Identification of a novel autophagy-related prognostic signature and small molecule drugs for glioblastoma by bioinformatics

• Main Authors: Dongjiao Wang (Author), Yuxue Jiang (Author), Tie Wang (Author), Zhe Wang (Author), Fei Zou (Author)
• Format: Book
• Published: BMC, 2022-05-01T00:00:00Z.
• Subjects: article
• Online Access: Connect to this object online.
• Notes: 10.1186/s12920-022-01261-5; 1755-8794
• Keywords: Autophagy; Gene signature; Prognosis; Glioblastoma; Mutation; LASSO cox regression analysis; Internal medicine; RC31-1245; Genetics; QH426-470
• Source: BMC Medical Genomics, Vol 15, Iss 1, Pp 1-11 (2022)

Abstract Objective To explore the autophagy-related prognostic signature (ARPs) via data mining in gene expression profiles for glioblastoma (GBM). Methods Using the Cancer Genome Atlas (TCGA) database, we obtained 156 GBM samples and 5 adjacent normal samples, and denoted them as discovery cohort. Univariate Cox regression analysis was used to screen autophagy genes that related to GBM prognosis. Then, the least absolute shrinkage and selection operator Cox regression model was used to construct an autophagy-based ARPs, which was validated in an external cohort containing 80 GBM samples. The patients in the above-mentioned cohorts were divided into low-risk group and high-risk group according to the median prognostic risk score, and the diagnostic performance of the model was assessed by receiver operating characteristic curve analyses. The gene ontology and Kyoto encyclopedia of genes and genomes pathway enrichment analyses were performed between the high-risk and low-risk patients. Additionally, the genetic features of ARPs, such as genetic variation profiles, correlations with tumor-infiltrating lymphocytes (TILs), and potential drug sensitivity, were further assessed in the TCGA-GBM data set. Results A signature of ARPs including NDUFB9 , BAK1 , SUPT3H , GAPDH , CDKN1B , CHMP6, and EGFR were detected and validated. We identified a autophagy-related prognosis 7-gene signature correlated survival prognosis, immune infiltration, level of cytokines, and cytokine receptor in tumor microenvironment. Furthermore, the signature was tested in several pathways related to disorders of tumor microenvironment, as well as cancer-related pathways. Additionally, a range of small molecular drugs, shown to have a potential therapeutic effect on GBM. Conclusions We constructed an autophagy-based 7-gene signature, which could serve as an independent prognostic indicator for cases of GBM and sheds light on the role of autophagy as a potential therapeutic target in GBM.