Determining the prognostic significance of alternative splicing events in soft tissue sarcoma using data from The Cancer Genome Atlas

Abstract

Background Surgery, adjuvant chemotherapy, and radiotherapy are the primary treatment options for soft tissue sarcomas (STSs). However, identifying ways to improve the prognosis of patients with STS remains a considerable challenge. Evidence shows that the dysregulation of alternative splicing (AS) events is involved in tumor pathogenesis and progression. The present study objective was to identify survival-associated AS events that could serve as prognostic biomarkers and potentially serve as tumor-selective STS drug targets. Methods STS-specific ‘percent spliced in’ (PSI) values for splicing events in 206 STS samples were downloaded from The Cancer Genome Atlas SpliceSeq ® database. Prognostic analyses were performed on seven types of AS events to determine their prognostic value in STS patients, for which prediction models were constructed with the risk score formula . Prediction models were also constructed to determine the prognostic value of AS events, and Spearman’s rank correlation coefficients were calculated to determine the degree of correlation between splicing factor expression and the PSI values. Results A total 10,439 events were found to significantly correlate with patient survival rates. The area under the time-dependent receiver operating characteristic curve for the prognostic predictor of STS overall survival was 0.826. Notably, the splicing events of certain STS key genes were significantly associated with STS 2-year overall survival in the present study, including exon skip (ES) events in MDM2 and EWSR1, alternate terminator events in CDKN2A and HMGA2 for dedifferentiated liposarcoma, ES in MDM2 and alternate promoter events in CDKN2A for leiomyosarcoma, and ES in EWSR1 for undifferentiated pleomorphic sarcoma. Moreover, splicing correlation networks between AS events and splicing factors revealed that almost all of the AS events showed negatively correlations with the expression of splicing factors. Conclusion An in-depth analysis of alternative RNA splicing could provide new insights into the mechanisms of STS oncogenesis and the potential for novel approaches to this type of cancer therapy.

Comprehensive profiling of immune-related genes in soft tissue sarcoma patients

“…We also constructed two comprehensive nomograms with satisfactory AUCs (OS: 0.832–0.926, PFS: 0.776–0.874) based on independent variables to assess the deterioration and survival of patients. To date, numerous studies have developed signatures based on sequencing data to stratify sarcoma patients, including CINSARC [ 64 ], alternative splicing events [ 65 ], relapse-related genes [ 66 ], and lncRNA [ 67 ]. However, none of them has been applied in clinical practice.…”

Intron retention is a robust marker of intertumoral heterogeneity in pancreatic ductal adenocarcinoma

“…In multiple tumor types, splicing has been reported to outperform gene expression analysis in predicting survival 64 . Specific AS events are prognostic for different cancer types such as cervical cancer 65 , endometrial cancer 66 , soft tissue sarcoma 67 , hepatocellular carcinoma 68 , and colorectal cancer 69 . Mutations in splicing factors are being recognized as important oncogenic events [26][27][28] .…”

DNA methylation patterns–based subtype distinction and identification of soft tissue sarcoma prognosis

“…Previously, several genomic and transcriptome data have focused on exploring effective diagnostic or prognostic markers in STSs, including alternative splicing, [ 8 ] copy number variation, [ 9 ] and genes expression. [ 10 ] As one of the core elements in tumorigenesis progression, DNA methylation occurs early and frequently in regulating a variety of genomic functions.…”