Identification of Novel Epigenetic Markers of Prostate Cancer by NotI-Microarray Analysis

Overview

Journal Dis Markers

Publisher Wiley

Specialty Biochemistry

Date 2015 Oct 23

PMID 26491211

Citations 27

Authors

Alexey A Dmitriev

Eugenia E Rosenberg

George S Krasnov

Ganna V Gerashchenko

Vasily V Gordiyuk

Tatiana V Pavlova

Anna V Kudryavtseva

Artemy D Beniaminov

Anastasia A Belova

Yuriy N Bondarenko

Rostislav O Danilets

Alexander I Glukhov

Aleksandr G Kondratov

Andrey Alexeyenko

Boris Y Alekseev

George Klein

Vera N Senchenko

Vladimir I Kashuba

Affiliations

Soon will be listed here.

Abstract

A significant need for reliable and accurate cancer diagnostics and prognosis compels the search for novel biomarkers that would be able to discriminate between indolent and aggressive tumors at the early stages of disease. The aim of this work was identification of potential diagnostic biomarkers for characterization of different types of prostate tumors. NotI-microarrays with 180 clones associated with chromosome 3 genes/loci were applied to determine genetic and epigenetic alterations in 33 prostate tumors. For 88 clones, aberrations were detected in more than 10% of tumors. The major types of alterations were DNA methylation and/or deletions. Frequent methylation of the discovered loci was confirmed by bisulfite sequencing on selective sampling of genes: FGF12, GATA2, and LMCD1. Three genes (BHLHE40, BCL6, and ITGA9) were tested for expression level alterations using qPCR, and downregulation associated with hypermethylation was shown in the majority of tumors. Based on these data, we proposed the set of potential biomarkers for detection of prostate cancer and discrimination between prostate tumors with different malignancy and aggressiveness: BHLHE40, FOXP1, LOC285205, ITGA9, CTDSPL, FGF12, LOC440944/SETD5, VHL, CLCN2, OSBPL10/ZNF860, LMCD1, FAM19A4, CAND2, MAP4, KY, and LRRC58. Moreover, we probabilistically estimated putative functional relations between the genes within each set using the network enrichment analysis.

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References

Alexeyenko A, Sonnhammer E . Global networks of functional coupling in eukaryotes from comprehensive data integration. Genome Res. 2009; 19(6):1107-16. PMC: 2694487. DOI: 10.1101/gr.087528.108. View

Kang J, Koo S, Kwon K, Park J, Kim J . Identification of novel candidate target genes, including EPHB3, MASP1 and SST at 3q26.2-q29 in squamous cell carcinoma of the lung. BMC Cancer. 2009; 9:237. PMC: 2716371. DOI: 10.1186/1471-2407-9-237. View

Smith A, Xian J, Richardson M, Johnstone K, Rabbitts P . Cre-loxP chromosome engineering of a targeted deletion in the mouse corresponding to the 3p21.3 region of homozygous loss in human tumours. Oncogene. 2002; 21(29):4521-9. DOI: 10.1038/sj.onc.1205530. View

Maldonado L, Brait M, Loyo M, Sullenberger L, Wang K, Peskoe S . GSTP1 promoter methylation is associated with recurrence in early stage prostate cancer. J Urol. 2014; 192(5):1542-8. PMC: 4390043. DOI: 10.1016/j.juro.2014.04.082. View

Ciriello G, Miller M, Aksoy B, Senbabaoglu Y, Schultz N, Sander C . Emerging landscape of oncogenic signatures across human cancers. Nat Genet. 2013; 45(10):1127-33. PMC: 4320046. DOI: 10.1038/ng.2762. View

Daniunaite K, Jarmalaite S, Kalinauskaite N, Petroska D, Laurinavicius A, Lazutka J . Prognostic value of RASSF1 promoter methylation in prostate cancer. J Urol. 2014; 192(6):1849-55. DOI: 10.1016/j.juro.2014.06.075. View

Alexeyenko A, Lee W, Pernemalm M, Guegan J, Dessen P, Lazar V . Network enrichment analysis: extension of gene-set enrichment analysis to gene networks. BMC Bioinformatics. 2012; 13:226. PMC: 3505158. DOI: 10.1186/1471-2105-13-226. View

Faria E, Chapin B, Muller R, Machado R, Reis R, Matin S . Radical Prostatectomy for Locally Advanced Prostate Cancer: Current Status. Urology. 2015; 86(1):10-5. DOI: 10.1016/j.urology.2015.03.012. View

Ahmadi H, Daneshmand S . Androgen deprivation therapy for prostate cancer: long-term safety and patient outcomes. Patient Relat Outcome Meas. 2014; 5:63-70. PMC: 4094624. DOI: 10.2147/PROM.S52788. View

10.

Miyamoto K, Fukutomi T, Akashi-Tanaka S, Hasegawa T, Asahara T, Sugimura T . Identification of 20 genes aberrantly methylated in human breast cancers. Int J Cancer. 2005; 116(3):407-14. DOI: 10.1002/ijc.21054. View

11.

Ferro M, Bruzzese D, Perdona S, Marino A, Mazzarella C, Perruolo G . Prostate Health Index (Phi) and Prostate Cancer Antigen 3 (PCA3) significantly improve prostate cancer detection at initial biopsy in a total PSA range of 2-10 ng/ml. PLoS One. 2013; 8(7):e67687. PMC: 3701535. DOI: 10.1371/journal.pone.0067687. View

12.

Sandoval J, Peiro-Chova L, Pallardo F, Garcia-Gimenez J . Epigenetic biomarkers in laboratory diagnostics: emerging approaches and opportunities. Expert Rev Mol Diagn. 2013; 13(5):457-71. DOI: 10.1586/erm.13.37. View

13.

Chetram M, Bethea D, Odero-Marah V, Don-Salu-Hewage A, Jones K, Hinton C . ROS-mediated activation of AKT induces apoptosis via pVHL in prostate cancer cells. Mol Cell Biochem. 2013; 376(1-2):63-71. PMC: 3578043. DOI: 10.1007/s11010-012-1549-7. View

14.

Ruepp A, Waegele B, Lechner M, Brauner B, Dunger-Kaltenbach I, Fobo G . CORUM: the comprehensive resource of mammalian protein complexes--2009. Nucleic Acids Res. 2009; 38(Database issue):D497-501. PMC: 2808912. DOI: 10.1093/nar/gkp914. View

15.

Lehto M, Laitinen S, Chinetti G, Johansson M, Ehnholm C, Staels B . The OSBP-related protein family in humans. J Lipid Res. 2001; 42(8):1203-13. View

16.

Dmitriev A, Kashuba V, Haraldson K, Senchenko V, Pavlova T, Kudryavtseva A . Genetic and epigenetic analysis of non-small cell lung cancer with NotI-microarrays. Epigenetics. 2012; 7(5):502-13. DOI: 10.4161/epi.19801. View

17.

Kanehisa M, Goto S, Kawashima S, Nakaya A . The KEGG databases at GenomeNet. Nucleic Acids Res. 2001; 30(1):42-6. PMC: 99091. DOI: 10.1093/nar/30.1.42. View

18.

Pavlova T, Kashuba V, Muravenko O, Yenamandra S, Ivanova T, Zabarovskaia V . [Technology of analysis of epigenetic and structural changes of epithelial tumors genome with NotI-microarrays by the example of human chromosome]. Mol Biol (Mosk). 2009; 43(2):339-47. View

19.

GUTMAN A, Gutman E . AN " ACID " PHOSPHATASE OCCURRING IN THE SERUM OF PATIENTS WITH METASTASIZING CARCINOMA OF THE PROSTATE GLAND. J Clin Invest. 1938; 17(4):473-8. PMC: 434803. DOI: 10.1172/JCI100974. View

20.

Kashuba V, Dmitriev A, Krasnov G, Pavlova T, Ignatjev I, Gordiyuk V . NotI microarrays: novel epigenetic markers for early detection and prognosis of high grade serous ovarian cancer. Int J Mol Sci. 2012; 13(10):13352-77. PMC: 3497331. DOI: 10.3390/ijms131013352. View