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@ARTICLE{Okonechnikov:186732,
      author       = {K. Okonechnikov$^*$ and A. Federico$^*$ and D. Schrimpf$^*$
                      and P. Sievers$^*$ and F. Sahm$^*$ and J. Koster and D.
                      Jones$^*$ and A. von Deimling$^*$ and S. Pfister$^*$ and M.
                      Kool$^*$ and A. Korshunov$^*$},
      title        = {{C}omparison of transcriptome profiles between
                      medulloblastoma primary and recurrent tumors uncovers novel
                      variance effects in relapses.},
      journal      = {Acta Neuropathologica Communications},
      volume       = {11},
      number       = {1},
      issn         = {2051-5960},
      address      = {London},
      publisher    = {Biomed Central},
      reportid     = {DKFZ-2023-00084},
      pages        = {7},
      year         = {2023},
      note         = {#EA:B062#LA:B300#},
      abstract     = {Nowadays medulloblastoma (MB) tumors can be treated with
                      risk-stratified approaches with up to $80\%$ success rate.
                      However, disease relapses occur in approximately $30\%$ of
                      patients and successful salvage treatment strategies at
                      relapse remain scarce. Acquired copy number changes or TP53
                      mutations are known to occur frequently in relapses, while
                      methylation profiles usually remain highly similar to those
                      of the matching primary tumors, indicating that in general
                      molecular subgrouping does not change during the course of
                      the disease. In the current study, we have used RNA
                      sequencing data to analyze the transcriptome profiles of 43
                      primary-relapse MB pairs in order to identify specific
                      molecular features of relapses within various tumor groups.
                      Gene variance analysis between primary and relapse samples
                      demonstrated the impact of age in SHH-MB: the changes in
                      gene expression relapse profiles were more pronounced in the
                      younger patients (< 10 years old), which were also
                      associated with increased DNA aberrations and somatic
                      mutations at relapse probably driving this effect. For Group
                      3/4 MB transcriptome data analysis uncovered clear sets of
                      genes either active or decreased at relapse that are
                      significantly associated with survival, thus could be
                      potential predictive markers. In addition, deconvolution
                      analysis of bulk transcriptome data identified
                      progression-associated differences in cell type enrichment.
                      The proportion of undifferentiated progenitors increased in
                      SHH-MB relapses with a concomitant decrease of
                      differentiated neuron-like cells, while in Group 3/4 MB
                      relapses cell cycle activity increases and differentiated
                      neuron-like cells proportion decreases as well. Thus, our
                      findings uncovered significant transcriptome changes in the
                      molecular signatures of relapsed MB and could be potentially
                      useful for further clinical purposes.},
      keywords     = {Medulloblastoma (Other) / Prognosis (Other) / Relapses
                      (Other) / Transcriptomics (Other)},
      cin          = {B062 / B300 / B360 / HD01},
      ddc          = {610},
      cid          = {I:(DE-He78)B062-20160331 / I:(DE-He78)B300-20160331 /
                      I:(DE-He78)B360-20160331 / 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:36635768},
      doi          = {10.1186/s40478-023-01504-1},
      url          = {https://inrepo02.dkfz.de/record/186732},
}