Related Experiment Video
Updated: Aug 14, 2026
Characterization of Functionally Associated miRNAs in Glioblastoma and their Engineering into Artificial Clusters for Gene Therapy
Published on: October 4, 2019
Gene Expression Profiling Identifies Two Chordoma Subtypes Associated with Distinct Molecular Mechanisms and Clinical
Jiwei Bai1,2,3, Jianxin Shi4, Yazhuo Zhang1,2,3,5
1Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.
Purpose:
Chordoma is a rare bone tumor with a high recurrence rate and limited treatment options. The aim of this study was to identify molecular subtypes of chordoma that may improve clinical management.
Experimental Design:
We conducted RNA sequencing in 48 tumors from patients with Chinese skull-base chordoma and identified two major molecular subtypes. We then replicated the classification using a NanoString panel in 48 patients with chordoma from North America.
Results:
Tumors in one subtype were more likely to have somatic mutations and reduced expression in chromatin remodeling genes, such as PBRM1 and SETD2, whereas the other subtype was characterized by the upregulation of genes in epithelial-mesenchymal transition and Sonic Hedgehog pathways. IHC staining of top differentially expressed genes between the two subtypes in 312 patients with Chinese chordoma with long-term follow-up data showed that the expression of some markers such as PTCH1 was significantly associated with survival outcomes.
Conclusions:
Our findings may improve the understanding of subtype-specific tumorigenesis of chordoma and inform clinical prognostication and targeted options.
Insights
This study identified two molecular subtypes of chordoma, a rare bone cancer. These subtypes, linked to specific gene pathways and mutations, may improve prognostication and targeted treatment for chordoma patients.
Area of Science:
- Oncology
- Genomics
- Molecular Biology
Background:
- Chordoma is a rare bone tumor with a high recurrence rate.
- Limited treatment options exist for chordoma.
- Understanding molecular heterogeneity is crucial for improved clinical management.
Purpose of the Study:
- To identify molecular subtypes of chordoma.
- To improve clinical management strategies for chordoma.
- To elucidate subtype-specific tumorigenesis.
Main Methods:
- RNA sequencing of 48 Chinese skull-base chordoma tumors.
- Replication of subtype classification using NanoString in 48 North American chordoma patients.
- Immunohistochemistry (IHC) staining of differentially expressed genes in 312 Chinese chordoma patients.
Main Results:
- Two major molecular subtypes of chordoma were identified.
- Subtype 1: associated with somatic mutations and reduced chromatin remodeling gene expression (e.g., PBRM1, SETD2).
- Subtype 2: characterized by upregulation of epithelial-mesenchymal transition and Sonic Hedgehog pathways; PTCH1 expression linked to survival outcomes.
Conclusions:
- Findings enhance understanding of chordoma tumorigenesis.
- Molecular subtypes can inform clinical prognostication.
- Potential for developing targeted therapeutic options based on identified subtypes.
More Related Videos
10:27Testing Targeted Therapies in Cancer using Structural DNA Alteration Analysis and Patient-Derived Xenografts
Published on: July 25, 2020
09:33Author Spotlight: Finding New Therapeutic Targets for Malignant Peripheral Nerve Sheath Tumor Through Genome-Scale shRNA Screens
Published on: August 25, 2023
Related Concept Videos
02:07Tumor Progression
Colon cancer is one of the best-documented examples of tumor progression. Early mutation in the APC gene in colon cells causes a small growth on the colon wall called a polyp. With time, this polyp grows into a benign, pre-cancerous tumor. Further...
02:07Tumor Progression
Colon cancer is one of the best-documented examples of tumor progression. Early mutation in the APC gene in colon cells causes a small growth on the colon wall called a polyp. With time, this polyp grows into a benign, pre-cancerous tumor. Further...