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Wheeler EC, Martin BJE, Doyle WC, Neaher S, Conway CA, Pitton CN, Gorelov RA, Donahue M, Jann JC, Abdel-Wahab O, Taylor J, Seiler M, Buonamici S, Pikman Y, Garcia JS, Belizaire R, Adelman K, Tothova Z. Splicing modulators impair DNA damage response and induce killing of cohesin-mutant MDS and AML. Sci Transl Med 2024; 16:eade2774. [PMID: 38170787 DOI: 10.1126/scitranslmed.ade2774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 10/08/2023] [Indexed: 01/05/2024]
Abstract
Splicing modulation is a promising treatment strategy pursued to date only in splicing factor-mutant cancers; however, its therapeutic potential is poorly understood outside of this context. Like splicing factors, genes encoding components of the cohesin complex are frequently mutated in cancer, including myelodysplastic syndromes (MDS) and secondary acute myeloid leukemia (AML), where they are associated with poor outcomes. Here, we showed that cohesin mutations are biomarkers of sensitivity to drugs targeting the splicing factor 3B subunit 1 (SF3B1) H3B-8800 and E-7107. We identified drug-induced alterations in splicing, and corresponding reduced gene expression, of a number of DNA repair genes, including BRCA1 and BRCA2, as the mechanism underlying this sensitivity in cell line models, primary patient samples and patient-derived xenograft (PDX) models of AML. We found that DNA damage repair genes are particularly sensitive to exon skipping induced by SF3B1 modulators due to their long length and large number of exons per transcript. Furthermore, we demonstrated that treatment of cohesin-mutant cells with SF3B1 modulators not only resulted in impaired DNA damage response and accumulation of DNA damage, but it sensitized cells to subsequent killing by poly(ADP-ribose) polymerase (PARP) inhibitors and chemotherapy and led to improved overall survival of PDX models of cohesin-mutant AML in vivo. Our findings expand the potential therapeutic benefits of SF3B1 splicing modulators to include cohesin-mutant MDS and AML.
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Affiliation(s)
- Emily C Wheeler
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Benjamin J E Martin
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - William C Doyle
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Sofia Neaher
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Caroline A Conway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Caroline N Pitton
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Rebecca A Gorelov
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Melanie Donahue
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Johann C Jann
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Omar Abdel-Wahab
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Justin Taylor
- Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Michael Seiler
- H3 Biomedicine Inc., 300 Technology Square, Cambridge, MA 02139, USA
| | - Silvia Buonamici
- H3 Biomedicine Inc., 300 Technology Square, Cambridge, MA 02139, USA
| | - Yana Pikman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02215 USA
| | - Jacqueline S Garcia
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Roger Belizaire
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Karen Adelman
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115, USA
| | - Zuzana Tothova
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115, USA
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2
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Gavory G, Ghandi M, d’Alessandro AC, Bonenfant D, Cabanski M, Cantagallo L, Chicas A, Chen Q, Diesslin A, King C, Massafra V, Narayan R, Osmont A, Peck D, Ortiz CP, Schillo M, Singh A, Tiedt R, Tortoioli S, Buonamici S, Janku F, Wallace O, Fasching B. Abstract 3449: Development of MRT-2359, an orally bioavailable GSPT1 molecular glue degrader, for the treatment of lung cancers with MYC-induced translational addiction. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-3449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
MYC transcription factors are well-established drivers of human cancers but despite being amongst the most frequently altered oncogenes, no approved therapy targeting MYC-driven tumors has been developed to date. MYC-driven cancers are known to be addicted to protein translation. This addiction creates a dependency on critical components of the translational machinery providing in turn a unique opportunity for therapeutic intervention. We hypothesized that targeting the translation termination factor GSPT1, a key regulator of protein synthesis, would constitute a vulnerability for MYC-driven tumors. Herein we further describe MRT-2359 a potent, selective and orally bioavailable degrader of GSPT1. MRT-2359 was rationally designed using our QuEENTM discovery engine and optimized to achieve a profound and preferential antiproliferative activity in MYC-driven cell lines, such as high N- and L-MYC mRNA expressing non-small cell lung cancer (NSCLC) and small cell lung cancer (SCLC) lines. In line with expectations, MRT-2359 activity is dependent on both CRBN and the GSPT1 G-loop degron. We further demonstrate using an inducible system that the sole expression of either N- or L-MYC is sufficient to sensitize initially resistant NSCLC cells to MRT-2359. These studies therefore establish a causal link between N- and L-MYC expression and sensitivity to MRT-2359. Unlike MRT-2359, agents targeting the protein translation initiation machinery or repressing MYC transcription (CDK9 inhibitor) failed to show such differential activity. Mechanistically, RiboSeq and polysome profiling revealed that treatment with MRT-2359 in the N- or L-MYC high cell lines induces ribosome stalling at the stop codon, increased monosomes and decreased polysomes. These changes are indicative of translational repression and were confirmed using puromycilation assays. Proteomics and RNAseq studies finally demonstrated a significant reduction in the total levels of N- or L-MYC leading in turn to the downmodulation of MYC target genes. Despite robust degradation of GSPT1, no marked effect was observed in these assays in low N- or L-MYC lines, confirming the selective activity of MRT-2359 in MYC-driven lung cancers. Last, the anti-tumor activity of MRT-2359 was assessed in >80 lung patient-derived xenografts (PDXs). MRT-2359 demonstrated preferential activity in N- and L-MYC high NSCLC and SCLC PDXs, including numerous instances of tumor regressions, when dosed orally daily or intermittently. Similar levels of anti-tumor activity were also observed in neuroendocrine lung cancer and lymphoma PDXs. Together these results warrant further investigations in the clinic. Oral MRT-2359 is currently in a Phase 1/2 clinical trial in selected cancer patients with MYC-driven NSCLC, SCLC, high grade neuroendocrine cancers and diffuse large B-cell lymphoma (NCT05546268).
Citation Format: Gerald Gavory, Mahmoud Ghandi, Anne-Cecile d’Alessandro, Debora Bonenfant, Maciej Cabanski, Lisa Cantagallo, Agustin Chicas, Qian Chen, Anna Diesslin, Christopher King, Vittoria Massafra, Rajiv Narayan, Arnaud Osmont, Dave Peck, Carolina Perdomo Ortiz, Martin Schillo, Ambika Singh, Ralph Tiedt, Simone Tortoioli, Silvia Buonamici, Filip Janku, Owen Wallace, Bernhard Fasching. Development of MRT-2359, an orally bioavailable GSPT1 molecular glue degrader, for the treatment of lung cancers with MYC-induced translational addiction [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3449.
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Affiliation(s)
| | | | | | | | | | | | | | - Qian Chen
- 1Monte Rosa Therapeutics, Inc., Basel, Switzerland
| | | | | | | | | | | | - Dave Peck
- 2Monte Rosa Therapeutics, Inc., Boston, MA
| | | | | | - Ambika Singh
- 1Monte Rosa Therapeutics, Inc., Basel, Switzerland
| | - Ralph Tiedt
- 1Monte Rosa Therapeutics, Inc., Basel, Switzerland
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3
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Gavory G, Ghandi M, d’Alessandro AC, Bonenfant D, Chicas A, Delobel F, Demarco B, Flohr A, King C, Laine AL, Massafra V, Narayan R, Osmont A, Ottaviani G, Peck D, Pessa S, Rubin N, Ryckmans T, Schillo M, Singh A, Tortoioli S, Vigil D, Zarayskiy V, Castle J, Janku F, Wallace O, Buonamici S, Fasching B. Abstract 3929: Identification of MRT-2359 a potent, selective and orally bioavailable GSPT1-directed molecular glue degrader (MGD) for the treatment of cancers with Myc-induced translational addiction. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Myc transcription factors are well-established drivers of human cancers. However, despite being amongst the most frequently mutated, translocated and overexpressed oncogenes, no therapy targeting the Myc family members directly has been developed to date. To sustain uncontrolled cell proliferation and tumor growth, Myc-driven cancers are known to be addicted to protein translation. This addiction creates a dependency on critical components of the translational machinery providing in turn a unique opportunity for therapeutic intervention. We hypothesized that targeting the translational termination factor GSPT1, a key regulator of protein synthesis, would constitute a vulnerability for Myc-driven tumors. GSPT1 contains a well-defined degron allowing for the recruitment of the E3 ligase cereblon (CRBN) and subsequent proteasomal degradation in the presence of molecular glue degraders. Herein we describe a novel orally bioavailable GSPT1-directed small molecule degrader MRT-2359, which has been rationally designed and optimized to selectively induce apoptosis in translationally addicted cells. MRT-2359 promotes complex formation between CRBN and GSPT1 and potently induces GSPT1 degradation in a CRBN- and degron-dependent manner. The high selectivity of MRT-2359 was subsequently demonstrated by the lack of activity in cells expressing a non-degradable GSPT1 mutant. Although MRT-2359 degrades GSPT1 in all the cell lines tested, profiling in a large panel of cancer lines revealed profound and preferential antiproliferative activity in Myc-driven cell lines, such as high N-Myc expressing non-small cell lung cancer (NSCLC) lines and high L-Myc expressing small cell lung cancer (SCLC) lines. In the Myc-driven cells, degradation of GSPT1 led to translational repression as manifested by a global shift from polysomes to monosomes resulting in the reduction of a subset of proteins as assessed by quantitative proteomics. In particular, N- or L-Myc protein levels decreased and as a consequence the known Myc target genes were downregulated at the mRNA level. Despite the robust degradation of GSPT1, no marked effect was observed in low N-Myc lines, confirming the selective activity of our GSPT1 degrader in Myc-driven lung cancers. Finally, oral administration of MRT-2359 in high N-Myc NSCLC xenografts and PDXs led to complete intratumoral GSPT1 degradation and concomitant decrease in N-Myc protein levels, resulting in tumor regression. In contrast, MRT-2359 had limited or no activity in low N-Myc NSCLC models, further corroborating the selective vulnerability of Myc-driven tumors to GSPT1 degradation. Together these data support the therapeutic potential of GSPT1-directed MGDs in Myc-driven solid tumors addicted to the protein translation machinery and warrant rapid evaluation towards the clinic.
Citation Format: Gerald Gavory, Mahmoud Ghandi, Anne-Cecile d’Alessandro, Debora Bonenfant, Agustin Chicas, Frederic Delobel, Brad Demarco, Alexander Flohr, Christopher King, Anne-Laure Laine, Vittoria Massafra, Rajiv Narayan, Arnaud Osmont, Giorgio Ottaviani, Dave Peck, Sarah Pessa, Nooreen Rubin, Thomas Ryckmans, Martin Schillo, Ambika Singh, Simone Tortoioli, Dominico Vigil, Vladislav Zarayskiy, John Castle, Filip Janku, Owen Wallace, Silvia Buonamici, Bernhard Fasching. Identification of MRT-2359 a potent, selective and orally bioavailable GSPT1-directed molecular glue degrader (MGD) for the treatment of cancers with Myc-induced translational addiction [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3929.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Dave Peck
- 2Monte Rosa Therapeutics, Boston, MA
| | | | | | | | | | | | | | | | | | - John Castle
- 1Monte Rosa Therapeutics, Basel, Switzerland
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4
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Gavory G, Fasching B, Bonenfant D, Sadok A, Singh A, Schillo M, Massafra V, d’Alessandro AC, Castle J, Ghandi M, Chicas A, Delobel F, Flohr A, Ottaviani G, Ryckmans T, Laine AL, Eidam O, Wang H, Bernett I, Chan L, Gorrini C, Roumiliotis T, Choudhary J, LeBihan YV, Cabry M, Stubbs M, Burke R, Van Montfort R, Caldwell J, Chopra R, Collins I, Buonamici S. Abstract LBA004: Identification of GSPT1-directed molecular glue degrader (MGD) for the treatment of Myc-driven breast cancer. Mol Cancer Ther 2021. [DOI: 10.1158/1535-7163.targ-21-lba004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The Myc family of transcription factors is a well-established driver of human cancers. However, despite being amongst the most frequently mutated, translocated and overexpressed oncogenes, no therapy directly targeting the Myc family members has been developed to date. Abnormal activation of Myc results in uncontrolled cell growth that is associated with high translational output and ramp up of the protein translational machinery. This creates a dependency to protein translation and in turn represents a potential therapeutic vulnerability for Myc-driven tumors. Based on these considerations, we hypothesized that targeting the translational termination factor GSPT1, a key player of protein synthesis, may constitute a vulnerability for Myc-driven tumors. Using our proprietary Quantitative and Engineered Elimination of Neosubstrates (QuEENTM) platform we characterized and explored the known G-loop degron in GSPT1 that renders it amenable to cereblon-induced degradation by molecular glue degraders (MGDs). We rationally designed and subsequently screened a proprietary library of cereblon-binding small molecules, including GSPT1-directed MGDs, in human mammary epithelial cells (HMECs) expressing doxycycline-inducible c-Myc. Doxycycline treatment led to sustained c-Myc expression and as a consequence to the induction of key biomarkers of enhanced protein translation, such as phospho 4EBP1 (p4EBP1). We identified MRT-048 as a potent and highly selective GSPT1 degrader and demonstrated its ability to induce cell death in Myc-driven HMEC cells whilst sparing control cells (EC50 0.64 μM vs 30 μM respectively). This confirmed the selective vulnerability of Myc-driven cell growth to GSPT1 degradation. In follow-up studies, we confirmed the correlation between p4EBP1 as biomarker of Myc-activation and sensitivity to MRT-048 in a large panel of breast cancer cell lines. Moreover, MRT-048 treatment of animals xenografted with breast cancer cells induced tumor regression and was associated with complete GSPT1 degradation. Mechanistically, we observed that GSPT1 degradation induced by MRT-048 led to inhibition of genes regulated by Myc and ribosomal stalling at stop codons of several mRNAs. Additionally, polysome profiling of cancer cells treated with MRT-048 was associated with a global reduction of the intensities of the polysome peaks and concomitant increase in the monosome peaks as previously observed in GSPT1 knockdown experiments, suggesting that GSPT1 degradation by our MGD molecules affects both the termination and initiation stages of protein translation. We believe these data support the therapeutic potential of GSPT1-directed MGDs in Myc-driven tumors dependent on protein translation machinery.
Citation Format: Gerald Gavory, Bernhard Fasching, Debora Bonenfant, Amine Sadok, Ambika Singh, Martin Schillo, Vittoria Massafra, Anne-Cecile d’Alessandro, John Castle, Mahmoud Ghandi, Agustin Chicas, Frederic Delobel, Alexander Flohr, Giorgio Ottaviani, Thomas Ryckmans, Anne-Laure Laine, Oliv Eidam, Hannah Wang, Ilona Bernett, Laura Chan, Chiara Gorrini, Theo Roumiliotis, Jyoti Choudhary, Yann-Vai LeBihan, Marc Cabry, Mark Stubbs, Rosemary Burke, Rob Van Montfort, John Caldwell, Rajesh Chopra, Ian Collins, Silvia Buonamici. Identification of GSPT1-directed molecular glue degrader (MGD) for the treatment of Myc-driven breast cancer [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr LBA004.
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Affiliation(s)
| | | | | | - Amine Sadok
- 1Monte Rosa Therapeutics AG, Basel, Switzerland,
| | - Ambika Singh
- 1Monte Rosa Therapeutics AG, Basel, Switzerland,
| | | | | | | | - John Castle
- 1Monte Rosa Therapeutics AG, Basel, Switzerland,
| | | | | | | | | | | | | | | | - Oliv Eidam
- 3Ridgeline Discovery, Basel, Switzerland,
| | - Hannah Wang
- 4The Institute of Cancer Research, London, United Kingdom,
| | - Ilona Bernett
- 4The Institute of Cancer Research, London, United Kingdom,
| | - Laura Chan
- 4The Institute of Cancer Research, London, United Kingdom,
| | - Chiara Gorrini
- 4The Institute of Cancer Research, London, United Kingdom,
| | | | | | | | - Marc Cabry
- 4The Institute of Cancer Research, London, United Kingdom,
| | - Mark Stubbs
- 4The Institute of Cancer Research, London, United Kingdom,
| | - Rosemary Burke
- 4The Institute of Cancer Research, London, United Kingdom,
| | | | - John Caldwell
- 4The Institute of Cancer Research, London, United Kingdom,
| | | | - Ian Collins
- 4The Institute of Cancer Research, London, United Kingdom,
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5
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Togami K, Chung SS, Madan V, Booth CAG, Kenyon CM, Cabal-Hierro L, Taylor J, Kim SS, Griffin GK, Ghandi M, Li J, Li YY, Angelot-Delettre F, Biichle S, Seiler M, Buonamici S, Lovitch SB, Louissaint A, Morgan EA, Jardin F, Piccaluga PP, Weinstock DM, Hammerman PS, Yang H, Konopleva M, Pemmaraju N, Garnache-Ottou F, Abdel-Wahab O, Koeffler HP, Lane AA. Sex-biased ZRSR2 mutations in myeloid malignancies impair plasmacytoid dendritic cell activation and apoptosis. Cancer Discov 2021; 12:522-541. [PMID: 34615655 PMCID: PMC8831459 DOI: 10.1158/2159-8290.cd-20-1513] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 08/17/2021] [Accepted: 10/01/2021] [Indexed: 11/16/2022]
Abstract
Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is an aggressive leukemia of plasmacytoid dendritic cells (pDCs). BPDCN occurs at least three times more frequently in men than women, but the reasons for this sex bias are unknown. Here, studying genomics of primary BPDCN and modeling disease-associated mutations, we link acquired alterations in RNA splicing to abnormal pDC development and inflammatory response through Toll-like receptors. Loss-of-function mutations in ZRSR2, an X chromosome gene encoding a splicing factor, are enriched in BPDCN and nearly all mutations occur in males. ZRSR2 mutation impairs pDC activation and apoptosis after inflammatory stimuli, associated with intron retention and inability to upregulate the transcription factor IRF7. In vivo, BPDCN-associated mutations promote pDC expansion and signatures of decreased activation. These data support a model in which male-biased mutations in hematopoietic progenitors alter pDC function and confer protection from apoptosis, which may impair immunity and predispose to leukemic transformation.
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Affiliation(s)
| | | | - Vikas Madan
- Cancer Science Institute of Singapore, National University of Singapore
| | | | | | | | - Justin Taylor
- Medicine/Hematology, Sylvester Comprehensive Cancer Center
| | | | | | | | - Jia Li
- National University of Singapore
| | - Yvonne Y Li
- Department of Medical Oncology, Dana-Farber Cancer Institute
| | | | | | | | | | | | | | | | | | - Pier Paolo Piccaluga
- Department of Experimental, Diagnostic, and Specialty Medicine, Bologna University
| | | | | | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore
| | - Marina Konopleva
- Department of Leukemia, The University of Texas MD Anderson Cancer Center
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6
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Zhang D, Hu Q, Liu X, Ji Y, Chao HP, Tracz A, Kirk J, Buonamici S, Zhu P, Wang J, liu S, Tang D. Abstract 2197: Dysregulated alternative splicing landscape identifies intron retention as a hallmark and spliceosome as a therapeutic vulnerability in aggressive prostate cancer. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-2197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Dysregulation of mRNA alternative splicing (AS) has been implicated in development and progression of hematological malignancies. How the global AS dysregulation contributes to the development and progression of solid tumors is under-studied and remains generally unclear. Here we describe the first comprehensive AS landscape in the spectrum of human prostate cancer (PCa) development, progression and therapy resistance. We find that the severity of splicing dysregulation correlates with disease progression and establish intron retention (IR) as a hallmark of PCa stemness and aggressiveness. Systematic interrogation of 274 splicing-regulatory genes (SRGs) uncovers prevalent SRG mutations associated with, mainly, copy number variations leading to mis-expression of ~68% of SRGs during PCa evolution. Consequently, we identify many SRGs as prognostic markers associated with splicing disruption and patient outcome. Interestingly, androgen receptor (AR) controls a splicing program distinct from its transcriptional regulation. The spliceosome modulator, E7107, reverses cancer aggressiveness and inhibits the growth of castration-resistant PCa (CRPC) xenograft models and of the autochthonous Hi-Myc tumors. Altogether, our studies establish aberrant AS landscape caused by dysregulated SRGs as a hallmark of PCa aggressiveness and a novel therapeutic vulnerability for CRPC.
Citation Format: Dingxiao Zhang, qiang Hu, Xiaozhuo Liu, Yibing Ji, Hsueh-Ping Chao, Amanda Tracz, Jason Kirk, Silvia Buonamici, Ping Zhu, Jianmin Wang, song liu, Dean Tang. Dysregulated alternative splicing landscape identifies intron retention as a hallmark and spliceosome as a therapeutic vulnerability in aggressive prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2197.
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Affiliation(s)
| | - qiang Hu
- 2Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Xiaozhuo Liu
- 2Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Yibing Ji
- 2Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Hsueh-Ping Chao
- 3University of Texas MD Anderson Cancer Center, Smithville, TX
| | - Amanda Tracz
- 2Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Jason Kirk
- 2Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | | | - Ping Zhu
- 4H3 Biomedicine, Inc., Cambridgee, MA
| | - Jianmin Wang
- 2Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - song liu
- 2Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Dean Tang
- 2Roswell Park Comprehensive Cancer Center, Buffalo, NY
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7
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Bowling EA, Wang JH, Gong F, Wu W, Neill NJ, Kim IS, Tyagi S, Orellana M, Kurley SJ, Dominguez-Vidaña R, Chung HC, Hsu TYT, Dubrulle J, Saltzman AB, Li H, Meena JK, Canlas GM, Chamakuri S, Singh S, Simon LM, Olson CM, Dobrolecki LE, Lewis MT, Zhang B, Golding I, Rosen JM, Young DW, Malovannaya A, Stossi F, Miles G, Ellis MJ, Yu L, Buonamici S, Lin CY, Karlin KL, Zhang XHF, Westbrook TF. Spliceosome-targeted therapies trigger an antiviral immune response in triple-negative breast cancer. Cell 2021; 184:384-403.e21. [PMID: 33450205 PMCID: PMC8635244 DOI: 10.1016/j.cell.2020.12.031] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/29/2020] [Accepted: 12/21/2020] [Indexed: 12/16/2022]
Abstract
Many oncogenic insults deregulate RNA splicing, often leading to hypersensitivity of tumors to spliceosome-targeted therapies (STTs). However, the mechanisms by which STTs selectively kill cancers remain largely unknown. Herein, we discover that mis-spliced RNA itself is a molecular trigger for tumor killing through viral mimicry. In MYC-driven triple-negative breast cancer, STTs cause widespread cytoplasmic accumulation of mis-spliced mRNAs, many of which form double-stranded structures. Double-stranded RNA (dsRNA)-binding proteins recognize these endogenous dsRNAs, triggering antiviral signaling and extrinsic apoptosis. In immune-competent models of breast cancer, STTs cause tumor cell-intrinsic antiviral signaling, downstream adaptive immune signaling, and tumor cell death. Furthermore, RNA mis-splicing in human breast cancers correlates with innate and adaptive immune signatures, especially in MYC-amplified tumors that are typically immune cold. These findings indicate that dsRNA-sensing pathways respond to global aberrations of RNA splicing in cancer and provoke the hypothesis that STTs may provide unexplored strategies to activate anti-tumor immune pathways.
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Affiliation(s)
- Elizabeth A Bowling
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jarey H Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fade Gong
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - William Wu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Nicholas J Neill
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ik Sun Kim
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Siddhartha Tyagi
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mayra Orellana
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sarah J Kurley
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rocio Dominguez-Vidaña
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hsiang-Ching Chung
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tiffany Y-T Hsu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Julien Dubrulle
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alexander B Saltzman
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Heyuan Li
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jitendra K Meena
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gino M Canlas
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Srinivas Chamakuri
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Swarnima Singh
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lukas M Simon
- Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Calla M Olson
- Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lacey E Dobrolecki
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michael T Lewis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bing Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ido Golding
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jeffrey M Rosen
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Damian W Young
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA; Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anna Malovannaya
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fabio Stossi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - George Miles
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Matthew J Ellis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lihua Yu
- H3Biomedicine, Cambridge, MA 02139, USA
| | | | - Charles Y Lin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kristen L Karlin
- Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xiang H-F Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Thomas F Westbrook
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA.
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8
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Zhang D, Hu Q, Liu X, Ji Y, Chao HP, Liu Y, Tracz A, Kirk J, Buonamici S, Zhu P, Wang J, Liu S, Tang DG. Intron retention is a hallmark and spliceosome represents a therapeutic vulnerability in aggressive prostate cancer. Nat Commun 2020; 11:2089. [PMID: 32350277 PMCID: PMC7190674 DOI: 10.1038/s41467-020-15815-7] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 03/31/2020] [Indexed: 02/06/2023] Open
Abstract
The role of dysregulation of mRNA alternative splicing (AS) in the development and progression of solid tumors remains to be defined. Here we describe the first comprehensive AS landscape in the spectrum of human prostate cancer (PCa) evolution. We find that the severity of splicing dysregulation correlates with disease progression and establish intron retention as a hallmark of PCa stemness and aggressiveness. Systematic interrogation of 274 splicing-regulatory genes (SRGs) uncovers prevalent genomic copy number variations (CNVs), leading to mis-expression of ~68% of SRGs during PCa development and progression. Consequently, many SRGs are prognostic. Surprisingly, androgen receptor controls a splicing program distinct from its transcriptional regulation. The spliceosome modulator, E7107, reverses cancer aggressiveness and inhibits castration-resistant PCa (CRPC) in xenograft and autochthonous PCa models. Altogether, our studies establish aberrant AS landscape caused by dysregulated SRGs as a hallmark of PCa aggressiveness and the spliceosome as a therapeutic vulnerability for CRPC.
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Affiliation(s)
- Dingxiao Zhang
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, New York, 14263, USA. .,College of Biology, Hunan University, Changsha, 410082, China. .,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Qiang Hu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, 14263, New York, USA
| | - Xiaozhuo Liu
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, New York, 14263, USA
| | - Yibing Ji
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, New York, 14263, USA
| | - Hsueh-Ping Chao
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, 78957, Texas, USA
| | - Yan Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Amanda Tracz
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, New York, 14263, USA
| | - Jason Kirk
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, New York, 14263, USA
| | - Silvia Buonamici
- H3 Biomedicine, Inc., 300 Technology Square, Cambridge, Massachusetts, 02139, USA
| | - Ping Zhu
- H3 Biomedicine, Inc., 300 Technology Square, Cambridge, Massachusetts, 02139, USA
| | - Jianmin Wang
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, 14263, New York, USA
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, 14263, New York, USA.
| | - Dean G Tang
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, New York, 14263, USA. .,Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, 78957, Texas, USA.
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9
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Seiler M, Peng S, Agrawal AA, Palacino J, Teng T, Zhu P, Smith PG, Buonamici S, Yu L. Somatic Mutational Landscape of Splicing Factor Genes and Their Functional Consequences across 33 Cancer Types. Cell Rep 2019; 23:282-296.e4. [PMID: 29617667 DOI: 10.1016/j.celrep.2018.01.088] [Citation(s) in RCA: 264] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 11/12/2017] [Accepted: 01/29/2018] [Indexed: 12/21/2022] Open
Abstract
Hotspot mutations in splicing factor genes have been recently reported at high frequency in hematological malignancies, suggesting the importance of RNA splicing in cancer. We analyzed whole-exome sequencing data across 33 tumor types in The Cancer Genome Atlas (TCGA), and we identified 119 splicing factor genes with significant non-silent mutation patterns, including mutation over-representation, recurrent loss of function (tumor suppressor-like), or hotspot mutation profile (oncogene-like). Furthermore, RNA sequencing analysis revealed altered splicing events associated with selected splicing factor mutations. In addition, we were able to identify common gene pathway profiles associated with the presence of these mutations. Our analysis suggests that somatic alteration of genes involved in the RNA-splicing process is common in cancer and may represent an underappreciated hallmark of tumorigenesis.
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Affiliation(s)
- Michael Seiler
- H3 Biomedicine, Inc., 300 Technology Square, Cambridge, MA 02139, USA
| | - Shouyong Peng
- H3 Biomedicine, Inc., 300 Technology Square, Cambridge, MA 02139, USA
| | - Anant A Agrawal
- H3 Biomedicine, Inc., 300 Technology Square, Cambridge, MA 02139, USA
| | - James Palacino
- H3 Biomedicine, Inc., 300 Technology Square, Cambridge, MA 02139, USA
| | - Teng Teng
- H3 Biomedicine, Inc., 300 Technology Square, Cambridge, MA 02139, USA
| | - Ping Zhu
- H3 Biomedicine, Inc., 300 Technology Square, Cambridge, MA 02139, USA
| | - Peter G Smith
- H3 Biomedicine, Inc., 300 Technology Square, Cambridge, MA 02139, USA
| | | | - Silvia Buonamici
- H3 Biomedicine, Inc., 300 Technology Square, Cambridge, MA 02139, USA.
| | - Lihua Yu
- H3 Biomedicine, Inc., 300 Technology Square, Cambridge, MA 02139, USA.
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10
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Aird D, Teng T, Huang CL, Pazolli E, Banka D, Cheung-Ong K, Eifert C, Furman C, Wu J, Seiler M, Buonamici S, Fekkes P, Karr C, Palacino J, Park E, Smith P, Yu L, Mizui Y, Warmuth M, Chicas A, Corson L, Zhu P. Abstract 281: Sensitivity to splicing modulation of BCL2 family genes reveals cancer therapeutic strategies for splicing modulators. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
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.
Citation Format: Daniel Aird, Teng Teng, Chia-Ling Huang, Ermira Pazolli, Deepti Banka, Kahlin Cheung-Ong, Cheryl Eifert, Craig Furman, Jeremy Wu, Michael Seiler, Silvia Buonamici, Peter Fekkes, Craig Karr, James Palacino, Eunice Park, Peter Smith, Lihua Yu, Yoshiharu Mizui, Markus Warmuth, Agustin Chicas, Laura Corson, Ping Zhu. Sensitivity to splicing modulation of BCL2 family genes reveals cancer therapeutic strategies for splicing modulators [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 281.
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11
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Tzelepis K, De Braekeleer E, Aspris D, Barbieri I, Vijayabaskar MS, Liu WH, Gozdecka M, Metzakopian E, Toop HD, Dudek M, Robson SC, Hermida-Prado F, Yang YH, Babaei-Jadidi R, Garyfallos DA, Ponstingl H, Dias JML, Gallipoli P, Seiler M, Buonamici S, Vick B, Bannister AJ, Rad R, Prinjha RK, Marioni JC, Huntly B, Batson J, Morris JC, Pina C, Bradley A, Jeremias I, Bates DO, Yusa K, Kouzarides T, Vassiliou GS. SRPK1 maintains acute myeloid leukemia through effects on isoform usage of epigenetic regulators including BRD4. Nat Commun 2018; 9:5378. [PMID: 30568163 PMCID: PMC6300607 DOI: 10.1038/s41467-018-07620-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 11/09/2018] [Indexed: 12/29/2022] Open
Abstract
We recently identified the splicing kinase gene SRPK1 as a genetic vulnerability of acute myeloid leukemia (AML). Here, we show that genetic or pharmacological inhibition of SRPK1 leads to cell cycle arrest, leukemic cell differentiation and prolonged survival of mice transplanted with MLL-rearranged AML. RNA-seq analysis demonstrates that SRPK1 inhibition leads to altered isoform levels of many genes including several with established roles in leukemogenesis such as MYB, BRD4 and MED24. We focus on BRD4 as its main isoforms have distinct molecular properties and find that SRPK1 inhibition produces a significant switch from the short to the long isoform at the mRNA and protein levels. This was associated with BRD4 eviction from genomic loci involved in leukemogenesis including BCL2 and MYC. We go on to show that this switch mediates at least part of the anti-leukemic effects of SRPK1 inhibition. Our findings reveal that SRPK1 represents a plausible new therapeutic target against AML.
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Affiliation(s)
- Konstantinos Tzelepis
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.
- Gurdon Institute and Department of Pathology, Tennis Court Road, Cambridge, CB2 1QN, UK.
| | - Etienne De Braekeleer
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Demetrios Aspris
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- Karaiskakio Foundation, Nicosia, Cyprus
| | - Isaia Barbieri
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Addenbrookes Hospital, CB2 0QQ, Cambridge, UK
| | - M S Vijayabaskar
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Wen-Hsin Liu
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), 81377, Munich, Germany
| | - Malgorzata Gozdecka
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Emmanouil Metzakopian
- UK Dementia Research Institute, University of Cambridge, Hills Rd, Cambridge, CB2 0AH, UK
| | - Hamish D Toop
- School of Chemistry, University of New South Wales, Sydney, Australia
- Exonate Ltd, Milton Science Park, Cambridge, UK
| | - Monika Dudek
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Samuel C Robson
- School of Pharmacy and Biomedical Science, University of Portsmouth, White Swan Road, Portsmouth, PO1 2DT, UK
| | - Francisco Hermida-Prado
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Yu Hsuen Yang
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | | | - Dimitrios A Garyfallos
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Hannes Ponstingl
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Joao M L Dias
- Cancer Molecular Diagnosis Laboratory, National Institute for Health Research, Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Paolo Gallipoli
- Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0XY, UK
- Department of Haematology, University of Cambridge, Cambridge, CB2 0PT, UK
- Department of Haematology, Cambridge University Hospitals NHS Trust, Cambridge, CB2 0QQ, UK
| | | | | | - Binje Vick
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), 81377, Munich, Germany
| | - Andrew J Bannister
- Gurdon Institute and Department of Pathology, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, Department of Medicine II and TranslaTUM Cancer Center, Technical University of Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, & German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Rab K Prinjha
- Epigenetics DPU, Immunoinflammation and Oncology TA Unit, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - John C Marioni
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
- European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
- Stem Cell Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Brian Huntly
- Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0XY, UK
- Department of Haematology, University of Cambridge, Cambridge, CB2 0PT, UK
- Department of Haematology, Cambridge University Hospitals NHS Trust, Cambridge, CB2 0QQ, UK
| | | | - Jonathan C Morris
- School of Chemistry, University of New South Wales, Sydney, Australia
- Exonate Ltd, Milton Science Park, Cambridge, UK
| | - Cristina Pina
- Department of Haematology, University of Cambridge, Cambridge, CB2 0PT, UK
| | - Allan Bradley
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Irmela Jeremias
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), 81377, Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, & German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatrics, Dr. von Hauner Children's Hospital, Ludwig Maximilians University München, 80337, Munich, Germany
| | - David O Bates
- Exonate Ltd, Milton Science Park, Cambridge, UK
- Cancer Biology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Queen's Medical Centre, Nottingham, NG2 7UH, UK
| | - Kosuke Yusa
- Stem Cell Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.
| | - Tony Kouzarides
- Gurdon Institute and Department of Pathology, Tennis Court Road, Cambridge, CB2 1QN, UK.
| | - George S Vassiliou
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.
- Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0XY, UK.
- Department of Haematology, University of Cambridge, Cambridge, CB2 0PT, UK.
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12
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Hacken ET, Valentin R, Regis FFD, Sun J, Yin S, Werner L, Deng J, Gruber M, Wong J, Zheng M, Gill AL, Seiler M, Smith P, Thomas M, Buonamici S, Ghia EM, Kim E, Rassenti LZ, Burger JA, Kipps TJ, Meyerson ML, Bachireddy P, Wang L, Reed R, Neuberg D, Carrasco RD, Brooks AN, Letai A, Davids MS, Wu CJ. Splicing modulation sensitizes chronic lymphocytic leukemia cells to venetoclax by remodeling mitochondrial apoptotic dependencies. JCI Insight 2018; 3:121438. [PMID: 30282833 PMCID: PMC6237462 DOI: 10.1172/jci.insight.121438] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 08/29/2018] [Indexed: 12/30/2022] Open
Abstract
The identification of targetable vulnerabilities in the context of therapeutic resistance is a key challenge in cancer treatment. We detected pervasive aberrant splicing as a characteristic feature of chronic lymphocytic leukemia (CLL), irrespective of splicing factor mutation status, which was associated with sensitivity to the spliceosome modulator, E7107. Splicing modulation affected CLL survival pathways, including members of the B cell lymphoma-2 (BCL2) family of proteins, remodeling antiapoptotic dependencies of human and murine CLL cells. E7107 treatment decreased myeloid cell leukemia-1 (MCL1) dependence and increased BCL2 dependence, sensitizing primary human CLL cells and venetoclax-resistant CLL-like cells from an Eμ-TCL1-based adoptive transfer murine model to treatment with the BCL2 inhibitor venetoclax. Our data provide preclinical rationale to support the combination of venetoclax with splicing modulators to reprogram apoptotic dependencies in CLL for treating venetoclax-resistant CLL cases.
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Affiliation(s)
- Elisa ten Hacken
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Rebecca Valentin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Fara Faye D. Regis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Jing Sun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Shanye Yin
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Lillian Werner
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Jing Deng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Michaela Gruber
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Jessica Wong
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Mei Zheng
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Amy L. Gill
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | | | - Peter Smith
- H3 Biomedicine Inc., Cambridge, Massachusetts, USA
| | | | | | - Emanuela M. Ghia
- Moores Cancer Center, University of California, San Diego, La Jolla, California, USA
| | - Ekaterina Kim
- University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Laura Z. Rassenti
- Moores Cancer Center, University of California, San Diego, La Jolla, California, USA
| | - Jan A. Burger
- University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Thomas J. Kipps
- Moores Cancer Center, University of California, San Diego, La Jolla, California, USA
| | - Matthew L. Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute, Cambridge, Massachusetts, USA
| | - Pavan Bachireddy
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Lili Wang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Robin Reed
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Donna Neuberg
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Ruben D. Carrasco
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA.,Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Angela N. Brooks
- Department of Biomolecular Engineering, University of California, Santa Cruz, California, USA
| | - Anthony Letai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Matthew S. Davids
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Catherine J. Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute, Cambridge, Massachusetts, USA.,Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
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13
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Schoepfer J, Jahnke W, Berellini G, Buonamici S, Cotesta S, Cowan-Jacob SW, Dodd S, Drueckes P, Fabbro D, Gabriel T, Groell JM, Grotzfeld RM, Hassan AQ, Henry C, Iyer V, Jones D, Lombardo F, Loo A, Manley PW, Pellé X, Rummel G, Salem B, Warmuth M, Wylie AA, Zoller T, Marzinzik AL, Furet P. Discovery of Asciminib (ABL001), an Allosteric Inhibitor of the Tyrosine Kinase Activity of BCR-ABL1. J Med Chem 2018; 61:8120-8135. [DOI: 10.1021/acs.jmedchem.8b01040] [Citation(s) in RCA: 175] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Joseph Schoepfer
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Wolfgang Jahnke
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | | | | | - Simona Cotesta
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Sandra W. Cowan-Jacob
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Stephanie Dodd
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Peter Drueckes
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | | | - Tobias Gabriel
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Jean-Marc Groell
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Robert M. Grotzfeld
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | | | - Chrystèle Henry
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | | | - Darryl Jones
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | | | - Alice Loo
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Paul W. Manley
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Xavier Pellé
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Gabriele Rummel
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Bahaa Salem
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | | | | | - Thomas Zoller
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Andreas L. Marzinzik
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Pascal Furet
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
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14
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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: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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15
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Puyang X, Furman C, Zheng GZ, Wu ZJ, Banka D, Aithal K, Agoulnik S, Bolduc DM, Buonamici S, Caleb B, Das S, Eckley S, Fekkes P, Hao MH, Hart A, Houtman R, Irwin S, Joshi JJ, Karr C, Kim A, Kumar N, Kumar P, Kuznetsov G, Lai WG, Larsen N, Mackenzie C, Martin LA, Melchers D, Moriarty A, Nguyen TV, Norris J, O'Shea M, Pancholi S, Prajapati S, Rajagopalan S, Reynolds DJ, Rimkunas V, Rioux N, Ribas R, Siu A, Sivakumar S, Subramanian V, Thomas M, Vaillancourt FH, Wang J, Wardell S, Wick MJ, Yao S, Yu L, Warmuth M, Smith PG, Zhu P, Korpal M. Discovery of Selective Estrogen Receptor Covalent Antagonists for the Treatment of ERα WT and ERα MUT Breast Cancer. Cancer Discov 2018; 8:1176-1193. [PMID: 29991605 DOI: 10.1158/2159-8290.cd-17-1229] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 05/11/2018] [Accepted: 06/19/2018] [Indexed: 11/16/2022]
Abstract
Mutations in estrogen receptor alpha (ERα) that confer resistance to existing classes of endocrine therapies are detected in up to 30% of patients who have relapsed during endocrine treatments. Because a significant proportion of therapy-resistant breast cancer metastases continue to be dependent on ERα signaling, there remains a critical need to develop the next generation of ERα antagonists that can overcome aberrant ERα activity. Through our drug-discovery efforts, we identified H3B-5942, which covalently inactivates both wild-type and mutant ERα by targeting Cys530 and enforcing a unique antagonist conformation. H3B-5942 belongs to a class of ERα antagonists referred to as selective estrogen receptor covalent antagonists (SERCA). In vitro comparisons of H3B-5942 with standard-of-care (SoC) and experimental agents confirmed increased antagonist activity across a panel of ERαWT and ERαMUT cell lines. In vivo, H3B-5942 demonstrated significant single-agent antitumor activity in xenograft models representing ERαWT and ERαY537S breast cancer that was superior to fulvestrant. Lastly, H3B-5942 potency can be further improved in combination with CDK4/6 or mTOR inhibitors in both ERαWT and ERαMUT cell lines and/or tumor models. In summary, H3B-5942 belongs to a class of orally available ERα covalent antagonists with an improved profile over SoCs.Significance: Nearly 30% of endocrine therapy-resistant breast cancer metastases harbor constitutively activating mutations in ERα. SERCA H3B-5942 engages C530 of both ERαWT and ERαMUT, promotes a unique antagonist conformation, and demonstrates improved in vitro and in vivo activity over SoC agents. Importantly, single-agent efficacy can be further enhanced by combining with CDK4/6 or mTOR inhibitors. Cancer Discov; 8(9); 1176-93. ©2018 AACR.This article is highlighted in the In This Issue feature, p. 1047.
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Affiliation(s)
| | | | | | | | | | - Kiran Aithal
- Aurigene Discovery Technologies Ltd., Bangalore, Karnataka, India
| | | | | | | | | | | | | | | | | | | | - René Houtman
- PamGene International, Den Bosch, the Netherlands
| | - Sean Irwin
- H3 Biomedicine, Inc., Cambridge, Massachusetts
| | | | - Craig Karr
- H3 Biomedicine, Inc., Cambridge, Massachusetts
| | - Amy Kim
- H3 Biomedicine, Inc., Cambridge, Massachusetts
| | | | - Pavan Kumar
- H3 Biomedicine, Inc., Cambridge, Massachusetts
| | | | | | | | | | - Lesley-Ann Martin
- Breast Cancer Now, Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | | | | | | | | | | | - Sunil Pancholi
- Breast Cancer Now, Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | | | | | | | | | | | - Ricardo Ribas
- Breast Cancer Now, Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Amy Siu
- Eisai Inc., Andover, Massachusetts
| | | | | | | | | | - John Wang
- H3 Biomedicine, Inc., Cambridge, Massachusetts
| | | | | | - Shihua Yao
- H3 Biomedicine, Inc., Cambridge, Massachusetts
| | - Lihua Yu
- H3 Biomedicine, Inc., Cambridge, Massachusetts
| | | | | | - Ping Zhu
- H3 Biomedicine, Inc., Cambridge, Massachusetts.
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16
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Albacker LA, Buonamici S, Frampton GM, Smith P, Stephens PJ, Warmuth M, Zhu P, Yu L. Abstract 3406: Comprehensive genomic profiling of hematologic malignancies identifies recurrent somatic splicing factor mutations in non-Hodgkin's lymphoma (NHL) and multiple myeloma (MM). Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-3406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Somatic mutations of splicing factors have been reported in multiple tumor types and have been recognized as a new hallmark of cancer. Although these mutations have been observed in myelodysplastic syndromes (MDS), acute myeloid leukemia (AML), chronic myelomonocytic leukemia (CMML) and chronic lymphocytic leukemia (CLL), the frequency of these mutations in other hematological malignancies is unknown.
We surveyed somatic mutations of several splicing factors (SF3B1, SRSF2, U2AF1, ZRSR2, DDX3X, ZMYM3, PCBP1 and U2AF2) in 6,235 patients across 15 hematological malignancies. 405 genes were analyzed by DNAseq at >500X coverage using FoundationOneHeme. Consistent with prior reports, we found that the hematopoietic malignancies with the most frequent splicing factor mutations were CMML (48.3%), MDS (36.9%), AML (25.3%) and CLL (22.5%). However, we also identified splicing factor mutations in NHL (13.8%) and MM (9%). In addition to mutations found across the different hematopoietic malignancies in SRSF2 (6%), SF3B1 (4.5%), U2AF1 (3.3%) and ZRSR2 (2.2%), we found DDX3X to be the fifth most frequently mutated gene at 1.6%, followed by ZMYM3 (0.8%), PCBP1 (0.5%) and U2AF2 (0.4%), indicating the importance of splicing dysregulation in hematological malignancies.
Within NHL, diffuse large B cell lymphoma (DLBCL) has the highest frequency of splicing factor mutations (18.3%), and these patients exhibited increased tumor mutation burden (TMB, 13.7 vs. 10.0 mutations per Mb, P < 0.05). Among the splicing factors, the RNA helicase DDX3X is the most frequently mutated in NHL (5.2%). DDX3X is a X chromosome gene and its mutations in NHL are associated with male gender (P = 0.006). Consistent with the reported mutations in CLL and natural killer/T-cell lymphoma, the majority of mutations are loss of function or missense mutations clustered in the two helicase domains. This suggests a pathological relevance of DDX3X in lymphoid malignancies.
In MM, SF3B1 and SRSF2 are two most frequently mutated genes at 3.8% and 1.9%, and patients with these mutations are associated with increased TMB (4.2 vs. 2.5, P < 0.001). Moreover, SF3B1 mutations occurred in 5.3% of samples with IGH-CCND1/2/3 or IGH-MAF/MAFB translocations, but <1% of samples with IGH-WHSC1/FGFR3 translocations. Although the most common SF3B1 mutation in hematopoietic malignancies is p.K700E, in MM the most frequent SF3B1 mutation is p.K666 (36.9% vs p.K700E 12.3%).
Here, we identify splicing factor mutations in NHL and MM, including hotspot somatic mutations of SF3B1, U2AF1 and SRSF2 and loss of function or missense mutations in DDX3X. Overall, our results broaden the disease association of splicing factor mutations in hematological malignancies and strengthen their role in disease pathogenesis.
Citation Format: Lee A. Albacker, Silvia Buonamici, Garrett M. Frampton, Peter Smith, Philip J. Stephens, Markus Warmuth,, Ping Zhu, Lihua Yu. Comprehensive genomic profiling of hematologic malignancies identifies recurrent somatic splicing factor mutations in non-Hodgkin's lymphoma (NHL) and multiple myeloma (MM) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3406.
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Affiliation(s)
| | | | | | | | | | | | - Ping Zhu
- 2H3 Biomedicine Inc., Cambridge, MA
| | - Lihua Yu
- 2H3 Biomedicine Inc., Cambridge, MA
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17
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Finci LI, Zhang X, Huang X, Zhou Q, Tsai J, Teng T, Agrawal A, Chan B, Irwin S, Karr C, Cook A, Zhu P, Reynolds D, Smith PG, Fekkes P, Buonamici S, Larsen NA. The cryo-EM structure of the SF3b spliceosome complex bound to a splicing modulator reveals a pre-mRNA substrate competitive mechanism of action. Genes Dev 2018; 32:309-320. [PMID: 29491137 PMCID: PMC5859971 DOI: 10.1101/gad.311043.117] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 02/07/2018] [Indexed: 12/16/2022]
Abstract
In this study, Finci et. al. present the cryo-EM structure of the SF3b subcomplex (SF3B1, SF3B3, PHF5A, and SF3B5), part of the U2 snRNP, bound to E7107 at 3.95 A. The structure suggests a model in which splicing modulators interfere with branch point adenosine recognition and supports a substrate competitive mechanism of action. Somatic mutations in spliceosome proteins lead to dysregulated RNA splicing and are observed in a variety of cancers. These genetic aberrations may offer a potential intervention point for targeted therapeutics. SF3B1, part of the U2 small nuclear RNP (snRNP), is targeted by splicing modulators, including E7107, the first to enter clinical trials, and, more recently, H3B-8800. Modulating splicing represents a first-in-class opportunity in drug discovery, and elucidating the structural basis for the mode of action opens up new possibilities for structure-based drug design. Here, we present the cryogenic electron microscopy (cryo-EM) structure of the SF3b subcomplex (SF3B1, SF3B3, PHF5A, and SF3B5) bound to E7107 at 3.95 Å. This structure shows that E7107 binds in the branch point adenosine-binding pocket, forming close contacts with key residues that confer resistance upon mutation: SF3B1R1074H and PHF5AY36C. The structure suggests a model in which splicing modulators interfere with branch point adenosine recognition and supports a substrate competitive mechanism of action (MOA). Using several related chemical probes, we validate the pose of the compound and support their substrate competitive MOA by comparing their activity against both strong and weak pre-mRNA substrates. Finally, we present functional data and structure–activity relationship (SAR) on the PHF5AR38C mutation that sensitizes cells to some chemical probes but not others. Developing small molecule splicing modulators represents a promising therapeutic approach for a variety of diseases, and this work provides a significant step in enabling structure-based drug design for these elaborate natural products. Importantly, this work also demonstrates that the utilization of cryo-EM in drug discovery is coming of age.
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Affiliation(s)
- Lorenzo I Finci
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaofeng Zhang
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiuliang Huang
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qiang Zhou
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jennifer Tsai
- H3 Biomedicine, Inc., Cambridge, Massachusetts 02139, USA
| | - Teng Teng
- H3 Biomedicine, Inc., Cambridge, Massachusetts 02139, USA
| | - Anant Agrawal
- H3 Biomedicine, Inc., Cambridge, Massachusetts 02139, USA
| | - Betty Chan
- H3 Biomedicine, Inc., Cambridge, Massachusetts 02139, USA
| | - Sean Irwin
- H3 Biomedicine, Inc., Cambridge, Massachusetts 02139, USA
| | - Craig Karr
- H3 Biomedicine, Inc., Cambridge, Massachusetts 02139, USA
| | - Andrew Cook
- H3 Biomedicine, Inc., Cambridge, Massachusetts 02139, USA
| | - Ping Zhu
- H3 Biomedicine, Inc., Cambridge, Massachusetts 02139, USA
| | | | - Peter G Smith
- H3 Biomedicine, Inc., Cambridge, Massachusetts 02139, USA
| | - Peter Fekkes
- H3 Biomedicine, Inc., Cambridge, Massachusetts 02139, USA
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18
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Seiler M, Yoshimi A, Darman R, Chan B, Keaney G, Thomas M, Agrawal AA, Caleb B, Csibi A, Sean E, Fekkes P, Karr C, Klimek V, Lai G, Lee L, Kumar P, Lee SCW, Liu X, Mackenzie C, Meeske C, Mizui Y, Padron E, Park E, Pazolli E, Peng S, Prajapati S, Taylor J, Teng T, Wang J, Warmuth M, Yao H, Yu L, Zhu P, Abdel-Wahab O, Smith PG, Buonamici S. H3B-8800, an orally available small-molecule splicing modulator, induces lethality in spliceosome-mutant cancers. Nat Med 2018; 24:497-504. [PMID: 29457796 PMCID: PMC6730556 DOI: 10.1038/nm.4493] [Citation(s) in RCA: 330] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 01/10/2018] [Indexed: 12/19/2022]
Abstract
Genomic analyses of cancer have identified recurrent point mutations in the RNA splicing factor-encoding genes SF3B1, U2AF1, and SRSF2 that confer an alteration of function. Cancer cells bearing these mutations are preferentially dependent on wild-type (WT) spliceosome function, but clinically relevant means to therapeutically target the spliceosome do not currently exist. Here we describe an orally available modulator of the SF3b complex, H3B-8800, which potently and preferentially kills spliceosome-mutant epithelial and hematologic tumor cells. These killing effects of H3B-8800 are due to its direct interaction with the SF3b complex, as evidenced by loss of H3B-8800 activity in drug-resistant cells bearing mutations in genes encoding SF3b components. Although H3B-8800 modulates WT and mutant spliceosome activity, the preferential killing of spliceosome-mutant cells is due to retention of short, GC-rich introns, which are enriched for genes encoding spliceosome components. These data demonstrate the therapeutic potential of splicing modulation in spliceosome-mutant cancers.
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Affiliation(s)
| | - Akihide Yoshimi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | - Betty Chan
- H3 Biomedicine Inc., Cambridge, Massachusetts, USA
| | - Gregg Keaney
- H3 Biomedicine Inc., Cambridge, Massachusetts, USA
| | | | | | | | | | | | - Peter Fekkes
- H3 Biomedicine Inc., Cambridge, Massachusetts, USA
| | - Craig Karr
- H3 Biomedicine Inc., Cambridge, Massachusetts, USA
| | - Virginia Klimek
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | - Linda Lee
- H3 Biomedicine Inc., Cambridge, Massachusetts, USA
| | - Pavan Kumar
- H3 Biomedicine Inc., Cambridge, Massachusetts, USA
| | - Stanley Chun-Wei Lee
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Xiang Liu
- H3 Biomedicine Inc., Cambridge, Massachusetts, USA
| | | | - Carol Meeske
- H3 Biomedicine Inc., Cambridge, Massachusetts, USA
| | | | - Eric Padron
- Department of Hematologic Malignancies and Immunology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Eunice Park
- H3 Biomedicine Inc., Cambridge, Massachusetts, USA
| | | | | | | | - Justin Taylor
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Teng Teng
- H3 Biomedicine Inc., Cambridge, Massachusetts, USA
| | - John Wang
- H3 Biomedicine Inc., Cambridge, Massachusetts, USA
| | | | - Huilan Yao
- H3 Biomedicine Inc., Cambridge, Massachusetts, USA
| | - Lihua Yu
- H3 Biomedicine Inc., Cambridge, Massachusetts, USA
| | - Ping Zhu
- H3 Biomedicine Inc., Cambridge, Massachusetts, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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19
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Cretu C, Agrawal AA, Cook A, Will CL, Fekkes P, Smith PG, Lührmann R, Larsen N, Buonamici S, Pena V. Structural Basis of Splicing Modulation by Antitumor Macrolide Compounds. Mol Cell 2018; 70:265-273.e8. [DOI: 10.1016/j.molcel.2018.03.011] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 02/07/2018] [Accepted: 03/07/2018] [Indexed: 12/22/2022]
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20
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Yamauchi T, Masuda T, Canver MC, Seiler M, Semba Y, Shboul M, Al-Raqad M, Maeda M, Schoonenberg VAC, Cole MA, Macias-Trevino C, Ishikawa Y, Yao Q, Nakano M, Arai F, Orkin SH, Reversade B, Buonamici S, Pinello L, Akashi K, Bauer DE, Maeda T. Genome-wide CRISPR-Cas9 Screen Identifies Leukemia-Specific Dependence on a Pre-mRNA Metabolic Pathway Regulated by DCPS. Cancer Cell 2018; 33:386-400.e5. [PMID: 29478914 PMCID: PMC5849534 DOI: 10.1016/j.ccell.2018.01.012] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 11/23/2017] [Accepted: 01/19/2018] [Indexed: 12/26/2022]
Abstract
To identify novel targets for acute myeloid leukemia (AML) therapy, we performed genome-wide CRISPR-Cas9 screening using AML cell lines, followed by a second screen in vivo. Here, we show that the mRNA decapping enzyme scavenger (DCPS) gene is essential for AML cell survival. The DCPS enzyme interacted with components of pre-mRNA metabolic pathways, including spliceosomes, as revealed by mass spectrometry. RG3039, a DCPS inhibitor originally developed to treat spinal muscular atrophy, exhibited anti-leukemic activity via inducing pre-mRNA mis-splicing. Humans harboring germline biallelic DCPS loss-of-function mutations do not exhibit aberrant hematologic phenotypes, indicating that DCPS is dispensable for human hematopoiesis. Our findings shed light on a pre-mRNA metabolic pathway and identify DCPS as a target for AML therapy.
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Affiliation(s)
- Takuji Yamauchi
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan; Department of Stem Cell Biology and Medicine, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Takeshi Masuda
- Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan
| | - Matthew C Canver
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | | | - Yuichiro Semba
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Mohammad Shboul
- Institute of Medical Biology, A∗STAR, 8A Biomedical Grove, Singapore 138648, Singapore
| | - Mohammed Al-Raqad
- Institute of Medical Biology, A∗STAR, 8A Biomedical Grove, Singapore 138648, Singapore; Al-Balqa Applied University, Faculty of Science, Al-Salt, Salt 19117, Jordan
| | - Manami Maeda
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Vivien A C Schoonenberg
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Mitchel A Cole
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Claudio Macias-Trevino
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Yuichi Ishikawa
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Qiuming Yao
- Department of Pathology & Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Michitaka Nakano
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Fumio Arai
- Department of Stem Cell Biology and Medicine, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Stuart H Orkin
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Bruno Reversade
- Institute of Medical Biology, A∗STAR, 8A Biomedical Grove, Singapore 138648, Singapore
| | | | - Luca Pinello
- Department of Pathology & Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Koichi Akashi
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan; Center for Cellular and Molecular Medicine, Kyushu University Hospital, Fukuoka 812-8582, Japan
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Takahiro Maeda
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Center for Cellular and Molecular Medicine, Kyushu University Hospital, Fukuoka 812-8582, Japan.
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Joshi JJ, Coffey H, Corcoran E, Tsai J, Huang CL, Ichikawa K, Prajapati S, Hao MH, Bailey S, Wu J, Rimkunas V, Karr C, Subramanian V, Kumar P, MacKenzie C, Hurley R, Satoh T, Yu K, Park E, Rioux N, Kim A, Lai WG, Yu L, Zhu P, Buonamici S, Larsen N, Fekkes P, Wang J, Warmuth M, Reynolds DJ, Smith PG, Selvaraj A. H3B-6527 Is a Potent and Selective Inhibitor of FGFR4 in FGF19-Driven Hepatocellular Carcinoma. Cancer Res 2018; 77:6999-7013. [PMID: 29247039 DOI: 10.1158/0008-5472.can-17-1865] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 08/23/2017] [Accepted: 10/10/2017] [Indexed: 01/18/2023]
Abstract
Activation of the fibroblast growth factor receptor FGFR4 by FGF19 drives hepatocellular carcinoma (HCC), a disease with few, if any, effective treatment options. While a number of pan-FGFR inhibitors are being clinically evaluated, their application to FGF19-driven HCC may be limited by dose-limiting toxicities mediated by FGFR1-3 receptors. To evade the potential limitations of pan-FGFR inhibitors, we generated H3B-6527, a highly selective covalent FGFR4 inhibitor, through structure-guided drug design. Studies in a panel of 40 HCC cell lines and 30 HCC PDX models showed that FGF19 expression is a predictive biomarker for H3B-6527 response. Moreover, coadministration of the CDK4/6 inhibitor palbociclib in combination with H3B-6527 could effectively trigger tumor regression in a xenograft model of HCC. Overall, our results offer preclinical proof of concept for H3B-6527 as a candidate therapeutic agent for HCC cases that exhibit increased expression of FGF19. Cancer Res; 77(24); 6999-7013. ©2017 AACR.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Jeremy Wu
- H3 Biomedicine, Cambridge, Massachusetts
| | | | - Craig Karr
- H3 Biomedicine, Cambridge, Massachusetts
| | | | | | | | | | | | - Kun Yu
- H3 Biomedicine, Cambridge, Massachusetts
| | | | | | - Amy Kim
- H3 Biomedicine, Cambridge, Massachusetts
| | | | - Lihua Yu
- H3 Biomedicine, Cambridge, Massachusetts
| | - Ping Zhu
- H3 Biomedicine, Cambridge, Massachusetts
| | | | | | | | - John Wang
- H3 Biomedicine, Cambridge, Massachusetts
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22
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Hacken ET, Wang L, Regis FF, Thomas M, Deng J, Baranowski K, Cartun Z, Buonamici S, Neuberg D, Letai A, Carrasco R, Wu CJ. Abstract 29: Characterization and treatment of a novel adoptive transfer model of Sf3b1mut/Atmdel chronic lymphocytic leukemia. Clin Cancer Res 2017. [DOI: 10.1158/1557-3265.hemmal17-29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The spliceosome component SF3B1 is among the most frequently mutated genes in CLL (Landau et al. Nature 2015), and its mutations are associated with transcriptomic changes in numerous pathways involved in the regulation of CLL-cell survival (Wang et al. Cancer Cell 2016). Across studies, the presence of SF3B1 mutations has been associated with poorer prognosis, and expansion of SF3B1-mutated subclones has been associated with resistance to current CLL therapies. Therefore, therapeutic options that selectively interfere with spliceosome components may represent an attractive therapeutic strategy for selected CLL patients.
We recently developed a novel mouse model of human CLL, based on the B-cell restricted coexpression of mutated Sf3b1 and deletion of Atm (Sf3b1mut/Atmdel), two commonly co-occurring genetic alterations in CLL. One of the main advantages of this model is its transplantability in either immunocompetent C57BL/6 or immunocompromised NSG hosts, with the engrafted mice rapidly succumbing to disease (3-4 months for C57BL/6, 4-6 weeks for NSG), thus providing a time frame for informative treatment studies. Sf3b1mut/Atmdelcells express unmutated IGHV B cell receptors (BCR), they show high BCR signaling responsiveness, and express high levels of the CD49d integrin and the chemokine receptor CXCR4, all phenotypic and functional features associated with aggressive human CLL. Sf3b1mut/Atmdel also express high levels of the aberrantly spliced isoforms of Tnpo3, Aurke, and Narfl1 genes, indicative of alternative splicing dysregulation.
We took advantage of the spliceosome modulator E7107, to test the effects of splicing inhibition in NSG mice challenged intravenously (i.v.) with 5 x 106 Sf3b1mut/Atmdel splenocytes. Fifteen days post-transplant, 40-50% circulating B220+CD5+Igk+ cells were detectable in the peripheral blood (PB) of recipient mice by flow cytometry. Mice were then randomized and treated i.v. for 5 days with either 4 mg/kg E7107 or vehicle control (3 controls/4 treated), then immediately euthanized. Three hours after the first E7107 dose, we observed significant reduction in Slc25a19 and Dph2 mature-RNA levels, two known targets of E7107, as analyzed by RT-PCR of PB cells collected from the treated animals. After the 5-day treatment, we observed a significant reduction in leukemia burden in the PB, bone marrow (BM), peritoneum (PLC), and spleen (SP) of the treated animals, associated to the presence of apoptotic AnnexinV+ Sf3b1mut/Atmdel cells. Interestingly, MCL1 protein and RNA levels were significantly reduced after the 5-day E7107 administration, as tested by RT-PCR and Western blot analysis of splenocytes harvested at sacrifice. Depletion of MCL1 total protein levels was also observed after 12 hours of in vitro treatment of Sf3b1mut/Atmdel cells with up to 1 μM E7107.
In conclusion, we propose a novel and valuable preclinical platform of Sf3b1mut/Atmdel CLL, with phenotypic and functional features similar to human CLL. We demonstrate that splicing modulation by E7107 treatment can reduce leukemia burden, not only in the PB, but also in the SP, BM, and PLC of these mice, by inducing CLL-cell apoptosis. Apoptosis induction is associated with depletion of MCL1 protein, an important antiapoptotic factor in CLL, which is commonly upregulated by microenvironmental interactions in lymphoid organs, and frequently associated with treatment resistance. Studies aimed at further evaluating E7107 selectivity towards Sf3b1mut as compared to Sf3b1wt cells are under way, along with combination treatments with standard or novel CLL therapeutics. These studies may provide the basis for personalized treatment strategies for patients harboring SF3B1 mutations, and novel therapeutic opportunities for refractory CLL patients carrying SF3B1mut subclones.
Citation Format: Elisa ten Hacken, Lili Wang, Fara Faye Regis, Michael Thomas, Jing Deng, Kaitlyn Baranowski, Zachary Cartun, Silvia Buonamici, Donna Neuberg, Anthony Letai, Ruben Carrasco, Catherine J. Wu. Characterization and treatment of a novel adoptive transfer model of Sf3b1mut/Atmdel chronic lymphocytic leukemia [abstract]. In: Proceedings of the Second AACR Conference on Hematologic Malignancies: Translating Discoveries to Novel Therapies; May 6-9, 2017; Boston, MA. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(24_Suppl):Abstract nr 29.
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Affiliation(s)
| | - Lili Wang
- 1Dana-Farber Cancer Institute, Boston, MA,
| | | | | | - Jing Deng
- 1Dana-Farber Cancer Institute, Boston, MA,
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23
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Chan S, Sridhar P, Kirchner R, Lock YJ, Herbert Z, Buonamici S, Smith P, Lieberman J, Petrocca F. Basal-A Triple-Negative Breast Cancer Cells Selectively Rely on RNA Splicing for Survival. Mol Cancer Ther 2017; 16:2849-2861. [PMID: 28878028 PMCID: PMC5997774 DOI: 10.1158/1535-7163.mct-17-0461] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 08/21/2017] [Accepted: 08/30/2017] [Indexed: 12/25/2022]
Abstract
Prognosis of triple-negative breast cancer (TNBC) remains poor. To identify shared and selective vulnerabilities of basal-like TNBC, the most common TNBC subtype, a directed siRNA lethality screen was performed in 7 human breast cancer cell lines, focusing on 154 previously identified dependency genes of 1 TNBC line. Thirty common dependency genes were identified, including multiple proteasome and RNA splicing genes, especially those associated with the U4/U6.U5 tri-snRNP complex (e.g., PRPF8, PRPF38A). PRPF8 or PRPF38A knockdown or the splicing modulator E7107 led to widespread intronic retention and altered splicing of transcripts involved in multiple basal-like TNBC dependencies, including protein homeostasis, mitosis, and apoptosis. E7107 treatment suppressed the growth of basal-A TNBC cell line and patient-derived basal-like TNBC xenografts at a well-tolerated dose. The antitumor response was enhanced by adding the proteasome inhibitor bortezomib. Thus, inhibiting both splicing and the proteasome might be an effective approach for treating basal-like TNBC. Mol Cancer Ther; 16(12); 2849-61. ©2017 AACR.
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Affiliation(s)
- Stefanie Chan
- Division of Computational Biomedicine, Department of Surgery, Boston University School of Medicine, Boston, Massachusetts
- Division of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Praveen Sridhar
- Division of Computational Biomedicine, Department of Surgery, Boston University School of Medicine, Boston, Massachusetts
- Division of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Rory Kirchner
- Bioinformatics Core, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Ying Jie Lock
- Division of Computational Biomedicine, Department of Surgery, Boston University School of Medicine, Boston, Massachusetts
- Division of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Zach Herbert
- Molecular Biology Core Facilities, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Peter Smith
- H3 Biomedicine Inc., Cambridge, Massachusetts
| | - Judy Lieberman
- Program in Cellular and Molecular Medicine, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts.
| | - Fabio Petrocca
- Division of Computational Biomedicine, Department of Surgery, Boston University School of Medicine, Boston, Massachusetts.
- Division of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
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24
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Agrawal AA, Yu L, Smith PG, Buonamici S. Targeting splicing abnormalities in cancer. Curr Opin Genet Dev 2017; 48:67-74. [PMID: 29136527 DOI: 10.1016/j.gde.2017.10.010] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 09/19/2017] [Accepted: 10/13/2017] [Indexed: 01/11/2023]
Abstract
Recently splicing has been recognized as a key pathway in cancer. Although aberrant splicing has been shown to be a consequence of mutations or the abnormal expression of splicing factors (trans-effect changes) or mutations in the splicing sequences (cis-effect mutations), the connections between aberrant splicing and cancer initiation or progression are still not well understood. Here we review the mutational landscape of splicing factors in cancer and associated splicing consequences, along with the most important examples of the therapeutic approaches targeting the spliceosome currently being investigated in oncology.
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Affiliation(s)
| | - Lihua Yu
- H3 Biomedicine, Inc., Cambridge, MA, USA
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25
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Tzelepis K, Braekeleer ED, Seiler M, Barbieri I, Robson S, Yang YH, Gozdecka M, Dudek M, Collord G, Dovey OM, Metzakopian E, Garyfallos D, Cooper JL, Buonamici S, Ponstingl H, Stratton MR, Bradley A, Huntly BJ, Pina C, Kouzarides T, Yusa K, Vassiliou GS. Abstract 1158: Modulation of splicing by inhibiting the kinase SRPK1 as a novel therapeutic strategy in myeloid leukemia. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-1158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Acute myeloid leukemia (AML) is an aggressive cancer with a poor prognosis, for which the therapeutic landscape has changed little for decades. Aberrant mRNA splicing plays a key role in cancer development and genes coding for several of the major components of the spliceosome are targeted by somatic mutations in numerous cancers including myelodysplastic syndromes and AML. Recently, myeloid neoplasms bearing spliceosome gene mutations were shown to be preferentially susceptible to pharmacological disruption of the spliceosome. Here we report that targeting the spliceosome can also be an effective therapeutic strategy in other types of AML.
Recently, we generated a comprehensive catalogue of genetic vulnerabilities in AML using CRISPR-Cas9 genome-wide recessive screens and reported several novel intuitive and non-intuitive therapeutic candidates. Amongst these we identify SRPK1, the gene coding for a serine-threonine kinase that phosphorylates the major spliceosome protein SRSF1. Here, we demonstrate that targeted genetic disruption of SRPK1 in AML driven by MLL-fusion genes, led to differentiation and apoptosis. Additionally, mice transplanted with human AML cell lines carrying the MLL-AF9 fusion gene, namely MOLM-13 and THP-1, presented a significant prolongation of survival when SRPK1 was genetically disrupted by CRISPR-Cas9 editing. Similar effects were seen with pharmacological inhibition of SRPK1 in vitro and in vivo. At the molecular level we show that genetic or pharmacological inhibition of SRPK1 was associated with profound changes in the splicing of multiple genes involved in the MLL leukemogenic program in association with significant changes in enzymatic modifications of core histone tails.
We proceeded to perform a genome-wide CRISPR drop-out screen for sensitizers of MOLM13 cells to pharmacological inhibition of SRPK1 and identified, amongst other genes, BRD4 as a sensitizer. We go on to show that the BRD inhibitor iBET-151 synergizes with SRPK1 inhibition to kill MOLM-13 both in vitro and in vivo. Preliminary data indicates that SRPK1 inhibition has overlapping molecular effects to BRD inhibition. We are currently investigating the molecular bases of this observation.
Our work identifies SRPK1 as a novel therapeutic target in AML that can be used alone or in conjunctions with drugs targeting epigenetic modifications to improve their anti-leukemic effects.
Citation Format: Konstantinos Tzelepis, Etienne De Braekeleer, Michael Seiler, Isaia Barbieri, Sam Robson, Yu Hsuen Yang, Malgorzata Gozdecka, Monika Dudek, Grace Collord, Oliver M. Dovey, Emmanouil Metzakopian, Dimitrios Garyfallos, Jonathan L. Cooper, Silvia Buonamici, Hannes Ponstingl, Michael R. Stratton, Allan Bradley, Brian J. Huntly, Cristina Pina, Tony Kouzarides, Kosuke Yusa, George S. Vassiliou. Modulation of splicing by inhibiting the kinase SRPK1 as a novel therapeutic strategy in myeloid leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1158. doi:10.1158/1538-7445.AM2017-1158
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Affiliation(s)
| | | | | | | | - Sam Robson
- 3Gurdon Institute, Cambridge, United Kingdom
| | - Yu Hsuen Yang
- 4University College of London, London, United Kingdom
| | | | | | | | | | | | | | | | | | | | | | | | - Brian J. Huntly
- 5Cambridge University Hospitals NHS Trust, Cambridge, United Kingdom
| | - Cristina Pina
- 6NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | | | - Kosuke Yusa
- 1Sanger Institute, Cambridge, United Kingdom
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26
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Teng T, Tsai J, Puyang X, Seiler M, Peng S, Aird D, Buonamici S, Caleb B, Chan B, Corson L, Feala J, Fekkes P, Karr C, Korpal M, Mizui Y, Park E, Palacino J, Smith P, Subramanian V, Wu J, Yu L, Chicas A, Warmuth M, Larsen N, Zhu P. Abstract 126: A chemogenomic approach reveals the action of splicing modulators at the branch point adenosine binding pocket defined by the PHF5A/SF3b complex. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Dysregulation of RNA splicing can cause various forms of cancer and neuromuscular disorders. Thus, developing compounds with splicing-modulating activity represents a promising therapeutic approach for these diseases. Natural products such as pladienolide, herboxidiene, and spliceostatin have been identified as potent splicing modulators that bind SF3B1, a member of the SF3b subcomplex that assembles into the U2 snRNP. Using integrated chemogenomic, structural and biochemical approaches, we show that PHF5A, another core component of the SF3b complex, is also targeted by these modulators. Whole exome sequencing of E7107 (pladienolide analogue) and herboxidiene resistant clones identified common mutations in either PHF5A-Y36, SF3B1-K1071, SF3B1-R1074, or SF3B1-V1078, which confers resistance to these modulators as assessed by splicing modulation and cell growth inhibition, suggesting a common site of interaction for these splicing modulators. We determine the crystal structure of human PHF5A and find that Y36 is located on the surface in a region of high sequence conservation. Analysis of the cryo-EM spliceosome Bact complex from yeast shows that these mutations cluster in a well-defined pocket surrounding the branch point adenosine suggesting a possible competitive mode of action for these modulators. Whole-transcriptome RNA-seq analysis reveals that PHF5A Y36C alters the profile of splicing modulators from inducing intron-retention events to exon-skipping events. Furthermore, the differential in GC content between adjacent introns and exons correlates with the relative intron strength, making some splicing events more susceptible to modulation. Collectively, we propose that PHF5A-SF3B1 is a central node for binding to these small-molecule splicing modulators offering novel approaches to modulate specific splicing events.
Citation Format: Teng Teng, Jennifer Tsai, Xiaoling Puyang, Michael Seiler, Shouyong Peng, Daniel Aird, Silvia Buonamici, Benjamin Caleb, Betty Chan, Laura Corson, Jacob Feala, Peter Fekkes, Craig Karr, Manav Korpal, Yoshiharu Mizui, Eunice Park, James Palacino, Peter Smith, Vanitha Subramanian, Jeremy Wu, Lihua Yu, Agustin Chicas, Markus Warmuth, Nicholas Larsen, Ping Zhu. A chemogenomic approach reveals the action of splicing modulators at the branch point adenosine binding pocket defined by the PHF5A/SF3b complex [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 126. doi:10.1158/1538-7445.AM2017-126
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Lihua Yu
- H3 Biomedicine Inc., Cambridge, MA
| | | | | | | | - Ping Zhu
- H3 Biomedicine Inc., Cambridge, MA
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27
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Buonamici S, Yoshimi A, Thomas M, Seiler M, Chan B, Caleb B, Csibi F, Darman R, Fekkes P, Karr C, Keaney G, Kim A, Klimek V, Kumar P, Kunii K, Lee SCW, Liu X, MacKenzie C, Meeske C, Mizui Y, Padron E, Park E, Pazolli E, Prajapati S, Rioux N, Taylor J, Wang J, Warmuth M, Yao H, Yu L, Zhu P, Abdel-Wahab O, Smith P. Abstract 1185: H3B-8800, a novel orally available SF3b modulator, shows preclinical efficacy across spliceosome mutant cancers. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-1185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Genomic characterization of hematologic and solid cancers has revealed recurrent somatic mutations affecting genes encoding the RNA splicing factors SF3B1, U2AF1, SRSF2 and ZRSR2. Recent data reveal that these mutations confer an alteration of function inducing aberrant splicing and rendering spliceosome mutant cells preferentially sensitive to splicing modulation compared with wildtype (WT) cells.
Here we describe a novel orally bioavailable small molecule SF3B1 modulator identified through a medicinal chemistry effort aimed at optimizing compounds for preferential lethality in spliceosome mutant cells. H3B-8800 potently binds to WT or mutant SF3b complexes and modulates splicing in in vitro biochemical splicing assays and cellular pharmacodynamic assays. The selectivity of H3B-8800 was confirmed by observing lack of activity in cells expressing SF3B1R1074H, the SF3B1 mutation previously shown to confer resistance to other splicing modulators.
Although H3B-8800 binds both WT and mutant SF3B1, it results in preferential lethality of cancer cells expressing SF3B1K700E, SRSF2P95H, or U2AF1S34F mutations compared to WT cells. In animals xenografted with SF3B1K700E knock-in leukemia K562 cells or mice transplanted with Srsf2P95H/MLL-AF9 mouse AML cells, oral H3B-8800 treatment demonstrated splicing modulation and inhibited tumor growth, while no therapeutic impact was seen in WT controls. These data were also evident in patient-derived xenografts (PDX) from patients with CMML where H3B-8800 resulted in a substantial reduction of leukemic burden only in SRSF2-mutant but not in WT CMML PDX models. Additionally, due to the high frequency of U2AF1 mutations in non-small cell lung cancer, H3B-8800 was tested in U2AF1S34F-mutant H441 lung cancer cells. Similar to the results from leukemia models, H3B-8800 demonstrated preferential lethality of U2AF1-mutant cells in vitro and in in vivo orthotopic xenografts at well tolerated doses.
RNA-seq of isogenic K562 cells treated with H3B-8800 revealed dose-dependent inhibition of splicing. Although global inhibition of RNA splicing was not observed; H3B-8800 treatment led to preferential intron retention of transcripts with shorter and more GC-rich regions compared to those unaffected by drug. Interestingly, H3B-8800-retained introns commonly disrupted the expression of spliceosomal genes, suggesting that the preferential effect of H3B-8800 on spliceosome mutant cells is due to the dependency of these cells on expression of WT spliceosomal genes.
These data identify a novel therapeutic approach with selective lethality in leukemias and lung cancers bearing a spliceosome mutation. Despite the essential nature of splicing, cancer cells without a spliceosome mutation were less sensitive to H3B-8800 compared with potent eradication of mutant counterparts. H3B-8800 is currently undergoing clinical evaluation in patients with MDS, AML, and CMML.
Citation Format: Silvia Buonamici, Akihide Yoshimi, Michael Thomas, Michael Seiler, Betty Chan, Benjamin Caleb, Fred Csibi, Rachel Darman, Peter Fekkes, Craig Karr, Gregg Keaney, Amy Kim, Virginia Klimek, Pavan Kumar, Kaiko Kunii, Stanley Chun-Wei Lee, Xiang Liu, Crystal MacKenzie, Carol Meeske, Yoshiharu Mizui, Eric Padron, Eunice Park, Ermira Pazolli, Sudeep Prajapati, Nathalie Rioux, Justin Taylor, John Wang, Markus Warmuth, Huilan Yao, Lihua Yu, Ping Zhu, Omar Abdel-Wahab, Peter Smith. H3B-8800, a novel orally available SF3b modulator, shows preclinical efficacy across spliceosome mutant cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1185. doi:10.1158/1538-7445.AM2017-1185
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Amy Kim
- 1H3 Biomedicine, Cambridge, MA
| | | | | | | | | | | | | | | | | | - Eric Padron
- 3Moffitt Cancer Center and Research Institute, Tampa, FL
| | | | | | | | | | - Justin Taylor
- 2Memorial Sloan Kettering Cancer Center, New York, NY
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Seiler M, Peng S, Agrawal A, Tsai J, Palacino J, Buonamici S, Yu L. Abstract 383: Survey of spliceosome gene mutations and associated splicing defects across 33 cancer types. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Hotspot mutations in the core spliceosome genes SF3B1, U2AF1, SRSF2 have been reported at high frequency in hematological malignancies and with lower occurrence in solid tumors. The TCGA Exome-seq and RNAseq data from 33 tumor types, the majority solid tumors, provides a unique opportunity to define the landscape of spliceosome mutations and associated splicing alterations in human malignancies.
To this end, we compiled a list of 404 genes known to be involved in splicing. We performed 2 different mutational analyses; for the first analysis each tumor type was evaluated independently using MutSig2CV and 68 significantly mutated genes (q ≤ 0.1) were identified. The second analysis was performed by systematically looking for genes across all tumor types with loss of function (LoF) or hotspot in-frame mutations, which identified an additional 12 genes. Among the 80 genes, EEF1A1, HNRNPCL1, PCBP1, PHF5A and ZC3H4 carry hotspot mutations in addition to the previously reported spliceosome genes SF1, SF3B1, SRSF2 and U2AF1. Interestingly, we observed that known leukemia mutation/deletion near P95 in SRSF2 were also present in uveal melanoma. Furthermore, the 2 hotspot mutations in U2AF1 identified in leukemia and lung adenocarcinoma (LUAD) were detected in an additional 9 tumor types. We identified new SF3B1 hotspot mutations p.L833F, p.E862K, p.E902K/G, and p.R957Q located in the heat domains (HD) 9-12 in AML, bladder (BLCA), and endometrial cancers. Unexpectedly, alternative exon usage was the most common splicing event observed in p.E902K mutant BLCA samples. This observation differs from the reported alternative 3’ splice site usage induced by SF3B1 hotspot mutations located in the HDs 4-8.
The majority of mutated spliceosome genes (52/80) contained LoF mutations across multiple tumor types. In particular, RBM10 showed the highest mutation frequency in LUAD (6.5%) and BLCA (3.8%), and FUBP1 in low grade glioma (8.0%). Differential splicing analysis comparing RBM10 LoF mutant and wild type LUAD identified exon inclusion and intron skipping as major splicing alterations, consistent with data showing RBM10 knock-down induces alternative exon usage within specific genes. Additionally, we identified cassette exon usage as the major splicing alteration in FUBP1 mutant versus wild type glioma samples. FUBP1 has been reported to bind and repress inclusion of AT rich exons, and confirming this finding we observed higher AT content in exons included in FUBP1 LoF mutant samples when compared to unaffected following exons. These findings suggest that LoF mutations in spliceosome genes impact splicing regulation and may play a critical role in cancer.
In conclusion, the landscape of hotspot and LoF mutations in multiple spliceosome genes and associated splicing alterations highlight the increasing importance of the splicing machinery in tumorigenesis in solid tumors beyond hematological malignancies.
Citation Format: Michael Seiler, Shouyong Peng, Anant Agrawal, Jennifer Tsai, James Palacino, Silvia Buonamici, Lihua Yu. Survey of spliceosome gene mutations and associated splicing defects across 33 cancer types [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 383. doi:10.1158/1538-7445.AM2017-383
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Affiliation(s)
| | | | | | | | | | | | - Lihua Yu
- H3 Biomedicine, Inc, Cambridge, MA
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Steensma DP, Maris MB, Yang J, Donnellan WB, Brunner AM, McMasters M, Greenberg P, Komrokji RS, Klimek VM, Goldberg JM, Rioux N, Kim A, Kumar P, Marino AJ, Buonamici S, Smith P, Sahmoud T, Warmuth M, Platzbecker U. H3B-8800-G0001-101: A first in human phase I study of a splicing modulator in patients with advanced myeloid malignancies. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.tps7075] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
TPS7075 Background: Dysregulated mRNA splicing is important in tumorigenesis and in resistance to cancer therapy. Somatic heterozygous mutations in core spliceosome genes (e.g. SF3B1, SRSF2, U2AF1) have been reported at high frequencies in patients with myelodysplastic syndromes (MDS), acute myeloid leukemia (AML), and chronic myelomonocytic leukemia (CMML). These mutations confer a change of function resulting in aberrant mRNA splicing that, in preclinical models, results in defects in hematopoietic cell development and myelodysplasia. Recurrent mutations in the spliceosome of patients with malignancies suggests importance in disease pathogenesis. Cells bearing splicing mutations depend on wild-type spliceosome function, suggesting the spliceosome as a therapeutic target. In vitro data indicate preferential induction of apoptosis (measured by caspase 3/7 activation) in SF3B1-mutant cells following treatment with the SF3B1 modulator H3B-8800. H3B-8800 inhibits growth in human AML cell lines, including those with mutations in U2AF1, SRSF2 or SF3B1. Oral administration of H3B-8800 modulates splicing and induces antitumor activity in xenograft leukemia models expressing mutant core spliceosome components. Methods: This study explores the safety of H3B-8800 in patients with myeloid cancers. Dose escalation (Cohort A) follows a 3+3 design with a starting dose of 1 mg daily for 5 consecutive days every 14 days in a 28 day cycle. Cohort A is open to patients with MDS, AML or CMML, irrespective of spliceosome mutations. In parallel to dose escalation, up to 6 patients with mutations of interest may be enrolled at doses determined to be safe in Cohort A (Cohort B). After determining the recommended phase 2 dose, 4 expansion cohorts will enroll patients with: (1) International Prognostic Scoring System (IPSS) low/int-1 risk MDS with SF3B1 mutations, (2) IPSS low/intermediate risk-1 MDS with mutations in SRSF2, U2AF1, or ZRSR2, (3) high/intermediate risk-2 MDS or AML, and (4) CMML; 3 and 4 having mutations in SF3B1, SRSF2, U2AF1, or ZRSR2. The first cohort enrolled 3 patients and the trial is currently enrolling patients at the second dose level. Clinical trial information: NCT02841540.
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Affiliation(s)
| | | | - Jay Yang
- Karmanos Cancer Institute, Detroit, MI
| | | | | | | | | | | | | | | | | | - Amy Kim
- H3 Biomedicine, Inc., Cambridge, MA
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Buonamici S, Yoshimi A, Thomas M, Seiler M, Chan B, Csibi A, Fekkes P, Klimek V, Kumar P, Lee S, Padron E, Pazolli E, Goldberg J, Sahmoud T, Taylor J, Warmuth M, Yu L, Zhu P, Abdel-Wahab O, Smith P. Characterization of Novel Oral Splicing Modulator, H3B-8800, Identifies the Mechanistic Basis for its Preferential Lethality Towards Spliceosome-Mutant Myeloid Malignancy Models. Leuk Res 2017. [DOI: 10.1016/s0145-2126(17)30133-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Mupo A, Seiler M, Sathiaseelan V, Pance A, Yang Y, Agrawal AA, Iorio F, Bautista R, Pacharne S, Tzelepis K, Manes N, Wright P, Papaemmanuil E, Kent DG, Campbell PC, Buonamici S, Bolli N, Vassiliou GS. Hemopoietic-specific Sf3b1-K700E knock-in mice display the splicing defect seen in human MDS but develop anemia without ring sideroblasts. Leukemia 2017; 31:720-727. [PMID: 27604819 PMCID: PMC5336192 DOI: 10.1038/leu.2016.251] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 08/19/2016] [Indexed: 02/06/2023]
Abstract
Heterozygous somatic mutations affecting the spliceosome gene SF3B1 drive age-related clonal hematopoiesis, myelodysplastic syndromes (MDS) and other neoplasms. To study their role in such disorders, we generated knock-in mice with hematopoietic-specific expression of Sf3b1-K700E, the commonest type of SF3B1 mutation in MDS. Sf3b1K700E/+ animals had impaired erythropoiesis and progressive anemia without ringed sideroblasts, as well as reduced hematopoietic stem cell numbers and host-repopulating fitness. To understand the molecular basis of these observations, we analyzed global RNA splicing in Sf3b1K700E/+ hematopoietic cells. Aberrant splicing was associated with the usage of cryptic 3' splice and branchpoint sites, as described for human SF3B1 mutants. However, we found a little overlap between aberrantly spliced mRNAs in mouse versus human, suggesting that anemia may be a consequence of globally disrupted splicing. Furthermore, the murine orthologues of genes associated with ring sideroblasts in human MDS, including Abcb7 and Tmem14c, were not aberrantly spliced in Sf3b1K700E/+ mice. Our findings demonstrate that, despite significant differences in affected transcripts, there is overlap in the phenotypes associated with SF3B1-K700E between human and mouse. Future studies should focus on understanding the basis of these similarities and differences as a means of deciphering the consequences of spliceosome gene mutations in MDS.
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Affiliation(s)
- A Mupo
- Haematological Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - M Seiler
- H3 Biomedicine, Inc., Cambridge, MA, USA
| | | | - A Pance
- Malaria Programme, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Y Yang
- Haematological Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | | | - F Iorio
- European Bioinformatics, Institute, Hinxton, Cambridge, UK
| | - R Bautista
- LIMS Compute and Infrastructure, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - S Pacharne
- Haematological Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - K Tzelepis
- Haematological Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - N Manes
- Haematological Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - P Wright
- Department of Pathology, Cambridge University Hospitals NHS Trust, Cambridge, UK
| | - E Papaemmanuil
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - D G Kent
- Cambridge Stem Cell Institute, Cambridge, UK
| | - P C Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | | | - N Bolli
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
- Dipartimento di Oncologia ed Onco-Ematologia, Universita' degli Studi di Milano, Milano, Italy
- Dipartimento di Ematologia ed Onco-Ematologia Pediatrica, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy
| | - G S Vassiliou
- Haematological Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
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Wang L, Brooks AN, Fan J, Wan Y, Gambe R, Li S, Hergert S, Yin S, Freeman SS, Levin JZ, Fan L, Seiler M, Buonamici S, Smith PG, Chau KF, Cibulskis CL, Zhang W, Rassenti LZ, Ghia EM, Kipps TJ, Fernandes S, Bloch DB, Kotliar D, Landau DA, Shukla SA, Aster JC, Reed R, DeLuca DS, Brown JR, Neuberg D, Getz G, Livak KJ, Meyerson MM, Kharchenko PV, Wu CJ. Transcriptomic Characterization of SF3B1 Mutation Reveals Its Pleiotropic Effects in Chronic Lymphocytic Leukemia. Cancer Cell 2016; 30:750-763. [PMID: 27818134 PMCID: PMC5127278 DOI: 10.1016/j.ccell.2016.10.005] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 09/01/2016] [Accepted: 10/04/2016] [Indexed: 12/16/2022]
Abstract
Mutations in SF3B1, which encodes a spliceosome component, are associated with poor outcome in chronic lymphocytic leukemia (CLL), but how these contribute to CLL progression remains poorly understood. We undertook a transcriptomic characterization of primary human CLL cells to identify transcripts and pathways affected by SF3B1 mutation. Splicing alterations, identified in the analysis of bulk cells, were confirmed in single SF3B1-mutated CLL cells and also found in cell lines ectopically expressing mutant SF3B1. SF3B1 mutation was found to dysregulate multiple cellular functions including DNA damage response, telomere maintenance, and Notch signaling (mediated through KLF8 upregulation, increased TERC and TERT expression, or altered splicing of DVL2 transcript, respectively). SF3B1 mutation leads to diverse changes in CLL-related pathways.
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Affiliation(s)
- Lili Wang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 540, 44 Binney Street, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Angela N Brooks
- Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 540, 44 Binney Street, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA; University of California, Santa Cruz, CA 95064, USA
| | - Jean Fan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Youzhong Wan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 540, 44 Binney Street, Boston, MA 02115, USA; National Engineering Laboratory of AIDS Vaccine, School of Life Science, Jilin University, Changchun, Jilin, PRC
| | - Rutendo Gambe
- Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 540, 44 Binney Street, Boston, MA 02115, USA
| | - Shuqiang Li
- Fluidigm Corporation, South San Francisco, CA 94080, USA
| | - Sarah Hergert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 540, 44 Binney Street, Boston, MA 02115, USA
| | - Shanye Yin
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Joshua Z Levin
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Lin Fan
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | | | | | | | | | | | - Wandi Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 540, 44 Binney Street, Boston, MA 02115, USA
| | - Laura Z Rassenti
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Emanuela M Ghia
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Thomas J Kipps
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Stacey Fernandes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 540, 44 Binney Street, Boston, MA 02115, USA
| | - Donald B Bloch
- Center for Immunology and Inflammatory Disease, Massachusetts General Hospital, Boston, MA 02115, USA
| | | | - Dan A Landau
- Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 540, 44 Binney Street, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Sachet A Shukla
- Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 540, 44 Binney Street, Boston, MA 02115, USA
| | - Jon C Aster
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Robin Reed
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - David S DeLuca
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Jennifer R Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 540, 44 Binney Street, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Donna Neuberg
- Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | | | - Matthew M Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 540, 44 Binney Street, Boston, MA 02115, USA
| | - Peter V Kharchenko
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 540, 44 Binney Street, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA.
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Obeng EA, Chappell RJ, Seiler M, Chen MC, Campagna DR, Schmidt PJ, Schneider RK, Lord AM, Wang L, Gambe RG, McConkey ME, Ali AM, Raza A, Yu L, Buonamici S, Smith PG, Mullally A, Wu CJ, Fleming MD, Ebert BL. Physiologic Expression of Sf3b1(K700E) Causes Impaired Erythropoiesis, Aberrant Splicing, and Sensitivity to Therapeutic Spliceosome Modulation. Cancer Cell 2016; 30:404-417. [PMID: 27622333 PMCID: PMC5023069 DOI: 10.1016/j.ccell.2016.08.006] [Citation(s) in RCA: 272] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 04/29/2016] [Accepted: 08/16/2016] [Indexed: 12/20/2022]
Abstract
More than 80% of patients with the refractory anemia with ring sideroblasts subtype of myelodysplastic syndrome (MDS) have mutations in Splicing Factor 3B, Subunit 1 (SF3B1). We generated a conditional knockin mouse model of the most common SF3B1 mutation, Sf3b1(K700E). Sf3b1(K700E) mice develop macrocytic anemia due to a terminal erythroid maturation defect, erythroid dysplasia, and long-term hematopoietic stem cell (LT-HSC) expansion. Sf3b1(K700E) myeloid progenitors and SF3B1-mutant MDS patient samples demonstrate aberrant 3' splice-site selection associated with increased nonsense-mediated decay. Tet2 loss cooperates with Sf3b1(K700E) to cause a more severe erythroid and LT-HSC phenotype. Furthermore, the spliceosome modulator, E7017, selectively kills SF3B1(K700E)-expressing cells. Thus, SF3B1(K700E) expression reflects the phenotype of the mutation in MDS and may be a therapeutic target in MDS.
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Affiliation(s)
- Esther A Obeng
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Division of Hematology/Oncology, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ryan J Chappell
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Michelle C Chen
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Dean R Campagna
- Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Paul J Schmidt
- Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Rebekka K Schneider
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Allegra M Lord
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Lili Wang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Rutendo G Gambe
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Marie E McConkey
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Abdullah M Ali
- Division of Hematology/Oncology, Columbia University Medical Center, New York, NY 10027, USA
| | - Azra Raza
- Division of Hematology/Oncology, Columbia University Medical Center, New York, NY 10027, USA
| | - Lihua Yu
- H3 Biomedicine, Inc., Cambridge, MA 03129, USA
| | | | | | - Ann Mullally
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Mark D Fleming
- Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Benjamin L Ebert
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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Bowman T, Cameron R, McKinstry M, De La Garza A, Nik S, Payne S, Smith P, Buonamici S, Bradley R. The spliceosomal component SF3B1 is essential for hematopoietic differentiation and splicing fidelity. Exp Hematol 2016. [DOI: 10.1016/j.exphem.2016.06.071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Aird D, Pazolli E, Furman C, Lee L, Kunii K, Park ES, Karr C, Chan B, Aicher M, Buonamici S, Wang JY, Feala J, Yu L, Warmuth M, Smith P, Fekkes P, Zhu P, Gerard B, Mizui Y, Corson L. Abstract C8: Targeting MCL1-dependent cancers with SF3B splicing modulators. Mol Cancer Ther 2015. [DOI: 10.1158/1535-7163.targ-15-c8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Myeloid cell leukemia 1 (MCL1) is a member of the BCL2 family of proteins governing the apoptosis pathway and is one of the most frequently amplified genes in cancer. MCL1 overexpression often results in dependence on MCL1 for survival and is linked to resistance to anticancer therapies. However, the development of direct MCL1 inhibitors has proven challenging and new modalities for targeting MCL1 are required. Alternative splicing of MCL1 converts the anti-apoptotic MCL1 long (MCL1L) isoform to the BH3-only MCL1 short (MCL1S) isoform, which has been reported to be pro-apoptotic. Thus, changing MCL1 isoform levels through modulation of RNA splicing may represent an attractive approach to targeting MCL1-amplified cancers. To this end, we tested a collection of small molecule SF3B modulators that impact RNA splicing on MCL1-dependent and MCL1-independent NSCLC cell lines.
SF3B modulators induced rapid downregulation of the long form and upregulation of the short- and intron-containing form of MCL1 across models; however, apoptosis was only observed in MCL1-dependent cells. Importantly, SF3B modulators preferentially killed MCL1-dependent cell lines and sensitivity correlated with MCL1 amplification. To dissect the mechanism of SF3B modulator-induced cytotoxicity, we overexpressed either the cDNA for the BH3-only short isoform or the full length isoform of MCL1. Surprisingly, overexpression of MCL1S cDNA had no significant effect on cells by itself and did not sensitize cells to SF3B modulator cytotoxicity. Conversely, MCL1L-specific shRNA knockdown was sufficient to kill MCL1-dependent cells and SF3B modulator cytotoxicity was rescued by expression of MCL1L cDNA. Together, these results argue that MCL1L modulation and not MCL1S upregulation is the effector of SF3B modulator cytotoxicity. In immunocompromised mice bearing MCL1-dependent xenograft models, SF3B1 modulator treatment resulted in significant downregulation of MCL1 levels accompanied by induction of apoptosis and robust efficacy at well-tolerated doses. Moreover, MCL1L cDNA expression in MCL1-dependent models rescued apoptosis induced by SF3B1 modulator treatment.
These studies provide proof-of-concept that splicing modulation is an effective strategy for targeting cancers dependent on MCL1.
Citation Format: Daniel Aird, Ermira Pazolli, Craig Furman, Linda Lee, Kaiko Kunii, Eun Sun Park, Craig Karr, Betty Chan, Michelle Aicher, Silvia Buonamici, John Yuan Wang, Jacob Feala, Lihua Yu, Markus Warmuth, Peter Smith, Peter Fekkes, Ping Zhu, Baudouin Gerard, Yoshiharu Mizui, Laura Corson. Targeting MCL1-dependent cancers with SF3B splicing modulators. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr C8.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Lihua Yu
- H3 Biomedicine Inc, Cambridge, MA
| | | | | | | | - Ping Zhu
- H3 Biomedicine Inc, Cambridge, MA
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Darman R, Seiler M, Agrawal A, Lim K, Peng S, Aird D, Bailey S, Bhavsar E, Chan B, Colla S, Corson L, Feala J, Fekkes P, Ichikawa K, Keaney G, Lee L, Kumar P, Kunii K, MacKenzie C, Matijevic M, Mizui Y, Myint K, Park E, Puyang X, Selvaraj A, Thomas M, Tsai J, Wang J, Warmuth M, Yang H, Zhu P, Garcia-Manero G, Furman R, Yu L, Smith P, Buonamici S. Cancer-Associated SF3B1 Hotspot Mutations Induce Cryptic 3′ Splice Site Selection through Use of a Different Branch Point. Cell Rep 2015; 13:1033-45. [DOI: 10.1016/j.celrep.2015.09.053] [Citation(s) in RCA: 247] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Revised: 08/21/2015] [Accepted: 09/18/2015] [Indexed: 10/22/2022] Open
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Kim E, Ilagan JO, Lee S, Ramakrishnan A, Chung YR, Micol JB, Murphy ME, Kim MK, Zebari AS, Buonamici S, Smith P, Deeg HJ, Lobry C, Aifantis I, Bradley RK, Abdel-Wahab O. Abstract IA36: SRSF2 mutations impair hematopoietic differentiation by altering exonic splicing enhancer preference. Clin Cancer Res 2015. [DOI: 10.1158/1557-3265.hemmal14-ia36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Spliceosomal mutations account for the most frequent class of mutations in patients with myelodysplastic syndromes, yet the mechanism by which these mutations perform their driver function is not well understood. Given the genetic heterogeneity of primary patient samples, we generated a model for conditional expression of the commonly occurring SRSF2P95H mutation from the endogenous murine locus of Srsf2 and compared expression of the Srsf2P95H mutation with genetic inactivation of 0, 1 or 2 copies of Srsf2.
Mx1-cre Srsf2P95H/wildtype mice exhibited significant morphologic dysplasia, leukopenia, macrocytic anemia, and preserved bone marrow (BM) cellularity as early as 2 weeks after mutation expression. Moreover, Mx1-cre Srsf2P95H/wildtype mice exhibited an increase in hematopoietic stem/progenitor cells (HSPCs) with an increase in lineage-negative Sca1+ c-Kit+ cells (LSK cells) in S-phase and early apoptosis. In competitive transplantation, Srsf2P95H mice HPSCs were expanded in the BM at 16 weeks post-transplantation despite having a reduced contribution to peripheral blood chimerism. In contrast, mice with homozygous deletion of Srsf2 exhibited anemia and leukopenia due to BM aplasia with striking loss of HSPCs. Collectively, these data show that Srsf2 is required for hematopoiesis, while mutations in Srsf2 provide a competitive advantage at the level of HSPCs but impair differentiation into mature circulating blood elements.
Next, to identify transcriptional alterations caused by SRSF2 mutations, we performed deep RNA-seq on sorted HSPC populations from wildtype and Srsf2P95H mice, stable K562 cell lines ectopically expressing an empty vector or a single allele of SRSF2 (WT, P95H, P95L, P95R), as well as primary CMML and AML patient samples. We quantified global changes in splicing of ~125,000 alternative splicing events and ~160,000 constitutive splice junctions associated with SRSF2 mutations in these datasets. Intersection of differentially spliced genes in primary murine HSPC, CMML, and AML samples identified 75 genes that were differentially spliced in association with SRSF2 mutations in murine HSPCs and at least one primary patient cohort. Many of the genes that were differentially spliced in SRSF2 mutant cells participate in biological processes of known importance in myeloid malignancies. For example, a cassette exon of EZH2 that alters the reading frame inducing nonsense-mediated decay was promoted by SRSF2 mutations. We next sought to determine how SRSF2 mutations alter SRSF2's normal role in RNA splicing. As SRSF2 recognizes exonic splicing enhancer (ESE) elements within the pre-mRNA to promote exon recognition, we hypothesized that SRSF2 mutations might alter its normal sequence-specific activity. To test this, we performed an ab initio motif identification screen to identify motifs that were enriched or depleted in cassette exons promoted versus repressed in primary Srsf2P95H cells relative to wildtype. This analysis identified CCAG and GGTG as the most enriched and depleted consensus motifs, respectively. A recent solution structure of SRSF2 in complex with RNA revealed that SRSF2 normally recognizes the motifs CCNG and GGNG equally well. Analysis of the spatial distribution of CCNG and GGNG motifs across genomic loci containing cassette exons that were promoted or repressed in association with SRSF2 mutations revealed that CCNG and GGNG were respectively enriched and depleted specifically over the cassette exons, that were differentially spliced in association with SRSF2 mutations. Together, our data indicate that mutant SRSF2 drives widespread changes in splicing due to alterations in its sequence-specific recognition of exonic splicing enhancers.
The biological as well as molecular data here identify an effect of the SRSF2P95H mutation distinct from haploinsufficient or complete loss of SRSF2 and reveal that mutations in SRSF2 alter ESE preference to contribute to key aspects of MDS.
Citation Format: Eunhee Kim, Janine O. Ilagan, Stanley Lee, Aravind Ramakrishnan, Young Rock Chung, Jean-Baptiste Micol, Michele E. Murphy, Min-Kyung Kim, Ahmad S. Zebari, Silvia Buonamici, Peter Smith, H. Joachim Deeg, Camille Lobry, Iannis Aifantis, Robert K. Bradley, Omar Abdel-Wahab. SRSF2 mutations impair hematopoietic differentiation by altering exonic splicing enhancer preference. [abstract]. In: Proceedings of the AACR Special Conference on Hematologic Malignancies: Translating Discoveries to Novel Therapies; Sep 20-23, 2014; Philadelphia, PA. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(17 Suppl):Abstract nr IA36.
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Affiliation(s)
- Eunhee Kim
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Stanley Lee
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | - Min-Kyung Kim
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Peter Smith
- 2Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | - Camille Lobry
- 3Cancer Institute, NYU Langone Medical Center, New York, NY
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Park ES, Aicher M, Aird D, Buonamici S, Chan B, Eifert C, Fekkes P, Furman C, Gerard B, Karr C, Keaney G, Kunii K, Lee L, Pazolli E, Prajapati S, Satoh T, Smith P, Wang JY, Wang K, Warmuth M, Yu L, Zhu P, Mizui Y, Corson LB. Abstract 2941: Targeting MCL1-dependent cancers through RNA splicing modulation. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-2941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Myeloid cell leukemia 1 (MCL1) is a member of the BCL2-family of proteins governing the apoptosis pathway and is one of the most frequently amplified genes in cancer. MCL1 overexpression often results in dependence on MCL1 for survival and is linked to resistance to anticancer therapies. However, the development of direct MCL1 inhibitors has proven challenging and thus far has been unsuccessful. Alternative splicing of MCL1 converts the anti-apoptotic MCL1 long (MCL1-L) isoform to the BH3-only containing MCL1 short (MCL1-S) isoform. As a potential approach for targeting MCL1-dependent cancers, we explored the use of MCL1 splicing modulators.
We screened a unique chemical library of compounds that span a range of splicing activities on various substrates in an in vitro assay. Interestingly, we found a subset of general splicing modulators, as well as a subset of SF3B1 inhibitors, that are capable of driving the distinctive alterations in MCL1 splicing that in turn can trigger preferential killing of MCL1-dependent cell lines. The best modulators induce a prominent down-regulation of MCL1-L, up-regulation of MCL1-S, and accumulation of intron-retained MCL1 transcript.
Somewhat surprisingly, several additional avenues of investigation pointed to MCL1-L down-regulation rather than MCL1-S up-regulation as the driver of preferential killing of MCL1-dependent cells. This includes the fact that compound-induced cytotoxicity can be rescued by expression of a MCL1-L cDNA and MCL1-L specific shRNA knockdown is sufficient to kill MCL1-dependent cells. On the other hand, overexpression of MCL1-S cDNA had no significant effect on cells and splicing modulators that induced very high levels of MCL1-S mRNA in the absence potent MCL1-L down-regulation exhibit minimal cytotoxicity. Biochemical characterization and understanding of these MCL1 splicing modulators has enabled further optimization of compounds that can induce potent and preferential killing of MCL1-dependent cancer cell lines in vitro. Preliminary studies in mice bearing MCL1-dependent NSCLC xenografts confirmed current lead compounds can indeed induce rapid down-regulation of MCL1-L, induction of apoptosis, and antitumor activity.
Collectively these data yield insight into mechanisms of MCL1 splicing modulation that can trigger acute apoptosis in MCL1-dependent cancers and provides support for the idea of using splicing modulators to target difficult-to-drug oncogenic drivers such as MCL1.
Citation Format: Eun Sun Park, Michelle Aicher, Daniel Aird, Silvia Buonamici, Betty Chan, Cheryl Eifert, Peter Fekkes, Craig Furman, Baudouin Gerard, Craig Karr, Gregg Keaney, Kaiko Kunii, Linda Lee, Ermira Pazolli, Sudeep Prajapati, Takashi Satoh, Peter Smith, John Yuan Wang, Karen Wang, Markus Warmuth, Lihua Yu, Ping Zhu, Yoshiharu Mizui, Laura B. Corson. Targeting MCL1-dependent cancers through RNA splicing modulation. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2941. doi:10.1158/1538-7445.AM2015-2941
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Buonamici S, Perino S, Lim KH, Feala J, Darman R, Obeng E, Furman RR, Bailey S, Keaney G, Kumar P, Mizui Y, Park E, Wang J, Warmuth M, Yu L, Zhu P, Ebert BL, Smith P. Abstract 2040: Mutations in SF3B1 lead to aberrant splicing through cryptic 3′ splice site selection and impair hematopoietic cell differentiation. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-2040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Heterozygous mutations in SF3B1, a component of the U2 complex involved in the recognition of 3′ splice sites (ss), have been reported with high frequency in refractory anemia with ring sideroblasts (RARS, a subtype of myelodysplastic syndrome, MDS) and have also been observed in chronic lymphocytic leukemia (CLL) and several solid tumors. To study the impact of SF3B1 mutations on splicing, RNAseq data obtained from breast cancer, melanoma, CLL and MDS samples with mutant (SF3B1MUT) or wild-type SF3B1 (SF3B1WT) were compared. The majority of aberrant junctions identified in the samples with mutant SF3B1 utilized an alternative 3′ss, suggesting its neomorphic function. Motif analysis of the sequences used by SF3B1MUT revealed the usage of a cryptic AG with a shorter and weaker polypyrimidine tract. Minigenes with modifications of these sites revealed the importance of both intronic and exonic sequence features for the recognition of the cryptic AG by SF3B1MUT. Of the aberrant junctions identified, several were common across all hotspot mutations and diseases; however, a unique aberrant splicing profile was found for each disease suggesting lineage and disease specific effects. The majority of splicing defects introduced a premature termination codon downstream of the cryptic AG leading to nonsense mediated decay (NMD) of aberrant transcripts and downregulation of gene expression, such as ABCB7. Gene-set enrichment analysis of aberrantly spliced and differentially expressed genes in SF3B1MUT MDS samples identified genes involved in cell differentiation and epigenetic pathways which are known to be deregulated in MDS. The impact on erythroid differentiation by SF3B1MUT was studied in transduced TF-1 cells following erythropoietin (EPO) stimulation. As expected, TF-1 SF3B1WT cells were able to differentiate normally after EPO treatment; however, expression of SF3B1K700E (the most common hotspot mutation found in RARS and CLL) induced a block in erythoid differentiation. This differentiation block was not observed with the expression of SF3B1G742D, a mutation found in CLL but not RARS, suggesting a context dependent role for SF3B1 mutations. Interestingly, the differentiation block observed in SF3B1K700E was associated with cytokine independent growth. Initial mining of RNAseq data from SF3B1MUT TF-1 cells highlighted several aberrantly spliced and NMD-downregulated genes previously implicated in MDS. Finally, a xenograft model was developed by subcutaneous implantation of transduced TF-1 cells. After several passages, an enrichment of TF-1 SF3B1K700E cells was observed, suggesting a growth advantage for SF3B1MUT cells over SF3B1WT cells. This data suggests that the K700E SF3B1 mutation can lead to a block in differentiation and competitive advantage as observed in human RARS.
Citation Format: Silvia Buonamici, Samantha Perino, Kian Huat Lim, Jacob Feala, Rachel Darman, Esther Obeng, Richard R. Furman, Suzanna Bailey, Gregg Keaney, Pavan Kumar, Yoshiharu Mizui, Eunice Park, John Wang, Markus Warmuth, Lihua Yu, Ping Zhu, Benjamin L. Ebert, Peter Smith. Mutations in SF3B1 lead to aberrant splicing through cryptic 3′ splice site selection and impair hematopoietic cell differentiation. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2040. doi:10.1158/1538-7445.AM2015-2040
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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: 410] [Impact Index Per Article: 45.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Buonamici S, Perino S, Lim K, Darman R, Feala J, Peng S, Bhavsar E, Corson L, Keaney G, Mizui Y, Obeng E, Park E, Wang J, Warmuth M, Yu L, Zhu P, Furman R, Ebert B, Smith P. 21 SF3B1 MUTATIONS INDUCE ABERRANT SPLICING LEADING TO A BLOCK IN ERYTHROID DIFFERENTIATION AND COMPETITIVE ADVANTAGE. Leuk Res 2015. [DOI: 10.1016/s0145-2126(15)30022-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Buonamici S, Ospina BE, Zhu JX, Yuan J, Hsiao K, Vattay A, Li F, Deeds J, Ostrom L, Monahan J, Williams J, Kelleher J, Peukert S, Pan S, Wu X, Warmuth M, Mosher R, Yao YM, Sellers WR, Dorsch M. Abstract 4290: The smoothened antagonist NVP-LDE225 targets stroma and cancer stem cells in primary human pancreatic tumor xenografts. Tumour Biol 2014. [DOI: 10.1158/1538-7445.am10-4290] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Russell P, Wickenden J, Cadwallader K, Maguire S, Joel J, Stockdale M, Chicas A, Banka D, Darman R, Perino S, Fekkes P, Smith P, Zhu P, Buonamici S, Moore J. 527 Is CRAF required for the maintenance of KRAS mutant non-small cell lung cancer? Eur J Cancer 2014. [DOI: 10.1016/s0959-8049(14)70653-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Abstract
T cell lymphoblastic leukemia (T-ALL) is an aggressive hematological cancer frequent within pediatric ALL patients. Recent findings suggested that the transmembrane receptor NOTCH1 is the major oncogene for the majority of T-ALL cases. In these cases activating mutations of NOTCH1 are responsible for the transformation of developing T cell progenitors. These observations prompted us to study the mechanisms of Notch1-induced T cell transformation. Using parallel studies in T cell progenitors and established T-ALL lines we have demonstrated that the NFkappaB signaling pathway is targeted and induced by Notch1 activation. Our studies suggested that NFkappaB activation by Notch1 can be direct, as Notch1 can bind and activate the promoters of the RELB and NFkappaB2 factors and indirect, as Notch1 can form a complex with the NFkappaB kinase IKK. NFkappaB appears to be important for the development of the disease as suppression of the pathway antagonizes T cell transformation both in vitro and in vivo, using animal models of T-ALL. We believe that these findings could be important for the understanding of Notch1 signaling and the therapeutic treatment of T-ALL.
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Affiliation(s)
- Iannis Aifantis
- Department of Pathology, New York University School of Medicine, New York, New York 10016, USA.
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Arai K, Buonamici S, Chan B, Corson L, Endo A, Gerard B, Hao MH, Karr C, Kira K, Lee L, Liu X, Lowe JT, Luo T, Marcaurelle LA, Mizui Y, Nevalainen M, O'Shea MW, Park ES, Perino SA, Prajapati S, Shan M, Smith PG, Tivitmahaisoon P, Wang JY, Warmuth M, Wu KM, Yu L, Zhang H, Zheng GZ, Keaney GF. Total synthesis of 6-deoxypladienolide D and Assessment of Splicing Inhibitory Activity in a Mutant SF3B1 cancer cell line. Org Lett 2014; 16:5560-3. [PMID: 25376106 DOI: 10.1021/ol502556c] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A total synthesis of the natural product 6-deoxypladienolide D (1) has been achieved. Two noteworthy attributes of the synthesis are (1) a late-stage allylic oxidation which proceeds with full chemo-, regio-, and diastereoselectivity and (2) the development of a scalable and cost-effective synthetic route to support drug discovery efforts. 6-Deoxypladienolide D (1) demonstrates potent growth inhibition in a mutant SF3B1 cancer cell line, high binding affinity to the SF3b complex, and inhibition of pre-mRNA splicing.
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Affiliation(s)
- Kenzo Arai
- H3 Biomedicine, Inc. 300 Technology Square, Cambridge, Massachusetts 02139, United States
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Buonamici S, Lim KH, Feala J, Park E, Corson L, Aicher M, Aird D, Chan B, Corcoran E, Darman R, Fekkes P, Keaney G, Kumar P, Kunii K, Lee L, Puyang X, Rodrigues J, Selvaraj A, Thomas M, Wang J, Warmuth M, Yu L, Zhu P, Smith P, Mizui Y. Abstract 2932: SF3B1 mutations induce aberrant mRNA splicing in cancer and confer sensitivity to spliceosome inhibition. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-2932] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Recurrent heterozygous mutations of the spliceosome protein SF3B1 have been identified in myelodysplastic syndromes, chronic lymphocytic leukemia (CLL), breast, pancreatic and skin cancers. SF3B1 is a component of the U2 snRNP complex which binds to the pre-mRNA branch point site and is involved in recognition and stabilization of the spliceosome at the 3′ splice site.
To understand the impact of SF3B1 mutations, we compared RNAseq profiles from tumor samples with SF3B1 hotspot mutations (SF3B1-MUT) or wild-type SF3B1 (SF3B1-WT) in breast cancer, melanoma and CLL. This analysis revealed significant increases in the usage of novel alternative splice junctions in SF3B1-MUT samples including selection of alternative 3′ splice sites and less frequently exon skipping. These events induce expression of alternative mRNAs that are translated into novel proteins or aberrant mRNAs that are decayed by cells. A common alternative splicing profile was shared across different hotspot mutations and lineages (e.g. ZDHHC16 and COASY); however, unique alternative splicing profiles were also observed suggesting lineage specific effects. RNAseq analysis of several cell lines with endogenous SF3B1 hotspot mutations confirmed the presence of the same spliced isoforms as observed in tumor samples. To prove that SF3B1-MUT were inducing alternative splicing, transient transfection of several SF3B1 hotspot mutations in 293FT cells induced the expression of the common alternatively spliced genes suggesting functional similarity. Selective shRNA depletion of mutant SF3B1 allele in SF3B1-MUT cells resulted in downregulation of the same splice isoforms. Furthermore, isogenic B-cell lines (NALM-6) expressing the most frequent SF3B1 mutation (K700E) were generated and profiled by RNAseq. As expected, similar alternatively spliced genes were observed in NALM-6 SF3B1-K700E cells exclusively. To investigate the role of nonsense-mediated mRNA decay (NMD) in eliminating aberrant mRNAs induced by SF3B1-MUT, we treated NALM-6 SF3B1-K700E cells with cycloheximide, a translation inhibitor known to inhibit NMD. In the treated samples, expression of several aberrant mRNAs was revealed and some of these transcripts were shown to be downregulated in patient samples. Taken together, these results confirm the association between different SF3B1 hotspot mutations and the presence of novel splice isoforms.
We demonstrated that E7107, a potent and selective inhibitor of wild-type SF3B1, also binds and inhibits SF3B1-MUT protein. In addition, E7107 represses the expression of several common aberrant splice mRNA products in SF3B1-MUT cells in vitro and in vivo. When tested in a NALM-6 mouse model, E7107 induced tumor regression and increased the overall survival of animals implanted with NALM-6 SF3B1-K700E cells. These data suggest splicing inhibitors as a promising therapeutic approach for cancer patients carrying SF3B1 mutations.
Citation Format: Silvia Buonamici, Kian Huat Lim, Jacob Feala, Eunice Park, Laura Corson, Michelle Aicher, Daniel Aird, Betty Chan, Erik Corcoran, Rachel Darman, Peter Fekkes, Gregg Keaney, Pavan Kumar, Kaiko Kunii, Linda Lee, Xiaoling Puyang, Jose Rodrigues, Anand Selvaraj, Michael Thomas, John Wang, Markus Warmuth, Lihua Yu, Ping Zhu, Peter Smith, Yoshiharu Mizui. SF3B1 mutations induce aberrant mRNA splicing in cancer and confer sensitivity to spliceosome inhibition. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2932. doi:10.1158/1538-7445.AM2014-2932
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Agarwal M, Nitta R, Dovat S, Li G, Arita H, Narita Y, Fukushima S, Tateishi K, Matsushita Y, Yoshida A, Miyakita Y, Ohno M, Collins VP, Kawahara N, Shibui S, Ichimura K, Kahn SA, Gholamin S, Junier MP, Chneiweiss H, Weissman I, Mitra S, Cheshier S, Avril T, Hamlat A, Le Reste PJ, Mosser J, Quillien V, Carrato C, Munoz-Marmol A, Serrano L, Pijuan L, Hostalot C, Villa SL, Ariza A, Etxaniz O, Balana C, Benveniste ET, Zheng Y, McFarland B, Drygin D, Bellis S, Bredel M, Lotsch D, Engelmaier C, Allerstorfer S, Grusch M, Pichler J, Weis S, Hainfellner J, Marosi C, Spiegl-Kreinecker S, Berger W, Bronisz A, Nowicki MO, Wang Y, Ansari K, Chiocca EA, Godlewski J, Brown K, Kwatra M, Brown K, Kwatra M, Bui T, Nitta R, Li G, Zhu S, Kozono D, Li J, Kushwaha D, Carter B, Chen C, Schulte J, Srikanth M, Das S, Zhang J, Lathia J, Yin L, Rich J, Olson E, Kessler J, Chenn A, Cherry A, Haas B, Lin YH, Ong SE, Stella N, Cifarelli CP, Griffin RJ, Cong D, Zhu W, Shi Y, Clark P, Kuo J, Hu S, Sun D, Bookland M, Darbinian N, Dey A, Robitaille M, Remke M, Faury D, Maier C, Malhotra A, Jabado N, Taylor M, Angers S, Kenney A, Ren X, Zhou H, Schur M, Baweja A, Singh M, Erdreich-Epstein A, Fu J, Koul D, Yao J, Saito N, Zheng S, Verhaak R, Lu Z, Yung WKA, Gomez G, Volinia S, Croce C, Brennan C, Cavenee W, Furnari F, Lopez SG, Qu D, Petritsch C, Gonzalez-Huarriz M, Aldave G, Ravi D, Rubio A, Diez-Valle R, Marigil M, Jauregi P, Vera B, Rocha AADL, Tejada-Solis S, Alonso MM, Gopal U, Isaacs J, Gruber-Olipitz M, Dabral S, Ramkissoon S, Kung A, Pak E, Chung J, Theisen M, Sun Y, Monrose V, Franchetti Y, Sun Y, Shulman D, Redjal N, Tabak B, Beroukhim R, Zhao J, Buonamici S, Ligon K, Kelleher J, Segal R, Haas B, Canton D, Diaz P, Scott J, Stella N, Hara K, Kageji T, Mizobuchi Y, Kitazato K, Okazaki T, Fujihara T, Nakajima K, Mure H, Kuwayama K, Hara T, Nagahiro S, Hill L, Botfield H, Hossain-Ibrahim K, Logan A, Cruickshank G, Liu Y, Gilbert M, Kyprianou N, Rangnekar V, Horbinski C, Hu Y, Vo C, Li Z, Ke C, Ru N, Hess KR, Linskey ME, Zhou YAH, Hu F, Vinnakota K, Wolf S, Kettenmann H, Jackson PJ, Larson JD, Beckmann DA, Moriarity BS, Largaespada DA, Jalali S, Agnihotri S, Singh S, Burrell K, Croul S, Zadeh G, Kang SH, Yu MO, Song NH, Park KJ, Chi SG, Chung YG, Kim SK, Kim JW, Kim JY, Kim JE, Choi SH, Kim TM, Lee SH, Kim SK, Park SH, Kim IH, Park CK, Jung HW, Koldobskiy M, Ahmed I, Ho G, Snowman A, Raabe E, Eberhart C, Snyder S, Agnihotri S, Gugel I, Remke M, Bornemann A, Pantazis G, Mack S, Shih D, Sabha N, Taylor M, Tatagiba M, Zadeh G, Krischek B, Schulte A, Liffers K, Kathagen A, Riethdorf S, Westphal M, Lamszus K, Lee JS, Xiao J, Patel P, Schade J, Wang J, Deneen B, Erdreich-Epstein A, Song HR, Leiss L, Gjerde C, Saed H, Rahman A, Lellahi M, Enger PO, Leung R, Gil O, Lei L, Canoll P, Sun S, Lee D, Ho ASW, Pu JKS, Zhang XQ, Lee NP, Dat PJR, Leung GKK, Loetsch D, Steiner E, Holzmann K, Spiegl-Kreinecker S, Pirker C, Hlavaty J, Petznek H, Hegedus B, Garay T, Mohr T, Sommergruber W, Grusch M, Berger W, Lukiw WJ, Jones BM, Zhao Y, Bhattacharjee S, Culicchia F, Magnus N, Garnier D, Meehan B, McGraw S, Hashemi M, Lee TH, Milsom C, Gerges N, Jabado N, Trasler J, Pawlinski R, Mackman N, Rak J, Maherally Z, Thorne A, An Q, Barbu E, Fillmore H, Pilkington G, Maherally Z, Tan SL, Tan S, An Q, Fillmore H, Pilkington G, Malhotra A, Choi S, Potts C, Ford DA, Nahle Z, Kenney AM, Matlaf L, Khan S, Zider A, Singer E, Cobbs C, Soroceanu L, McFarland BC, Hong SW, Rajbhandari R, Twitty GB, Gray GK, Yu H, Benveniste EN, Nozell SE, Minata M, Kim S, Mao P, Kaushal J, Nakano I, Mizowaki T, Sasayama T, Tanaka K, Mizukawa K, Nishihara M, Nakamizo S, Tanaka H, Kohta M, Hosoda K, Kohmura E, Moeckel S, Meyer K, Leukel P, Bogdahn U, Riehmenschneider MJ, Bosserhoff AK, Spang R, Hau P, Mukasa A, Watanabe A, Ogiwara H, Saito N, Aburatani H, Mukherjee J, Obha S, See W, Pieper R, Nakajima K, Hara K, Kageji T, Mizobuchi Y, Kitazato K, Fujihara T, Otsuka R, Kung D, Nagahiro S, Rajbhandari R, Sinha T, Meares G, Benveniste EN, Nozell S, Ott M, Litzenburger U, Rauschenbach K, Bunse L, Pusch S, Ochs K, Sahm F, Opitz C, von Deimling A, Wick W, Platten M, Peruzzi P, Chiocca EA, Godlewski J, Read R, Fenton T, Gomez G, Wykosky J, Vandenberg S, Babic I, Iwanami A, Yang H, Cavenee W, Mischel P, Furnari F, Thomas J, Ronellenfitsch MW, Thiepold AL, Harter PN, Mittelbronn M, Steinbach JP, Rybakova Y, Kalen A, Sarsour E, Goswami P, Silber J, Harinath G, Aldaz B, Fabius AWM, Turcan S, Chan TA, Huse JT, Sonabend AM, Bansal M, Guarnieri P, Lei L, Soderquist C, Leung R, Yun J, Kennedy B, Sisti J, Bruce S, Bruce R, Shakya R, Ludwig T, Rosenfeld S, Sims PA, Bruce JN, Califano A, Canoll P, Stockhausen MT, Kristoffersen K, Olsen LS, Poulsen HS, Stringer B, Day B, Barry G, Piper M, Jamieson P, Ensbey K, Bruce Z, Richards L, Boyd A, Sufit A, Burleson T, Le JP, Keating AK, Sundstrom T, Varughese JK, Harter P, Prestegarden L, Petersen K, Azuaje F, Tepper C, Ingham E, Even L, Johnson S, Skaftnesmo KO, Lund-Johansen M, Bjerkvig R, Ferrara K, Thorsen F, Takeshima H, Yamashita S, Yokogami K, Mizuguchi S, Nakamura H, Kuratsu J, Fukushima T, Morishita K, Tanaka H, Sasayama T, Tanaka K, Nakamizo S, Mizukawa K, Kohmura E, Tang Y, Vaka D, Chen S, Ponnuswami A, Cho YJ, Monje M, Tateishi K, Narita Y, Nakamura T, Cahill D, Kawahara N, Ichimura K, Tiemann K, Hedman H, Niclou SP, Timmer M, Tjiong R, Rohn G, Goldbrunner R, Timmer M, Tjiong R, Stavrinou P, Rohn G, Perrech M, Goldbrunner R, Tokita M, Mikheev S, Sellers D, Mikheev A, Kosai Y, Rostomily R, Tritschler I, Seystahl K, Schroeder JJ, Weller M, Wade A, Robinson AE, Phillips JJ, Gong Y, Ma Y, Cheng Z, Thompson R, Wang J, Fan QW, Cheng C, Gustafson W, Charron E, Zipper P, Wong R, Chen J, Lau J, Knobbe-Thosen C, Weller M, Jura N, Reifenberger G, Shokat K, Weiss W, Wu S, Fu J, Zheng S, Koul D, Yung WKA, Wykosky J, Hu J, Taylor T, Villa GR, Gomez G, Mischel PS, Gonias SL, Cavenee W, Furnari F, Yamashita D, Kondo T, Takahashi H, Inoue A, Kohno S, Harada H, Ohue S, Ohnishi T, Li P, Ng J, Yuelling L, Du F, Curran T, Yang ZJ, Zhu D, Castellino RC, Van Meir EG, Zhu W, Begum G, Wang Q, Clark P, Yang SS, Lin SH, Kahle K, Kuo J, Sun D. CELL BIOLOGY AND SIGNALING. Neuro Oncol 2013. [DOI: 10.1093/neuonc/not174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Filbin MG, Dabral SK, Pazyra-Murphy MF, Ramkissoon S, Kung AL, Pak E, Chung J, Theisen MA, Sun Y, Franchetti Y, Sun Y, Shulman DS, Redjal N, Tabak B, Beroukhim R, Wang Q, Zhao J, Dorsch M, Buonamici S, Ligon KL, Kelleher JF, Segal RA. Coordinate activation of Shh and PI3K signaling in PTEN-deficient glioblastoma: new therapeutic opportunities. Nat Med 2013; 19:1518-23. [PMID: 24076665 DOI: 10.1038/nm.3328] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2013] [Accepted: 08/06/2013] [Indexed: 01/17/2023]
Abstract
In glioblastoma, phosphatidylinositol 3-kinase (PI3K) signaling is frequently activated by loss of the tumor suppressor phosphatase and tensin homolog (PTEN). However, it is not known whether inhibiting PI3K represents a selective and effective approach for treatment. We interrogated large databases and found that sonic hedgehog (SHH) signaling is activated in PTEN-deficient glioblastoma. We demonstrate that the SHH and PI3K pathways synergize to promote tumor growth and viability in human PTEN-deficient glioblastomas. A combination of PI3K and SHH signaling inhibitors not only suppressed the activation of both pathways but also abrogated S6 kinase (S6K) signaling. Accordingly, targeting both pathways simultaneously resulted in mitotic catastrophe and tumor apoptosis and markedly reduced the growth of PTEN-deficient glioblastomas in vitro and in vivo. The drugs tested here appear to be safe in humans; therefore, this combination may provide a new targeted treatment for glioblastoma.
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Affiliation(s)
- Mariella Gruber Filbin
- 1] Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA. [2] Department of Pediatric Oncology, Dana-Farber Cancer Institute and Children's Hospital Boston, Harvard Medical School, Boston, Massachusetts, USA. [3] Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA. [4] Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
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Peukert S, He F, Dai M, Zhang R, Sun Y, Miller-Moslin K, McEwan M, Lagu B, Wang K, Yusuff N, Bourret A, Ramamurthy A, Maniara W, Amaral A, Vattay A, Wang A, Guo R, Yuan J, Green J, Williams J, Buonamici S, Kelleher JF, Dorsch M. Cover Picture: Discovery of NVP-LEQ506, a Second-Generation Inhibitor of Smoothened (ChemMedChem 8/2013). ChemMedChem 2013. [DOI: 10.1002/cmdc.201390030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Peukert S, He F, Dai M, Zhang R, Sun Y, Miller-Moslin K, McEwan M, Lagu B, Wang K, Yusuff N, Bourret A, Ramamurthy A, Maniara W, Amaral A, Vattay A, Wang A, Guo R, Yuan J, Green J, Williams J, Buonamici S, Kelleher JF, Dorsch M. Discovery of NVP-LEQ506, a Second-Generation Inhibitor of Smoothened. ChemMedChem 2013; 8:1261-5. [DOI: 10.1002/cmdc.201300217] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Indexed: 01/17/2023]
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