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<p>Locally advanced esophageal adenocarcinoma remains difficult to treat and the ecological and evolutionary dynamics responsible for resistance and recurrence are incompletely understood. Here, we performed longitudinal multiomic analysis of patients with esophageal adenocarcinoma in the MEMORI trial. Multi-region multi-timepoint whole-exome and paired transcriptome sequencing was performed on 27 patients before, during and after neoadjuvant treatment. We found major transcriptomic changes during treatment with upregulation of immune, stromal and oncogenic pathways. Genetic data revealed that clonal sweeps through treatment were rare. Imaging mass cytometry and T cell receptor sequencing revealed remodeling of the tumor microenvironment during treatment. The presence of genetic immune escape, a less-cytotoxic T cell phenotype and a lack of clonal T cell expansions were linked to poor treatment response. In summary, there were widespread transcriptional and environmental changes through treatment, with limited clonal replacement, suggestive of phenotypic plasticity.</p>

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Evolutionary and immune microenvironment dynamics during neoadjuvant treatment of esophageal adenocarcinoma

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2025年5月14日

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  • Melissa Barroux,
  • Jacob Househam,
  • Eszter Lakatos,
  • Tahel Ronel,
  • Ann-Marie Baker,
  • Henrike Salié,
  • Maximilian Mossner,
  • Kane Smith,
  • Chris Kimberley,
  • Salpie Nowinski,
  • Alison Berner,
  • Vinaya Gunasri,
  • Martin Borgmann,
  • Sven Liffers,
  • Marnix Jansen,
  • Giulio Caravagna,
  • Katja Steiger,
  • Julia Slotta-Huspenina,
  • Wilko Weichert,
  • Luis Zapata,
  • Eleftheria Giota,
  • Sylvie Lorenzen,
  • Markus Alberstmeier,
  • Benny Chain,
  • Helmut Friess,
  • Bertram Bengsch,
  • Roland M. Schmid,
  • Jens T. Siveke,
  • Michael Quante,
  • Trevor A. Graham

摘要

Locally advanced esophageal adenocarcinoma remains difficult to treat and the ecological and evolutionary dynamics responsible for resistance and recurrence are incompletely understood. Here, we performed longitudinal multiomic analysis of patients with esophageal adenocarcinoma in the MEMORI trial. Multi-region multi-timepoint whole-exome and paired transcriptome sequencing was performed on 27 patients before, during and after neoadjuvant treatment. We found major transcriptomic changes during treatment with upregulation of immune, stromal and oncogenic pathways. Genetic data revealed that clonal sweeps through treatment were rare. Imaging mass cytometry and T cell receptor sequencing revealed remodeling of the tumor microenvironment during treatment. The presence of genetic immune escape, a less-cytotoxic T cell phenotype and a lack of clonal T cell expansions were linked to poor treatment response. In summary, there were widespread transcriptional and environmental changes through treatment, with limited clonal replacement, suggestive of phenotypic plasticity.