Systematic pan‐cancer analysis identifies RBM39 as an immunological and prognostic biomarker

Abstract

RNA‐binding Motif Protein39 (RBM39) is identified as a splicing factor and transcription coactivator. Despite mounting evidence that RBM39 plays a critical role in the development of specific malignancies, no systematic pan‐cancer investigation of RBM39 has been conducted. As a result, we set out to investigate RBM39’s prognostic significance and putative immunological activities in 33 different cancers. Based on TCGA and CCLE, GTEx, cBioportal and HPA, we used a series of bioinformatics approaches to explore the potential oncogenic role of RBM39, including analysis of the expression of the pan‐cancer species RBM39, the prognostic relationship between RBM39 expression and overall survival (OS), disease‐specific survival (DSS) and progression‐free interval (PFI), the relationship between RBM39 expression and clinical phenotype, analysis of the relationship between RBM39 expression and tumour mutational burden (TMB), microsatellite instability (MSI), DNA methylation and immune cell infiltration. Our results showed that RBM39 is overexpressed in most cancers. RBM39 was positively or negatively correlated with the prognosis of different tumours. RBM39 expression was associated with TMB and MSI in 9 and 12 cancer types. In addition, RBM39 expression was associated with DNA methylation in almost all tumours. There are eight tumours were screened for further study, including BRCA, COAD, HNSC, LIHC, LUSC, SKCM, STAD, UCEC. In the screed tumours, RBM39 was found to be negatively correlated with the infiltration of most immune cells. In addition, the correlation with RBM39 expression varied by immune cell subtype. Based on RBM39’s role in tumorigenesis and tumour immunity, we suggest it can serve as a surrogate prognostic marker.

Identification of hub genes and potential molecular mechanisms in MSS/MSI classifier primary colorectal cancer based on multiple datasets

“…Previous studies have also shown that RBM39 is a proto-oncogene that plays an important role in the development of malignant tumors [42]. Recent studies have found that RBM39 has been identi ed as a marker of pan-cancer and is negatively correlated with in ltration of most immune cells [43]. In particular, RBM39 expression was substantially associated with tumor stage and MSI, which is similar to the ndings of this study.…”

Oncogenic and immunological role of EDIL3 in human tumours: From pan-cancer analysis to validation in gastric cancer

“…Recent reports revealed that TME plays critical functions in tumour progression and influences final prognosis [ 41 ]. Furthermore, reports have demonstrated that TME is associated with various cancer genes [ 42 ]. Our results indicated that EDIL3 was highly associated with the levels of various tumour-infiltrating immune cells in multiple cancers.…”

Therapeutic Targeting of RNA Splicing in Cancer

“…Increased RBM39 expression has also been identified across a host of solid tumors and hematologic malig-nancies [103]. A pan-cancer analysis of RBM39 correlates expression with clinical outcome for patients in terms of overall survival, dependent on tumor type [104]. Additionally, RBM39 has been proposed as a unique vulnerability in leukemias bearing splicing factor mutations [105].…”