Establishment and validation of a ubiquitination-related gene signature associated with prognosis in pancreatic duct adenocarcinoma

Abstract

BackgroundPatients with pancreatic duct adenocarcinoma (PDAC) have varied prognoses that depend on numerous variables. However, additional research is required to uncover the latent impact of ubiquitination-related genes (URGs) on determining PDAC patients’ prognoses.MethodsThe URGs clusters were discovered via consensus clustering, and the prognostic differentially expressed genes (DEGs) across clusters were utilized to develop a signature using a least absolute shrinkage and selection operator (LASSO) regression analysis of data from TCGA-PAAD. Verification analyses were conducted across TCGA-PAAD, GSE57495 and ICGC-PACA-AU to show the robustness of the signature. RT-qPCR was used to verify the expression of risk genes. Lastly, we formulated a nomogram to improve the clinical efficacy of our predictive tool.ResultsThe URGs signature, comprised of three genes, was developed and was shown to be highly correlated with the prognoses of PAAD patients. The nomogram was established by combining the URGs signature with clinicopathological characteristics. We discovered that the URGs signature was remarkably superior than other individual predictors (age, grade, T stage, et al). Also, the immune microenvironment analysis indicated that ESTIMATEscore, ImmuneScores, and StromalScores were elevated in the low-risk group. The immune cells that infiltrated the tissues were different between the two groups, as did the expression of immune-related genes.ConclusionThe URGs signature could act as the biomarker of prognosis and selecting appropriate therapeutic drugs for PDAC patients.

A novel model based on ubiquitination-related gene to predict prognosis and immunotherapy response in hepatocellular carcinoma

“…Currently, there is insufficient research on URGs in patients with liver cancer. Some previous studies have confirmed the prognostic role of URGs in certain cancers, such as pancreatic cancer and prostate cancer [ 53 , 54 ]. The research validated the prognostic significance of URGs in liver cancer and investigated the potential use of immunotherapy, offering valuable guidance for tailored clinical interventions.…”

Elevated ADH5 expression suggested better prognosis in kidney renal clear cell carcinoma (KIRC) and related to immunity through single-cell and bulk RNA-sequencing

“…The relevance between ADH5 and immune cell infiltration in KIRC was investigated by the TIMER analysis tool ( https://cistrome.shinyapps.io/timer/ ). The ESTIMATE method utilizes existing gene expression profiles to estimate the degree of infiltration of stromal or immune cells into the tumor [ 16 ]. So, based on the ADH5 expression matrix, we executed the ESTIMATE algorithm to calculate the immune, stromal, and ESTIMATE scores.…”