Investigation of Androgen Responsive Elements in Some Autophagy Related Genes via In Silico Analysis

Öz

Amaç: Otofaji, hasarlı organellerin, hatalı katlanmış veya uzun ömürlü proteinlerin, ökaryotik hücrelerde lizozom aracılı uzaklaştırılmasından sorumlu olan majör bir hücresel yoldur ve mayadan memelilere kadar iyi düzeyde korunmuş fizyolojik mekanizmadır. Otofaji, nörodejeneratif hastalıklar, bulaşıcı hastalıklar, metabolik hastalıklar ve kanserinde dahil olduğu çok çeşitli patolojilerle ilişkilendirilmiştir. Son çalışmalar otofajinin prostat kanserindeki rolünü vurgulamaktadır. Bu nedenle, otofajinin bilinmeyen mekanizmalar ile gerçekleşen regülasyonu ve özellikle androjen aracılı gerçekleşen regülasyonu hakkındaki bilinmeyen süreçlerin anlaşılması önem taşımaktadır. Bu çalışmada otofaji ile ilişkili genlerin promotor bölgesinde in silico analizler ile varsayılan ARE’leri araştırmayı amaçladık. Materyal-Metod: Otofaji ile ilişkili hedef genlerin promotör dizileri UCSC ve EPD veri tabanından ekstrakte edilerek, androjen resepötörü bağlanma motifi için varsayılan bağlanma bölgeleri matinspector biyoinformatik aracı ile analiz edildi.

Bulgular: İn silico analiz sonuçlara göre otofaji ile ilişkili 33 farklı genin promotor bölgesinde varsayılan ARE’ler tanımlandı.

Sonuç: Sonuçlarımız otofaji ile ilişkili komponentlerin androjen sinyalizasyonu ile sıkı şekilde düzenlenebileceğini önermektedir.

Anahtar Kelimeler

• Otofaji,Androjen cevap elementleri,Prostat kanseri,in silico analiz

Investigation of Androgen Responsive Elements in Some Autophagy Related Genes via in silico Analysis

Öz

Objective: Autophagy is a major cellular pathway that is responsible for removal of damaged organelles, misfolded or long-lived proteins by lysosome in eukaryotic cells, and it is a well conserved physiological mechanism from the yeast to mammalian. Autophagy has been associated with several pathologies, including neurodegenerative diseases, infectious diseases, metabolic diseases and cancer. Recent studies highlight the role of autophagy in prostate cancer. Thus, it is important to understand the unknown processes about regulation of autophagy with its different mechanisms, especially androgen mediated regulation. In this study, our aim was to investigate the putative AREs in promoter sequence of autophagy related genes by in silico analysis. Material-Method: Promoter sequences of the autophagy related target genes extracted from UCSC and EPD databases and then analyzed putative binding sites for androgen receptor binding motif by matinspector bioinformatics tool. Results: The result of the in silico analysis indicates that putative AREs in the promoter region of 33 different genes associated with autophagy are identified. Conclusions: Our data the positive correlation between suggest that autophagy related components may be tightly regulated by androgen signaling.

Anahtar Kelimeler

• Autophagy,androgen responsive elements (AREs),Prostate cancer,İn silico analysis

Kaynakça

1. 1. Farhan H, Kundu M, Ferro-Novick S. The link between autophagy and secretion: a story of multitasking proteins. Mol Biol Cell. 2017;28(9):1161-4.
2. 2. Manjithaya R, Subramani S. Role of autophagy in unconventional protein secretion. Autophagy. 2010;6(5):650-1.
3. 3. Shimizu S, Yoshida T, Tsujioka M, Arakawa S. Autophagic cell death and cancer. Int J Mol Sci. 2014;15(2):3145-53.
4. 4. Beau I, Esclatine A, Codogno P. Lost to translation: when autophagy targets mature ribosomes. Trends Cell Biol. 2008;18(7):311-4.
5. 5. Kraft C, Reggiori F, Peter M. Selective types of autophagy in yeast. Biochim Biophys Acta. 2009;1793(9):1404-12.
6. 6. van der Vaart A, Mari M, Reggiori F. A picky eater: exploring the mechanisms of selective autophagy in human pathologies. Traffic. 2008;9(3):281-9.
7. 7. Levine B, Kroemer G. Autophagy in the pathogenesis of disease. Cell. 2008;132(1):27-42.
8. 8. Button RW, Roberts SL, Willis TL, Hanemann CO, Luo S. Accumulation of autophagosomes confers cytotoxicity. J Biol Chem. 2017;292(33):13599-614.

9. 9. Mizushima N, Yoshimori T, Ohsumi Y. The role of Atg proteins in autophagosome formation. Annu Rev Cell Dev Biol. 2011;27:107-32.
10. 10. Ganley IG, Lam du H, Wang J, Ding X, Chen S, Jiang X. ULK1.ATG13. FIP200 complex mediates mTOR signaling and is essential for autophagy. J Biol Chem. 2009;284(18):12297-305.
11. 11. Morris DH, Yip CK, Shi Y, Chait BT, Wang QJ. Beclin1-VPS34 complex architecture: understanding the nuts and bolts of therapeutic targets. Front Biol. 2015;10(5):398-426.
12. 12. Obara K, Sekito T, Niimi K, Ohsumi Y. The Atg18-Atg2 complex is recruited to autophagic membranes via phosphatidylinositol 3-phosphate and exerts an essential function. J Biol Chem. 2008;283(35):23972-80.
13. 13. Tamura H, Shibata M, Koike M, Sasaki M, Uchiyama Y. Atg9A protein, an autophagy-related membrane protein, is localized in the neurons of mouse brains. J Histochem Cytochem. 2010;58(5):443-53.
14. 14. Otomo C, Metlagel Z, Takaesu G, Otomo T. Structure of the human ATG12~ATG5 conjugate required for LC3 lipidation in autophagy. Nat Struct Mol Biol. 2013;20(1):59-66.
15. 15. Lee Y-K, Lee J-A. Role of the Mammalian ATG8/LC3 Family in Autophagy: Differential and Compensatory Roles in the Spatiotemporal Regulation of Autophagy. BMB reports. 2016;49(8):424-30.
16. 16. Miller KD, Siegel RL, Lin CC, Mariotto AB, Kramer JL, Rowland JH, et al. Cancer treatment and survivorship statistics. CA Cancer J Clin. 2016;66(4):271-89.
17. 17. Siegel RL, Miller KD, Jemal A. Cancer statistics. CA Cancer J Clin. 2016;66:7–30.
18. 18. Jiang M, Ma Y, Chen C, Fu X, Yang S, Li X, et al. Androgen-responsive gene database: integrated knowledge on androgen-responsive genes. Mol Endocrinol. 2009;23(11):1927-33.
19. 19. Massie CE, Mills IG. Global identification of androgen response elements. Methods Mol Biol. 2011;776:255-73.
20. 20. Shaffer PL, Jivan A, Dollins DE, Claessens F, Gewirth DT. Structural basis of androgen receptor binding to selective androgen response elements. Proc Natl Acad Sci USA. 2004;101(14):4758-63.
21. 21. Horie-Inoue K, Bono H, Okazaki Y, Inoue S. Identification and functional analysis of consensus androgen response elements in human prostate cancer cells. Biochem Biophys Res Commun. 2004;325(4):1312-7.
22. 22. Culig Z. Proinflammatory cytokine interleukin-6 in prostate carcinogenesis. Am J Clin Exp Urol. 2014;2(3):231-8.
23. 23. Amaravadi R, Kimmelman AC, White E. Recent insights into the function of autophagy in cancer. Genes Dev. 2016;30(17):1913-30.
24. 24. Blessing AM, Rajapakshe K, Reddy Bollu L, Shi Y, White MA, Pham AH, et al. Transcriptional regulation of core autophagy and lysosomal genes by the androgen receptor promotes prostate cancer progression. Autophagy. 2017;13(3):506-21.
25. 25. Masuda, K, Werner T, Maheshwari S, Frisch M, Oh S, Petrovics G, et al. Androgen receptor binding sites identified by a GREF_GATA model. J Mol Biol. 2005;353(4):763–71.
26. 26. Cavin Périer R, Junier T, Bucher P. The Eukaryotic Promoter Database EPD. Nucleic Acids Res. 1998;26(1):353–7.
27. 27. Proikas-Cezanne T, Takacs Z, Dönnes P, Kohlbacher O. WIPI proteins: essential PtdIns3P effectors at the nascent autophagosome. J Cell Sci. 2015;128(2):207-17.
28. 28. Velikkakath AK, Nishimura T, Oita E, Ishihara N, Mizushima N. Mammalian Atg2 proteins are essential for autophagosome formation and important for regulation of size and distribution of lipid droplets. Mol Biol Cell. 2012;23(5):896-909.
29. 29. Li M, Hou Y, Wang J, Chen X, Shao ZM, Yin XM. Kinetics comparisons of mammalian Atg4 homologues indicate selective preferences toward diverse Atg8 substrates. J Biol Chem. 2011;286(9):7327-38.
30. 30. Komatsu M, Wang QJ, Holstein GR, Friedrich VL Jr, Iwata J, Kominami E, et al. Essential role for autophagy protein Atg7 in the maintenance of axonal homeostasis and the prevention of axonal degeneration. Proc Natl Acad Sci USA. 2007;104(36):14489-94.
31. 31. Rogov V, Dötsch V, Johansen T, Kirkin V. Interactions between autophagy receptors and ubiquitin-like proteins form the molecular basis for selective autophagy. Mol Cell. 2014;53(2):167-78.
32. 32. Pontano Vaites L, Paulo JA, Huttlin EL, Harper JW. Systematic analysis of human cells lacking ATG8 proteins uncovers roles for GABARAPs and the CCZ1/MON1 regulator C18orf8/RMC1 in macro and selective autophagic flux. Mol Cell Biol. 2017;38(1):pii:e00392-17.
33. 33. Phillips AR, Suttangkakul A, Vierstra RD. The ATG12-conjugating enzyme ATG10 is essential for autophagic vesicle formation in Arabidopsis thaliana. Genetics. 2008;178(3):1339-53.
34. 34. Suzuki H, Kaizuka T, Mizushima N, Noda NN. Structure of the Atg101-Atg13 complex reveals essential roles of Atg101 in autophagy initiation. Nat Struct Mol Biol. 2015;22(7):572-80.
35. 35. Mizushima N, Levine B, Cuervo AM, Klionsky DJ. Autophagy fights disease through cellular self-digestion. Nature. 2008;451(7182):1069-75.
36. 36. Davis S, Wang J, Ferro-Novick S. Crosstalk between the Secretory and Autophagy Pathways Regulates Autophagosome Formation. Dev Cell. 2017;41(1):23-32.
37. 37. Bennett HL, Fleming JT, O'Prey J, Ryan KM, Leung HY. Androgens modulate autophagy and cell death via regulation of the endoplasmic reticulum chaperone glucose-regulated protein 78/BiP in prostate cancer cells. Cell Death Dis. 2010;9(1):e72.
38. 38. Hao K, Zhao S, Cui D, Zhang Y, Jiang C, Jing Y, et al. Androgen receptor antagonist bicalutamide induces autophagy and apoptosis via ULK2 upregulation
in human bladder cancer cells. Int J Clin Exp Pathol. 2017;10(7):7603-15.
39. 39. Shi Y, Han JJ, Tennakoon JB, Mehta FF, Merchant FA, Burns AR, et al. Androgens promote prostate cancer cell growth through induction of autophagy. Mol Endocrinol 2013;27(2):280-95.