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Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer
Open accessAbstract
Beginning with precursor lesions, aberrant DNA methylation marks the entire spectrum of prostate cancer progression. We mapped the global DNA methylation patterns in select prostate tissues and cell lines using MethylPlex–next-generation sequencing (M-NGS). Hidden Markov model–based next-generation sequence analysis identified ∼68,000 methylated regions per sample. While global CpG island (CGI) methylation was not differential between benign adjacent and cancer samples, overall promoter CGI methylation significantly increased from ∼12.6% in benign samples to 19.3% and 21.8% in localized and metastatic cancer tissues, respectively ( P -value < 2 × 10 −16 ). We found distinct patterns of promoter methylation around transcription start sites, where methylation occurred not only on the CGIs, but also on flanking regions and CGI sparse promoters. Among the 6691 methylated promoters in prostate tissues, 2481 differentially methylated regions (DMRs) are cancer-specific, including numerous novel DMRs. A novel cancer-specific DMR in the WFDC2 promoter showed frequent methylation in cancer (17/22 tissues, 6/6 cell lines), but not in the benign tissues (0/10) and normal PrEC cells. Integration of LNCaP DNA methylation and H3K4me3 data suggested an epigenetic mechanism for alternate transcription start site utilization, and these modifications segregated into distinct regions when present on the same promoter. Finally, we observed differences in repeat element methylation, particularly LINE-1, between ERG gene fusion-positive and -negative cancers, and we confirmed this observation using pyrosequencing on a tissue panel. This comprehensive methylome map will further our understanding of epigenetic regulation in prostate cancer progression.
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“The statistically significant correlations that were observed, however, accounted for relatively small effects.”
From A survey of best practices for RNA-seq data analysis (2016) · cites this paper as [138]
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“Pairwise DNA-methylation and RNA-seq integration, for the most part, has consisted of the analysis of the correlation between DEGs and methylation patterns [138–140].”
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Vandesompele, J., De Preter, K., Pattyn, F., Poppe, B., Van Roy, N., De Paepe, A., & Speleman, F. (2002) · Genome Biology · doi:10.1186/gb-2002-3-7-research0034 · Cited by 20,038
In silico prediction of protein-protein interactions in human macrophages
Souiai, O., Guerfali, F. Z., Miled, S. B., Brun, C., & Benkahla, A. (2014) · BMC Research Notes · doi:10.1186/1756-0500-7-157 · Cited by 10,785
Significance analysis of microarrays applied to the ionizing radiation response
Tusher, V. G., Tibshirani, R., & Chu, G. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.091062498 · Cited by 10,568
DNA methylation patterns and epigenetic memory
Bird, A. (2002) · Genes & Development · doi:10.1101/gad.947102 · Cited by 7,124
A bivalent chromatin structure marks key developmental genes in embryonic stem cells
Bernstein, B. E., Mikkelsen, T. S., Xie, X., Kamal, M., Huebert, D. J., Cuff, J., Fry, B., Meissner, A., Wernig, M., Plath, K., et al. (2006) · Cell · doi:10.1016/j.cell.2006.02.041 · Cited by 5,361
Jones, P. A., & Baylin, S. B. (2007) · Cell · doi:10.1016/j.cell.2007.01.029 · Cited by 4,515
MethPrimer: designing primers for methylation PCRs
Li, L.-C., & Dahiya, R. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.11.1427 · Cited by 2,741
Genome-scale DNA methylation maps of pluripotent and differentiated cells
Meissner, A., Mikkelsen, T. S., Gu, H., Wernig, M., Hanna, J., Sivachenko, A., Zhang, X., Bernstein, B. E., Nusbaum, C., Jaffe, D. B., et al. (2008) · Nature · doi:10.1038/nature07107 · Cited by 2,536
Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning
Cokus, S. J., Feng, S.-H., Zhang, X.-Y., Chen, Z., Merriman, B., Haudenschild, C., Pradhan, S., Nelson, S., Pellegrini, M., & Jacobsen, S. (2008) · Nature · doi:10.1038/nature06745 · Cited by 2,278
Irizarry, R. A., Ladd-Acosta, C., Wen, B., Wu, Z., Montano, C., Onyango, P., Cui, H., Gabo, K., Rongione, M., Webster, M., et al. (2009) · Nature Genetics · doi:10.1038/ng.298 · Cited by 2,177
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Self-citationTumor origin detection with tissue-specific miRNA and DNA methylation markers
Tang, W., Wan, S., Yang, Z., Teschendorff, A. E., & Zou, Q. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx622 · Cited by 348
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Liu, Z., Xiao, X., Qiu, W., & Chou, K. (2015) · Analytical Biochemistry · doi:10.1016/j.ab.2014.12.009 · Cited by 252
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Kregel, S., Kiriluk, K. J., Rosen, A. M., Cai, Y., Reyes, E. E., Otto, K. B., Tom, W. R., Paner, G., Szmulewitz, R., & Griend, D. V. V. (2013) · PLoS ONE · doi:10.1371/journal.pone.0053701 · Cited by 177
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Börno, S. T., Fischer, A., Kerick, M., Fälth, M., Laible, M., Brase, J. C., Kuner, R., Dahl, A., Grimm, C., Sayanjali, B., et al. (2012) · Cancer Discovery · doi:10.1158/2159-8290.cd-12-0041 · Cited by 137
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Alkhateeb, A., Rezaeian, I., Singireddy, S., Cavallo‐Medved, D., Porter, L. A., & Rueda, L. G. (2019) · Cancer Informatics · doi:10.1177/1176935119835522 · Cited by 86
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Kim, J. H., Sartor, M. A., Rozek, L. S., Faulk, C. D., Anderson, O. S., Jones, T. R., Nahar, M. S., & Dolinoy, D. C. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-30 · Cited by 84
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Heller, G., Babinsky, V. N., Ziegler, B., Weinzierl, M., Noll, C., Altenberger, C., Müllauer, L., Dekan, G., Grin, Y., Láng, G., et al. (2012) · Carcinogenesis · doi:10.1093/carcin/bgs363 · Cited by 82
Schoenborn, J. R., Nelson, P., & Fang, M. (2013) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-12-3606 · Cited by 86
Chen, J., Zhang, D., Yan, W., Yang, D., & Shen, B. (2013) · BioMed Research International · doi:10.1155/2013/901578 · Cited by 86
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Lin, P., Γιαννοπούλου, Ε., Park, K., Mosquera, J. M., Sboner, A., Tewari, A. K., Garraway, L. A., Beltran, H., Rubin, M. A., & Elemento, O. (2013) · Neoplasia · doi:10.1593/neo.122146 · Cited by 77
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Wang, Z., Li, X., Jiang, Y. W., Shao, Q., Liu, Q., Chen, B., & Huang, D. (2015) · PLoS ONE · doi:10.1371/journal.pone.0132866 · Cited by 70
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Lorincz, A. T. (2014) · Expert Review of Molecular Diagnostics · doi:10.1586/14737159.2014.897610 · Cited by 70
Saied, M. H., Marzec, J., Khalid, S., Smith, P., Down, T. A., Rakyan, V. K., Molloy, G., Raghavan, M., Debernardi, S., & Young, B. D. (2012) · PLoS ONE · doi:10.1371/journal.pone.0033213 · Cited by 68
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Levenson, V., & Melnikov, A. A. (2012) · Pharmaceuticals · doi:10.3390/ph5010094 · Cited by 66
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Wong, K. Y., Huang, X., & Chim, C. S. (2012) · Carcinogenesis · doi:10.1093/carcin/bgs212 · Cited by 66
dos Reis, M. B., Barros‐Filho, M. C., Marchi, F. A., Beltrami, C. M., Kuasne, H., Pinto, C. A. L., Ambatipudi, S., Herceg, Z., Kowalski, L. P., & Rogatto, S. R. (2017) · The Journal of Clinical Endocrinology & Metabolism · doi:10.1210/jc.2017-00881 · Cited by 67
Kim, J. W., Kim, S., Turner, A. R., Young, T., Smith, S. G., Liu, W., Lindberg, J., Egevad, L., Grönberg, H., Isaacs, W. B., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0048455 · Cited by 63
Self-citationLi, Y., Zhang, Y., Li, S., Lu, J., Chen, J., Wang, Y., Li, Y., Xu, J., & Li, X. (2015) · Scientific Reports · doi:10.1038/srep08790 · Cited by 64
Faulk, C. D., Kim, J. H., Jones, T. R., McEachin, R. C., Nahar, M. S., Dolinoy, D. C., & Sartor, M. A. (2015) · Current Zoology · doi:10.1093/eep/dvv006 · Cited by 64
Self-citationRhee, J., Kim, K., Chae, H., Evans, J. M., Yan, P. S., Zhang, B.-T., Gray, J. W., Spellman, P. T., Huang, T. H. ‐., Nephew, K. P., et al. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt643 · Cited by 61
Theodore, S., Davis, M. B., Zhao, F., Wang, H., Chen, D., Rhim, J. S., Dean-Colomb, W. M., Turner, T., Ji, W., Zeng, G., et al. (2014) · Oncotarget · doi:10.18632/oncotarget.1953 · Cited by 60
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Goering, W., Kloth, M. T., & Schulz, W. A. (2012) · Methods in molecular biology · doi:10.1007/978-1-61779-612-8_4 · Cited by 60
Kron, K. J., Liu, L., Trudel, D., Pethe, V. V., Trachtenberg, J., Fleshner, N. E., Bapat, B. V., & van der Kwast, T. (2012) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-11-2901 · Cited by 60
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Geybels, M. S., Zhao, S., Wong, C.-J., Bibikova, M. V., Klotzle, B., Wu, M. C., Ostrander, E. A., Fan, J., Feng, Z., & Stanford, J. L. (2015) · The Prostate · doi:10.1002/pros.23093 · Cited by 60
Yu, Y. P., Ding, Y., Chen, R., Liao, S. G., Ren, B., Michalopoulos, A., Michalopoulos, G. K., Nelson, J. B., Tseng, G. C., & Luo, J. (2013) · American Journal Of Pathology · doi:10.1016/j.ajpath.2013.08.018 · Cited by 57
Faulk, C. D., Kim, J. H., Anderson, O. S., Nahar, M. S., Jones, T. R., Sartor, M. A., & Dolinoy, D. C. (2016) · Epigenetics · doi:10.1080/15592294.2016.1183856 · Cited by 57
Self-citationKirby, M. K., Ramaker, R. C., Roberts, B. S., Lasseigne, B. N., Gunther, D. S., Burwell, T. C., Davis, N. S., Gulzar, Z. G., Absher, D., Cooper, S. J., et al. (2017) · BMC Cancer · doi:10.1186/s12885-017-3252-2 · Cited by 55
Parrillo, L., Costa, V., Raciti, G. A., Longo, M., Spinelli, R., Esposito, R., Nigro, C., Vastolo, V., Desiderio, A., Zatterale, F., et al. (2016) · International Journal of Obesity · doi:10.1038/ijo.2016.36 · Cited by 52
Luo, J., Ding, Y., Chen, R., Michalopoulos, G. K., Nelson, J. B., Tseng, G. C., & Yu, Y. P. (2013) · American Journal Of Pathology · doi:10.1016/j.ajpath.2013.02.040 · Cited by 50
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Esposito, S., Russo, M. V., Airoldi, I., Tupone, M. G., Sorrentino, C., Barbarito, G., Meo, S. D., & Carlo, E. D. (2015) · Oncotarget · doi:10.18632/oncotarget.2736 · Cited by 49
Bhasin, J., Lee, B., Matkin, L., Taylor, M. G., Hu, B., Xu, Y., Magi‐Galluzzi, C., Klein, E. A., & Ting, A. H. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.10.078 · Cited by 48
Hájková, H., Marková, J., Haškovec, C., Šárová, I., Fuchs, O., Kostečka, A., Cetkovský, P., Michalova, K., & Schwarz, J. (2012) · Leukemia Research · doi:10.1016/j.leukres.2012.05.012 · Cited by 47
Wyatt, A. W., Mo, F., Wang, Y. Z., & Collins, C. C. (2013) · Asian Journal of Andrology · doi:10.1038/aja.2013.13 · Cited by 45
Møller, M., Strand, S. H., Mundbjerg, K., Liang, G., Gill, I. S., Haldrup, C., Borre, M., Høyer, S., Orntoft, T. F., & Sørensen, K. D. (2017) · Scientific Reports · doi:10.1038/srep40636 · Cited by 45
Li, Y., Camarillo, C., Xu, J., Arana, T. B., Xiao, Y., Zhao, Z., Chen, H., Ramírez, M., Zavala, J., Escamilla, M., et al. (2015) · BioMed Research International · doi:10.1155/2015/201587 · Cited by 42
Using Epigenome-Wide Association Scans of DNA Methylation in Age-Related Complex Human Traits
Tsai, P.-C., Spector, T. D., & Bell, J. T. (2012) · Epigenomics · doi:10.2217/epi.12.45 · Cited by 40
Heterogeneous epigenetic regulation ofTIMP3in prostate cancer
Shinojima, T., Yu, Q., Huang, S. K., Li, M., Mizuno, R., Liu, E. T., Hoon, D. S. �., & Lessard, L. (2012) · Epigenetics · doi:10.4161/epi.22333 · Cited by 41
Geybels, M. S., Alumkal, J. J., Luedeke, M., Rinckleb, A. E., Zhao, S., Shui, I. M., Bibikova, M. V., Klotzle, B., van den Brandt, P. A., Ostrander, E. A., et al. (2015) · Clinical Epigenetics · doi:10.1186/s13148-015-0161-6 · Cited by 41
Kukkonen, K., Taavitsainen, S., Huhtala, L., Uusi-Mäkelä, J., Granberg, K. J., Nykter, M., & Urbanucci, A. (2021) · Cancers · doi:10.3390/cancers13133325 · Cited by 47
Hartung, T., Zhang, L., Kanwar, R., Khrebtukova, I., Reinhardt, M., Wang, C., Therneau, T. M., Banck, M. S., Schroth, G. P., & Beutler, A. S. (2012) · Epigenetics · doi:10.4161/epi.19565 · Cited by 35
SFRP1 repression in prostate cancer is triggered by two different epigenetic mechanisms
García-Tobilla, P., Solórzano, S. R., Salido-Guadarrama, I., González-Covarrubias, V., Morales-Montor, G., Díaz‐Otañez, C. E., & Rodríguez‐Dorantes, M. (2016) · Gene · doi:10.1016/j.gene.2016.08.030 · Cited by 36
Han, J., Liu, S., Sun, Z., Zhang, Y., Zhang, F., Zhang, C., Shang, D., Yang, H., Su, F., Xu, Y., et al. (2017) · Scientific Reports · doi:10.1038/srep46566 · Cited by 36
Human methionine synthase A2756G polymorphism increases susceptibility to prostate cancer
Shao, H., Ren, K., Gao, S., Zou, J.-G., Mi, Y., Zhang, L.-F., Zuo, L., Okada, A., & Yasui, T. (2018) · Aging · doi:10.18632/aging.101509 · Cited by 36
Raheem, O. A., Kulidjian, A., Wu, C., Jeong, Y. B., Yamaguchi, T., Smith, K. M., Goff, D. J., Leu, H. S., Morris, S., Cacalano, N. A., et al. (2011) · Journal of Translational Medicine · doi:10.1186/1479-5876-9-185 · Cited by 36
Nüsgen, N., Goering, W., Daukša, A., Biswas, A., Jamil, M. A., Dimitriou, I. M., Sharma, A., Singer, H., Fimmers, R., Fröhlich, H., et al. (2015) · Clinical Epigenetics · doi:10.1186/s13148-015-0051-y · Cited by 35
Jiang, Y., Liu, S., Chen, X. '., Cao, Y., & Tao, Y. (2012) · Biochimica et Biophysica Acta (BBA) - Reviews on Cancer · doi:10.1016/j.bbcan.2012.12.003 · Cited by 36
Chen, D.-P., Lin, Y., & Fann, C. S. J. (2016) · Briefings in Functional Genomics · doi:10.1093/bfgp/elw018 · Cited by 38
DNA Methylation-Guided Prediction of Clinical Failure in High-Risk Prostate Cancer
Litovkin, K., Eynde, A. V., Joniau, S., Lerut, E., Laenen, A., Gevaert, T., Gevaert, O., Spahn, M., Kneitz, B., Gramme, P., et al. (2015) · PLoS ONE · doi:10.1371/journal.pone.0130651 · Cited by 35
Varışlı, L. (2013) · Genetic Testing and Molecular Biomarkers · doi:10.1089/gtmb.2012.0524 · Cited by 34
Tian, F., Zhan, F., VanderKraats, N. D., Hiken, J., Edwards, J. R., Zhang, H., Zhao, K., & Song, J. (2013) · Epigenetics · doi:10.4161/epi.24361 · Cited by 37
Copy-number-aware differential analysis of quantitative DNA sequencing dataPreprint
Robinson, M. D., Strbenac, D., Stirzaker, C., Statham, A. L., Song, J. Z., Speed, T. P., & Clark, S. J. (2012) · Genome Research · doi:10.1101/gr.139055.112 · Cited by 35
Functional roles of antisense enhancer RNA for promoting prostate cancer progression
Pan, C., Wen, S., Chen, L., Wei, Y., Niu, Y., & Zhao, Y. (2020) · Theranostics · doi:10.7150/thno.51931 · Cited by 29
The evolution of CpG density and lifespan in conserved primate and mammalian promoters
McLain, A. T., & Faulk, C. D. (2018) · Aging · doi:10.18632/aging.101413 · Cited by 32
Pan, J., Chen, J., Zhang, B., Chen, X., Huang, B., Zhuang, J., Mo, C., & Qiu, S. (2013) · PLoS ONE · doi:10.1371/journal.pone.0075283 · Cited by 31
DKK1 and Kremen Expression Predicts the Osteoblastic Response to Bone Metastasis
Clines, K. L., & Clines, G. A. (2018) · Translational Oncology · doi:10.1016/j.tranon.2018.04.013 · Cited by 31
Targeting the methionine addiction of cancer.
Sedillo, J. C., & Cryns, V. L. (2022) · PubMed Central · Cited by 30
Recent advances in understanding DNA methylation of prostate cancer
Shin, H. J., Hua, J. T., & Li, H. (2023) · Frontiers in Oncology · doi:10.3389/fonc.2023.1182727 · Cited by 32
Peng, Y., Song, Y., & Wang, H. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.723466 · Cited by 31
The Genomic Landscape of Prostate Cancer
Spans, L., Clinckemalie, L., Helsen, C., Vanderschueren, D., Boonen, S., Lerut, E., Joniau, S., & Claessens, F. (2013) · International Journal of Molecular Sciences · doi:10.3390/ijms140610822 · Cited by 32
Pan, J., Chen, Y., Mo, C., Wang, D., Chen, J., Mao, X., Guo, S., Zhuang, J., & Qiu, S. (2014) · PLoS ONE · doi:10.1371/journal.pone.0092815 · Cited by 29
Patel, L. R., Nykter, M., Chen, K., & Zhang, W. (2012) · Cancer Letters · doi:10.1016/j.canlet.2012.10.018 · Cited by 28
Singh, R. K., Srivastava, A., Ponnusamy, K., Manvati, S., Chopra, R., & Bamezai, R. N. K. (2014) · Scientific Reports · doi:10.1038/srep06571 · Cited by 28
Kacprzyk, L. A., Laible, M., Andrasiuk, T., Brase, J. C., Börno, S. T., Fälth, M., Kuner, R., Lehrach, H., Schweiger, M. R., & Sültmann, H. (2013) · PLoS ONE · doi:10.1371/journal.pone.0059976 · Cited by 27
Haldrup, C., Lynnerup, A.-S., Storebjerg, T. M., Vang, S., Wild, P. J., Visakorpi, T., Arsov, C., Schulz, W. A., Lindberg, J., Grönberg, H., et al. (2016) · Molecular Oncology · doi:10.1016/j.molonc.2016.02.001 · Cited by 28
Daniūnaitė, K., Bakavičius, A., Žukauskaitė, K., Rauluševičiūtė, I., Lazutka, J. R., Ulys, A., Jankevičius, F., & Jarmalaitė, S. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22116091 · Cited by 28
Zseq: An Approach for Preprocessing Next-Generation Sequencing Data
Alkhateeb, A., & Rueda, L. G. (2017) · Journal of Computational Biology · doi:10.1089/cmb.2017.0021 · Cited by 27
Investigative pathology: leading the post-genomic revolution
Berman, D. M., Bosenberg, M., Orwant, R., Thurberg, B. L., Draetta, G. F., Fletcher, C. D. �., & Loda, M. F. (2011) · Laboratory Investigation · doi:10.1038/labinvest.2011.147 · Cited by 27
Kron, K. J., Trudel, D., Pethe, V. V., Briollais, L., Fleshner, N. E., van der Kwast, T., & Bapat, B. V. (2013) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-12-3139 · Cited by 26
Erfani, S. F., Hua, H., Pan, Y.-Y., Zhou, B., & Yang, X.-W. H. (2021) · Cancers · doi:10.3390/cancers13092005 · Cited by 20
Kuroyanagi, J., Shimada, Y., Zhang, B., Ariyoshi, M., Umemoto, N., Nishimura, Y., & Tanaka, T. (2014) · FEBS Letters · doi:10.1016/j.febslet.2014.07.033 · Cited by 26
Danziger, O., Shai, B., Sabo, Y., Bacharach, E., & Ehrlich, M. (2016) · Oncotarget · doi:10.18632/oncotarget.10313 · Cited by 25
Integrative analysis reveals disease-associated genes and biomarkers for prostate cancer progression
Li, Y., Vongsangnak, W., Chen, L., & Shen, B. (2014) · BMC Medical Genomics · doi:10.1186/1755-8794-7-s1-s3 · Cited by 24
Cruz, S. P., Zhang, Q., Devarajan, R., Paia, C., Luo, B., Zhang, K., Koivusalo, S., Qin, L., Xia, J., Ahtikoski, A. M., et al. (2024) · Advanced Science · doi:10.1002/advs.202305547 · Cited by 22
Common gene pathways and families altered by DNA methylation in breast and prostate cancers
Day, T. K., & Bianco‐Miotto, T. (2013) · Endocrine Related Cancer · doi:10.1530/erc-13-0204 · Cited by 23
Identification of specific DNA methylation sites on the Y-chromosome as biomarker in prostate cancer
Yao, L., Ren, S., Zhang, M., Du, F., Zhu, Y., Yu, H., Zhang, C., Li, X., Yang, C., Liu, H., et al. (2015) · Oncotarget · doi:10.18632/oncotarget.6141 · Cited by 22
Genome-wide methylated CpG island profiles of melanoma cells reveal a melanoma coregulation network
Li, J.-L., Mazar, J., Zhong, C., Faulkner, G. J., Govindarajan, S. S., Zhang, Z., Dinger, M. E., Meredith, G., Adams, C., Zhang, S., et al. (2013) · Scientific Reports · doi:10.1038/srep02962 · Cited by 21
Manipulating the epigenome for the treatment of urological malignancies
O’Rourke, C. J., Knabben, V., Bolton, E. M., Moran, D. C., Lynch, T. H., Hollywood, D. P., & Perry, A. S. (2013) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2013.01.007 · Cited by 22
Metadata
- Authors
- Kim, J. H., Dhanasekaran, S. M., Prensner, J. R., Cao, X., Robinson, D., Kalyana-Sundaram, S., Huang, C., Shankar, S., Jing, X., Iyer, M., Hu, M., Sam, L., Grasso, C., Maher, C. A., Palanisamy, N., Mehra, R., Kominsky, H. D., Siddiqui, J., Yu, J., Qin, Z. S., & Chinnaiyan, A. M.
- Affiliations
- University of Michigan (US)
- Harvard University (US)
- Northwestern University (US)
- Emory University (US)
- ORCID
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2011-07
- Volume
- 21
- Issue
- 7
- Pages
- 1028-1041
- ISSN
- 1088-9051 (ISSN-L)
- PMC
- PMC3129246
- OpenAlex
- W2114884175
- Cited by
- 188
- References
- 61
- Citations by year
- 2026: 7 · 2025: 2 · 2024: 4 · 2023: 4 · 2022: 7 · 2021: 9 · 2020: 11 · 2019: 12 · 2018: 8 · 2017: 15 · 2016: 14 · 2015: 20 · 2014: 20 · 2013: 25 · 2012: 27
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- HighWire Press Open Archive (submittedVersion)
- Funders
- U.S. Department of Defense (W81XWH, BC075023)
- Howard Hughes Medical Institute
- Prostate Cancer Foundation
- Amgen
- University of Michigan (P50CA69568)
- Canary Foundation
- National Institutes of Health (W81XWH, CA009676)
- National Institute on Drug Abuse (U54DA021519)
- National Human Genome Research Institute (R01HG005119)
- National Cancer Institute (P50-CA-69568, R01CA132874, U01CA111275, CA009676-18, R00CA129565, K99CA129565, P50CA069568, T32CA009676)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Prostate Cancer Treatment and Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Cancer-related gene regulation
- Keywords
- prostate cancer, DNA methylation, methylome, promoter methylation, CpG island methylation, differentially methylated regions, HE4, H3K4me3, tumor progression, metastatic prostate cancer, epigenetic regulation
- MeSH terms
- DNA, Neoplasm, Epithelial Cells, Humans, Male, Markov Chains, Neoplasm Metastasis, Promoter Regions, Genetic, Prostate, Prostatic Neoplasms, Gene Library, Polymerase Chain Reaction, Sequence Analysis, RNA, CpG Islands, DNA Methylation, Oligonucleotide Array Sequence Analysis, Gene Expression Profiling, Transcription Initiation Site, Cell Line, Tumor, Epigenomics, High-Throughput Nucleotide Sequencing
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