Theoretical and Natural Science
- The Open Access Proceedings Series for Conferences
Theoretical and Natural Science
Vol. 8, 13 November 2023
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Identification of key genes for glioblastoma microenvironment
* Author to whom correspondence should be addressed.
Abstract
Glioblastoma(GBM), as a common kind of brain cancer, has a poor prognosis and a recurrence rate of nearly 100 percent. Tumor immune microenvironment is a crucial factor for glioblastoma progression. Some prognostically relevant genes in the immunologic microenvironment of glioblastoma remain to be further explored. This article aims to ascertain genes involved in the immune microenvironment of glioblastoma, and this topic has not been identified before. R version 4.2.1 and the appropriate packages were used for all analyses in this paper. Relevant transcriptomic data for GBMs as well as clinical data were extracted from immune score data in the TCGA database, and stromal score data were acquired from this URL (http://www.cbioportal.org/). Differentially expressed genes were obtained from immune score data and Stromal score data. After intersections of all these genes, the PPI interaction network was applied. According to functional analysis, these genes are intensively distributed in immune-related pathways. Eventually LncRNAs co-expressing with immune-related genes were positively identified. We characterized genes related to the GBM tumor microenvironment not previously identified in similar studies, as well as some lncRNAs that co-expressed with these immune genes
Keywords
Tumor Immune Microenvironment, Transcriptomics, Glioblastoma, Individual Prognostic Genesintroduction
References
1. Jia L, et al Prevalence, risk factors, and management of dementia and mild cognitive impairment in adults aged 60 years or older in China: a cross-sectional study. 2020 Lancet Public Health 5 e661-e71
2. Rini BI, Campbell SCand Escudier B Renal cell carcinoma. 2009 Lancet 373 1119-32
3. Lan MJ, Rizk MM, Pantazatos SP, Rubin-Falcone H, Miller JM, Sublette ME, Oquendo MA, Keilp JGand Mann JJ Resting-state amplitude of low-frequency fluctuation is associated with suicidal ideation. 2019 Depress Anxiety 36 433-41
4. Cao J, et al Resting-state functional MRI of abnormal baseline brain activity in young depressed patients with and without suicidal behavior. 2016 J Affect Disord 205 252-63
5. Khazaei Z, et al The association between incidence and mortality of brain cancer and human development index (HDI): an ecological study. 2020 BMC Public Health 20 1696
6. Schwartzbaum JA, Fisher JL, Aldape KDand Wrensch M Epidemiology and molecular pathology of glioma. 2006 Nat Clin Pract Neurol 2
7. Brandes AA, et al Temozolomide as a second-line systemic regimen in recurrent high-grade glioma: a phase II study. 2001 Ann Oncol 12 255-7
8. Krex D, et al Long-term survival with glioblastoma multiforme. 2007 Brain 130 2596-606
9. Omuro Aand DeAngelis LM Glioblastoma and other malignant gliomas: a clinical review. 2013 JAMA 310 1842-50
10. Anand P, Kunnumakkara AB, Sundaram C, Harikumar KB, Tharakan ST, Lai OS, Sung Band Aggarwal BB Cancer is a preventable disease that requires major lifestyle changes. 2008 Pharm Res 25 2097-116
11. Merlo LMF, Pepper JW, Reid BJand Maley CC Cancer as an evolutionary and ecological process. 2006 Nat Rev Cancer 6 924-35
12. Tantillo E, Vannini E, Cerri C, Spalletti C, Colistra A, Mazzanti CM, Costa Mand Caleo M Differential roles of pyramidal and fast-spiking, GABAergic neurons in the control of glioma cell proliferation. 2020 Neurobiol Dis 141 104942
13. Yoshihara K, et al Inferring tumour purity and stromal and immune cell admixture from expression data. 2013 Nat Commun 4 2612
14. Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi Wand Smyth GK limma powers differential expression analyses for RNA-sequencing and microarray studies. 2015 Nucleic Acids Res 43 e47
15. Szklarczyk D, et al STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. 2019 Nucleic Acids Res 47 D607-D13
16. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski Band Ideker T Cytoscape: a software environment for integrated models of biomolecular interaction networks. 2003 Genome Res 13 2498-504
17. Yu G, Wang L-G, Han Yand He Q-Y clusterProfiler: an R package for comparing biological themes among gene clusters. 2012 OMICS 16 284-7
18. Weller M, et al Glioma. 2015 Nat Rev Dis Primers 1 15017
19. Louis DN, et al The 2016 World Health Organization Classification of Tumors of the Central Nervous System: a summary. 2016 Acta Neuropathol 131 803-20
20. Verhaak RGW, et al Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. 2010 Cancer Cell 17
21. Lenting K, Verhaak R, Ter Laan M, Wesseling Pand Leenders W Glioma: experimental models and reality. 2017 Acta Neuropathol 133 263-82
22. Tan AC, Ashley DM, López GY, Malinzak M, Friedman HSand Khasraw M Management of glioblastoma: State of the art and future directions. 2020 CA Cancer J Clin 70 299-312
23. Gilbert MR, et al Dose-dense temozolomide for newly diagnosed glioblastoma: a randomized phase III clinical trial. 2013 J Clin Oncol 31 4085-91
24. Chinot OL, et al Bevacizumab plus radiotherapy-temozolomide for newly diagnosed glioblastoma. 2014 N Engl J Med 370 709-22
25. Gilbert MR, et al A randomized trial of bevacizumab for newly diagnosed glioblastoma. 2014 N Engl J Med 370 699-708
26. Wen PYand Reardon DA Neuro-oncology in 2015: Progress in glioma diagnosis, classification and treatment. 2016 Nat Rev Neurol 12 69-70
27. Stupp R, et al Effect of Tumor-Treating Fields Plus Maintenance Temozolomide vs Maintenance Temozolomide Alone on Survival in Patients With Glioblastoma: A Randomized Clinical Trial. 2017 JAMA 318 2306-16
28. Chen N, Alieva M, van der Most T, Klazen JAZ, Vollmann-Zwerenz A, Hau Pand Vrisekoop N Neutrophils Promote Glioblastoma Tumor Cell Migration after Biopsy. 2022 Cells 11
29. Xu M, Wang Y, Xia R, Wei Yand Wei X Role of the CCL2-CCR2 signalling axis in cancer: Mechanisms and therapeutic targeting. 2021 Cell Prolif 54 e13115
30. Knebel FH, Uno M, Galatro TF, Bellé LP, Oba-Shinjo SM, Marie SKNand Campa A Serum amyloid A1 is upregulated in human glioblastoma. 2017 J Neurooncol 132 383-91
31. Lin C-Y, et al Serum amyloid A1 in combination with integrin αVβ3 increases glioblastoma cells mobility and progression. 2018 Mol Oncol 12 756-71
32. Zhang H, et al SAA1 knockdown promotes the apoptosis of glioblastoma cells via downregulation of AKT signaling. 2021 J Cancer 12 2756-67
33. Cao K, Jiang X, Wang B, Ni Zand Chen Y SAA1 Expression as a Potential Prognostic Marker of the Tumor Microenvironment in Glioblastoma. 2022 Front Neurol 13 905561
34. Cui Gand Xiao Y Identification of SAA1 as a prognostic biomarker associated with immune infiltration in glioblastoma. 2022 Autoimmunity 55 418-27
35. Filippova N, Grimes JM, Leavenworth JW, Namkoong D, Yang X, King PH, Crowley M, Crossman DKand Nabors LB Targeting the TREM1-positive myeloid microenvironment in glioblastoma. 2022 Neurooncol Adv 4 vdac149
36. Jin X, et al Fc gamma receptor IIb in tumor-associated macrophages and dendritic cells drives poor prognosis of recurrent glioblastoma through immune-associated signaling pathways. 2022 Front Genet 13 1046008
37. Mao P, Wang T, Du C-W, Yu Xand Wang M-D CXCL5 promotes tumorigenesis and angiogenesis of glioblastoma via JAK-STAT/NF-κb signaling pathways. 2023 Mol Biol Rep
38. Ji H, Liu Z, Wang F, Sun H, Wang N, Liu Y, Hu Sand You C Novel macrophage-related gene prognostic index for glioblastoma associated with M2 macrophages and T cell dysfunction. 2022 Front Immunol 13 941556
39. Wu P, Guo Y, Xiao L, Yuan J, Tang C, Dong Jand Qian Z LILRB2-containing small extracellular vesicles from glioblastoma promote tumor progression by promoting the formation and expansion of myeloid-derived suppressor cells. 2023 Cancer Immunol Immunother 72 2179-93
40. Peng WX, Koirala Pand Mo YY LncRNA-mediated regulation of cell signaling in cancer. 2017 Oncogene 36 5661-7
41. Li Z, et al Glioblastoma Cell-Derived lncRNA-Containing Exosomes Induce Microglia to Produce Complement C5, Promoting Chemotherapy Resistance. 2021 Cancer Immunol Res 9 1383-99
42. Chen Q, et al Long Noncoding RNA NEAT1, Regulated by the EGFR Pathway, Contributes to Glioblastoma Progression Through the WNT/β-Catenin Pathway by Scaffolding EZH2. 2018 Clin Cancer Res 24 684-95
43. Banelli B, Forlani A, Allemanni G, Morabito A, Pistillo MPand Romani M MicroRNA in Glioblastoma: An Overview. 2017 Int J Genomics 2017 7639084
44. Yang L, Ma Y, Xin Y, Han R, Li Rand Hao X Role of the microRNA 181 family in glioma development. 2018 Mol Med Rep 17 322-9
Data Availability
The datasets used and/or analyzed during the current study will be available from the authors upon reasonable request.
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- Volume Title
- Proceedings of the 2nd International Conference on Modern Medicine and Global Health
- ISBN (Print)
- 978-1-83558-111-7
- ISBN (Online)
- 978-1-83558-112-4
- Published Date
- 13 November 2023
- Series
- Theoretical and Natural Science
- ISSN (Print)
- 2753-8818
- ISSN (Online)
- 2753-8826
- DOI
- 10.54254/2753-8818/8/20240355
- Copyright
- 13 November 2023
- Open Access
- This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited