The ceRNA Network Has Potential Prognostic Value in Clear Cell Renal Cell Carcinoma: A Study Based on TCGA Database

Liu, Haosheng; Zhu, Zhaowen; Fang, Jianxiong; Liu, Tianqi; Zhang, Zhenhui; Zhao, Chao; Pu, Xiao‐Yong; Liu, Jiumin

doi:10.1155/2020/4830847

Cited by 5 publications

(2 citation statements)

References 30 publications

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“…LINC00973-miR-7109-Siglec-15 axis was involved in immune activations in ccRCC [9]. Additionally, in recent years, some studies used bioinformatic methods to construct ceRNA networks which displayed satisfactory prognostic value for ccRCC [10,11]. All these findings drove us to explore the connection between ceRNA network and tumor immune microenvironment.…”

Section: Introductionmentioning

confidence: 96%

KCNN4 may weaken anti-tumor immune response via raising Tregs and diminishing resting mast cells in clear cell renal cell carcinoma

Cui

Shen

et al. 2022

Cancer Cell Int

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Background Studies over the past decade have shown that competitive endogenous RNA (ceRNA) plays an essential role in the tumorigenesis and progression of clear cell renal cell carcinoma (ccRCC). Meanwhile, immune checkpoint blocker is gradually moving towards the first-line treatment of ccRCC. Hence, it’s urgent to develop a new prediction model for the efficiency of immunotherapy. At present, there is no study to reveal the effect of ceRNA network on the efficiency of immunotherapy for ccRCC. Methods To systematically analyze the effect of ceRNA hub genes in ccRCCon immune response, we constructed prognosis models based on ceRNAs and immune cells, respectively. We constructed ceRNA network using hypergeometric distribution test and correlation analysis with R script based on The Cancer Genome Atlas (TCGA) database. We then applied the Cibersort algorithm to simulate the infiltration overview of immune cells in kidney renal clear carcinoma (KIRC) samples. Prognosis-related immune cells were screened and a predictive model of these cells was constructed. Prognosis-related immune cells and ceRNA hub genes were performed with co-expression analysis. Finally, qRT-PCR and immunofluorescence assays were performed to validate the results. Results The construction of ceRNA related prognosis model contained 8 hub genes, including RELT, MYO9B, KCNN4, SIX1, OTOGL, MALAT1, hsa-miR-130b-3p, and hsa-miR-21-5p. The area under the receiver operating characteristic curve (AUC) was 0.77 at 5 years. For the construction of immune cells prognosis model, 3 immune cells (T cells regulatory, Macrophages, Mast cells resting) were adopted, and the AUC was 0.65 at 5 years. We then merged the two models by correlation analysis and co-expression analysis. Finally, we found that KCNN4 positively correlates with T cells regulatory (Tregs) and negatively correlates with mast cells resting significantly. Furthermore, higher expression of KCNN4 may lead to a higher potential for immune evasion and lower efficiency for immune checkpoint inhibitors (ICIs). Conclusions Generally, this is the first study to assess the prognostic value of immune related ceRNA hub genes in ccRCC, and KCNN4 was finally demonstrated to be a key regulatory factor with strong correlation with Tregs and mast cells resting.

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Section: Introductionmentioning

confidence: 96%

KCNN4 may weaken anti-tumor immune response via raising Tregs and diminishing resting mast cells in clear cell renal cell carcinoma

Cui

Shen

et al. 2022

Cancer Cell Int

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“…RNA species play diverse roles in cells, and non-coding RNAs (ncRNAs) with distinct functions have been identified, including circular RNAs (circRNAs) [4,5] . Although generally classified as ncRNAs, certain circR-NAs have been shown to yield polypeptides [6,7] .…”

Section: Introductionmentioning

confidence: 99%

Identification and Functional Analysis of Circular RNAs in Ankylosing Spondylitis Patient Peripheral Blood Mononuclear Cells

Huang,

Liu,

WANG

et al. 2024

Preprint

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Objectives:To analyze the function and roles of circRNAs in the peripheral blood mononuclear cells (PBMCs) of ankylosing spondylitis (AS) patients. Methods: The expression of AS-related circRNAs were detected by high-throughput RNA-sequencing within the PBMCs of 5 AS cases and healthy controls. After profiling circRNA expression in these samples, differentially expressed circRNAs (DECs) were identified, and a qPCR-based validation approach was used to confirm the differential expression of six of these DECs in patient samples. Spearman’s correlation tests and ROC curve analyses were further used to assess the relationship between disease severity and the expression of DECs of interest in AS patients, after which a putative circRNA-microRNAs (miRNAs) interaction network was constructed leading to the detection of six validated DECs with competing endogenous RNA (ceRNA) functionality. Besides, cell experiments were also performed to investigate the potential mechanism of key circRNA in AS. Results: 10,441 circRNAs were identified in these 10 PBMC samples, with 131 total DECs including 89 and 42 that were up- and down-regulated, respectively. In qPCR validation assays, patterns of hsa_circ_0000702, hsa_circ_0006209, hsa_circ_0047920, hsa_circ_0001543, hsa_circ_0072697 and hsa_circ_0005076 were confirmed to align well with RNA-seq results. In addition, the expression levels of hsa_circ_0006209, hsa_circ_0047920, and hsa_circ_0072697 were detected to be positively correlated with disease severity. ROC curve analyses suggested that hsa_circ_0072697 may offer value as a diagnostic biomarker for AS. Cell experiments indicated that hsa_circ_0072697 could suppress the progression of AS by targeting NF-κB pathway Conclusions: The identification of six circRNAs with putative ceRNA functionality in AS patients highlights potential molecular mechanisms governing this debilitating disease. However, further research will be necessary to formally confirm the roles of these DECs and their target miRNAs in AS. Further, hsa_circ_0072697 has a good diagnostic value in AS patients, and it could suppress the progression of AS by targeting NF-κB pathwa

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Uncovering the ceRNA Network Related to the Prognosis of Stomach Adenocarcinoma Among 898 Patient Samples

Liu,

Petinrin

et al. 2024

Biochem Genet

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Stomach adenocarcinoma (STAD) patients are often associated with significantly high mortality rates and poor prognoses worldwide. Among STAD patients, competing endogenous RNAs (ceRNAs) play key roles in regulating one another at the post-transcriptional stage by competing for shared miRNAs. In this study, we aimed to elucidate the roles of lncRNAs in the ceRNA network of STAD, uncovering the molecular biomarkers for target therapy and prognosis. Specifically, a multitude of differentially expressed lncRNAs, miRNAs, and mRNAs (i.e., 898 samples in total) was collected and processed from TCGA. Cytoplasmic lncRNAs were kept for evaluating overall survival (OS) time and constructing the ceRNA network. Differentially expressed mRNAs in the ceRNA network were also investigated for functional and pathological insights. Interestingly, we identified one ceRNA network including 13 lncRNAs, 25 miRNAs, and 9 mRNAs. Among them, 13 RNAs were found related to the patient survival time; their individual risk score can be adopted for prognosis inference. Finally, we constructed a comprehensive ceRNA regulatory network for STAD and developed our own risk-scoring system that can predict the OS time of STAD patients by taking into account the above.

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The ceRNA Network Has Potential Prognostic Value in Clear Cell Renal Cell Carcinoma: A Study Based on TCGA Database

Cited by 5 publications

References 30 publications

KCNN4 may weaken anti-tumor immune response via raising Tregs and diminishing resting mast cells in clear cell renal cell carcinoma

KCNN4 may weaken anti-tumor immune response via raising Tregs and diminishing resting mast cells in clear cell renal cell carcinoma

Identification and Functional Analysis of Circular RNAs in Ankylosing Spondylitis Patient Peripheral Blood Mononuclear Cells

Uncovering the ceRNA Network Related to the Prognosis of Stomach Adenocarcinoma Among 898 Patient Samples

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