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@ARTICLE{Riegel:210399,
      author       = {D. Riegel and E. Romero-Fernández and M. Simon$^*$ and A.
                      R. Adenugba and K. Singer and R. Mayr and F. Weber and M.
                      Kleemann and C. D. Imbusch$^*$ and M. Kreutz and B.
                      Brors$^*$ and I. Ugele and J. M. Werner and P. J. Siska and
                      C. Schmidl},
      title        = {{I}ntegrated single-cell profiling dissects
                      cell-state-specific enhancer landscapes of human
                      tumor-infiltrating {CD}8+ {T} cells.},
      journal      = {Molecular cell},
      volume       = {83},
      number       = {4},
      issn         = {1097-2765},
      address      = {New York, NY},
      publisher    = {Elsevier},
      reportid     = {DKFZ-2023-00123},
      pages        = {622-636.e10.},
      year         = {2023},
      note         = {#EA:B330# / 83(4), pp. 622-636.e10. 2023},
      abstract     = {Despite extensive studies on the chromatin landscape of
                      exhausted T cells, the transcriptional wiring underlying the
                      heterogeneous functional and dysfunctional states of human
                      tumor-infiltrating lymphocytes (TILs) is incompletely
                      understood. Here, we identify gene-regulatory landscapes in
                      a wide breadth of functional and dysfunctional CD8+ TIL
                      states covering four cancer entities using single-cell
                      chromatin profiling. We map enhancer-promoter interactions
                      in human TILs by integrating single-cell chromatin
                      accessibility with single-cell RNA-seq data from
                      tumor-entity-matching samples and prioritize
                      cell-state-specific genes by super-enhancer analysis.
                      Besides revealing entity-specific chromatin remodeling in
                      exhausted TILs, our analyses identify a common chromatin
                      trajectory to TIL dysfunction and determine key enhancers,
                      transcriptional regulators, and deregulated genes involved
                      in this process. Finally, we validate enhancer regulation at
                      immunotherapeutically relevant loci by targeting non-coding
                      regulatory elements with potent CRISPR activators and
                      repressors. In summary, our study provides a framework for
                      understanding and manipulating cell-state-specific
                      gene-regulatory cues from human tumor-infiltrating
                      lymphocytes.},
      keywords     = {CRISPR activation (Other) / CRISPR interference (Other) / T
                      cell exhaustion (Other) / cancer immunology (Other) /
                      chromatin accessibility (Other) / enhancer (Other) / gene
                      regulation (Other) / single-cell ATAC-seq (Other) /
                      tumor-infiltrating T cells (Other)},
      cin          = {B330 / HD01},
      ddc          = {610},
      cid          = {I:(DE-He78)B330-20160331 / I:(DE-He78)HD01-20160331},
      pnm          = {312 - Funktionelle und strukturelle Genomforschung
                      (POF4-312)},
      pid          = {G:(DE-HGF)POF4-312},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:36657444},
      doi          = {10.1016/j.molcel.2022.12.029},
      url          = {https://inrepo02.dkfz.de/record/210399},
}