Revealing Endoplasmic Reticulum Stress-Related CAF Subpopulations Associated with Chordoma Progression

Genetics Life Sciences Immunology Oncology Medicine Cell Biology
Endoplasmic Reticulum Stress Cancer-Associated Fibroblasts Chordoma Single-Cell RNA Sequencing Spatial Transcriptomics

Title Page

Introduction

Chordoma is a rare and locally aggressive mesenchymal tumor, believed to originate from the remnant tissues of the primitive notochord. The incidence of chordoma is approximately 0.8 per million, with a predilection for the sacral and skull base regions. Currently, the optimal treatment strategy is maximal safe surgical resection followed by radiotherapy. However, due to the invasive growth pattern of the tumor and its proximity to critical neurovascular structures, complete resection remains challenging. Consequently, many patients experience local recurrence or even distant metastasis after surgery, leading to poor prognosis. Therefore, elucidating the molecular biological characteristics of chordoma is crucial for developing more effective therapeutic strategies.

Research Background

The prominent matrix-rich feature of chordoma tissues may be closely related to its progressive development. Previous retrospective studies have shown that the tumor-matrix ratio is positively correlated with the invasive phenotype, immunosuppressive microenvironment, and poor prognosis of chordoma. As the main component of the matrix cells, cancer-associated fibroblasts (CAFs) play a critical role in the tumor microenvironment. However, the impact of CAFs on the biological behavior of chordoma remains unclear.

Single-cell RNA sequencing (scRNA-seq) can help delineate different cell types and their complex lineages within the tumor microenvironment. The recently established spatial transcriptomics technique allows the analysis of cell types and their gene expression changes at the structural and spatial levels. This study aimed to determine the types, spatial distribution, and clinical significance of CAFs in the chordoma microenvironment by combining these two sequencing technologies.

Research Team and Publication

This study was a collaborative effort by a multidisciplinary team from the Indiana University School of Medicine, USA, the University of Toledo College of Medicine, USA, Hunan University Affiliated Hospital, China, and Peking University People’s Hospital, China. The relevant findings were published in the prestigious international journal Neuro-Oncology (Volume 26, Issue 2, 2024).

Main Research Content and Findings

1. Single-cell transcriptomic analysis revealed a unique CAF subgroup associated with chordoma progression

Researchers performed scRNA-seq on samples from 6 chordoma patients (3 primary and 3 recurrent) and 3 normal nucleus pulposus samples. A total of 10 major cell types were identified, including epithelial-like cells (potentially tumor cells), monocytes/macrophages, T cells, endothelial cells, neutrophils, B cells, osteoblasts, fibroblasts, chondrocytes, and smooth muscle cells.

Further analysis revealed that CAFs could be divided into 4 subgroups (CAF-1, CAF-2, CAF-3, and CAF-4). Among these, the CAF-2 subgroup was enriched in recurrent tumors, highly expressed stress-related genes (e.g., hspa1a, hspa1b, dnajb1) and hypoxia-related genes (e.g., hif1a, vegfa), and was closely associated with the endoplasmic reticulum stress response (ERS). Trajectory analysis suggested that CAF-2 originated from normal fibroblasts and could extensively interact with tumor cells and immune cells.

2. Bulk RNA sequencing validated the association between the ERS-CAF subgroup score and chordoma progression and prognosis

Using bulk RNA sequencing data from 126 chordoma patients, researchers found that the ERS-CAF subgroup score was significantly associated with the invasive phenotype, higher-grade differentiation, and poor prognosis of the tumors.

3. Spatial transcriptomics confirmed the existence of the ERS-CAF subgroup and its proximity to tumor cells

Spatial transcriptomics analysis of 3 fresh tumor samples verified the existence of the ERS-CAF subgroup in chordoma tissues. Further analysis revealed that the ERS-CAF subgroup exhibited the strongest affinity for surrounding tumor cells compared to other cell types.

4. Immunofluorescence analysis confirmed the association between the density of the ERS-CAF subgroup, its proximity to tumor cells, and patient prognosis

Using multiplex immunofluorescence analysis on tumor samples from 105 chordoma patients, the researchers found that:

  • The ERS-CAF subgroup was abundant in the chordoma microenvironment and localized in areas adjacent to tumor cells.
  • The density of ERS-CAFs and their distance from tumor cells were significantly associated with the invasive phenotype and poor prognosis of the tumors.

5. Cell-cell communication analysis suggested that ERS-CAFs may promote chordoma progression through direct crosstalk with tumor cells

Through cell-cell communication analysis, researchers predicted that ERS-CAFs might directly interact with tumor cells through multiple signaling pathways, such as JAM2/ITGB1, TNC/SDC4, and THBS1/CD47, thereby influencing the biological behavior of tumor cells.

Research Significance

This study is the first to reveal the heterogeneous characteristics of CAFs in the chordoma microenvironment and identify a unique ERS-CAF subgroup closely associated with disease progression. The ERS-CAF subgroup may promote the malignant progression of chordoma through direct interactions with tumor cells, providing new insights for the development of precision therapeutic targets. The research findings lay the foundation for a deeper understanding of the role of CAFs in the pathogenesis and development of chordoma.