Prediction and Depiction of Potential RNA-Based Therapeutics for Oncogenic E6 and E7 Genes of Human Papilloma Virus Types 16 & 18: A New Class of Treatment for Lung Cancer
Cancer Research Journal
Volume 6, Issue 2, June 2018, Pages: 62-69
Received: Feb. 2, 2018;
Accepted: Feb. 25, 2018;
Published: Apr. 2, 2018
Views 729 Downloads 32
Moinul Abedin Shuvo, Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong, Chittagong, Bangladesh
Sayeedul Alam Prince, Institute of Nuclear Medicine and Allied Sciences, Bangladesh Atomic Energy Commission, Cox’s Bazar, Bangladesh
Arifuzzaman, Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong, Chittagong, Bangladesh
Unlike almost all the cervical, penile, vulvar, and anal cancers, where Human papilloma virus has long known to play a vital role, a causative link between carcinogenic Human papilloma virus and lung cancer have been found to be highly variable and contradictory. Data also shows geography and race-dependenty. Apart from etiological factors, viral carcinogen can manipulate the cell cycle, hamper cell apoptosis and also interrupt the cell division in host cell which lead to the lung cancer. Molecular studies of carcinogenic Human papilloma virus have found that E6/E7 acts as mitotic mutators which play an important role in pathogenicity and oncogenicity. Analysis of genome sequence of Human papilloma virus revealed that ORF having conserved in early region, E6 and E7 required for viral pathogenicity and oncogenicity can be the suitable target for RNAi technology. RNAi works by silencing or turning off gene expression to control pathogenicity and oncogenicity by blocking its replication processes. Therefore, the work is done on the basis of rational siRNA designing method by targeting viral oncogenic E6 and E7 genes of Human papilloma virus types16 & 18. Searching siRNA target sequences, multiple sequence alignment, forecasting secondary structure and RNA-RNA interaction prediction was done by various computational software tools for designing RNA-based therapeutics (siRNA). In this study, four effective siRNA were predicted rationally for oncogenic E6 and E7 genes of Human papilloma virus types 16 & 18 which might be used as a potential RNA based therapeutics to control the rate of carcinogenesis and degree of oncogenicity. The outcome of this study provides a basis of the researchers towards understating to development of RNA-based therapeutics (siRNA) at genomic level.
Moinul Abedin Shuvo,
Sayeedul Alam Prince,
Prediction and Depiction of Potential RNA-Based Therapeutics for Oncogenic E6 and E7 Genes of Human Papilloma Virus Types 16 & 18: A New Class of Treatment for Lung Cancer, Cancer Research Journal.
Vol. 6, No. 2,
2018, pp. 62-69.
Mathers CD, Loncar D. Projections of global mortality and burden of disease from 2002 to 2030. PLoS Med. 2006; 3:e422.
Jemal, A. Siegel, R, Ward, E et al. Cancer statistics, 2008. CA Cancer J Clin. 2008; 58 (2):71-96.
Talukder, M. H, Jabeen. S, Islam J, Karim, N. Annual report, 2005. Natil. Inst.
Alberg AJ, Samet JM, Epidemiology of lung cancer, Chest, 2003; 123:21S-49S.
Wang XR, Chiu YL, qiu H, Au JS, Yu IT. The roles of smoking and cooking emissions in lung cancer risk among chiness women in Hong kong. Ann Oncol 2009; 20:746-51.
Grosche B, Kreuzer m, Kerisheimer M, Schnelzer M, Tschense A. Lung Cancer risk among German male uranium miners: A cohort study, 19946-1998. Br J Cancer 2006; 95:1280-7.
Pukkala E, Martinsen JI, Lynge e, Gunnarsdottir HK et al. Occupation and cancer-follow-up of 15 million people in five Nordic countries. Acta Oncol 2009; 48:646-790.
Alberg AJ, Ford JG, Samet JM; American college of Chest Physicians. Epidemiology of lung cancer: ACCP evidence-based clinical practice guidelines (2nd edition). Chest. 2007; 132 (3 suppl): 29S-55S.
Grant WB. Air pollution in relation to U.S. cancer mortality rates: An ecological study; likely role of carbonaceous aerosols and polycyclic aromatic hydrocarbons. Anticancer Res 2009; 29:3537-45.
Andres C, Ihrler S, Puchta U, Flaig MJ. Merkel Cell polymavirus is prevalent in a subset of small cell lung cancer: a study of 31 patients. Thorax 2009; 64:1007-1008.
Giuliani L, Jaxmar T, Casadio C, et al. Detection of oncogenic viruss SV40, BKV, JCV, HCMV, HPV and p53 codon 72 plymorphism in lung carcinoma. Lung Cancer 2007; 57:273-281.
Joh J, Jenson AB, Moore GD et al. Human papillomavirus (HPV) and Merkel cell polyomavirus (MCPyV) in non small cell lung cancer. Exp Mol Pathol. 2010; 89:222-226.
Cheng YW, Chiou HL, Sheu GT et al. The association of human papillomavirus 16/18 infection with lung cancer among nonsmoking Taiwanese women. Cancer Res. 2001; 61:2799-803.
Walboomers JM, Jacobs MV, Manos MM et al. Human papillomavirus is a necessary cause of invasive cervical cancer worldwide. J Pathol. 1999; 189:12-19.
Heideman DA, Water boer T, Pawlita M et al. Human Papillomavirus -16 is the predominant type etiologically involved in panile squamous cell carcinoma. J Clin Oncol. 2007; 25:4550-4556.
Steenbergen Rd, de Wilde J, Wilting SM, Brink AA, Snijders PJ, Meijer CJ. HPV-mediated transformation of anogenital tract. J Clin Virol. 2005; 32 Suppl 1: S25-S33.
Syrjänen K. Detection of human papilloma in lung cancer: systematic review and meta-analysis. Anticancer Res. 2012; 32: 3235-50.
Hirayasu T, Iwamasa T, Kamada Y, Koyanagi Y, Usuda H, Genka K. Human papillomavirus DNA in sequamous cell carcinoma of the lung. J Clin Pathol. 1996; 49:810-7.
Chen YC, Chen JH, Richard K, Chen PY, Christiani DC. Lung adenocarcinoma and human papillomavirus infection. Cancer. 2004; 101:1428-36.
Goto A, Li CP, Ota S, et al. Human papillomavirus infection in lung and esophageal cancer: analysis of 485 Asian cases. J Med Virol. 2011; 132:1565-1571.
Klein F, Amin Kotb WF, Petersen I. Incidence of human papilloma virus in lung cancer. Lung Cancer. 2009; 65:13-18.
Koshiol J, Rotunno M, Gillison ML, et al. Assesment of human papillomavirus in lung tumor tissue. J Natl Cancer Inst. 2011; 103:501-507.
Srinivasan M, Taioli E, Ragin CC. Human papillomavirus type 16 and 18 in primary lung cancers-a meta-analysis. Carcinogenesis. 2009; 30:1722-1728.
Tsuhako K, Nakazato I, Hirayasu T, Sunakawa H, Iwamasa T. Human papillovirus DNA in adenosquamous carcinoma of the lung cancer. J Clin Pathol. 1998; 51:741-9.
Soini Y, Nuorva K, Kamel D et al. Presence of Human papillomavirus DNA and abnormal p53 protein accumulation in lung carcinoma. Thorax. 1996; 51:887-93.
Review of Medical Microbiology and Immunology: Edited by: Warren Levinson. Mc GrawHill; 10. 2008:270-275.
J. Betiol, L. L Villa and L. Sichero. Impect of HPV infection on the development of head and neck cancer. Braz J Med Biol Res. 2003; 46:217-226.
IARC Working Group on the Evalution of Carcinogenic Risks to Humans. Human Papillomaviruses. IARC Monogr Eval Carcinog Risks Hum. 2007; 90:1-636.
Schiffman M, Clifford G, Buonaguro FM. Classification of weakly carcinogenic Human papillomavirus types: Addresing the limits of epidemiology at the borderline. Infect Agent Cancer. 2009; 4:6.
Rabia Faridi, Amreen Zahra, Khalida Khan and Muhammad Idrees. Oncogenic potential of Human Papillomavirus (HPV) and its relation with cervical cancer. Virology Journal. 2011; 8:269.
Longwort MS, Laimins LA. Pathogenesis of human papillomaviruses in differentiating epithelia. Mircobial Mol Bio Rev 2004; 68:362-372.
McLaughlin-Drubin ME, Munger K. Oncogenic activities of human papillomaviruses. Virus Res. 2009; 143:195-208.
Nobelprize.org. [Retrieval date: 04/04/2016] http://www.nobelprize.org/nobel_prizes/medicine/laureaters/2006/.
Burger K, Gullerova M. Swiss army knives: non-canonical functions of nuclear Dorsha and Dicer. Nat Rev Mol Cell Bio. 2015.
Saengkrit N, Sanitrum P, woramongkolchai N, et al. The PEI-introduced CS shell/PMMA core nonopartical for silencing the expression of E6/E7 oncogenes in human cervical cells. Carbohydr polym. 2012; 90:1323-1329.
Geall AJ, Verma A, Otten GR, et al. Nonviral delivery of self-amplifying RNA vaccines. Proc Natl Acad Sci USA. 2012; 109:1460-14609.
National Center of Biotechnology Information (NCBI) [Retrieval date: 13/06/2016] (http://www.ncbi.nlm.nih.gov).
Y. Naito, J. Yoshimura, S. Morishita, et.al. siDirect 2.0: update software for designing functional siRNA with reduced seed-dependent off-target effect. BMC Bioformatics. 2009; 10, pp. 392. (http://sidirect2.rnai.jp/design.cgi).
Ui-Tei K, Naito Y, Takahashi F, Haraguchi T, OhkiHamazaki H, Juni A, et al. Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference. Nucleic Acids Res. 2004; 32, 936-948.
Amarzguioui M, Prydz H, An algorithm for selection of functional siRNA sequences. Biochem. Biophys. Res. Commun. 2004; 316, 1050-1058.
Reynolds A, Leake D, Boese Q, Scaringe S, Marshall WS, et al. Rational siRNA design for RNA interference. Nat. Biotechnol. 2004; 22, 326330.
J. D. Thompson, D. G. Higgins and T. J. Gibson. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acid Research, 1994; vol. 22, no 22, pp. 4673-4680. [Retrieval date: 14/06/2016] (http://www.genome.jp/tools/ClustalW).
DNA/RNA GC content calculator. [Retrieval date:14/06/2016](http://www.endmemo.com/bio/gc.php).
Altschul SF., Gish W., Miller W., Myers EW., Lipman DJ. Basic local alignment search tool, J Mol Biol. 1990; 215:403-410. [Retrieval date: 14/06/2016] (http://genome.ucsc.edu/cgi-bin/hgBlat).
mfoldserver [Retrieval date: 14/06/2016] (http://unafold.rna.albany.edu/?q=mfold).
RNAcofold [Retrieval date:14/06/2016] (http://rna.tbi.univie.ac.at/cgi-bin/RNAcofold.cgi).
Taxman DJ, Livingstone LR, Zhang J, et al. Criteria for effective design, construction, and gene knockdown by shRNA vectors, BMC Biotechnol. 2006; 6:7.
Chan CY, Carmack CS, Long DD, et al. A structural interpretation of effect of GC-content on efficiency of RNA interference. BMC Bioinform. 2009; 10:S33.
UiTei K, Naito Y, Nishi K, Juni A, Saigo K. Thermodynamic stability and WatsonCrick base pairing in the seed duplex are major determinants of the efficiency of the siRNA based off target effect. Nucleic Acids Res. 2008; 36, 7100-7109.
M. A Hashem, Moinul Abedin Shuvo and Arifuzzaman. A Computational Approach to Design Potential Antiviral RNA for 3’UTR Post Transcriptional Gene Silencing of Different Strains of Zika Virus. J Young Pharm. 2017; 9 (1):23-30.
Singh S, Gupta SK, Nischal A et al. Design of Potential siRNA molecules for hepatitis delta virus gene silencing. Bioinformation. 2012; 8:749-757.