news and views
Linking the SWI/SNF complex to prostate cancer
npg
© 2013 Nature America, Inc. All rights reserved.
Ryan S Lee & Charles W M Roberts Genes encoding subunits of the SWI/SNF chromatin-remodeling complex constitute, collectively, one of the most frequently mutated targets in cancer. Although mutations in SWI/SNF genes are uncommon in prostate cancer, a new study shows that SChLAP1, a long noncoding RNA frequently expressed in aggressive prostate tumors, drives cancer by directly disrupting SNF5, a core subunit of the SWI/SNF complex. Despite improvements in screening and early detection, prostate cancer remains the second leading cause of cancer mortality in men1. However, individual cases of prostate cancer can display markedly different clinical behavior, ranging from indolent to highly aggressive, metastatic cancers. Thus, ongoing efforts are aimed at identifying biomarkers of aggressive disease and investigating underlying mechanisms. For example, one subset of more aggressive prostate tumors is characterized by the overexpression of EZH2, a member of the PRC2 epigenetic regulatory complex2. Recently, the examination of causal links has expanded to include long noncoding RNAs (lncRNAs) aberrantly expressed in cancer, although the mechanisms by which these lncRNAs drive oncogenesis are just beginning to be understood3,4. In prostate cancer alone, multiple lncRNAs have been described as being abnormally expressed at high levels in cancer cells, with nearly a quarter of transcripts found to be lncRNAs or to be derived from otherwise unannotated sequences4–6. On page 1392 of this issue, Arul Chinnaiyan and colleagues7 focus on one of these lncRNAs, called SChLAP1, and identify a mechanism by which it contributes to prostate cancer growth. SChLAP1 inhibits SNF5 Prensner et al.7 began by searching for lncRNAs expressed at especially high levels Ryan S. Lee and Charles W. M. Roberts are affiliated with the Department of Pediatric Oncology, Dana-Farber Cancer Institute, the Division of Hematology-Oncology, Boston Children’s Hospital and the Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA. e-mail: [email protected]
1268
in a subset of aggressive prostate cancers. They identified a particular lncRNA, which they called SChLAP1 (second chromosome locus associated with prostate-1), that was a predictor of shorter time to recurrence and was associated with increased risk of progression and mortality in an independent cohort of individuals with prostate cancer. Next, they showed that knockdown of SChLAP1 led to reduced cell invasion and proliferation in both cell lines and mouse models, confirming the role of SChLAP1 as an oncogene. Inversely, they found that overexpression of SChLAP1 restored the aggressive phenotype of cells with SChLAP1 knockdown and induced increased invasiveness in benign cells with normally low levels of SChLAP1. Next, Prensner et al.7 explored potential mechanisms by which SChLAP1 expression drives malignancy and found a correlation with gene sets regulated by the SWI/SNF (BAF) complex. The evolutionarily conserved SWI/SNF complex, whose subunits are frequently mutated in human cancer, canonically modulates
transcription by using ATP hydrolysis to remodel chromatin and mobilize nucleosomes8. In particular, the authors focused their attention on the core SWI/SNF subunit SNF5 (also called SMARCB1, INI1 and BAF47) because, when examining gene expression in cells with SChLAP1 knockdown, they observed effects that were anticorrelated with the effects previously reported for SNF5 knockdown. Next, by performing chromatin and RNA immunoprecipitation, the authors identified direct binding of SChLAP1 to SNF5. Mechanistically, they found that binding of SChLAP1 to SNF5 caused a decrease in SNF5 binding to 30% of its target promoters (Fig. 1), which correlated with reduced expression of these genes. SWI/SNF dysregulation in cancer The role of the SWI/SNF complex in cancer has become more apparent in recent years owing to the identification of mutations in genes encoding SWI/SNF subunits in nearly 20% of tumors examined across a wide spectrum
SChLAP1
SWI/SNF SChLAP1
SWI/SNF
SNF5
SNF5 Promoter
Gene
Promoter
Gene
Figure 1 Aberrantly high expression of SChLAP1 in aggressive prostate cancers inhibits SWI/SNFmediated epigenetic regulation. SChLAP1, a long noncoding RNA, binds directly to SNF5. This interaction prevents the SWI/SNF complex from binding to target promoters, resulting in decreased expression of target genes.
volume 45 | number 11 | NOVEMBER 2013 | nature genetics
npg
© 2013 Nature America, Inc. All rights reserved.
news and views of cancer types8–10. Consequently, the complex has been identified as the most frequently mutated chromatin regulatory complex in cancer and one of the most frequently mutated targets overall. The gene encoding SNF5 (SMARCB1) is mutated in pediatric rhabdoid tumors and in a few other rare cancers, but it is not widely mutated across cancer types8. However, mechanisms that indirectly disrupt SNF5 are now being identified in additional types of cancer. For instance, a recent study has shown that the SS18-SSX fusion in synovial sarcoma promotes tumorigenesis by disrupting SNF5 integration into the SWI/SNF complex11. The work of Prensner et al.7 now illustrates how lncRNA-mediated disruption of this SWI/SNF complex subunit can also drive malignancy. The new findings of Prensner et al.7 suggest that SChLAP1 may specifically affect the targeting mechanism of the SWI/SNF complex, a function that remains poorly understood. Although decreased SNF5 binding was observed at some promoters, leading to decreased expression of downstream genes, the specific effect of reduced SNF5 binding
on epigenetic regulation needs to be explored further. The SWI/SNF complex is canonically described as a regulator of gene expression via remodeling of nucleosomes, especially at promoters12,13. Thus, it is possible that SChLAP1 expression leads to disordered nucleosomes or other changes in chromatin structure at proximal promoter sites. Taking these results together with those for EZH2 and BAF57, another SWI/SNF subunit, a theme may be emerging in which aberrantly expressed epigenetic regulators contribute to aggressive prostate cancers14,15. SChLAP1 can be added to a growing list of lncRNAs associated with prostate cancer6. In addition, the ability of SChLAP1 to inhibit SNF5 binding further emphasizes the central role that chromatin regulators have in driving cancer. In essence, SChLAP1 expression in prostate cancer ties together two frontiers in cancer biology: noncoding RNAs and chromatin regulators. By uncovering the interaction between SChLAP1 and SNF5, this new study demonstrates both a mechanism through which lncRNAs can act to drive malignancy
and an additional mechanism by which SWI/ SNF activity can be disrupted in a way that affects cancer growth. COMPETING FINANCIAL INTERESTS The authors declare no competing financial interests. 1. Siegel, R., Naishadham, D. & Jemal, A. CA Cancer J. Clin. 63, 11–30 (2013). 2. Varambally, S. et al. Nature 419, 624–629 (2002). 3. Prensner, J.R. & Chinnaiyan, A.M. Cancer Discov. 1, 391–407 (2011). 4. Du, Z. et al. Nat. Struct. Mol. Biol. 20, 908–913 (2013). 5. Prensner, J.R. et al. Nat. Biotechnol. 29, 742–749 (2011). 6. Yang, L. et al. Nature 500, 598–602 (2013). 7. Prensner, J.R. et al. Nat. Genet. 45, 1392–1398 (2013). 8. Wilson, B.G. & Roberts, C.W.M. Nat. Rev. Cancer 11, 481–492 (2011). 9. Lee, R.S. et al. J. Clin. Invest. 122, 2983–2988 (2012). 10. Kadoch, C. et al. Nat. Genet. 45, 592–601 (2013). 11. Kadoch, C. & Crabtree, G.R. Cell 153, 71–85 (2013). 12. You, J.S. et al. PLoS Genet. 9, e1003459 (2013). 13. Tolstorukov, M.Y. et al. Proc. Natl. Acad. Sci. USA 110, 10165–10170 (2013). 14. Link, K.A. et al. Cancer Res. 68, 4551–4558 (2008). 15. Balasubramaniam, S. et al. Clin. Cancer Res. 19, 2657–2667 (2013).
Mining the epigenetic landscape in ALL Lindsay M LaFave & Ross L Levine The significance of epigenomic aberrations in cancer development has been underscored by the discovery of mutations in key chromatin modifiers, most notably in hematological malignancies. A new study of pediatric acute lymphoblastic leukemia (ALL) demonstrates the usefulness of mapping global epigenetic signatures and applying these data in a framework to identify and characterize underlying somatic genetic alterations in human cancers. Epigenetic dysregulation has become a cardinal feature of human malignancies, warranting the development of innovative approaches to identify epigenetic driver alterations. Numerous large-scale sequencing studies, including targeted exome, transcriptome and whole genome, have led to the identification of mutations or expression changes in genes critical for normal Lindsay M. LaFave and Ross L. Levine are affiliated with the Human Oncology and Pathogenesis Program, Memorial SloanKettering Cancer Center, New York, New York, USA. Lindsay M. LaFave is also affiliated with Gerstner Sloan-Kettering Graduate School, Memorial Sloan-Kettering Cancer Center, New York, New York, USA. Ross L. Levine is also affiliated with the Leukemia Service, Department of Medicine, Memorial SloanKettering Cancer Center, New York, New York, USA. e-mail: [email protected]
epigenetic regulation in a spectrum of cancer types, including in hematological malignancies. For example, oncogenic mutations in histone methyltransferases that modify key lysine residues on histone tails have been identified in leukemias and lymphomas. These findings have led to the development of selective small molecule histone methyltransferase inhibitors for therapeutic applications. Selective inhibitors targeting gain-of-function alterations in EZH2 (refs. 1,2), the catalytic methyltransferase in the PRC2 complex that mediates repressive trimethylation of histone H3 at lysine 27 (H3K27me3), and DOT1L3, the methyltransferase that methylates histone H3 at lysine 79 (H3K79), are being tested in EZH2-mutant B cell lymphoma and MLL-rearranged leukemia, respectively. The successful development of EZH2 and DOT1L inhibitors has driven efforts to assess mutations in histone methyltransferases that drive cancer development and progression and represent tractable therapeutic targets. In this
nature genetics | volume 45 | number 11 | NOVEMBER 2013
issue of Nature Genetics, Frank Stegmeier, Levi Garraway and colleagues describe an innovative approach coupling histone mass spectroscopy analyses with mutational data for the identification of genetic alterations in the NSD2 gene, which encodes a H3K36 methyltransferase4. Global chromatin profiling Stegmeier and colleagues used a tandem mass spectroscopy strategy to measure chromatin marks on extracted histone proteins, a technique they term ‘global chromatin profiling’. Mass spectrometry circumvents the use of antibodies for the analysis of chromatin marks, which is advantageous given that the lack of specific antibodies for many histone marks remains a significant challenge for the field. Whereas a typical study design for the identification of driver mutations involves elucidating genetic alterations by sequencing and then studying the mechanisms by which these alterations contribute to disease pathogenesis, Stegmeier 1269
Linking the SWI/SNF complex to prostate cancer
npg
© 2013 Nature America, Inc. All rights reserved.
Ryan S Lee & Charles W M Roberts Genes encoding subunits of the SWI/SNF chromatin-remodeling complex constitute, collectively, one of the most frequently mutated targets in cancer. Although mutations in SWI/SNF genes are uncommon in prostate cancer, a new study shows that SChLAP1, a long noncoding RNA frequently expressed in aggressive prostate tumors, drives cancer by directly disrupting SNF5, a core subunit of the SWI/SNF complex. Despite improvements in screening and early detection, prostate cancer remains the second leading cause of cancer mortality in men1. However, individual cases of prostate cancer can display markedly different clinical behavior, ranging from indolent to highly aggressive, metastatic cancers. Thus, ongoing efforts are aimed at identifying biomarkers of aggressive disease and investigating underlying mechanisms. For example, one subset of more aggressive prostate tumors is characterized by the overexpression of EZH2, a member of the PRC2 epigenetic regulatory complex2. Recently, the examination of causal links has expanded to include long noncoding RNAs (lncRNAs) aberrantly expressed in cancer, although the mechanisms by which these lncRNAs drive oncogenesis are just beginning to be understood3,4. In prostate cancer alone, multiple lncRNAs have been described as being abnormally expressed at high levels in cancer cells, with nearly a quarter of transcripts found to be lncRNAs or to be derived from otherwise unannotated sequences4–6. On page 1392 of this issue, Arul Chinnaiyan and colleagues7 focus on one of these lncRNAs, called SChLAP1, and identify a mechanism by which it contributes to prostate cancer growth. SChLAP1 inhibits SNF5 Prensner et al.7 began by searching for lncRNAs expressed at especially high levels Ryan S. Lee and Charles W. M. Roberts are affiliated with the Department of Pediatric Oncology, Dana-Farber Cancer Institute, the Division of Hematology-Oncology, Boston Children’s Hospital and the Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA. e-mail: [email protected]
1268
in a subset of aggressive prostate cancers. They identified a particular lncRNA, which they called SChLAP1 (second chromosome locus associated with prostate-1), that was a predictor of shorter time to recurrence and was associated with increased risk of progression and mortality in an independent cohort of individuals with prostate cancer. Next, they showed that knockdown of SChLAP1 led to reduced cell invasion and proliferation in both cell lines and mouse models, confirming the role of SChLAP1 as an oncogene. Inversely, they found that overexpression of SChLAP1 restored the aggressive phenotype of cells with SChLAP1 knockdown and induced increased invasiveness in benign cells with normally low levels of SChLAP1. Next, Prensner et al.7 explored potential mechanisms by which SChLAP1 expression drives malignancy and found a correlation with gene sets regulated by the SWI/SNF (BAF) complex. The evolutionarily conserved SWI/SNF complex, whose subunits are frequently mutated in human cancer, canonically modulates
transcription by using ATP hydrolysis to remodel chromatin and mobilize nucleosomes8. In particular, the authors focused their attention on the core SWI/SNF subunit SNF5 (also called SMARCB1, INI1 and BAF47) because, when examining gene expression in cells with SChLAP1 knockdown, they observed effects that were anticorrelated with the effects previously reported for SNF5 knockdown. Next, by performing chromatin and RNA immunoprecipitation, the authors identified direct binding of SChLAP1 to SNF5. Mechanistically, they found that binding of SChLAP1 to SNF5 caused a decrease in SNF5 binding to 30% of its target promoters (Fig. 1), which correlated with reduced expression of these genes. SWI/SNF dysregulation in cancer The role of the SWI/SNF complex in cancer has become more apparent in recent years owing to the identification of mutations in genes encoding SWI/SNF subunits in nearly 20% of tumors examined across a wide spectrum
SChLAP1
SWI/SNF SChLAP1
SWI/SNF
SNF5
SNF5 Promoter
Gene
Promoter
Gene
Figure 1 Aberrantly high expression of SChLAP1 in aggressive prostate cancers inhibits SWI/SNFmediated epigenetic regulation. SChLAP1, a long noncoding RNA, binds directly to SNF5. This interaction prevents the SWI/SNF complex from binding to target promoters, resulting in decreased expression of target genes.
volume 45 | number 11 | NOVEMBER 2013 | nature genetics
npg
© 2013 Nature America, Inc. All rights reserved.
news and views of cancer types8–10. Consequently, the complex has been identified as the most frequently mutated chromatin regulatory complex in cancer and one of the most frequently mutated targets overall. The gene encoding SNF5 (SMARCB1) is mutated in pediatric rhabdoid tumors and in a few other rare cancers, but it is not widely mutated across cancer types8. However, mechanisms that indirectly disrupt SNF5 are now being identified in additional types of cancer. For instance, a recent study has shown that the SS18-SSX fusion in synovial sarcoma promotes tumorigenesis by disrupting SNF5 integration into the SWI/SNF complex11. The work of Prensner et al.7 now illustrates how lncRNA-mediated disruption of this SWI/SNF complex subunit can also drive malignancy. The new findings of Prensner et al.7 suggest that SChLAP1 may specifically affect the targeting mechanism of the SWI/SNF complex, a function that remains poorly understood. Although decreased SNF5 binding was observed at some promoters, leading to decreased expression of downstream genes, the specific effect of reduced SNF5 binding
on epigenetic regulation needs to be explored further. The SWI/SNF complex is canonically described as a regulator of gene expression via remodeling of nucleosomes, especially at promoters12,13. Thus, it is possible that SChLAP1 expression leads to disordered nucleosomes or other changes in chromatin structure at proximal promoter sites. Taking these results together with those for EZH2 and BAF57, another SWI/SNF subunit, a theme may be emerging in which aberrantly expressed epigenetic regulators contribute to aggressive prostate cancers14,15. SChLAP1 can be added to a growing list of lncRNAs associated with prostate cancer6. In addition, the ability of SChLAP1 to inhibit SNF5 binding further emphasizes the central role that chromatin regulators have in driving cancer. In essence, SChLAP1 expression in prostate cancer ties together two frontiers in cancer biology: noncoding RNAs and chromatin regulators. By uncovering the interaction between SChLAP1 and SNF5, this new study demonstrates both a mechanism through which lncRNAs can act to drive malignancy
and an additional mechanism by which SWI/ SNF activity can be disrupted in a way that affects cancer growth. COMPETING FINANCIAL INTERESTS The authors declare no competing financial interests. 1. Siegel, R., Naishadham, D. & Jemal, A. CA Cancer J. Clin. 63, 11–30 (2013). 2. Varambally, S. et al. Nature 419, 624–629 (2002). 3. Prensner, J.R. & Chinnaiyan, A.M. Cancer Discov. 1, 391–407 (2011). 4. Du, Z. et al. Nat. Struct. Mol. Biol. 20, 908–913 (2013). 5. Prensner, J.R. et al. Nat. Biotechnol. 29, 742–749 (2011). 6. Yang, L. et al. Nature 500, 598–602 (2013). 7. Prensner, J.R. et al. Nat. Genet. 45, 1392–1398 (2013). 8. Wilson, B.G. & Roberts, C.W.M. Nat. Rev. Cancer 11, 481–492 (2011). 9. Lee, R.S. et al. J. Clin. Invest. 122, 2983–2988 (2012). 10. Kadoch, C. et al. Nat. Genet. 45, 592–601 (2013). 11. Kadoch, C. & Crabtree, G.R. Cell 153, 71–85 (2013). 12. You, J.S. et al. PLoS Genet. 9, e1003459 (2013). 13. Tolstorukov, M.Y. et al. Proc. Natl. Acad. Sci. USA 110, 10165–10170 (2013). 14. Link, K.A. et al. Cancer Res. 68, 4551–4558 (2008). 15. Balasubramaniam, S. et al. Clin. Cancer Res. 19, 2657–2667 (2013).
Mining the epigenetic landscape in ALL Lindsay M LaFave & Ross L Levine The significance of epigenomic aberrations in cancer development has been underscored by the discovery of mutations in key chromatin modifiers, most notably in hematological malignancies. A new study of pediatric acute lymphoblastic leukemia (ALL) demonstrates the usefulness of mapping global epigenetic signatures and applying these data in a framework to identify and characterize underlying somatic genetic alterations in human cancers. Epigenetic dysregulation has become a cardinal feature of human malignancies, warranting the development of innovative approaches to identify epigenetic driver alterations. Numerous large-scale sequencing studies, including targeted exome, transcriptome and whole genome, have led to the identification of mutations or expression changes in genes critical for normal Lindsay M. LaFave and Ross L. Levine are affiliated with the Human Oncology and Pathogenesis Program, Memorial SloanKettering Cancer Center, New York, New York, USA. Lindsay M. LaFave is also affiliated with Gerstner Sloan-Kettering Graduate School, Memorial Sloan-Kettering Cancer Center, New York, New York, USA. Ross L. Levine is also affiliated with the Leukemia Service, Department of Medicine, Memorial SloanKettering Cancer Center, New York, New York, USA. e-mail: [email protected]
epigenetic regulation in a spectrum of cancer types, including in hematological malignancies. For example, oncogenic mutations in histone methyltransferases that modify key lysine residues on histone tails have been identified in leukemias and lymphomas. These findings have led to the development of selective small molecule histone methyltransferase inhibitors for therapeutic applications. Selective inhibitors targeting gain-of-function alterations in EZH2 (refs. 1,2), the catalytic methyltransferase in the PRC2 complex that mediates repressive trimethylation of histone H3 at lysine 27 (H3K27me3), and DOT1L3, the methyltransferase that methylates histone H3 at lysine 79 (H3K79), are being tested in EZH2-mutant B cell lymphoma and MLL-rearranged leukemia, respectively. The successful development of EZH2 and DOT1L inhibitors has driven efforts to assess mutations in histone methyltransferases that drive cancer development and progression and represent tractable therapeutic targets. In this
nature genetics | volume 45 | number 11 | NOVEMBER 2013
issue of Nature Genetics, Frank Stegmeier, Levi Garraway and colleagues describe an innovative approach coupling histone mass spectroscopy analyses with mutational data for the identification of genetic alterations in the NSD2 gene, which encodes a H3K36 methyltransferase4. Global chromatin profiling Stegmeier and colleagues used a tandem mass spectroscopy strategy to measure chromatin marks on extracted histone proteins, a technique they term ‘global chromatin profiling’. Mass spectrometry circumvents the use of antibodies for the analysis of chromatin marks, which is advantageous given that the lack of specific antibodies for many histone marks remains a significant challenge for the field. Whereas a typical study design for the identification of driver mutations involves elucidating genetic alterations by sequencing and then studying the mechanisms by which these alterations contribute to disease pathogenesis, Stegmeier 1269
