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Hunter O, Talkish J, Quick-Cleveland J, Igel H, Tan A, Kuersten S, Katzman S, Donohue JP, S Jurica M, Ares M. Broad variation in response of individual introns to splicing inhibitors in a humanized yeast strain. RNA (NEW YORK, N.Y.) 2024; 30:149-170. [PMID: 38071476 PMCID: PMC10798247 DOI: 10.1261/rna.079866.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 11/14/2023] [Indexed: 12/19/2023]
Abstract
Intron branchpoint (BP) recognition by the U2 snRNP is a critical step of splicing, vulnerable to recurrent cancer mutations and bacterial natural product inhibitors. The BP binds a conserved pocket in the SF3B1 (human) or Hsh155 (yeast) U2 snRNP protein. Amino acids that line this pocket affect the binding of splicing inhibitors like Pladienolide-B (Plad-B), such that organisms differ in their sensitivity. To study the mechanism of splicing inhibitor action in a simplified system, we modified the naturally Plad-B resistant yeast Saccharomyces cerevisiae by changing 14 amino acids in the Hsh155 BP pocket to those from human. This humanized yeast grows normally, and splicing is largely unaffected by the mutation. Splicing is inhibited within minutes after the addition of Plad-B, and different introns appear inhibited to different extents. Intron-specific inhibition differences are also observed during cotranscriptional splicing in Plad-B using single-molecule intron tracking to minimize gene-specific transcription and decay rates that cloud estimates of inhibition by standard RNA-seq. Comparison of Plad-B intron sensitivities to those of the structurally distinct inhibitor Thailanstatin-A reveals intron-specific differences in sensitivity to different compounds. This work exposes a complex relationship between the binding of different members of this class of inhibitors to the spliceosome and intron-specific rates of BP recognition and catalysis. Introns with variant BP sequences seem particularly sensitive, echoing observations from mammalian cells, where monitoring individual introns is complicated by multi-intron gene architecture and alternative splicing. The compact yeast system may hasten the characterization of splicing inhibitors, accelerating improvements in selectivity and therapeutic efficacy.
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Affiliation(s)
- Oarteze Hunter
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
| | - Jason Talkish
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
| | - Jen Quick-Cleveland
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
| | - Haller Igel
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
| | - Asako Tan
- Illumina, Inc., Madison, Wisconsin 53719, USA
| | | | - Sol Katzman
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
| | - John Paul Donohue
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
| | - Melissa S Jurica
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
| | - Manuel Ares
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
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2
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Hunter O, Talkish J, Quick-Cleveland J, Igel H, Tan A, Kuersten S, Katzman S, Donohue JP, Jurica M, Ares M. Broad variation in response of individual introns to splicing inhibitors in a humanized yeast strain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.05.560965. [PMID: 37873484 PMCID: PMC10592967 DOI: 10.1101/2023.10.05.560965] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Intron branch point (BP) recognition by the U2 snRNP is a critical step of splicing, vulnerable to recurrent cancer mutations and bacterial natural product inhibitors. The BP binds a conserved pocket in the SF3B1 (human) or Hsh155 (yeast) U2 snRNP protein. Amino acids that line this pocket affect binding of splicing inhibitors like Pladienolide-B (Plad-B), such that organisms differ in their sensitivity. To study the mechanism of splicing inhibitor action in a simplified system, we modified the naturally Plad-B resistant yeast Saccharomyces cerevisiae by changing 14 amino acids in the Hsh155 BP pocket to those from human. This humanized yeast grows normally, and splicing is largely unaffected by the mutation. Splicing is inhibited within minutes after addition of Plad-B, and different introns appear inhibited to different extents. Intron-specific inhibition differences are also observed during co-transcriptional splicing in Plad-B using single-molecule intron tracking (SMIT) to minimize gene-specific transcription and decay rates that cloud estimates of inhibition by standard RNA-seq. Comparison of Plad-B intron sensitivities to those of the structurally distinct inhibitor Thailanstatin-A reveals intron-specific differences in sensitivity to different compounds. This work exposes a complex relationship between binding of different members of this class of inhibitors to the spliceosome and intron-specific rates of BP recognition and catalysis. Introns with variant BP sequences seem particularly sensitive, echoing observations from mammalian cells, where monitoring individual introns is complicated by multi-intron gene architecture and alternative splicing. The compact yeast system may hasten characterization of splicing inhibitors, accelerating improvements in selectivity and therapeutic efficacy.
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Affiliation(s)
- Oarteze Hunter
- Center for Molecular Biology of RNA, University of California, Santa Cruz, CA 95064
| | - Jason Talkish
- Center for Molecular Biology of RNA, University of California, Santa Cruz, CA 95064
| | - Jen Quick-Cleveland
- Center for Molecular Biology of RNA, University of California, Santa Cruz, CA 95064
| | - Haller Igel
- Center for Molecular Biology of RNA, University of California, Santa Cruz, CA 95064
| | | | | | - Sol Katzman
- Center for Molecular Biology of RNA, University of California, Santa Cruz, CA 95064
| | - John Paul Donohue
- Center for Molecular Biology of RNA, University of California, Santa Cruz, CA 95064
| | - Melissa Jurica
- Center for Molecular Biology of RNA, University of California, Santa Cruz, CA 95064
| | - Manuel Ares
- Center for Molecular Biology of RNA, University of California, Santa Cruz, CA 95064
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3
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Zhou S, Zhao F, Zhu D, Zhang Q, Dai Z, Wu Z. Coupling of co-transcriptional splicing and 3' end Pol II pausing during termination in Arabidopsis. Genome Biol 2023; 24:206. [PMID: 37697420 PMCID: PMC10496290 DOI: 10.1186/s13059-023-03050-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 09/04/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND In Arabidopsis, RNA Polymerase II (Pol II) often pauses within a few hundred base pairs downstream of the polyadenylation site, reflecting efficient transcriptional termination, but how such pausing is regulated remains largely elusive. RESULT Here, we analyze Pol II dynamics at 3' ends by combining comprehensive experiments with mathematical modelling. We generate high-resolution serine 2 phosphorylated (Ser2P) Pol II positioning data specifically enriched at 3' ends and define a 3' end pause index (3'PI). The position but not the extent of the 3' end pause correlates with the termination window size. The 3'PI is not decreased but even mildly increased in the termination deficient mutant xrn3, indicating 3' end pause is a regulatory step early during the termination and before XRN3-mediated RNA decay that releases Pol II. Unexpectedly, 3'PI is closely associated with gene exon numbers and co-transcriptional splicing efficiency. Multiple exons genes often display stronger 3' end pauses and more efficient on-chromatin splicing than genes with fewer exons. Chemical inhibition of splicing strongly reduces the 3'PI and disrupts its correlation with exon numbers but does not globally impact 3' end readthrough levels. These results are further confirmed by fitting Pol II positioning data with a mathematical model, which enables the estimation of parameters that define Pol II dynamics. CONCLUSION Our work highlights that the number of exons via co-transcriptional splicing is a major determinant of Pol II pausing levels at the 3' end of genes in plants.
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Affiliation(s)
- Sixian Zhou
- Harbin Institute of Technology, Harbin, 150001, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Fengli Zhao
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Danling Zhu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Qiqi Zhang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Ziwei Dai
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Zhe Wu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
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4
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Zhang F, Chen L. Molecular Threat of Splicing Factor Mutations to Myeloid Malignancies and Potential Therapeutic Modulations. Biomedicines 2022; 10:biomedicines10081972. [PMID: 36009519 PMCID: PMC9405558 DOI: 10.3390/biomedicines10081972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/08/2022] [Accepted: 08/10/2022] [Indexed: 11/21/2022] Open
Abstract
Splicing factors are frequently mutated in myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML). These mutations are presumed to contribute to oncogenic transformation, but the underlying mechanisms remain incompletely understood. While no specific treatment option is available for MDS/AML patients with spliceosome mutations, novel targeting strategies are actively explored, leading to clinical trials of small molecule inhibitors that target the spliceosome, DNA damage response pathway, and immune response pathway. Here, we review recent progress in mechanistic understanding of splicing factor mutations promoting disease progression and summarize potential therapeutic strategies, which, if successful, would provide clinical benefit to patients carrying splicing factor mutations.
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5
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Pan YJ, Liu BW, Pei DS. The Role of Alternative Splicing in Cancer: Regulatory Mechanism, Therapeutic Strategy, and Bioinformatics Application. DNA Cell Biol 2022; 41:790-809. [PMID: 35947859 DOI: 10.1089/dna.2022.0322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
[Formula: see text] Alternative splicing (AS) can generate distinct transcripts and subsequent isoforms that play differential functions from the same pre-mRNA. Recently, increasing numbers of studies have emerged, unmasking the association between AS and cancer. In this review, we arranged AS events that are closely related to cancer progression and presented promising treatments based on AS for cancer therapy. Obtaining proliferative capacity, acquiring invasive properties, gaining angiogenic features, shifting metabolic ability, and getting immune escape inclination are all splicing events involved in biological processes. Spliceosome-targeted and antisense oligonucleotide technologies are two novel strategies that are hopeful in tumor therapy. In addition, bioinformatics applications based on AS were summarized for better prediction and elucidation of regulatory routines mingled in. Together, we aimed to provide a better understanding of complicated AS events associated with cancer biology and reveal AS a promising target of cancer treatment in the future.
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Affiliation(s)
- Yao-Jie Pan
- Department of Pathology, Laboratory of Clinical and Experimental Pathology, Xuzhou Medical University, Xuzhou, China
| | - Bo-Wen Liu
- Department of General Surgery, Xuzhou Medical University, Xuzhou, China
| | - Dong-Sheng Pei
- Department of Pathology, Laboratory of Clinical and Experimental Pathology, Xuzhou Medical University, Xuzhou, China
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6
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Boghaert ER, Cox MC, Vaidya KS. Pathophysiological and pharmacological considerations to improve the design and application of antibody-drug conjugates. Cancer Res 2022; 82:1858-1869. [PMID: 35298624 DOI: 10.1158/0008-5472.can-21-3236] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 03/01/2022] [Accepted: 03/14/2022] [Indexed: 11/16/2022]
Abstract
Antibody-drug conjugates (ADC) have emerged as one of the pillars of clinical disease management in oncology. The biggest hurdle to widespread development and application of ADCs has been a narrow therapeutic index. Advances in antibody technologies and formats as well as novel linker and payload chemistries have begun to facilitate structural improvements to ADCs. However, the interplay of structural characteristics with physiologic and pharmacologic factors determining therapeutic success has garnered less attention. This review elaborates on the pharmacology of ADCs, the pathophysiology of cancerous tissues, and the reciprocal consequences on ADC properties and functions. While most currently approved ADCs utilize either microtubule inhibition or DNA damage as primary mechanisms of action, we present arguments to expand this repertoire and highlight the need for payload mechanisms that exploit disease-specific vulnerabilities. We promote the idea that the choice of antibody format, targeting antigen, linker properties, and payload of an ADC should be deliberately fit for purpose by taking the pathophysiology of disease and the specific pharmacology of the drug entity into account, thus allowing a higher probability of clinical success.
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Affiliation(s)
| | - Megan C Cox
- Abbvie, Inc., North Chicago, IL, United States
| | - Kedar S Vaidya
- Jazz Pharmaceuticals (United States), Palo Alto, CA, United States
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7
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Peng Q, Zhou Y, Oyang L, Wu N, Tang Y, Su M, Luo X, Wang Y, Sheng X, Ma J, Liao Q. Impacts and mechanisms of alternative mRNA splicing in cancer metabolism, immune response, and therapeutics. Mol Ther 2022; 30:1018-1035. [PMID: 34793975 PMCID: PMC8899522 DOI: 10.1016/j.ymthe.2021.11.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/29/2021] [Accepted: 11/11/2021] [Indexed: 02/08/2023] Open
Abstract
Alternative pre-mRNA splicing (AS) provides the potential to produce diversity at RNA and protein levels. Disruptions in the regulation of pre-mRNA splicing can lead to diseases. With the development of transcriptome and genome sequencing technology, increasing diseases have been identified to be associated with abnormal splicing of mRNAs. In tumors, abnormal alternative splicing frequently plays critical roles in cancer pathogenesis and may be considered as new biomarkers and therapeutic targets for cancer intervention. Metabolic abnormalities and immune disorders are important hallmarks of cancer. AS produces multiple different isoforms and diversifies protein expression, which is utilized by the immune and metabolic reprogramming systems to expand gene functions. The abnormal splicing events contributed to tumor progression, partially due to effects on immune response and metabolic reprogramming. Herein, we reviewed the vital role of alternative splicing in regulating cancer metabolism and immune response. We discussed how alternative splicing regulates metabolic reprogramming of cancer cells and antitumor immune response, and the possible strategies to targeting alternative splicing pathways or splicing-regulated metabolic pathway in the context of anticancer immunotherapy. Further, we highlighted the challenges and discuss the perspectives for RNA-based strategies for the treatment of cancer with abnormally alternative splicing isoforms.
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Affiliation(s)
- Qiu Peng
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China,Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China
| | - Yujuan Zhou
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China,Hunan Key Laboratory of Translational Radiation Oncology, 283 Tongzipo Road, Changsha 410013, Hunan, China
| | - Linda Oyang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Nayiyuan Wu
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Yanyan Tang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Min Su
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Xia Luo
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Ying Wang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Xiaowu Sheng
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Jian Ma
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China; Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China.
| | - Qianjin Liao
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China; Hunan Key Laboratory of Translational Radiation Oncology, 283 Tongzipo Road, Changsha 410013, Hunan, China.
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8
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Isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomic analysis of mRNA splicing relevant proteins in aging HSPCs. Aging Clin Exp Res 2021; 33:3123-3134. [PMID: 32141009 DOI: 10.1007/s40520-020-01509-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 02/10/2020] [Indexed: 10/24/2022]
Abstract
BACKGROUND HSPC (hematopoietic stem/progenitor cell) aging was closely associated with the organism aging, senile diseases and hematopoietic related diseases. Therefore, study on HSPC aging is of great significance to further elucidate the mechanisms of aging and to treat hematopoietic disease resulting from HSPC aging. Little attention had been paid to mRNA splicing as a mechanism underlying HSPC senescence. RESULTS We used our lab's patented in vitro aging model of HSPCs to analyze mRNA splicing relevant protein alterations with iTRAQ-based proteomic analysis. We found that not only the notable mRNA splicing genes such as SR, hnRNP, WBP11, Sf3b1, Ptbp1 and U2AF1 but also the scarcely reported mRNA splicing relevant genes such as Rbmxl1, Dhx16, Pcbp2, Pabpc1 were significantly down-regulated. We further verified their gene expressions by qRT-PCR. In addition, we reported the effect of Spliceostatin A (SSA), which inhibits mRNA splicing in vivo and in vitro, on HSPC aging. CONCLUSIONS It was concluded that mRNA splicing emerged as an important factor for the vulnerability of HSPC aging. This study improved our understanding of the role of mRNA splicing in the HSPC aging process.
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9
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Urabe VK, Stevers M, Ghosh AK, Jurica MS. U2 snRNA structure is influenced by SF3A and SF3B proteins but not by SF3B inhibitors. PLoS One 2021; 16:e0258551. [PMID: 34648557 PMCID: PMC8516221 DOI: 10.1371/journal.pone.0258551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/29/2021] [Indexed: 11/19/2022] Open
Abstract
U2 snRNP is an essential component of the spliceosome. It is responsible for branch point recognition in the spliceosome A-complex via base-pairing of U2 snRNA with an intron to form the branch helix. Small molecule inhibitors target the SF3B component of the U2 snRNP and interfere with A-complex formation during spliceosome assembly. We previously found that the first SF3B inhibited-complex is less stable than A-complex and hypothesized that SF3B inhibitors interfere with U2 snRNA secondary structure changes required to form the branch helix. Using RNA chemical modifiers, we probed U2 snRNA structure in A-complex and SF3B inhibited splicing complexes. The reactivity pattern for U2 snRNA in the SF3B inhibited-complex is indistinguishable from that of A-complex, suggesting that they have the same secondary structure conformation, including the branch helix. This observation suggests SF3B inhibited-complex instability does not stem from an alternate RNA conformation and instead points to the inhibitors interfering with protein component interactions that normally stabilize U2 snRNP’s association with an intron. In addition, we probed U2 snRNA in the free U2 snRNP in the presence of SF3B inhibitor and again saw no differences. However, increased protection of nucleotides upstream of Stem I in the absence of SF3A and SF3B proteins suggests a change of secondary structure at the very 5′ end of U2 snRNA. Chemical probing of synthetic U2 snRNA in the absence of proteins results in similar protections and predicts a previously uncharacterized extension of Stem I. Because this stem must be disrupted for SF3A and SF3B proteins to stably join the snRNP, the structure has the potential to influence snRNP assembly and recycling after spliceosome disassembly.
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Affiliation(s)
- Veronica K. Urabe
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, California, United States of America
| | - Meredith Stevers
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, California, United States of America
| | - Arun K. Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, Indiana, United States of America
| | - Melissa S. Jurica
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, California, United States of America
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California, United States of America
- * E-mail:
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10
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A synthetic small molecule stalls pre-mRNA splicing by promoting an early-stage U2AF2-RNA complex. Cell Chem Biol 2021; 28:1145-1157.e6. [PMID: 33689684 PMCID: PMC8380659 DOI: 10.1016/j.chembiol.2021.02.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/25/2021] [Accepted: 02/11/2021] [Indexed: 12/20/2022]
Abstract
Dysregulated pre-mRNA splicing is an emerging Achilles heel of cancers and myelodysplasias. To expand the currently limited portfolio of small-molecule drug leads, we screened for chemical modulators of the U2AF complex, which nucleates spliceosome assembly and is mutated in myelodysplasias. A hit compound specifically enhances RNA binding by a U2AF2 subunit. Remarkably, the compound inhibits splicing of representative substrates and stalls spliceosome assembly at the stage of U2AF function. Computational docking, together with structure-guided mutagenesis, indicates that the compound bridges the tandem U2AF2 RNA recognition motifs via hydrophobic and electrostatic moieties. Cells expressing a cancer-associated U2AF1 mutant are preferentially killed by treatment with the compound. Altogether, our results highlight the potential of trapping early spliceosome assembly as an effective pharmacological means to manipulate pre-mRNA splicing. By extension, we suggest that stabilizing assembly intermediates may offer a useful approach for small-molecule inhibition of macromolecular machines.
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11
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Ghosh AK, Allu SR, Reddy GC, Lopez AG, Mendez P, Jurica MS. Design and synthesis of herboxidiene derivatives that potently inhibit in vitro splicing. Org Biomol Chem 2021; 19:1365-1377. [PMID: 33480941 DOI: 10.1039/d0ob02532a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Herboxidiene is a potent antitumor agent that targets the SF3B subunit of the spliceosome. Herboxidiene possesses a complex structural architecture with nine stereocenters and design of potent less complex structures would be of interest as a drug lead as well as a tool for studying SF3B1 function in splicing. We investigated a number of C-6 modified herboxidiene derivatives in an effort to eliminate this stereocenter and, also to understand the importance of this functionality. The syntheses of structural variants involved a Suzuki-Miyaura cross-coupling reaction as the key step. The functionalized tetrahydrofuran core has been constructed from commercially available optically active tri-O-acetyl-d-glucal. We investigated the effect of these derivatives on splicing chemistry. The C-6 alkene derivative showed very potent splicing inhibitory activity similar to herboxidiene. Furthermore, the C-6 gem-dimethyl derivative also exhibited very potent in vitro splicing inhibitory activity comparable to herboxidiene.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry and Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, USA.
| | - Srinivasa Rao Allu
- Department of Chemistry and Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, USA.
| | - Guddeti Chandrashekar Reddy
- Department of Chemistry and Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, USA.
| | - Adriana Gamboa Lopez
- Department of Molecular Cell and Developmental Biology and Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
| | - Patricia Mendez
- Department of Molecular Cell and Developmental Biology and Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
| | - Melissa S Jurica
- Department of Molecular Cell and Developmental Biology and Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
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12
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Kovalenko TF, Larionova TD, Antipova NV, Shakhparonov MI, Pavlyukov MS. The Role of Non-coding RNAs in the Pathogenesis of Glial Tumors. Acta Naturae 2021; 13:38-51. [PMID: 34707896 PMCID: PMC8526181 DOI: 10.32607/actanaturae.11270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 03/15/2021] [Indexed: 11/25/2022] Open
Abstract
Among the many malignant neoplasms, glioblastoma (GBM) leads to one of the worst prognosis for patients and has an almost 100% recurrence rate. The only chemotherapeutic drug that is widely used for treating glioblastoma is temozolomide, a DNA alkylating agent. Its impact, however, is only minor; it increases patients' survival just by 12 to 14 months. Multiple highly selective compounds that affect specific proteins and have performed well in other types of cancer have proved ineffective against glioblastoma. Hence, there is an urgent need for novel methods that could help achieve the long-awaited progress in glioblastoma treatment. One of the potentially promising approaches is the targeting of non-coding RNAs (ncRNAs). These molecules are characterized by extremely high multifunctionality and often act as integrators by coordinating multiple key signaling pathways within the cell. Thus, the impact on ncRNAs has the potential to lead to a broader and stronger impact on cells, as opposed to the more focused action of inhibitors targeting specific proteins. In this review, we summarize the functions of long noncoding RNAs, circular RNAs, as well as microRNAs, PIWI-interacting RNAs, small nuclear and small nucleolar RNAs. We provide a classification of these transcripts and describe their role in various signaling pathways and physiological processes. We also provide examples of oncogenic and tumor suppressor ncRNAs belonging to each of these classes in the context of their involvement in the pathogenesis of gliomas and glioblastomas. In conclusion, we considered the potential use of ncRNAs as diagnostic markers and therapeutic targets for the treatment of glioblastoma.
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Affiliation(s)
- T. F. Kovalenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences, Moscow, 117997 Russia
| | - T. D. Larionova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences, Moscow, 117997 Russia
| | - N. V. Antipova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences, Moscow, 117997 Russia
| | - M. I. Shakhparonov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences, Moscow, 117997 Russia
| | - M. S. Pavlyukov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences, Moscow, 117997 Russia
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13
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Biology of the mRNA Splicing Machinery and Its Dysregulation in Cancer Providing Therapeutic Opportunities. Int J Mol Sci 2021; 22:ijms22105110. [PMID: 34065983 PMCID: PMC8150589 DOI: 10.3390/ijms22105110] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/07/2021] [Accepted: 05/07/2021] [Indexed: 12/13/2022] Open
Abstract
Dysregulation of messenger RNA (mRNA) processing—in particular mRNA splicing—is a hallmark of cancer. Compared to normal cells, cancer cells frequently present aberrant mRNA splicing, which promotes cancer progression and treatment resistance. This hallmark provides opportunities for developing new targeted cancer treatments. Splicing of precursor mRNA into mature mRNA is executed by a dynamic complex of proteins and small RNAs called the spliceosome. Spliceosomes are part of the supraspliceosome, a macromolecular structure where all co-transcriptional mRNA processing activities in the cell nucleus are coordinated. Here we review the biology of the mRNA splicing machinery in the context of other mRNA processing activities in the supraspliceosome and present current knowledge of its dysregulation in lung cancer. In addition, we review investigations to discover therapeutic targets in the spliceosome and give an overview of inhibitors and modulators of the mRNA splicing process identified so far. Together, this provides insight into the value of targeting the spliceosome as a possible new treatment for lung cancer.
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14
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Yoshimoto R, Chhipi-Shrestha JK, Schneider-Poetsch T, Furuno M, Burroughs AM, Noma S, Suzuki H, Hayashizaki Y, Mayeda A, Nakagawa S, Kaida D, Iwasaki S, Yoshida M. Spliceostatin A interaction with SF3B limits U1 snRNP availability and causes premature cleavage and polyadenylation. Cell Chem Biol 2021; 28:1356-1365.e4. [PMID: 33784500 DOI: 10.1016/j.chembiol.2021.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 01/07/2021] [Accepted: 03/09/2021] [Indexed: 12/01/2022]
Abstract
RNA splicing, a highly conserved process in eukaryotic gene expression, is seen as a promising target for anticancer agents. Splicing is associated with other RNA processing steps, such as transcription and nuclear export; however, our understanding of the interaction between splicing and other RNA regulatory mechanisms remains incomplete. Moreover, the impact of chemical splicing inhibition on long non-coding RNAs (lncRNAs) has been poorly understood. Here, we demonstrate that spliceostatin A (SSA), a chemical splicing modulator that binds to the SF3B subcomplex of the U2 small nuclear ribonucleoprotein particle (snRNP), limits U1 snRNP availability in splicing, resulting in premature cleavage and polyadenylation of MALAT1, a nuclear lncRNA, as well as protein-coding mRNAs. Therefore, truncated transcripts are exported into the cytoplasm and translated, resulting in aberrant protein products. Our work demonstrates that active recycling of the splicing machinery maintains homeostasis of RNA processing beyond intron excision.
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Affiliation(s)
- Rei Yoshimoto
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan; Division of Gene Expression Mechanism, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | - Jagat K Chhipi-Shrestha
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan; Department of Biotechnology, Graduate School of Agricultural Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tilman Schneider-Poetsch
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Masaaki Furuno
- RIKEN Center for Integrative Medical Sciences, Tsurumi-ku, Yokohama 230-0045, Japan
| | - A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Shohei Noma
- RIKEN Center for Integrative Medical Sciences, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Harukazu Suzuki
- RIKEN Center for Integrative Medical Sciences, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Yoshihide Hayashizaki
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan
| | - Akila Mayeda
- Division of Gene Expression Mechanism, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Hokkaido 060-0812, Japan
| | - Daisuke Kaida
- Department of Gene Expression and Regulation, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Sugitani, Toyama 930-0194, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan; AMED-CREST, Japan Agency for Medical Research and Development, Chiyoda-ku, Tokyo 100-0004 Japan.
| | - Minoru Yoshida
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan; Department of Biotechnology, Graduate School of Agricultural Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.
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15
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Gamboa Lopez A, Allu SR, Mendez P, Chandrashekar Reddy G, Maul-Newby HM, Ghosh AK, Jurica MS. Herboxidiene Features That Mediate Conformation-Dependent SF3B1 Interactions to Inhibit Splicing. ACS Chem Biol 2021; 16:520-528. [PMID: 33617218 DOI: 10.1021/acschembio.0c00965] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Small molecules that target the spliceosome SF3B complex are potent inhibitors of cancer cell growth. The compounds affect an early stage of spliceosome assembly when U2 snRNP first engages the branch point sequence of an intron. Employing an inactive herboxidiene analog (iHB) as a competitor, we investigated factors that influence inhibitor interactions with SF3B to interfere with pre-mRNA splicing in vitro. Order-of-addition experiments show that inhibitor interactions are long lasting and affected by both temperature and the presence of ATP. Our data are also consistent with the model that not all SF3B conformations observed in structural studies are conducive to productive inhibitor interactions. Notably, SF3B inhibitors do not impact an ATP-dependent rearrangement in U2 snRNP that exposes the branch binding sequence for base pairing. We also report extended structure-activity relationship analysis of the splicing inhibitor herboxidiene. We identified features of the tetrahydropyran ring that mediate its interactions with SF3B and its ability to interfere with splicing. In the context of recent structures of SF3B bound to inhibitor, our results lead us to extend the model for early spliceosome assembly and inhibitor mechanism. We postulate that interactions between a carboxylic acid substituent of herboxidiene and positively charged SF3B1 side chains in the inhibitor binding channel are needed to maintain inhibitor occupancy while counteracting the SF3B transition to a closed state that is required for stable U2 snRNP interactions with the intron.
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Affiliation(s)
| | - Srinivasa Rao Allu
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | | | - Guddeti Chandrashekar Reddy
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | | | - Arun K. Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
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16
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Caizzi L, Monteiro-Martins S, Schwalb B, Lysakovskaia K, Schmitzova J, Sawicka A, Chen Y, Lidschreiber M, Cramer P. Efficient RNA polymerase II pause release requires U2 snRNP function. Mol Cell 2021; 81:1920-1934.e9. [PMID: 33689748 DOI: 10.1016/j.molcel.2021.02.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 01/07/2021] [Accepted: 02/10/2021] [Indexed: 12/21/2022]
Abstract
Transcription by RNA polymerase II (Pol II) is coupled to pre-mRNA splicing, but the underlying mechanisms remain poorly understood. Co-transcriptional splicing requires assembly of a functional spliceosome on nascent pre-mRNA, but whether and how this influences Pol II transcription remains unclear. Here we show that inhibition of pre-mRNA branch site recognition by the spliceosome component U2 snRNP leads to a widespread and strong decrease in new RNA synthesis from human genes. Multiomics analysis reveals that inhibition of U2 snRNP function increases the duration of Pol II pausing in the promoter-proximal region, impairs recruitment of the pause release factor P-TEFb, and reduces Pol II elongation velocity at the beginning of genes. Our results indicate that efficient release of paused Pol II into active transcription elongation requires the formation of functional spliceosomes and that eukaryotic mRNA biogenesis relies on positive feedback from the splicing machinery to the transcription machinery.
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Affiliation(s)
- Livia Caizzi
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Sara Monteiro-Martins
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Björn Schwalb
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Kseniia Lysakovskaia
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Jana Schmitzova
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Anna Sawicka
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Ying Chen
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Michael Lidschreiber
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
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17
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Larsen NA. The SF3b Complex is an Integral Component of the Spliceosome and Targeted by Natural Product-Based Inhibitors. Subcell Biochem 2021; 96:409-432. [PMID: 33252738 DOI: 10.1007/978-3-030-58971-4_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
In this chapter, the essential role of the SF3b multi-protein complex will be discussed in the context of the overall spliceosome. SF3b is critical during spliceosome assembly for recognition of the branch point (BP) adenosine and, by de facto, selection of the 3' splice site. This complex is highly dynamic, undergoing significant conformational changes upon loading of the branch duplex RNA and in its relative positioning during spliceosomal remodeling from the A, pre-B, B, Bact and B* complexes. Ultimately, during the spliceosome activation phase, SF3b must be displaced to unmask the branch point adenosine for the first splicing reaction to occur. In certain cancers, such as the hematological malignancies CML, CLL and MDS, the SF3b subunit SF3B1 is frequently mutated. Recent studies suggest these mutations lead to inappropriate branch point selection and mis-splicing events that appear to be drivers of disease. Finally, the SF3b complex is the target for at least three different classes of natural product-based inhibitors. These inhibitors bind in the BP adenosine-binding pocket and demonstrate a pre-mRNA competitive mechanism of action resulting in either intron retention or exon skipping. These compounds are extremely useful as chemical probes to isolate and characterize early stages of spliceosome assembly. They are also being explored preclinically and clinically as possible agents for hematological cancers.
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18
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Jiang W, Chen L. Alternative splicing: Human disease and quantitative analysis from high-throughput sequencing. Comput Struct Biotechnol J 2020; 19:183-195. [PMID: 33425250 PMCID: PMC7772363 DOI: 10.1016/j.csbj.2020.12.009] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 11/26/2020] [Accepted: 12/11/2020] [Indexed: 02/07/2023] Open
Abstract
Alternative splicing contributes to the majority of protein diversity in higher eukaryotes by allowing one gene to generate multiple distinct protein isoforms. It adds another regulation layer of gene expression. Up to 95% of human multi-exon genes undergo alternative splicing to encode proteins with different functions. Moreover, around 15% of human hereditary diseases and cancers are associated with alternative splicing. Regulation of alternative splicing is attributed to a set of delicate machineries interacting with each other in aid of important biological processes such as cell development and differentiation. Given the importance of alternative splicing events, their accurate mapping and quantification are paramount for downstream analysis, especially for associating disease with alternative splicing. However, deriving accurate isoform expression from high-throughput RNA-seq data remains a challenging task. In this mini-review, we aim to illustrate I) mechanisms and regulation of alternative splicing, II) alternative splicing associated human disease, III) computational tools for the quantification of isoforms and alternative splicing from RNA-seq.
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Affiliation(s)
- Wei Jiang
- Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089, United States
| | - Liang Chen
- Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089, United States
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19
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Zhang D, Meng F. A Comprehensive Overview of Structure-Activity Relationships of Small-Molecule Splicing Modulators Targeting SF3B1 as Anticancer Agents. ChemMedChem 2020; 15:2098-2120. [PMID: 33037739 DOI: 10.1002/cmdc.202000642] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 09/19/2020] [Indexed: 02/06/2023]
Abstract
The pre-mRNA splicing factor SF3B1 shows recurrent mutations among hematologic malignancies and some solid tumors. In 2007, the identification of two cytotoxic natural products, which showed splicing inhibition by binding to SF3b, prompted the development of small-molecule splicing modulators of SF3B1 as therapeutics for cancer. Recent studies suggested that spliceosome-mutant cells are preferentially sensitive to pharmacologic splicing modulation; therefore, exploring the clinical utility of splicing modulator therapies in patients with spliceosome-mutant hematologic malignancies who have failed current therapies is greatly needed, as these patients have few treatment options. H3B-8800 had unique pharmacological activity and exhibited favorable data in phase I clinical trials to treat patients with advanced myeloid malignancies, indicating that further clinical trials are promising. The most established small-molecule modulators of SF3B1 can be categorized into three classes: the bicycles, the monopyranes, and the 12-membered macrolides. This review provides a comprehensive overview of the structure-activity relationships of small-molecule SF3B1 modulators, with a detailed analysis of interactions between modulators and protein binding pocket. The future strategy for splicing modulators development is also discussed.
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Affiliation(s)
- Datong Zhang
- School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), 3501 Daxue Road, Jinan, 250353, P. R. China
| | - Fancui Meng
- Tianjin Institute of Pharmaceutical Research, 306 Huiren Road, Tianjin, 300301, P. R. China
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20
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Ghosh AK, Born JR, Veitschegger AM, Jurica MS. Copper-Catalyzed Stille Cross-Coupling Reaction and Application in the Synthesis of the Spliceostatin Core Structure. J Org Chem 2020; 85:8111-8120. [PMID: 32515594 DOI: 10.1021/acs.joc.0c00976] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
An efficient palladium-free Stille cross-coupling reaction of allylic bromides and functionalized organostannylfuran using catalytic copper halide has been developed. The coupling reaction was optimized using CuI and low catalyst loading (down to 5 mol %). The reaction was conveniently carried out at ambient temperature in the presence of inorganic base to afford the coupling product in good-to-excellent yields. The utility of this reaction was demonstrated in the synthesis of a furan with sensitive functionalities. A sulfolene moiety was utilized as a masking group for the sensitive diene. Noyori asymmetric reduction, Achmatowicz reaction, and Kishi reduction steps converted sulfolene to a highly substituted tetrahydropyran intermediate used in the synthesis of the highly potent antitumor agents, spliceostatins, and their derivatives.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry and Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Joshua R Born
- Department of Chemistry and Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Anne M Veitschegger
- Department of Chemistry and Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Melissa S Jurica
- Department of Molecular Cell and Developmental Biology and Center for Molecular Biology of RNA, University of California, Santa Cruz, Santa Cruz, California 95064, United States
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21
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Sebbag-Sznajder N, Brody Y, Hochberg-Laufer H, Shav-Tal Y, Sperling J, Sperling R. Dynamic Supraspliceosomes Are Assembled on Different Transcripts Regardless of Their Intron Number and Splicing State. Front Genet 2020; 11:409. [PMID: 32499811 PMCID: PMC7243799 DOI: 10.3389/fgene.2020.00409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 03/31/2020] [Indexed: 11/13/2022] Open
Abstract
Splicing and alternative splicing of pre-mRNA are key sources in the formation of diversity in the human proteome. These processes have a central role in the regulation of the gene expression pathway. Yet, how spliceosomes are assembled on a multi-intronic pre-mRNA is at present not well understood. To study the spliceosomes assembled in vivo on transcripts with variable number of introns, we examined a series of three related transcripts derived from the β-globin gene, where two transcript types contained increasing number of introns, while one had only an exon. Each transcript had multiple MS2 sequence repeats that can be bound by the MS2 coat protein. Using our protocol for isolation of endogenous spliceosomes under native conditions from cell nuclei, we show that all three transcripts are found in supraspliceosomes – 21 MDa dynamic complexes, sedimenting at 200S in glycerol gradients, and composed of four native spliceosomes connected by the transcript. Affinity purification of complexes assembled on the transcript with most introns (termed E6), using the MS2 tag, confirmed the assembly of E6 in supraspliceosomes with components such as Sm proteins and PSF. Furthermore, splicing inhibition by spliceostatin A did not inhibit the assembly of supraspliceosomes on the E6 transcript, yet increased the percentage of E6 pre-mRNA supraspliceosomes. These findings were corroborated in intact cells, using RNA FISH to detect the MS2-tagged E6 mRNA, together with GFP-tagged splicing factors, showing the assembly of splicing factors SRSF2, U1-70K, and PRP8 onto the E6 transcripts under normal conditions and also when splicing was inhibited. This study shows that different transcripts with different number of introns, or lacking an intron, are assembled in supraspliceosomes even when splicing is inhibited. This assembly starts at the site of transcription and can continue during the life of the transcript in the nucleoplasm. This study further confirms the dynamic and universal nature of supraspliceosomes that package RNA polymerase II transcribed pre-mRNAs into complexes composed of four native spliceosomes connected by the transcript, independent of their length, number of introns, or splicing state.
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Affiliation(s)
| | - Yehuda Brody
- The Mina and Everard Goodman Faculty of Life Sciences and The Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Hodaya Hochberg-Laufer
- The Mina and Everard Goodman Faculty of Life Sciences and The Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Yaron Shav-Tal
- The Mina and Everard Goodman Faculty of Life Sciences and The Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Joseph Sperling
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| | - Ruth Sperling
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem, Israel
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22
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Fujita KI, Ishizuka T, Mitsukawa M, Kurata M, Masuda S. Regulating Divergent Transcriptomes through mRNA Splicing and Its Modulation Using Various Small Compounds. Int J Mol Sci 2020; 21:ijms21062026. [PMID: 32188117 PMCID: PMC7139312 DOI: 10.3390/ijms21062026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/11/2020] [Accepted: 03/12/2020] [Indexed: 12/14/2022] Open
Abstract
Human transcriptomes are more divergent than genes and contribute to the sophistication of life. This divergence is derived from various isoforms arising from alternative splicing. In addition, alternative splicing regulated by spliceosomal factors and RNA structures, such as the RNA G-quadruplex, is important not only for isoform diversity but also for regulating gene expression. Therefore, abnormal splicing leads to serious diseases such as cancer and neurodegenerative disorders. In the first part of this review, we describe the regulation of divergent transcriptomes using alternative mRNA splicing. In the second part, we present the relationship between the disruption of splicing and diseases. Recently, various compounds with splicing inhibitor activity were established. These splicing inhibitors are recognized as a biological tool to investigate the molecular mechanism of splicing and as a potential therapeutic agent for cancer treatment. Food-derived compounds with similar functions were found and are expected to exhibit anticancer effects. In the final part, we describe the compounds that modulate the messenger RNA (mRNA) splicing process and their availability for basic research and future clinical potential.
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23
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Bressin RK, Osman S, Pohorilets I, Basu U, Koide K. Total Synthesis of Meayamycin B. J Org Chem 2020; 85:4637-4647. [DOI: 10.1021/acs.joc.9b03370] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Robert K. Bressin
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Sami Osman
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Ivanna Pohorilets
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Upamanyu Basu
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Kazunori Koide
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
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24
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Dong X, Chen R. Understanding aberrant RNA splicing to facilitate cancer diagnosis and therapy. Oncogene 2019; 39:2231-2242. [PMID: 31819165 DOI: 10.1038/s41388-019-1138-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 11/22/2019] [Accepted: 11/27/2019] [Indexed: 12/31/2022]
Abstract
Almost all genes in normal cells undergo alternative RNA splicing to generate a greater extent of diversification of gene products for normal cellular functions. RNA splicing is tightly regulated and closely interplays with genetic and epigenetic machinery. While DNA polymorphism and somatic mutations modulate alternative splicing patterns, RNA splicing also controls genomic stability, chromatin organization, and transcriptome. Tumor cells, in turn, often take advantage of aberrant RNA splicing to develop, grow and progress into therapy-resistant tumors. Understanding alternative RNA splicing in tumor cells would, therefore, provide us opportunities to gain further insights into tumor biology, identify diagnostic or prognosis biomarkers, as well as to design effective therapeutic means to control tumor progression. Here, we provide an overview of RNA splicing mechanisms and use prostate cancer as an example to review recent advancements in our understanding of RNA splicing in cancer progression and therapy resistance. We also discuss emerging diagnostic and therapeutic potentials of RNA splicing events or RNA splicing factors.
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Affiliation(s)
- Xuesen Dong
- Department of Urologic Sciences, Faculty of Medicine, The University of British Columbia, 2660 Oak Street, Vancouver, BC, V6H 3Z6, Canada. .,The Vancouver Prostate Centre, Vancouver General Hospital, 2660 Oak Street, Vancouver, BC, V6H 3Z6, Canada.
| | - Ruiqi Chen
- Faculty of Medicine, University of Toronto, 27 King's College Circle 8, Toronto, ON, M5S 1A1, Canada
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25
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van der Feltz C, Hoskins AA. Structural and functional modularity of the U2 snRNP in pre-mRNA splicing. Crit Rev Biochem Mol Biol 2019; 54:443-465. [PMID: 31744343 DOI: 10.1080/10409238.2019.1691497] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The U2 small nuclear ribonucleoprotein (snRNP) is an essential component of the spliceosome, the cellular machine responsible for removing introns from precursor mRNAs (pre-mRNAs) in all eukaryotes. U2 is an extraordinarily dynamic splicing factor and the most frequently mutated in cancers. Cryo-electron microscopy (cryo-EM) has transformed our structural and functional understanding of the role of U2 in splicing. In this review, we synthesize these and other data with respect to a view of U2 as an assembly of interconnected functional modules. These modules are organized by the U2 small nuclear RNA (snRNA) for roles in spliceosome assembly, intron substrate recognition, and protein scaffolding. We describe new discoveries regarding the structure of U2 components and how the snRNP undergoes numerous conformational and compositional changes during splicing. We specifically highlight large scale movements of U2 modules as the spliceosome creates and rearranges its active site. U2 serves as a compelling example for how cellular machines can exploit the modular organization and structural plasticity of an RNP.
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Affiliation(s)
| | - Aaron A Hoskins
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
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26
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Coltri PP, Dos Santos MGP, da Silva GHG. Splicing and cancer: Challenges and opportunities. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1527. [PMID: 30773852 DOI: 10.1002/wrna.1527] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/14/2018] [Accepted: 01/17/2019] [Indexed: 12/11/2022]
Abstract
Cancer arises from alterations in several metabolic processes affecting proliferation, growth, replication and death of cells. A fundamental challenge in the study of cancer biology is to uncover molecular mechanisms that lead to malignant cellular transformation. Recent genomic analyses revealed that many molecular alterations observed in cancers come from modifications in the splicing process, including mutations in pre-mRNA regulatory sequences, mutations in spliceosome components, and altered ratio of specific splicing regulators. While alterations in splice site preferences might generate alternative isoforms enabling different biological functions, these might also be responsible for nonfunctional isoforms that can eventually cause dysregulation in cellular processes. Molecular characteristics of regulatory sequences and proteins might also be important prognostic tools revealing a cancer-specific splicing pattern and linking splicing control to cancer development. The connection between cancer biology and splicing regulation is of primary importance to understand the mechanisms leading to disease and also to improve development of therapeutic approaches. Splicing modulation is being explored in new anti-cancer therapies and further investigation of targeted splicing factors is critical for the success of these strategies. This article is categorized under: RNA Processing > Splicing Mechanisms RNA-Based Catalysis > RNA Catalysis in Splicing and Translation RNA Processing > Splicing Regulation/Alternative Splicing RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Patricia P Coltri
- Department of Cell and Developmental Biology, Institute for Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Maria G P Dos Santos
- Department of Cell and Developmental Biology, Institute for Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Guilherme H G da Silva
- Department of Cell and Developmental Biology, Institute for Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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27
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Yosudjai J, Wongkham S, Jirawatnotai S, Kaewkong W. Aberrant mRNA splicing generates oncogenic RNA isoforms and contributes to the development and progression of cholangiocarcinoma. Biomed Rep 2019; 10:147-155. [PMID: 30906543 PMCID: PMC6403481 DOI: 10.3892/br.2019.1188] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 01/04/2019] [Indexed: 12/13/2022] Open
Abstract
Cholangiocarcinoma is a lethal biliary cancer, with an unclear molecular pathogenesis. Alternative splicing is a post-transcriptional modification that generates mature mRNAs, which are subsequently translated into proteins. Aberrant alternative splicing has been reported to serve a role in tumor initiation, maintenance and metastasis in several types of human cancer, including cholangiocarcinoma. In this review, the aberrant splicing of genes and the functional contributions of the spliced genes, in the carcinogenesis, progression and aggressiveness of cholangiocarcinoma are summarized. In addition, factors that influence this aberrant splicing that may be relevant as therapeutic targets or prognosis markers for cholangiocarcinoma are discussed.
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Affiliation(s)
- Juthamas Yosudjai
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Sopit Wongkham
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Siwanon Jirawatnotai
- Siriraj Center for Research of Excellence (SiCORE) for System Pharmacology, Department of Pharmacology, Faculty of Medicine, Siriraj Medical School, Mahidol University, Bangkok 10700, Thailand
| | - Worasak Kaewkong
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand
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Ghosh AK, Reddy GC, Kovela S, Relitti N, Urabe VK, Prichard BE, Jurica MS. Enantioselective Synthesis of a Cyclopropane Derivative of Spliceostatin A and Evaluation of Bioactivity. Org Lett 2018; 20:7293-7297. [PMID: 30394756 PMCID: PMC6519444 DOI: 10.1021/acs.orglett.8b03228] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Spliceostatin A is a potent inhibitor of spliceosomes and exhibits excellent anticancer activity against multiple human cancer cell lines. We describe here the design and synthesis of a stable cyclopropane derivative of spliceostatin A. The synthesis involved a cross-metathesis or a Suzuki cross-coupling reaction as the key step. The functionalized epoxy alcohol ring was constructed from commercially available optically active tri- O-acetyl-d-glucal. The biological properties of the cyclopropyl derivative revealed that it is active in human cells and inhibits splicing in vitro comparable to spliceostatin A.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry and Department of Medicinal Chemistry , Purdue University , 560 Oval Drive , West Lafayette , Indiana 47907 , United States
| | - Guddeti Chandrashekar Reddy
- Department of Chemistry and Department of Medicinal Chemistry , Purdue University , 560 Oval Drive , West Lafayette , Indiana 47907 , United States
| | - Satish Kovela
- Department of Chemistry and Department of Medicinal Chemistry , Purdue University , 560 Oval Drive , West Lafayette , Indiana 47907 , United States
| | - Nicola Relitti
- Department of Chemistry and Department of Medicinal Chemistry , Purdue University , 560 Oval Drive , West Lafayette , Indiana 47907 , United States
| | - Veronica K Urabe
- Department of Molecular Cell and Developmental Biology and Center for Molecular Biology of RNA , University of California , Santa Cruz , California 95064 , United States
| | - Beth E Prichard
- Department of Molecular Cell and Developmental Biology and Center for Molecular Biology of RNA , University of California , Santa Cruz , California 95064 , United States
| | - Melissa S Jurica
- Department of Molecular Cell and Developmental Biology and Center for Molecular Biology of RNA , University of California , Santa Cruz , California 95064 , United States
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29
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Structural studies of the spliceosome: past, present and future perspectives. Biochem Soc Trans 2018; 46:1407-1422. [PMID: 30420411 DOI: 10.1042/bst20170240] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 09/24/2018] [Accepted: 09/25/2018] [Indexed: 12/18/2022]
Abstract
The spliceosome is a multi-subunit RNA-protein complex involved in the removal of non-coding segments (introns) from between the coding regions (exons) in precursors of messenger RNAs (pre-mRNAs). Intron removal proceeds via two transesterification reactions, occurring between conserved sequences at intron-exon junctions. A tightly regulated, hierarchical assembly with a multitude of structural and compositional rearrangements posed a great challenge for structural studies of the spliceosome. Over the years, X-ray crystallography dominated the field, providing valuable high-resolution structural information that was mostly limited to individual proteins and smaller sub-complexes. Recent developments in the field of cryo-electron microscopy allowed the visualisation of fully assembled yeast and human spliceosomes, providing unprecedented insights into substrate recognition, catalysis, and active site formation. This has advanced our mechanistic understanding of pre-mRNA splicing enormously.
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30
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Wu G, Fan L, Edmonson MN, Shaw T, Boggs K, Easton J, Rusch MC, Webb TR, Zhang J, Potter PM. Inhibition of SF3B1 by molecules targeting the spliceosome results in massive aberrant exon skipping. RNA (NEW YORK, N.Y.) 2018; 24:1056-1066. [PMID: 29844105 PMCID: PMC6049506 DOI: 10.1261/rna.065383.117] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 05/14/2018] [Indexed: 05/22/2023]
Abstract
The recent identification of compounds that interact with the spliceosome (sudemycins, spliceostatin A, and meayamycin) indicates that these molecules modulate aberrant splicing via SF3B1 inhibition. Through whole transcriptome sequencing, we have demonstrated that treatment of Rh18 cells with sudemycin leads to exon skipping as the predominant aberrant splicing event. This was also observed following reanalysis of published RNA-seq data sets derived from HeLa cells after spliceostatin A exposure. These results are in contrast to previous reports that indicate that intron retention was the major consequence of SF3B1 inhibition. Analysis of the exon junctions up-regulated by these small molecules indicated that these sequences were absent in annotated human genes, suggesting that aberrant splicing events yielded novel RNA transcripts. Interestingly, the length of preferred downstream exons was significantly longer than the skipped exons, although there was no difference between the lengths of introns flanking skipped exons. The reading frame of the aberrantly skipped exons maintained a ratio of 2:1:1, close to that of the cassette exons (3:1:1) present in naturally occurring isoforms, suggesting negative selection by the nonsense-mediated decay (NMD) machinery for out-of-frame transcripts. Accordingly, genes involved in NMD and RNAs encoding proteins involved in the splicing process were enriched in both data sets. Our findings, therefore, further elucidate the mechanisms by which SF3B1 inhibition modulates pre-mRNA splicing.
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Affiliation(s)
- Gang Wu
- Department of Computational Biology
| | - Liying Fan
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105-2794, USA
| | | | | | | | | | | | - Thomas R Webb
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105-2794, USA
| | | | - Philip M Potter
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105-2794, USA
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31
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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: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [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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32
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Ghosh AK, Veitschegger AM, Nie S, MacRae NRAJ, Jurica MS. Enantioselective Synthesis of Thailanstatin A Methyl Ester and Evaluation of in Vitro Splicing Inhibition. J Org Chem 2018; 83:5187-5198. [PMID: 29696980 PMCID: PMC5972027 DOI: 10.1021/acs.joc.8b00593] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thailanstatin A has been isolated recently from the fermentation broth of B. thailandensis MSMB43. We describe here an enantioselective convergent synthesis of thailanstatin A methyl ester and evaluation of its splicing activity. Synthesis of both highly functionalized tetrahydropyran rings were carried out from commercially available tri- O-acetyl-d-glucal as the key starting material. Our convergent synthesis involved the synthesis of both tetrahydropyran fragments in a highly stereoselective manner. The fragments were then coupled using cross-metathesis as the key step. The synthesis of the diene subunit included a highly stereoselective Claisen rearrangement, a Cu(I)-mediated conjugate addition of MeLi to set the C-14 methyl stereochemistry, a reductive amination reaction to install the C16-amine functionality, and a Wittig olefination reaction to incorporate the diene unit. The epoxy alcohol subunit was synthesized by a highly selective anomeric allylation, a Peterson olefination, and a vanadium catalyzed epoxidation that installed the epoxide stereoselectively. Cross-metathesis of the olefins provided the methyl ester derivative of thailanstatin A. We have carried out in vitro splicing studies of the methyl ester derivative, which proved to be a potent inhibitor of the spliceosome.
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Affiliation(s)
- Arun K. Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907
| | - Anne M. Veitschegger
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907
| | - Shenyou Nie
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907
| | - Nicola Relitti Andrew J. MacRae
- Department of Molecular, Cell and Developmental Biology and Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064
| | - Melissa S. Jurica
- Department of Molecular, Cell and Developmental Biology and Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064
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33
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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] [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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34
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35
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Alternative Splicing as a Target for Cancer Treatment. Int J Mol Sci 2018; 19:ijms19020545. [PMID: 29439487 PMCID: PMC5855767 DOI: 10.3390/ijms19020545] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 01/29/2018] [Accepted: 01/29/2018] [Indexed: 02/06/2023] Open
Abstract
Alternative splicing is a key mechanism determinant for gene expression in metazoan. During alternative splicing, non-coding sequences are removed to generate different mature messenger RNAs due to a combination of sequence elements and cellular factors that contribute to splicing regulation. A different combination of splicing sites, exonic or intronic sequences, mutually exclusive exons or retained introns could be selected during alternative splicing to generate different mature mRNAs that could in turn produce distinct protein products. Alternative splicing is the main source of protein diversity responsible for 90% of human gene expression, and it has recently become a hallmark for cancer with a full potential as a prognostic and therapeutic tool. Currently, more than 15,000 alternative splicing events have been associated to different aspects of cancer biology, including cell proliferation and invasion, apoptosis resistance and susceptibility to different chemotherapeutic drugs. Here, we present well established and newly discovered splicing events that occur in different cancer-related genes, their modification by several approaches and the current status of key tools developed to target alternative splicing with diagnostic and therapeutic purposes.
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36
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Ghosh AK, Reddy GC, MacRae AJ, Jurica MS. Enantioselective Synthesis of Spliceostatin G and Evaluation of Bioactivity of Spliceostatin G and Its Methyl Ester. Org Lett 2017; 20:96-99. [PMID: 29218995 DOI: 10.1021/acs.orglett.7b03456] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An enantioselective total synthesis of spliceostatin G has been accomplished. The synthesis involved a Suzuki cross-coupling reaction as a key step. The functionalized tetrahydropyran ring was constructed from commercially available optically active tri-O-acetyl-d-glucal. Other key reactions include a highly stereoselective Claisen rearrangement, a Cu(I)-mediated 1,4 addition of MeLi to install the C8 methyl group, and a reductive amination to incorporate the C10 amine functionality of spliceostatin G. Biological evaluation of synthetic spliceostatin G and its methyl ester revealed that it does not inhibit splicing in vitro.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University , 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Guddeti Chandrashekar Reddy
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University , 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Andrew J MacRae
- Department of Molecular Cell and Developmental Biology and Center for Molecular Biology of RNA, University of California , Santa Cruz, California 95064, United States
| | - Melissa S Jurica
- Department of Molecular Cell and Developmental Biology and Center for Molecular Biology of RNA, University of California , Santa Cruz, California 95064, United States
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37
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Wegener M, Müller-McNicoll M. Nuclear retention of mRNAs - quality control, gene regulation and human disease. Semin Cell Dev Biol 2017; 79:131-142. [PMID: 29102717 DOI: 10.1016/j.semcdb.2017.11.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 10/30/2017] [Accepted: 11/01/2017] [Indexed: 12/21/2022]
Abstract
Nuclear retention of incompletely spliced or mature mRNAs emerges as a novel, previously underappreciated layer of gene regulation, which enables the cell to rapidly respond to stress, viral infection, differentiation cues or changing environmental conditions. Focusing on mammalian cells, we discuss recent insights into the mechanisms and functions of nuclear retention, describe retention-promoting features in protein-coding transcripts and propose mechanisms for their regulated release into the cytoplasm. Moreover, we discuss examples of how aberrant nuclear retention of mRNAs may lead to human diseases.
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Affiliation(s)
- Marius Wegener
- RNA Regulation Group, Cluster of Excellence 'Macromolecular Complexes', Goethe University Frankfurt, Institute of Cell Biology and Neuroscience, Max-von-Laue-Str. 13, 60438 Frankfurt/Main, Germany
| | - Michaela Müller-McNicoll
- RNA Regulation Group, Cluster of Excellence 'Macromolecular Complexes', Goethe University Frankfurt, Institute of Cell Biology and Neuroscience, Max-von-Laue-Str. 13, 60438 Frankfurt/Main, Germany.
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38
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Lee SCW, Abdel-Wahab O. Therapeutic targeting of splicing in cancer. Nat Med 2017; 22:976-86. [PMID: 27603132 DOI: 10.1038/nm.4165] [Citation(s) in RCA: 384] [Impact Index Per Article: 54.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 07/13/2016] [Indexed: 02/07/2023]
Abstract
Recent studies have highlighted that splicing patterns are frequently altered in cancer and that mutations in genes encoding spliceosomal proteins, as well as mutations affecting the splicing of key cancer-associated genes, are enriched in cancer. In parallel, there is also accumulating evidence that several molecular subtypes of cancer are highly dependent on splicing function for cell survival. These findings have resulted in a growing interest in targeting splicing catalysis, splicing regulatory proteins, and/or specific key altered splicing events in the treatment of cancer. Here we present strategies that exist and that are in development to target altered dependency on the spliceosome, as well as aberrant splicing, in cancer. These include drugs to target global splicing in cancer subtypes that are preferentially dependent on wild-type splicing for survival, methods to alter post-translational modifications of splicing-regulating proteins, and strategies to modulate pathologic splicing events and protein-RNA interactions in cancer.
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Affiliation(s)
- Stanley Chun-Wei Lee
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA.,Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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39
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Pham D, Koide K. Discoveries, target identifications, and biological applications of natural products that inhibit splicing factor 3B subunit 1. Nat Prod Rep 2017; 33:637-47. [PMID: 26812544 DOI: 10.1039/c5np00110b] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Covering: 1992 to 2015The natural products FR901464, pladienolide, and herboxidiene were discovered as activators of reporter gene systems. Unexpectedly, these compounds target neither transcription nor translation; rather, they target splicing factor 3B subunit 1 of the spliceosome, causing changes in splicing patterns. All of them showed anticancer activity in a low nanomolar range. Since their discovery, these molecules have been used in a variety of biological applications.
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Affiliation(s)
- Dianne Pham
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, USA.
| | - Kazunori Koide
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, USA.
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40
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Multivalent peptidic linker enables identification of preferred sites of conjugation for a potent thialanstatin antibody drug conjugate. PLoS One 2017; 12:e0178452. [PMID: 28558059 PMCID: PMC5448779 DOI: 10.1371/journal.pone.0178452] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 05/12/2017] [Indexed: 11/19/2022] Open
Abstract
Antibody drug conjugates (ADCs) are no longer an unknown entity in the field of cancer therapy with the success of marketed ADCs like ADCETRIS and KADCYLA and numerous others advancing through clinical trials. The pursuit of novel cytotoxic payloads beyond the mictotubule inhibitors and DNA damaging agents has led us to the recent discovery of an mRNA splicing inhibitor, thailanstatin, as a potent ADC payload. In our previous work, we observed that the potency of this payload was uniquely tied to the method of conjugation, with lysine conjugates showing much superior potency as compared to cysteine conjugates. However, the ADC field is rapidly shifting towards site-specific ADCs due to their advantages in manufacturability, characterization and safety. In this work we report the identification of a highly efficacious site-specific thailanstatin ADC. The site of conjugation played a critical role on both the in vitro and in vivo potency of these ADCs. During the course of this study, we developed a novel methodology of loading a single site with multiple payloads using an in situ generated multi-drug carrying peptidic linker that allowed us to rapidly screen for optimal conjugation sites. Using this methodology, we were able to identify a double-cysteine mutant ADC delivering four-loaded thailanstatin that was very efficacious in a gastric cancer xenograft model at 3mg/kg and was also shown to be efficacious against T-DM1 resistant and MDR1 overexpressing tumor cell lines.
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41
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Kim YD, Lee J, Kim HS, Lee MO, Son MY, Yoo CH, Choi JK, Lee SC, Cho YS. The unique spliceosome signature of human pluripotent stem cells is mediated by SNRPA1, SNRPD1, and PNN. Stem Cell Res 2017; 22:43-53. [PMID: 28595116 DOI: 10.1016/j.scr.2017.05.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 05/25/2017] [Accepted: 05/26/2017] [Indexed: 12/21/2022] Open
Abstract
Spliceosomes are the core host of pre-mRNA splicing, allowing multiple protein isoforms to be produced from a single gene. Herein, we reveal that spliceosomes are more abundant in human pluripotent stem cells (hPSs), including human embryonic stem cells (hESs) and human induced pluripotent stem cells (hiPSs), than non-hPSs, and their presence is associated with high transcriptional activity. Supportively, spliceosomal components involved in the catalytically active pre-mRNA splicing step were mainly co-localized with hPS spliceosomes. By profiling the gene expression of 342 selected splicing factors, we found that 71 genes were significantly altered during the reprogramming of human somatic cells into hiPSs. Among them, SNRPA1, SNRPD1, and PNN were significantly up-regulated during the early stage of reprogramming, identified as hub genes by interaction network and cluster analysis. SNRPA1, SNRPD1, or PNN depletion led to a pronounced loss of pluripotency and significantly blocked hiPS generation. SNRPA1, SNRPD1, and PNN co-localized with the hPS spliceosomes, physically interacted with each other, and positively influenced the appearance of hPS spliceosomes. Our data suggest that SNRPA1, SNRPD1, and PNN are key players in the regulation of pluripotency-specific spliceosome assembly and the acquisition and maintenance of pluripotency.
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Affiliation(s)
- Young-Dae Kim
- Stem Cell Research Laboratory, Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Jungwoon Lee
- Stem Cell Research Laboratory, Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Han-Seop Kim
- Stem Cell Research Laboratory, Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Mi-Ok Lee
- Stem Cell Research Laboratory, Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Mi-Young Son
- Stem Cell Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Chae Hwa Yoo
- Stem Cell Research Laboratory, Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Jung-Kyun Choi
- Stem Cell Research Laboratory, Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea; Department of Bioscience, KRIBB School, University of Science & Technology, 113 Gwahak-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Sang Chul Lee
- Research Center for Metabolic Regulation, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Yee Sook Cho
- Stem Cell Research Laboratory, Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea; Department of Bioscience, KRIBB School, University of Science & Technology, 113 Gwahak-ro, Yuseong-gu, Daejeon 34113, Republic of Korea.
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42
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Kozlovski I, Siegfried Z, Amar-Schwartz A, Karni R. The role of RNA alternative splicing in regulating cancer metabolism. Hum Genet 2017; 136:1113-1127. [PMID: 28429085 DOI: 10.1007/s00439-017-1803-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 04/13/2017] [Indexed: 12/12/2022]
Abstract
Tumor cells alter their metabolism by a wide array of mechanisms to promote growth and proliferation. Dysregulated expression and/or somatic mutations of key components of the glycolytic pathway/TCA cycle as well as other metabolic pathways allow tumor cells to improve their ability to survive harsh conditions such as hypoxia and the presence of reactive oxygen species, as well as the ability to obtain nutrients to increase lipids, protein, and nucleic acids biogenesis. Approximately 95% of the human protein encoding genes undergo alternative splicing (AS), a regulated process of gene expression that greatly diversifies the proteome by creating multiple proteins from a single gene. In recent years, a growing body of evidence suggests that unbalanced AS, the formation of certain pro-tumorigenic isoforms and the reduction of anti-tumorigenic isoforms, is implicated in a variety of cancers. It is becoming increasingly clear that cancer-associated AS contributes to increased growth and proliferation, partially due to effects on metabolic reprogramming. Here, we summarize the known roles of AS in regulating cancer metabolism. We present evidence supporting the idea that AS, in many types of cancer, acts as a molecular switch that alters metabolism to drive tumorigenesis. We propose that the elucidation of misregulated AS and its downstream effects on cancer metabolism emphasizes the need for new therapeutic approaches aiming to modulate the splicing machinery to selectively target cancer cells.
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Affiliation(s)
- Itamar Kozlovski
- Department of Biochemistry and Molecular Biology, IMRIC, Hebrew University-Hadassah Medical School, Ein Karem, 91120, Jerusalem, Israel
| | - Zahava Siegfried
- Department of Biochemistry and Molecular Biology, IMRIC, Hebrew University-Hadassah Medical School, Ein Karem, 91120, Jerusalem, Israel
| | - Adi Amar-Schwartz
- Department of Biochemistry and Molecular Biology, IMRIC, Hebrew University-Hadassah Medical School, Ein Karem, 91120, Jerusalem, Israel
| | - Rotem Karni
- Department of Biochemistry and Molecular Biology, IMRIC, Hebrew University-Hadassah Medical School, Ein Karem, 91120, Jerusalem, Israel.
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Carvalho T, Martins S, Rino J, Marinho S, Carmo-Fonseca M. Pharmacological inhibition of the spliceosome subunit SF3b triggers exon junction complex-independent nonsense-mediated decay. J Cell Sci 2017; 130:1519-1531. [PMID: 28302904 DOI: 10.1242/jcs.202200] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 03/06/2017] [Indexed: 12/12/2022] Open
Abstract
Spliceostatin A, meayamycin, and pladienolide B are small molecules that target the SF3b subunit of the spliceosomal U2 small nuclear ribonucleoprotein (snRNP). These compounds are attracting much attention as tools to manipulate splicing and for use as potential anti-cancer drugs. We investigated the effects of these inhibitors on mRNA transport and stability in human cells. Upon splicing inhibition, unspliced pre-mRNAs accumulated in the nucleus, particularly within enlarged nuclear speckles. However, a small fraction of the pre-mRNA molecules were exported to the cytoplasm. We identified the export adaptor ALYREF as being associated with intron-containing transcripts and show its requirement for the nucleo-cytoplasmic transport of unspliced pre-mRNA. In contrast, the exon junction complex (EJC) core protein eIF4AIII failed to form a stable complex with intron-containing transcripts. Despite the absence of EJC, unspliced transcripts in the cytoplasm were degraded by nonsense-mediated decay (NMD), suggesting that unspliced transcripts are degraded by an EJC-independent NMD pathway. Collectively, our results indicate that although blocking the function of SF3b elicits a massive accumulation of unspliced pre-mRNAs in the nucleus, intron-containing transcripts can still bind the ALYREF export factor and be transported to the cytoplasm, where they trigger an alternative NMD pathway.
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Affiliation(s)
- Teresa Carvalho
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
| | - Sandra Martins
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
| | - José Rino
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
| | - Sérgio Marinho
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
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44
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Sidarovich A, Will CL, Anokhina MM, Ceballos J, Sievers S, Agafonov DE, Samatov T, Bao P, Kastner B, Urlaub H, Waldmann H, Lührmann R. Identification of a small molecule inhibitor that stalls splicing at an early step of spliceosome activation. eLife 2017; 6. [PMID: 28300534 PMCID: PMC5354520 DOI: 10.7554/elife.23533] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 02/26/2017] [Indexed: 11/13/2022] Open
Abstract
Small molecule inhibitors of pre-mRNA splicing are important tools for identifying new spliceosome assembly intermediates, allowing a finer dissection of spliceosome dynamics and function. Here, we identified a small molecule that inhibits human pre-mRNA splicing at an intermediate stage during conversion of pre-catalytic spliceosomal B complexes into activated Bact complexes. Characterization of the stalled complexes (designated B028) revealed that U4/U6 snRNP proteins are released during activation before the U6 Lsm and B-specific proteins, and before recruitment and/or stable incorporation of Prp19/CDC5L complex and other Bact complex proteins. The U2/U6 RNA network in B028 complexes differs from that of the Bact complex, consistent with the idea that the catalytic RNA core forms stepwise during the B to Bact transition and is likely stabilized by the Prp19/CDC5L complex and related proteins. Taken together, our data provide new insights into the RNP rearrangements and extensive exchange of proteins that occurs during spliceosome activation. DOI:http://dx.doi.org/10.7554/eLife.23533.001
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Affiliation(s)
- Anzhalika Sidarovich
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Cindy L Will
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Maria M Anokhina
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Javier Ceballos
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Sonja Sievers
- Compound Management and Screening Center, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Dmitry E Agafonov
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Timur Samatov
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Penghui Bao
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Berthold Kastner
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytics Group, Institute for Clinical Chemistry Göttingen, University Medical Center, Göttingen, Germany
| | - Herbert Waldmann
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Reinhard Lührmann
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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45
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Paolella BR, Gibson WJ, Urbanski LM, Alberta JA, Zack TI, Bandopadhayay P, Nichols CA, Agarwalla PK, Brown MS, Lamothe R, Yu Y, Choi PS, Obeng EA, Heckl D, Wei G, Wang B, Tsherniak A, Vazquez F, Weir BA, Root DE, Cowley GS, Buhrlage SJ, Stiles CD, Ebert BL, Hahn WC, Reed R, Beroukhim R. Copy-number and gene dependency analysis reveals partial copy loss of wild-type SF3B1 as a novel cancer vulnerability. eLife 2017; 6. [PMID: 28177281 PMCID: PMC5357138 DOI: 10.7554/elife.23268] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/06/2017] [Indexed: 12/13/2022] Open
Abstract
Genomic instability is a hallmark of human cancer, and results in widespread somatic copy number alterations. We used a genome-scale shRNA viability screen in human cancer cell lines to systematically identify genes that are essential in the context of particular copy-number alterations (copy-number associated gene dependencies). The most enriched class of copy-number associated gene dependencies was CYCLOPS (Copy-number alterations Yielding Cancer Liabilities Owing to Partial losS) genes, and spliceosome components were the most prevalent. One of these, the pre-mRNA splicing factor SF3B1, is also frequently mutated in cancer. We validated SF3B1 as a CYCLOPS gene and found that human cancer cells harboring partial SF3B1 copy-loss lack a reservoir of SF3b complex that protects cells with normal SF3B1 copy number from cell death upon partial SF3B1 suppression. These data provide a catalog of copy-number associated gene dependencies and identify partial copy-loss of wild-type SF3B1 as a novel, non-driver cancer gene dependency.
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Affiliation(s)
- Brenton R Paolella
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - William J Gibson
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Laura M Urbanski
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - John A Alberta
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Department of Neurobiology, Harvard Medical School, Boston, United States
| | - Travis I Zack
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Pratiti Bandopadhayay
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Caitlin A Nichols
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Pankaj K Agarwalla
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, United States
| | - Meredith S Brown
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Rebecca Lamothe
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Yong Yu
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Peter S Choi
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Esther A Obeng
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Dirk Heckl
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Guo Wei
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States
| | - Belinda Wang
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Aviad Tsherniak
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States
| | - Francisca Vazquez
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States
| | - Barbara A Weir
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States
| | - David E Root
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States
| | - Glenn S Cowley
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States
| | - Sara J Buhrlage
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Charles D Stiles
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Department of Neurobiology, Harvard Medical School, Boston, United States
| | - Benjamin L Ebert
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - William C Hahn
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, United States
| | - Robin Reed
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Rameen Beroukhim
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, United States
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46
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Yoshimoto R, Kaida D, Furuno M, Burroughs AM, Noma S, Suzuki H, Kawamura Y, Hayashizaki Y, Mayeda A, Yoshida M. Global analysis of pre-mRNA subcellular localization following splicing inhibition by spliceostatin A. RNA (NEW YORK, N.Y.) 2017; 23:47-57. [PMID: 27754875 PMCID: PMC5159648 DOI: 10.1261/rna.058065.116] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 10/03/2016] [Indexed: 05/27/2023]
Abstract
Spliceostatin A (SSA) is a methyl ketal derivative of FR901464, a potent antitumor compound isolated from a culture broth of Pseudomonas sp no. 2663. These compounds selectively bind to the essential spliceosome component SF3b, a subcomplex of the U2 snRNP, to inhibit pre-mRNA splicing. However, the mechanism of SSA's antitumor activity is unknown. It is noteworthy that SSA causes accumulation of a truncated form of the CDK inhibitor protein p27 translated from CDKN1B pre-mRNA, which is involved in SSA-induced cell-cycle arrest. However, it is still unclear whether pre-mRNAs are uniformly exported from the nucleus following SSA treatment. We performed RNA-seq analysis on nuclear and cytoplasmic fractions of SSA-treated cells. Our statistical analyses showed that intron retention is the major consequence of SSA treatment, and a small number of intron-containing pre-mRNAs leak into the cytoplasm. Using a series of reporter plasmids to investigate the roles of intronic sequences in the pre-mRNA leakage, we showed that the strength of the 5' splice site affects pre-mRNA leakage. Additionally, we found that the level of pre-mRNA leakage is related to transcript length. These results suggest that the strength of the 5' splice site and the length of the transcripts are determinants of the pre-mRNA leakage induced by SF3b inhibitors.
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Affiliation(s)
- Rei Yoshimoto
- Chemical Genetics Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
- Division of Gene Expression Mechanism, Institute for Comprehensive Medical Science, Fujita Health University, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan
| | - Daisuke Kaida
- Chemical Genetics Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
- Frontier Research Core for Life Sciences, University of Toyama, Toyama-shi, Toyama 930-0194, Japan
- Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama-shi, Toyama 930-0194, Japan
| | - Masaaki Furuno
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - A Maxwell Burroughs
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Shohei Noma
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Harukazu Suzuki
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yumi Kawamura
- Chemical Genetics Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
| | - Yoshihide Hayashizaki
- RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Akila Mayeda
- Division of Gene Expression Mechanism, Institute for Comprehensive Medical Science, Fujita Health University, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan
| | - Minoru Yoshida
- Chemical Genetics Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
- Japan Science and Technology Corporation, CREST Research Project, Kawaguchi, Saitama 332-0012, Japan
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47
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Microbial and Natural Metabolites That Inhibit Splicing: A Powerful Alternative for Cancer Treatment. BIOMED RESEARCH INTERNATIONAL 2016; 2016:3681094. [PMID: 27610372 PMCID: PMC5004037 DOI: 10.1155/2016/3681094] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 06/27/2016] [Accepted: 07/03/2016] [Indexed: 02/06/2023]
Abstract
In eukaryotes, genes are frequently interrupted with noncoding sequences named introns. Alternative splicing is a nuclear mechanism by which these introns are removed and flanking coding regions named exons are joined together to generate a message that will be translated in the cytoplasm. This mechanism is catalyzed by a complex machinery known as the spliceosome, which is conformed by more than 300 proteins and ribonucleoproteins that activate and regulate the precision of gene expression when assembled. It has been proposed that several genetic diseases are related to defects in the splicing process, including cancer. For this reason, natural products that show the ability to regulate splicing have attracted enormous attention due to its potential use for cancer treatment. Some microbial metabolites have shown the ability to inhibit gene splicing and the molecular mechanism responsible for this inhibition is being studied for future applications. Here, we summarize the main types of natural products that have been characterized as splicing inhibitors, the recent advances regarding molecular and cellular effects related to these molecules, and the applications reported so far in cancer therapeutics.
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48
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Rakesh R, Joseph AP, Bhaskara RM, Srinivasan N. Structural and mechanistic insights into human splicing factor SF3b complex derived using an integrated approach guided by the cryo-EM density maps. RNA Biol 2016; 13:1025-1040. [PMID: 27618338 DOI: 10.1080/15476286.2016.1218590] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Pre-mRNA splicing in eukaryotes is performed by the spliceosome, a highly complex macromolecular machine. SF3b is a multi-protein complex which recognizes the branch point adenosine of pre-mRNA as part of a larger U2 snRNP or U11/U12 di-snRNP in the dynamic spliceosome machinery. Although a cryo-EM map is available for human SF3b complex, the structure and relative spatial arrangement of all components in the complex are not yet known. We have recognized folds of domains in various proteins in the assembly and generated comparative models. Using an integrative approach involving structural and other experimental data, guided by the available cryo-EM density map, we deciphered a pseudo-atomic model of the closed form of SF3b which is found to be a "fuzzy complex" with highly flexible components and multiplicity of folds. Further, the model provides structural information for 5 proteins (SF3b10, SF3b155, SF3b145, SF3b130 and SF3b14b) and localization information for 4 proteins (SF3b10, SF3b145, SF3b130 and SF3b14b) in the assembly for the first time. Integration of this model with the available U11/U12 di-snRNP cryo-EM map enabled elucidation of an open form. This now provides new insights on the mechanistic features involved in the transition between closed and open forms pivoted by a hinge region in the SF3b155 protein that also harbors cancer causing mutations. Moreover, the open form guided model of the 5' end of U12 snRNA, which includes the branch point duplex, shows that the architecture of SF3b acts as a scaffold for U12 snRNA: pre-mRNA branch point duplex formation with potential implications for branch point adenosine recognition fidelity.
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Affiliation(s)
- Ramachandran Rakesh
- a Molecular Biophysics Unit, Indian Institute of Science , Bangalore , India
| | - Agnel Praveen Joseph
- b National Center for Biological Sciences, TIFR, GKVK Campus , Bangalore , India
| | - Ramachandra M Bhaskara
- a Molecular Biophysics Unit, Indian Institute of Science , Bangalore , India.,b National Center for Biological Sciences, TIFR, GKVK Campus , Bangalore , India
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49
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Puthenveetil S, Loganzo F, He H, Dirico K, Green M, Teske J, Musto S, Clark T, Rago B, Koehn F, Veneziale R, Falahaptisheh H, Han X, Barletta F, Lucas J, Subramanyam C, O'Donnell CJ, Tumey LN, Sapra P, Gerber HP, Ma D, Graziani EI. Natural Product Splicing Inhibitors: A New Class of Antibody-Drug Conjugate (ADC) Payloads. Bioconjug Chem 2016; 27:1880-8. [PMID: 27412791 DOI: 10.1021/acs.bioconjchem.6b00291] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
There is a considerable ongoing work to identify new cytotoxic payloads that are appropriate for antibody-based delivery, acting via mechanisms beyond DNA damage and microtubule disruption, highlighting their importance to the field of cancer therapeutics. New modes of action will allow a more diverse set of tumor types to be targeted and will allow for possible mechanisms to evade the drug resistance that will invariably develop to existing payloads. Spliceosome inhibitors are known to be potent antiproliferative agents capable of targeting both actively dividing and quiescent cells. A series of thailanstatin-antibody conjugates were prepared in order to evaluate their potential utility in the treatment of cancer. After exploring a variety of linkers, we found that the most potent antibody-drug conjugates (ADCs) were derived from direct conjugation of the carboxylic acid-containing payload to surface lysines of the antibody (a "linker-less" conjugate). Activity of these lysine conjugates was correlated to drug-loading, a feature not typically observed for other payload classes. The thailanstatin-conjugates were potent in high target expressing cells, including multidrug-resistant lines, and inactive in nontarget expressing cells. Moreover, these ADCs were shown to promote altered splicing products in N87 cells in vitro, consistent with their putative mechanism of action. In addition, the exposure of the ADCs was sufficient to result in excellent potency in a gastric cancer xenograft model at doses as low as 1.5 mg/kg that was superior to the clinically approved ADC T-DM1. The results presented herein therefore open the door to further exploring splicing inhibition as a potential new mode-of-action for novel ADCs.
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Affiliation(s)
| | - Frank Loganzo
- Oncology-Rinat Research & Development, Pfizer , 401 North Middletown Road, Pearl River, New York 10965, United States
| | | | | | | | | | - Sylvia Musto
- Oncology-Rinat Research & Development, Pfizer , 401 North Middletown Road, Pearl River, New York 10965, United States
| | | | | | | | - Robert Veneziale
- Drug Safety Research and Development, Pfizer , 401 North Middletown Road, Pearl River, New York 10977, United States
| | - Hadi Falahaptisheh
- Drug Safety Research and Development, Pfizer , 401 North Middletown Road, Pearl River, New York 10977, United States
| | | | | | - Judy Lucas
- Oncology-Rinat Research & Development, Pfizer , 401 North Middletown Road, Pearl River, New York 10965, United States
| | | | | | | | - Puja Sapra
- Oncology-Rinat Research & Development, Pfizer , 401 North Middletown Road, Pearl River, New York 10965, United States
| | - Hans Peter Gerber
- Oncology-Rinat Research & Development, Pfizer , 401 North Middletown Road, Pearl River, New York 10965, United States
| | - Dangshe Ma
- Oncology-Rinat Research & Development, Pfizer , 401 North Middletown Road, Pearl River, New York 10965, United States
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50
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Effenberger KA, Urabe VK, Jurica MS. Modulating splicing with small molecular inhibitors of the spliceosome. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27440103 DOI: 10.1002/wrna.1381] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 06/06/2016] [Accepted: 06/28/2016] [Indexed: 12/23/2022]
Abstract
Small molecule inhibitors that target components of the spliceosome have great potential as tools to probe splicing mechanism and dissect splicing regulatory networks in cells. These compounds also hold promise as drug leads for diseases in which splicing regulation plays a critical role, including many cancers. Because the spliceosome is a complicated and dynamic macromolecular machine comprised of many RNA and protein components, a variety of compounds that interfere with different aspects of spliceosome assembly is needed to probe its function. By screening chemical libraries with high-throughput splicing assays, several labs have added to the collection of splicing inhibitors, although the mechanistic insight into splicing yielded from the initial compound hits is somewhat limited so far. In contrast, SF3B1 inhibitors stand out as a great example of what can be accomplished with small molecule tools. This group of compounds were first discovered as natural products that are cytotoxic to cancer cells, and then later shown to target the core spliceosome protein SF3B1. The inhibitors have since been used to uncover details of SF3B1 mechanism in the spliceosome and its impact on gene expression in cells. Continuing structure activity relationship analysis of the compounds is also making progress in identifying chemical features key to their function, which is critical in understanding the mechanism of SF3B1 inhibition. The knowledge is also important for the design of analogs with new and useful features for both splicing researchers and clinicians hoping to exploit splicing as pressure point to target in cancer therapy. WIREs RNA 2017, 8:e1381. doi: 10.1002/wrna.1381 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Kerstin A Effenberger
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA.,Center for Molecular Biology of RNA, University of California, Santa Cruz, CA, USA
| | - Veronica K Urabe
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA.,Center for Molecular Biology of RNA, University of California, Santa Cruz, CA, USA
| | - Melissa S Jurica
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA.,Center for Molecular Biology of RNA, University of California, Santa Cruz, CA, USA
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