Nature Communications (Sep 2024)

Proteogenomic characterization of skull-base chordoma

  • Qilin Zhang,
  • Ziyan Xu,
  • Rui Han,
  • Yunzhi Wang,
  • Zhen Ye,
  • Jiajun Zhu,
  • Yixin Cai,
  • Fan Zhang,
  • Jiangyan Zhao,
  • Boyuan Yao,
  • Zhaoyu Qin,
  • Nidan Qiao,
  • Ruofan Huang,
  • Jinwen Feng,
  • Yongfei Wang,
  • Wenting Rui,
  • Fuchu He,
  • Yao Zhao,
  • Chen Ding

DOI
https://doi.org/10.1038/s41467-024-52285-7
Journal volume & issue
Vol. 15, no. 1
pp. 1 – 32

Abstract

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Abstract Skull-base chordoma is a rare, aggressive bone cancer with a high recurrence rate. Despite advances in genomic studies, its molecular characteristics and effective therapies remain unknown. Here, we conduct integrative genomics, transcriptomics, proteomics, and phosphoproteomics analyses of 187 skull-base chordoma tumors. In our study, chromosome instability is identified as a prognostic predictor and potential therapeutic target. Multi-omics data reveals downstream effects of chromosome instability, with RPRD1B as a putative target for radiotherapy-resistant patients. Chromosome 1q gain, associated with chromosome instability and upregulated mitochondrial functions, lead to poorer clinical outcomes. Immune subtyping identify an immune cold subtype linked to chromosome 9p/10q loss and immune evasion. Proteomics-based classification reveals subtypes (P-II and P-III) with high chromosome instability and immune cold features, with P-II tumors showing increased invasiveness. These findings, confirmed in 17 paired samples, provide insights into the biology and treatment of skull-base chordoma.