Single-cell RNA-seq identification of four differentially expressed survival-related genes by a TARGET: Osteosarcoma database analysis

M. Feleke; W. Feng; E. Rothzerg; D. Song; Q. Wei; S. Kõks; D. Wood; Y. Liu; J. Xu

doi:10.1177/15353702221080131

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Single-cell RNA-seq identification of four differentially expressed survival-related genes by a TARGET: Osteosarcoma database analysis

Journal article

Peer reviewed

Single-cell RNA-seq identification of four differentially expressed survival-related genes by a TARGET: Osteosarcoma database analysis

M. Feleke, W. Feng, E. Rothzerg, D. Song, Q. Wei, S. Kõks, D. Wood, Y. Liu and J. Xu

Experimental Biology and Medicine

2022

DOI: https://doi.org/10.1177/15353702221080131

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Abstract

Osteosarcoma (OS) differentially expressed genes (DEGs) have been predicted using the data portal of the Therapeutically Applicable Research to Generate Effective Treatments (TARGET). In this study, we sought to identify cell types that specially express key DEGs (MUC1, COL13A1, JAG2, and KAZALD1) in each of the nine identified cell populations derived from tissues of OS tumors with single-cell RNA-sequencing data. Gene expression levels were pairwise compared between cell clusters and a p value < 0.05 was considered differentially expressed. It was revealed that MUC1 is expressed at high levels in osteoblastic OS cells followed by carcinoma-associated fibroblasts (CAFs) and plasmocytes, respectively. COL13A1 is highly expressed in osteoblastic OS cells, CAFs, and endothelial cells (ECs), respectively. The KAZALD1 gene is expressed in CAFs and osteoblastic OS cells at high levels, but at very low levels in plasmocytes, osteoclasts, NK/T, myeloid cells 1, myeloid cells 2, ECs, and B cells. JAG2 is expressed at significantly high levels in ECs and osteoblastic OS cells, and at relatively lower levels in all other cell types. Interestingly, LSAMP, as an established gene in the development of OS shows high expression in osteoblastic OS cells and CAFs but low in other cells such as osteoclasts. Our findings here highlight the heterogeneity of OS cells and cell-type-dependent DEGs which have potential as therapeutic targets in OS.

Details

Title: Single-cell RNA-seq identification of four differentially expressed survival-related genes by a TARGET: Osteosarcoma database analysis
Authors/Creators: M. Feleke (Author/Creator) - The University of Western Australia
W. Feng (Author/Creator) - First Affiliated Hospital of GuangXi Medical University
E. Rothzerg (Author/Creator) - The University of Western Australia
D. Song (Author/Creator) - Guangxi Medical University
Q. Wei (Author/Creator) - First Affiliated Hospital of GuangXi Medical University
S. Kõks (Author/Creator) - Murdoch University
D. Wood (Author/Creator) - The University of Western Australia
Y. Liu (Author/Creator) - First Affiliated Hospital of GuangXi Medical University
J. Xu (Author/Creator) - The University of Western Australia
Publication Details: Experimental Biology and Medicine
Publisher: SAGE Publications
Identifiers: 991005540003907891
Copyright: © 2022 by The Society for Experimental Biology and Medicine
Murdoch Affiliation: Centre for Molecular Medicine and Innovative Therapeutics
Language: English
Resource Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Citation topics: 1 Clinical & Life Sciences; 1.118 Soft Tissue, Bone & Nerve Cancers; 1.118.300 Sarcoma Research
Web Of Science research areas: Medicine, Research & Experimental
ESI research areas: Clinical Medicine