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:: Volume 26, Issue 1 (Bimonthly 2022) ::
Feyz Med Sci J 2022, 26(1): 9-21 Back to browse issues page
In Silico design and in vitro validation for siRNA targeting PTX3 gene in glioma cell line
Reza Ahmadi-Beni , Shirin Shahbazi * , Alireza Khoshnevisan , Javad Behroozi
Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, I.R. Iran. , sh.shahbazi@modares.ac.ir
Abstract:   (1316 Views)
Background: Identification of underlying mechanisms of gliomas pathogenesis is of particular importance. The overexpression of PTX3 gene is profoundly implicated in glioma development. The RNA interference (RNAi)-based knockdown of target gene by means of double-stranded RNA molecules including siRNA can be harvested as a therapeutic tool for oncogene silencing. The present study aimed to induce apoptosis in U-87 glioma cell line by knockdown of PTX3 gene.
Materials and Methods: A variety of in silico methods were applied for siRNA design to silence PTX3 gene. Scoring of candidate siRNAs was performed according to design rules. The best siRNA against the PTX3 gene as well as scrambled siRNA were selected. The efficacy of PTX3 silencing in the U-87 cells was evaluated by Real‐time PCR assay. To assess the effect of PTX3 knock down on cellular apoptosis, the mortality rate of transfected cells was compared with control groups by flow cytometry.
Results: Designed PTX3‐siRNAs (n=53) were assessed and scored from different aspects and the best one was suggested in PTX3 gene expression knockdown assay. The 72-hour treatment of U-87 cells with designed PTX3‐siRNA in 100 nM concentration affected the gene expression by decreasing to 69%. Flowcytometry results indicated the induction of apoptosis in 65% of the cells.
Conclusion: The efficiency of designed siRNA was approved in vitro, with significant effect on the downregulation of PTX3 gene and induction of apoptosis in U-87 glioma cells. Based on our finding, targeting PTX3 via siRNA can be considered as an anti-cancer strategy.
Keywords: PTX3, Glioma, siRNA, Apoptosis, U-87
Full-Text [PDF 888 kb]   (973 Downloads)    
Type of Study: Research | Subject: medicine, paraclinic
Received: 2021/12/8 | Revised: 2022/04/9 | Accepted: 2022/02/13 | Published: 2022/04/4
References
1. Delgado-López PD, Corrales-García EM. Survival in glioblastoma: a review on the impact of treatment modalities. Clin Transl Oncol 2016; 18(11): 1062-71.
2. Pessina F, Navarria P, Cozzi L, Ascolese AM, Simonelli M, Santoro A, et al. Maximize surgical resection beyond contrast-enhancing boundaries in newly diagnosed glioblastoma multiforme: is it useful and safe? A single institution retrospective experience. J Neurooncol 2017; 135(1): 129-39.
3. Ahmadi-Beni R, Khoshnevisan A. An overview of crucial genes involved in stemness of glioblastoma multiforme. Neurochem J 2017; 11(4): 259-65.
4. Ahmadi-Beni R, Najafi A, Savar SM, Mohebbi N, Khoshnevisan A. Role of dimethyl fumarate in the treatment of glioblastoma multiforme: A review article. Iran J Neurol 2019;18(3):127.
5. Noori-Daloii M-R, Ahmadi-beni R. Glioblastoma gene therapy and related delivery systems. Med Sci 2017; 27(3): 149-63. [in Persian]
6. Garlanda C, Bottazzi B, Magrini E, Inforzato A, Mantovani A. PTX3, a humoral pattern recognition molecule, in innate immunity, tissue repair, and cancer. Physiol Rev 2018; 98(2): 623-39.
7. Wang Z, Wang X, Zou H, Dai Z, Feng S, Zhang M, et al. The Basic Characteristics of the Pentraxin Family and Their Functions in Tumor Progression. Front Immunol 2020; 11: 1757.
8. Giacomini A, Ghedini GC, Presta M, Ronca R. Long pentraxin 3: A novel multifaceted player in cancer. Biochim Biophys Acta Rev Cancer 2018; 1869(1): 53-63.
9. Doni A, Stravalaci M, Inforzato A, Magrini E, Mantovani A, Garlanda C, et al. The long pentraxin PTX3 as a link between innate immunity, tissue remodeling, and cancer. Front Immunol 2019; 10: 712.
10. Wang Z, Wang X, Zhang N, Zhang H, Dai Z, Zhang M, et al. Pentraxin 3 promotes glioblastoma progression by negative regulating cells autophagy. Front Cell Dev Biol 2020; 8: 795.
11. Petterson SA, Sørensen MD, Kristensen BW. Expression profiling of primary and recurrent glioblastomas reveals a reduced level of pentraxin 3 in recurrent glioblastomas. J Neuropathol Exp Neurol 2020; 79(9): 975-85.
12. Locatelli M, Ferrero S, Boneschi FM, Boiocchi L, Zavanone M, Gaini SM, et al. The long pentraxin PTX3 as a correlate of cancer-related inflammation and prognosis of malignancy in gliomas. J Neuroimmunol 2013; 260(1-2): 99-106.
13. Yeh CM, Lin CW, Chuang CY, Liu YF, Chou CH, Yang SF, et al. Functional genetic variant of long PENTRAXIN 3 gene is associated With clinical aspects of oral cancer in male patients. Front Oncol 2019; 9: 581.
14. Gluszek S, Matykiewicz J, Grabowska U, Chrapek M, Nawacki L, Wawrzycka I, et al. Clinical usefulness of pentraxin 3 (PTX3) as a biomarker of acute pancreatitis and pancreatic cancer. Stud Med 2020; 36(1): 6-13.
15. Goulart MR, Watt J, Siddiqui I, Lawlor RT, Imrali A, Hughes C, et al. Pentraxin 3 is a stromally-derived biomarker for detection of pancreatic ductal adenocarcinoma. NPJ Precis Oncol 2021; 5(1): 1-10.
16. Choi B, Lee E-J, Shin M-K, Park YS, Ryu M-H, Kim S-M, et al. Upregulation of brain-derived neurotrophic factor in advanced gastric cancer contributes to bone metastatic osteolysis by inducing long pentraxin 3. Oncotarget 2016; 7(34): 55506.
17. Choi B, Lee EJ, Park YS, Kim S-M, Kim EY, Song Y, et al. Pentraxin-3 silencing suppresses gastric cancer-related inflammation by inhibiting chemotactic migration of macrophages. Anticancer Res 2015; 35(5): 2663-8.
18. Hu T, Qiao L, Li H, Ren H, Ning Q, Zhou H, et al. Pentraxin 3 (PTX-3) Levels in Bronchoalveolar Lavage Fluid as a Lung Cancer Biomarker. Dis Markers 2020; 2020.
19. Ahmmed B, Kampo S, Khan M, Faqeer A, Kumar SP, Yulin L, et al. Rg3 inhibits gemcitabine‐induced lung cancer cell invasiveness through ROS‐dependent, NF‐κB‐and HIF‐1α‐mediated downregulation of PTX3. J Cell Physiol 2019; 234(7): 10680-97.
20. Ying TH, Lee CH, Chiou HL, Yang SF, Lin CL, Hung CH, et al. Knockdown of Pentraxin 3 suppresses tumorigenicity and metastasis of human cervical cancer cells. Sci Rep 2016; 6(1): 1-12.
21. Yu LM, Wang WW, Qi R, Leng TG, Zhang XL. MicroRNA‐224 inhibition prevents progression of cervical carcinoma by targeting PTX3. J Cell Biochem 2018; 119(12): 10278-90.
22. Kampo S, Ahmmed B, Zhou T, Owusu L, Anabah TW, Doudou NR, et al. Scorpion venom analgesic peptide, BmK AGAP inhibits stemness, and epithelial-mesenchymal transition by down-regulating PTX3 in breast cancer. Front Oncol 2019; 9: 21.
23. Zhang P, Liu Y, Lian C, Cao X, Wang Y, Li X, et al. SH3RF3 promotes breast cancer stem-like properties via JNK activation and PTX3 upregulation. Nat Commun 2020;11(1):1-13.
24. Wills CA, Liu X, Chen L, Zhao Y, Dower CM, Sundstrom J, et al. Chemotherapy-induced upregulation of small extracellular vesicle-associated PTX3 accelerates breast cancer metastasis. Cancer Res 2021;81(2):452-63.
25. Chang X, Li D, Liu C, Zhang Z, Wang T. Pentraxin 3 is a diagnostic and prognostic marker for ovarian epithelial cancer patients based on comprehensive bioinformatics and experiments. Cancer Cell Int 2021; 21(1): 1-13.
26. Stallone G, Netti GS, Cormio L, Castellano G, Infante B, Pontrelli P, et al. Modulation of complement activation by pentraxin-3 in prostate cancer. Sci Rep 2020; 10(1): 1-11.
27. Güzel Ö, Kösem A, Aslan Y, Asfuroglu A, Balci M, Senel C, et al. The Role of Pentraxin-3, Fetuin-A and Sirtuin-7 in the Diagnosis of Prostate Cancer. Urol J 2021: 6626.
28. Falagario UG, Busetto GM, Netti GS, Sanguedolce F, Selvaggio O, Infante B, et al. Prospective Validation of Pentraxin-3 as a Novel Serum Biomarker to Predict the Risk of Prostate Cancer in Patients Scheduled for Prostate Biopsy. Cancers (Basel) 2021; 13(7): 1611.
29. Netti GS, Lucarelli G, Spadaccino F, Castellano G, Gigante M, Divella C, et al. PTX3 modulates the immunoflogosis in tumor microenvironment and is a prognostic factor for patients with clear cell renal cell carcinoma. Aging (Albany NY) 2020; 12(8): 7585.
30. Liu B, Zhao Y, Guo L. Increased serum pentraxin-3 level predicts poor prognosis in patients with colorectal cancer after curative surgery, a cohort study. Medicine (Baltimore) 2018;97(40).
31. Deng H, Fan X, Wang X, Zeng L, Zhang K, Zhang X, et al. Serum pentraxin 3 as a biomarker of hepatocellular carcinoma in chronic hepatitis B virus infection. Sci Rep 2020;10(1):1-10.
32. Cabiati M, Gaggini M, De Simone P, Del Ry S. Do pentraxin 3 and neural pentraxin 2 have different facet function in hepatocellular carcinoma? Clin Exp Med 2021:1-8.
33. Carmo RF, Aroucha D, Vasconcelos LRS, Pereira L, Moura P, Cavalcanti MSM. Genetic variation in PTX 3 and plasma levels associated with hepatocellular carcinoma in patients with HCV. J Viral Hepat 2016;23(2):116-22.
34. Rathore M, Girard C, Ohanna M, Tichet M, Jouira RB, Garcia E, et al. Cancer cell-derived long pentraxin 3 (PTX3) promotes melanoma migration through a toll-like receptor 4 (TLR4)/NF-κB signaling pathway. Oncogene 2019; 38(30): 5873-89.
35. Guo P, Zhang SZ, He H, Zhu Y-T, Tseng SCG. PTX3 controls activation of matrix metalloproteinase 1 and apoptosis in conjunctivochalasis fibroblasts. Invest Ophthalmol Vis Sci 2012; 53(7): 3414-23.
36. Lee HH, Kim SY, Na JC, Yoon YE, Han WK. Exogenous pentraxin-3 inhibits the reactive oxygen species-mitochondrial and apoptosis pathway in acute kidney injury. PloS One 2018; 13(4): e0195758.
37. Lian C, Huang Q, Zhong X, He Z, Liu B, Zeng H, et al. Pentraxin 3 secreted by human adipose‐derived stem cells promotes dopaminergic neuron repair in Parkinson's disease via the inhibition of apoptosis. FASEB J 2021;35(7):e21748.
38. He D, Yan L. MiR-29b-3p aggravates cardiac hypoxia/reoxygenation injury via targeting PTX3. Cytotechnology 2021; 1-10.
39. Chang WC, Wu SL, Huang WC, Hsu JY, Chan SH, Wang JM, et al. PTX3 gene activation in EGF-induced head and neck cancer cell metastasis. Oncotarget 2015; 6(10): 7741.
40. Ahmmed B, Khan MN, Nisar MA, Kampo S, Zheng Q, Li Y, et al. Tunicamycin enhances the suppressive effects of cisplatin on lung cancer growth through PTX3 glycosylation via AKT/NF-κB signaling pathway. Int J Oncol 2019; 54(2): 431-42.
41. Chan SH, Tsai JP, Shen CJ, Liao YH, Chen BK. Oleate-induced PTX3 promotes head and neck squamous cell carcinoma metastasis through the up-regulation of vimentin. Oncotarget 2017; 8(25): 41364.
42. Thomas C, Henry W, Cuiffo BG, Collmann AY, Marangoni E, Benhamo V, et al. Pentraxin-3 is a PI3K signaling target that promotes stem cell–like traits in basal-like breast cancers. Sci Signal 2017; 10(467).
43. O’Keefe EP. siRNAs and shRNAs: Tools for protein knockdown by gene silencing. Mater Methods 2013; 3: 197.
44. Jinek M, Doudna JA. A three-dimensional view of the molecular machinery of RNA interference. Nature 2009; 457(7228): 405-12.
45. Paddison PJ, Caudy AA, Bernstein E, Hannon GJ, Conklin DS. Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells. Genes Dev 2002; 16(8): 948-58.
46. Malekshahi SS, Arefian E, Salimi V, Azad TM, Yavarian J. Potential siRNA molecules for nucleoprotein and M2/L overlapping region of respiratory syncytial virus: In silico design. Jundishapur J Microbiol 2016; 9(4).
47. Tuschl T. Tom Tuschl's motif siRNA design rules and siRNA rational design. Protocol Online 2009. Available at: http://www.protocol-online.org/prot/Protocols/Rules-of-siRNA-design-for-RNA-interference--RNAi--3210.html
48. Baghban-Kohnehrouz B, Nayeri S. Design, simplified cloning, and in-silico analysis of multisite small interfering RNA-targeting cassettes. Mol Biol Res Commun 2016; 5(1): 31.
49. McIntyre GJ, Yu YH, Lomas M, Fanning GC. The effects of stem length and core placement on shRNA activity. BMC Mol Biol 2011; 12(1): 1-12.
50. Bofill-De Ros X, Gu S. Guidelines for the optimal design of miRNA-based shRNAs. Methods 2016; 103: 157-66.
51. Fakhr E, Zare F, Teimoori-Toolabi L. Precise and efficient siRNA design: a key point in competent gene silencing. Cancer Gene Ther 2016; 23(4): 73-82.
52. Tung JN, Ko CP, Yang SF, Cheng CW, Chen P-N, Chang CY, et al. Inhibition of pentraxin 3 in glioma cells impairs proliferation and invasion in vitro and in vivo. J Neurooncol 2016;129(2):201-9.
53. Liu Q, Wang XY, Qin YY, Yan XL, Chen HM, Huang QD, et al. SPOCD1 promotes the proliferation and metastasis of glioma cells by up-regulating PTX3. Am J Cancer Res 2018;8(4):624.
54. Ke HH, Hueng DY, Tsai WC. Low expression of pentraxin 3 and nuclear factor-like 2 implying a relatively longer overall survival time in gliomas. Chin J Physiol 2019; 62(1): 35.
55. Li Y, Song X, Niu J, Ren M, Tang G, Sun Z, et al. Pentraxin 3 acts as a functional effector of Akt/NF-κB signaling to modulate the progression and cisplatin-resistance in non-small cell lung cancer. Arch Biochem Biophys 2021; 701: 108818.
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Ahmadi-Beni R, Shahbazi S, Khoshnevisan A, Behroozi J. In Silico design and in vitro validation for siRNA targeting PTX3 gene in glioma cell line. Feyz Med Sci J 2022; 26 (1) :9-21
URL: http://feyz.kaums.ac.ir/article-1-4518-en.html


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Volume 26, Issue 1 (Bimonthly 2022) Back to browse issues page
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