Effects of antioxidants in human cancers: Differential effects on non-coding intronic RNA expression

Antioxidants

Volumn 5, Issue 1, 2016, Pages

  Menon, Shreya ^a   Lu, Chunxia ^b   Menon, Rajasree ^b   Schwartz, Jessica ^b   Guan, Yuanfang ^b  

^a Skyline High School Library   (United States)

^b UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

Author keywords

Antioxidants; Intronic RNA; Lung cancer; Prostate cancer

Indexed keywords

EID: 85010399587     PISSN: None     EISSN: 20763921     Source Type: Journal    
DOI: 10.3390/antiox5010001     Document Type: Article

References (55)

1. Cui, H.; Kong, Y.; Zhang, H. Oxidative stress, mitochondrial dysfunction, and aging. J. Signal Transduct. 2012, 2012, 646354.
2. Mates, J.M.; Perez-Gomez, C.; Nunez de Castro, I. Antioxidant enzymes and human diseases. Clin. Biochem. 1999, 32, 595–603.
3. Hennekens, C.H.; Buring, J.E.; Manson, J.E.; Stampfer, M.; Rosner, B.; Cook, N.R.; Belanger, C.; LaMotte, F.; Gaziano, J.M.; Ridker, P.M.; et al. Lack of effect of long-term supplementation with beta carotene on the incidence of malignant neoplasms and cardiovascular disease. N. Engl. J. Med. 1996, 334, 1145–1149.
4. Hercberg, S.; Galan, P.; Preziosi, P.; Bertrais, S.; Mennen, L.; Malvy, D.; Roussel, A.M.; Favier, A.; Briancon, S. The SU.VI.MAX Study: A randomized, placebo-controlled trial of the health effects of antioxidant vitamins and minerals. Arch. Intern. Med. 2004, 164, 2335–2342.
5. Ushakova, T.; Melkonyan, H.; Nikonova, L.; Afanasyev, V.; Gaziev, A.I.; Mudrik, N.; Bradbury, R.; Gogvadze, V. Modification of gene expression by dietary antioxidants in radiation-induced apoptosis of mice splenocytes. Free Radic. Biol. Med. 1999, 26, 887–891.
6. vasculature. Circ. Res. 1999, 85, 753–766.
7. Canali, R.; Natarelli, L.; Leoni, G.; Azzini, E.; Comitato, R.; Sancak, O.; Barella, L.; Virgili, F. Vitamin C supplementation modulates gene expression in peripheral blood mononuclear cells specifically upon an inflammatory stimulus: A pilot study in healthy subjects. Genes Nutr. 2014, 9, 390.
8. Luan, H.; Meng, N.; Fu, J.; Chen, X.; Xu, X.; Feng, Q.; Jiang, H.; Dai, J.; Yuan, X.; Lu, Y.; et al. Genome-wide transcriptome and antioxidant analyses on gamma-irradiated phases of deinococcus radiodurans R1. PLoS ONE 2014, 9, e85649.
9. Matsumoto, A.; Mason, S.R.; Flatscher-Bader, T.; Ward, L.C.; Marsh, S.A.; Wilce, P.A.; Fassett, R.G.; de Haan, J.B.; Coombes, J.S. Effects of exercise and antioxidant supplementation on endothelial gene expression. Int. J. Cardiol. 2012, 158, 59–65.
10. Tsai, P.H.; Liu, J.J.; Yeh, C.L.; Chiu, W.C.; Yeh, S.L. Effects of glutamine supplementation on oxidative stress-related gene expression and antioxidant properties in rats with streptozotocin-induced type 2 diabetes. Br. J. Nutr. 2012, 107, 1112–1118.
11. : Expression noise or expression choice? Genomics 2009, 93, 291–298.
12. Martianov, I.; Ramadass, A.; Serra Barros, A.; Chow, N.; Akoulitchev, A. Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript. Nature 2007, 445, 666–670.
13. Brito, G.C.; Fachel, Â.A.; Vettore, A.L.; Vignal, G.M.; Gimba, E.R.P.; Campos, F.S.; Barcinski, M.A.; Verjovski-Almeida, S.; Reis, E.M. Identification of protein-coding and intronic noncoding RNAs down-regulated in clear cell renal carcinoma. Mol. Carcinog. 2008, 47, 757–767.
14. Reis, E.M.; Nakaya, H.I.; Louro, R.; Canavez, F.C.; Flatschart, A.V.F.; Almeida, G.T.; Egidio, C.M.; Paquola, A.C.; Machado, A.A.; Festa, F.; et al. Antisense intronic non-coding RNA levels correlate to the degree of tumor differentiation in prostate cancer. Oncogene 2004, 23, 6684–6692.
15. Olson, J.H.; Erie, J.C.; Bakri, S.J. Nutritional supplementation and age-related macular degeneration. Semin. Ophthalmol. 2011, 26, 131–136.
16. Mathew, M.C.; Ervin, A.M.; Tao, J.; Davis, R.M. Antioxidant vitamin supplementation for preventing and slowing the progression of age-related cataract. Cochrane Database Syst. Rev. 2012, 6, Cd004567.
17. Tarozzi, A.; Angeloni, C.; Malaguti, M.; Morroni, F.; Hrelia, S.; Hrelia, P. Sulforaphane as a Potential Protective Phytochemical against Neurodegenerative Diseases. Oxidative Med. Cell. Longevity 2013, 2013, 10.
18. : The search for chemopreventive agents and supportive therapeutics. Pharmaceuticals (Basel) 2014, 7, 913–942.
19. Bjelakovic, G.; Nikolova, D.; Gluud, C. Antioxidant supplements to prevent mortality. JAMA 2013, 310, 1178–1179.
20. Sablina, A.A.; Budanov, A.V.; Ilyinskaya, G.V.; Agapova, L.S.; Kravchenko, J.E.; Chumakov, P.M. The antioxidant function of the p53 tumor suppressor. Nat. Med. 2005, 11, 1306–1313.
21. Sultan, M.; Schulz, M.H.; Richard, H.; Magen, A.; Klingenhoff, A.; Scherf, M.; Seifert, M.; Borodina, T.; Soldatov, A.; Parkhomchuk, D.; et al. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 2008, 321, 956–960.
22. Mortazavi, A.; Williams, B.A.; McCue, K.; Schaeffer, L.; Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 2008, 5, 621–628.
23. Gaidatzis, D.; Burger, L.; Florescu, M.; Stadler, M.B. Analysis of intronic and exonic reads in RNA-seq data characterizes transcriptional and post-transcriptional regulation. 2015, 33, 722–729.
24. Li, L.; Tan, J.; Zhang, Y.; Han, N.; Di, X.; Xiao, T.; Cheng, S.; Gao, Y.; Liu, Y. DLK1 promotes lung cancer cell invasion through upregulation of MMP9 expression depending on Notch signaling. PLoS ONE 2014, 9, e91509.
25. Li, Y.; Zhang, Y.; Qiu, F.; Qiu, Z. Proteomic identification of exosomal LRG1: A potential urinary biomarker for detecting NSCLC. Electrophoresis 2011, 32, 1976–1983.
26. Wang, Z.; Gerstein, M.; Snyder, M. RNA-Seq: A revolutionary tool for transcriptomics. Nat. Rev. Genet. 2009, 10, 57–63.
27. Sayin, V.I.; Ibrahim, M.X.; Larsson, E.; Nilsson, J.A.; Lindahl, P.; Bergo, M.O. Antioxidants Accelerate Lung Cancer Progression in Mice. Sci. Transl. Med. 2014, 6, 221ra15.
28. Beaver, L.M.; Buchanan, A.; Sokolowski, E.I.; Riscoe, A.N.; Wong, C.P.; Chang, J.H.; Lohr, C.V.; Williams, D.E.; Dashwood, R.H.; Ho, E. Transcriptome analysis reveals a dynamic and differential transcriptional response to sulforaphane in normal and prostate cancer cells and suggests a role for Sp1 in chemoprevention. Mol. Nutr. Food Res. 2014, 58, 2001–2013.
29. Illumina iGenomes. Available online: https://support.illumina.com/sequencing/sequencing_software/ igenome.html (accessed on 26 December 2014).
30. Kim, D.; Pertea, G.; Trapnell, C.; Pimentel, H.; Kelley, R.; Salzberg, S.L. TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013, 14, R36.
31. Langmead, B.; Trapnell, C.; Pop, M.; Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009, 10, R25.
32. SA Mtools. Available online: http://samtools.sourceforge.net/ (accessed on 26 December 2014).
33. UCSC Genome Bioinformatics. Available online: https://genome.ucsc.edu/cgi-bin/hgTables (accessed on 15 December 2014).
34. Robinson, M.D.; McCarthy, D.J.; Smyth, G.K. edge R: A Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010, 26, 139–140.
35. P. adjust {stats}. Available online: https://stat.ethz.ch/R-manual/R-devel/library/stats/html/p.adjust.html (accessed on 15 January 2015).
36. GSEA Gene Set Enrichment Analysis. Available online: http://software.broadinstitute.org/gsea/msigdb (accessed on 30 January 2015).
37. Yu, Y.; Bae, S.; Kim, H.; Kim, Y.; Chu, N.B.; Chu, N.K.; Kang, J.S.; Lee, W.J. The Anti-tumor Activity of Vitamin C via the Increase of Fas (CD95) and MHC I Expression on Human Stomach Cancer Cell Line, SNU1. Immune Netw. 2011, 11, 210–215.
38. Kang, T.H.; Knoff, J.; Yeh, W.H.; Yang, B.; Wang, C.; Kim, Y.S.; Kim, T.W.; Wu, T.C.; Hung, C.F. Treatment of tumors with vitamin E suppresses myeloid derived suppressor cells and enhances CD8+ T cell-mediated antitumor effects. PLoS ONE 2014, 9, e103562.
39. Shanafelt, T.D.; Lee, Y.K.; Geyer, S.M.; Grote, D.; Stenson, M.; Zincke, S.; Ansell, S.M.; Witzig, T.E.; Kay, N.E. The Green Tea Extract Epigallocatechin Induces in Vitro Cell Death in Primary Human Lymphoma Cells through an ROS Dependent Mechanism. ASH Annu. Meet. Abstr. 2006, 108, 234.
40. Vahdati-Mashhadian, N.; Jafari, M.R.; Sharghi, N.; Sanati, T. Protective Effects of Vitamin C and NAC on the Toxicity of Rifampin on Hepg2 Cells. Iran J. Pharm. Res. 2013, 12, 141–146.
41. Bio-Rad Protein Assay. Available online: http://www.bio-rad.com/LifeScience/pdf/Bulletin_9004.pdf (accessed on 10 February 2015).
42. Superoxide Dismutase Assay Kit. Available online: https://www.caymanchem.com/pdfs/706002.pdf (accessed on 10 February 2015).
43. Primer3 (v0.4.0). Available online: http://bioinfo.ut.ee/primer3-0.4.0/ (accessed on 25 May 2015).
44. Sweet-Cordero, A.; Mukherjee, S.; Subramanian, A.; You, H.; Roix, J.J.; Ladd-Acosta, C.; Mesirov, J.; Golub, T.R.; Jacks, T. An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis. Nat. Genet. 2005, 37, 48–55.
45. Klein, E.A.; Thompson, I.M., Jr.; Tangen, C.M.; Crowley, J.J.; Lucia, M.S.; Goodman, P.J.; Minasian, L.M.; Ford, L.G.; Parnes, H.L.; Gaziano, J.M.; et al. Vitamin E and the risk of prostate cancer: The Selenium and Vitamin E Cancer Prevention Trial (SELECT). JAMA 2011, 306, 1549–1556.
46. Jerome-Morais, A.; Diamond, A.M.; Wright, M.E. Dietary supplements and human health: For better or for worse? Mol. Nutr. Food Res. 2011, 55, 122–135.
47. getable intake and mortality from ischaemic heart disease: Results from the European Prospective Investigation into Cancer and Nutrition (EPIC)-Heart study. Eur. Heart J. 2011, 32, 1235–1243.
48. DeBerardinis, R.J. Is cancer a disease of abnormal cellular metabolism?: New angles on an old idea. Genet. Med.: Off. J. Am. Coll. Med. Genet. 2008, 10, 767–777.
49. Takashima, Y.; Ohtsuka, T.; Gonzalez, A.; Miyachi, H.; Kageyama, R. Intronic delay is essential for oscillatory expression in the segmentation clock. Proc. Natl. Acad. Sci. USA 2011, 108, 3300–3305.
50. Chorev, M.; Carmel, L. The Function of Introns. Front. Genet. 2012, 3, 55.
51. Nakaya, H.I.; Amaral, P.P.; Louro, R.; Lopes, A.; Fachel, A.A.; Moreira, Y.B.; El-Jundi, T.A.; da Silva, A.M.; Reis, E.M.; Verjovski-Almeida, S. Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription. Genome Biol. 2007, 8, R43.
52. Yazdi, M.H.; Mahdavi, M.; Kheradmand, E.; Shahverdi, A.R. The preventive oral supplementation of a selenium nanoparticle-enriched probiotic increases the immune response and lifespan of 4T1 breast cancer bearing mice. Arzneimittelforschung 2012, 62, 525–531.
53. Lu, L.Y.; Ou, N.; Lu, Q.B. Antioxidant induces DNA damage, cell death and mutagenicity in human lung and skin normal cells. Sci. Rep. 2013, 3, 3169.
54. Watson, J. Oxidants, antioxidants and the current incurability of metastatic cancers. Open Biol. 2013, 3, 120144.
55. Liu, Y.; Luo, X.; Hu, H.; Wang, R.; Sun, Y.; Zeng, R.; Chen, H. Integrative proteomics and tissue microarray profiling indicate the association between overexpressed serum proteins and non-small cell lung cancer. PLoS ONE 2012, 7, e51748.