Quantitative Evaluation of Stem-like Markers of Human Glioblastoma Using Single-Cell RNA Sequencing Datasets

Abstract

Targeting glioblastoma (GBM) stem-like cells (GSCs) is a common interest in both the laboratory investigation and clinical treatment of GBM. Most of the currently applied GBM stem-like markers lack validation and comparison with common standards regarding their efficiency and feasibility in various targeting methods. Using single-cell RNA sequencing datasets from 37 GBM patients, we obtained a large pool of 2173 GBM stem-like marker candidates. To evaluate and select these candidates quantitatively, we characterized the efficiency of the candidate markers in targeting the GBM stem-like cells by their frequencies and significance of being the stem-like cluster markers. This was followed by further selection based on either their differential expression in GBM stem-like cells compared with normal brain cells or their relative expression level compared with other expressed genes. The cellular location of the translated protein was also considered. Different combinations of selection criteria highlight different markers for different application scenarios. By comparing the commonly used GSCs marker CD133 (PROM1) with markers selected by our method regarding their universality, significance, and abundance, we revealed the limitations of CD133 as a GBM stem-like marker. Overall, we propose BCAN, PTPRZ1, SOX4, etc. for laboratory-based assays with samples free of normal cells. For in vivo targeting applications that require high efficiency in targeting the stem-like subtype, the ability to distinguish GSCs from normal brain cells, and a high expression level, we recommend the intracellular marker TUBB3 and the surface markers PTPRS and GPR56.

Protein Tyrosine Phosphatase Receptor Zeta 1 as a Potential Target in Cancer Therapy and Diagnosis

“…Finally, a recent study that used single-cell RNA-sequencing datasets from 37 GBM patients to look for GBM stem-like marker candidates identified PTPRZ1 as one of the most highly expressed surface markers to be used for GBM stem cell isolation and identification [129].…”

Biomarkers in the Era of Precision Oncology

“…The authors also proposed the use of validated biomarkers, such as TMB, mismatch repair deficiency, and the PD-L1 expression level combined with novel emerging biomarkers linked to the immune TME to guide the selection of appropriate individualized therapeutic strategies and to improve the clinical benefits. In these lines, He et al [ 17 ] proposed the therapeutic targeting of GBM stem-like cells (GSCs) via the discovery of GSCs specific markers. They have identified such markers using publicly available scRNA-seq data and by taking into account various reality-relevant parameters including the universality and significance of these markers, their unique expression in GSCs (and not normal brain cells), as well as the level of expression and their cellular location.…”