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@ARTICLE{Fincke:182309,
      author       = {V. E. Fincke and M. E. Krulik and P. Joshi$^*$ and M. C.
                      Frühwald and Y.-B. Chen and P. Johann$^*$},
      title        = {{R}enal {M}edullary {C}arcinomas {H}arbor a {D}istinct
                      {M}ethylation {P}henotype and {D}isplay {A}berrant
                      {M}ethylation of {G}enes {R}elated to {E}arly
                      {N}ephrogenesis.},
      journal      = {Cancers},
      volume       = {14},
      number       = {20},
      issn         = {2072-6694},
      address      = {Basel},
      publisher    = {MDPI},
      reportid     = {DKFZ-2022-02566},
      pages        = {5044},
      year         = {2022},
      note         = {#LA:B062#},
      abstract     = {Renal medullary carcinomas (RMC) are rare aggressive tumors
                      of the kidneys, characterized by a loss of SMARCB1.
                      Characteristically, these tumors arise in patients with
                      sickle cell trait or other hemoglobinopathies. Recent
                      characterization efforts have unraveled oncogenic pathways
                      that drive tumorigenesis. Among these, gene sets that
                      characterize replicative stress and the innate immune
                      response are upregulated in RMCs. Despite comprehensive
                      genetic and transcriptomic characterizations, commonalities
                      or differences to other SMARCB1 deficient entities so far
                      have not been investigated. We analyzed the methylome of
                      seven primary RMC and compared it to other SMARCB1 deficient
                      entities such as rhabdoid tumors (RT) and epithelioid
                      sarcomas using 850 K methylation arrays. Moreover, we
                      evaluated the differential gene expression of RMC using
                      RNA-sequencing in comparison to other rhabdoid tumors. In
                      accordance with previous gene expression data, we found that
                      RMCs separate from other SMARCB1 deficient entities,
                      pointing to a potentially different cell of origin and a
                      role of additional genetic aberrations that may drive
                      tumorigenesis and thus alter the methylome when compared to
                      rhabdoid tumors. In a focused analysis of genes that are
                      important for nephrogenesis, we particularly detected genes
                      that govern early nephrogenesis such as FOXI1 to be
                      hypomethylated and expressed at high levels in RMC. Overall,
                      our analyses underscore the fact that RMCs represent a
                      separate entity with limited similarities to rhabdoid
                      tumors, warranting specific treatment tailored to the
                      aggressiveness of the disease.},
      keywords     = {DNA methylation (Other) / SMARCB1 loss (Other) / renal
                      medullary carcinoma (Other)},
      cin          = {B062 / HD01},
      ddc          = {610},
      cid          = {I:(DE-He78)B062-20160331 / 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:36291828},
      doi          = {10.3390/cancers14205044},
      url          = {https://inrepo02.dkfz.de/record/182309},
}