Immune-Related LncRNAs Affect the Prognosis of Osteosarcoma, Which Are Related to the Tumor Immune Microenvironment

Identification and prognostic evaluation of differentially expressed long noncoding RNAs associated with immune infiltration in osteosarcoma

Osteosarcoma is a malignant bone cancer that originates from the bone with the strongest invasiveness. Tumor formation strongly correlates with immune cell infiltration into the tumor immune microenvironment (TIME). Therefore, we aimed to identify TIME-related biomarkers as potential prognostic markers of osteosarcoma. The mRNA and long noncoding RNA (lncRNA) transcriptome data of 88 patients with osteosarcoma and the expression profile of GSE99671 were downloaded from The Cancer Genome Atlas and Gene Expression Omnibus, respectively. Immune infiltration scores and types were evaluated using ESTIMATE and CIBERSORT. A linear model was established to identify the differentially expressed genes (DEGs) and lncRNAs (DElncRNAs). Functional enrichment analysis of DEGs was conducted by Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, gene set enrichment analysis, and gene set variation analysis. DElncRNAs were analyzed using a weighted gene co-expression network. Least absolute shrinkage and selection operator regression was applied to screen for prognostic markers. Patient survival was predicted by the risk score and analyzed by receiver operating characteristic curve. Clinical features affecting patient survival were assessed. Immune infiltration positively correlated with osteosarcoma patient survival. Different immune cell infiltrates in patients with osteosarcma may serve as prognostic indicators and targets for immunotherapy. In total, 1125 DEGs, 80 DElncRNAs, and 11 pairs of co-expressed lncRNA-mRNAs were identified. DEGs in the three modules were associated with immune infiltration into the TIME. Four DElncRNAs, namely AC015819.1, AC015911.3, AL365361.1, and USP30-AS1, showed good prognostic ability for osteosarcoma and were positively correlated with the immune score. Tumor metastasis and risk scores alone were good prognostic indicators, and a combination of the two variables can better predict the prognosis of osteosarcoma. We identified four lncRNAs, AC015819.1, AC015911.3, AL365361.1, and USP30-AS1, as potential biomarkers for osteosarcoma prognosis.

LINC00960 affects osteosarcoma treatment and prognosis by regulating the tumor immune microenvironment

Background

Osteosarcoma (OS), the commonest primary malignant bone tumor, is mainly seen in children and teenagers. LINC00960, a newly discovered long intergenic non-protein coding RNA, has been shown to be important in certain cancers. The objective of this study was to assess LINC00960's prognostic and therapeutic value and analyze its mechanism of action in osteosarcoma.

Methods

With the transcriptome information of 85 osteosarcomas from the TARGET database, the Cox regression analyses, K-M curve, and ROC curve, were conducted for survival and prognostic analysis. The functional analysis was conducted using GO, KEGG, GSEA, and GSVA. The ESTIMATE, ssGSEA, MCP-counter, ImmuCellAI algorithms, and immune checkpoint correlation analysis were performed for immune-related analysis. The single-cell RNA sequencing data of 6 osteosarcoma patients was obtained from the Gene Expression Omnibus database. The Tumor Immune Dysfunction and Exclusion algorithm and the "pRRophetic" R package were performed to predict the response to immunotherapy and chemotherapy.

Results

LINC00960 overexpression is associated with osteosarcoma metastasis and poor prognosis. Based on the LINC00960 expression, the nomogram prediction model was created, which showed good accuracy and precision to predict the overall survival of osteosarcoma. Single-cell and immune-related analysis showed that LINC00960 is mainly highly expressed in the tumor-exhausted CD8 T cells in osteosarcoma. In osteosarcoma, the expression of LIC00960 was favorably connected with immune checkpoint-related genes and negatively correlated with immune infiltration. TIDE analysis indicated that low LINC00960 expression patients might have a better response to immunotherapy. Drug sensitivity analysis showed that high LINC00960 expression patients might have better responses to Bleomycin and Doxorubicin.

Conclusion

LINC00960 has the potential to be a novel biomarker for predicting overall survival in osteosarcoma patients and to guide more individualized treatment and clinical decision-making.

A Newly Established Cuproptosis-Associated Long Non-Coding RNA Signature for Predicting Prognosis and Indicating Immune Microenvironment Features in Soft Tissue Sarcoma

Cuproptosis, a new type of programmed cell death, is involved in the development and progression of malignancies. The study of cuproptosis-associated long non-coding RNAs (lncRNAs) in soft tissue sarcomas (STSs) is however limited. There is also uncertainty regarding the prognostic accuracy of cuproptosis-associated lncRNAs in STSs and their relationship to the tumor immune microenvironment. The aim of this study was to determine the prognostic significance of cuprotosis-associated lncRNAs in STSs and their relationship to the tumor immune microenvironment. Transcriptomic and clinical data from patients with STSs were obtained through The Cancer Genome Atlas (TCGA). Overall, 259 patients were randomly allocated to a training group or a testing group. In the training group, a cuproptosis-associated lncRNA signature was constructed, and the signature was verified in the testing group. On the basis of risk scores and clinical features, we later developed a hybrid nomogram. We also performed functional and tumor immune microenvironment analysis based on the cuproptosis-associated lncRNA signature. A signature of 5 cuproptosis-associated lncRNAs was created. Based on this signature, we categorized STS patients into high-risk and low-risk groups. The study showed that patients at high risk had a worse prognosis than those at low risk. A nomogram was then constructed combining clinical characteristics with the risk scores, and it was shown to have credible predictive power. Functional enrichment and tumor immune microenvironmental analyses showed that high-risk STSs tend to be immunologically sensitive tumors. In our study, we found a cuproptosis-associated lncRNAs signature, which serves as an independent prognostic indicator. Cuproptosis-associated lncRNAs may play a role in the tumor immune microenvironment, which might be a therapeutic target for patients with STSs.