Construction of ceRNA Networks Associated With CD8 T Cells in Breast Cancer

Abstract

BackgroundThe infiltration of CD8 T cells is usually linked to a favorable prognosis and may predict the therapeutic response of breast cancer patients to immunotherapy. The purpose of this research is to investigate the competing endogenous RNA (ceRNA) network correlated with the infiltration of CD8 T cells.MethodsBased on expression profiles, CD8 T cell abundances for each breast cancer (BC) patient were inferred using the bioinformatic method by immune markers and expression profiles. We were able to extract the differentially expressed RNAs (DEmRNAs, DEmiRNAs, and DElncRNAs) between low and high CD8 T-cell samples. The ceRNA network was constructed using Cytoscape. Machine learning models were built by lncRNAs to predict CD8 T-cell abundances. The lncRNAs were used to develop a prognostic model that could predict the survival rates of BC patients. The expression of selected lncRNA (XIST) was validated by quantitative real-time PCR (qRT-PCR).ResultsA total of 1,599 DElncRNAs, 89 DEmiRNAs, and 1,794 DEmRNAs between high and low CD8 T-cell groups were obtained. Two ceRNA networks that have positive or negative correlations with CD8 T cells were built. Among the two ceRNA networks, nine lncRNAs (MIR29B2CHG, NEAT1, MALAT1, LINC00943, LINC01146, AC092718.4, AC005332.4, NORAD, and XIST) were selected for model construction. Among six prevalent machine learning models, artificial neural networks performed best, with an area under the curve (AUC) of 0.855. Patients from the high-risk category with BC had a lower survival rate compared to those from the low-risk group. The qRT-PCR results revealed significantly reduced XIST expression in normal breast samples, which was consistent with our integrated analysis.ConclusionThese results potentially provide insights into the ceRNA networks linked with T-cell infiltration and provide accurate models for T-cell prediction.

Construction of a Cuproptosis-Related lncRNA Signature for Predicting Prognosis and Immune Response in Cervical Cancer

“…was just the opposite. Combined with relevant studies [33,37] , we believe that the signal regulation involved by lnc-AL031775 and lnc-AC005332.4 may play a protective role in the cancer prognosis. We used ROC and c-index curves to validate the prognostic accuracy of the model.…”

“…It was also involved in the competing endogenous RNA network correlated with the in ltration of CD8 T cells. It may predict the therapeutic response of breast cancer and osteosarcoma patients to immunotherapy [37,38] . Lnc-KLF7-IT1 is a novel lncRNA identi ed as a cuproptosis-related lncRNA in our study that has not been previously reported, which can help us to nd a new target for cancer therapy mainly.…”

Development and validation of an autophagy-related long non-coding RNA prognostic signature for cervical squamous cell carcinoma and endocervical adenocarcinoma

“…Although MIR9-3HG was highly expressed in cervical cancer and could regulate apoptosis in cervical cancer cells by affecting the mitochondria-mediated apoptosis pathway ( 42 ), a study has shown that MIR9-3HG is a protective gene ( 39 ). Meanwhile, AC005332.4 has also been reported in colorectal cancer ( 43 ), cervical cancer ( 44 ), breast cancer ( 45 ), and osteosarcoma ( 46 ).…”

“…reported in colorectal cancer (43), cervical cancer (44), breast cancer (45), and osteosarcoma (46).…”

Analysis of Long Noncoding RNAs-Related Regulatory Mechanisms in Duchenne Muscular Dystrophy Using a Disease-Related lncRNA-mRNA Pathway Network

“…GAS5 reportedly promotes wound healing by activating the HIF1A/ VEGF pathway [43]. Dysregulation of the lncRNAs MBNL1-AS1, CCDC18-AS1, LINC01290, MIR29B2CHG, and PSMB8-AS1 has been observed in many cancers [44][45][46][47][48]. NF-κB signaling is activated during DMD pathogenesis and leads to infammation and muscle degeneration [49].…”