Dataset Information

Comprehensive Analysis of Splicing Factor and Alternative Splicing Event to Construct Subtype-Specific Prognosis-Predicting Models for Breast Cancer.

ABSTRACT: Recent evidence suggests that splicing factors (SFs) and alternative splicing (AS) play important roles in cancer progression. We constructed four SF-risk-models using 12 survival-related SFs. In Luminal-A, Luminal-B, Her-2, and Basal-Like BRCA, SF-risk-models for three genes (PAXBP1, NKAP, and NCBP2), four genes (RBM15B, PNN, ACIN1, and SRSF8), three genes (LSM3, SNRNP200, and SNU13), and three genes (SRPK3, PUF60, and PNN) were constructed. These models have a promising prognosis-predicting power. The co-expression and protein-protein interaction analysis suggest that the 12 SFs are highly functional-connected. Pathway analysis and gene set enrichment analysis suggests that the functional role of the selected 12 SFs is highly context-dependent among different BRCA subtypes. We further constructed four AS-risk-models with good prognosis predicting ability in four BRCA subtypes by integrating the four SF-risk-models and 21 survival-related AS-events. This study proposed that SFs and ASs were potential multidimensional biomarkers for the diagnosis, prognosis, and treatment of BRCA.

SUBMITTER: Zhang H

PROVIDER: S-EPMC8497829 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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Comprehensive Analysis of Splicing Factor and Alternative Splicing Event to Construct Subtype-Specific Prognosis-Predicting Models for Breast Cancer.

Zhang He H Han Baoai B Han Xingxing X Zhu Yuying Y Liu Hui H Wang Zhiyong Z Cui Yanfen Y Tian Ran R Gao Zicong Z Tian Ruinan R Ren Sixin S Zuo Xiaoyan X Tian Jianfei J Zhang Fei F Niu Ruifang R

Frontiers in genetics 20210924

Recent evidence suggests that splicing factors (SFs) and alternative splicing (AS) play important roles in cancer progression. We constructed four SF-risk-models using 12 survival-related SFs. In Luminal-A, Luminal-B, Her-2, and Basal-Like BRCA, SF-risk-models for three genes (PAXBP1, NKAP, and NCBP2), four genes (RBM15B, PNN, ACIN1, and SRSF8), three genes (LSM3, SNRNP200, and SNU13), and three genes (SRPK3, PUF60</ ...[more]

PMID: 34630526

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Project description:BackgroundAlternative splicing (AS) is important in the regulation of gene expression and aberrant AS is emerging as a major factor in the pathogenesis of human conditions, including cancer. Triple-negative breast cancer (TNBC) is the most challenging subtype of breast cancer with strong invasion, high rate of metastasis, and poor prognosis. Here we report a systematic profiling of aberrant AS in TNBC.MethodsThe percent spliced in (PSI) values for AS events in 151 TNBC patients were obtained from The Cancer Genome Atlas (TCGA) SpliceSeq database. Univariate Cox and stepwise Multivariate Cox regression analyses were conducted to find the best prognostic AS model. Splicing regulatory networks were constructed by prognosis-related spliceosome and aberrant AS events. Additionally, pathway enrichment and gene set enrichment analysis (GSEA) were further employed to reveal the significant pathways for prognosis-related AS genes. Finally, splicing regulatory networks were constructed via Spearman's rank correlation coefficients between prognosis-related AS events and splicing factor expressions.ResultsA total of 1,397 prognosis-associated AS events were identified in TNBC. The majority of the parent genes of prognostic AS events exhibited direct interactions to each other in the STRING gene network. Pathways of focal adhesion (p < 0.001), RNA splicing (p = 0.007), homologous recombination (p = 0.042) and ECM-receptor interaction (p = 0.046) were found to be significantly enriched for prognosis-related AS. Additionally, the area under curve (AUC) of the best AS prognostic predictor model reached 0.949, showing a powerful capability to predict outcomes. The Exon Skip (ES) type of AS events displayed more robust and efficient capacity in predicting performance than any other specific AS events type in terms of prognosis. The ES AS signature might confer a strong oncogenic phenotype in the high-risk group with elevated activities in cell cycle and SUMOylating pathways of tumorigenesis, while programmed cell death and metabolism pathways were found to be enriched in the low-risk group of TNBC. The splicing correlation network also revealed a regulatory mode of prognostic splicing factors (SFs) in TNBC.ConclusionOur analysis of AS events in TNBC could not only contribute to elucidating the tumorigenesis mechanism of AS but also provide clues to uncovering underlying prognostic biomarkers and therapeutic targets for further study.

Project description:BackgroundAlternative splicing (AS) is a critical mechanism of post-transcriptional regulation and has been widely reported to be associated with the tumor progression and tumor microenvironment (TME) formation. However, the role of AS in lung adenocarcinoma (LUAD) has not been clearly elucidated. This study presents a comprehensive analysis exploring the impact of AS on prognosis and TME in LUAD.MethodsThe gene expression transcriptome profiles and survival data were obtained from The Cancer Genome Atlas (TCGA) database, and the splicing profiles were obtained from the TCGA SpliceSeq database. Base on prognostic AS events, a prognostic signature was constructed using Least Absolute Shrinkage and Selection Operator (LASSO) regression followed by multivariate Cox regression analysis. Survival outcomes was analyzed using the Kaplan-Meier method and the predictive performance of the signature was evaluated using receiver operating characteristic (ROC) curve analysis. Furthermore, the landscape of the TME was assessed by ESTIMATE, Microenvironment Cell Population (MCP)-counter, and single-sample Gene-Set Enrichment Analysis (ssGSEA) algorithms.ResultsA total of 127 prognostic AS events with P value <0.001 from 89 genes in LUAD were confirmed. A prognostic signature was constructed based on 20 prognostic AS events. Kaplan-Meier survival analysis demonstrated that higher risk scores were associated with poorer overall survival (OS). The area under the ROC curve of risk scores predicting the 1-, 3-, and 5-year survival probability were 0.791, 0.847, and 0.832, respectively. Furthermore, significant relationship was observed between the prognostic signature and the landscape of the TME. High-risk patients had lower stromal/immune scores, higher tumor purity, and significantly decreased abundance of majority immune cells, and immune-related signatures (P<0.05). Finally, a potential regulatory mechanism of the AS events is displayed in a regulatory network.ConclusionsThis research highlights the prognostic value of AS events for patients with LUAD and provide new insight into the regulation of the TME by AS. Notably, AS may affect the patient's prognosis by altering the TME. Our findings provide important guidance for the development of novel biomarkers and therapeutic targets in patients with LUAD.

Dataset Information

Comprehensive Analysis of Splicing Factor and Alternative Splicing Event to Construct Subtype-Specific Prognosis-Predicting Models for Breast Cancer.

Publications

Comprehensive Analysis of Splicing Factor and Alternative Splicing Event to Construct Subtype-Specific Prognosis-Predicting Models for Breast Cancer.

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