Long Non-Coding RNA CRNDE, LINC00957, and AC072061.1 as a Promising Diagnostic and Prognostic Biomarker in Glioblastoma Multiforme
-
Arash Poursheikhani
,
Meysam Mosallaei
,
Mehrdad Nasrollahzadeh Sabet
,
Mohammad Foad Heidari
,
Mohsen Rajaeinejad
,
Mohsen Chamanara
,
Mojtaba Yousefi zoshk
,
Peyman Aslani
,
Ebrahim Hazrati
,
Mojgan Mohammadimehr
,
Javad Behroozi
Abstract
Background: Glioblastoma multiforme (GBM) is one of the most invasive types of brain cancer. LncRNAs can be considered a new prognostic and diagnostic biomarker in GBM. This study comprehensively explored the interaction of lncRNAs with mRNAs in the TCGA database and proposed a novel promising biomarker with favorable diagnostic and prognostic values.
Methods: The public data of RNA-seq and related clinical data were downloaded from the TCGA database. Differential expression analysis was conducted in R. GO and KEGG signaling pathways were used for enrichment. The STRING database was used for PPI analysis. CE-network was constructed by STAR database. Kaplan-Meier survival analysis and ROC curve analysis to indicate the biomarkers' diagnostic and prognostic values.
Results: Differentially expressed data illustrated that 4428 mRNAs were differentially expressed in GBM. The GO and KEGG pathway analysis showed that the differentially expressed mRNAs were enriched in critical biological processes. The PPI showed that WEE1, BARD1, and CDK6 were the important PPI hubs. The ceRNA network data demonstrated critical lncRNAs. The data revealed that the lncRNA CRNDE, LINC00957, AC072061.1, AC068888.1, and DBH-AS1 are potential diagnostic prognostic biomarkers in the GBM patients.
Conclusion: Altogether, we demonstrated lncRNA, and mRNA interaction and mentioned regulatory networks, considered a therapeutic option in GBM. In addition, we proposed potential diagnostic and prognostic biomarkers for the patients.
1. Tan L, Liu J, Yang M, Ju T, Zhang Y (2020). LncRNA ASB16-AS1 promotes proliferation and inhibits apoptosis of non small cell lung cancer cells by activating the Wnt/β catenin signaling pathway. Eur Rev Med Pharmacol Sci, 24 (4):1870-1876.
2. Sun M, Jin FY, Xia R, et al (2014). Decreased expression of long noncoding RNA GAS5 indicates a poor prognosis and promotes cell proliferation in gastric cancer. BMC Cancer, 14:319.
3. Wang G, Lin X, Han H, et al (2022). lncRNA H19 promotes glioblastoma multiforme development by activating autophagy by sponging miR-491-5p. Bioengineered, 13 (5):11440-11455.
4. Wei P, Jiang J, Xiao M, et al (2022). The transcript ENST00000444125 of lncRNA LINC01503 promotes cancer stem cell properties of glioblastoma cells via reducing FBXW1 mediated GLI2 degradation. Exp Cell Res, 412 (1):113009.
5. Lee SY (2016). Temozolomide resistance in glioblastoma multiforme. Genes Dis, 3 (3):198-210.
6. Zhang L, Wang Q, Wang F, Zhang X, Tang Y, Wang S (2018). LncRNA LINC01446 promotes glioblastoma progression by modulating miR-489-3p/TPT1 axis. Biochem Biophys Res Commun, 503 (3):1484-1490.
7. Vojdani S, Ghaderian SMH, Zali A, et al (2021). Altered expression of EGFR and miR-34a derived from serum and tumoral tissue was associated with glioblastoma multiform. Exp Mol Pathol, 121:104655.
8. Liu S, Mitra R, Zhao MM, et al (2016). The potential roles of long noncoding RNAs (lncRNA) in glioblastoma development. Mol Cancer Ther, 15 (12):2977-2986.
9. Li M, Long S, Hu J, Wang Z, Geng C, Ou S (2019). Systematic identification of lncRNA-based prognostic biomarkers for glioblastoma. Aging (Albany NY), 11 (21):9405-9423.
10. Poursheikhani A, Abbaszadegan MR, Kerachian MA (2021). Mechanisms of long non‐coding RNA function in colorectal cancer tumorigenesis. Asia Pac J Clin Oncol, 17 (1):7-23.
11. Poursheikhani A, Abbaszadegan MR, Nokhandani N, Kerachian MA (2020). Integration analysis of long non-coding RNA (lncRNA) role in tumorigenesis of colon adenocarcinoma. BMC Med Genomics, 13 (1):108.
12. Poursheikhani A, Bahmanpour Z, Razmara E, et al (2020). Non-coding RNAs underlying chemoresistance in gastric cancer. Cell Oncol, 43(6):961-988.
13. Poursheikhani A, Nokhandani N, Yousefi H, Rad DM, Sahebkar A (2020). Clinicopathological Significance of Long Non-Coding RNA GHET1 in Human Cancers: A Meta-Analysis. Curr Pharm Biotechnol, 21 (14):1422-1432.
14. Liu B, Zhou J, Wang C, et al (2020). LncRNA SOX2OT promotes temozolomide resistance by elevating SOX2 expression via ALKBH5-mediated epigenetic regulation in glioblastoma. Cell Death Dis, 11 (5):384.
15. Poursheikhani A, Abbaszadegan MR, Kerachian MA (2022). Long non-coding RNA AC087388. 1 as a novel biomarker in colorectal cancer. BMC Cancer, 22 (1):196.
16. Lv T, Jin Y, Miao Y, et al (2021). LncRNA PVT1 promotes tumorigenesis of glioblastoma by recruiting COPS5 to deubiquitinate and stabilize TRIM24. Mol Ther Nucleic Acids, 27:109-121.
17. Chen X, Yan GY (2013). Novel human lncRNA–disease association inference based on lncRNA expression profiles. Bioinformatics, 29 (20):2617-2624.
18. Yang G, Lu X, Yuan L (2014). LncRNA: a link between RNA and cancer. Biochim Biophys Acta, 1839 (11):1097-1109.
19. Han L, Zhang K, Shi Z, et al (2012). LncRNA profile of glioblastoma reveals the potential role of lncRNAs in contributing to glioblastoma pathogenesis. Int J Oncol, 40 (6):2004-2012.
20. Yadav G, Kulshreshtha R (2022). Metastasis associated long noncoding RNAs in glioblastoma: Biomarkers and therapeutic targets. J Cell Physiol, 237 (1):401-420.
21. Chen L, Gong X, Huang M (2019). YY1-activated long noncoding RNA SNHG5 promotes Glioblastoma cell proliferation through p38/MAPK signaling pathway. Cancer Biother Radiopharm, 34 (9):589-596.
22. Han N, Yang L, Zhang X, et al (2019). LncRNA MATN1-AS1 prevents glioblastoma cell from proliferation and invasion via RELA regulation and MAPK signaling pathway. Ann Transl Med, 7 (23):784.
23. Li J, Zhu Y, Wang H, Ji X (2018). Targeting long noncoding RNA in glioma: a pathway perspective. Mol Ther Nucleic Acids, 13:431-441.
24. Chen Y, Bao C, Zhang X, Lin X, Huang H, Wang Z (2019). Long non‐coding RNA HCG11 modulates glioma progression through cooperating with miR‐496/CPEB3 axis. Cell Prolif, 52 (5):e12615.
25. Li H, Yuan X, Yan D, et al (2017). Long non-coding RNA MALAT1 decreases the sensitivity of resistant glioblastoma cell lines to temozolomide. Cell Physiol Biochem, 42 (3):1192-1201.
26. Wang L, Du L, Duan W, Yan S, Xie Y, Wang C (2018). Overexpression of long noncoding RNA NORAD in colorectal cancer associates with tumor progression. Onco Targets Ther, 11:6757-6766.
27. Bahmanpour Z, Sheervalilou R, Khaniani MS, et al (2022). In Silico and Experimental Analysis of miR-125b-5 and miR-485-5p Expression in Serum of Patients with Breast Cancer. Microrna, 10.2174/2211536611666220523100057.
28. Quintavalle C, Donnarumma E, Iaboni M, et al (2013). Effect of miR-21 and miR-30b/c on TRAIL-induced apoptosis in glioma cells. Oncogene, 32 (34):4001-4008.
29. Chen L, Wang X, Wang H, et al (2012). miR-137 is frequently down-regulated in glioblastoma and is a negative regulator of Cox-2. Eur J Cancer, 48 (16):3104-3111.
30. Silber J, Lim DA, Petritsch C, et al (2008). miR-124 and miR-137 inhibit proliferation of glioblastoma multiforme cells and induce differentiation of brain tumor stem cells. BMC Med, 6 :14.
31. Pan C, Gao H, Zheng N, Gao Q, Si Y, Zhao Y (2017). MiR-320 inhibits the growth of glioma cells through downregulating PBX3. Biol Res, 50 (1):31.
32. Sun JY, Xiao WZ, Wang F, et al (2015). MicroRNA-320 inhibits cell proliferation in glioma by targeting E2F1. Mol Med Rep, 12 (2):2355-2359.
33. Pang H, Zheng Y, Zhao Y, Xiu X, Wang J (2015). miR-590-3p suppresses cancer cell migration, invasion and epithelial–mesenchymal transition in glioblastoma multiforme by targeting ZEB1 and ZEB2. Biochem Biophys Res Commun, 468 (4):739-745.
34. Song J, Ma Q, Hu M, Qian D, Wang B, He N (2018). The inhibition of miR-144-3p on cell proliferation and metastasis by targeting TOP2A in HCMV-positive glioblastoma cells. Molecules, 23 (12):3259.
35. Yan Z, Che S, Wang J, Jiao Y, Wang C, Meng Q (2015). miR-155 contributes to the progression of glioma by enhancing Wnt/β-catenin pathway. Tumour Biol, 36 (7):5323-5331.
36. D'Urso PI, D'Urso OF, Storelli C, et al (2012). miR-155 is up-regulated in primary and secondary glioblastoma and promotes tumour growth by inhibiting GABA receptors. Int J Oncol, 41 (1):228-234.
37. Chen L, Li H, Han L, et al (2011). Expression and function of miR-27b in human glioma. Oncol Rep, 26 (6):1617-1621.
38. Tang H, Wang Z, Liu X, et al (2012). LRRC4 inhibits glioma cell growth and invasion through a miR-185-dependent pathway. Curr Cancer Drug Targets, 12 (8):1032-1042.
39. Wu W, Yu T, Wu Y, et al (2019). The miR155HG/miR-185/ANXA2 loop contributes to glioblastoma growth and progression. J Exp Clin Cancer Res, 38 (1):133.
40. Feng L, Ma J, Ji H, Liu Y, Hu W (2017). miR-330-5p suppresses glioblastoma cell proliferation and invasiveness through targeting ITGA5. Biosci Rep, 37 (3): BSR20170019.
41. Zhu B, Liu W, Liu H, Xu Q, Xu W (2020). LINC01094 down-regulates miR-330-3p and enhances the expression of MSI1 to promote the progression of glioma. Cancer Manag Res, 12:6511-6521.
42. Qiu S, Lin S, Hu D, Feng Y, Tan Y, Peng Y (2013). Interactions of miR-323/miR-326/miR-329 and miR-130a/miR-155/miR-210 as prognostic indicators for clinical outcome of glioblastoma patients. J Transl Med, 11:10.
43. Nawaz Z, Patil V, Paul Y, et al (2016). PI3 kinase pathway regulated miRNome in glioblastoma: identification of miR-326 as a tumour suppressor miRNA. Mol Cancer, 15 (1):74.
44. Du W, Liu X, Chen L, et al (2015). Targeting the SMO oncogene by miR-326 inhibits glioma biological behaviors and stemness. Neuro Oncol, 17 (2):243-253.
2. Sun M, Jin FY, Xia R, et al (2014). Decreased expression of long noncoding RNA GAS5 indicates a poor prognosis and promotes cell proliferation in gastric cancer. BMC Cancer, 14:319.
3. Wang G, Lin X, Han H, et al (2022). lncRNA H19 promotes glioblastoma multiforme development by activating autophagy by sponging miR-491-5p. Bioengineered, 13 (5):11440-11455.
4. Wei P, Jiang J, Xiao M, et al (2022). The transcript ENST00000444125 of lncRNA LINC01503 promotes cancer stem cell properties of glioblastoma cells via reducing FBXW1 mediated GLI2 degradation. Exp Cell Res, 412 (1):113009.
5. Lee SY (2016). Temozolomide resistance in glioblastoma multiforme. Genes Dis, 3 (3):198-210.
6. Zhang L, Wang Q, Wang F, Zhang X, Tang Y, Wang S (2018). LncRNA LINC01446 promotes glioblastoma progression by modulating miR-489-3p/TPT1 axis. Biochem Biophys Res Commun, 503 (3):1484-1490.
7. Vojdani S, Ghaderian SMH, Zali A, et al (2021). Altered expression of EGFR and miR-34a derived from serum and tumoral tissue was associated with glioblastoma multiform. Exp Mol Pathol, 121:104655.
8. Liu S, Mitra R, Zhao MM, et al (2016). The potential roles of long noncoding RNAs (lncRNA) in glioblastoma development. Mol Cancer Ther, 15 (12):2977-2986.
9. Li M, Long S, Hu J, Wang Z, Geng C, Ou S (2019). Systematic identification of lncRNA-based prognostic biomarkers for glioblastoma. Aging (Albany NY), 11 (21):9405-9423.
10. Poursheikhani A, Abbaszadegan MR, Kerachian MA (2021). Mechanisms of long non‐coding RNA function in colorectal cancer tumorigenesis. Asia Pac J Clin Oncol, 17 (1):7-23.
11. Poursheikhani A, Abbaszadegan MR, Nokhandani N, Kerachian MA (2020). Integration analysis of long non-coding RNA (lncRNA) role in tumorigenesis of colon adenocarcinoma. BMC Med Genomics, 13 (1):108.
12. Poursheikhani A, Bahmanpour Z, Razmara E, et al (2020). Non-coding RNAs underlying chemoresistance in gastric cancer. Cell Oncol, 43(6):961-988.
13. Poursheikhani A, Nokhandani N, Yousefi H, Rad DM, Sahebkar A (2020). Clinicopathological Significance of Long Non-Coding RNA GHET1 in Human Cancers: A Meta-Analysis. Curr Pharm Biotechnol, 21 (14):1422-1432.
14. Liu B, Zhou J, Wang C, et al (2020). LncRNA SOX2OT promotes temozolomide resistance by elevating SOX2 expression via ALKBH5-mediated epigenetic regulation in glioblastoma. Cell Death Dis, 11 (5):384.
15. Poursheikhani A, Abbaszadegan MR, Kerachian MA (2022). Long non-coding RNA AC087388. 1 as a novel biomarker in colorectal cancer. BMC Cancer, 22 (1):196.
16. Lv T, Jin Y, Miao Y, et al (2021). LncRNA PVT1 promotes tumorigenesis of glioblastoma by recruiting COPS5 to deubiquitinate and stabilize TRIM24. Mol Ther Nucleic Acids, 27:109-121.
17. Chen X, Yan GY (2013). Novel human lncRNA–disease association inference based on lncRNA expression profiles. Bioinformatics, 29 (20):2617-2624.
18. Yang G, Lu X, Yuan L (2014). LncRNA: a link between RNA and cancer. Biochim Biophys Acta, 1839 (11):1097-1109.
19. Han L, Zhang K, Shi Z, et al (2012). LncRNA profile of glioblastoma reveals the potential role of lncRNAs in contributing to glioblastoma pathogenesis. Int J Oncol, 40 (6):2004-2012.
20. Yadav G, Kulshreshtha R (2022). Metastasis associated long noncoding RNAs in glioblastoma: Biomarkers and therapeutic targets. J Cell Physiol, 237 (1):401-420.
21. Chen L, Gong X, Huang M (2019). YY1-activated long noncoding RNA SNHG5 promotes Glioblastoma cell proliferation through p38/MAPK signaling pathway. Cancer Biother Radiopharm, 34 (9):589-596.
22. Han N, Yang L, Zhang X, et al (2019). LncRNA MATN1-AS1 prevents glioblastoma cell from proliferation and invasion via RELA regulation and MAPK signaling pathway. Ann Transl Med, 7 (23):784.
23. Li J, Zhu Y, Wang H, Ji X (2018). Targeting long noncoding RNA in glioma: a pathway perspective. Mol Ther Nucleic Acids, 13:431-441.
24. Chen Y, Bao C, Zhang X, Lin X, Huang H, Wang Z (2019). Long non‐coding RNA HCG11 modulates glioma progression through cooperating with miR‐496/CPEB3 axis. Cell Prolif, 52 (5):e12615.
25. Li H, Yuan X, Yan D, et al (2017). Long non-coding RNA MALAT1 decreases the sensitivity of resistant glioblastoma cell lines to temozolomide. Cell Physiol Biochem, 42 (3):1192-1201.
26. Wang L, Du L, Duan W, Yan S, Xie Y, Wang C (2018). Overexpression of long noncoding RNA NORAD in colorectal cancer associates with tumor progression. Onco Targets Ther, 11:6757-6766.
27. Bahmanpour Z, Sheervalilou R, Khaniani MS, et al (2022). In Silico and Experimental Analysis of miR-125b-5 and miR-485-5p Expression in Serum of Patients with Breast Cancer. Microrna, 10.2174/2211536611666220523100057.
28. Quintavalle C, Donnarumma E, Iaboni M, et al (2013). Effect of miR-21 and miR-30b/c on TRAIL-induced apoptosis in glioma cells. Oncogene, 32 (34):4001-4008.
29. Chen L, Wang X, Wang H, et al (2012). miR-137 is frequently down-regulated in glioblastoma and is a negative regulator of Cox-2. Eur J Cancer, 48 (16):3104-3111.
30. Silber J, Lim DA, Petritsch C, et al (2008). miR-124 and miR-137 inhibit proliferation of glioblastoma multiforme cells and induce differentiation of brain tumor stem cells. BMC Med, 6 :14.
31. Pan C, Gao H, Zheng N, Gao Q, Si Y, Zhao Y (2017). MiR-320 inhibits the growth of glioma cells through downregulating PBX3. Biol Res, 50 (1):31.
32. Sun JY, Xiao WZ, Wang F, et al (2015). MicroRNA-320 inhibits cell proliferation in glioma by targeting E2F1. Mol Med Rep, 12 (2):2355-2359.
33. Pang H, Zheng Y, Zhao Y, Xiu X, Wang J (2015). miR-590-3p suppresses cancer cell migration, invasion and epithelial–mesenchymal transition in glioblastoma multiforme by targeting ZEB1 and ZEB2. Biochem Biophys Res Commun, 468 (4):739-745.
34. Song J, Ma Q, Hu M, Qian D, Wang B, He N (2018). The inhibition of miR-144-3p on cell proliferation and metastasis by targeting TOP2A in HCMV-positive glioblastoma cells. Molecules, 23 (12):3259.
35. Yan Z, Che S, Wang J, Jiao Y, Wang C, Meng Q (2015). miR-155 contributes to the progression of glioma by enhancing Wnt/β-catenin pathway. Tumour Biol, 36 (7):5323-5331.
36. D'Urso PI, D'Urso OF, Storelli C, et al (2012). miR-155 is up-regulated in primary and secondary glioblastoma and promotes tumour growth by inhibiting GABA receptors. Int J Oncol, 41 (1):228-234.
37. Chen L, Li H, Han L, et al (2011). Expression and function of miR-27b in human glioma. Oncol Rep, 26 (6):1617-1621.
38. Tang H, Wang Z, Liu X, et al (2012). LRRC4 inhibits glioma cell growth and invasion through a miR-185-dependent pathway. Curr Cancer Drug Targets, 12 (8):1032-1042.
39. Wu W, Yu T, Wu Y, et al (2019). The miR155HG/miR-185/ANXA2 loop contributes to glioblastoma growth and progression. J Exp Clin Cancer Res, 38 (1):133.
40. Feng L, Ma J, Ji H, Liu Y, Hu W (2017). miR-330-5p suppresses glioblastoma cell proliferation and invasiveness through targeting ITGA5. Biosci Rep, 37 (3): BSR20170019.
41. Zhu B, Liu W, Liu H, Xu Q, Xu W (2020). LINC01094 down-regulates miR-330-3p and enhances the expression of MSI1 to promote the progression of glioma. Cancer Manag Res, 12:6511-6521.
42. Qiu S, Lin S, Hu D, Feng Y, Tan Y, Peng Y (2013). Interactions of miR-323/miR-326/miR-329 and miR-130a/miR-155/miR-210 as prognostic indicators for clinical outcome of glioblastoma patients. J Transl Med, 11:10.
43. Nawaz Z, Patil V, Paul Y, et al (2016). PI3 kinase pathway regulated miRNome in glioblastoma: identification of miR-326 as a tumour suppressor miRNA. Mol Cancer, 15 (1):74.
44. Du W, Liu X, Chen L, et al (2015). Targeting the SMO oncogene by miR-326 inhibits glioma biological behaviors and stemness. Neuro Oncol, 17 (2):243-253.
| Files | ||
| Issue | Vol 53 No 9 (2024) | |
| Section | Original Article(s) | |
| DOI | https://doi.org/10.18502/ijph.v53i9.16462 | |
| Keywords | ||
| Glioblastoma multiforme Tumorigenesis Long non-coding RNAs | ||
| Rights and permissions | |
|
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License. |
How to Cite
1.
Poursheikhani A, Mosallaei M, Nasrollahzadeh Sabet M, Foad Heidari M, Rajaeinejad M, Chamanara M, Yousefi zoshk M, Aslani P, Hazrati E, Mohammadimehr M, Behroozi J. Long Non-Coding RNA CRNDE, LINC00957, and AC072061.1 as a Promising Diagnostic and Prognostic Biomarker in Glioblastoma Multiforme. Iran J Public Health. 2024;53(9):2090-2102.
