Comprehensive Analysis of Prognostic Alternative Splicing Signatures in Endometrial Cancer

Chen, Peigen; He, Junxian; Ye, Huixia; Jiang, Senwei; Li, Yunhui; Li, Xiaomao; Wan, Jing

doi:10.3389/fgene.2020.00456

Cited by 9 publications

(8 citation statements)

References 40 publications

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“…The PSI of AS events in patients with OC was supplemented by Knn function in the R language Impute package, which was then integrated with patient survival time and survival status. Univariate Cox regression was used to evaluate the correlation between PSI value and overall survival of patients with OC and screen the survival-associated AS events with a P -value < 0.05 27 . Upset plots were created by UpSet R to visualize the intersections of all seven types of survival-related AS events in OC.…”

Section: Methodsmentioning

confidence: 99%

Comprehensive characterization of 11 prognostic alternative splicing events in ovarian cancer interacted with the immune microenvironment

Yue

Zhao

Zhang

et al. 2022

Sci Rep

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Alternative splicing (AS) events play a crucial role in the tumorigenesis and progression of cancer. Transcriptome data and Percent Spliced In (PSI) values of ovarian cancer patients were downloaded from TCGA database and TCGA SpliceSeq. Totally we identified 1472 AS events that were associated with survival of ovarian serous cystadenocarcinoma (OC) and exon skipping (ES) was the most important type. Univariate and multivariate Cox regression analysis were performed to identify survival-associated AS events and developed the prognostic model based on 11-AS events. The immune cells and different response to cytotoxic T lymphocyte associated antigen 4 (CTLA-4) and programmed cell death protein 1 (PD-1) blockers in low-risk and high-risk group of OC patients were analyzed. Ten kinds of immune cells were found up-regulated in low-risk group. Activated B cell, natural killer T cell, natural killer cell and regulatory T cell were associated with survival of OC. The patients in low-risk group had good response to CTLA-4 and PD-1 blockers treatment. Moreover, a regulatory network was established according to the correlation between AS events and splicing factors (SFs). The present study provided valuable insights into the underlying mechanisms of OC. AS events that were correlated with the immune system might be potential therapeutic targets.

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Section: Methodsmentioning

confidence: 99%

Comprehensive characterization of 11 prognostic alternative splicing events in ovarian cancer interacted with the immune microenvironment

Yue

Zhao

Zhang

et al. 2022

Sci Rep

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“…A risk model was developed with the training group, and this model was established with published methodologies [ 17 , 18 ]. Univariate analysis was performed with the “survival” package, and the genes with p < 0.05 were identified as survival-related.…”

Section: Methodsmentioning

confidence: 99%

Identification of a five-immune gene model as an independent prognostic factor in hepatocellular carcinoma

Chen

Xiao

et al. 2021

BMC Cancer

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Background Hepatocellular carcinoma (HCC) is a common malignant tumor with a poor prognosis. We aimed to identify a new prognostic model of HCC based on differentially expressed (DE) immune genes. Methods The DE immune genes were identified based on an analysis of 374 cases of HCC and 50 adjacent non-tumor specimens from the Cancer Genome Atlas (TCGA) database. Univariate Cox analysis, Lasso regression, and multivariate Cox analysis were used to construct the model based on the training group. Survival analysis and the receiver operating characteristic (ROC) curves were used to evaluate model performance. The testing group and the entire group were subsequently used for validation of the model. Results A five-immune gene model consisted of HSPA4, ISG20L2, NDRG1, EGF, and IL17D was identified. Based on the model, the overall survival was significantly different between the high-risk and low-risk groups (P = 7.953e-06). The AUCs for the model at 1- and 3-year were 0.849 and 0.74, respectively. The reliability of the model was confirmed using the validation groups. The risk score was identified as an independent prognostic parameter and closely related to the content of immune cells from human HCC specimens. Conclusion We identified a five-immune gene model that can be used as an independent prognostic marker for HCC.

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“…Patients with a follow-up of fewer than 90 days were excluded because these patients might die due to other factors, such as surgical complications. Univariate Cox regression was used to screen the survival-associated AS events with a P-value < 0.05 23 . Upset plots were created by UpSet R to visualize the intersections of all seven types of survival-related AS events in OV.…”

Section: Methodsmentioning

confidence: 99%

Survival-associated 11-AS Events Interact with the Immune Microenvironment in Ovarian Cancer

Yue

Zhao

Zhang

et al. 2021

Preprint

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Alternative splicing (AS) events play a crucial role in the tumorigenesis and progression of cancer. Transcriptome data and Percent Spliced In (PSI) values of OV patients were downloaded from TCGA database and TCGA SpliceSeq. Totally we identified 1,472 AS events that were associated with survival of OV and exon skipping (ES) was the most important type. Univariate and multivariate Cox regression analysis were performed to identify survival-associated AS events and develop the prognostic model based on 11-AS events. The immune cells and different response to cytotoxic T lymphocyte associated antigen 4 (CTLA-4) and programmed cell death protein 1 (PD-1) blockers in low-risk and high-risk group of OV patients were analyzed. Ten kinds of immune cells were found up-regulated in low-risk group. Activated B cell, natural killer T cell, natural killer cell and regulatory T cell were associated with survival of OV. The patients in low-risk group had good response to CTLA-4 and PD-1 blockers treatment. Moreover, a regulatory network was established according to the correlation between AS events and splicing factors (SFs). The present study provided valuable insights into the underlying mechanisms of OV. AS events that were correlated with the immune system might be potential therapeutic targets.

show abstract

Comprehensive Analysis of Prognostic Alternative Splicing Signatures in Endometrial Cancer

Cited by 9 publications

References 40 publications

Comprehensive characterization of 11 prognostic alternative splicing events in ovarian cancer interacted with the immune microenvironment

Comprehensive characterization of 11 prognostic alternative splicing events in ovarian cancer interacted with the immune microenvironment

Identification of a five-immune gene model as an independent prognostic factor in hepatocellular carcinoma

Survival-associated 11-AS Events Interact with the Immune Microenvironment in Ovarian Cancer

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