Liquid biopsy-based identification of prognostic and immunotherapeutically relevant gene signatures in lower grade glioma

Abstract

Background Recent studies have shown that immunotherapies, including peptide vaccines, remain promising strategies for patients with lower grade glioma (LGG); however new biomarkers need to be developed to identify patients who may benefit from therapy. We aimed to investigate the feasibility of liquid biopsy-based gene signatures in predicting the prognosis of LGG patients, as well as the benefits of immunotherapy. Methods We evaluated the association between circulating immune cells and treatment response by analyzing peripheral blood mononuclear cell (PBMC) samples from LGG patients receiving peptide vaccine immunotherapy, identified response-related genes (RRGs), and constructed RRG-related Response Score. In addition, RRG-related RiskScore was constructed in LGG tumor samples based on RRGs; association analysis for RiskScore and characteristics of TME as well as patient prognosis were performed in two LGG tumor datasets. The predictive power of RiskScore for immunotherapy benefits was analyzed in an anti-PD-1 treatment cohort. Results This study demonstrated the importance of circulating immune cells, including monocytes, in the immunotherapeutic response and prognosis of patients with LGG. Overall, 43 significant RRGs were identified, and three clusters with different characteristics were identified in PBMC samples based on RRGs. The constructed RRG-related Response Score could identify patients who produced a complete response to peptide vaccine immunotherapy and could predict prognosis. Additionally, three subtypes were identified in LGG tumors based on RRGs, with subtype 2 being an immune “hot” phenotype suitable for immune checkpoint therapy. The constructed RRG-related RiskScore was significantly positively correlated with the level of tumor immune cell infiltration. Patients with high RiskScore had a worse prognosis and were more likely to respond to immune checkpoint therapy. The therapeutic advantage and clinical benefits of patients with a high RiskScore were confirmed in an anti-PD-1 treatment cohort. Conclusion This study confirmed the potential of liquid biopsy for individualized treatment selection in LGG patients and determined the feasibility of circulating immune cells as biomarkers for LGG. Scoring systems based on RRGs can predict the benefits of immunotherapy and prognosis in patients with LGG. This work would help to increase our understanding of the clinical significance of liquid biopsy and more effectively guide individualized immunotherapy strategies.

Identification of molecular subtypes and a risk model based on inflammation-related genes in patients with low grade glioma

“…The 245 prognostic IRGs were used to identify potential inflammation-related molecular subtypes in LGG. We utilized the “ConsensusClusterPlus” R package to conduct the cluster analysis, with the parameters set according to our previous description [ 25 ].…”

Single-Cell Transcriptomics of Glioblastoma Reveals Pericytes Contributing to Blood–Brain Tumor Barrier and Tumor Progression

“…Prognostically relevant DEGs with prognostic value in all three cohorts were screened using Venn diagrams. Subsequently, risk models were constructed in the CGGA cohort using a similar approach as before [50]. Brie y, the prognosis relevant DEGs were downscaled for further screening using the least absolute shrinkage and selector operation (LASSO) algorithm.…”