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Zhao X, Joshi JJ, Aird D, Karr C, Yu K, Huang C, Colombo F, Virrankoski M, Prajapati S, Selvaraj A. Combined inhibition of FGFR4 and VEGFR signaling enhances efficacy in FGF19 driven hepatocellular carcinoma. Am J Cancer Res 2022; 12:2733-2743. [PMID: 35812049 PMCID: PMC9251677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/07/2022] [Indexed: 06/15/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is an aggressive liver malignancy that is difficult to treat with no approved biomarker based targeted therapies. FGF19-FGFR4 signaling blockade has been recently identified as a promising avenue for treatment of a subset of HCC patients. Using HCC relevant xenograft and PDX models, we show that Lenvatinib, an approved multi-kinase inhibitor, strongly enhanced the efficacy of FGFR4 inhibitor H3B-6527. This enhanced combination effect is not due to enhanced FGFR4 inhibition and it is likely due to cell non-autonomous VEGFR activity of Lenvatinib. This cell non-autonomous mode of action was further supported by strong in vivo combination efficacy with the mouse specific VEGFR2 antibody, DC101, which cannot cell-autonomously inhibit pathways in human xenografts. Mechanistic studies showed that the combination resulted in enhanced efficacy through increased anti-angiogenic and anti-tumorigenic activities. Overall, our results indicate that this combination can be a highly effective treatment option for FGF19 driven HCC patients, and provide preclinical validation of a combination that can be readily tested in the clinical setting.
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Fenoglio S, Cristo AM, Tepper J, Teng T, Meier SR, Choi A, Zhang H, Zhao SC, Liu S, Ahronian LG, Aird D, Das NM, Yu Y, Sjin RTT, Andersen JN, Huang A, Li F, Pan X. Abstract P183: CRISPR screens identify sensitizers to trametinib in KRAS mutant cancer cell lines. Mol Cancer Ther 2021. [DOI: 10.1158/1535-7163.targ-21-p183] [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
KRAS is the most frequently mutated oncogene in human tumors and drives tumorigenesis across multiple lineages. Specifically, KRAS is mutated in about 30% of lung cancer and over 90% of pancreatic cancer. Despite recent progress in developing mutant selective KRASG12C inhibitors, patient treatment options for RAS activated cancers remain very limited. Targeting the MAPK pathway by means of MEK and ERK inhibitors has been explored as an alternative strategy for KRAS mutant cancer. However, the clinical benefit is modest due to drug resistance caused by reactivation of the MAPK pathway and potentially other pathways and/or bypass mechanisms. Here we used CRISPR-based screens to identify potential combination therapy targets to enhance trametinib response in KRAS mutant cancers. We screened in five KRAS mutant cell lines of lung and pancreatic lineages and identified both known as well as novel modulators of MEK inhibitor response. Consistent with previous reports, gene knockouts that impair the reactivation of ERK downstream of MEK inhibition scored as top hits in our drop-out screens. Knocking out MAPK1, RAF1, BRAF and PTPN11 sensitized all five cell lines to trametinib treatment supporting these as candidate drug combination targets for MAPK pathway inhibition. Our screens also identified multiple genes within the heparan sulfate pathway (EXT1, EXT2, EXTL3, XYLT2, ALG6, B3GAT3, B4GALT7 and HS2ST1) and the MAPK7 pathway (MAPK7 and MAP2K5) that sensitize multiple but not all cell lines to trametinib. As part of our target discovery platform, we further validated these screening results using various phenotypic assays. Altogether, our results suggest that resistance to MEK inhibitors is driven by reactivation of the MAPK pathway as previously demonstrated and that impairing such reactivation restores the sensitivity of KRAS mutant cancer cells to trametinib. The genetic mechanisms driving the MAPK pathway rebound are likely different in different cancers and understanding such mechanisms will be key for achieving clinical success.
Citation Format: Silvia Fenoglio, Aileen M. Cristo, James Tepper, Teng Teng, Samuel R. Meier, Ashley Choi, Hongxiang Zhang, Shan-chuan Zhao, Shangtao Liu, Leanne G. Ahronian, Daniel Aird, Nikitha M. Das, Yi Yu, Robert Tjin Tham Sjin, Jannik N. Andersen, Alan Huang, Fang Li, Xuewen Pan. CRISPR screens identify sensitizers to trametinib in KRAS mutant cancer cell lines [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 P183.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Yi Yu
- Tango Therapeutics, Cambridge, MA
| | | | | | | | - Fang Li
- Tango Therapeutics, Cambridge, MA
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Ahronian LG, Fenoglio S, Das N, Aird D, Guerin D, Whittington D, Jahic H, Brophy E, McCarren P, McMillan B, Tepper J, Mentzer M, Li F, Zhang H, Pan X, Maxwell J, Andersen J, Huang A, Sjin RTT. Abstract P146: Loss of HS2ST1 cooperates with MAPK inhibition to impair growth of mesenchymal KRAS mutant NSCLC. Mol Cancer Ther 2021. [DOI: 10.1158/1535-7163.targ-21-p146] [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
Activating mutations in the KRAS oncogene occur in approximately 30% of non-small cell lung cancers (NSCLC). Hence, multiple therapeutic strategies have been explored to block RAS including inhibition of downstream effector molecules in the MAPK pathway and direct pharmacological inhibition of the KRAS G12C mutant protein. However, inhibition of the RAS-RAF-MEK-ERK cascade with MEK inhibitor monotherapy has been insufficient to induce robust clinical responses. To identify novel drug targets that are synthetic lethal with MEK inhibition, CRISPR screens were conducted in multiple KRAS mutant NSCLC cell lines with or without trametinib treatment. Consistent with previous reports, several known MAPK-pathway genes, including KRAS, MEK, ERK, and FGFR1, were identified as top sensitizers validating our functional genomics approach. Interestingly, several novel targets were ranked among these top hits, including several members of the heparan sulfate biosynthesis pathway, such as the heparan sulfate 2-O-sulfotransferase (HS2ST1). In cells, HS2ST1 is responsible for transferring a sulfate from PAPS (3-phosphoadenosine-5’-phosphosulfate) to the 2-O position of a growing heparan sulfate chain. These chains partner with receptor tyrosine kinases at the cell surface to facilitate their interactions with growth factors. In this case, the interaction of FGF2 and FGFR1 has been shown to require HS2ST1-mediated 2-O sulfation, making HS2ST1 a novel druggable target in a well-validated FGFR-MAPK adaptive signaling axis. Here, we report that HS2ST1 is required for the feedback activation of the MAPK pathway that occurs downstream and in response to MEK or KRAS G12C inhibition via genetic validations studies. Knockout of HS2ST1 results in reduced feedback activation via FGFR1 and reduced MAPK pathway signaling. This reduced signaling leads to a reduction in cell growth in the presence of a MEK inhibitor, such as trametinib or selumetinib, or a KRAS G12C inhibitor like sotorasib. Our screen results reiterate the findings of others which indicate that effective MAPK suppression is key to inhibiting KRAS-mutant NSCLC cell growth. We find that HS2ST1 blockade would aid in maintaining the suppression of MAPK pathway signaling in KRAS-mutant NSCLC, leading to reduced cell viability and growth suppression. While others have described pairing receptor tyrosine kinase inhibitors with MAPK pathway inhibitors, this would be a novel approach to reducing upstream MAPK pathway feedback that may lead to reduced toxicity in patients.
Citation Format: Leanne G. Ahronian, Silvia Fenoglio, Nikitha Das, Daniel Aird, David Guerin, Douglas Whittington, Haris Jahic, Erin Brophy, Patrick McCarren, Brian McMillan, James Tepper, Michaela Mentzer, Fang Li, Hongxiang Zhang, Xuewen Pan, John Maxwell, Jannik Andersen, Alan Huang, Robert Tjin Tham Sjin. Loss of HS2ST1 cooperates with MAPK inhibition to impair growth of mesenchymal KRAS mutant NSCLC [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 P146.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Fang Li
- Tango Therapeutics, Cambridge, MA
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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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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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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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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, 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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Rakestraw JA, Aird D, Aha PM, Baynes BM, Lipovsek D. Secretion-and-capture cell-surface display for selection of target-binding proteins. Protein Eng Des Sel 2011; 24:525-30. [DOI: 10.1093/protein/gzr008] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [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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Aird D, Ross MG, Chen WS, Danielsson M, Fennell T, Russ C, Jaffe DB, Nusbaum C, Gnirke A. Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol 2011; 12:R18. [PMID: 21338519 PMCID: PMC3188800 DOI: 10.1186/gb-2011-12-2-r18] [Citation(s) in RCA: 735] [Impact Index Per Article: 56.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Revised: 12/23/2010] [Accepted: 02/21/2011] [Indexed: 01/18/2023] Open
Abstract
Despite the ever-increasing output of Illumina sequencing data, loci with extreme base compositions are often under-represented or absent. To evaluate sources of base-composition bias, we traced genomic sequences ranging from 6% to 90% GC through the process by quantitative PCR. We identified PCR during library preparation as a principal source of bias and optimized the conditions. Our improved protocol significantly reduces amplification bias and minimizes the previously severe effects of PCR instrument and temperature ramp rate.
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Affiliation(s)
- Daniel Aird
- Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA 02141, USA
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Aird D, Ross MG, Chen WS, Danielsson M, Fennell T, Russ C, Jaffe DB, Nusbaum C, Gnirke A. Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol 2011. [PMID: 21338519 DOI: 10.1186/1465-6906-12-s1-i18] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
Despite the ever-increasing output of Illumina sequencing data, loci with extreme base compositions are often under-represented or absent. To evaluate sources of base-composition bias, we traced genomic sequences ranging from 6% to 90% GC through the process by quantitative PCR. We identified PCR during library preparation as a principal source of bias and optimized the conditions. Our improved protocol significantly reduces amplification bias and minimizes the previously severe effects of PCR instrument and temperature ramp rate.
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Affiliation(s)
- Daniel Aird
- Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA 02141, USA
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Aird D, Chen WS, Ross M, Connolly K, Meldrim J, Russ C, Fisher S, Jaffe D, Nusbaum C, Gnirke A. Analyzing and minimizing bias in Illumina sequencing libraries. Genome Biol 2010. [PMCID: PMC3026259 DOI: 10.1186/gb-2010-11-s1-p3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Daniel Aird
- Broad Institute, Genome Sequencing, Cambridge, MA 02141, USA
| | - Wei-Shen Chen
- Broad Institute, Genome Sequencing, Cambridge, MA 02141, USA
| | - Michael Ross
- Broad Institute, Genome Sequencing, Cambridge, MA 02141, USA
| | | | - Jim Meldrim
- Broad Institute, Genome Sequencing, Cambridge, MA 02141, USA
| | - Carsten Russ
- Broad Institute, Genome Sequencing, Cambridge, MA 02141, USA
| | - Sheila Fisher
- Broad Institute, Genome Sequencing, Cambridge, MA 02141, USA
| | - David Jaffe
- Broad Institute, Genome Sequencing, Cambridge, MA 02141, USA
| | - Chad Nusbaum
- Broad Institute, Genome Sequencing, Cambridge, MA 02141, USA
| | - Andreas Gnirke
- Broad Institute, Genome Sequencing, Cambridge, MA 02141, USA
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Sui J, Hwang WC, Perez S, Wei G, Aird D, Chen LM, Santelli E, Stec B, Cadwell G, Ali M, Wan H, Murakami A, Yammanuru A, Han T, Cox NJ, Bankston LA, Donis RO, Liddington RC, Marasco WA. Structural and functional bases for broad-spectrum neutralization of avian and human influenza A viruses. Nat Struct Mol Biol 2009; 16:265-73. [PMID: 19234466 PMCID: PMC2692245 DOI: 10.1038/nsmb.1566] [Citation(s) in RCA: 947] [Impact Index Per Article: 63.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2008] [Accepted: 01/22/2009] [Indexed: 02/03/2023]
Abstract
A group of neutralizing monoclonal antibodies (mAbs) targeting the influenza A hemagglutinin has been selected and characterized. Remarkably, these mAbs were able to neutralize a broad array of group 1 strains and could protect mice from infection when given prophylactically or therapeutically. The crystal structure of one such mAb in complex with hemagglutinin provides insight into its mechanism of neutralization and broad specificity. Influenza virus remains a serious health threat, owing to its ability to evade immune surveillance through rapid genetic drift and reassortment. Here we used a human non-immune antibody phage-display library and the H5 hemagglutinin ectodomain to select ten neutralizing antibodies (nAbs) that were effective against all group 1 influenza viruses tested, including H5N1 'bird flu' and the H1N1 'Spanish flu'. The crystal structure of one such nAb bound to H5 shows that it blocks infection by inserting its heavy chain into a conserved pocket in the stem region, thus preventing membrane fusion. Nine of the nAbs employ the germline gene VH1-69, and all seem to use the same neutralizing mechanism. Our data further suggest that this region is recalcitrant to neutralization escape and that nAb-based immunotherapy is a promising strategy for broad-spectrum protection against seasonal and pandemic influenza viruses.
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Affiliation(s)
- Jianhua Sui
- Department of Cancer Immunology & AIDS, Dana-Farber Cancer Institute, Harvard Medical School, 44 Binney Street JFB 826, Boston, Massachusetts 02115, USA.
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15
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Taube R, Zhu Q, Xu C, Diaz-Griffero F, Sui J, Kamau E, Dwyer M, Aird D, Marasco WA. Lentivirus display: stable expression of human antibodies on the surface of human cells and virus particles. PLoS One 2008; 3:e3181. [PMID: 18784843 PMCID: PMC2527531 DOI: 10.1371/journal.pone.0003181] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [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: 07/08/2008] [Accepted: 08/11/2008] [Indexed: 01/12/2023] Open
Abstract
Background Isolation of human antibodies using current display technologies can be limited by constraints on protein expression, folding and post-translational modifications. Here we describe a discovery platform that utilizes self-inactivating (SIN) lentiviral vectors for the surface display of high-affinity single-chain variable region (scFv) antibody fragments on human cells and lentivirus particles. Methodology/Principal Findings Bivalent scFvFc human antibodies were fused in frame with different transmembrane (TM) anchoring moieties to allow efficient high-level expression on human cells and the optimal TM was identified. The addition of an eight amino acid HIV-1 gp41 envelope incorporation motif further increased scFvFc expression on human cells and incorporation into lentiviral particles. Both antibody-displaying human cells and virus particles bound antigen specifically. Sulfation of CDR tyrosine residues, a property recently shown to broaden antibody binding affinity and antigen recognition was also demonstrated. High level scFvFc expression and stable integration was achieved in human cells following transduction with IRES containing bicistronic SIN lentivectors encoding ZsGreen when scFvFc fusion proteins were expressed from the first cassette. Up to 106-fold enrichment of antibody expressing cells was achieved with one round of antigen coupled magnetic bead pre-selection followed by FACS sorting. Finally, the scFvFc displaying human cells could be used directly in functional biological screens with remarkable sensitivity. Conclusions/Significance This antibody display platform will complement existing technologies by virtue of providing properties unique to lentiviruses and antibody expression in human cells, which, in turn, may aid the discovery of novel therapeutic human mAbs.
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Affiliation(s)
- Ran Taube
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Quan Zhu
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Chen Xu
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Felipe Diaz-Griffero
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Pathology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jianhua Sui
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Erick Kamau
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Markryan Dwyer
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Daniel Aird
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Wayne A. Marasco
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
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