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

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

Quantitative Evaluation of Stem-like Markers of Human Glioblastoma Using Single-Cell RNA Sequencing Datasets. / He, Yue; Døssing, Kristina B.V.; Sloth, Ane Beth; He, Xuening; Rossing, Maria; Kjaer, Andreas.

In: Cancers, Vol. 15, No. 5, 1557, 2023.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

He, Y, Døssing, KBV, Sloth, AB, He, X, Rossing, M & Kjaer, A 2023, 'Quantitative Evaluation of Stem-like Markers of Human Glioblastoma Using Single-Cell RNA Sequencing Datasets', Cancers, vol. 15, no. 5, 1557. https://doi.org/10.3390/cancers15051557

APA

He, Y., Døssing, K. B. V., Sloth, A. B., He, X., Rossing, M., & Kjaer, A. (2023). Quantitative Evaluation of Stem-like Markers of Human Glioblastoma Using Single-Cell RNA Sequencing Datasets. Cancers, 15(5), [1557]. https://doi.org/10.3390/cancers15051557

Vancouver

He Y, Døssing KBV, Sloth AB, He X, Rossing M, Kjaer A. Quantitative Evaluation of Stem-like Markers of Human Glioblastoma Using Single-Cell RNA Sequencing Datasets. Cancers. 2023;15(5). 1557. https://doi.org/10.3390/cancers15051557

Author

He, Yue ; Døssing, Kristina B.V. ; Sloth, Ane Beth ; He, Xuening ; Rossing, Maria ; Kjaer, Andreas. / Quantitative Evaluation of Stem-like Markers of Human Glioblastoma Using Single-Cell RNA Sequencing Datasets. In: Cancers. 2023 ; Vol. 15, No. 5.

Bibtex

@article{0cdf2e8063614b1499a02c8e614677ed,
title = "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.",
keywords = "CD133, CD15, CD24, GBM stem-like markers, glioblastoma stem cells, quantitative evaluation, single-cell RNA sequencing, SOX2",
author = "Yue He and D{\o}ssing, {Kristina B.V.} and Sloth, {Ane Beth} and Xuening He and Maria Rossing and Andreas Kjaer",
note = "Publisher Copyright: {\textcopyright} 2023 by the authors.",
year = "2023",
doi = "10.3390/cancers15051557",
language = "English",
volume = "15",
journal = "Cancers",
issn = "2072-6694",
publisher = "M D P I AG",
number = "5",

}

RIS

TY - JOUR

T1 - Quantitative Evaluation of Stem-like Markers of Human Glioblastoma Using Single-Cell RNA Sequencing Datasets

AU - He, Yue

AU - Døssing, Kristina B.V.

AU - Sloth, Ane Beth

AU - He, Xuening

AU - Rossing, Maria

AU - Kjaer, Andreas

N1 - Publisher Copyright: © 2023 by the authors.

PY - 2023

Y1 - 2023

N2 - 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.

AB - 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.

KW - CD133

KW - CD15

KW - CD24

KW - GBM stem-like markers

KW - glioblastoma stem cells

KW - quantitative evaluation

KW - single-cell RNA sequencing

KW - SOX2

UR - http://www.scopus.com/inward/record.url?scp=85149812819&partnerID=8YFLogxK

U2 - 10.3390/cancers15051557

DO - 10.3390/cancers15051557

M3 - Journal article

C2 - 36900348

AN - SCOPUS:85149812819

VL - 15

JO - Cancers

JF - Cancers

SN - 2072-6694

IS - 5

M1 - 1557

ER -

ID: 340405363