Structural variation drives enhancer hijacking via 3D genome disruption in ccRCC - Scorecard - MDSpire

Structural variation drives enhancer hijacking via 3D genome disruption in ccRCC

  • By

  • Yu Dong

  • Wenjiao Xia

  • Zitong Yang

  • Liangliang Ren

  • Hongru Wang

  • Yiyang Zhou

  • Qinchen Li

  • Zhi Chen

  • Zhinan Xia

  • Yichun Zheng

  • Feifan Wang

  • Ning He

  • Bing Cheng

  • Dongmei Ma

  • Wei Shao

  • Wei Guo

  • Shuwen Wang

  • Ziqiao Liu

  • Junxiao Shen

  • Yiming Qi

  • Xuke Gong

  • Juan Jin

  • Bo Xie

  • Guixin Zhu

  • Cheng Zhang

  • January 6, 2026

  • 0 min

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Clinical Scorecard: Enhancer Hijacking in Clear Cell Renal Cell Carcinoma is Driven by Structural Variation and Disruption of 3D Genome Architecture

At a Glance

CategoryDetail
ConditionClear cell renal cell carcinoma (ccRCC), a predominant and aggressive subtype of renal cell carcinoma
Key MechanismsStructural variants (SVs) disrupt 3D genome architecture leading to enhancer hijacking and aberrant oncogene activation
Target PopulationPatients with clear cell renal cell carcinoma, including those with primary tumors and metastatic disease
Care SettingOncology and urology clinical settings focusing on diagnosis, surgical treatment, and molecular targeted therapy development

Key Highlights

  • ccRCC is characterized by high heterogeneity, aggressiveness, and resistance to radiotherapy and chemotherapy, with poor survival outcomes.
  • Long-read sequencing reveals extensive structural variants that alter 3D chromatin organization, influencing gene regulation in ccRCC.
  • A novel enhancer hijacking event activating proto-oncogene SEMA5B was identified, providing potential therapeutic and prognostic targets.

Guideline-Based Recommendations

Diagnosis

  • Utilize next-generation and long-read whole-genome sequencing to detect structural variants in ccRCC.
  • Incorporate 3D genomic interaction assays such as Hi-C sequencing to assess chromatin architecture disruptions.

Management

  • Standard treatment remains radical nephrectomy or partial nephrectomy.
  • Develop targeted therapies addressing SV-driven oncogenic mechanisms, including enhancer hijacking events.

Monitoring & Follow-up

  • Monitor for disease recurrence and progression post-surgery due to high relapse rates.
  • Employ molecular profiling to guide prognosis and therapeutic decisions.

Risks

  • High risk of metastasis at diagnosis (25–30%) and recurrence (20–40%) after surgery.
  • Intrinsic resistance to radiotherapy and chemotherapy limits treatment options.

Patient & Prescribing Data

Patients diagnosed with clear cell renal cell carcinoma, including those undergoing surgical and molecular diagnostic evaluation.

Current treatments are primarily surgical; molecular insights into SVs and enhancer hijacking may inform future targeted therapies and prognostic models.

Clinical Best Practices

  • Incorporate advanced genomic sequencing techniques to characterize SVs and 3D genome alterations in ccRCC.
  • Use integrative multi-omics approaches (WGS, Hi-C, ChIP-seq, RNA-seq) for comprehensive tumor profiling.
  • Consider molecular findings such as enhancer hijacking events in developing personalized treatment and prognostic strategies.

References

Original Source(s)

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