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@ARTICLE{Lopez:179850,
      author       = {C. Lopez and N. Schleussner and S. H. Bernhart and K.
                      Kleinheinz and S. Sungalee and H. L. Sczakiel and H.
                      Kretzmer and U. H. Toprak$^*$ and S. Glaser and R. Wagener
                      and O. Ammerpohl and S. Bens and M. Giefing and J. C. G.
                      Sanchez and G. Apic and D. Hubschmann$^*$ and M. Janz and M.
                      Kreuz and A. Mottok and J. M. Muller and J. Seufert$^*$ and
                      S. Hoffmann and J. O. Korbel and R. B. Russell and R. Schule
                      and L. Trumper and W. Klapper and B. Radlwimmer$^*$ and P.
                      Lichter$^*$ and R. Kuppers$^*$ and M. Schlesner$^*$ and S.
                      Mathas and R. Siebert},
      title        = {{F}ocal structural variants revealed by whole genome
                      sequencing disrupt the histone demethylase {KDM}4{C} in {B}
                      cell lymphomas.},
      journal      = {Haematologica},
      volume       = {108},
      number       = {2},
      issn         = {0390-6078},
      address      = {Pavia},
      publisher    = {Ferrata Storti Foundation},
      reportid     = {DKFZ-2022-00924},
      pages        = {543-554},
      year         = {2023},
      note         = {2023 Feb 1;108(2):543-554},
      abstract     = {Histone methylation-modifiers, like EZH2 and KMT2D, are
                      recurrently altered in B-cell lymphomas. To comprehensively
                      describe the landscape of alterations affecting genes
                      encoding histone methylation-modifiers in lymphomagenesis we
                      investigated whole genome and transcriptome data of 186
                      mature B-cell lymphomas sequenced in the ICGC MMML-Seq
                      project. Besides confirming common alterations of KMT2D
                      $(47\%$ of cases), EZH2 $(17\%),$ SETD1B $(5\%),$ PRDM9
                      $(4\%),$ KMT2C $(4\%),$ and SETD2 $(4\%)$ also identified by
                      prior exome or RNAseq studies, we here unravel KDM4C in
                      chromosome 9p24, encoding a histone demethylase, to be
                      recurrently altered. Focal structural variation was the main
                      mechanism of KDM4C alterations, which was independent from
                      9p24 amplification. We identified KDM4C alterations also in
                      lymphoma cell lines including a focal homozygous deletion in
                      a classical Hodgkin lymphoma cell line. By integrating
                      RNAseq and genome sequencing data we predict KDM4C
                      structural variants to result in loss-of-function. By
                      functional reconstitution studies in cell lines, we provide
                      evidence that KDM4C can act as tumor suppressor. Thus, we
                      show that identification of structural variants in whole
                      genome sequencing data adds to the comprehensive description
                      of the mutational landscape of lymphomas and, moreover,
                      establish KDM4C as putative tumor suppressive gene
                      recurrently altered in subsets of B-cell derived lymphomas.},
      cin          = {B240 / B087 / HD01 / B060 / ED01},
      ddc          = {610},
      cid          = {I:(DE-He78)B240-20160331 / I:(DE-He78)B087-20160331 /
                      I:(DE-He78)HD01-20160331 / I:(DE-He78)B060-20160331 /
                      I:(DE-He78)ED01-20160331},
      pnm          = {312 - Funktionelle und strukturelle Genomforschung
                      (POF4-312)},
      pid          = {G:(DE-HGF)POF4-312},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:35522148},
      doi          = {10.3324/haematol.2021.280005},
      url          = {https://inrepo02.dkfz.de/record/179850},
}