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@ARTICLE{Barroux:301315,
      author       = {M. Barroux$^*$ and J. Househam and E. Lakatos and T. Ronel
                      and A.-M. Baker and H. Salié and M. Mossner and K. Smith
                      and C. Kimberley and S. Nowinski and A. Berner and V.
                      Gunasri and M. Borgmann and S. Liffers$^*$ and M. Jansen and
                      G. Caravagna and K. Steiger and J. Slotta-Huspenina and W.
                      Weichert and L. Zapata and E. Giota and S. Lorenzen and M.
                      Alberstmeier and B. Chain and H. Friess and B. Bengsch$^*$
                      and R. M. Schmid$^*$ and J. Siveke$^*$ and M. Quante$^*$ and
                      T. A. Graham},
      title        = {{E}volutionary and immune microenvironment dynamics during
                      neoadjuvant treatment of esophageal adenocarcinoma.},
      journal      = {Nature cancer},
      volume       = {6},
      number       = {5},
      issn         = {2662-1347},
      address      = {London},
      publisher    = {Nature Research},
      reportid     = {DKFZ-2025-00987},
      pages        = {820-837},
      year         = {2025},
      note         = {2025 May;6(5):820-837},
      abstract     = {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.},
      cin          = {MU01 / ED01 / FR01},
      ddc          = {610},
      cid          = {I:(DE-He78)MU01-20160331 / I:(DE-He78)ED01-20160331 /
                      I:(DE-He78)FR01-20160331},
      pnm          = {899 - ohne Topic (POF4-899)},
      pid          = {G:(DE-HGF)POF4-899},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:40369175},
      doi          = {10.1038/s43018-025-00955-w},
      url          = {https://inrepo02.dkfz.de/record/301315},
}