A five metastasis-related long noncoding RNA risk signature for osteosarcoma survival prediction

Yu, Siyuan; Shao, Fengling; Liu, Huijun; Liu, Qingqing

doi:10.1186/s12920-021-00972-5

Cited by 6 publications

(7 citation statements)

References 38 publications

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“…Based on the risk scores, we divided the patients into a high-risk group (>0.975) and a low-risk group (<0.975), and then calculated the five-year survival rate by Kaplan–Meier analysis. In comparison with other signatures, our AUC value of 0.784 was larger than the 0.745 AUC value of SiYuan Yu’s signature ( Yu et al, 2021 ). This confirmed that our prognostic signature was convincing and had the potential to evaluate the survival of patients with osteosarcoma.…”

Section: Discussioncontrasting

confidence: 73%

“…Although several previous studies have identified a series of lncRNAs that play an important role in osteosarcoma, proof of the efficacy of lncRNAs as prognostic markers of osteosarcoma is still limited. SiYuan Yu et al identified a five-lncRNA, metastasis-related risk signature for osteosarcoma survival prediction, and the AUC for predicting 5-year survival was 0.745 ( Yu et al, 2021 ). Gao et al (2020 ) constructed a multivariable Cox regression model based on seven lncRNAs for prognosis prediction, among which AC011442.1 was assumed to act as an oncogenic driver in osteosarcoma.…”

Section: Discussionmentioning

confidence: 99%

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A four-lncRNA risk signature for prognostic prediction of osteosarcoma

et al. 2023

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Aim: Osteosarcoma is the most common primary malignant tumor of bone. However, our understanding of the prognostic indicators and the genetic mechanisms of the disease progression are still incomplete. The aim of this study was to identify a long noncoding RNA (lncRNA) risk signature for osteosarcoma survival prediction.Methods: RNA sequencing data and relevant clinical information of osteosarcoma patients were downloaded from the database of Therapeutically Applicable Research to Generate Effective Treatments (TARGET). We analyzed the differentially expressed lncRNAs between deceased and living patients by univariate and multivariate Cox regression analysis to identify a risk signature. We calculated a prognostic risk score for each sample according to this prognosis signature, and divided patients into high-risk and low-risk groups according to the median value of the risk score (0.975). Kaplan–Meier analysis and receiver operating characteristic (ROC) curve statistics were used to evaluate the performance of the signature. Next, we analyzed the signature’s potential function through Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene-set enrichment analysis (GSEA). Lastly, qRT-PCR was used to validate the expression levels of the four lncRNAs in clinical samples.Results: Twenty-six differentially expressed lncRNAs were identified between deceased and living patients. Four of these lncRNAs (CTB-4E7.1, RP11-553A10.1, RP11-24N18.1, and PVRL3-AS1) were identified as independent prognostic factors, and a risk signature of these four lncRNAs for osteosarcoma survival prediction was constructed. Kaplan–Meier analysis showed that the five-year survival time in high-risk and low-risk groups was 33.1% and 82.5%, and the area under the curve (AUC) of the ROC was 0.784, which demonstrated that the prognostic signature was reliable and had the potential to predict the survival of patients with osteosarcoma. The expression level of the four lncRNAs in osteosarcoma tissues and cells was determined by qRT-PCR. Functional enrichment analysis suggested that the signature might be related to osteosarcoma through regulation of the MAPK signaling pathway, the PI3K-Akt signaling pathway, and the extracellular matrix and also provided new insights into the study of osteosarcoma, including the role of papillomavirus infection, olfactory receptor activity, and olfactory transduction in osteosarcoma.Conclusion: We constructed a novel lncRNA risk signature that served as an independent biomarker for predicting the prognosis of osteosarcoma patients.

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Section: Discussioncontrasting

confidence: 73%

Section: Discussionmentioning

confidence: 99%

A four-lncRNA risk signature for prognostic prediction of osteosarcoma

et al. 2023

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“…The four EMGs identified included the well-characterized genes MYC, TERT, EIF4E3, and RBM34 [ 73 ]. Consulting the same TARGET database, Yu et al, 2021 found that five lncRNAs (RP11-128N14.5, RP11-231/13.2, RP5-894D12.4, LAMA5-AS1, and RP11-346L1.2) served as a reliable prognostic signature for OS patients with an AUC (area under the curve) prediction for the 5-year survival rate at a 0.745 accuracy [ 74 ]. Both of these studies offer promise for improving the prognoses of OS patients.…”

Section: Treatmentsmentioning

confidence: 99%

Epigenetic Changes Associated with Osteosarcoma: A Comprehensive Review

Twenhafel,

Moreno,

Punt

et al. 2023

Cells

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Osteosarcoma is the most common malignant primary bone tumor in children and adolescents. While clinical outcomes have improved, the 5-year survival rate is only around 60% if discovered early and can require debilitating treatments, such as amputations. A better understanding of the disease could lead to better clinical outcomes for patients with osteosarcoma. One promising avenue of osteosarcoma research is in the field of epigenetics. This research investigates changes in genetic expression that occur above the genome rather than in the genetic code itself. The epigenetics of osteosarcoma is an active area of research that is still not fully understood. In a narrative review, we examine recent advances in the epigenetics of osteosarcoma by reporting biomarkers of DNA methylation, histone modifications, and non-coding RNA associated with disease progression. We also show how cancer tumor epigenetic profiles are being used to predict and improve patient outcomes. The papers in this review cover a large range of epigenetic target genes and pathways that modulate many aspects of osteosarcoma, including but not limited to metastases and chemotherapy resistance. Ultimately, this review will shed light on the recent advances in the epigenetics of osteosarcoma and illustrate the clinical benefits of this field of research.

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“…Similarly, high level of HULC is also link to poor prognosis of OS patients (83, 84). Yu and colleagues interrogated the OS dataset from TARGET (84). Among a total of 97 samples that have RNA-seq results, they found 24 metastatic samples and 73 non-metastatic samples; and then identified RP11-128N14.5, RP11-231|13.2, RP5-894D12.4, LAMA5-AS1 and RP11-346L1.2 as metastasis-related lncRNAs that can be used as potential prognostic indicator for OS.…”

Section: Lncrna Acts As a Predictive Biomarkermentioning

confidence: 99%

Roles of lncRNAs in childhood cancer: Current landscape and future perspectives

et al. 2023

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According to World Health Organization (WHO), cancer is the leading cause of death for children and adolescents. Leukemias, brain cancers, lymphomas and solid tumors, such as neuroblastoma, ostesarcoma and Wilms tumors are the most common types of childhood cancers. Approximately 400,000 children and adolescents between the ages of 0 and 19 are diagnosed with cancer each year worldwide. The cancer incidence rates have been rising for the past few decades. Generally, the prognosis of childhood cancers is favorable, but the survival rate for many unresectable or recurring cancers is substantially worse. Although random genetic mutations, persistent infections, and environmental factors may serve as contributing factors for many pediatric malignancies, the underlying mechanisms are yet unknown. Long non-coding RNAs (lncRNAs) are a group of transcripts with longer than 200 nucleotides that lack the coding capacity. However, increasing evidence indicates that lncRNAs play vital regulatory roles in cancer initiation and development in both adults and children. In particular, many lncRNAs are stable in cancer patients’ body fluids such as blood and urine, suggesting that they could be used as novel biomarkers. In support of this notion, lncRNAs have been identified in liquid biopsy samples from pediatric cancer patients. In this review, we look at the regulatory functions and underlying processes of lncRNAs in the initiation and progression of children cancer and discuss the potential of lncRNAs as biomarkers for early detection. We hope that this article will help researchers explore lncRNA functions and clinical applications in pediatric cancers.

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A five metastasis-related long noncoding RNA risk signature for osteosarcoma survival prediction

Cited by 6 publications

References 38 publications

A four-lncRNA risk signature for prognostic prediction of osteosarcoma

A four-lncRNA risk signature for prognostic prediction of osteosarcoma

Epigenetic Changes Associated with Osteosarcoma: A Comprehensive Review

Roles of lncRNAs in childhood cancer: Current landscape and future perspectives

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