Construction and analysis of a ceRNA network and patterns of immune infiltration in bladder cancer

Abstract

Background: Bladder cancer (BC) is the ninth most common malignant tumor, accounting for an estimate of 549,000 new BC cases and 200,000 BC-related deaths worldwide in 2018. The prognosis of BC has not substantially improved despite significant advances in the diagnosis and treatment of the disease. Methods:The RNA sequencing (RNA-seq) data and clinical information of BC patients were downloaded from The Cancer Genome Atlas (TCGA) database. The Cell-type Identification By Estimating Relative Subsets Of RNA Transcripts (CIBERSORT) algorithm was used to assess immune infiltration. The survival analyses were performed using the selected components of a ceRNA network and selected immune cell types by least absolute shrinkage and selection operator (LASSO) Cox regression to calculate the risk score. The accuracy of prognosis prediction was determined by receiver operating characteristic (ROC) curves, survival curves, and nomograms. Finally, the correlation analysis was performed to investigate the relationships between the signature components of the ceRNA network and the immune cell signature.Results: Two completed survival analyses included selected components of the ceRNA network (ELN, SREBF1, DSC2, TTLL7, DIP2C, SATB1, hsa-miR-20a-5p, and hsa-miR-29c-3p) and selected immune cell types (M0 macrophages, M2 macrophages, resting mast cells, and neutrophils). ROC curves, survival curves (all P values <0.05), nomograms, and calibration curves indicated that the accuracy of the two survival analyses was acceptable. Moreover, the correlations between TTLL7 and resting mast cells (R=0.24, P<0.001), DSC2 and resting mast cells (R=−0.23, P<0.001), ELN and resting mast cells (R=0.44, P<0.001), and hsa-miR-29c-3p and M0 macrophages (R=−0.29, P<0.001) were significant, indicating that interactions of these factors may play significant roles in the prognosis of BC.Conclusions: TTLL7, DSC2, ELN, hsa-miR-29c-3p, resting mast cells, and M0 macrophages may play an important role in the development of BC. However, additional studies are needed to confirm this hypothesis.

Validation the role of desmocollin-2 in osteosarcoma based on single cell and bulk RNA seq and experimental analyses

“…Tumor immune microenvironment plays a key role in the occurrence and development of tumors 22 . Research have released that DSC2 was associated with immune cell infiltration in bladder cancer 23 . Similarly, we also found that DSC2 was strongly associated with most immune cell infiltration, such as Neutrophils, M2 Macrophages, Eosinophils, resting Dendritic cells, CD8 T cells and CD4 memory activated T cells.…”

A Prognostic Model of Colon Cancer Based on the Microenvironment Component ScoreviaSingle Cell Sequencing

“…The Cibersort analytical tool can be used to calculate the relative content of 22 specific immune cell subtypes in the TME based on machine learning algorithms (9). Based on this approach, several studies have established prognostic models for various types of cancer (10)(11)(12)(13)(14). Cibersortx, an upgraded version of Cibersort, could be applied to establish multi-gene signatures of cell subpopulations based on scRNA-seq data and be used to analyse the relative content of these subpopulations (15).…”