Large-scale transcriptomics-driven approach revealed overexpression of CRNDE as a poor survival prognosis biomarker in glioblastoma

Sorokin, Maxim (author), Raevskiy, Mikhail (author), Zottel, Alja (author), Šamec, Neja (author), Skoblar Vidmar, Marija (author), Matjašič, Alenka (author), Zupan, Andrej (author), Mlakar, Jernej (author), Suntsova, Maria (author), Kuzmin, Denis V. (author), Buzdin, Anton A. (author), Jovchevska, Ivana (author)

Glioblastoma is the most common and malignant brain malignancy worldwide, with a 10-year survival of only 0.7%. Aggressive multimodal treatment is not enough to increase life expectancy and provide good quality of life for glioblastoma patients. In addition, despite decades of research, there are no established biomarkers for early disease diagnosis and monitoring of patient response to treatment. High throughput sequencing technologies allow for the identification of unique molecules from large clinically annotated datasets. Thus, the aim of our study was to identify significant molecular changes between short- and long-term glioblastoma survivors by transcriptome RNA sequencing profiling, followed by differential pathway-activation-level analysis. We used data from the publicly available repositories The Cancer Genome Atlas (TCGA; number of annotated cases = 135) and Chinese Glioma Genome Atlas (CGGA; number of annotated cases = 218), and experimental clinically annotated glioblastoma tissue samples from the Institute of Pathology, Faculty of Medicine in Ljubljana corresponding to 2-58 months overall survival (n = 16). We found one differential gene for long noncoding RNA CRNDE whose overexpression showed correlation to poor patient OS. Moreover, we identified overlapping sets of congruently regulated differential genes involved in cell growth, division, and migration, structure and dynamics of extracellular matrix, DNA methylation, and regulation through noncoding RNAs. Gene ontology analysis can provide additional information about the function of protein- and nonprotein-coding genes of interest and the processes in which they are involved. In the future, this can shape the design of more targeted therapeutic approaches.

• Language: English
• Keywords: glioblastoma, noncoding RNA, long-term survival, CRNDE, RNA sequencing
• Work type: Article
• Typology: 1.01 - Original Scientific Article
• Organization: MF - Faculty of Medicine
• Publication status: Published
• Publication version: Version of Record
• Year: 2021
• Number of pages: 18 str.
• Numbering: Vol. 13, iss. 14, art. 3419
• PID: 20.500.12556/RUL-135720
• UDC: 616-006
• ISSN on article: 2072-6694
• DOI: 10.3390/cancers13143419
• COBISS.SI-ID: 69980163
• Publication date in RUL: 29.03.2022

Record is a part of a journal

• Title: Cancers
• Shortened title: Cancers
• Publisher: MDPI
• ISSN: 2072-6694
• COBISS.SI-ID: 517914137

Licences

• License: CC BY 4.0, Creative Commons Attribution 4.0 International
• Link: http://creativecommons.org/licenses/by/4.0/
• Description: This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.
• Licensing start date: 08.07.2021

Secondary language

• Language: Slovenian
• Keywords: glioblastom, nekodirajoča RNA, dolgoročno preživetje