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Volume 31, Issue 149 (November & December 2023)
J Adv Med Biomed Res 2023, 31(149): 594-601 |
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Ghorbanlou M, Marzban H, Mehdizadeh M. Targeting Positive Regulators of Sonic Hedgehog Signaling Pathway in Medulloblastoma by Designing CRISPR/Cas9 Single Guide RNAs. J Adv Med Biomed Res 2023; 31 (149) :594-601
URL: http://journal.zums.ac.ir/article-1-7249-en.html
URL: http://journal.zums.ac.ir/article-1-7249-en.html
1- Dept. of Anatomy, School of medicine, Iran University of Medical Sciences, Tehran, Iran
2- Children’s Hospital Research Institute of Manitoba (CHRIM), College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
3- Reproductive Sciences and Technology Research Center, School of Medicine, Iran University of Medical Sciences, Tehran, Iran ,mehdizadeh.m@iums.ac.ir
2- Children’s Hospital Research Institute of Manitoba (CHRIM), College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
3- Reproductive Sciences and Technology Research Center, School of Medicine, Iran University of Medical Sciences, Tehran, Iran ,
Abstract: (1522 Views)
Background and Objective: Medulloblastoma formation is importantly related to granular cell proliferation and differentiation, processes which are under the influence of sonic hedgehog (SHH) signaling. Exons of genes encoding different components of this signaling pathway (e.g., ligands, co-receptor, transcription factors, and target genes) were investigated to identify the proper single guide RNAs for selective targeting of positive regulators of the SHH pathway.
Materials and Methods: The genomic DNA sequences of corresponding genes of several positive regulators of the SHH pathway (in Homo Sapiens), including SHH, SMO, GLI1, GLI2, MYCN, and MYC, were retrieved from the National Center for Biotechnology Information (NCBI) gene database. Next, the exon sequences of these genes were identified using protospacer adjacent motif (PAM) of NGG and Streptococcus pyogenes Cas9 nuclease and evaluated by CRISPOR software to select the best sgRNA for each target gene.
Results: The analyses revealed the best sgRNAs for the SHH, SMO, GLI1, GLI2, MYCN, and MYC genes targeted exon 1, -4, -4, -5, -2 and -2, respectively. Proper sgRNAs for targeting each exon in each gene were also identified.
Conclusion: This study revealed possible specific exonic targets of components of the SHH signaling pathway through designing proper sgRNAs using the CRISPR/Cas9 genome editing approach.
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✅ This study revealed possible specific exonic targets of components of the SHH signaling pathway through designing proper sgRNAs using the CRISPR/Cas9 genome editing approach.
Type of Study: Original Research Article |
Subject:
Medical Biology
Received: 2023/09/9 | Accepted: 2023/12/5 | Published: 2024/01/29
Received: 2023/09/9 | Accepted: 2023/12/5 | Published: 2024/01/29
References
1. Marzban H, Del Bigio MR, Alizadeh J, Ghavami S, Zachariah RM, Rastegar M. Cellular commitment in the developing cerebellum. Front Cell Neurosci. 2014;8:450. [DOI:10.3389/fncel.2014.00450] [PMID] [PMCID]
2. Jiao X, Rahimi Balaei M, Abu-El-Rub E, Casoni F, Pezeshgi Modarres H, Dhingra S, et al. Reduced Granule Cell Proliferation and Molecular Dysregulation in the Cerebellum of Lysosomal Acid Phosphatase 2 (ACP2) Mutant Mice. International journal of molecular sciences. 2021;22(6):2994. [DOI:10.3390/ijms22062994] [PMID] [PMCID]
3. Taylor MD, Northcott PA, Korshunov A, et al. Molecular subgroups of medulloblastoma: the current consensus. Acta Neuropathol. 2012;123(4):465-72. [DOI:10.1007/s00401-011-0922-z] [PMID] [PMCID]
4. Northcott PA, Hielscher T, Dubuc A, et al. Pediatric and adult sonic hedgehog medulloblastomas are clinically and molecularly distinct. Acta Neuropathol. 2011;122(2):231-40. [DOI:10.1007/s00401-011-0846-7] [PMID] [PMCID]
5. Hatten ME, Roussel MF. Development and cancer of the cerebellum. Trends Neurosci. 2011;34(3):134-42. [DOI:10.1016/j.tins.2011.01.002] [PMID] [PMCID]
6. Sigafoos AN, Paradise BD, Fernandez-Zapico ME. Hedgehog/GLI signaling pathway: transduction, regulation, and implications for disease. Cancers (Basel). 2021;13(14):3410 [DOI:10.3390/cancers13143410] [PMID] [PMCID]
7. Carballo GB, Honorato JR, de Lopes GPF, Spohr T. A highlight on Sonic hedgehog pathway. Cell Commun Signal. 2018;16(1):11. [DOI:10.1186/s12964-018-0220-7] [PMID] [PMCID]
8. Skoda AM, Simovic D, Karin V, Kardum V, Vranic S, Serman L. The role of the Hedgehog signaling pathway in cancer: A comprehensive review. Bosnian J Basic Med Sci. 2018;18(1):8-20. [DOI:10.17305/bjbms.2018.2756] [PMID] [PMCID]
9. Jiang F, Doudna JA. CRISPR-Cas9 structures and mechanisms. Annu Rev Biophys. 2017;46:505-29. [DOI:10.1146/annurev-biophys-062215-010822] [PMID]
10. Concordet JP, Haeussler M. CRISPOR: intuitive guide selection for CRISPR/Cas9 genome editing experiments and screens. Nucl Acid Res. 2018;46(W1):W242-W5. [DOI:10.1093/nar/gky354] [PMID] [PMCID]
11. Haeussler M, Schönig K, Eckert H, et al. Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR. Gen Biol. 2016;17(1):148. [DOI:10.1186/s13059-016-1012-2] [PMID] [PMCID]
12. Liu G, Zhang Y, Zhang T. Computational approaches for effective CRISPR guide RNA design and evaluation. Comput Struct Biotechnol J. 2020;18:35-44. [DOI:10.1016/j.csbj.2019.11.006] [PMID] [PMCID]
13. Doench JG, Fusi N, Sullender M, et al. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nature Biotechnol. 2016;34(2):184-91. [DOI:10.1038/nbt.3437] [PMID]
14. Moreno-Mateos MA, Vejnar CE, Beaudoin JD, et al. CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo. Nature Method. 2015;12(10):982-8. [DOI:10.1038/nmeth.3543] [PMID] [PMCID]
15. Gupta S, Takebe N, Lorusso P. Targeting the Hedgehog pathway in cancer. Therapeut Adv Med Oncol. 2010;2(4):237-50. [DOI:10.1177/1758834010366430] [PMID] [PMCID]
16. Evangelista M, Tian H, de Sauvage FJ. The hedgehog signaling pathway in cancer. Clin Cancer Res. 2006;12(20 Pt 1):5924-8. [DOI:10.1158/1078-0432.CCR-06-1736] [PMID]
17. Watkins DN, Berman DM, Burkholder SG, Wang B, Beachy PA, Baylin SB. Hedgehog signalling within airway epithelial progenitors and in small-cell lung cancer. Nature. 2003;422(6929):313-7. [DOI:10.1038/nature01493] [PMID]
18. McMahon AP. More surprises in the Hedgehog signaling pathway. Cell. 2000;100(2):185-8. [DOI:10.1016/S0092-8674(00)81555-X] [PMID]
19. Ruiz i Altaba A. Catching a Gli-mpse of Hedgehog. Cell. 1997;90(2):193-6. [DOI:10.1016/S0092-8674(00)80325-6] [PMID]
20. Northcott PA, Korshunov A, Witt H, et al. Medulloblastoma comprises four distinct molecular variants. J Clin Oncol. 2011;29(11):1408-14. [DOI:10.1200/JCO.2009.27.4324] [PMID] [PMCID]
21. Kenney AM, Cole MD, Rowitch DH. Nmyc upregulation by sonic hedgehog signaling promotes proliferation in developing cerebellar granule neuron precursors. Develop. 2003;130(1):15-28. [DOI:10.1242/dev.00182] [PMID]
22. Hatton BA, Knoepfler PS, Kenney AM, et al. N-myc is an essential downstream effector of Shh signaling during both normal and neoplastic cerebellar growth. Cancer Res. 2006;66(17):8655-61. [DOI:10.1158/0008-5472.CAN-06-1621] [PMID]
23. Amakye D, Jagani Z, Dorsch M. Unraveling the therapeutic potential of the Hedgehog pathway in cancer. Nat Med. 2013;19(11):1410-22. [DOI:10.1038/nm.3389] [PMID]
24. Chen JK, Taipale J, Cooper MK, Beachy PA. Inhibition of Hedgehog signaling by direct binding of cyclopamine to Smoothened. Genes Dev. 2002;16(21):2743-8. [DOI:10.1101/gad.1025302] [PMID] [PMCID]
25. Sekulic A, Migden MR, Oro AE, et al. Efficacy and safety of vismodegib in advanced basal-cell carcinoma. N Engl J Med. 2012;366(23):2171-9. [DOI:10.1056/NEJMoa1113713] [PMID] [PMCID]
26. Lou E, Schomaker M, Wilson JD, Ahrens M, Dolan M, Nelson AC. Complete and sustained response of adult medulloblastoma to first-line sonic hedgehog inhibition with vismodegib. Cancer Biol Ther. 2016;17(10):1010-6. [DOI:10.1080/15384047.2016.1220453] [PMID] [PMCID]
27. Li Y, Song Q, Day BW. Phase I and phase II sonidegib and vismodegib clinical trials for the treatment of paediatric and adult MB patients: a systemic review and meta-analysis. Acta Neuropathol Commun. 2019;7(1):123. [DOI:10.1186/s40478-019-0773-8] [PMID] [PMCID]
28. Gampala S, Zhang G, Chang CJ, Yang JY. Activation of AMPK sensitizes medulloblastoma to Vismodegib and overcomes Vismodegib-resistance. FASEB Bio Adv. 2021;3(6):459-69. [DOI:10.1096/fba.2020-00032] [PMID] [PMCID]
29. Kim J, Aftab BT, Tang JY, et al. Itraconazole and arsenic trioxide inhibit Hedgehog pathway activation and tumor growth associated with acquired resistance to smoothened antagonists. Cancer Cell. 2013;23(1):23-34. [DOI:10.1016/j.ccr.2012.11.017] [PMID] [PMCID]
30. Lauth M, Bergström A, Shimokawa T, Toftgård R. Inhibition of GLI-mediated transcription and tumor cell growth by small-molecule antagonists. Proc Natl Acad Sci USA. 2007;104(20):8455-60. [DOI:10.1073/pnas.0609699104] [PMID] [PMCID]
31. Yauch RL, Dijkgraaf GJ, Alicke B, et al. Smoothened mutation confers resistance to a Hedgehog pathway inhibitor in medulloblastoma. Science. 2009;326(5952):572-4. [DOI:10.1126/science.1179386] [PMID] [PMCID]
32. Buonamici S, Williams J, Morrissey M, et al. Interfering with resistance to smoothened antagonists by inhibition of the PI3K pathway in medulloblastoma. Sci Transl Med. 2010;2(51):51ra70. [DOI:10.1126/scitranslmed.3001599] [PMID] [PMCID]
33. Atwood SX, Li M, Lee A, Tang JY, Oro AE. GLI activation by atypical protein kinase C ι/λ regulates the growth of basal cell carcinomas. Nature. 2013;494(7438):484-8. [DOI:10.1038/nature11889] [PMID] [PMCID]
34. Jiang K, Liu Y, Fan J, et al. Hedgehog-regulated atypical PKC promotes phosphorylation and activation of Smoothened and Cubitus interruptus in Drosophila. Proc Natl Acad Sci U S A. 2014;111(45):E4842-E50. [DOI:10.1073/pnas.1417147111] [PMID] [PMCID]
35. Baliou S, Adamaki M, Kyriakopoulos AM, et al. CRISPR therapeutic tools for complex genetic disorders and cancer (Review). Int J Oncol. 2018;53(2):443-68. [DOI:10.3892/ijo.2018.4434] [PMID] [PMCID]
36. Li X, Qian X, Wang B, et al. Programmable base editing of mutated TERT promoter inhibits brain tumour growth. Nat Cell Biol. 2020;22(3):282-8. [DOI:10.1038/s41556-020-0471-6] [PMID]
37. Salimi-Jeda A, Esghaei M, Hossein k, Bokharaei-Salim F, Teimoori A, Abdoli A. Inhibition of HIV-1 replication using the CRISPR/cas9-no NLS system as a prophylactic strategy. Heliyon. 2022;8(9):e10483. [DOI:10.1016/j.heliyon.2022.e10483] [PMID] [PMCID]
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