Comprehensive Analysis of Pyroptosis-Related Long Noncoding RNA Immune Infiltration and Prediction of Prognosis in Patients with Colon Cancer

Liu, Li; Chen, Wenzheng; Li, Yebei; Fu, Pengcheng; Cao, Yi; Li, Zhengrong; Xiong, Jianbo; Jie, Zhigang

doi:10.1155/2022/2035808

Cited by 11 publications

(8 citation statements)

References 62 publications

(70 reference statements)

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“…More importantly, previous studies have confirmed that the NRlncRNA signature also can be used to predict the prognosis of tumors. For instance, the NRlncRNAs have vital functions in Colon Cancer, and the signature composed of NRlncRNAs can predict the prognosis of Colon Cancer (CC) and be used to customize CC treatment in the future ( Liu et al, 2022 ). However, the relationship between NRlncRNAs and STS is still unknown.…”

Section: Discussionmentioning

confidence: 99%

A Necroptosis-Related lncRNA Signature Predicts Prognosis and Indicates the Immune Microenvironment in Soft Tissue Sarcomas

Liu

Feng

2022

Front. Genet.

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Background: The necroptosis and long noncoding RNA (lncRNA) are critical in the occurrence and development of malignancy, while the association between the necroptosis-related lncRNAs (NRlncRNAs) and soft tissue sarcoma (STS) remains controversial. Therefore, the present study aims to construct a novel signature based on NRlncRNAs to predict the prognosis of STS patients and investigate its possible role.Methods: The transcriptome data and clinical characteristics were extracted from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression database (GTEx). A novel NRlncRNA signature was established and verified by the COX regression analysis and least absolute shrinkage and selection operator (LASSO) regression analysis. Subsequently, the K-M survival analysis, ROC, univariate, multivariate Cox regression analysis, and nomogram were used to evaluate the predictive value of the signature. Also, a variety of bioinformatic analysis algorithms explored the differences between the potential mechanism, tumor immune status, and drug sensitivity in the two-risk group. Finally, the RT-qPCR was performed to evaluate the expression of signature NRlncRNAs.Results: A novel signature consisting of seven NRlncRNAs was successfully established and verified with stable prediction performance and general applicability for STS. Next, the GSEA showed that the patients in the high-risk group were mainly enriched with tumor-related pathways, while the low-risk patients were significantly involved in immune-related pathways. In parallel, we found that the STS patients in the low-risk group had a better immune status than that in the high-risk group. Additionally, there were significant differences in the sensitivity to anti-tumor agents between the two groups. Finally, the RT-qPCR results indicated that these signature NRlncRNAs were abnormally expressed in STS.Conclusion: To the best of our knowledge, it is the first study to construct an NRlncRNA signature for STS. More importantly, the novel signature displays stable value and translational potential for predicting prognosis, tumor immunogenicity, and therapeutic response in STS.

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Section: Discussionmentioning

confidence: 99%

A Necroptosis-Related lncRNA Signature Predicts Prognosis and Indicates the Immune Microenvironment in Soft Tissue Sarcomas

Liu

Feng

2022

Front. Genet.

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“…For instance, Luo et al studied the association of lncRNAs with stomach adenocarcinoma, focusing on a twelve NRL signature which included LASTR, one of the lncRNAs identified in this work as NRL for KIRC [ 40 ]. Liu et al studied lncRNAs in colon cancer and identified MYOSLID as associated to pyroptosis, linking this lncRNA to regulation of SKP1 expression via MIR-589-5p and to the miR-29c-3p-mcl-1 axis [ 41 ]. The function of lncRNAs in sequestering and inactivating one or more miRNA species was studied also in the necroptosis response in HCC [ 42 ].…”

Section: Discussionmentioning

confidence: 99%

Qualification of Necroptosis-Related lncRNA to Forecast the Treatment Outcome, Immune Response, and Therapeutic Effect of Kidney Renal Clear Cell Carcinoma

Yin

Tian

Ren

et al. 2022

Journal of Oncology

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Background. Kidney renal clear cell carcinoma (KIRC) is considered as a highly immune infiltrative tumor. Necroptosis is an inflammatory programmed cell death associated with a wide range of diseases. Long noncoding RNAs (lncRNAs) play important roles in gene regulation and immune function. lncRNA associated with necroptosis could systematically explore the prognostic value, regulate tumor microenvironment (TME), etc. Method. The patients’ data was collected from TCGA datasets. We used the univariate Cox regression (UCR) to select prediction lncRNAs that are related to necroptosis. Meanwhile, risk models were constructed using LASSO Cox regression (LCR). Kaplan–Meier (KM) analysis, accompanied with receiver operating characteristic (ROC) curves, was performed to assess the independent risk factors of different clinical characteristics. The evaluated factors are age, gender, disease staging, grade, and their related risk score. Databases such as Gene Ontology (GO), Kyoto encyclopedia of genes and genomes (KEGG), and Gene set enrichment analysis (GSEA) were used to search the probable biological characteristics that could influence the risk groups, containing signaling pathway and immue-related pathways. The single-sample gene set enrichment analysis (ssGSEA) was chosen to perform gene set variation analysis (GSVA), and the GSEABase package was selected to detect the immune and inflammatory infiltration profiles. The TIDE and I C 50 evaluation were used to estimate the effectiveness of clinical treatment on KIRC. Results. Based on the above analysis, we have got a conclusion that patients who show high risk had higher immune infiltration, immune checkpoint expression, and poorer prognosis. We identified 19 novel prognostic necroptosis-related lncRNAs, which could offer opinions for a deeper study of KIRC. Conclusion. The risk model we constructed makes it possible to predict the prognosis of KIRC patients and offers directions for further research on the prognostication and treatment strategies for KIRC.

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“…Several recent studies have proposed prognostic models for COAD [22][23][24]. However, the studies' predictive performances have not been validated in COAD, and the differences in immune infiltrating cells and immune checkpoint blockade-, immune checkpoint-, and m6A-related genes between the high and low risks of the prediction model were not analyzed.…”

Section: Discussionmentioning

confidence: 99%

Construction and Validation of Pyroptosis-Related lncRNA Prediction Model for Colon Adenocarcinoma and Immune Infiltration Analysis

et al. 2022

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Objective Colon adenocarcinoma (COAD) is one of the most prevalent cancers worldwide. However, the pyroptosis-related lncRNAs of COAD have not been deeply examined and validated. Here, we constructed and validated a risk model on pyroptosis-related lncRNAs in COAD. Methods The RNA sequencing transcriptome and clinical data of COAD patients were downloaded from The Cancer Genome Atlas (TCGA) database. Differentially expressed pyroptosis-related mRNAs and mRNA-lncRNA coexpression network were identified. After univariate and multifactorial cox analyses of prognosis-related lncRNAs, a risk model was constructed. Next, we analyzed the differences in immune infiltration, immune checkpoint blockade-, immune checkpoint-, and N6-methyladenosine-related gene expressions between the high- and low-risk groups. RT-qPCR was used to validate the expression of lncRNAs. Result A risk model was constructed based on 9 pyroptosis-related lncRNAs and separated COAD patients into the high- and low-risk groups. Immune infiltration analysis and immune checkpoint blockade-, immune checkpoint-, and N6-methyladenosine-related genes showed significant differences between the two subgroups. RT-qPCR showed that the 9 pyroptosis-related lncRNAs could be used as prognostic indicators. Conclusion A novel risk model based on pyroptosis-related lncRNAs was constructed and demonstrated that these lncRNAs might be used as independent prognostic biomarkers. This will also assist shed light on the COAD prognosis and therapy.

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Comprehensive Analysis of Pyroptosis-Related Long Noncoding RNA Immune Infiltration and Prediction of Prognosis in Patients with Colon Cancer

Cited by 11 publications

References 62 publications

A Necroptosis-Related lncRNA Signature Predicts Prognosis and Indicates the Immune Microenvironment in Soft Tissue Sarcomas

A Necroptosis-Related lncRNA Signature Predicts Prognosis and Indicates the Immune Microenvironment in Soft Tissue Sarcomas

Qualification of Necroptosis-Related lncRNA to Forecast the Treatment Outcome, Immune Response, and Therapeutic Effect of Kidney Renal Clear Cell Carcinoma

Construction and Validation of Pyroptosis-Related lncRNA Prediction Model for Colon Adenocarcinoma and Immune Infiltration Analysis

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