An analysis of TCGA RNA-seq datasets to identify differentially expressed genes in glioma

Gliomas makes up ۸۱% of malignancies in the central nervous system (CNS). The primary source of these tumors is glial or precursor cells in the brain and spinal cord. Depending on the type of cells affected, gliomas are classified into four major types: astrocytomas, oligodendrogliomas, ependymomas, and oligoastrocytomas. According to the World Health Organization's grading system, gliomas range in grade from grade ۱ (i.e., pilocytic astrocytomas) to grade ۴ (i.e., glioblastomas). Nausea and vomiting, memory loss, speech difficulties, and personality changes are some of the symptoms of glioma. A glioma is diagnosed through a combination of tests, including a CT scan, MRI and genetic testing. In spite of advances in neuro-oncology, high-grade gliomas continue to pose treatment and management challenges. With the recent developments in cancer genomics, the use of molecular biomarkers, such as mRNAs, lncRNAs, or miRNAs , has become one of the emerging methods of glioma diagnosis. These markers, which are stable in body fluids and have high specificity and sensitivity, have been shown to have significant prognostic and diagnostic values. This study utilizes TCGA RNA-seq data to identify and analyze differentially expressed genes in glioma, proposing possible targets for diagnostics. Methods: The transcriptomic data of glioma patients were obtained from the GDC portal. The given data was then analyzed in R, using TCGAbiolinks, limma, and edger packages. The molecular pathways involved in glioma were investigated using ClusterProfiler and gprofiler packages. Results: After analyzing TCGA-GBM samples, the list of the up-regulated (such as RIPK۱, CDK۴, and DKC۱) and the down-regulated genes (such as CACNA۱D, CAMK۲B, and CALM۳) was obtained. Additionally, pathway analysis of these differentially expressed genes revealed multiple glioma-associated pathways. Conclusion: A genome-wide analysis of RNA-Seq data enabled us to identify genes that are differentially expressed in glioma, which could lead to more effective methods of identifying brain tumors through molecular techniques.

کلیدواژه ها:

Glioma ، TCGA ، RNA-seq ، Differentially Expressed Genes