Selection of lncRNAs That Influence the Prognosis of Osteosarcoma Based on Copy Number Variation Data

Zhang, Jian; Huang, Chi Yo; Zhu, Gui‐Qi; He, Guanyi; Xu, Wenbo; Li, Jianming; Wang, Dong; Han, Kecheng; Shen, Zancong; Liu, Jianyu

doi:10.1155/2022/8024979

Cited by 8 publications

(8 citation statements)

References 39 publications

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“…Moreover, the GSEA analysis of signaling pathways revealed signi cant enrichment of RAMP1 in the olfactory transduction processes, providing insight into the mechanisms underlying its prognostic role. Consistent with the current conclusion, earlier research has indicated that olfactory transduction processes may be a potential mechanism associated with OS prognosis 24 . In addition, the KEGG pathway analysis revealed an abundance of genes involved in the Hippo and Wnt signaling pathway.…”

Section: Discussionsupporting

confidence: 92%

RAMP1 as a Novel Prognostic Biomarker in Pan-cancer and Osteosarcoma

Xie

Xiao

Fang

et al. 2023

Preprint

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Receptor activity modifying protein 1 (RAMP1) facilitates the localization of the calcitonin-like receptor (CLR) to the plasma membrane, but its role in osteosarcoma (OS) remains unclear. We evaluated the RAMP1 expression and prognostic value across different cancers, studying tumor immune infiltration. The prognostic value was analyzed using the GSE39058 and TARGET datasets. Differential gene expression was evaluated. a protein-protein interaction network was constructed, and gene set enrichment analysis was performed. The function of RAMP1 in the tumor microenvironment was analyzed, and its expression in OS cell lines was validated using quantitative real-time PCR. High RAMP1 expression correlated with poor prognosis relative to low RAMP1 expression (p < 0.05). Low RAMP1 expression correlated with an abundance of CD4 + memory-activated T cells. whereas a high expression level correlated with a high proportion of gamma-delta T cells (γδ T cells). Differentially expressed genes from TARGET was enriched in olfactory transduction pathways (normalized enrichment scores [NES] = 1.6998, p < 0.0001). RAMP1 expression negatively correlated with CD44 expression but positively correlated with TNFSF9 expression. The RAMP1 gene is substantially expressed in OS cells compared to the normal osteoblast cell line hFOB1.19. Thus, RAMP1 may be a prognostic biomarker and potential therapeutic target in OS.

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Section: Discussionsupporting

confidence: 92%

RAMP1 as a Novel Prognostic Biomarker in Pan-cancer and Osteosarcoma

Xie

Xiao

Fang

et al. 2023

Preprint

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show abstract

“…Moreover, the GSEA analysis of signaling pathways revealed significant enrichment of RAMP1 in the olfactory transduction processes, providing insight into the mechanisms underlying its prognostic role. Consistent with the current conclusion, earlier research has indicated that olfactory transduction processes may be a potential mechanism associated with OS prognosis [ 25 ]. In addition, the KEGG pathway analysis revealed an abundance of genes involved in the Hippo and Wnt signaling pathway.…”

Section: Discussionsupporting

confidence: 92%

RAMP1 as a novel prognostic biomarker in pan-cancer and osteosarcoma

Xie,

Xiao,

Fang

et al. 2023

PLoS ONE

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Receptor activity modifying protein 1 (RAMP1) facilitates the localization of the calcitonin-like receptor (CLR) to the plasma membrane, but its role in osteosarcoma (OS) remains unclear. We evaluated the RAMP1 expression and prognostic value across different cancers, studying tumor immune infiltration. The prognostic value was analyzed using the GSE39058 and TARGET datasets. Differential gene expression was evaluated. a protein-protein interaction network was constructed, and gene set enrichment analysis was performed. The function of RAMP1 in the tumor microenvironment was analyzed, and its expression in OS cell lines was validated using quantitative real-time PCR. High RAMP1 expression correlated with poor prognosis relative to low RAMP1 expression (p < 0.05). Low RAMP1 expression correlated with an abundance of CD4+ memory-activated T cells. whereas a high expression level correlated with a high proportion of gamma-delta T cells (γδ T cells). Differentially expressed genes from TARGET was enriched in olfactory transduction pathways (normalized enrichment scores [NES] = 1.6998, p < 0.0001). RAMP1 expression negatively correlated with CD44 expression but positively correlated with TNFSF9 expression. The RAMP1 gene is substantially expressed in OS cells compared to the normal osteoblast cell line hFOB1.19. Thus, RAMP1 may be a prognostic biomarker and potential therapeutic target in OS.

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“…The study of Zhang et al [ 25 ] and Yang et al [ 26 ] were included into our study to compare the AUC values between our model and their models. By comparing the AUC values of 1-year, 3-years, and 5-years between models, we found that the model in our study was more effective (Figures 6(j–l) ).…”

Section: Resultsmentioning

confidence: 99%

The Cuproptosis-Related Long Noncoding RNA Signature Predicts Prognosis and Tumour Immune Analysis in Osteosarcoma

Jiang

Chu

Lai³

et al. 2022

Computational and Mathematical Methods in Medicine

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Background. Cuprotopsis is a type of programmed cell death discovered in recent years. Long noncoding RNAs (lncRNAs) play an important regulatory role in programmed cell death. The effect of cuproptosis-related lncRNAs on osteosarcoma is unknown. Our work, based on cuproptosis-related lncRNAs, proposes a gene signature to assess the prognosis of patients with osteosarcoma. Methods. Osteosarcoma gene expression data from The Cancer Genome Atlas (TCGA), clinical features of osteosarcoma and RNA sequencing data of normal adipose tissue were obtained from the UCSC Xena database. A cuproptosis-related lncRNA risk model was established to calculate the risk score. At the same time, cluster analysis, clinicopathological analysis, functional enrichment analysis, and prediction of compounds with potential therapeutic value were evaluated. We analyzed whether there was a correlation between the risk score and tumour immunity. RT-qPCR was used to verify the expression level of lncRNA. Results. Nine lncRNAs (AC124798.1, AC006033.2, AL450344.2, AL512625.2, LINC01060, LINC00837, AC004943.2, AC064836.3, and AC100821.2) were identified to create a risk model and indicate the prognosis of patients with osteosarcoma. The high-risk group had a worse prognosis than the low-risk group. Analysis of clinicopathological features, principal component analysis, receiver operating characteristic curve, c-index curve, and comparative analysis of models proved that the model is reliable. Functional enrichment analysis suggests that the risk score may correlate with cell energy metabolism and tumour-related biological function. Three potentially therapeutic compounds have been predicted. These analyses may be beneficial to the treatment of osteosarcoma in the future. RT-qPCR verified the expression level of three lncRNA (LINC01060, NKILA, and SNHG8). Conclusions. Cuproptosis-related lncRNAs have a strong relationship with osteosarcoma patients. Nine lncRNA models can effectively forecast the prognosis of osteosarcoma and may play a significant role in the individualized treatment of osteosarcoma patients in the future.

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Selection of lncRNAs That Influence the Prognosis of Osteosarcoma Based on Copy Number Variation Data

Cited by 8 publications

References 39 publications

RAMP1 as a Novel Prognostic Biomarker in Pan-cancer and Osteosarcoma

RAMP1 as a Novel Prognostic Biomarker in Pan-cancer and Osteosarcoma

RAMP1 as a novel prognostic biomarker in pan-cancer and osteosarcoma

The Cuproptosis-Related Long Noncoding RNA Signature Predicts Prognosis and Tumour Immune Analysis in Osteosarcoma

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