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Knockdown of PHF5A Inhibits Migration and Invasion of HCC Cells via Downregulating NF- κB Signaling. BIOMED RESEARCH INTERNATIONAL 2019; 2019:1621854. [PMID: 30766880 PMCID: PMC6350539 DOI: 10.1155/2019/1621854] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 11/29/2018] [Accepted: 12/23/2018] [Indexed: 02/07/2023]
Abstract
Background Inflammation is the major risk factor for the progression of hepatocellular carcinoma (HCC), and the nuclear factor-κB (NF-κB) signaling plays the central role in the inflammation process. However, the activated mechanism of NF-κB signaling in HCC is unclear. Methods The expression of PHF5A is examined by qPCR, western blotting, and immunohistochemistry (IHC) assay. The potential of PHF5A (PHD-finger domain protein 5a) for migration and invasion is examined by wound healing and Transwell assay. Luciferase reporter assay, western blotting, and qPCR were applied to explore the mechanism by which PHF5A is involved in progression of HCC. Results PHF5A was significantly upregulated in HCC tissues and cells. Downregulation of PHF5A inhibits the migration and invasion of HCC cells. Further study demonstrated that PHF5A is implicated in HCC progression through NF-κB signaling. In addition, blocking the NF-κB signaling can weaken the stimulatory effect of PHF5A on migration and invasion of HCC cells. Conclusion PHF5A expression is upregulated in HCC tissues, and depletion of PHF5A inhibits the migration and invasion of HCC cells. Further experiments demonstrated that PHF5A is implicated in NF-κB signaling and knockdown of PHF5A downregulates the activity of NF-κB pathway to inhibit the tumor progression. The above results provide the evidence that PHF5A plays an indispensable role in progressive effect of NF-κB pathway in HCC and may be a novel therapeutic target of HCC.
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Sensitivity to splicing modulation of BCL2 family genes defines cancer therapeutic strategies for splicing modulators. Nat Commun 2019; 10:137. [PMID: 30635584 PMCID: PMC6329755 DOI: 10.1038/s41467-018-08150-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 12/18/2018] [Indexed: 11/24/2022] Open
Abstract
Dysregulation of RNA splicing by spliceosome mutations or in cancer genes is increasingly recognized as a hallmark of cancer. Small molecule splicing modulators have been introduced into clinical trials to treat solid tumors or leukemia bearing recurrent spliceosome mutations. Nevertheless, further investigation of the molecular mechanisms that may enlighten therapeutic strategies for splicing modulators is highly desired. Here, using unbiased functional approaches, we report that the sensitivity to splicing modulation of the anti-apoptotic BCL2 family genes is a key mechanism underlying preferential cytotoxicity induced by the SF3b-targeting splicing modulator E7107. While BCL2A1, BCL2L2 and MCL1 are prone to splicing perturbation, BCL2L1 exhibits resistance to E7107-induced splicing modulation. Consequently, E7107 selectively induces apoptosis in BCL2A1-dependent melanoma cells and MCL1-dependent NSCLC cells. Furthermore, combination of BCLxL (BCL2L1-encoded) inhibitors and E7107 remarkably enhances cytotoxicity in cancer cells. These findings inform mechanism-based approaches to the future clinical development of splicing modulators in cancer treatment. Small molecule modulators of RNA splicing have therapeutic potential in tumours bearing spliceosome mutations. Here, the authors identify BCL2 genes have differential sensitivities to SF3b-targeting splicing modulators and combination of SF3b-targeting splicing modulators and BCLxL inhibition induces synergistic cytotoxicity in cancer cells.
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53
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A peptide encoded by circular form of LINC-PINT suppresses oncogenic transcriptional elongation in glioblastoma. Nat Commun 2018; 9:4475. [PMID: 30367041 PMCID: PMC6203777 DOI: 10.1038/s41467-018-06862-2] [Citation(s) in RCA: 448] [Impact Index Per Article: 74.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 10/02/2018] [Indexed: 01/12/2023] Open
Abstract
Circular RNAs (circRNAs) are a large class of transcripts in the mammalian genome. Although the translation of circRNAs was reported, additional coding circRNAs and the functions of their translated products remain elusive. Here, we demonstrate that an endogenous circRNA generated from a long noncoding RNA encodes regulatory peptides. Through ribosome nascent-chain complex-bound RNA sequencing (RNC-seq), we discover several peptides potentially encoded by circRNAs. We identify an 87-amino-acid peptide encoded by the circular form of the long intergenic non-protein-coding RNA p53-induced transcript (LINC-PINT) that suppresses glioblastoma cell proliferation in vitro and in vivo. This peptide directly interacts with polymerase associated factor complex (PAF1c) and inhibits the transcriptional elongation of multiple oncogenes. The expression of this peptide and its corresponding circRNA are decreased in glioblastoma compared with the levels in normal tissues. Our results establish the existence of peptides encoded by circRNAs and demonstrate their potential functions in glioblastoma tumorigenesis. Functional peptides can be encoded by short open reading frames in non-coding RNA. Here, the authors identify a 87aa peptide encoded by the circular form of the long intergenic non-protein-coding RNA p53-induced transcript (LINC-PINT) that can reduce glioblastoma proliferation via interaction with PAF1 which sequentially inhibits the transcriptional elongation of some oncogenes.
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54
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Lee SCW, North K, Kim E, Jang E, Obeng E, Lu SX, Liu B, Inoue D, Yoshimi A, Ki M, Yeo M, Zhang XJ, Kim MK, Cho H, Chung YR, Taylor J, Durham BH, Kim YJ, Pastore A, Monette S, Palacino J, Seiler M, Buonamici S, Smith PG, Ebert BL, Bradley RK, Abdel-Wahab O. Synthetic Lethal and Convergent Biological Effects of Cancer-Associated Spliceosomal Gene Mutations. Cancer Cell 2018; 34:225-241.e8. [PMID: 30107174 PMCID: PMC6373472 DOI: 10.1016/j.ccell.2018.07.003] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 04/25/2018] [Accepted: 07/12/2018] [Indexed: 02/07/2023]
Abstract
Mutations affecting RNA splicing factors are the most common genetic alterations in myelodysplastic syndrome (MDS) patients and occur in a mutually exclusive manner. The basis for the mutual exclusivity of these mutations and how they contribute to MDS is not well understood. Here we report that although different spliceosome gene mutations impart distinct effects on splicing, they are negatively selected for when co-expressed due to aberrant splicing and downregulation of regulators of hematopoietic stem cell survival and quiescence. In addition to this synthetic lethal interaction, mutations in the splicing factors SF3B1 and SRSF2 share convergent effects on aberrant splicing of mRNAs that promote nuclear factor κB signaling. These data identify shared consequences of splicing-factor mutations and the basis for their mutual exclusivity.
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Affiliation(s)
- Stanley Chun-Wei Lee
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, Zuckerman 701, 408 East 69(th) Street, New York, NY 10065, USA
| | - Khrystyna North
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Mailstop: M1-B514, Seattle, WA 98109-1024, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Eunhee Kim
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Eunjung Jang
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Esther Obeng
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sydney X Lu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, Zuckerman 701, 408 East 69(th) Street, New York, NY 10065, USA
| | - Bo Liu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, Zuckerman 701, 408 East 69(th) Street, New York, NY 10065, USA
| | - Daichi Inoue
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, Zuckerman 701, 408 East 69(th) Street, New York, NY 10065, USA
| | - Akihide Yoshimi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, Zuckerman 701, 408 East 69(th) Street, New York, NY 10065, USA
| | - Michelle Ki
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, Zuckerman 701, 408 East 69(th) Street, New York, NY 10065, USA
| | - Mirae Yeo
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Xiao Jing Zhang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, Zuckerman 701, 408 East 69(th) Street, New York, NY 10065, USA
| | - Min Kyung Kim
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, Zuckerman 701, 408 East 69(th) Street, New York, NY 10065, USA
| | - Hana Cho
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, Zuckerman 701, 408 East 69(th) Street, New York, NY 10065, USA
| | - Young Rock Chung
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, Zuckerman 701, 408 East 69(th) Street, New York, NY 10065, USA
| | - Justin Taylor
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, Zuckerman 701, 408 East 69(th) Street, New York, NY 10065, USA
| | - Benjamin H Durham
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, Zuckerman 701, 408 East 69(th) Street, New York, NY 10065, USA
| | - Young Joon Kim
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, Zuckerman 701, 408 East 69(th) Street, New York, NY 10065, USA
| | - Alessandro Pastore
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, Zuckerman 701, 408 East 69(th) Street, New York, NY 10065, USA
| | - Sebastien Monette
- Laboratory of Comparative Pathology, Memorial Sloan Kettering Cancer Center, Weill Cornell Medicine, The Rockefeller University, New York, NY, USA
| | | | | | | | | | - Benjamin L Ebert
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Mailstop: M1-B514, Seattle, WA 98109-1024, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, Zuckerman 701, 408 East 69(th) Street, New York, NY 10065, USA; Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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55
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Targeting the spliceosome for cutaneous squamous cell carcinoma therapy: a role for c-MYC and wild-type p53 in determining the degree of tumour selectivity. Oncotarget 2018; 9:23029-23046. [PMID: 29796170 PMCID: PMC5955416 DOI: 10.18632/oncotarget.25196] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 04/04/2018] [Indexed: 12/25/2022] Open
Abstract
We show that suppression of the spliceosome has potential for the treatment of cutaneous squamous cell carcinoma (cSCC). The small-molecule inhibitors of the spliceosome at the most advanced stage of development target the splicing factor SF3B1/SF3b155. The majority of cSCC cell lines are more sensitive than normal skin cells to death induced by the SF3B1 inhibitor pladienolide B. Knockdown of SF3B1 and a range of other splicing factors with diverse roles in the spliceosome can also selectively kill cSCC cells. We demonstrate that endogenous c-MYC participates in conferring sensitivity to spliceosome inhibition. c-MYC expression is elevated in cSCC lines and its knockdown reduces alterations in mRNA splicing and attenuates cell death caused by interference with the spliceosome. In addition, this study provides further support for a key role of the p53 pathway in the response to spliceosome disruption. SF3B1 inhibition causes wild-type p53 upregulation associated with altered mRNA splicing and reduced protein expression of both principal p53 negative regulators MDMX/MDM4 and MDM2. We observed that wild-type p53 can promote pladienolide B-induced death in tumour cells. However, p53 is commonly inactivated by mutation in cSCCs and p53 participates in killing normal skin cells at high concentrations of pladienolide B. This may limit the therapeutic window of SF3B1 inhibitors for cSCC. We provide evidence that, while suppression of SF3B1 has promise for treating cSCCs with mutant p53, inhibitors which target the spliceosome through SF3B1-independent mechanisms could have greater cSCC selectivity as a consequence of reduced p53 upregulation in normal cells.
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56
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Zheng YZ, Xue MZ, Shen HJ, Li XG, Ma D, Gong Y, Liu YR, Qiao F, Xie HY, Lian B, Sun WL, Zhao HY, Yao L, Zuo WJ, Li DQ, Wang P, Hu X, Shao ZM. PHF5A Epigenetically Inhibits Apoptosis to Promote Breast Cancer Progression. Cancer Res 2018; 78:3190-3206. [PMID: 29700004 DOI: 10.1158/0008-5472.can-17-3514] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 03/15/2018] [Accepted: 04/19/2018] [Indexed: 11/16/2022]
Abstract
Alternative splicing (AS) and its regulation play critical roles in cancer, yet the dysregulation of AS and its molecular bases in breast cancer development have not yet been elucidated. Using an in vivo CRISPR screen targeting RNA-binding proteins, we identified PHD finger protein 5A (PHF5A) as a key splicing factor involved in tumor progression. PHF5A expression was frequently upregulated in breast cancer and correlated with poor survival, and knockdown of PHF5A significantly suppressed cell proliferation, migration, and tumor formation. PHF5A was required for SF3b spliceosome stability and linked the complex to histones, and the PHF5A-SF3b complex modulated AS changes in apoptotic signaling. In addition, expression of a short truncated FAS-activated serine/threonine kinase (FASTK) protein was increased after PHF5A ablation and facilitated Fas-mediated apoptosis. This PHF5A-modulated FASTK-AS axis was widely present in breast cancer specimens, particularly those of the triple-negative subtype. Taken together, our findings reveal that PHF5A serves as an epigenetic suppressor of apoptosis and thus provides a mechanistic basis for breast cancer progression and may be a valuable therapeutic target.Significance: This study provides an epigenetic mechanistic basis for the aggressive biology of breast cancer and identifies a translatable therapeutic target. Cancer Res; 78(12); 3190-206. ©2018 AACR.
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Affiliation(s)
- Yi-Zi Zheng
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Meng-Zhu Xue
- SARI center for Stem Cell and Nanomedicine, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Hong-Jie Shen
- Epigenetics Laboratory, Institutes of Biomedical Sciences and School of Basic Medicine, Shanghai Medical College of Fudan University, Shanghai, China
| | - Xiao-Guang Li
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Ding Ma
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yue Gong
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yi-Rong Liu
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Feng Qiao
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Hong-Yan Xie
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Bi Lian
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wei-Li Sun
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Hai-Yun Zhao
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ling Yao
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Wen-Jia Zuo
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Da-Qiang Li
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Peng Wang
- Bio-Med Big Data Center, Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xin Hu
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China. .,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhi-Ming Shao
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China. .,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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57
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Ding Y, Herman JA, Toledo CM, Lang JM, Corrin P, Girard EJ, Basom R, Delrow JJ, Olson JM, Paddison PJ. ZNF131 suppresses centrosome fragmentation in glioblastoma stem-like cells through regulation of HAUS5. Oncotarget 2018; 8:48545-48562. [PMID: 28596487 PMCID: PMC5564707 DOI: 10.18632/oncotarget.18153] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 05/05/2017] [Indexed: 12/17/2022] Open
Abstract
Zinc finger domain genes comprise ∼3% of the human genome, yet many of their functions remain unknown. Here we investigated roles for the vertebrate-specific BTB domain zinc finger gene ZNF131 in the context of human brain tumors. We report that ZNF131 is broadly required for Glioblastoma stem-like cell (GSC) viability, but dispensable for neural progenitor cell (NPC) viability. Examination of gene expression changes after ZNF131 knockdown (kd) revealed that ZNF131 activity notably promotes expression of Joubert Syndrome ciliopathy genes, including KIF7, NPHP1, and TMEM237, as well as HAUS5, a component of Augmin/HAUS complex that facilitates microtubule nucleation along the mitotic spindle. Of these genes only kd of HAUS5 displayed GSC-specific viability loss. Critically, HAUS5 ectopic expression was sufficient to suppress viability defects of ZNF131 kd cells. Moreover, ZNF131 and HAUS5 kd phenocopied each other in GSCs, each causing: mitotic arrest, centrosome fragmentation, loss of Augmin/HAUS complex on the mitotic spindle, and loss of GSC self-renewal and tumor formation capacity. In control NPCs, we observed centrosome fragmentation and lethality only when HAUS5 kd was combined with kd of HAUS2 or HAUS4, demonstrating that the complex is essential in NPCs, but that GSCs have heightened requirement. Our results suggest that GSCs differentially rely on ZNF131-dependent expression of HAUS5 as well as the Augmin/HAUS complex activity to maintain the integrity of centrosome function and viability.
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Affiliation(s)
- Yu Ding
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Novartis Institute for Biomedical Research, Shanghai, China
| | - Jacob A Herman
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Chad M Toledo
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA.,Nurix Inc., San Francisco, CA, USA
| | - Jackie M Lang
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Philip Corrin
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Emily J Girard
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ryan Basom
- Genomics and Bioinformatics Shared Resources, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jeffrey J Delrow
- Genomics and Bioinformatics Shared Resources, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - James M Olson
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Patrick J Paddison
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
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58
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Yang Y, Zhu J, Zhang T, Liu J, Li Y, Zhu Y, Xu L, Wang R, Su F, Ou Y, Wu Q. PHD-finger domain protein 5A functions as a novel oncoprotein in lung adenocarcinoma. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2018; 37:65. [PMID: 29566713 PMCID: PMC5863814 DOI: 10.1186/s13046-018-0736-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 03/14/2018] [Indexed: 12/30/2022]
Abstract
BACKGROUND PHD-finger domain protein 5A (PHF5A) is a highly conserved small transcriptional regulator also involved in pre-mRNA splicing; however, its biological functions and molecular mechanisms in non-small cell lung cancer (NSCLC) have not yet been investigated. The purpose of this study was to determine the functional relevance and therapeutic potential of PHF5A in lung adenocarcinoma (LAC). METHODS The expression of PHF5A in LAC tissues and adjacent non-tumor (ANT) tissues was investigated using immunohistochemistry of a tissue microarray, qRT-PCR, western blot and bioinformatics. The function of PHF5A was determined using several in vitro assays and also in vivo assay by lentiviral vector-mediated PHF5A depletion in LAC cell lines. RESULTS PHF5A was highly upregulated in LAC tissues compared with the ANT counterparts, and closely associated with tumor progression and poor patient prognosis. These results were further confirmed by findings of the TCGA database. Moreover, functional studies demonstrated that PHF5A knockdown not only resulted in reduced cell proliferation, increased cell apoptosis, and cell cycle arrest, but also suppressed migration and invasion in LAC cells. PHF5A silencing was also found to inhibit LAC tumor growth in nude mice. Microarray and bioinformatics analyses revealed that PHF5A depletion led to dysregulation of multiple tumor signaling pathways; selected factors in key signaling pathways were verified in vitro. CONCLUSIONS The data suggest for the first time that PHF5A is an oncoprotein that contributes to LAC progression by regulating multiple signaling pathways, and may constitute a prognostic factor and potential new therapeutic target in NSCLC.
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Affiliation(s)
- Yan Yang
- Department of Medical Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233004, People's Republic of China.
| | - Jian Zhu
- Department of Cardiology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233004, People's Republic of China
| | - Tiantian Zhang
- Department of Medical Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233004, People's Republic of China
| | - Jing Liu
- Department of Medical Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233004, People's Republic of China
| | - Yumei Li
- Department of Medical Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233004, People's Republic of China
| | - Yue Zhu
- Department of Medical Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233004, People's Republic of China
| | - Lingjie Xu
- Department of Medical Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233004, People's Republic of China
| | - Rui Wang
- Department of Medical Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233004, People's Republic of China
| | - Fang Su
- Department of Medical Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233004, People's Republic of China
| | - Yurong Ou
- Department of Pathology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233004, Anhui, People's Republic of China
| | - Qiong Wu
- Department of Medical Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233004, People's Republic of China.
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Molecular basis of differential 3' splice site sensitivity to anti-tumor drugs targeting U2 snRNP. Nat Commun 2017; 8:2100. [PMID: 29235465 PMCID: PMC5727392 DOI: 10.1038/s41467-017-02007-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 10/30/2017] [Indexed: 01/21/2023] Open
Abstract
Several splicing-modulating compounds, including Sudemycins and Spliceostatin A, display anti-tumor properties. Combining transcriptome, bioinformatic and mutagenesis analyses, we delineate sequence determinants of the differential sensitivity of 3′ splice sites to these drugs. Sequences 5′ from the branch point (BP) region strongly influence drug sensitivity, with additional functional BPs reducing, and BP-like sequences allowing, drug responses. Drug-induced retained introns are typically shorter, displaying higher GC content and weaker polypyrimidine-tracts and BPs. Drug-induced exon skipping preferentially affects shorter alternatively spliced regions with weaker BPs. Remarkably, structurally similar drugs display both common and differential effects on splicing regulation, SSA generally displaying stronger effects on intron retention, and Sudemycins more acute effects on exon skipping. Collectively, our results illustrate how splicing modulation is exquisitely sensitive to the sequence context of 3′ splice sites and to small structural differences between drugs. Several families of natural compounds target core components of the pre-mRNA splicing machinery and display anti-tumor activity. Here the authors show that particular sequence features can be linked to drug response, and that drugs with very similar chemical structures display substantially different effects on splicing regulation.
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60
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61
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Lee E, Pain M, Wang H, Herman JA, Toledo CM, DeLuca JG, Yong RL, Paddison P, Zhu J. Sensitivity to BUB1B Inhibition Defines an Alternative Classification of Glioblastoma. Cancer Res 2017; 77:5518-5529. [PMID: 28855212 DOI: 10.1158/0008-5472.can-17-0736] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 07/26/2017] [Accepted: 08/22/2017] [Indexed: 12/21/2022]
Abstract
Glioblastoma multiforme (GBM) remains a mainly incurable disease in desperate need of more effective treatments. In this study, we develop evidence that the mitotic spindle checkpoint molecule BUB1B may offer a predictive marker for aggressiveness and effective drug response. A subset of GBM tumor isolates requires BUB1B to suppress lethal kinetochore-microtubule attachment defects. Using gene expression data from GBM stem-like cells, astrocytes, and neural progenitor cells that are sensitive or resistant to BUB1B inhibition, we created a computational framework to predict sensitivity to BUB1B inhibition. Applying this framework to tumor expression data from patients, we stratified tumors into BUB1B-sensitive (BUB1BS) or BUB1B-resistant (BUB1BR) subtypes. Through this effort, we found that BUB1BS patients have a significantly worse prognosis regardless of tumor development subtype (i.e., classical, mesenchymal, neural, proneural). Functional genomic profiling of BUB1BR versus BUB1BS isolates revealed a differential reliance of genes enriched in the BUB1BS classifier, including those involved in mitotic cell cycle, microtubule organization, and chromosome segregation. By comparing drug sensitivity profiles, we predicted BUB1BS cells to be more sensitive to type I and II topoisomerase inhibitors, Raf inhibitors, and other drugs, and experimentally validated some of these predictions. Taken together, the results show that our BUB1BR/S classification of GBM tumors can predict clinical course and sensitivity to drug treatment. Cancer Res; 77(20); 5518-29. ©2017 AACR.
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Affiliation(s)
- Eunjee Lee
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Margaret Pain
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Huaien Wang
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jacob A Herman
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado
| | - Chad M Toledo
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Molecular and Cellular Biology Program, University of Washington, Seattle, Washington
| | - Jennifer G DeLuca
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado
| | - Raymund L Yong
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Patrick Paddison
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Molecular and Cellular Biology Program, University of Washington, Seattle, Washington
| | - Jun Zhu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York. .,Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York.,Sema4 Genomics, Icahn School of Medicine at Mount Sinai, New York, New York
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62
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McDonald ER, de Weck A, Schlabach MR, Billy E, Mavrakis KJ, Hoffman GR, Belur D, Castelletti D, Frias E, Gampa K, Golji J, Kao I, Li L, Megel P, Perkins TA, Ramadan N, Ruddy DA, Silver SJ, Sovath S, Stump M, Weber O, Widmer R, Yu J, Yu K, Yue Y, Abramowski D, Ackley E, Barrett R, Berger J, Bernard JL, Billig R, Brachmann SM, Buxton F, Caothien R, Caushi JX, Chung FS, Cortés-Cros M, deBeaumont RS, Delaunay C, Desplat A, Duong W, Dwoske DA, Eldridge RS, Farsidjani A, Feng F, Feng J, Flemming D, Forrester W, Galli GG, Gao Z, Gauter F, Gibaja V, Haas K, Hattenberger M, Hood T, Hurov KE, Jagani Z, Jenal M, Johnson JA, Jones MD, Kapoor A, Korn J, Liu J, Liu Q, Liu S, Liu Y, Loo AT, Macchi KJ, Martin T, McAllister G, Meyer A, Mollé S, Pagliarini RA, Phadke T, Repko B, Schouwey T, Shanahan F, Shen Q, Stamm C, Stephan C, Stucke VM, Tiedt R, Varadarajan M, Venkatesan K, Vitari AC, Wallroth M, Weiler J, Zhang J, Mickanin C, Myer VE, Porter JA, Lai A, Bitter H, Lees E, Keen N, Kauffmann A, Stegmeier F, Hofmann F, Schmelzle T, Sellers WR. Project DRIVE: A Compendium of Cancer Dependencies and Synthetic Lethal Relationships Uncovered by Large-Scale, Deep RNAi Screening. Cell 2017; 170:577-592.e10. [PMID: 28753431 DOI: 10.1016/j.cell.2017.07.005] [Citation(s) in RCA: 405] [Impact Index Per Article: 57.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 06/02/2017] [Accepted: 07/06/2017] [Indexed: 12/13/2022]
Abstract
Elucidation of the mutational landscape of human cancer has progressed rapidly and been accompanied by the development of therapeutics targeting mutant oncogenes. However, a comprehensive mapping of cancer dependencies has lagged behind and the discovery of therapeutic targets for counteracting tumor suppressor gene loss is needed. To identify vulnerabilities relevant to specific cancer subtypes, we conducted a large-scale RNAi screen in which viability effects of mRNA knockdown were assessed for 7,837 genes using an average of 20 shRNAs per gene in 398 cancer cell lines. We describe findings of this screen, outlining the classes of cancer dependency genes and their relationships to genetic, expression, and lineage features. In addition, we describe robust gene-interaction networks recapitulating both protein complexes and functional cooperation among complexes and pathways. This dataset along with a web portal is provided to the community to assist in the discovery and translation of new therapeutic approaches for cancer.
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Affiliation(s)
- E Robert McDonald
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA.
| | - Antoine de Weck
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Michael R Schlabach
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Eric Billy
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Konstantinos J Mavrakis
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Gregory R Hoffman
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Dhiren Belur
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Deborah Castelletti
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Elizabeth Frias
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Kalyani Gampa
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Javad Golji
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Iris Kao
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Li Li
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Philippe Megel
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Thomas A Perkins
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Nadire Ramadan
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - David A Ruddy
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Serena J Silver
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Sosathya Sovath
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Mark Stump
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Odile Weber
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Roland Widmer
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Jianjun Yu
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Kristine Yu
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Yingzi Yue
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Dorothee Abramowski
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Elizabeth Ackley
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Rosemary Barrett
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Joel Berger
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Julie L Bernard
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Rebecca Billig
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Saskia M Brachmann
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Frank Buxton
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Roger Caothien
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Justina X Caushi
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Franklin S Chung
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Marta Cortés-Cros
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Rosalie S deBeaumont
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Clara Delaunay
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Aurore Desplat
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - William Duong
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Donald A Dwoske
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Richard S Eldridge
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Ali Farsidjani
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Fei Feng
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - JiaJia Feng
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Daisy Flemming
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - William Forrester
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Giorgio G Galli
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Zhenhai Gao
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - François Gauter
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Veronica Gibaja
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Kristy Haas
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Marc Hattenberger
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Tami Hood
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Kristen E Hurov
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Zainab Jagani
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Mathias Jenal
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Jennifer A Johnson
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Michael D Jones
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Avnish Kapoor
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Joshua Korn
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Jilin Liu
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Qiumei Liu
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Shumei Liu
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Yue Liu
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Alice T Loo
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Kaitlin J Macchi
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Typhaine Martin
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Gregory McAllister
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Amandine Meyer
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Sandra Mollé
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Raymond A Pagliarini
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Tanushree Phadke
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Brian Repko
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Tanja Schouwey
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Frances Shanahan
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Qiong Shen
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Christelle Stamm
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Christine Stephan
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Volker M Stucke
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Ralph Tiedt
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Malini Varadarajan
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Kavitha Venkatesan
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Alberto C Vitari
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Marco Wallroth
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Jan Weiler
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Jing Zhang
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Craig Mickanin
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Vic E Myer
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Jeffery A Porter
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Albert Lai
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Hans Bitter
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Emma Lees
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Nicholas Keen
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Audrey Kauffmann
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Frank Stegmeier
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Francesco Hofmann
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
| | - Tobias Schmelzle
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA.
| | - William R Sellers
- Novartis Institutes for Biomedical Research, Oncology Disease Area, Basel 4002, Switzerland; Cambridge, MA 02139, USA; and Emeryville, CA 94608, USA
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Lee SCW, Abdel-Wahab O. Therapeutic targeting of splicing in cancer. Nat Med 2017; 22:976-86. [PMID: 27603132 DOI: 10.1038/nm.4165] [Citation(s) in RCA: 385] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 07/13/2016] [Indexed: 02/07/2023]
Abstract
Recent studies have highlighted that splicing patterns are frequently altered in cancer and that mutations in genes encoding spliceosomal proteins, as well as mutations affecting the splicing of key cancer-associated genes, are enriched in cancer. In parallel, there is also accumulating evidence that several molecular subtypes of cancer are highly dependent on splicing function for cell survival. These findings have resulted in a growing interest in targeting splicing catalysis, splicing regulatory proteins, and/or specific key altered splicing events in the treatment of cancer. Here we present strategies that exist and that are in development to target altered dependency on the spliceosome, as well as aberrant splicing, in cancer. These include drugs to target global splicing in cancer subtypes that are preferentially dependent on wild-type splicing for survival, methods to alter post-translational modifications of splicing-regulating proteins, and strategies to modulate pathologic splicing events and protein-RNA interactions in cancer.
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Affiliation(s)
- Stanley Chun-Wei Lee
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA.,Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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64
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Dhanjal JK, Radhakrishnan N, Sundar D. Identifying synthetic lethal targets using CRISPR/Cas9 system. Methods 2017; 131:66-73. [PMID: 28710008 DOI: 10.1016/j.ymeth.2017.07.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 07/06/2017] [Accepted: 07/08/2017] [Indexed: 12/26/2022] Open
Abstract
Synthetic lethality occurs when co-occurrence of two genetic events is unfavorable for the survival of the cell or organism. The conventional approach of high throughput screening of synthetic lethal targets using chemical compounds has been replaced by RNAi technology. CRISPR/Cas9, an RNA guided endonuclease system is the most recent technology for this work. Here, we have discussed the major considerations involved in designing a CRISPR/Cas9 based screening experiment for identification of synthetic lethal targets. It mainly includes CRISPR library to be used, cell types for conducting the experiment, the most appropriate screening strategy and ways of selecting the desired phenotypes from the complete cell population. The complete knockdown of genes can be achieved using CRISPR/Cas9 knockout libraries. For higher quality loss-of-function screens, haploid cells with defective homology-directed DNA repair mechanism could be used. Two widely used screening formats include arrayed and pooled screens followed by negative or positive selection of the cells with desired phenotype. However, pooled screening format with negative selection of cells serves the best. The advantages of using CRISPR/Cas9 system over the other RNAi approaches have also been discussed. Finally, some studies using CRISPR/Cas9 for genome-wide knockout screening in human cells and computational approaches for identification of synthetic lethal interactions have been discussed.
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Affiliation(s)
- Jaspreet Kaur Dhanjal
- Department of Biochemical Engineering and Biotechnology, DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
| | - Navaneethan Radhakrishnan
- Department of Biochemical Engineering and Biotechnology, DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
| | - Durai Sundar
- Department of Biochemical Engineering and Biotechnology, DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
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65
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RNA processing as an alternative route to attack glioblastoma. Hum Genet 2017; 136:1129-1141. [PMID: 28608251 DOI: 10.1007/s00439-017-1819-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 06/02/2017] [Indexed: 02/07/2023]
Abstract
Genomic analyses have become an important tool to identify new avenues for therapy. This is especially true for cancer types with extremely poor outcomes, since our lack of effective therapies offers no tangible clinical starting point to build upon. The highly malignant brain tumor glioblastoma (GBM) exemplifies such a refractory cancer, with only 15 month average patient survival. Analyses of several hundred GBM samples compiled by the TCGA (The Cancer Genome Atlas) have produced an extensive transcriptomic map, identified prevalent chromosomal alterations, and defined important driver mutations. Unfortunately, clinical trials based on these results have not yet delivered an improvement on outcome. It is, therefore, necessary to characterize other regulatory routes known for playing a role in tumor relapse and response to treatment. Alternative splicing affects more than 90% of the human coding genes and it is an important source for transcript variation and gene regulation. Mutations and alterations in splicing factors are highly prevalent in multiple cancers, demonstrating the potential for splicing to act as a tumor driver. As a result, numerous genes are expressed as cancer-specific splicing isoforms that are functionally distinct from the canonical isoforms found in normal tissue. These include genes that regulate cancer-critical pathways such as apoptosis, DNA repair, cell proliferation, and migration. Splicing defects can even induce genomic instability, a common characteristic of cancer, and a driver of tumor evolution. Importantly, components of the splicing machinery are targetable; multiple drugs can inhibit splicing factors or promote changes in splicing which could be exploited to begin improving clinical outcomes. Here, we review the current literature and present a case for exploring RNA processing as therapeutic route for the treatment of GBM.
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66
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Splicing modulators act at the branch point adenosine binding pocket defined by the PHF5A-SF3b complex. Nat Commun 2017; 8:15522. [PMID: 28541300 PMCID: PMC5458519 DOI: 10.1038/ncomms15522] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 04/05/2017] [Indexed: 01/28/2023] Open
Abstract
Pladienolide, herboxidiene and spliceostatin have been identified as splicing modulators that target SF3B1 in the SF3b subcomplex. Here we report that PHF5A, another component of this subcomplex, is also targeted by these compounds. Mutations in PHF5A-Y36, SF3B1-K1071, SF3B1-R1074 and SF3B1-V1078 confer resistance to these modulators, suggesting a common interaction site. RNA-seq analysis reveals that PHF5A-Y36C has minimal effect on basal splicing but inhibits the global action of splicing modulators. Moreover, PHF5A-Y36C alters splicing modulator-induced intron-retention/exon-skipping profile, which correlates with the differential GC content between adjacent introns and exons. We determine the crystal structure of human PHF5A demonstrating that Y36 is located on a highly conserved surface. Analysis of the cryo-EM spliceosome Bact complex shows that the resistance mutations cluster in a pocket surrounding the branch point adenosine, suggesting a competitive mode of action. Collectively, we propose that PHF5A–SF3B1 forms a central node for binding to these splicing modulators. A number of natural occurring small-molecule splicing modulators are known. Here, the authors combine chemogenomic, structural and biochemical methods and show that these compounds also target the spliceosome-associated protein PHF5A and propose a potential modulator binding site in the PHF5A–SF3B1 complex.
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67
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O'Duibhir E, Carragher NO, Pollard SM. Accelerating glioblastoma drug discovery: Convergence of patient-derived models, genome editing and phenotypic screening. Mol Cell Neurosci 2017; 80:198-207. [PMID: 27825983 PMCID: PMC6128397 DOI: 10.1016/j.mcn.2016.11.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 10/05/2016] [Accepted: 11/02/2016] [Indexed: 12/27/2022] Open
Abstract
Patients diagnosed with glioblastoma (GBM) continue to face a bleak prognosis. It is critical that new effective therapeutic strategies are developed. GBM stem cells have molecular hallmarks of neural stem and progenitor cells and it is possible to propagate both non-transformed normal neural stem cells and GBM stem cells, in defined, feeder-free, adherent culture. These primary stem cell lines provide an experimental model that is ideally suited to cell-based drug discovery or genetic screens in order to identify tumour-specific vulnerabilities. For many solid tumours, including GBM, the genetic disruptions that drive tumour initiation and growth have now been catalogued. CRISPR/Cas-based genome editing technologies have recently emerged, transforming our ability to functionally annotate the human genome. Genome editing opens prospects for engineering precise genetic changes in normal and GBM-derived neural stem cells, which will provide more defined and reliable genetic models, with critical matched pairs of isogenic cell lines. Generation of more complex alleles such as knock in tags or fluorescent reporters is also now possible. These new cellular models can be deployed in cell-based phenotypic drug discovery (PDD). Here we discuss the convergence of these advanced technologies (iPS cells, neural stem cell culture, genome editing and high content phenotypic screening) and how they herald a new era in human cellular genetics that should have a major impact in accelerating glioblastoma drug discovery.
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Affiliation(s)
- Eoghan O'Duibhir
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK; Institute of Genetics and Molecular Medicine, CRUK Edinburgh Centre, University of Edinburgh, UK
| | - Neil O Carragher
- Institute of Genetics and Molecular Medicine, CRUK Edinburgh Centre, University of Edinburgh, UK.
| | - Steven M Pollard
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK; Institute of Genetics and Molecular Medicine, CRUK Edinburgh Centre, University of Edinburgh, UK.
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68
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Bressan RB, Dewari PS, Kalantzaki M, Gangoso E, Matjusaitis M, Garcia-Diaz C, Blin C, Grant V, Bulstrode H, Gogolok S, Skarnes WC, Pollard SM. Efficient CRISPR/Cas9-assisted gene targeting enables rapid and precise genetic manipulation of mammalian neural stem cells. Development 2017; 144:635-648. [PMID: 28096221 PMCID: PMC5312033 DOI: 10.1242/dev.140855] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 12/15/2016] [Indexed: 01/09/2023]
Abstract
Mammalian neural stem cell (NSC) lines provide a tractable model for discovery across stem cell and developmental biology, regenerative medicine and neuroscience. They can be derived from foetal or adult germinal tissues and continuously propagated in vitro as adherent monolayers. NSCs are clonally expandable, genetically stable, and easily transfectable - experimental attributes compatible with targeted genetic manipulations. However, gene targeting, which is crucial for functional studies of embryonic stem cells, has not been exploited to date in NSC lines. Here, we deploy CRISPR/Cas9 technology to demonstrate a variety of sophisticated genetic modifications via gene targeting in both mouse and human NSC lines, including: (1) efficient targeted transgene insertion at safe harbour loci (Rosa26 and AAVS1); (2) biallelic knockout of neurodevelopmental transcription factor genes; (3) simple knock-in of epitope tags and fluorescent reporters (e.g. Sox2-V5 and Sox2-mCherry); and (4) engineering of glioma mutations (TP53 deletion; H3F3A point mutations). These resources and optimised methods enable facile and scalable genome editing in mammalian NSCs, providing significant new opportunities for functional genetic analysis.
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Affiliation(s)
| | - Pooran Singh Dewari
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Maria Kalantzaki
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Ester Gangoso
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Mantas Matjusaitis
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Claudia Garcia-Diaz
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Carla Blin
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Vivien Grant
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Harry Bulstrode
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Sabine Gogolok
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - William C Skarnes
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Steven M Pollard
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
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69
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Suda K, Rozeboom L, Yu H, Ellison K, Rivard CJ, Mitsudomi T, Hirsch FR. Potential effect of spliceosome inhibition in small cell lung cancer irrespective of the MYC status. PLoS One 2017; 12:e0172209. [PMID: 28192473 PMCID: PMC5305228 DOI: 10.1371/journal.pone.0172209] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 02/01/2017] [Indexed: 11/18/2022] Open
Abstract
Small cell lung cancer (SCLC) is a highly aggressive malignancy with few therapeutic advances in the treatment in recent decades. Based on a recent study that identified the spliceosome as a therapeutic vulnerability in MYC-driven breast cancers, we evaluated the efficacy of a spliceosome inhibitor in SCLC cell lines and analyzed the correlation with MYC status. Among 23 SCLC cell lines examined, eight showed high MYC protein expression (> 80% positive cells) by immunohistochemistry (IHC), while 10 cell lines demonstrated no staining for MYC. The remaining five cell lines showed weak staining (< 40% positive cells). All four cell lines that were previously demonstrated to have MYC gene amplification were positive for MYC by IHC. Four cell lines with high MYC expression and four with low MYC expression were used in further analysis. A spliceosome inhibitor, pladienolide B, showed high efficacy (IC50 < 12nM) in all eight cell lines tested, irrespective of the MYC IHC or MYC gene amplification status. We observed that the four cell lines with higher sensitivity to the spliceosome inhibitor were established from patients with prior chemotherapy. Therefore we chronically treated H1048 cells, that were established from a treatment-naïve patient, with cisplatin for 4 weeks, and found that H1048-cisplatin treated cells became more sensitive to pladienolide B. In conclusion, our in vitro results indicate that spliceosome inhibitors would be promising molecular target drugs in SCLC irrespective of the MYC status, especially in the second-line settings after an effective front-line chemotherapy.
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Affiliation(s)
- Kenichi Suda
- Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America.,Division of Thoracic Surgery, Department of Surgery, Kindai University Faculty of Medicine, Osaka-Sayama, Japan
| | - Leslie Rozeboom
- Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Hui Yu
- Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Kim Ellison
- Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Christopher J Rivard
- Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Tetsuya Mitsudomi
- Division of Thoracic Surgery, Department of Surgery, Kindai University Faculty of Medicine, Osaka-Sayama, Japan
| | - Fred R Hirsch
- Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
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70
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Screen for reactivation of MeCP2 on the inactive X chromosome identifies the BMP/TGF-β superfamily as a regulator of XIST expression. Proc Natl Acad Sci U S A 2017; 114:1619-1624. [PMID: 28143937 DOI: 10.1073/pnas.1621356114] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Rett syndrome (RS) is a debilitating neurological disorder affecting mostly girls with heterozygous mutations in the gene encoding the methyl-CpG-binding protein MeCP2 on the X chromosome. Because restoration of MeCP2 expression in a mouse model reverses neurologic deficits in adult animals, reactivation of the wild-type copy of MeCP2 on the inactive X chromosome (Xi) presents a therapeutic opportunity in RS. To identify genes involved in MeCP2 silencing, we screened a library of 60,000 shRNAs using a cell line with a MeCP2 reporter on the Xi and found 30 genes clustered in seven functional groups. More than half encoded proteins with known enzymatic activity, and six were members of the bone morphogenetic protein (BMP)/TGF-β pathway. shRNAs directed against each of these six genes down-regulated X-inactive specific transcript (XIST), a key player in X-chromosome inactivation that encodes an RNA that coats the silent X chromosome, and modulation of regulators of this pathway both in cell culture and in mice demonstrated robust regulation of XIST. Moreover, we show that Rnf12, an X-encoded ubiquitin ligase important for initiation of X-chromosome inactivation and XIST transcription in ES cells, also plays a role in maintenance of the inactive state through regulation of BMP/TGF-β signaling. Our results identify pharmacologically suitable targets for reactivation of MeCP2 on the Xi and a genetic circuitry that maintains XIST expression and X-chromosome inactivation in differentiated cells.
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71
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Abstract
Single-cell cell cycle analysis is an emerging technique that requires detailed exploration of the image analysis process. In this study, we established a microfluidic single-cell cell cycle analysis method that can analyze cells in small numbers and in situ on a microfluidic chip. In addition, factors that influenced the analysis were carefully investigated. U87 or HeLa cells were seeded and attached to microfluidic channels before measurement. Cell nucleic DNA was imaged by 4′-6-diamidino-2-phenylindole (DAPI) staining under a fluorescent microscope and subsequently fluorescent intensities of the cell nuclei DNA were converted to depict histograms for cell cycle phases. DAPI concentration, microscopic magnification, exposure time and cell number were examined for optimal cell cycle analysis conditions. The results showed that as few as a few hundred cells could be measured by DAPI staining in the range of 0.4–0.6 μg/mL to depict histograms with typical cell cycle phase distribution. Microscopic magnification during image acquisition, however, could distort the phase distribution. Exposure time did not significantly affect the cell cycle analysis. Furthermore, cell cycle inhibitor rapamycin treatment changed the cell cycle phase distribution as expected. In conclusion, a method for microfluidic single-cell cell cycle analysis of spread cells in situ was developed. Factors such as dye concentration and microscopic magnification had more influence on cell cycle phase distribution. Further studies will focus on detail differentiation of cell cycle phases and the application of such a method for biological meanings.
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72
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Makowski K, Vigevani L, Albericio F, Valcárcel J, Álvarez M. Sudemycin K: A Synthetic Antitumor Splicing Inhibitor Variant with Improved Activity and Versatile Chemistry. ACS Chem Biol 2017; 12:163-173. [PMID: 28103691 DOI: 10.1021/acschembio.6b00562] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Important links exist between the process of pre-mRNA splicing and cancer, as illustrated by the frequent mutation of splicing factors in tumors and the emergence of various families of antitumor drugs that target components of the splicing machinery, notably SF3B1, a protein subunit of spliceosomal U2 small nuclear ribonucleoprotein particle (snRNP). Sudemycins are synthetic compounds that harbor a pharmacophore common to various classes of splicing inhibitors. Here, we describe the synthesis and functional characterization of novel sudemycin analogues that functionally probe key chemical groups within this pharmacophore. Our results confirm the importance of a conjugated diene group and in addition reveal significant spatial flexibility in this region of the molecule. Sudemycin K, a derivative that replaces the pharmacophore's oxycarbonyl by an amide group, displays improved potency as an inhibitor of cancer cell proliferation, as a regulator of alternative splicing in cultured cells and as an inhibitor of in vitro spliceosome assembly. Sudemycin K displays higher stability, likely related to the replacement of the oxycarbonyl group, which can be a substrate of esterases, by an amide group. The activity and special reactivity of sudemycin K can pave the way to the synthesis and evaluation of a variety of novel sudemycin derivatives.
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Affiliation(s)
- Kamil Makowski
- Centre
for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- Institute for Research in Biomedicine (IRB-Barcelona), Baldiri i Reixac 10, 08028, Barcelona, Spain
| | - Luisa Vigevani
- Centre
for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr.
Aiguader 88, 08003 Barcelona, Spain
| | - Fernando Albericio
- Institute for Research in Biomedicine (IRB-Barcelona), Baldiri i Reixac 10, 08028, Barcelona, Spain
- Department
of Organic Chemistry, Faculty of Chemistry, University of Barcelona, Martí Franqués 1, 08028 Barcelona,Spain
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona, Spain
| | - Juan Valcárcel
- Centre
for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr.
Aiguader 88, 08003 Barcelona, Spain
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Mercedes Álvarez
- Institute for Research in Biomedicine (IRB-Barcelona), Baldiri i Reixac 10, 08028, Barcelona, Spain
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona, Spain
- Laboratory
of Organic Chemistry, Faculty of Pharmacy, University of Barcelona, Joan XXIII s/n, 08028 Barcelona, Spain
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73
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Shi Y, Park J, Lagisetti C, Zhou W, Sambucetti LC, Webb TR. A triple exon-skipping luciferase reporter assay identifies a new CLK inhibitor pharmacophore. Bioorg Med Chem Lett 2016; 27:406-412. [PMID: 28049589 DOI: 10.1016/j.bmcl.2016.12.056] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 12/20/2016] [Accepted: 12/21/2016] [Indexed: 12/19/2022]
Abstract
The splicing of pre-mRNA is a critical process in normal cells and is deregulated in cancer. Compounds that modulate this process have recently been shown to target a specific vulnerability in tumors. We have developed a novel cell-based assay that specifically activates luciferase in cells exposed to SF3B1 targeted compounds, such as sudemycin D6. This assay was used to screen a combined collection of approved drugs and bioactive compounds. This screening approach identified several active hits, the most potent of which were CGP-74514A and aminopurvalanol A, both have been reported to be cyclin-dependent kinases (CDKs) inhibitors. We found that these compounds, and their analogs, show significant cdc2-like kinase (CLK) inhibition and clear structure-activity relationships (SAR) at CLKs. We prepared a set of analogs and were able to 'dial out' the CDK activity and simultaneously developed CLK inhibitors with low nanomolar activity. Thus, we have demonstrated the utility of our exon-skipping assay and identified new molecules that exhibit potency and selectivity for CLK, as well as some structurally related dual CLK/CDK inhibitors.
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Affiliation(s)
- Yihui Shi
- Division of Biosciences, SRI International, 333 Ravenswood Ave., Menlo Park, CA 94025, USA
| | - Jaehyeon Park
- Division of Biosciences, SRI International, 333 Ravenswood Ave., Menlo Park, CA 94025, USA
| | - Chandraiah Lagisetti
- Division of Biosciences, SRI International, 333 Ravenswood Ave., Menlo Park, CA 94025, USA
| | - Wei Zhou
- Division of Biosciences, SRI International, 333 Ravenswood Ave., Menlo Park, CA 94025, USA
| | - Lidia C Sambucetti
- Division of Biosciences, SRI International, 333 Ravenswood Ave., Menlo Park, CA 94025, USA
| | - Thomas R Webb
- Division of Biosciences, SRI International, 333 Ravenswood Ave., Menlo Park, CA 94025, USA.
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Yoshimi A, Abdel-Wahab O. Molecular Pathways: Understanding and Targeting Mutant Spliceosomal Proteins. Clin Cancer Res 2016; 23:336-341. [PMID: 27836865 DOI: 10.1158/1078-0432.ccr-16-0131] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 10/09/2016] [Accepted: 10/11/2016] [Indexed: 02/06/2023]
Abstract
Splicing of precursor messenger RNA is a critical step in regulating gene expression, and major advances are being made in understanding the composition and structure of the enzymatic complex that performs splicing, which is termed the "spliceosome." In parallel, there has been increased appreciation for diverse mechanisms by which alterations in splicing contribute to cancer pathogenesis. Key among these include change-of-function mutations in genes encoding spliceosomal proteins. Such mutations are among the most common genetic alterations in myeloid and lymphoid leukemias, making efforts to therapeutically target cells bearing these mutations critical. To this end, recent studies have clarified that pharmacologic modulation of splicing may be preferentially lethal for cells bearing spliceosomal mutations and may also have a role in the therapy of MYC-driven cancers. This has culminated in the initiation of a clinical trial of a novel oral spliceosome modulatory compound targeting the SF3B complex, and several novel alternative approaches to target splicing are in development as reviewed here. There is now, therefore, a great need to understand the mechanistic basis of altered spliceosomal function in cancers and to study the effects of spliceosomal modulatory compounds in preclinical settings and in well-designed clinical trials. Clin Cancer Res; 23(2); 336-41. ©2016 AACR.
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Affiliation(s)
- Akihide Yoshimi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York.
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
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75
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Strikoudis A, Lazaris C, Trimarchi T, Galvao Neto AL, Yang Y, Ntziachristos P, Rothbart S, Buckley S, Dolgalev I, Stadtfeld M, Strahl BD, Dynlacht BD, Tsirigos A, Aifantis I. Regulation of transcriptional elongation in pluripotency and cell differentiation by the PHD-finger protein Phf5a. Nat Cell Biol 2016; 18:1127-1138. [PMID: 27749823 PMCID: PMC5083132 DOI: 10.1038/ncb3424] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 09/15/2016] [Indexed: 12/12/2022]
Abstract
Pluripotent embryonic stem cells (ESCs) self-renew or differentiate into all tissues of the developing embryo and cell-specification factors are necessary to balance gene expression. Here we delineate the function of the PHD-finger protein 5a (Phf5a) in ESC self-renewal and ascribe its role in regulating pluripotency, cellular reprogramming, and myoblast specification. We demonstrate that Phf5a is essential for maintaining pluripotency, since depleted ESCs exhibit hallmarks of differentiation. Mechanistically, we attribute Phf5a function to the stabilization of the Paf1 transcriptional complex and control of RNA polymerase II elongation on pluripotency loci. Apart from an ESC-specific factor, we demonstrate that Phf5a controls differentiation of adult myoblasts. Our findings suggest a potent mode of regulation by the Phf5a in stem cells, which directs their transcriptional program ultimately regulating maintenance of pluripotency and cellular reprogramming.
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Affiliation(s)
- Alexandros Strikoudis
- Department of Pathology, NYU School of Medicine, New York, New York 10016, USA.,Laura &Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York 10016, USA.,Helen L. &Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, New York 10016, USA
| | - Charalampos Lazaris
- Department of Pathology, NYU School of Medicine, New York, New York 10016, USA.,Laura &Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York 10016, USA.,Helen L. &Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, New York 10016, USA.,Center for Health Informatics and Bioinformatics, NYU School of Medicine, New York, New York 10016, USA
| | - Thomas Trimarchi
- Department of Pathology, NYU School of Medicine, New York, New York 10016, USA.,Laura &Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York 10016, USA.,Helen L. &Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, New York 10016, USA
| | - Antonio L Galvao Neto
- Department of Pathology, NYU School of Medicine, New York, New York 10016, USA.,Ronald O. Perelman Department of Dermatology, NYU School of Medicine, New York, New York 10016, USA
| | - Yan Yang
- Department of Pathology, NYU School of Medicine, New York, New York 10016, USA.,Laura &Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York 10016, USA
| | - Panagiotis Ntziachristos
- Department of Pathology, NYU School of Medicine, New York, New York 10016, USA.,Laura &Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York 10016, USA.,Helen L. &Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, New York 10016, USA
| | - Scott Rothbart
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, North Carolina 27599, USA
| | - Shannon Buckley
- Department of Pathology, NYU School of Medicine, New York, New York 10016, USA.,Laura &Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York 10016, USA.,Helen L. &Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, New York 10016, USA
| | - Igor Dolgalev
- Department of Pathology, NYU School of Medicine, New York, New York 10016, USA.,Laura &Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York 10016, USA.,Helen L. &Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, New York 10016, USA.,Center for Health Informatics and Bioinformatics, NYU School of Medicine, New York, New York 10016, USA.,Genome Technology Center, Office of Collaborative Science, NYU School of Medicine, New York, New York 10016, USA
| | - Matthias Stadtfeld
- Helen L. &Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, New York 10016, USA.,Department of Cell Biology, NYU School of Medicine, New York, New York 10016, USA
| | - Brian D Strahl
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, North Carolina 27599, USA
| | - Brian D Dynlacht
- Department of Pathology, NYU School of Medicine, New York, New York 10016, USA.,Laura &Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York 10016, USA
| | - Aristotelis Tsirigos
- Department of Pathology, NYU School of Medicine, New York, New York 10016, USA.,Laura &Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York 10016, USA.,Center for Health Informatics and Bioinformatics, NYU School of Medicine, New York, New York 10016, USA
| | - Iannis Aifantis
- Department of Pathology, NYU School of Medicine, New York, New York 10016, USA.,Laura &Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York 10016, USA.,Helen L. &Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, New York 10016, USA
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Li Y, Min W, Li M, Han G, Dai D, Zhang L, Chen X, Wang X, Zhang Y, Yue Z, Liu J. Identification of hub genes and regulatory factors of glioblastoma multiforme subgroups by RNA-seq data analysis. Int J Mol Med 2016; 38:1170-8. [PMID: 27572852 PMCID: PMC5029949 DOI: 10.3892/ijmm.2016.2717] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 08/04/2016] [Indexed: 11/24/2022] Open
Abstract
Glioblastoma multiforme (GBM) is the most common malignant brain tumor. This study aimed to identify the hub genes and regulatory factors of GBM subgroups by RNA sequencing (RNA-seq) data analysis, in order to explore the possible mechanisms responsbile for the progression of GBM. The dataset RNASeqV2 was downloaded by TCGA-Assembler, containing 169 GBM and 5 normal samples. Gene expression was calculated by the reads per kilobase per million reads measurement, and nor malized with tag count comparison. Following subgroup classification by the non-negative matrix factorization, the differentially expressed genes (DEGs) were screened in 4 GBM subgroups using the method of significance analysis of microarrays. Functional enrichment analysis was performed by DAVID, and the protein-protein interaction (PPI) network was constructed based on the HPRD database. The subgroup-related microRNAs (miRNAs or miRs), transcription factors (TFs) and small molecule drugs were predicted with predefined criteria. A cohort of 19,515 DEGs between the GBM and control samples was screened, which were predominantly enriched in cell cycle- and immunoreaction-related pathways. In the PPI network, lymphocyte cytosolic protein 2 (LCP2), breast cancer 1 (BRCA1), specificity protein 1 (Sp1) and chromodomain-helicase-DNA-binding protein 3 (CHD3) were the hub nodes in subgroups 1–4, respectively. Paired box 5 (PAX5), adipocyte protein 2 (aP2), E2F transcription factor 1 (E2F1) and cAMP-response element-binding protein-1 (CREB1) were the specific TFs in subgroups 1–4, respectively. miR-147b, miR-770-5p, miR-220a and miR-1247 were the particular miRNAs in subgroups 1–4, respectively. Natalizumab was the predicted small molecule drug in subgroup 2. In conclusion, the molecular regulatory mechanisms of GBM pathogenesis were distinct in the different subgroups. Several crucial genes, TFs, miRNAs and small molecules in the different GBM subgroups were identified, which may be used as potential markers. However, further experimental validations may be required.
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Affiliation(s)
- Yanan Li
- Department of Neurosurgery, Changhai Hospital, The Second Military Medical University, Shanghai 200433, P.R. China
| | - Weijie Min
- Department of Neurosurgery, Changhai Hospital, The Second Military Medical University, Shanghai 200433, P.R. China
| | - Mengmeng Li
- Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, The Second Military Medical University, Shanghai 200003, P.R. China
| | - Guosheng Han
- Department of Neurosurgery, Changhai Hospital, The Second Military Medical University, Shanghai 200433, P.R. China
| | - Dongwei Dai
- Department of Neurosurgery, Changhai Hospital, The Second Military Medical University, Shanghai 200433, P.R. China
| | - Lei Zhang
- Department of Neurosurgery, Changhai Hospital, The Second Military Medical University, Shanghai 200433, P.R. China
| | - Xin Chen
- Department of Neurosurgery, Changhai Hospital, The Second Military Medical University, Shanghai 200433, P.R. China
| | - Xinglai Wang
- Department of Neurosurgery, Changhai Hospital, The Second Military Medical University, Shanghai 200433, P.R. China
| | - Yuhui Zhang
- Department of Neurosurgery, Changhai Hospital, The Second Military Medical University, Shanghai 200433, P.R. China
| | - Zhijian Yue
- Department of Neurosurgery, Changhai Hospital, The Second Military Medical University, Shanghai 200433, P.R. China
| | - Jianmin Liu
- Department of Neurosurgery, Changhai Hospital, The Second Military Medical University, Shanghai 200433, P.R. China
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Abstract
The recent genomic characterization of cancers has revealed recurrent somatic point mutations and copy number changes affecting genes encoding RNA splicing factors. Initial studies of these 'spliceosomal mutations' suggest that the proteins bearing these mutations exhibit altered splice site and/or exon recognition preferences relative to their wild-type counterparts, resulting in cancer-specific mis-splicing. Such changes in the splicing machinery may create novel vulnerabilities in cancer cells that can be therapeutically exploited using compounds that can influence the splicing process. Further studies to dissect the biochemical, genomic and biological effects of spliceosomal mutations are crucial for the development of cancer therapies targeted at these mutations.
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Affiliation(s)
- Heidi Dvinge
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Eunhee Kim
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Leukemia Service, Dept. of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Robert K. Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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Levin VA, Tonge PJ, Gallo JM, Birtwistle MR, Dar AC, Iavarone A, Paddison PJ, Heffron TP, Elmquist WF, Lachowicz JE, Johnson TW, White FM, Sul J, Smith QR, Shen W, Sarkaria JN, Samala R, Wen PY, Berry DA, Petter RC. CNS Anticancer Drug Discovery and Development Conference White Paper. Neuro Oncol 2016; 17 Suppl 6:vi1-26. [PMID: 26403167 DOI: 10.1093/neuonc/nov169] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Following the first CNS Anticancer Drug Discovery and Development Conference, the speakers from the first 4 sessions and organizers of the conference created this White Paper hoping to stimulate more and better CNS anticancer drug discovery and development. The first part of the White Paper reviews, comments, and, in some cases, expands on the 4 session areas critical to new drug development: pharmacological challenges, recent drug approaches, drug targets and discovery, and clinical paths. Following this concise review of the science and clinical aspects of new CNS anticancer drug discovery and development, we discuss, under the rubric "Accelerating Drug Discovery and Development for Brain Tumors," further reasons why the pharmaceutical industry and academia have failed to develop new anticancer drugs for CNS malignancies and what it will take to change the current status quo and develop the drugs so desperately needed by our patients with malignant CNS tumors. While this White Paper is not a formal roadmap to that end, it should be an educational guide to clinicians and scientists to help move a stagnant field forward.
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Affiliation(s)
- Victor A Levin
- Kaiser Permanente, Redwood City, California, USA (V.A.L.); University of Texas MD Anderson Cancer Center, Houston, TX, USA (V.A.L.); University of California, San Francisco, CA, USA (V.A.L.); SUNY Stony Brook University, Stony Brook, NY, USA (P.J.T.); Icahn School of Medicine at Mount Sinai, New York, NY, USA (J.M.G., M.R.B., A.C.D.); Columbia University Institute for Cancer Genetics, New York, NY, USA (A.I.); Fred Hutchinson Cancer Research Center, Seattle, WA, USA (P.J.P.); Genentech, Inc., South San Francisco, CA, USA (T.P.H.); University of Minnesota School of Pharmacy, Minneapolis, MN, USA (W.F.E.); Angiochem, Inc., Montreal, Quebec, Canada (J.E.L.); Pfizer Oncology, San Diego, CA, USA (T.W.J.); Massachusetts Institute of Technology, Cambridge, MA, USA (F.M.W.); US Food and Drug Administration, Silver Spring, MD, USA (J.S.); Texas Tech University School of Pharmacy, Amarillo, TX, USA (Q.R.S., R.S.); NewGen Therapeutics, Inc., Menlo Park, CA, USA (W.S.); Mayo Clinic, Rochester, MN, USA (J.N.S.); Dana-Farber Cancer Institute, Boston, MA, USA (P.Y.W.); University of Texas MD Anderson Cancer Center, Houston, TX, USA (D.A.B.); Celgene Avilomics Research, Bedford, MA, USA (R.C.P.)
| | - Peter J Tonge
- Kaiser Permanente, Redwood City, California, USA (V.A.L.); University of Texas MD Anderson Cancer Center, Houston, TX, USA (V.A.L.); University of California, San Francisco, CA, USA (V.A.L.); SUNY Stony Brook University, Stony Brook, NY, USA (P.J.T.); Icahn School of Medicine at Mount Sinai, New York, NY, USA (J.M.G., M.R.B., A.C.D.); Columbia University Institute for Cancer Genetics, New York, NY, USA (A.I.); Fred Hutchinson Cancer Research Center, Seattle, WA, USA (P.J.P.); Genentech, Inc., South San Francisco, CA, USA (T.P.H.); University of Minnesota School of Pharmacy, Minneapolis, MN, USA (W.F.E.); Angiochem, Inc., Montreal, Quebec, Canada (J.E.L.); Pfizer Oncology, San Diego, CA, USA (T.W.J.); Massachusetts Institute of Technology, Cambridge, MA, USA (F.M.W.); US Food and Drug Administration, Silver Spring, MD, USA (J.S.); Texas Tech University School of Pharmacy, Amarillo, TX, USA (Q.R.S., R.S.); NewGen Therapeutics, Inc., Menlo Park, CA, USA (W.S.); Mayo Clinic, Rochester, MN, USA (J.N.S.); Dana-Farber Cancer Institute, Boston, MA, USA (P.Y.W.); University of Texas MD Anderson Cancer Center, Houston, TX, USA (D.A.B.); Celgene Avilomics Research, Bedford, MA, USA (R.C.P.)
| | - James M Gallo
- Kaiser Permanente, Redwood City, California, USA (V.A.L.); University of Texas MD Anderson Cancer Center, Houston, TX, USA (V.A.L.); University of California, San Francisco, CA, USA (V.A.L.); SUNY Stony Brook University, Stony Brook, NY, USA (P.J.T.); Icahn School of Medicine at Mount Sinai, New York, NY, USA (J.M.G., M.R.B., A.C.D.); Columbia University Institute for Cancer Genetics, New York, NY, USA (A.I.); Fred Hutchinson Cancer Research Center, Seattle, WA, USA (P.J.P.); Genentech, Inc., South San Francisco, CA, USA (T.P.H.); University of Minnesota School of Pharmacy, Minneapolis, MN, USA (W.F.E.); Angiochem, Inc., Montreal, Quebec, Canada (J.E.L.); Pfizer Oncology, San Diego, CA, USA (T.W.J.); Massachusetts Institute of Technology, Cambridge, MA, USA (F.M.W.); US Food and Drug Administration, Silver Spring, MD, USA (J.S.); Texas Tech University School of Pharmacy, Amarillo, TX, USA (Q.R.S., R.S.); NewGen Therapeutics, Inc., Menlo Park, CA, USA (W.S.); Mayo Clinic, Rochester, MN, USA (J.N.S.); Dana-Farber Cancer Institute, Boston, MA, USA (P.Y.W.); University of Texas MD Anderson Cancer Center, Houston, TX, USA (D.A.B.); Celgene Avilomics Research, Bedford, MA, USA (R.C.P.)
| | - Marc R Birtwistle
- Kaiser Permanente, Redwood City, California, USA (V.A.L.); University of Texas MD Anderson Cancer Center, Houston, TX, USA (V.A.L.); University of California, San Francisco, CA, USA (V.A.L.); SUNY Stony Brook University, Stony Brook, NY, USA (P.J.T.); Icahn School of Medicine at Mount Sinai, New York, NY, USA (J.M.G., M.R.B., A.C.D.); Columbia University Institute for Cancer Genetics, New York, NY, USA (A.I.); Fred Hutchinson Cancer Research Center, Seattle, WA, USA (P.J.P.); Genentech, Inc., South San Francisco, CA, USA (T.P.H.); University of Minnesota School of Pharmacy, Minneapolis, MN, USA (W.F.E.); Angiochem, Inc., Montreal, Quebec, Canada (J.E.L.); Pfizer Oncology, San Diego, CA, USA (T.W.J.); Massachusetts Institute of Technology, Cambridge, MA, USA (F.M.W.); US Food and Drug Administration, Silver Spring, MD, USA (J.S.); Texas Tech University School of Pharmacy, Amarillo, TX, USA (Q.R.S., R.S.); NewGen Therapeutics, Inc., Menlo Park, CA, USA (W.S.); Mayo Clinic, Rochester, MN, USA (J.N.S.); Dana-Farber Cancer Institute, Boston, MA, USA (P.Y.W.); University of Texas MD Anderson Cancer Center, Houston, TX, USA (D.A.B.); Celgene Avilomics Research, Bedford, MA, USA (R.C.P.)
| | - Arvin C Dar
- Kaiser Permanente, Redwood City, California, USA (V.A.L.); University of Texas MD Anderson Cancer Center, Houston, TX, USA (V.A.L.); University of California, San Francisco, CA, USA (V.A.L.); SUNY Stony Brook University, Stony Brook, NY, USA (P.J.T.); Icahn School of Medicine at Mount Sinai, New York, NY, USA (J.M.G., M.R.B., A.C.D.); Columbia University Institute for Cancer Genetics, New York, NY, USA (A.I.); Fred Hutchinson Cancer Research Center, Seattle, WA, USA (P.J.P.); Genentech, Inc., South San Francisco, CA, USA (T.P.H.); University of Minnesota School of Pharmacy, Minneapolis, MN, USA (W.F.E.); Angiochem, Inc., Montreal, Quebec, Canada (J.E.L.); Pfizer Oncology, San Diego, CA, USA (T.W.J.); Massachusetts Institute of Technology, Cambridge, MA, USA (F.M.W.); US Food and Drug Administration, Silver Spring, MD, USA (J.S.); Texas Tech University School of Pharmacy, Amarillo, TX, USA (Q.R.S., R.S.); NewGen Therapeutics, Inc., Menlo Park, CA, USA (W.S.); Mayo Clinic, Rochester, MN, USA (J.N.S.); Dana-Farber Cancer Institute, Boston, MA, USA (P.Y.W.); University of Texas MD Anderson Cancer Center, Houston, TX, USA (D.A.B.); Celgene Avilomics Research, Bedford, MA, USA (R.C.P.)
| | - Antonio Iavarone
- Kaiser Permanente, Redwood City, California, USA (V.A.L.); University of Texas MD Anderson Cancer Center, Houston, TX, USA (V.A.L.); University of California, San Francisco, CA, USA (V.A.L.); SUNY Stony Brook University, Stony Brook, NY, USA (P.J.T.); Icahn School of Medicine at Mount Sinai, New York, NY, USA (J.M.G., M.R.B., A.C.D.); Columbia University Institute for Cancer Genetics, New York, NY, USA (A.I.); Fred Hutchinson Cancer Research Center, Seattle, WA, USA (P.J.P.); Genentech, Inc., South San Francisco, CA, USA (T.P.H.); University of Minnesota School of Pharmacy, Minneapolis, MN, USA (W.F.E.); Angiochem, Inc., Montreal, Quebec, Canada (J.E.L.); Pfizer Oncology, San Diego, CA, USA (T.W.J.); Massachusetts Institute of Technology, Cambridge, MA, USA (F.M.W.); US Food and Drug Administration, Silver Spring, MD, USA (J.S.); Texas Tech University School of Pharmacy, Amarillo, TX, USA (Q.R.S., R.S.); NewGen Therapeutics, Inc., Menlo Park, CA, USA (W.S.); Mayo Clinic, Rochester, MN, USA (J.N.S.); Dana-Farber Cancer Institute, Boston, MA, USA (P.Y.W.); University of Texas MD Anderson Cancer Center, Houston, TX, USA (D.A.B.); Celgene Avilomics Research, Bedford, MA, USA (R.C.P.)
| | - Patrick J Paddison
- Kaiser Permanente, Redwood City, California, USA (V.A.L.); University of Texas MD Anderson Cancer Center, Houston, TX, USA (V.A.L.); University of California, San Francisco, CA, USA (V.A.L.); SUNY Stony Brook University, Stony Brook, NY, USA (P.J.T.); Icahn School of Medicine at Mount Sinai, New York, NY, USA (J.M.G., M.R.B., A.C.D.); Columbia University Institute for Cancer Genetics, New York, NY, USA (A.I.); Fred Hutchinson Cancer Research Center, Seattle, WA, USA (P.J.P.); Genentech, Inc., South San Francisco, CA, USA (T.P.H.); University of Minnesota School of Pharmacy, Minneapolis, MN, USA (W.F.E.); Angiochem, Inc., Montreal, Quebec, Canada (J.E.L.); Pfizer Oncology, San Diego, CA, USA (T.W.J.); Massachusetts Institute of Technology, Cambridge, MA, USA (F.M.W.); US Food and Drug Administration, Silver Spring, MD, USA (J.S.); Texas Tech University School of Pharmacy, Amarillo, TX, USA (Q.R.S., R.S.); NewGen Therapeutics, Inc., Menlo Park, CA, USA (W.S.); Mayo Clinic, Rochester, MN, USA (J.N.S.); Dana-Farber Cancer Institute, Boston, MA, USA (P.Y.W.); University of Texas MD Anderson Cancer Center, Houston, TX, USA (D.A.B.); Celgene Avilomics Research, Bedford, MA, USA (R.C.P.)
| | - Timothy P Heffron
- Kaiser Permanente, Redwood City, California, USA (V.A.L.); University of Texas MD Anderson Cancer Center, Houston, TX, USA (V.A.L.); University of California, San Francisco, CA, USA (V.A.L.); SUNY Stony Brook University, Stony Brook, NY, USA (P.J.T.); Icahn School of Medicine at Mount Sinai, New York, NY, USA (J.M.G., M.R.B., A.C.D.); Columbia University Institute for Cancer Genetics, New York, NY, USA (A.I.); Fred Hutchinson Cancer Research Center, Seattle, WA, USA (P.J.P.); Genentech, Inc., South San Francisco, CA, USA (T.P.H.); University of Minnesota School of Pharmacy, Minneapolis, MN, USA (W.F.E.); Angiochem, Inc., Montreal, Quebec, Canada (J.E.L.); Pfizer Oncology, San Diego, CA, USA (T.W.J.); Massachusetts Institute of Technology, Cambridge, MA, USA (F.M.W.); US Food and Drug Administration, Silver Spring, MD, USA (J.S.); Texas Tech University School of Pharmacy, Amarillo, TX, USA (Q.R.S., R.S.); NewGen Therapeutics, Inc., Menlo Park, CA, USA (W.S.); Mayo Clinic, Rochester, MN, USA (J.N.S.); Dana-Farber Cancer Institute, Boston, MA, USA (P.Y.W.); University of Texas MD Anderson Cancer Center, Houston, TX, USA (D.A.B.); Celgene Avilomics Research, Bedford, MA, USA (R.C.P.)
| | - William F Elmquist
- Kaiser Permanente, Redwood City, California, USA (V.A.L.); University of Texas MD Anderson Cancer Center, Houston, TX, USA (V.A.L.); University of California, San Francisco, CA, USA (V.A.L.); SUNY Stony Brook University, Stony Brook, NY, USA (P.J.T.); Icahn School of Medicine at Mount Sinai, New York, NY, USA (J.M.G., M.R.B., A.C.D.); Columbia University Institute for Cancer Genetics, New York, NY, USA (A.I.); Fred Hutchinson Cancer Research Center, Seattle, WA, USA (P.J.P.); Genentech, Inc., South San Francisco, CA, USA (T.P.H.); University of Minnesota School of Pharmacy, Minneapolis, MN, USA (W.F.E.); Angiochem, Inc., Montreal, Quebec, Canada (J.E.L.); Pfizer Oncology, San Diego, CA, USA (T.W.J.); Massachusetts Institute of Technology, Cambridge, MA, USA (F.M.W.); US Food and Drug Administration, Silver Spring, MD, USA (J.S.); Texas Tech University School of Pharmacy, Amarillo, TX, USA (Q.R.S., R.S.); NewGen Therapeutics, Inc., Menlo Park, CA, USA (W.S.); Mayo Clinic, Rochester, MN, USA (J.N.S.); Dana-Farber Cancer Institute, Boston, MA, USA (P.Y.W.); University of Texas MD Anderson Cancer Center, Houston, TX, USA (D.A.B.); Celgene Avilomics Research, Bedford, MA, USA (R.C.P.)
| | - Jean E Lachowicz
- Kaiser Permanente, Redwood City, California, USA (V.A.L.); University of Texas MD Anderson Cancer Center, Houston, TX, USA (V.A.L.); University of California, San Francisco, CA, USA (V.A.L.); SUNY Stony Brook University, Stony Brook, NY, USA (P.J.T.); Icahn School of Medicine at Mount Sinai, New York, NY, USA (J.M.G., M.R.B., A.C.D.); Columbia University Institute for Cancer Genetics, New York, NY, USA (A.I.); Fred Hutchinson Cancer Research Center, Seattle, WA, USA (P.J.P.); Genentech, Inc., South San Francisco, CA, USA (T.P.H.); University of Minnesota School of Pharmacy, Minneapolis, MN, USA (W.F.E.); Angiochem, Inc., Montreal, Quebec, Canada (J.E.L.); Pfizer Oncology, San Diego, CA, USA (T.W.J.); Massachusetts Institute of Technology, Cambridge, MA, USA (F.M.W.); US Food and Drug Administration, Silver Spring, MD, USA (J.S.); Texas Tech University School of Pharmacy, Amarillo, TX, USA (Q.R.S., R.S.); NewGen Therapeutics, Inc., Menlo Park, CA, USA (W.S.); Mayo Clinic, Rochester, MN, USA (J.N.S.); Dana-Farber Cancer Institute, Boston, MA, USA (P.Y.W.); University of Texas MD Anderson Cancer Center, Houston, TX, USA (D.A.B.); Celgene Avilomics Research, Bedford, MA, USA (R.C.P.)
| | - Ted W Johnson
- Kaiser Permanente, Redwood City, California, USA (V.A.L.); University of Texas MD Anderson Cancer Center, Houston, TX, USA (V.A.L.); University of California, San Francisco, CA, USA (V.A.L.); SUNY Stony Brook University, Stony Brook, NY, USA (P.J.T.); Icahn School of Medicine at Mount Sinai, New York, NY, USA (J.M.G., M.R.B., A.C.D.); Columbia University Institute for Cancer Genetics, New York, NY, USA (A.I.); Fred Hutchinson Cancer Research Center, Seattle, WA, USA (P.J.P.); Genentech, Inc., South San Francisco, CA, USA (T.P.H.); University of Minnesota School of Pharmacy, Minneapolis, MN, USA (W.F.E.); Angiochem, Inc., Montreal, Quebec, Canada (J.E.L.); Pfizer Oncology, San Diego, CA, USA (T.W.J.); Massachusetts Institute of Technology, Cambridge, MA, USA (F.M.W.); US Food and Drug Administration, Silver Spring, MD, USA (J.S.); Texas Tech University School of Pharmacy, Amarillo, TX, USA (Q.R.S., R.S.); NewGen Therapeutics, Inc., Menlo Park, CA, USA (W.S.); Mayo Clinic, Rochester, MN, USA (J.N.S.); Dana-Farber Cancer Institute, Boston, MA, USA (P.Y.W.); University of Texas MD Anderson Cancer Center, Houston, TX, USA (D.A.B.); Celgene Avilomics Research, Bedford, MA, USA (R.C.P.)
| | - Forest M White
- Kaiser Permanente, Redwood City, California, USA (V.A.L.); University of Texas MD Anderson Cancer Center, Houston, TX, USA (V.A.L.); University of California, San Francisco, CA, USA (V.A.L.); SUNY Stony Brook University, Stony Brook, NY, USA (P.J.T.); Icahn School of Medicine at Mount Sinai, New York, NY, USA (J.M.G., M.R.B., A.C.D.); Columbia University Institute for Cancer Genetics, New York, NY, USA (A.I.); Fred Hutchinson Cancer Research Center, Seattle, WA, USA (P.J.P.); Genentech, Inc., South San Francisco, CA, USA (T.P.H.); University of Minnesota School of Pharmacy, Minneapolis, MN, USA (W.F.E.); Angiochem, Inc., Montreal, Quebec, Canada (J.E.L.); Pfizer Oncology, San Diego, CA, USA (T.W.J.); Massachusetts Institute of Technology, Cambridge, MA, USA (F.M.W.); US Food and Drug Administration, Silver Spring, MD, USA (J.S.); Texas Tech University School of Pharmacy, Amarillo, TX, USA (Q.R.S., R.S.); NewGen Therapeutics, Inc., Menlo Park, CA, USA (W.S.); Mayo Clinic, Rochester, MN, USA (J.N.S.); Dana-Farber Cancer Institute, Boston, MA, USA (P.Y.W.); University of Texas MD Anderson Cancer Center, Houston, TX, USA (D.A.B.); Celgene Avilomics Research, Bedford, MA, USA (R.C.P.)
| | - Joohee Sul
- Kaiser Permanente, Redwood City, California, USA (V.A.L.); University of Texas MD Anderson Cancer Center, Houston, TX, USA (V.A.L.); University of California, San Francisco, CA, USA (V.A.L.); SUNY Stony Brook University, Stony Brook, NY, USA (P.J.T.); Icahn School of Medicine at Mount Sinai, New York, NY, USA (J.M.G., M.R.B., A.C.D.); Columbia University Institute for Cancer Genetics, New York, NY, USA (A.I.); Fred Hutchinson Cancer Research Center, Seattle, WA, USA (P.J.P.); Genentech, Inc., South San Francisco, CA, USA (T.P.H.); University of Minnesota School of Pharmacy, Minneapolis, MN, USA (W.F.E.); Angiochem, Inc., Montreal, Quebec, Canada (J.E.L.); Pfizer Oncology, San Diego, CA, USA (T.W.J.); Massachusetts Institute of Technology, Cambridge, MA, USA (F.M.W.); US Food and Drug Administration, Silver Spring, MD, USA (J.S.); Texas Tech University School of Pharmacy, Amarillo, TX, USA (Q.R.S., R.S.); NewGen Therapeutics, Inc., Menlo Park, CA, USA (W.S.); Mayo Clinic, Rochester, MN, USA (J.N.S.); Dana-Farber Cancer Institute, Boston, MA, USA (P.Y.W.); University of Texas MD Anderson Cancer Center, Houston, TX, USA (D.A.B.); Celgene Avilomics Research, Bedford, MA, USA (R.C.P.)
| | - Quentin R Smith
- Kaiser Permanente, Redwood City, California, USA (V.A.L.); University of Texas MD Anderson Cancer Center, Houston, TX, USA (V.A.L.); University of California, San Francisco, CA, USA (V.A.L.); SUNY Stony Brook University, Stony Brook, NY, USA (P.J.T.); Icahn School of Medicine at Mount Sinai, New York, NY, USA (J.M.G., M.R.B., A.C.D.); Columbia University Institute for Cancer Genetics, New York, NY, USA (A.I.); Fred Hutchinson Cancer Research Center, Seattle, WA, USA (P.J.P.); Genentech, Inc., South San Francisco, CA, USA (T.P.H.); University of Minnesota School of Pharmacy, Minneapolis, MN, USA (W.F.E.); Angiochem, Inc., Montreal, Quebec, Canada (J.E.L.); Pfizer Oncology, San Diego, CA, USA (T.W.J.); Massachusetts Institute of Technology, Cambridge, MA, USA (F.M.W.); US Food and Drug Administration, Silver Spring, MD, USA (J.S.); Texas Tech University School of Pharmacy, Amarillo, TX, USA (Q.R.S., R.S.); NewGen Therapeutics, Inc., Menlo Park, CA, USA (W.S.); Mayo Clinic, Rochester, MN, USA (J.N.S.); Dana-Farber Cancer Institute, Boston, MA, USA (P.Y.W.); University of Texas MD Anderson Cancer Center, Houston, TX, USA (D.A.B.); Celgene Avilomics Research, Bedford, MA, USA (R.C.P.)
| | - Wang Shen
- Kaiser Permanente, Redwood City, California, USA (V.A.L.); University of Texas MD Anderson Cancer Center, Houston, TX, USA (V.A.L.); University of California, San Francisco, CA, USA (V.A.L.); SUNY Stony Brook University, Stony Brook, NY, USA (P.J.T.); Icahn School of Medicine at Mount Sinai, New York, NY, USA (J.M.G., M.R.B., A.C.D.); Columbia University Institute for Cancer Genetics, New York, NY, USA (A.I.); Fred Hutchinson Cancer Research Center, Seattle, WA, USA (P.J.P.); Genentech, Inc., South San Francisco, CA, USA (T.P.H.); University of Minnesota School of Pharmacy, Minneapolis, MN, USA (W.F.E.); Angiochem, Inc., Montreal, Quebec, Canada (J.E.L.); Pfizer Oncology, San Diego, CA, USA (T.W.J.); Massachusetts Institute of Technology, Cambridge, MA, USA (F.M.W.); US Food and Drug Administration, Silver Spring, MD, USA (J.S.); Texas Tech University School of Pharmacy, Amarillo, TX, USA (Q.R.S., R.S.); NewGen Therapeutics, Inc., Menlo Park, CA, USA (W.S.); Mayo Clinic, Rochester, MN, USA (J.N.S.); Dana-Farber Cancer Institute, Boston, MA, USA (P.Y.W.); University of Texas MD Anderson Cancer Center, Houston, TX, USA (D.A.B.); Celgene Avilomics Research, Bedford, MA, USA (R.C.P.)
| | - Jann N Sarkaria
- Kaiser Permanente, Redwood City, California, USA (V.A.L.); University of Texas MD Anderson Cancer Center, Houston, TX, USA (V.A.L.); University of California, San Francisco, CA, USA (V.A.L.); SUNY Stony Brook University, Stony Brook, NY, USA (P.J.T.); Icahn School of Medicine at Mount Sinai, New York, NY, USA (J.M.G., M.R.B., A.C.D.); Columbia University Institute for Cancer Genetics, New York, NY, USA (A.I.); Fred Hutchinson Cancer Research Center, Seattle, WA, USA (P.J.P.); Genentech, Inc., South San Francisco, CA, USA (T.P.H.); University of Minnesota School of Pharmacy, Minneapolis, MN, USA (W.F.E.); Angiochem, Inc., Montreal, Quebec, Canada (J.E.L.); Pfizer Oncology, San Diego, CA, USA (T.W.J.); Massachusetts Institute of Technology, Cambridge, MA, USA (F.M.W.); US Food and Drug Administration, Silver Spring, MD, USA (J.S.); Texas Tech University School of Pharmacy, Amarillo, TX, USA (Q.R.S., R.S.); NewGen Therapeutics, Inc., Menlo Park, CA, USA (W.S.); Mayo Clinic, Rochester, MN, USA (J.N.S.); Dana-Farber Cancer Institute, Boston, MA, USA (P.Y.W.); University of Texas MD Anderson Cancer Center, Houston, TX, USA (D.A.B.); Celgene Avilomics Research, Bedford, MA, USA (R.C.P.)
| | - Ramakrishna Samala
- Kaiser Permanente, Redwood City, California, USA (V.A.L.); University of Texas MD Anderson Cancer Center, Houston, TX, USA (V.A.L.); University of California, San Francisco, CA, USA (V.A.L.); SUNY Stony Brook University, Stony Brook, NY, USA (P.J.T.); Icahn School of Medicine at Mount Sinai, New York, NY, USA (J.M.G., M.R.B., A.C.D.); Columbia University Institute for Cancer Genetics, New York, NY, USA (A.I.); Fred Hutchinson Cancer Research Center, Seattle, WA, USA (P.J.P.); Genentech, Inc., South San Francisco, CA, USA (T.P.H.); University of Minnesota School of Pharmacy, Minneapolis, MN, USA (W.F.E.); Angiochem, Inc., Montreal, Quebec, Canada (J.E.L.); Pfizer Oncology, San Diego, CA, USA (T.W.J.); Massachusetts Institute of Technology, Cambridge, MA, USA (F.M.W.); US Food and Drug Administration, Silver Spring, MD, USA (J.S.); Texas Tech University School of Pharmacy, Amarillo, TX, USA (Q.R.S., R.S.); NewGen Therapeutics, Inc., Menlo Park, CA, USA (W.S.); Mayo Clinic, Rochester, MN, USA (J.N.S.); Dana-Farber Cancer Institute, Boston, MA, USA (P.Y.W.); University of Texas MD Anderson Cancer Center, Houston, TX, USA (D.A.B.); Celgene Avilomics Research, Bedford, MA, USA (R.C.P.)
| | - Patrick Y Wen
- Kaiser Permanente, Redwood City, California, USA (V.A.L.); University of Texas MD Anderson Cancer Center, Houston, TX, USA (V.A.L.); University of California, San Francisco, CA, USA (V.A.L.); SUNY Stony Brook University, Stony Brook, NY, USA (P.J.T.); Icahn School of Medicine at Mount Sinai, New York, NY, USA (J.M.G., M.R.B., A.C.D.); Columbia University Institute for Cancer Genetics, New York, NY, USA (A.I.); Fred Hutchinson Cancer Research Center, Seattle, WA, USA (P.J.P.); Genentech, Inc., South San Francisco, CA, USA (T.P.H.); University of Minnesota School of Pharmacy, Minneapolis, MN, USA (W.F.E.); Angiochem, Inc., Montreal, Quebec, Canada (J.E.L.); Pfizer Oncology, San Diego, CA, USA (T.W.J.); Massachusetts Institute of Technology, Cambridge, MA, USA (F.M.W.); US Food and Drug Administration, Silver Spring, MD, USA (J.S.); Texas Tech University School of Pharmacy, Amarillo, TX, USA (Q.R.S., R.S.); NewGen Therapeutics, Inc., Menlo Park, CA, USA (W.S.); Mayo Clinic, Rochester, MN, USA (J.N.S.); Dana-Farber Cancer Institute, Boston, MA, USA (P.Y.W.); University of Texas MD Anderson Cancer Center, Houston, TX, USA (D.A.B.); Celgene Avilomics Research, Bedford, MA, USA (R.C.P.)
| | - Donald A Berry
- Kaiser Permanente, Redwood City, California, USA (V.A.L.); University of Texas MD Anderson Cancer Center, Houston, TX, USA (V.A.L.); University of California, San Francisco, CA, USA (V.A.L.); SUNY Stony Brook University, Stony Brook, NY, USA (P.J.T.); Icahn School of Medicine at Mount Sinai, New York, NY, USA (J.M.G., M.R.B., A.C.D.); Columbia University Institute for Cancer Genetics, New York, NY, USA (A.I.); Fred Hutchinson Cancer Research Center, Seattle, WA, USA (P.J.P.); Genentech, Inc., South San Francisco, CA, USA (T.P.H.); University of Minnesota School of Pharmacy, Minneapolis, MN, USA (W.F.E.); Angiochem, Inc., Montreal, Quebec, Canada (J.E.L.); Pfizer Oncology, San Diego, CA, USA (T.W.J.); Massachusetts Institute of Technology, Cambridge, MA, USA (F.M.W.); US Food and Drug Administration, Silver Spring, MD, USA (J.S.); Texas Tech University School of Pharmacy, Amarillo, TX, USA (Q.R.S., R.S.); NewGen Therapeutics, Inc., Menlo Park, CA, USA (W.S.); Mayo Clinic, Rochester, MN, USA (J.N.S.); Dana-Farber Cancer Institute, Boston, MA, USA (P.Y.W.); University of Texas MD Anderson Cancer Center, Houston, TX, USA (D.A.B.); Celgene Avilomics Research, Bedford, MA, USA (R.C.P.)
| | - Russell C Petter
- Kaiser Permanente, Redwood City, California, USA (V.A.L.); University of Texas MD Anderson Cancer Center, Houston, TX, USA (V.A.L.); University of California, San Francisco, CA, USA (V.A.L.); SUNY Stony Brook University, Stony Brook, NY, USA (P.J.T.); Icahn School of Medicine at Mount Sinai, New York, NY, USA (J.M.G., M.R.B., A.C.D.); Columbia University Institute for Cancer Genetics, New York, NY, USA (A.I.); Fred Hutchinson Cancer Research Center, Seattle, WA, USA (P.J.P.); Genentech, Inc., South San Francisco, CA, USA (T.P.H.); University of Minnesota School of Pharmacy, Minneapolis, MN, USA (W.F.E.); Angiochem, Inc., Montreal, Quebec, Canada (J.E.L.); Pfizer Oncology, San Diego, CA, USA (T.W.J.); Massachusetts Institute of Technology, Cambridge, MA, USA (F.M.W.); US Food and Drug Administration, Silver Spring, MD, USA (J.S.); Texas Tech University School of Pharmacy, Amarillo, TX, USA (Q.R.S., R.S.); NewGen Therapeutics, Inc., Menlo Park, CA, USA (W.S.); Mayo Clinic, Rochester, MN, USA (J.N.S.); Dana-Farber Cancer Institute, Boston, MA, USA (P.Y.W.); University of Texas MD Anderson Cancer Center, Houston, TX, USA (D.A.B.); Celgene Avilomics Research, Bedford, MA, USA (R.C.P.)
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79
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Carugo A, Genovese G, Seth S, Nezi L, Rose JL, Bossi D, Cicalese A, Shah PK, Viale A, Pettazzoni PF, Akdemir KC, Bristow CA, Robinson FS, Tepper J, Sanchez N, Gupta S, Estecio MR, Giuliani V, Dellino GI, Riva L, Yao W, Di Francesco ME, Green T, D'Alesio C, Corti D, Kang Y, Jones P, Wang H, Fleming JB, Maitra A, Pelicci PG, Chin L, DePinho RA, Lanfrancone L, Heffernan TP, Draetta GF. In Vivo Functional Platform Targeting Patient-Derived Xenografts Identifies WDR5-Myc Association as a Critical Determinant of Pancreatic Cancer. Cell Rep 2016; 16:133-147. [PMID: 27320920 DOI: 10.1016/j.celrep.2016.05.063] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 03/21/2016] [Accepted: 05/16/2016] [Indexed: 12/28/2022] Open
Abstract
Current treatment regimens for pancreatic ductal adenocarcinoma (PDAC) yield poor 5-year survival, emphasizing the critical need to identify druggable targets essential for PDAC maintenance. We developed an unbiased and in vivo target discovery approach to identify molecular vulnerabilities in low-passage and patient-derived PDAC xenografts or genetically engineered mouse model-derived allografts. Focusing on epigenetic regulators, we identified WDR5, a core member of the COMPASS histone H3 Lys4 (H3K4) MLL (1-4) methyltransferase complex, as a top tumor maintenance hit required across multiple human and mouse tumors. Mechanistically, WDR5 functions to sustain proper execution of DNA replication in PDAC cells, as previously suggested by replication stress studies involving MLL1, and c-Myc, also found to interact with WDR5. We indeed demonstrate that interaction with c-Myc is critical for this function. By showing that ATR inhibition mimicked the effects of WDR5 suppression, these data provide rationale to test ATR and WDR5 inhibitors for activity in this disease.
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Affiliation(s)
- Alessandro Carugo
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Molecular and Cellular Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy.
| | - Giannicola Genovese
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Molecular and Cellular Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sahil Seth
- Institute for Applied Cancer Science, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Luigi Nezi
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Molecular and Cellular Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Johnathon Lynn Rose
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Molecular and Cellular Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Daniela Bossi
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
| | - Angelo Cicalese
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
| | | | - Andrea Viale
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Molecular and Cellular Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Piergiorgio Francesco Pettazzoni
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Molecular and Cellular Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kadir Caner Akdemir
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Frederick Scott Robinson
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Molecular and Cellular Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - James Tepper
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Molecular and Cellular Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nora Sanchez
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Molecular and Cellular Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sonal Gupta
- Sheikh Ahmed Bin Zayed Al Nahyan Center for Pancreatic Cancer Research, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Marcos Roberto Estecio
- Department of Epigenetics and Molecular Carcinogenesis, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Virginia Giuliani
- Institute for Applied Cancer Science, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Gaetano Ivan Dellino
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy; Department of Oncology and Hemato-oncology, University of Milan, Milan 20139, Italy
| | - Laura Riva
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milan 20139, Italy
| | - Wantong Yao
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Molecular and Cellular Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Maria Emilia Di Francesco
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Institute for Applied Cancer Science, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Tessa Green
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Molecular and Cellular Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Carolina D'Alesio
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
| | - Denise Corti
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Molecular and Cellular Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ya'an Kang
- Department of Surgical Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Philip Jones
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Institute for Applied Cancer Science, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Huamin Wang
- Department of Pathology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jason Bates Fleming
- Department of Surgical Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Anirban Maitra
- Sheikh Ahmed Bin Zayed Al Nahyan Center for Pancreatic Cancer Research, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy; Department of Oncology and Hemato-oncology, University of Milan, Milan 20139, Italy
| | - Lynda Chin
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Institute for Applied Cancer Science, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Luisa Lanfrancone
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy.
| | | | - Giulio Francesco Draetta
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Institute for Applied Cancer Science, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Molecular and Cellular Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA.
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80
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Full-length LGR5-positive cells have chemoresistant characteristics in colorectal cancer. Br J Cancer 2016; 114:1251-60. [PMID: 27140312 PMCID: PMC4891500 DOI: 10.1038/bjc.2016.112] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 03/28/2016] [Accepted: 03/31/2016] [Indexed: 12/22/2022] Open
Abstract
Background: Leucine-rich repeat-containing G-protein-coupled receptor 5 (LGR5) is a target of Wnt signalling and considered both a cancer stem cell marker and intestinal stem cell marker. We found first some splice variants of LGR5 in human intestine and elucidated the functional feature of full-length LGR5 (LGR5FL). Methods: Reverse transcript PCR using mRNA extracted from intestine revealed the existence of LGR5 splice variants. We designed an antibody that recognises only LGR5FL and assessed immunohistochemically the distribution of LGR5FL-positive cells and Ki-67-positive cells in clinical samples. Results: Two LGR5 splice variants were expressed in the human intestine crypt cells; one lacked exon 5 and the other lacked exons 5–8. Only LGR5FL appeared during cell cycle arrest, whereas the transcript variants appeared when the cell cycle was proceeding. Immunohistochemistry and in situ hybridisation showed that LGR5FL-positive cells were negative for Ki-67. Comparing prechemotherapy and post-chemotherapy specimens, the population of LGR5FL-positive cells significantly increased with therapy (P<0.01). Conclusions: The function of LGR5FL-positive cells had low cell proliferative ability compared with the cells, which expressed splice variants of LGR5 and remained after chemotherapy. Designing therapeutic strategies that target LGR5FL-positive cells seems to be important in colorectal cancer.
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81
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Modulation of splicing catalysis for therapeutic targeting of leukemia with mutations in genes encoding spliceosomal proteins. Nat Med 2016; 22:672-8. [PMID: 27135740 PMCID: PMC4899191 DOI: 10.1038/nm.4097] [Citation(s) in RCA: 257] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 04/06/2016] [Indexed: 12/15/2022]
Abstract
Mutations in spliceosomal genes are commonly found in patients with myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML)1–3. These mutations occur at highly recurrent amino acid residues and perturb normal splice site and exon recognition4–6. Spliceosomal mutations are always heterozygous and rarely co-occur with one another, suggesting that cells may only tolerate a partial deviation from normal splicing activity. To test this hypothesis, we engineered mice that express the SRSF2P95H mutation, which commonly occurs in MDS and AML, in an inducible hemizygous manner in hematopoietic cells. These mice developed lethal bone marrow failure, demonstrating that Srsf2-mutant cells depend on the wildtype Srsf2 allele for survival. In the context of leukemia, treatment with the spliceosome inhibitor E71077,8 resulted in significant reductions in leukemic burden specifically in isogenic mouse leukemias and patient-derived xenograft (PDX) AMLs carrying spliceosomal mutations. While in vivo E7107 exposure resulted in widespread intron retention and cassette exon skipping regardless of Srsf2 genotype, the magnitude of splicing inhibition following E7107 treatment was greater in Srsf2-mutant versus wildtype leukemias, consistent with its differential effect on survival in these two genotypes. Collectively, these data provide genetic and pharmacologic evidence that leukemias with spliceosomal mutations are preferentially susceptible to additional splicing perturbations in vivo compared with wildtype counterparts. Modulation of spliceosome function may provide a novel therapeutic avenue in genetically defined subsets of MDS and AML patients.
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82
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Abstract
MYC is a transcription factor, which not only directly modulates multiple aspects of transcription and co‐transcriptional processing (e.g. RNA‐Polymerase II initiation, elongation, and mRNA capping), but also indirectly influences several steps of RNA metabolism, including both constitutive and alternative splicing, mRNA stability, and translation efficiency. As MYC is an oncoprotein whose expression is deregulated in multiple human cancers, identifying its critical downstream activities in tumors is of key importance for designing effective therapeutic strategies. With this knowledge and recent technological advances, we now have multiple angles to reach the goal of targeting MYC in tumors, ranging from the direct reduction of MYC levels, to the dampening of selected house‐keeping functions in MYC‐overexpressing cells, to more targeted approaches based on MYC‐induced secondary effects.
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Affiliation(s)
- Cheryl M Koh
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Arianna Sabò
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - Ernesto Guccione
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,National Cancer Centre Singapore, Singapore
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83
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Toledo CM, Ding Y, Hoellerbauer P, Davis RJ, Basom R, Girard EJ, Lee E, Corrin P, Hart T, Bolouri H, Davison J, Zhang Q, Hardcastle J, Aronow BJ, Plaisier CL, Baliga NS, Moffat J, Lin Q, Li XN, Nam DH, Lee J, Pollard SM, Zhu J, Delrow JJ, Clurman BE, Olson JM, Paddison PJ. Genome-wide CRISPR-Cas9 Screens Reveal Loss of Redundancy between PKMYT1 and WEE1 in Glioblastoma Stem-like Cells. Cell Rep 2015; 13:2425-2439. [PMID: 26673326 PMCID: PMC4691575 DOI: 10.1016/j.celrep.2015.11.021] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 10/12/2015] [Accepted: 11/03/2015] [Indexed: 12/31/2022] Open
Abstract
To identify therapeutic targets for glioblastoma (GBM), we performed genome-wide CRISPR-Cas9 knockout (KO) screens in patient-derived GBM stem-like cells (GSCs) and human neural stem/progenitors (NSCs), non-neoplastic stem cell controls, for genes required for their in vitro growth. Surprisingly, the vast majority GSC-lethal hits were found outside of molecular networks commonly altered in GBM and GSCs (e.g., oncogenic drivers). In vitro and in vivo validation of GSC-specific targets revealed several strong hits, including the wee1-like kinase, PKMYT1/Myt1. Mechanistic studies demonstrated that PKMYT1 acts redundantly with WEE1 to inhibit cyclin B-CDK1 activity via CDK1-Y15 phosphorylation and to promote timely completion of mitosis in NSCs. However, in GSCs, this redundancy is lost, most likely as a result of oncogenic signaling, causing GBM-specific lethality.
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Affiliation(s)
- Chad M Toledo
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Yu Ding
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Pia Hoellerbauer
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Ryan J Davis
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Ryan Basom
- Genomics and Bioinformatics Shared Resources, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Emily J Girard
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Eunjee Lee
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Philip Corrin
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Traver Hart
- Department of Molecular Genetics, University of Toronto and Donnelly Centre, Toronto, ON M5S3E1, Canada; Canadian Institute for Advanced Research, Toronto, ON M5G1Z8, Canada
| | - Hamid Bolouri
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jerry Davison
- Genomics and Bioinformatics Shared Resources, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Qing Zhang
- Genomics and Bioinformatics Shared Resources, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Justin Hardcastle
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Bruce J Aronow
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | | | | | - Jason Moffat
- Department of Molecular Genetics, University of Toronto and Donnelly Centre, Toronto, ON M5S3E1, Canada; Canadian Institute for Advanced Research, Toronto, ON M5G1Z8, Canada
| | - Qi Lin
- Brain Tumor Program, Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xiao-Nan Li
- Brain Tumor Program, Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Do-Hyun Nam
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul 135-710, Korea
| | - Jeongwu Lee
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44192, USA
| | - Steven M Pollard
- Edinburgh CRUK Cancer Research Centre and MRC Centre for Regenerative Medicine, The University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Jun Zhu
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jeffery J Delrow
- Genomics and Bioinformatics Shared Resources, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Bruce E Clurman
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - James M Olson
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
| | - Patrick J Paddison
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA.
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84
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Abstract
In a recent issue of Nature, Hsu and colleagues report that oncogenic MYC activation is synthetic lethal with inhibition of the core spliceosome, because MYC-driven growth and increased transcription leave tumors dependent on pre-mRNA processing for survival. As direct targeting of MYC has remained elusive, synthetic lethal strategies are attractive.
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Affiliation(s)
- Zachary E Stine
- Abramson Family Cancer Research Institute, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Chi V Dang
- Abramson Family Cancer Research Institute, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA.
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85
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Abstract
Two opposing models have been proposed to describe the function of the MYC oncoprotein in shaping cellular transcriptomes: one posits that MYC amplifies transcription at all active loci; the other that MYC differentially controls discrete sets of genes, the products of which affect global transcript levels. Here, we argue that differential gene regulation by MYC is the sole unifying model that is consistent with all available data. Among other effects, MYC endows cells with physiological and metabolic changes that have the potential to feed back on global RNA production, processing and turnover. The field is progressing steadily towards a full characterization of the MYC-regulated genes and pathways that mediate these biological effects and - by the same token - endow MYC with its pervasive oncogenic potential.
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Affiliation(s)
- Theresia R Kress
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT) and Department of Experimental Oncology, European Institute of Oncology (IEO), Via Adamello 16, 20139 Milan, Italy
| | - Arianna Sabò
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT) and Department of Experimental Oncology, European Institute of Oncology (IEO), Via Adamello 16, 20139 Milan, Italy
| | - Bruno Amati
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT) and Department of Experimental Oncology, European Institute of Oncology (IEO), Via Adamello 16, 20139 Milan, Italy
- Department of Experimental Oncology, European Institute of Oncology (IEO), Via Adamello 16, 20139 Milan, Italy
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86
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Hsu TYT, Simon LM, Neill NJ, Marcotte R, Sayad A, Bland CS, Echeverria GV, Sun T, Kurley SJ, Tyagi S, Karlin KL, Dominguez-Vidaña R, Hartman JD, Renwick A, Scorsone K, Bernardi RJ, Skinner SO, Jain A, Orellana M, Lagisetti C, Golding I, Jung SY, Neilson JR, Zhang XHF, Cooper TA, Webb TR, Neel BG, Shaw CA, Westbrook TF. The spliceosome is a therapeutic vulnerability in MYC-driven cancer. Nature 2015; 525:384-8. [PMID: 26331541 PMCID: PMC4831063 DOI: 10.1038/nature14985] [Citation(s) in RCA: 343] [Impact Index Per Article: 38.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 07/24/2015] [Indexed: 12/14/2022]
Abstract
c-MYC (MYC) overexpression or hyperactivation is one of the most common drivers of human cancer. Despite intensive study, the MYC oncogene remains recalcitrant to therapeutic inhibition. MYC is a transcription factor, and many of its pro-tumorigenic functions have been attributed to its ability to regulate gene expression programs1–3. Notably, oncogenic MYC activation has also been shown to increase total RNA and protein production in many tissue and disease contexts4–7. While such increases in RNA and protein production may endow cancer cells with pro-tumor hallmarks, this elevation in synthesis may also generate new or heightened burden on MYC-driven cancer cells to properly process these macromolecules8. Herein, we discover the spliceosome as a new target of oncogenic stress in MYC-driven cancers. We identify BUD31 as a MYC-synthetic lethal gene, and demonstrate that BUD31 is a component of the core spliceosome required for its assembly and catalytic activity. Core spliceosomal factors (SF3B1, U2AF1, and others) associated with BUD31 are also required to tolerate oncogenic MYC. Notably, MYC hyperactivation induces an increase in total pre-mRNA synthesis, suggesting an increased burden on the core spliceosome to process pre-mRNA. In contrast to normal cells, partial inhibition of the spliceosome in MYC-hyperactivated cells leads to global intron retention, widespread defects in pre-mRNA maturation, and deregulation of many essential cell processes. Importantly, genetic or pharmacologic inhibition of the spliceosome in vivo impairs survival, tumorigenicity, and metastatic proclivity of MYC-dependent breast cancers. Collectively, these data suggest that oncogenic MYC confers a collateral stress on splicing and that components of the spliceosome may be therapeutic entry points for aggressive MYC-driven cancers.
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Affiliation(s)
- Tiffany Y-T Hsu
- Verna &Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.,Interdepartmental Program in Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, Texas 77030, USA.,Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Lukas M Simon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Nicholas J Neill
- Verna &Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Richard Marcotte
- Princess Margaret Cancer Centre, University Health Network, Toronto M5G 2C4, Canada
| | - Azin Sayad
- Princess Margaret Cancer Centre, University Health Network, Toronto M5G 2C4, Canada
| | - Christopher S Bland
- Verna &Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Gloria V Echeverria
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Tingting Sun
- Verna &Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Sarah J Kurley
- Verna &Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Siddhartha Tyagi
- Verna &Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Kristen L Karlin
- Verna &Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Rocio Dominguez-Vidaña
- Verna &Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.,Interdepartmental Program in Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jessica D Hartman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Alexander Renwick
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Kathleen Scorsone
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Ronald J Bernardi
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Samuel O Skinner
- Verna &Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Physics, University of Illinois, Urbana, Illinois 61801, USA
| | - Antrix Jain
- Verna &Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Mayra Orellana
- Verna &Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Chandraiah Lagisetti
- Center for Chemical Biology, Bioscience Division, SRI International, Menlo Park, California 94025, USA
| | - Ido Golding
- Verna &Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Physics, University of Illinois, Urbana, Illinois 61801, USA
| | - Sung Y Jung
- Verna &Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Joel R Neilson
- Interdepartmental Program in Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Xiang H-F Zhang
- The Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Thomas A Cooper
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Thomas R Webb
- Center for Chemical Biology, Bioscience Division, SRI International, Menlo Park, California 94025, USA
| | - Benjamin G Neel
- Princess Margaret Cancer Centre, University Health Network, Toronto M5G 2C4, Canada.,Department of Medical Biophysics, University of Toronto, Toronto M5S 2J7, Canada
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Thomas F Westbrook
- Verna &Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.,Interdepartmental Program in Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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87
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Schreiber CA, Sakuma T, Izumiya Y, Holditch SJ, Hickey RD, Bressin RK, Basu U, Koide K, Asokan A, Ikeda Y. An siRNA Screen Identifies the U2 snRNP Spliceosome as a Host Restriction Factor for Recombinant Adeno-associated Viruses. PLoS Pathog 2015; 11:e1005082. [PMID: 26244496 PMCID: PMC4526370 DOI: 10.1371/journal.ppat.1005082] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 07/13/2015] [Indexed: 12/02/2022] Open
Abstract
Adeno-associated viruses (AAV) have evolved to exploit the dynamic reorganization of host cell machinery during co-infection by adenoviruses and other helper viruses. In the absence of helper viruses, host factors such as the proteasome and DNA damage response machinery have been shown to effectively inhibit AAV transduction by restricting processes ranging from nuclear entry to second-strand DNA synthesis. To identify host factors that might affect other key steps in AAV infection, we screened an siRNA library that revealed several candidate genes including the PHD finger-like domain protein 5A (PHF5A), a U2 snRNP-associated protein. Disruption of PHF5A expression selectively enhanced transgene expression from AAV by increasing transcript levels and appears to influence a step after second-strand synthesis in a serotype and cell type-independent manner. Genetic disruption of U2 snRNP and associated proteins, such as SF3B1 and U2AF1, also increased expression from AAV vector, suggesting the critical role of U2 snRNP spliceosome complex in this host-mediated restriction. Notably, adenoviral co-infection and U2 snRNP inhibition appeared to target a common pathway in increasing expression from AAV vectors. Moreover, pharmacological inhibition of U2 snRNP by meayamycin B, a potent SF3B1 inhibitor, substantially enhanced AAV vector transduction of clinically relevant cell types. Further analysis suggested that U2 snRNP proteins suppress AAV vector transgene expression through direct recognition of intact AAV capsids. In summary, we identify U2 snRNP and associated splicing factors, which are known to be affected during adenoviral infection, as novel host restriction factors that effectively limit AAV transgene expression. Concurrently, we postulate that pharmacological/genetic manipulation of components of the spliceosomal machinery might enable more effective gene transfer modalities with recombinant AAV vectors. Mammalian cells have developed diverse innate/intrinsic immune strategies to counteract viral infections. Post-entry infection steps of a single-strand DNA virus, adeno-associated virus (AAV), are subject to such restrictions. Here, we screened an siRNA library to identify a novel cellular factor involved in AAV restriction. We found PHF5A, a component of the U2 snRNP mRNA splicing factor, blocks expression from recombinant AAV vectors. Disruption of PHF5A expression specifically enhanced AAV vector performance. Moreover, genetic and pharmacological inhibition of other U2 snRNP proteins, but not spliceosome proteins involved in other splicing steps, strongly increased transgene expression from AAV vectors. Further study demonstrated that U2 snRNP proteins recognize incoming AAV capsids to mediate this cellular restriction at the step after second-strand synthesis. In summary, we identify the U2 snRNP spliceosome complex as novel host factors that effectively restrict recombinant AAV vectors. Considering frequent reorganization of host splicing machinery in DNA virus infections, it is conceivable that U2 snRNP plays a role as a broad spectrum antiviral factor and helper viruses have evolved to counteract this restriction through sequestration of snRNP proteins.
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Affiliation(s)
- Claire A. Schreiber
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Toshie Sakuma
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Yoshihiro Izumiya
- Department of Dermatology, UC Davis School of Medicine, Sacramento, California, United States of America
| | - Sara J. Holditch
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Raymond D. Hickey
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Robert K. Bressin
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Upamanyu Basu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Kazunori Koide
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Aravind Asokan
- Gene Therapy Center and Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Yasuhiro Ikeda
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
- * E-mail:
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88
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Shi Y, Joyner AS, Shadrick W, Palacios G, Lagisetti C, Potter PM, Sambucetti LC, Stamm S, Webb TR. Pharmacodynamic assays to facilitate preclinical and clinical development of pre-mRNA splicing modulatory drug candidates. Pharmacol Res Perspect 2015; 3:e00158. [PMID: 26171237 PMCID: PMC4492733 DOI: 10.1002/prp2.158] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 05/22/2015] [Indexed: 12/29/2022] Open
Abstract
The spliceosome has recently emerged as a new target for cancer chemotherapy and novel antitumor spliceosome targeted agents are under development. Here, we describe two types of novel pharmacodynamic assays that facilitate drug discovery and development of this intriguing class of innovative therapeutics; the first assay is useful for preclinical optimization of small-molecule agents that target the SF3B1 spliceosomal protein in animals, the second assay is an ex vivo validated, gel-based assay for the measurement of drug exposure in human leukocytes. The first assay utilizes a highly specific bioluminescent splicing reporter, based on the skipping of exons 4–11 of a Luc-MDM2 construct, which specifically yields active luciferase when treated with small-molecule spliceosome modulators. We demonstrate that this reporter can be used to monitor alternative splicing in whole cells in vitro. We describe here that cell lines carrying the reporter can be used in vivo for the efficient pharmacodynamic analysis of agents during drug optimization and development. We also demonstrate dose- and time-dependent on-target activity of sudemycin D6 (SD6), which leads to dramatic tumor regression. The second assay relies on the treatment of freshly drawn human blood with SD6 ex vivo treatment. Changes in alternative splicing are determined by RT-PCR using genes previously identified in in vitro experiments. The Luc-MDM2 alternative splicing bioluminescent reporter and the splicing changes observed in human leukocytes should allow for the more facile translation of novel splicing modulators into clinical application.
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Affiliation(s)
- Yihui Shi
- Division of Biosciences, SRI International Menlo Park, California, 94025
| | - Amanda S Joyner
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital Memphis, Tennessee, 38105
| | - William Shadrick
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital Memphis, Tennessee, 38105
| | - Gustavo Palacios
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital Memphis, Tennessee, 38105
| | | | - Philip M Potter
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital Memphis, Tennessee, 38105
| | - Lidia C Sambucetti
- Division of Biosciences, SRI International Menlo Park, California, 94025
| | - Stefan Stamm
- Department of Molecular and Cellular Biochemistry, University of Kentucky 741 South Limestone, Lexington, Kentucky, 40536
| | - Thomas R Webb
- Division of Biosciences, SRI International Menlo Park, California, 94025
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89
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Worley MJ, Liu S, Hua Y, Kwok JSL, Samuel A, Hou L, Shoni M, Lu S, Sandberg EM, Keryan A, Wu D, Ng SK, Kuo WP, Parra-Herran CE, Tsui SKW, Welch W, Crum C, Berkowitz RS, Ng SW. Molecular changes in endometriosis-associated ovarian clear cell carcinoma. Eur J Cancer 2015; 51:1831-42. [PMID: 26059197 DOI: 10.1016/j.ejca.2015.05.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 05/12/2015] [Accepted: 05/14/2015] [Indexed: 01/16/2023]
Abstract
BACKGROUND Endometriosis is frequently associated with and thought of having propensity to develop into ovarian clear cell carcinoma (OCCC), although the molecular transformation mechanism is not completely understood. METHODS We employed immunohistochemical (IHC) staining for marker expression along the potential progression continuum. Expression profiling of microdissected endometriotic and OCCC cells from patient-matched formalin-fixed, paraffin-embedded samples was performed to explore the carcinogenic pathways. Function of novel biomarkers was confirmed by knockdown experiments. RESULTS PTEN was significantly lost in both endometriosis and invasive tumour tissues, while oestrogen receptor (ER) expression was lost in OCCC relative to endometriosis. XRCC5, PTCH2, eEF1A2 and PPP1R14B were significantly overexpressed in OCCC and associated endometriosis, but not in benign endometriosis (p ⩽ 0.004). Knockdown experiments with XRCC5 and PTCH2 in a clear cell cancer cell line resulted in significant growth inhibition. There was also significant silencing of a panel of target genes with histone H3 lysine 27 trimethylation, a signature of polycomb chromatin-remodelling complex in OCCC. IHC confirmed the loss of expression of one such polycomb target gene, the serous ovarian cancer lineage marker Wilms' tumour protein 1 (WT1) in OCCC, while endometriotic tissues showed significant co-expression of WT1 and ER. CONCLUSIONS Loss of PTEN expression is proposed as an early and permissive event in endometriosis development, while the loss of ER and polycomb-mediated transcriptional reprogramming for pluripotency may play an important role in the ultimate transformation process. Our study provides new evidence to redefine the pathogenic programme for lineage-specific transformation of endometriosis to OCCC.
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Affiliation(s)
- Michael J Worley
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Shubai Liu
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yuanyuan Hua
- Department of Obstetrics & Gynecology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, PR China; Division of Gynecologic Oncology, Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jamie Sui-Lam Kwok
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Anicka Samuel
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Lei Hou
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Melina Shoni
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Shi Lu
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Evelien M Sandberg
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Anna Keryan
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Di Wu
- Statistics Department, Harvard University, Boston, MA, USA
| | - Shu-Kay Ng
- School of Medicine, Griffith University, Meadowbrook, Australia
| | - Winston P Kuo
- Harvard Catalyst Laboratory for Innovative Translational Technologies, Harvard Medical School, Boston, MA, USA
| | - Carlos E Parra-Herran
- Division of Women's and Perinatal Pathology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Stephen K W Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong
| | - William Welch
- Division of Women's and Perinatal Pathology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Christopher Crum
- Division of Women's and Perinatal Pathology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ross S Berkowitz
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Shu-Wing Ng
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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90
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Dvinge H, Bradley RK. Widespread intron retention diversifies most cancer transcriptomes. Genome Med 2015; 7:45. [PMID: 26113877 PMCID: PMC4480902 DOI: 10.1186/s13073-015-0168-9] [Citation(s) in RCA: 217] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 04/30/2015] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Somatic mutations affecting components of the RNA splicing machinery occur with high frequencies across many tumor types. These mutations give rise to distinct alterations in normal splice site and exon recognition, such as unusual 3' splice site preferences, that likely contribute to tumorigenesis. METHODS We analyzed genome-wide patterns of RNA splicing across 805 matched tumor and normal control samples from 16 distinct cancer types to identify signals of abnormal cancer-associated splicing. RESULTS We found that abnormal RNA splicing, typified by widespread intron retention, is common across cancers even in the absence of mutations directly affecting the RNA splicing machinery. Almost all liquid and solid cancer types exhibited frequent retention of both alternative and constitutive introns relative to control normal tissues. The sole exception was breast cancer, where intron retention typified adjacent normal rather than cancer tissue. Different introns were preferentially retained in specific cancer types, although a small subset of introns enriched for genes encoding RNA splicing and export factors exhibited frequent retention across diverse cancers. The extent of intron retention correlated with the presence of IDH1 and IDH2 mutations in acute myeloid leukemia and across molecular subtypes in breast cancer. Many introns that were preferentially retained in primary cancers were present at high levels in the cytoplasmic mRNA pools of cancer cell lines. CONCLUSIONS Our data indicate that abnormal RNA splicing is a common characteristic of cancers even in the absence of mutational insults to the splicing machinery, and suggest that intron-containing mRNAs contribute to the transcriptional diversity of many cancers.
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Affiliation(s)
- Heidi Dvinge
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA ; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA ; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA
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91
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Koh CM, Bezzi M, Low DHP, Ang WX, Teo SX, Gay FPH, Al-Haddawi M, Tan SY, Osato M, Sabò A, Amati B, Wee KB, Guccione E. MYC regulates the core pre-mRNA splicing machinery as an essential step in lymphomagenesis. Nature 2015; 523:96-100. [PMID: 25970242 DOI: 10.1038/nature14351] [Citation(s) in RCA: 269] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 02/24/2015] [Indexed: 12/29/2022]
Abstract
Deregulated expression of the MYC transcription factor occurs in most human cancers and correlates with high proliferation, reprogrammed cellular metabolism and poor prognosis. Overexpressed MYC binds to virtually all active promoters within a cell, although with different binding affinities, and modulates the expression of distinct subsets of genes. However, the critical effectors of MYC in tumorigenesis remain largely unknown. Here we show that during lymphomagenesis in Eµ-myc transgenic mice, MYC directly upregulates the transcription of the core small nuclear ribonucleoprotein particle assembly genes, including Prmt5, an arginine methyltransferase that methylates Sm proteins. This coordinated regulatory effect is critical for the core biogenesis of small nuclear ribonucleoprotein particles, effective pre-messenger-RNA splicing, cell survival and proliferation. Our results demonstrate that MYC maintains the splicing fidelity of exons with a weak 5' donor site. Additionally, we identify pre-messenger-RNAs that are particularly sensitive to the perturbation of the MYC-PRMT5 axis, resulting in either intron retention (for example, Dvl1) or exon skipping (for example, Atr, Ep400). Using antisense oligonucleotides, we demonstrate the contribution of these splicing defects to the anti-proliferative/apoptotic phenotype observed in PRMT5-depleted Eµ-myc B cells. We conclude that, in addition to its well-documented oncogenic functions in transcription and translation, MYC also safeguards proper pre-messenger-RNA splicing as an essential step in lymphomagenesis.
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Affiliation(s)
- Cheryl M Koh
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore
| | - Marco Bezzi
- 1] Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore [2] Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
| | - Diana H P Low
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore
| | - Wei Xia Ang
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore
| | - Shun Xie Teo
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore
| | - Florence P H Gay
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore
| | - Muthafar Al-Haddawi
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore
| | - Soo Yong Tan
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore
| | - Motomi Osato
- Cancer Science Institute of Singapore (CSI), National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore
| | - Arianna Sabò
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139 Milan, Italy
| | - Bruno Amati
- 1] Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139 Milan, Italy [2] Department of Experimental Oncology, European Institute of Oncology (IEO), Via Adamello 16, 20139 Milan, Italy
| | - Keng Boon Wee
- 1] Institute of High Performance Computing (IHPC), A*STAR (Agency for Science, Technology and Research), Connexis, Singapore 138632, Singapore [2] Bioinformatics Institute (BII), A*STAR (Agency for Science, Technology and Research), Singapore 138671, Singapore
| | - Ernesto Guccione
- 1] Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore [2] Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore [3] Cancer Science Institute of Singapore (CSI), National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore
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92
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Kim E, Ilagan JO, Liang Y, Daubner GM, Lee SCW, Ramakrishnan A, Li Y, Chung YR, Micol JB, Murphy ME, Cho H, Kim MK, Zebari AS, Aumann S, Park CY, Buonamici S, Smith PG, Deeg HJ, Lobry C, Aifantis I, Modis Y, Allain FHT, Halene S, Bradley RK, Abdel-Wahab O. SRSF2 Mutations Contribute to Myelodysplasia by Mutant-Specific Effects on Exon Recognition. Cancer Cell 2015; 27:617-30. [PMID: 25965569 PMCID: PMC4429920 DOI: 10.1016/j.ccell.2015.04.006] [Citation(s) in RCA: 424] [Impact Index Per Article: 47.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 02/19/2015] [Accepted: 04/10/2015] [Indexed: 12/14/2022]
Abstract
Mutations affecting spliceosomal proteins are the most common mutations in patients with myelodysplastic syndromes (MDS), but their role in MDS pathogenesis has not been delineated. Here we report that mutations affecting the splicing factor SRSF2 directly impair hematopoietic differentiation in vivo, which is not due to SRSF2 loss of function. By contrast, SRSF2 mutations alter SRSF2's normal sequence-specific RNA binding activity, thereby altering the recognition of specific exonic splicing enhancer motifs to drive recurrent mis-splicing of key hematopoietic regulators. This includes SRSF2 mutation-dependent splicing of EZH2, which triggers nonsense-mediated decay, which, in turn, results in impaired hematopoietic differentiation. These data provide a mechanistic link between a mutant spliceosomal protein, alterations in the splicing of key regulators, and impaired hematopoiesis.
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Affiliation(s)
- Eunhee Kim
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Janine O Ilagan
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Yang Liang
- Hematology, Yale Comprehensive Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Gerrit M Daubner
- Institute for Molecular Biology and Biophysics, ETH, 8093 Zürich, Switzerland
| | - Stanley C-W Lee
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Aravind Ramakrishnan
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Division of Medical Oncology, School of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Yue Li
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Young Rock Chung
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jean-Baptiste Micol
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Michele E Murphy
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Hana Cho
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Min-Kyung Kim
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ahmad S Zebari
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Shlomzion Aumann
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Christopher Y Park
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | | | - H Joachim Deeg
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Division of Medical Oncology, School of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Camille Lobry
- Institut National de la Santé et de la Recherche Medicale (INSERM) U1009, Institut Gustave Roussy, 94805 Villejuif, France; Université Paris-Sud, 91400 Orsay, France
| | - Iannis Aifantis
- Howard Hughes Medical Institute and Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Yorgo Modis
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Frederic H-T Allain
- Institute for Molecular Biology and Biophysics, ETH, 8093 Zürich, Switzerland
| | - Stephanie Halene
- Hematology, Yale Comprehensive Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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93
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Gupte A, Baker EK, Wan SS, Stewart E, Loh A, Shelat AA, Gould CM, Chalk AM, Taylor S, Lackovic K, Karlström Å, Mutsaers AJ, Desai J, Madhamshettiwar PB, Zannettino ACW, Burns C, Huang DCS, Dyer MA, Simpson KJ, Walkley CR. Systematic Screening Identifies Dual PI3K and mTOR Inhibition as a Conserved Therapeutic Vulnerability in Osteosarcoma. Clin Cancer Res 2015; 21:3216-29. [PMID: 25862761 PMCID: PMC4506243 DOI: 10.1158/1078-0432.ccr-14-3026] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 03/26/2015] [Indexed: 01/08/2023]
Abstract
PURPOSE Osteosarcoma is the most common cancer of bone occurring mostly in teenagers. Despite rapid advances in our knowledge of the genetics and cell biology of osteosarcoma, significant improvements in patient survival have not been observed. The identification of effective therapeutics has been largely empirically based. The identification of new therapies and therapeutic targets are urgently needed to enable improved outcomes for osteosarcoma patients. EXPERIMENTAL DESIGN We have used genetically engineered murine models of human osteosarcoma in a systematic, genome-wide screen to identify new candidate therapeutic targets. We performed a genome-wide siRNA screen, with or without doxorubicin. In parallel, a screen of therapeutically relevant small molecules was conducted on primary murine- and primary human osteosarcoma-derived cell cultures. All results were validated across independent cell cultures and across human and mouse osteosarcoma. RESULTS The results from the genetic and chemical screens significantly overlapped, with a profound enrichment of pathways regulated by PI3K and mTOR pathways. Drugs that concurrently target both PI3K and mTOR were effective at inducing apoptosis in primary osteosarcoma cell cultures in vitro in both human and mouse osteosarcoma, whereas specific PI3K or mTOR inhibitors were not effective. The results were confirmed with siRNA and small molecule approaches. Rationale combinations of specific PI3K and mTOR inhibitors could recapitulate the effect on osteosarcoma cell cultures. CONCLUSIONS The approaches described here have identified dual inhibition of the PI3K-mTOR pathway as a sensitive, druggable target in osteosarcoma, and provide rationale for translational studies with these agents.
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Affiliation(s)
- Ankita Gupte
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia. Department of Medicine, St. Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, Australia
| | - Emma K Baker
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia. Department of Medicine, St. Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, Australia
| | - Soo-San Wan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia. Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Elizabeth Stewart
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Amos Loh
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Anang A Shelat
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Cathryn M Gould
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | - Alistair M Chalk
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia. Department of Medicine, St. Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, Australia
| | - Scott Taylor
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia. Department of Medicine, St. Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, Australia
| | - Kurt Lackovic
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia. Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Åsa Karlström
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Anthony J Mutsaers
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia. Department of Medicine, St. Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, Australia. Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Jayesh Desai
- Department of Medical Oncology, Royal Melbourne Hospital, Melbourne, Victoria, Australia. Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Piyush B Madhamshettiwar
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Andrew C W Zannettino
- Myeloma Research Laboratory, School of Medical Sciences, Faculty of Health Sciences, University of Adelaide, Adelaide, South Australia, Australia. Cancer Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Chris Burns
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia. Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - David C S Huang
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia. Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Michael A Dyer
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee. Howard Hughes Medical Institute, Chevy Chase, Maryland.
| | - Kaylene J Simpson
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia. Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Carl R Walkley
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia. Department of Medicine, St. Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, Australia. ACRF Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia.
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94
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Carroll PA, Diolaiti D, McFerrin L, Gu H, Djukovic D, Du J, Cheng PF, Anderson S, Ulrich M, Hurley JB, Raftery D, Ayer DE, Eisenman RN. Deregulated Myc requires MondoA/Mlx for metabolic reprogramming and tumorigenesis. Cancer Cell 2015; 27:271-85. [PMID: 25640402 PMCID: PMC4326605 DOI: 10.1016/j.ccell.2014.11.024] [Citation(s) in RCA: 157] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 09/02/2014] [Accepted: 11/21/2014] [Indexed: 12/16/2022]
Abstract
Deregulated Myc transcriptionally reprograms cell metabolism to promote neoplasia. Here we show that oncogenic Myc requires the Myc superfamily member MondoA, a nutrient-sensing transcription factor, for tumorigenesis. Knockdown of MondoA, or its dimerization partner Mlx, blocks Myc-induced reprogramming of multiple metabolic pathways, resulting in apoptosis. Identification and knockdown of genes coregulated by Myc and MondoA have allowed us to define metabolic functions required by deregulated Myc and demonstrate a critical role for lipid biosynthesis in survival of Myc-driven cancer. Furthermore, overexpression of a subset of Myc and MondoA coregulated genes correlates with poor outcome of patients with diverse cancers. Coregulation of cancer metabolism by Myc and MondoA provides the potential for therapeutics aimed at inhibiting MondoA and its target genes.
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Affiliation(s)
- Patrick A Carroll
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, MS A2-025, P.O. Box 19024, Seattle, WA 98109-1024, USA
| | - Daniel Diolaiti
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, MS A2-025, P.O. Box 19024, Seattle, WA 98109-1024, USA
| | - Lisa McFerrin
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, MS A2-025, P.O. Box 19024, Seattle, WA 98109-1024, USA
| | - Haiwei Gu
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican Street, Room S148, P.O. Box 358057, Seattle, WA 98109-8057, USA
| | - Danijel Djukovic
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican Street, Room S148, P.O. Box 358057, Seattle, WA 98109-8057, USA
| | - Jianhai Du
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Pei Feng Cheng
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, MS A2-025, P.O. Box 19024, Seattle, WA 98109-1024, USA
| | - Sarah Anderson
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, MS A2-025, P.O. Box 19024, Seattle, WA 98109-1024, USA
| | - Michelle Ulrich
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, MS A2-025, P.O. Box 19024, Seattle, WA 98109-1024, USA
| | - James B Hurley
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Department of Ophthalmology, University of Washington, Seattle, WA 98195, USA
| | - Daniel Raftery
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican Street, Room S148, P.O. Box 358057, Seattle, WA 98109-8057, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N, Seattle, WA 98109, USA
| | - Donald E Ayer
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope, Salt Lake City, UT 84112, USA
| | - Robert N Eisenman
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, MS A2-025, P.O. Box 19024, Seattle, WA 98109-1024, USA.
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95
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Feng Q, Snider L, Jagannathan S, Tawil R, van der Maarel SM, Tapscott SJ, Bradley RK. A feedback loop between nonsense-mediated decay and the retrogene DUX4 in facioscapulohumeral muscular dystrophy. eLife 2015; 4. [PMID: 25564732 PMCID: PMC4383350 DOI: 10.7554/elife.04996] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 01/07/2015] [Indexed: 12/22/2022] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is a muscular dystrophy caused by
inefficient epigenetic repression of the D4Z4 macrosatellite array and somatic
expression of the DUX4 retrogene. DUX4 is a double homeobox
transcription factor that is normally expressed in the testis and causes apoptosis
and FSHD when misexpressed in skeletal muscle. The mechanism(s) of DUX4 toxicity in
muscle is incompletely understood. We report that DUX4-triggered proteolytic
degradation of UPF1, a central component of the nonsense-mediated decay (NMD)
machinery, is associated with profound NMD inhibition, resulting in global
accumulation of RNAs normally degraded as NMD substrates. DUX4 mRNA is itself
degraded by NMD, such that inhibition of NMD by DUX4 protein stabilizes DUX4 mRNA
through a double-negative feedback loop in FSHD muscle cells. This feedback loop
illustrates an unexpected mode of autoregulatory behavior of a transcription factor,
is consistent with ‘bursts’ of DUX4 expression in FSHD
muscle, and has implications for FSHD pathogenesis. DOI:http://dx.doi.org/10.7554/eLife.04996.001 Genes are sequences of DNA that contain instructions for the cell that must be
carefully controlled because it is not always appropriate or safe for these
instructions to be followed. When genes are active, copies of the DNA are made using
molecules of ribonucleic acid (RNA) and these can then be used as templates to make
proteins. One way genes can be controlled is by adding small chemical tags that mark them out
to be activated or deactivated, known as epigenetic control. The muscle disease
facioscapulohumeral muscular dystrophy (FSHD) is caused by the loss of the chemical
tags that normally keep certain genes switched off in many cell types. One of these
genes is DUX4, which in healthy males is normally only active in the
testes, but in FSHD patients it is also active in other parts of the body. Another way to control genes is by nonsense-mediated decay, where incorrect or
incomplete RNA molecules are destroyed before they can be used to make defective
proteins. In this study, Feng et al. show that when DUX4 is
activated following the failure of epigenetic control in FSHD patients, the
effectiveness of nonsense-mediated decay is also reduced. This results in the
build-up of incorrect RNA molecules inside muscle cells, which can harm the cell. In
fact, 13% of the incorrect RNA molecules that are normally destroyed in cells were
found at higher levels when DUX4 was active. To investigate how DUX4 could work, Feng et al. focused on another
gene called UPF1 because cells without the protein encoded by this
gene have similar defects in nonsense-mediated decay as cells with active
DUX4. No difference was found in how often the
UPF1 gene is activated in FSHD cells and normal cells. However,
the amount of the protein encoded by UPF1 was lower in cells with
FSHD than in normal muscle cells. The experiments show that the protein encoded by
UPF1 is broken down as a result of the activation of the
DUX4 gene, leading to problems with nonsense-mediated decay,
which may result in the worsening of FSHD symptoms. The twist in the tale is that DUX4 itself is also controlled by
nonsense-mediated decay under normal circumstances. Therefore, in diseased cells, a
failure in epigenetic control allows DUX4 to prevent its own
destruction by tampering with nonsense-mediated decay. These findings offer new
insights into the role of the DUX4 gene in FSHD. The next step is to
test whether these defects in nonsense-mediated decay can explain any of the symptoms
of FSHD, such as muscle inflammation. DOI:http://dx.doi.org/10.7554/eLife.04996.002
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Affiliation(s)
- Qing Feng
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Lauren Snider
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Sujatha Jagannathan
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Rabi Tawil
- Department of Neurology, University of Rochester, Rochester, United States
| | | | - Stephen J Tapscott
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States
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96
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Ilagan JO, Ramakrishnan A, Hayes B, Murphy ME, Zebari AS, Bradley P, Bradley RK. U2AF1 mutations alter splice site recognition in hematological malignancies. Genome Res 2015; 25:14-26. [PMID: 25267526 PMCID: PMC4317169 DOI: 10.1101/gr.181016.114] [Citation(s) in RCA: 208] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2014] [Accepted: 09/25/2014] [Indexed: 01/30/2023]
Abstract
Whole-exome sequencing studies have identified common mutations affecting genes encoding components of the RNA splicing machinery in hematological malignancies. Here, we sought to determine how mutations affecting the 3' splice site recognition factor U2AF1 alter its normal role in RNA splicing. We find that U2AF1 mutations influence the similarity of splicing programs in leukemias, but do not give rise to widespread splicing failure. U2AF1 mutations cause differential splicing of hundreds of genes, affecting biological pathways such as DNA methylation (DNMT3B), X chromosome inactivation (H2AFY), the DNA damage response (ATR, FANCA), and apoptosis (CASP8). We show that U2AF1 mutations alter the preferred 3' splice site motif in patients, in cell culture, and in vitro. Mutations affecting the first and second zinc fingers give rise to different alterations in splice site preference and largely distinct downstream splicing programs. These allele-specific effects are consistent with a computationally predicted model of U2AF1 in complex with RNA. Our findings suggest that U2AF1 mutations contribute to pathogenesis by causing quantitative changes in splicing that affect diverse cellular pathways, and give insight into the normal function of U2AF1's zinc finger domains.
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Affiliation(s)
- Janine O Ilagan
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Aravind Ramakrishnan
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; Division of Medical Oncology, School of Medicine, University of Washington, Seattle, Washington 98109, USA
| | - Brian Hayes
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Michele E Murphy
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Ahmad S Zebari
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Philip Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA;
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA;
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97
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Herman JA, Toledo CM, Olson JM, DeLuca JG, Paddison PJ. Molecular pathways: regulation and targeting of kinetochore-microtubule attachment in cancer. Clin Cancer Res 2014; 21:233-9. [PMID: 25104085 DOI: 10.1158/1078-0432.ccr-13-0645] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Kinetochores are large protein structures assembled on centromeric DNA during mitosis that bind to microtubules of the mitotic spindle to orchestrate and power chromosome movements. Deregulation of kinetochore-microtubule (KT-MT) attachments has been implicated in driving chromosome instability and cancer evolution; however, the nature and source of KT-MT attachment defects in cancer cells remain largely unknown. Here, we highlight recent findings suggesting that oncogene-driven changes in kinetochore regulation occur in glioblastoma multiforme (GBM) and possibly other cancers exhibiting chromosome instability, giving rise to novel therapeutic opportunities. In particular, we consider the GLE2p-binding sequence domains of BubR1 and the newly discovered BuGZ, two kinetochore-associated proteins, as candidate therapeutic targets for GBM.
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Affiliation(s)
- Jacob A Herman
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado
| | - Chad M Toledo
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington. Molecular and Cellular Biology Program, University of Washington, Seattle, Washington
| | - James M Olson
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Jennifer G DeLuca
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado.
| | - Patrick J Paddison
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington. Molecular and Cellular Biology Program, University of Washington, Seattle, Washington.
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98
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Weng MT, Luo J. The enigmatic ERH protein: its role in cell cycle, RNA splicing and cancer. Protein Cell 2014; 4:807-12. [PMID: 24078386 DOI: 10.1007/s13238-013-3056-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 08/26/2013] [Indexed: 12/21/2022] Open
Abstract
Enhancer of rudimentary homolog (ERH) is a small, highly conserved protein among eukaryotes. Since its discovery nearly 20 years ago, its molecular function has remained enigmatic. It has been implicated to play a role in transcriptional regulation and in cell cycle. We recently showed that ERH binds to the Sm complex and is required for the mRNA splicing of the mitotic motor protein CENP-E. Furthermore, cancer cells driven by mutations in the KRAS oncogene are particularly sensitive to RNAi-mediated suppression of ERH function, and ERH expression is inversely correlated with survival in colorectal cancer patients whose tumors harbor KRAS mutation. These recent findings indicate that ERH plays an important role in cell cycle through its mRNA splicing activity and is critically required for genomic stability and cancer cell survival.
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99
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Chudnovsky Y, Kim D, Zheng S, Whyte WA, Bansal M, Bray MA, Gopal S, Theisen MA, Bilodeau S, Thiru P, Muffat J, Yilmaz OH, Mitalipova M, Woolard K, Lee J, Nishimura R, Sakata N, Fine HA, Carpenter AE, Silver SJ, Verhaak RGW, Califano A, Young RA, Ligon KL, Mellinghoff IK, Root DE, Sabatini DM, Hahn WC, Chheda MG. ZFHX4 interacts with the NuRD core member CHD4 and regulates the glioblastoma tumor-initiating cell state. Cell Rep 2014; 6:313-24. [PMID: 24440720 PMCID: PMC4041390 DOI: 10.1016/j.celrep.2013.12.032] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2013] [Revised: 11/27/2013] [Accepted: 12/18/2013] [Indexed: 12/18/2022] Open
Abstract
Glioblastoma (GBM) harbors subpopulations of therapy-resistant tumor-initiating cells (TICs) that are self-renewing and multipotent. To understand the regulation of the TIC state, we performed an image-based screen for genes regulating GBM TIC maintenance and identified ZFHX4, a 397 kDa transcription factor. ZFHX4 is required to maintain TIC-associated and normal human neural precursor cell phenotypes in vitro, suggesting that ZFHX4 regulates differentiation, and its suppression increases glioma-free survival in intracranial xenografts. ZFHX4 interacts with CHD4, a core member of the nucleosome remodeling and deacetylase (NuRD) complex. ZFHX4 and CHD4 bind to overlapping sets of genomic loci and control similar gene expression programs. Using expression data derived from GBM patients, we found that ZFHX4 significantly affects CHD4-mediated gene expression perturbations, which defines ZFHX4 as a master regulator of CHD4. These observations define ZFHX4 as a regulatory factor that links the chromatin-remodeling NuRD complex and the GBM TIC state.
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Affiliation(s)
- Yakov Chudnovsky
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Dohoon Kim
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Siyuan Zheng
- Department of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Warren A Whyte
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Mukesh Bansal
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032, USA
| | | | - Shuba Gopal
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Matthew A Theisen
- Department of Medical Oncology, Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Steve Bilodeau
- Centre de Recherche sur le Cancer and Centre de Recherche du CHU de Québec (Hôtel-Dieu de Québec), Université Laval, QC G1R 2J6, Canada; Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Faculté de Médecine, Université Laval, QC G1R 2J6, Canada
| | - Prathapan Thiru
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Julien Muffat
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Omer H Yilmaz
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02139, USA
| | - Maya Mitalipova
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Kevin Woolard
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Jeongwu Lee
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland, OH 44195, USA
| | - Riko Nishimura
- Department of Molecular and Cellular Biochemistry, Osaka University Graduate School of Dentistry, Suita, Osaka 565-0871, Japan
| | - Nobuo Sakata
- Department of Biochemistry, Showa Pharmaceutical University, Machida, Tokyo 194-8543, Japan
| | - Howard A Fine
- Division of Hematology and Medical Oncology, New York University Cancer Institute, New York University Langone Medical Center, New York, NY 10016, USA; Brain Tumor Center, New York University Cancer Institute, New York University Langone Medical Center, New York, NY 10016, USA
| | | | - Serena J Silver
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Roel G W Verhaak
- Department of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Andrea Califano
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032, USA; Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Keith L Ligon
- Department of Medical Oncology, Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Ingo K Mellinghoff
- Department of Neurology, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Department of Pharmacology, Weill-Cornell Graduate School of Biomedical Sciences, New York, NY 10021, USA
| | - David E Root
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - David M Sabatini
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA.
| | - William C Hahn
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
| | - Milan G Chheda
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Neurology, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
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100
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Toledo CM, Herman JA, Olsen JB, Ding Y, Corrin P, Girard EJ, Olson JM, Emili A, DeLuca JG, Paddison PJ. BuGZ is required for Bub3 stability, Bub1 kinetochore function, and chromosome alignment. Dev Cell 2014; 28:282-94. [PMID: 24462187 DOI: 10.1016/j.devcel.2013.12.014] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Revised: 12/12/2013] [Accepted: 12/20/2013] [Indexed: 01/01/2023]
Abstract
During mitosis, the spindle assembly checkpoint (SAC) monitors the attachment of kinetochores (KTs) to the plus ends of spindle microtubules (MTs) and prevents anaphase onset until chromosomes are aligned and KTs are under proper tension. Here, we identify a SAC component, BuGZ/ZNF207, from an RNAi viability screen in human glioblastoma multiforme (GBM) brain tumor stem cells. BuGZ binds to and stabilizes Bub3 during interphase and mitosis through a highly conserved GLE2p-binding sequence (GLEBS) domain. Inhibition of BuGZ results in loss of both Bub3 and its binding partner Bub1 from KTs, reduction of Bub1-dependent phosphorylation of centromeric histone H2A, attenuation of KT-based Aurora B kinase activity, and lethal chromosome congression defects in cancer cells. Phylogenetic analysis indicates that BuGZ orthologs are highly conserved among eukaryotes, but are conspicuously absent from budding and fission yeasts. These findings suggest that BuGZ has evolved to facilitate Bub3 activity and chromosome congression in higher eukaryotes.
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Affiliation(s)
- Chad M Toledo
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Jacob A Herman
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Jonathan B Olsen
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Yu Ding
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Philip Corrin
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Emily J Girard
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - James M Olson
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Andrew Emili
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Jennifer G DeLuca
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA.
| | - Patrick J Paddison
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA.
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