% IMPORTANT: The following is UTF-8 encoded.  This means that in the presence
% of non-ASCII characters, it will not work with BibTeX 0.99 or older.
% Instead, you should use an up-to-date BibTeX implementation like “bibtex8” or
% “biber”.

@ARTICLE{Vlachavas:298342,
      author       = {E.-I. Vlachavas$^*$ and K. Voutetakis and V. Kosmidou and
                      S. Tsikalakis$^*$ and S. Roditis and K. Pateas and R. Kim
                      and K. Pagel and S. Wolf$^*$ and G. Warsow$^*$ and A.
                      Dimitrakopoulou-Strauss$^*$ and G. N. Zografos and A.
                      Pintzas and J. Betge$^*$ and O. Papadodima and S.
                      Wiemann$^*$},
      title        = {{M}olecular and functional profiling unravels targetable
                      vulnerabilities in colorectal cancer.},
      journal      = {Molecular oncology},
      volume       = {19},
      number       = {6},
      issn         = {1574-7891},
      address      = {Hoboken, NJ},
      publisher    = {John Wiley $\&$ Sons, Inc.},
      reportid     = {DKFZ-2025-00246},
      pages        = {1751-1774},
      year         = {2025},
      note         = {#EA:B050#LA:B050# / 2025 Jun;19(6):1751-1774},
      abstract     = {Colorectal cancer (CRC) patients with microsatellite-stable
                      (MSS) tumors are mostly treated with chemotherapy. Clinical
                      benefits of targeted therapies depend on mutational states
                      and tumor location. Many tumors carry mutations in KRAS
                      proto-oncogene, GTPase (KRAS) or B-Raf proto-oncogene,
                      serine/threonine kinase (BRAF), rendering them more
                      resistant to therapies. We performed whole-exome sequencing
                      and RNA-Sequencing of 28 tumors of the Athens Comprehensive
                      Cancer Center CRC cohort, and molecularly characterized CRC
                      patients based on their microsatellite instability (MSI)
                      status, single-nucleotide variations (SNVs)/copy number
                      alterations (CNAs), and pathway/transcription factor
                      activities at the individual patient level. Variants were
                      classified using a computational score for integrative
                      cancer variant annotation and prioritization. Complementing
                      this with public multi-omics datasets, we identified
                      activation of transforming growth factor beta (TGFβ)
                      signaling to be more strongly activated in MSS patients,
                      whereas Janus kinase (JAK)-signal transducer and activator
                      of transcription (STAT) and mitogen-activated protein kinase
                      (MAPK) molecular cascades were activated specifically in MSI
                      tumors. We unraveled mechanisms consistently perturbed in
                      the transcriptional and mutational circuits and identified
                      Runt-related transcription factors (RUNX transcription
                      factors) as putative biomarkers in CRC, given their role in
                      the regulation of pathways involved in tumor progression and
                      immune evasion. Assessing the immunogenicity of CRC tumors
                      in the context of RAS/RAF mutations and MSI/MSS status
                      revealed a critical impact that KRAS mutations have on
                      immunogenicity, particularly in the MSS patient subgroup,
                      with implications for diagnosis and treatment.},
      keywords     = {CRC (Other) / MSI status (Other) / RAS/RAF (Other) /
                      SNVs/CNAs (Other) / WES/RNA‐sequencing (Other) /
                      pathway/TF activity (Other)},
      cin          = {B050 / W190 / W610 / E060 / B440},
      ddc          = {610},
      cid          = {I:(DE-He78)B050-20160331 / I:(DE-He78)W190-20160331 /
                      I:(DE-He78)W610-20160331 / I:(DE-He78)E060-20160331 /
                      I:(DE-He78)B440-20160331},
      pnm          = {312 - Funktionelle und strukturelle Genomforschung
                      (POF4-312)},
      pid          = {G:(DE-HGF)POF4-312},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:39876058},
      doi          = {DOI:10.1002/1878-0261.13814},
      url          = {https://inrepo02.dkfz.de/record/298342},
}