Identification of LARS as an essential gene for osteosarcoma proliferation through large-Scale CRISPR-Cas9 screening database and experimental verification

Abstract

Background Osteosarcoma is one of the most malignant tumors, and it occurs mostly in children and adolescents. Currently, surgery and chemotherapy are the main treatments. The recurrence rate is high and the prognosis is often poor. Finding an effective target gene therapy for osteosarcoma may effectively improve its prognosis. Method In this study, genes essential for the survival of osteosarcoma cells were identified by genome-wide screening of CRISPR-Cas9 based on the DepMap database. The expression of these essential genes in osteosarcoma patients’ tissues and normal tissues was identified in the GSE19276 database. Functional pathway enrichment analysis, protein interaction network construction, and LASSO were performed to construct a prognostic risk model based on these essential genes. CCK8 assay was used to detect the effect of essential gene-LARS (Leucyl-TRNA Synthetase 1) on the proliferation of osteosarcoma. Results In this study, 785 genes critical for osteosarcoma cell proliferation were identified from the DepMap. Among these 785 essential genes, 59 DEGs were identified in osteosarcoma tissues. In the functional enrichment analysis, these 59 essential genes were mainly enriched in cell cycle-related signaling pathways. Furthermore, we established a risk score module, including LARS and DNAJC17, screened from these 59 genes, and this module could divide osteosarcoma patients into the low-risk and high-risk groups. In addition, knockdown of LARS expression inhibited the proliferative ability of osteosarcoma cells. A significant correlation was found between LARS expression and Monocytic lineage, T cells, and Fibroblasts. Conclusion In conclusion, LARS was identified as an essential gene for survival in osteosarcoma based on the DepMap database. Knockdown of LARS expression significantly inhibited the proliferation of osteosarcoma cells, suggesting that it is involved in the formation and development of osteosarcoma. The results are useful as a foundation for further studies to elucidate a potential osteosarcoma diagnostic index and therapeutic targets.

Essential genes analysis reveals small ribosomal subunit protein eS28 may be a prognostic factor and potential vulnerability in osteosarcoma

“…In the present research, we first identified essential genes based on the DepMap database, a large-scale CRISPR-Cas9 and RNAi database. Gene dependencies in 13 kinds of osteosarcoma cell lines are recorded in the database [20] . GSEA analysis revealed that these essential genes were mainly enriched in the ribosome pathway.…”

CRISPR-Cas9 identifies growth-related subtypes of glioblastoma with therapeutical significance through cell line knockdown

“…Growth-related genes screened by CRISPR-Cas 9 have already been used in several studies [ 9 , 10 ]. GGSs were established based on growth-related genes of GBM obtained by CRISPR-Case 9 screening, and we found that growth-related genes of GBM all were indicators of poor prognosis.…”

“…To further verify that LARS is an essential gene for osteosarcoma growth, cellular experiments were conducted. It provides a new perspective on the risk stratification of osteosarcoma [9]. Similarly, Ho et al used the lung adenocarcinoma growth-related genes obtained from the DepMap database to perform consensus clustering, which divided patients into subgroups with different prognoses, further enriching the classification of lung adenocarcinoma [10].…”

Exosomal miRNA Changes Associated with Restoration to Sinus Rhythm in Atrial Fibrillation Patients

“…Its downregulation may impact cardiovascular responses and adaptations to physical activity, showing improved exercise tolerance. LARS regulates protein synthesis, especially the attachment of leucine to tRNA, and suppresses osteosarcoma cells [32]. Its downregulation might influence protein synthesis and metabolic processes.…”