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Prostate Cancer Epigenomics
Prostate Cancer Epigenomics EPIGENETIC alterations are regarded as a hallmark of prostate cancer. Undoubtedly, the best characterized of them is promoter hypermethylation, and concomitant silencing of tumor suppressor genes and genes with important regulatory functions. At least 100 individual genes with a diverse range of functional capabilities have been described as de novo methylated during prostate carcinogenesis. These discoveries have largely been achieved through candidate gene based approaches and have identified several prognostic DNA methylation biomarkers. In a landmark study in 2004 Yegnasubramanian et al performed a comprehensive quantitative methylation analysis of 16 loci (of which the majority had never previously been described in prostate cancer) and found that, somewhat surprisingly, methylation patterns appear to be clonally maintained during metastatic progression of prostate cancer.1 This gave substantial support to the theory that an “epigenetic catastrophe” occurs in the earliest stages of prostate carcinogenesis and is maintained during disease progression. Naturally, there are exceptions, for example promoter hypermethylation of EDNRB, PTGS2 and APC genes has been associated with disease severity, clinical recurrence and lethality, respectively.1–3 In this issue of The Journal Desotelle et al (page 329) investigated aberration DNA methylation during senescence.4 Induction of filamin A interacting protein 1-like (FILIP1L) is a marker of senescence, although its precise role in this process is unknown. It is one of several genes that become elevated as prostate epithelial cells enter senescence, and is down-regulated in immortalized prostate cancer cell lines. Previously called DOC1 (down-regulated in ovarian cancer), it is down-regulated in several cancer types and hypermethylated in another endocrine related malignancy, cancer of the ovary.5 It has recently been shown that it is transcriptionally induced by OCT1 and it mediates apoptosis in response to topoisomerase II targeting drugs, although its mechanism of action remains unclear.6 It is also induced by angiogenesis inhibitors, whereby it inhibits proliferation and migration, and induces apoptosis.7 In the current study 1 of the 3 isoforms 0022-5347/13/1891-0010/0 THE JOURNAL OF UROLOGY® © 2013 by AMERICAN UROLOGICAL ASSOCIATION EDUCATION
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(isoform 2) of FILIP1L was shown to be induced during senescence but frequently hypermethylated and concurrently down-regulated in a cohort of 14 primary prostate cancers, suggesting that loss of senescence may favor prostate cancer progression. Further functional investigations are warranted to decipher its promiscuous modes of action in cancer pathways and the significance of its 3 variant isoforms. Recent technological advances in high throughput, next generation sequencing and microarrays have meant that a new wave of global assessment of DNA methylation (or epigenetic aberrations) is now possible. This has facilitated whole genome methylome analysis in prostate cancer.3,8,9 Interestingly, although these newer approaches enable interrogation of more than 27,000 individual CpG sites (Illumina® Infinium® HumanMethylation27 BeadChip), the number of hypermethylated genes has not jumped dramatically and remains relatively constant. Of course, new targets of epigenetic silencing (eg HIF3A and HAAO) have been identified through these studies and must now be validated in independent cohorts to fully evaluate their functional role in prostate carcinogenesis and their potential biomarker capabilities. Notably, these studies clearly confirm that promoter hypermethylation is more widespread in prostate cancer than conventional mechanisms of gene inactivation, such as mutation and deletion.10 Furthermore, they support data from the last decade, which showed that genes become hypermethylated in precursor lesions and early stage prostate cancers, driving malignant initiation rather than tumor progression. It seems that during metastatic progression epigenetic changes become markedly more heterogeneous.3 Interestingly, FILIP1L was identified by the Illumina methylation array as frequently methylated (93% or 55 of 59 cases) in primary prostate cancer.8 Akin to GSTP1 hypermethylation, which is the most common somatic alteration in prostate cancer, FILIP1L methylation was not found to be significantly associated with tumor grade or other clinicopathological variables, indicating that it most likely occurs as an early, initiating event during prostate carcinogenesis. http://dx.doi.org/10.1016/j.juro.2012.10.015 Vol. 189, 10-11, January 2013 Printed in U.S.A.
PROSTATE CANCER EPIGENOMICS
Undoubtedly, as technology continues to advance, so too will our (epi)genomic interrogation capabilities. Studies to date have been largely biased in favor of detecting promoter methylation changes and do not provide an accurate reflection of the 28 million CpG sites present in the human genome. Promoter hypermethylation acts in a concerted effort with a diverse range of histone modifications (acetylation, methylation and phosphorylation, to name but a few) and nucleosome remodeling factors to stably regulate gene expression through modifying chromatin structure. Therefore, an integrative approach analyzing DNA methylation in conjunction with other epigenetic marks, namely specific histone modifications, will be necessary to gain a better understanding of the role of epigenomics in prostate cancer biology. Furthermore, we have yet to
11
harness the power of these next generation technologies to fully investigate the significance of intragenic methylation and promoter hypomethylation of proto-oncogenes and oncomiRs in prostate cancer. There is a hint that 5-hydroxymethylcytosine may also have an important role in tissue differentiation and, thus, human cancers, including prostate cancer.11 The broad range of clinical behavior of prostate tumors reflects complex genomic and epigenomic diversity, which can only be truly investigated by analyzing these aberrations in parallel rather than in isolation. Antoinette S. Perry Prostate Molecular Oncology Institute of Molecular Medicine Trinity College Dublin Dublin, Ireland
REFERENCES 1. Yegnasubramanian S, Kowalski J, Gonzalgo ML et al: Hypermethylation of CpG islands in primary and metastatic human prostate cancer. Cancer Res 2004; 64: 1975. 2. Richiardi L, Fiano V, Vizzini L et al: Promoter methylation in APC, RUNX3, and GSTP1 and mortality in prostate cancer patients. J Clin Oncol 2009; 27: 3161. 3. Mahapatra S, Klee EW, Young CY et al: Global methylation profiling for risk prediction of prostate cancer. Clin Cancer Res 2012; 18: 2882. 4. Desotelle J, Truong M, Ewald J et al: CpG island hypermethylation frequently silences FILIP1L isoform 2 expression in prostate cancer. J Urol 2013; 189: 329.
5. Burton ER, Gaffar A, Lee SJ et al: Downregulation of Filamin A interacting protein 1-like is associated with promoter methylation and induces an invasive phenotype in ovarian cancer. Mol Cancer Res 2011; 9: 1126. 6. Lu H and Hallstrom TC: Sensitivity to TOP2 targeting chemotherapeutics is regulated by Oct1 and FILIP1L. PLoS One 2012; 7: e42921. 7. Kwon M, Hanna E, Lorang D et al: Functional characterization of filamin a interacting protein 1-like, a novel candidate for antivascular cancer therapy. Cancer Res 2008; 68: 7332. 8. Kobayashi Y, Absher DM, Gulzar ZG et al: DNA methylation profiling reveals novel biomarkers
and important roles for DNA methyltransferases in prostate cancer. Genome Res 2011; 21: 1017. 9. Kron K, Pethe V, Briollais L et al: Discovery of novel hypermethylated genes in prostate cancer using genomic CpG island microarrays. PLoS One 2009; 4: e4830. 10. Barbieri CE, Baca SC, Lawrence MS et al: Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer. Nat Genet 2012; 44: 685. 11. Haffner MC, Chaux A, Meeker AK et al: Global 5-hydroxymethylcytosine content is significantly reduced in tissue stem/progenitor cell compartments and in human cancers. Oncotarget 2011; 2: 627.
10
www.jurology.com
AND
RESEARCH, INC.
(isoform 2) of FILIP1L was shown to be induced during senescence but frequently hypermethylated and concurrently down-regulated in a cohort of 14 primary prostate cancers, suggesting that loss of senescence may favor prostate cancer progression. Further functional investigations are warranted to decipher its promiscuous modes of action in cancer pathways and the significance of its 3 variant isoforms. Recent technological advances in high throughput, next generation sequencing and microarrays have meant that a new wave of global assessment of DNA methylation (or epigenetic aberrations) is now possible. This has facilitated whole genome methylome analysis in prostate cancer.3,8,9 Interestingly, although these newer approaches enable interrogation of more than 27,000 individual CpG sites (Illumina® Infinium® HumanMethylation27 BeadChip), the number of hypermethylated genes has not jumped dramatically and remains relatively constant. Of course, new targets of epigenetic silencing (eg HIF3A and HAAO) have been identified through these studies and must now be validated in independent cohorts to fully evaluate their functional role in prostate carcinogenesis and their potential biomarker capabilities. Notably, these studies clearly confirm that promoter hypermethylation is more widespread in prostate cancer than conventional mechanisms of gene inactivation, such as mutation and deletion.10 Furthermore, they support data from the last decade, which showed that genes become hypermethylated in precursor lesions and early stage prostate cancers, driving malignant initiation rather than tumor progression. It seems that during metastatic progression epigenetic changes become markedly more heterogeneous.3 Interestingly, FILIP1L was identified by the Illumina methylation array as frequently methylated (93% or 55 of 59 cases) in primary prostate cancer.8 Akin to GSTP1 hypermethylation, which is the most common somatic alteration in prostate cancer, FILIP1L methylation was not found to be significantly associated with tumor grade or other clinicopathological variables, indicating that it most likely occurs as an early, initiating event during prostate carcinogenesis. http://dx.doi.org/10.1016/j.juro.2012.10.015 Vol. 189, 10-11, January 2013 Printed in U.S.A.
PROSTATE CANCER EPIGENOMICS
Undoubtedly, as technology continues to advance, so too will our (epi)genomic interrogation capabilities. Studies to date have been largely biased in favor of detecting promoter methylation changes and do not provide an accurate reflection of the 28 million CpG sites present in the human genome. Promoter hypermethylation acts in a concerted effort with a diverse range of histone modifications (acetylation, methylation and phosphorylation, to name but a few) and nucleosome remodeling factors to stably regulate gene expression through modifying chromatin structure. Therefore, an integrative approach analyzing DNA methylation in conjunction with other epigenetic marks, namely specific histone modifications, will be necessary to gain a better understanding of the role of epigenomics in prostate cancer biology. Furthermore, we have yet to
11
harness the power of these next generation technologies to fully investigate the significance of intragenic methylation and promoter hypomethylation of proto-oncogenes and oncomiRs in prostate cancer. There is a hint that 5-hydroxymethylcytosine may also have an important role in tissue differentiation and, thus, human cancers, including prostate cancer.11 The broad range of clinical behavior of prostate tumors reflects complex genomic and epigenomic diversity, which can only be truly investigated by analyzing these aberrations in parallel rather than in isolation. Antoinette S. Perry Prostate Molecular Oncology Institute of Molecular Medicine Trinity College Dublin Dublin, Ireland
REFERENCES 1. Yegnasubramanian S, Kowalski J, Gonzalgo ML et al: Hypermethylation of CpG islands in primary and metastatic human prostate cancer. Cancer Res 2004; 64: 1975. 2. Richiardi L, Fiano V, Vizzini L et al: Promoter methylation in APC, RUNX3, and GSTP1 and mortality in prostate cancer patients. J Clin Oncol 2009; 27: 3161. 3. Mahapatra S, Klee EW, Young CY et al: Global methylation profiling for risk prediction of prostate cancer. Clin Cancer Res 2012; 18: 2882. 4. Desotelle J, Truong M, Ewald J et al: CpG island hypermethylation frequently silences FILIP1L isoform 2 expression in prostate cancer. J Urol 2013; 189: 329.
5. Burton ER, Gaffar A, Lee SJ et al: Downregulation of Filamin A interacting protein 1-like is associated with promoter methylation and induces an invasive phenotype in ovarian cancer. Mol Cancer Res 2011; 9: 1126. 6. Lu H and Hallstrom TC: Sensitivity to TOP2 targeting chemotherapeutics is regulated by Oct1 and FILIP1L. PLoS One 2012; 7: e42921. 7. Kwon M, Hanna E, Lorang D et al: Functional characterization of filamin a interacting protein 1-like, a novel candidate for antivascular cancer therapy. Cancer Res 2008; 68: 7332. 8. Kobayashi Y, Absher DM, Gulzar ZG et al: DNA methylation profiling reveals novel biomarkers
and important roles for DNA methyltransferases in prostate cancer. Genome Res 2011; 21: 1017. 9. Kron K, Pethe V, Briollais L et al: Discovery of novel hypermethylated genes in prostate cancer using genomic CpG island microarrays. PLoS One 2009; 4: e4830. 10. Barbieri CE, Baca SC, Lawrence MS et al: Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer. Nat Genet 2012; 44: 685. 11. Haffner MC, Chaux A, Meeker AK et al: Global 5-hydroxymethylcytosine content is significantly reduced in tissue stem/progenitor cell compartments and in human cancers. Oncotarget 2011; 2: 627.