature, Nature, vol. 543(7643), pages 65-71, March.
    3. Nicholas K. Hayward & James S. Wilmott & Nicola Waddell & Peter A. Johansson & Matthew A. Field & Katia Nones & Ann-Marie Patch & Hojabr Kakavand & Ludmil B. Alexandrov & Hazel Burke & Valerie Jakrot , 2017. "Whole-genome landscapes of major melanoma subtypes," Nature, Nature, vol. 545(7653), pages 175-180, May.
    4. Serena Nik-Zainal & Helen Davies & Johan Staaf & Manasa Ramakrishna & Dominik Glodzik & Xueqing Zou & Inigo Martincorena & Ludmil B. Alexandrov & Sancha Martin & David C. Wedge & Peter Van Loo & Young, 2016. "Landscape of somatic mutations in 560 breast cancer whole-genome sequences," Nature, Nature, vol. 534(7605), pages 47-54, June.
    5. Ludmil B. Alexandrov & Serena Nik-Zainal & David C. Wedge & Samuel A. J. R. Aparicio & Sam Behjati & Andrew V. Biankin & Graham R. Bignell & Niccolò Bolli & Ake Borg & Anne-Lise Børresen-Dale & Sandri, 2013. "Correction: Corrigendum: Signatures of mutational processes in human cancer," Nature, Nature, vol. 502(7470), pages 258-258, October.
    6. Sarah Song & Katia Nones & David Miller & Ivon Harliwong & Karin S Kassahn & Mark Pinese & Marina Pajic & Anthony J Gill & Amber L Johns & Matthew Anderson & Oliver Holmes & Conrad Leonard & Darrin Ta, 2012. "qpure: A Tool to Estimate Tumor Cellularity from Genome-Wide Single-Nucleotide Polymorphism Profiles," PLOS ONE, Public Library of Science, vol. 7(9), pages 1-7, September.
    7. Katia Nones & Nicola Waddell & Nicci Wayte & Ann-Marie Patch & Peter Bailey & Felicity Newell & Oliver Holmes & J. Lynn Fink & Michael C. J. Quinn & Yue Hang Tang & Guy Lampe & Kelly Quek & Kelly A. L, 2014. "Genomic catastrophes frequently arise in esophageal adenocarcinoma and drive tumorigenesis," Nature Communications, Nature, vol. 5(1), pages 1-9, December.
    8. Ludmil B. Alexandrov & Serena Nik-Zainal & David C. Wedge & Samuel A. J. R. Aparicio & Sam Behjati & Andrew V. Biankin & Graham R. Bignell & Niccolò Bolli & Ake Borg & Anne-Lise Børresen-Dale & Sandri, 2013. "Signatures of mutational processes in human cancer," Nature, Nature, vol. 500(7463), pages 415-421, August.
    9. Ankur Chakravarthy & Andrew Furness & Kroopa Joshi & Ehsan Ghorani & Kirsty Ford & Matthew J. Ward & Emma V. King & Matt Lechner & Teresa Marafioti & Sergio A. Quezada & Gareth J. Thomas & Andrew Febe, 2018. "Pan-cancer deconvolution of tumour composition using DNA methylation," Nature Communications, Nature, vol. 9(1), pages 1-13, December.
    10. Michael S. Lawrence & Petar Stojanov & Craig H. Mermel & James T. Robinson & Levi A. Garraway & Todd R. Golub & Matthew Meyerson & Stacey B. Gabriel & Eric S. Lander & Gad Getz, 2014. "Discovery and saturation analysis of cancer genes across 21 tumour types," Nature, Nature, vol. 505(7484), pages 495-501, January.
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