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McCleland ML, Mesh K, Lorenzana E, Chopra VS, Segal E, Watanabe C, Haley B, Mayba O, Yaylaoglu M, Gnad F, Firestein R. CCAT1 is an enhancer-templated RNA that predicts BET sensitivity in colorectal cancer. J Clin Invest 2016; 126:639-52. [PMID: 26752646 DOI: 10.1172/jci83265] [Citation(s) in RCA: 166] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 11/18/2015] [Indexed: 01/17/2023] Open
Abstract
Colon tumors arise in a stepwise fashion from either discrete genetic perturbations or epigenetic dysregulation. To uncover the key epigenetic regulators that drive colon cancer growth, we used a CRISPR loss-of-function screen and identified a number of essential genes, including the bromodomain and extraterminal (BET) protein BRD4. We found that BRD4 is critical for colon cancer proliferation, and its knockdown led to differentiation effects in vivo. JQ1, a BET inhibitor, preferentially reduced growth in a subset of epigenetically dysregulated colon cancers characterized by the CpG island methylator phenotype (CIMP). Integrated transcriptomic and genomic analyses defined a distinct superenhancer in CIMP+ colon cancers that regulates cMYC transcription. We found that the long noncoding RNA colon cancer-associated transcript 1 (CCAT1) is transcribed from this superenhancer and is exquisitely sensitive to BET inhibition. Concordantly, cMYC transcription and cell growth were tightly correlated with the presence of CCAT1 RNA in a variety of tumor types. Taken together, we propose that CCAT1 is a clinically tractable biomarker for identifying patients who are likely to benefit from BET inhibitors.
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MESH Headings
- Animals
- Azepines/pharmacology
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Cell Cycle Proteins
- Cell Line, Tumor
- Cell Proliferation
- Colorectal Neoplasms
- CpG Islands
- DNA Methylation/drug effects
- DNA, Neoplasm/genetics
- DNA, Neoplasm/metabolism
- Female
- Gene Knockdown Techniques
- Humans
- Mice
- Mice, Nude
- Nuclear Proteins/antagonists & inhibitors
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Proto-Oncogene Proteins c-myc/genetics
- Proto-Oncogene Proteins c-myc/metabolism
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Neoplasm/genetics
- RNA, Neoplasm/metabolism
- Transcription Factors/antagonists & inhibitors
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Triazoles/pharmacology
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McCleland ML, Soukup TM, Liu SD, Esensten JH, de Sousa e Melo F, Yaylaoglu M, Warming S, Roose-Girma M, Firestein R. Cdk8 deletion in the Apc(Min) murine tumour model represses EZH2 activity and accelerates tumourigenesis. J Pathol 2015; 237:508-19. [PMID: 26235356 DOI: 10.1002/path.4596] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 07/09/2015] [Accepted: 07/28/2015] [Indexed: 01/29/2023]
Abstract
CDK8 is a dissociable kinase module of the Mediator complex and has been shown to play an important role in transcriptional regulation in organisms as diverse as yeast and humans. Recent studies suggest that CDK8 functions as an oncoprotein in melanoma and colon cancer. Importantly, these studies were conducted using in vitro cell line models and the role of CDK8 in tumourigenesis in vivo has not been explored. We have generated a mouse with a Cdk8 conditional knockout allele and examined the consequences of Cdk8 loss on normal tissue homeostasis and tumour development in vivo. Cdk8 deletion in the young adult mouse did not induce any gross or histopathological abnormalities, implying that Cdk8 is largely dispensable for somatic cellular homeostasis. In contrast, Cdk8 deletion in the Apc(Min) intestinal tumour model shortened the animals' survival and increased tumour burden. Although Cdk8 deletion did not affect tumour initiation, intestinal tumour size and growth rate were significantly increased in Cdk8-null animals. Transcriptome analysis performed on Cdk8-null intestinal cells revealed up-regulation of genes that are governed by the Polycomb group (PcG) complex. In support of these findings, Cdk8-null intestinal cells and tumours displayed a reduction in histone H3K27 trimethylation, both globally and at the promoters of a number of PcG-regulated genes involved in oncogenic signalling. Together, our findings uncover a tumour suppressor function for CDK8 in vivo and suggest that the role of CDK8 activity in driving oncogenesis is context-specific. Sequencing data were deposited at GEO (Accession No. GSE71385).
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Affiliation(s)
- Mark L McCleland
- Department of Pathology, Genentech Inc, South San Francisco, CA, USA
| | - Tim M Soukup
- Department of Molecular Biology, Genentech Inc, South San Francisco, CA, USA
| | - Scot D Liu
- Department of Pathology, Genentech Inc, South San Francisco, CA, USA
| | | | | | - Murat Yaylaoglu
- Department of Pathology, Genentech Inc, South San Francisco, CA, USA
| | - Soren Warming
- Department of Molecular Biology, Genentech Inc, South San Francisco, CA, USA
| | - Merone Roose-Girma
- Department of Molecular Biology, Genentech Inc, South San Francisco, CA, USA
| | - Ron Firestein
- Department of Pathology, Genentech Inc, South San Francisco, CA, USA
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Fuji RN, Flagella M, Baca M, S. Baptista MA, Brodbeck J, Chan BK, Fiske BK, Honigberg L, Jubb AM, Katavolos P, Lee DW, Lewin-Koh SC, Lin T, Liu X, Liu S, Lyssikatos JP, O’Mahony J, Reichelt M, Roose-Girma M, Sheng Z, Sherer T, Smith A, Solon M, Sweeney ZK, Tarrant J, Urkowitz A, Warming S, Yaylaoglu M, Zhang S, Zhu H, Estrada AA, Watts RJ. Effect of selective LRRK2 kinase inhibition on nonhuman primate lung. Sci Transl Med 2015; 7:273ra15. [DOI: 10.1126/scitranslmed.aaa3634] [Citation(s) in RCA: 242] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Jia G, Chandriani S, Abbas A, DePianto D, N'Diaye E, Yaylaoglu M, Collard H, Wolters P, Egen J, Scalori A, Ackrill A, Hou J, Kaminski J, Maher T, Arron J. P23 Target And Biomarker Discovery For Hedgehog Pathway Activity In Idiopathic Pulmonary Fibrosis In Support Of A Phase 2 Randomised, Double-blind, Placebo-controlled Study To Assess Efficacy And Safety Of Vismodegib In Ipf (island). Thorax 2014. [DOI: 10.1136/thoraxjnl-2014-206260.173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Firestein R, Adler A, McCleland M, Yaylaoglu M, Zhang Z, Liu J, Jiang Z. 553 PRPF6, a tri-snRNP spliceosome protein, regulates the alternative splicing of a distinct oncogenic ZAK variant and promotes colon tumor growth. Eur J Cancer 2014. [DOI: 10.1016/s0959-8049(14)70679-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Adler AS, McCleland ML, Yee S, Yaylaoglu M, Hussain S, Cosino E, Quinones G, Modrusan Z, Seshagiri S, Torres E, Chopra VS, Haley B, Zhang Z, Blackwood EM, Singh M, Junttila M, Stephan JP, Liu J, Pau G, Fearon ER, Jiang Z, Firestein R. An integrative analysis of colon cancer identifies an essential function for PRPF6 in tumor growth. Genes Dev 2014; 28:1068-84. [PMID: 24788092 PMCID: PMC4035536 DOI: 10.1101/gad.237206.113] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The spliceosome machinery is composed of multimeric protein complexes that generate a diverse repertoire of mRNA. Here, Adler et al. discover that PRPF6, a member of the tri-snRNP spliceosome complex, drives cancer proliferation. Inhibition of PRPF6 and other tri-snRNP complex proteins selectively abrogated growth in cancer cells with high tri-snRNP levels. Reducing PRPF6 altered the splicing of a discrete number of genes, including an oncogenic isoform of the ZAK kinase. This study identifies an essential role for PRPF6 in cancer via splicing of distinct growth-related gene products. The spliceosome machinery is composed of multimeric protein complexes that generate a diverse repertoire of mRNA through coordinated splicing of heteronuclear RNAs. While somatic mutations in spliceosome components have been discovered in several cancer types, the molecular bases and consequences of spliceosome aberrations in cancer are poorly understood. Here we report for the first time that PRPF6, a member of the tri-snRNP (small ribonucleoprotein) spliceosome complex, drives cancer proliferation by preferential splicing of genes associated with growth regulation. Inhibition of PRPF6 and other tri-snRNP complex proteins, but not other snRNP spliceosome complexes, selectively abrogated growth in cancer cells with high tri-snRNP levels. High-resolution transcriptome analyses revealed that reduced PRPF6 alters the constitutive and alternative splicing of a discrete number of genes, including an oncogenic isoform of the ZAK kinase. These findings implicate an essential role for PRPF6 in cancer via splicing of distinct growth-related gene products.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Eric Torres
- Department of Biochemical and Cellular Pharmacology
| | | | | | - Zemin Zhang
- Department of Bioinformatics, Genentech, Inc., South San Francisco, California 94080, USA
| | | | | | | | | | - Jinfeng Liu
- Department of Bioinformatics, Genentech, Inc., South San Francisco, California 94080, USA
| | - Gregoire Pau
- Department of Bioinformatics, Genentech, Inc., South San Francisco, California 94080, USA
| | - Eric R Fearon
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Zhaoshi Jiang
- Department of Bioinformatics, Genentech, Inc., South San Francisco, California 94080, USA
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Ziskin JL, Dunlap D, Yaylaoglu M, Fodor IK, Forrest WF, Patel R, Ge N, Hutchins GG, Pine JK, Quirke P, Koeppen H, Jubb AM. In situ validation of an intestinal stem cell signature in colorectal cancer. Gut 2013; 62:1012-23. [PMID: 22637696 DOI: 10.1136/gutjnl-2011-301195] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
OBJECTIVE Wnt/Tcf, Lgr5, Ascl2 and/or Bmi1 signalling is believed to define the mouse intestinal stem cell niche(s) from which adenomas arise. The aim of this study was to determine the relevance of these putative intestinal stem cell markers to human colorectal cancer. DESIGN 19 putative intestinal stem cell markers, including Ascl2 and Lgr5, were identified from published data and an evaluation of a human colorectal gene expression database. Associations between these genes were assessed by isotopic in situ hybridisation (ISH) in 57 colorectal adenocarcinomas. Multiplex fluorescent ISH and chromogenic non-isotopic ISH were performed to confirm expression patterns. The prognostic significance of Lgr5 was assessed in 891 colorectal adenocarcinomas. RESULTS Ascl2 and Lgr5 were expressed in 85% and 74% of cancers respectively, and expression was positively correlated (p=0.003). Expression of Bmi1 was observed in 47% of cancers but was very weak in 98% of cases with expression. Both Ascl2 and/or Lgr5 were positively correlated with the majority of genes in the signature but neither was correlated with Cdk6, Gpx2, Olfm4 or Tnfrsf19. Lgr5 did not have prognostic significance. CONCLUSION These data suggest that 74-85% of colorectal cancers express a Lgr5/Ascl2 associated signature and support the hypothesis that they derive from Lgr5(+)/Ascl2(+) crypt stem cells, not Bmi1(+) stem cells. However, Olfm4 was not found to be a useful marker of Lgr5(+) cells in normal colon or tumours. In this large series, Lgr5 expression is not associated with increased tumour aggressiveness, as might be expected from a cancer stem cell marker.
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Affiliation(s)
- Jennifer L Ziskin
- Department of Pathology, Stanford University Medical Center, Stanford, California, USA
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Kraszucka K, Burfeind P, Nayernia K, Köhler M, Schmid M, Yaylaoglu M, Engel W. Developmental stage- and germ cell-regulated expression of a calcium-binding protein mRNA in mouse Sertoli cells. Mol Reprod Dev 1999; 54:232-43. [PMID: 10497345 DOI: 10.1002/(sici)1098-2795(199911)54:3<232::aid-mrd4>3.0.co;2-f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
There is considerable evidence that germ cells, mainly spermatocytes and spermatids, contribute to the regulation of Sertoli cell activity. We developed an in vitro system to investigate the genes involved in Sertoli cell-germ cell interaction in the mouse by using the differential mRNA display technique. One of the isolated differentially expressed genes, named calgizzarin, belongs to the family of S100 calcium-binding proteins and shows a decreased expression in Sertoli cell-germ cell cocultures compared to cultured Sertoli cells alone. Calgizzarin is expressed in all adult tissues examined, including testis and ovary; however, a high mRNA level for calgizzarin in mouse testis is maintained until day 15 of postnatal development and then declines dramatically, whereas the expression pattern in the ovary remains constantly high. Furthermore, Northern blot studies on testicular RNA from different mouse mutants with defects in spermatogenesis revealed that high levels of calgizzarin transcripts can only be detected in testes of mouse mutants with either no germ cells or primary spermatocytes, but only weak signals for calgizzarin are observed in testes of mutants containing spermatids. In addition, using both RT-PCR analysis and whole-mount in situ hybridization on dissected gonads it was demonstrated that mouse calgizzarin expression starts at 13.5 dpc in the prenatal male gonad and at 16.5 dpc in the embryonic ovary, respectively. The mouse calgizzarin gene was localized on mouse chromosome 5, region E-F. Taken together, our results indicate that calgizzarin expression could be repressed by factors originated from pachytene spermatocytes and/or spermatids.
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Affiliation(s)
- K Kraszucka
- Institute of Human Genetics, University of Göttingen, Göttingen, Germany
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