1
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Paul T, Zhang P, Zhang Z, Fargason T, De Silva NIU, Powell E, Ekpenyong E, Jamal S, Yu Y, Prevelige P, Lu R, Zhang J. The U1-70K and SRSF1 interaction is modulated by phosphorylation during the early stages of spliceosome assembly. Protein Sci 2024; 33:e5117. [PMID: 39023093 PMCID: PMC11255866 DOI: 10.1002/pro.5117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 06/22/2024] [Accepted: 07/01/2024] [Indexed: 07/20/2024]
Abstract
In eukaryotes, pre-mRNA splicing is vital for RNA processing and orchestrated by the spliceosome, whose assembly starts with the interaction between U1-70K and SR proteins. Despite the significance of the U1-70K/SR interaction, the dynamic nature of the complex and the challenges in obtaining soluble U1-70K have impeded a comprehensive understanding of the interaction at the structural level for decades. We overcome the U1-70K solubility issues, enabling us to characterize the interaction between U1-70K and SRSF1, a representative SR protein. We unveil specific interactions: phosphorylated SRSF1 RS with U1-70K BAD1, and SRSF1 RRM1 with U1-70K RRM. The RS/BAD1 interaction plays a dominant role, whereas the interaction between the RRM domains further enhances the stability of the U1-70K/SRSF1 complex. The RRM interaction involves the C-terminal extension of U1-70K RRM and the conserved acid patches on SRSF1 RRM1 that is involved in SRSF1 phase separation. Our circular dichroism spectra reveal that BAD1 adapts an α-helical conformation and RS is intrinsically disordered. Intriguingly, BAD1 undergoes a conformation switch from α-helix to β-strand and random coil upon RS binding. In addition to the regulatory mechanism via SRSF1 phosphorylation, the U1-70K/SRSF1 interaction is also regulated by U1-70K BAD1 phosphorylation. We find that U1-70K phosphorylation inhibits the U1-70K and SRSF1 interaction. Our structural findings are validated through in vitro splicing assays and in-cell saturated domain scanning using the CRISPR method, providing new insights into the intricate regulatory mechanisms of pre-mRNA splicing.
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Affiliation(s)
- Trent Paul
- Department of ChemistryUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Pengcheng Zhang
- Department of Medicine, Division of Hematology/OncologyUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Zihan Zhang
- Department of ChemistryUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Talia Fargason
- Department of ChemistryUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | | | - Erin Powell
- Department of ChemistryUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Ethan Ekpenyong
- Department of ChemistryUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Shariq Jamal
- Department of ChemistryUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Yanbao Yu
- Department of Chemistry and BiochemistryUniversity of DelawareNewarkDelawareUSA
| | - Peter Prevelige
- Department of MicrobiologyUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Rui Lu
- Department of Medicine, Division of Hematology/OncologyUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Jun Zhang
- Department of ChemistryUniversity of Alabama at BirminghamBirminghamAlabamaUSA
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2
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Cai G, Bao Y, Li Q, Hsu PH, Xia J, Ngo JCK. Design of a covalent protein-protein interaction inhibitor of SRPKs to suppress angiogenesis and invasion of cancer cells. Commun Chem 2024; 7:144. [PMID: 38937565 PMCID: PMC11211491 DOI: 10.1038/s42004-024-01230-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 06/19/2024] [Indexed: 06/29/2024] Open
Abstract
Serine-arginine (SR) proteins are splicing factors that play essential roles in both constitutive and alternative pre-mRNA splicing. Phosphorylation of their C-terminal RS domains by SR protein kinases (SRPKs) regulates their localization and diverse cellular activities. Dysregulation of phosphorylation has been implicated in many human diseases, including cancers. Here, we report the development of a covalent protein-protein interaction inhibitor, C-DBS, that targets a lysine residue within the SRPK-specific docking groove to block the interaction and phosphorylation of the prototypic SR protein SRSF1. C-DBS exhibits high specificity and conjugation efficiency both in vitro and in cellulo. This self-cell-penetrating inhibitor attenuates the phosphorylation of endogenous SR proteins and subsequently inhibits the angiogenesis, migration, and invasion of cancer cells. These findings provide a new foundation for the development of covalent SRPK inhibitors for combatting diseases such as cancer and viral infections and overcoming the resistance encountered by ATP-competitive inhibitors.
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Affiliation(s)
- Gongli Cai
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Yishu Bao
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Qingyun Li
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou, 450001, China
| | - Pang-Hung Hsu
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Jiang Xia
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Jacky Chi Ki Ngo
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China.
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China.
- Center of Novel Biomaterials, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China.
- Center for Protein Science and Crystallography, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China.
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3
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Zhuravskaya A, Yap K, Hamid F, Makeyev EV. Alternative splicing coupled to nonsense-mediated decay coordinates downregulation of non-neuronal genes in developing mouse neurons. Genome Biol 2024; 25:162. [PMID: 38902825 PMCID: PMC11188260 DOI: 10.1186/s13059-024-03305-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 06/07/2024] [Indexed: 06/22/2024] Open
Abstract
BACKGROUND The functional coupling between alternative pre-mRNA splicing (AS) and the mRNA quality control mechanism called nonsense-mediated decay (NMD) can modulate transcript abundance. Previous studies have identified several examples of such a regulation in developing neurons. However, the systems-level effects of AS-NMD in this context are poorly understood. RESULTS We developed an R package, factR2, which offers a comprehensive suite of AS-NMD analysis functions. Using this tool, we conducted a longitudinal analysis of gene expression in pluripotent stem cells undergoing induced neuronal differentiation. Our analysis uncovers hundreds of AS-NMD events with significant potential to regulate gene expression. Notably, this regulation is significantly overrepresented in specific functional groups of developmentally downregulated genes. Particularly strong association with gene downregulation is detected for alternative cassette exons stimulating NMD upon their inclusion into mature mRNA. By combining bioinformatic analyses with CRISPR/Cas9 genome editing and other experimental approaches we show that NMD-stimulating cassette exons regulated by the RNA-binding protein PTBP1 dampen the expression of their genes in developing neurons. We also provided evidence that the inclusion of NMD-stimulating cassette exons into mature mRNAs is temporally coordinated with NMD-independent gene repression mechanisms. CONCLUSIONS Our study provides an accessible workflow for the discovery and prioritization of AS-NMD targets. It further argues that the AS-NMD pathway plays a widespread role in developing neurons by facilitating the downregulation of functionally related non-neuronal genes.
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Affiliation(s)
- Anna Zhuravskaya
- Centre for Developmental Neurobiology, King's College London, London, SE1 1UL, UK
| | - Karen Yap
- Centre for Developmental Neurobiology, King's College London, London, SE1 1UL, UK
| | - Fursham Hamid
- Centre for Developmental Neurobiology, King's College London, London, SE1 1UL, UK.
| | - Eugene V Makeyev
- Centre for Developmental Neurobiology, King's College London, London, SE1 1UL, UK.
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4
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Roesmann F, Müller L, Klaassen K, Heß S, Widera M. Interferon-Regulated Expression of Cellular Splicing Factors Modulates Multiple Levels of HIV-1 Gene Expression and Replication. Viruses 2024; 16:938. [PMID: 38932230 PMCID: PMC11209495 DOI: 10.3390/v16060938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
Type I interferons (IFN-Is) are pivotal in innate immunity against human immunodeficiency virus I (HIV-1) by eliciting the expression of IFN-stimulated genes (ISGs), which encompass potent host restriction factors. While ISGs restrict the viral replication within the host cell by targeting various stages of the viral life cycle, the lesser-known IFN-repressed genes (IRepGs), including RNA-binding proteins (RBPs), affect the viral replication by altering the expression of the host dependency factors that are essential for efficient HIV-1 gene expression. Both the host restriction and dependency factors determine the viral replication efficiency; however, the understanding of the IRepGs implicated in HIV-1 infection remains greatly limited at present. This review provides a comprehensive overview of the current understanding regarding the impact of the RNA-binding protein families, specifically the two families of splicing-associated proteins SRSF and hnRNP, on HIV-1 gene expression and viral replication. Since the recent findings show specifically that SRSF1 and hnRNP A0 are regulated by IFN-I in various cell lines and primary cells, including intestinal lamina propria mononuclear cells (LPMCs) and peripheral blood mononuclear cells (PBMCs), we particularly discuss their role in the context of the innate immunity affecting HIV-1 replication.
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Affiliation(s)
- Fabian Roesmann
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Paul-Ehrlich-Str. 40, 60596 Frankfurt am Main, Germany
| | - Lisa Müller
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Katleen Klaassen
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Paul-Ehrlich-Str. 40, 60596 Frankfurt am Main, Germany
| | - Stefanie Heß
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Paul-Ehrlich-Str. 40, 60596 Frankfurt am Main, Germany
| | - Marek Widera
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Paul-Ehrlich-Str. 40, 60596 Frankfurt am Main, Germany
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5
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Kramárek M, Souček P, Réblová K, Grodecká L, Freiberger T. Splicing analysis of STAT3 tandem donor suggests non-canonical binding registers for U1 and U6 snRNAs. Nucleic Acids Res 2024; 52:5959-5974. [PMID: 38426935 PMCID: PMC11162779 DOI: 10.1093/nar/gkae147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 02/02/2024] [Accepted: 02/16/2024] [Indexed: 03/02/2024] Open
Abstract
Tandem donor splice sites (5'ss) are unique regions with at least two GU dinucleotides serving as splicing cleavage sites. The Δ3 tandem 5'ss are a specific subclass of 5'ss separated by 3 nucleotides which can affect protein function by inserting/deleting a single amino acid. One 5'ss is typically preferred, yet factors governing particular 5'ss choice are not fully understood. A highly conserved exon 21 of the STAT3 gene was chosen as a model to study Δ3 tandem 5'ss splicing mechanisms. Based on multiple lines of experimental evidence, endogenous U1 snRNA most likely binds only to the upstream 5'ss. However, the downstream 5'ss is used preferentially, and the splice site choice is not dependent on the exact U1 snRNA binding position. Downstream 5'ss usage was sensitive to exact nucleotide composition and dependent on the presence of downstream regulatory region. The downstream 5'ss usage could be best explained by two novel interactions with endogenous U6 snRNA. U6 snRNA enables the downstream 5'ss usage in STAT3 exon 21 by two mechanisms: (i) binding in a novel non-canonical register and (ii) establishing extended Watson-Crick base pairing with the downstream regulatory region. This study suggests that U6:5'ss interaction is more flexible than previously thought.
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Affiliation(s)
- Michal Kramárek
- Centre for Cardiovascular Surgery and Transplantation, 656 91 Brno, Czech Republic
- Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | - Přemysl Souček
- Centre for Cardiovascular Surgery and Transplantation, 656 91 Brno, Czech Republic
- Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic
| | - Kamila Réblová
- Centre of Molecular Biology and Genetics, University Hospital and Masaryk University, Brno, Czech Republic
| | - Lucie Kajan Grodecká
- Centre for Cardiovascular Surgery and Transplantation, 656 91 Brno, Czech Republic
| | - Tomáš Freiberger
- Centre for Cardiovascular Surgery and Transplantation, 656 91 Brno, Czech Republic
- Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic
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6
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Fingerhut JM, Lannes R, Whitfield TW, Thiru P, Yamashita YM. Co-transcriptional splicing facilitates transcription of gigantic genes. PLoS Genet 2024; 20:e1011241. [PMID: 38870220 PMCID: PMC11207136 DOI: 10.1371/journal.pgen.1011241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 06/26/2024] [Accepted: 05/31/2024] [Indexed: 06/15/2024] Open
Abstract
Although introns are typically tens to thousands of nucleotides, there are notable exceptions. In flies as well as humans, a small number of genes contain introns that are more than 1000 times larger than typical introns, exceeding hundreds of kilobases (kb) to megabases (Mb). It remains unknown why gigantic introns exist and how cells overcome the challenges associated with their transcription and RNA processing. The Drosophila Y chromosome contains some of the largest genes identified to date: multiple genes exceed 4Mb, with introns accounting for over 99% of the gene span. Here we demonstrate that co-transcriptional splicing of these gigantic Y-linked genes is important to ensure successful transcription: perturbation of splicing led to the attenuation of transcription, leading to a failure to produce mature mRNA. Cytologically, defective splicing of the Y-linked gigantic genes resulted in disorganization of transcripts within the nucleus suggestive of entanglement of transcripts, likely resulting from unspliced long RNAs. We propose that co-transcriptional splicing maintains the length of nascent transcripts of gigantic genes under a critical threshold, preventing their entanglement and ensuring proper gene expression. Our study reveals a novel biological significance of co-transcriptional splicing.
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Affiliation(s)
- Jaclyn M. Fingerhut
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Cambridge, Massachusetts, United States of America
| | - Romain Lannes
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Troy W. Whitfield
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Prathapan Thiru
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Yukiko M. Yamashita
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Cambridge, Massachusetts, United States of America
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
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7
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DePew AT, Bruckner JJ, O'Connor-Giles KM, Mosca TJ. Neuronal LRP4 directs the development, maturation and cytoskeletal organization of Drosophila peripheral synapses. Development 2024; 151:dev202517. [PMID: 38738619 PMCID: PMC11190576 DOI: 10.1242/dev.202517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 05/02/2024] [Indexed: 05/14/2024]
Abstract
Synaptic development requires multiple signaling pathways to ensure successful connections. Transmembrane receptors are optimally positioned to connect the synapse and the rest of the neuron, often acting as synaptic organizers to synchronize downstream events. One such organizer, the LDL receptor-related protein LRP4, is a cell surface receptor that has been most well-studied postsynaptically at mammalian neuromuscular junctions. Recent work, however, identified emerging roles, but how LRP4 acts as a presynaptic organizer and the downstream mechanisms of LRP4 are not well understood. Here, we show that LRP4 functions presynaptically at Drosophila neuromuscular synapses, acting in motoneurons to instruct pre- and postsynaptic development. Loss of presynaptic LRP4 results in multiple defects, impairing active zone organization, synapse growth, physiological function, microtubule organization, synaptic ultrastructure and synapse maturation. We further demonstrate that LRP4 promotes most aspects of presynaptic development via a downstream SR-protein kinase, SRPK79D. These data demonstrate a function for presynaptic LRP4 as a peripheral synaptic organizer, highlight a downstream mechanism conserved with its CNS function in Drosophila, and underscore previously unappreciated but important developmental roles for LRP4 in cytoskeletal organization, synapse maturation and active zone organization.
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Affiliation(s)
- Alison T. DePew
- Department of Neuroscience, Vickie and Jack Farber Institute of Neuroscience, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Joseph J. Bruckner
- Cell and Molecular Biology Training Program, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kate M. O'Connor-Giles
- Department of Neuroscience, Brown University, Providence, RI 02912, USA
- Carney Institute for Brain Science, Brown University, Providence, RI 02912, USA
| | - Timothy J. Mosca
- Department of Neuroscience, Vickie and Jack Farber Institute of Neuroscience, Thomas Jefferson University, Philadelphia, PA 19107, USA
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8
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Zhang YE, Stuelten CH. Alternative splicing in EMT and TGF-β signaling during cancer progression. Semin Cancer Biol 2024; 101:1-11. [PMID: 38614376 PMCID: PMC11180579 DOI: 10.1016/j.semcancer.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 11/20/2023] [Accepted: 04/04/2024] [Indexed: 04/15/2024]
Abstract
Epithelial to mesenchymal transition (EMT) is a physiological process during development where epithelial cells transform to acquire mesenchymal characteristics, which allows them to migrate and colonize secondary tissues. Many cellular signaling pathways and master transcriptional factors exert a myriad of controls to fine tune this vital process to meet various developmental and physiological needs. Adding to the complexity of this network are post-transcriptional and post-translational regulations. Among them, alternative splicing has been shown to play important roles to drive EMT-associated phenotypic changes, including actin cytoskeleton remodeling, cell-cell junction changes, cell motility and invasiveness. In advanced cancers, transforming growth factor-β (TGF-β) is a major inducer of EMT and is associated with tumor cell metastasis, cancer stem cell self-renewal, and drug resistance. This review aims to provide an overview of recent discoveries regarding alternative splicing events and the involvement of splicing factors in the EMT and TGF-β signaling. It will emphasize the importance of various splicing factors involved in EMT and explore their regulatory mechanisms.
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Affiliation(s)
- Ying E Zhang
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.
| | - Christina H Stuelten
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
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9
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Abd El-Rahman YA, Chen PJ, ElHady AK, Chen SH, Lin HC, El-Gamil DS, Aboushady Y, Abadi AH, Engel M, Abdel-Halim M. Development of 5-hydroxybenzothiophene derivatives as multi-kinase inhibitors with potential anti-cancer activity. Future Med Chem 2024; 16:1239-1254. [PMID: 38989990 PMCID: PMC11249150 DOI: 10.1080/17568919.2024.2342708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 04/09/2024] [Indexed: 07/12/2024] Open
Abstract
Aim: Chemoresistance in cancer challenges the classical therapeutic strategy of 'one molecule-one target'. To combat this, multi-target therapies that inhibit various cancer-relevant targets simultaneously are proposed. Methods & results: We introduce 5-hydroxybenzothiophene derivatives as effective multi-target kinase inhibitors, showing notable growth inhibitory activity across different cancer cell lines. Specifically, compound 16b, featuring a 5-hydroxybenzothiophene hydrazide scaffold, emerged as a potent inhibitor, displaying low IC50 values against key kinases and demonstrating significant anti-cancer effects, particularly against U87MG glioblastoma cells. It induced G2/M cell cycle arrest, apoptosis and inhibited cell migration by modulating apoptotic markers. Conclusion: 16b represents a promising lead for developing new anti-cancer agents targeting multiple kinases with affinity to the hydroxybenzothiophene core.
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Affiliation(s)
- Yara A Abd El-Rahman
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy & Biotechnology, German University in Cairo, Cairo, 11835, Egypt
| | - Po-Jen Chen
- Department of Medical Research, E-Da Hospital, I-Shou University, Kaohsiung, 824410, Taiwan
- Graduate Institute of Medicine, I-Shou University, Kaohsiung, 824410, Taiwan
| | - Ahmed K ElHady
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy & Biotechnology, German University in Cairo, Cairo, 11835, Egypt
- School of Life & Medical Sciences, University of Hertfordshire hosted by Global Academic Foundation, New Administrative Capital, Cairo, Egypt
| | - Shun-Hua Chen
- School of Nursing, Fooyin University, Kaohsiung, 831301, Taiwan
| | - Hsin-Chieh Lin
- Department of Chinese Medicine, E-Da Cancer Hospital, Kaohsiung, 824410, Taiwan
| | - Dalia S El-Gamil
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy & Biotechnology, German University in Cairo, Cairo, 11835, Egypt
- Department of Chemistry, Faculty of Pharmacy, Ahram Canadian University, Cairo, 12451, Egypt
| | - Youssef Aboushady
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy & Biotechnology, German University in Cairo, Cairo, 11835, Egypt
| | - Ashraf H Abadi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy & Biotechnology, German University in Cairo, Cairo, 11835, Egypt
| | - Matthias Engel
- Pharmaceutical & Medicinal Chemistry, Saarland University, Campus C2.3, D-66123, Saarbrücken, Germany
| | - Mohammad Abdel-Halim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy & Biotechnology, German University in Cairo, Cairo, 11835, Egypt
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10
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Song X, Tiek D, Miki S, Huang T, Lu M, Goenka A, Iglesia R, Yu X, Wu R, Walker M, Zeng C, Shah H, Weng SHS, Huff A, Zhang W, Koga T, Hubert C, Horbinski CM, Furnari FB, Hu B, Cheng SY. RNA splicing analysis deciphers developmental hierarchies and reveals therapeutic targets in adult glioma. J Clin Invest 2024; 134:e173789. [PMID: 38662454 PMCID: PMC11142752 DOI: 10.1172/jci173789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 04/16/2024] [Indexed: 06/02/2024] Open
Abstract
Widespread alterations in RNA alternative splicing (AS) have been identified in adult gliomas. However, their regulatory mechanism, biological significance, and therapeutic potential remain largely elusive. Here, using a computational approach with both bulk and single-cell RNA-Seq, we uncover a prognostic AS signature linked with neural developmental hierarchies. Using advanced iPSC glioma models driven by glioma driver mutations, we show that this AS signature could be enhanced by EGFRvIII and inhibited by in situ IDH1 mutation. Functional validations of 2 isoform switching events in CERS5 and MPZL1 show regulations of sphingolipid metabolism and SHP2 signaling, respectively. Analysis of upstream RNA binding proteins reveals PTBP1 as a key regulator of the AS signature where targeting of PTBP1 suppresses tumor growth and promotes the expression of a neuron marker TUJ1 in glioma stem-like cells. Overall, our data highlights the role of AS in affecting glioma malignancy and heterogeneity and its potential as a therapeutic vulnerability for treating adult gliomas.
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Affiliation(s)
- Xiao Song
- The Ken & Ruth Davee Department of Neurology, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Deanna Tiek
- The Ken & Ruth Davee Department of Neurology, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Shunichiro Miki
- Department of Medicine, Division of Regenerative Medicine, Sanford Stem Cell Institute, UCSD, La Jolla, California, USA
| | - Tianzhi Huang
- The Ken & Ruth Davee Department of Neurology, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Minghui Lu
- The Ken & Ruth Davee Department of Neurology, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Anshika Goenka
- The Ken & Ruth Davee Department of Neurology, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Rebeca Iglesia
- The Ken & Ruth Davee Department of Neurology, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Xiaozhou Yu
- The Ken & Ruth Davee Department of Neurology, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Runxin Wu
- The Ken & Ruth Davee Department of Neurology, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Maya Walker
- The Ken & Ruth Davee Department of Neurology, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Chang Zeng
- Department of Preventive Medicine, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Hardik Shah
- Metabolomics Platform, Comprehensive Cancer Center, and
| | - Shao Huan Samuel Weng
- Proteomics Platform, Office of Shared Research Facilities, Biological Sciences Division, The University of Chicago, Chicago, Illinois, USA
| | - Allen Huff
- Proteomics Platform, Office of Shared Research Facilities, Biological Sciences Division, The University of Chicago, Chicago, Illinois, USA
| | - Wei Zhang
- Department of Preventive Medicine, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Tomoyuki Koga
- Department of Neurosurgery, The University of Minnesota, Minneapolis, Minnesota, USA
| | - Christopher Hubert
- Department of Biochemistry, School of Medicine, Case Western Reserved University, Cleveland, Ohio, USA
| | - Craig M. Horbinski
- Departments of Pathology and Neurological Surgery, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Frank B. Furnari
- Department of Medicine, Division of Regenerative Medicine, Sanford Stem Cell Institute, UCSD, La Jolla, California, USA
| | - Bo Hu
- The Ken & Ruth Davee Department of Neurology, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Shi-Yuan Cheng
- The Ken & Ruth Davee Department of Neurology, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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11
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Lee FFY, Harris C, Alper S. RNA Binding Proteins that Mediate LPS-induced Alternative Splicing of the MyD88 Innate Immune Regulator. J Mol Biol 2024; 436:168497. [PMID: 38369277 PMCID: PMC11001520 DOI: 10.1016/j.jmb.2024.168497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 02/08/2024] [Accepted: 02/14/2024] [Indexed: 02/20/2024]
Abstract
Inflammation driven by Toll-like receptor (TLR) signaling pathways is required to combat infection. However, inflammation can damage host tissues; thus it is essential that TLR signaling ultimately is terminated to prevent chronic inflammatory disorders. One mechanism that terminates persistent TLR signaling is alternative splicing of the MyD88 signaling adaptor, which functions in multiple TLR signaling pathways. While the canonical long isoform of MyD88 (MyD88-L) mediates TLR signaling and promotes inflammation, an alternatively-spliced shorter isoform of MyD88 (MyD88-S) produces a dominant negative inhibitor of TLR signaling. MyD88-S production is induced by inflammatory agonists including lipopolysaccharide (LPS), and thus MyD88-S induction is thought to act as a negative feedback loop that prevents chronic inflammation. Despite the potential role that MyD88-S production plays in inflammatory disorders, the mechanisms controlling MyD88 alternative splicing remain unclear. Here, we identify two RNA binding proteins, SRSF1 and HNRNPU, that regulate LPS-induced alternative splicing of MyD88.
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Affiliation(s)
- Frank Fang Yao Lee
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO 80206, USA; Center for Genes, Environment and Health, National Jewish Health, Denver, CO 80206, USA; Department of Immunology and Microbiology, University of Colorado School of Medicine, Anschutz, CO 80045, USA
| | - Chelsea Harris
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO 80206, USA; Center for Genes, Environment and Health, National Jewish Health, Denver, CO 80206, USA; Department of Immunology and Microbiology, University of Colorado School of Medicine, Anschutz, CO 80045, USA
| | - Scott Alper
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO 80206, USA; Center for Genes, Environment and Health, National Jewish Health, Denver, CO 80206, USA; Department of Immunology and Microbiology, University of Colorado School of Medicine, Anschutz, CO 80045, USA.
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12
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Forman TE, Sajek MP, Larson ED, Mukherjee N, Fantauzzo KA. PDGFRα signaling regulates Srsf3 transcript binding to affect PI3K signaling and endosomal trafficking. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.03.587975. [PMID: 38617350 PMCID: PMC11014628 DOI: 10.1101/2024.04.03.587975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Signaling through the platelet-derived growth factor receptor alpha (PDGFRa) plays a critical role in craniofacial development, as mutations in PDGFRA are associated with cleft lip/palate in humans and Pdgfra mutant mouse models display varying degrees of facial clefting. Phosphatidylinositol 3-kinase (PI3K)/Akt is the primary effector of PDGFRα signaling during skeletal development in the mouse. We previously demonstrated that Akt phosphorylates the RNA-binding protein serine/arginine-rich splicing factor 3 (Srsf3) downstream of PI3K-mediated PDGFRa signaling in mouse embryonic palatal mesenchyme (MEPM) cells, leading to its nuclear translocation. We further showed that ablation of Srsf3 in the murine neural crest lineage results in severe midline facial clefting, due to defects in proliferation and survival of cranial neural crest cells, and widespread alternative RNA splicing (AS) changes. Here, we sought to determine the molecular mechanisms by which Srsf3 activity is regulated downstream of PDGFRa signaling to control AS of transcripts necessary for craniofacial development. We demonstrated via enhanced UV-crosslinking and immunoprecipitation (eCLIP) of MEPM cells that PDGF-AA stimulation leads to preferential binding of Srsf3 to exons and loss of binding to canonical Srsf3 CA-rich motifs. Through the analysis of complementary RNA-seq data, we showed that Srsf3 activity results in the preferential inclusion of exons with increased GC content and lower intron to exon length ratio. Moreover, we found that the subset of transcripts that are bound by Srsf3 and undergo AS upon PDGFRα signaling commonly encode regulators of PI3K signaling and early endosomal trafficking. Functional validation studies further confirmed that Srsf3 activity downstream of PDGFRα signaling leads to retention of the receptor in early endosomes and increases in downstream PI3K-mediated Akt signaling. Taken together, our findings reveal that growth factor-mediated phosphorylation of an RNA-binding protein underlies gene expression regulation necessary for mammalian craniofacial development.
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Affiliation(s)
- Thomas E. Forman
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Medical Scientist Training Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Marcin P. Sajek
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Eric D. Larson
- Department of Otolaryngology – Head and Neck Surgery, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Basic and Translational Sciences, Penn Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Neelanjan Mukherjee
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Katherine A. Fantauzzo
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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13
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Scott HM, Smith MH, Coleman AK, Armijo KS, Chapman MJ, Apostalo SL, Wagner AR, Watson RO, Patrick KL. Serine/arginine-rich splicing factor 7 promotes the type I interferon response by activating Irf7 transcription. Cell Rep 2024; 43:113816. [PMID: 38393946 PMCID: PMC11056844 DOI: 10.1016/j.celrep.2024.113816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 12/19/2023] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
Tight regulation of macrophage immune gene expression is required to fight infection without risking harmful inflammation. The contribution of RNA-binding proteins (RBPs) to shaping the macrophage response to pathogens remains poorly understood. Transcriptomic analysis reveals that a member of the serine/arginine-rich (SR) family of mRNA processing factors, SRSF7, is required for optimal expression of a cohort of interferon-stimulated genes in macrophages. Using genetic and biochemical assays, we discover that in addition to its canonical role in regulating alternative splicing, SRSF7 drives transcription of interferon regulatory transcription factor 7 (IRF7) to promote antiviral immunity. At the Irf7 promoter, SRSF7 maximizes STAT1 transcription factor binding and RNA polymerase II elongation via cooperation with the H4K20me1 histone methyltransferase KMT5a (SET8). These studies define a role for an SR protein in activating transcription and reveal an RBP-chromatin network that orchestrates macrophage antiviral gene expression.
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Affiliation(s)
- Haley M Scott
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health, College of Medicine, Bryan, TX 77807, USA
| | - Mackenzie H Smith
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health, College of Medicine, Bryan, TX 77807, USA
| | - Aja K Coleman
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health, College of Medicine, Bryan, TX 77807, USA
| | - Kaitlyn S Armijo
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health, College of Medicine, Bryan, TX 77807, USA
| | - Morgan J Chapman
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health, College of Medicine, Bryan, TX 77807, USA
| | - Summer L Apostalo
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health, College of Medicine, Bryan, TX 77807, USA
| | - Allison R Wagner
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health, College of Medicine, Bryan, TX 77807, USA
| | - Robert O Watson
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health, College of Medicine, Bryan, TX 77807, USA
| | - Kristin L Patrick
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health, College of Medicine, Bryan, TX 77807, USA.
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14
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Zhao R, Wu WA, Huang YH, Li XK, Han JQ, Jiao W, Su YN, Zhao H, Zhou Y, Cao WQ, Zhang X, Wei W, Zhang WK, Song QX, He XJ, Ma B, Chen SY, Tao JJ, Yin CC, Zhang JS. An RRM domain protein SOE suppresses transgene silencing in rice. THE NEW PHYTOLOGIST 2024. [PMID: 38509454 DOI: 10.1111/nph.19686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 03/01/2024] [Indexed: 03/22/2024]
Abstract
Gene expression is regulated at multiple levels, including RNA processing and DNA methylation/demethylation. How these regulations are controlled remains unclear. Here, through analysis of a suppressor for the OsEIN2 over-expressor, we identified an RNA recognition motif protein SUPPRESSOR OF EIN2 (SOE). SOE is localized in nuclear speckles and interacts with several components of the spliceosome. We find SOE associates with hundreds of targets and directly binds to a DNA glycosylase gene DNG701 pre-mRNA for efficient splicing and stabilization, allowing for subsequent DNG701-mediated DNA demethylation of the transgene promoter for proper gene expression. The V81M substitution in the suppressor mutant protein mSOE impaired its protein stability and binding activity to DNG701 pre-mRNA, leading to transgene silencing. SOE mutation enhances grain size and yield. Haplotype analysis in c. 3000 rice accessions reveals that the haplotype 1 (Hap 1) promoter is associated with high 1000-grain weight, and most of the japonica accessions, but not indica ones, have the Hap 1 elite allele. Our study discovers a novel mechanism for the regulation of gene expression and provides an elite allele for the promotion of yield potentials in rice.
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Affiliation(s)
- Rui Zhao
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wen-Ai Wu
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yi-Hua Huang
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xin-Kai Li
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jia-Qi Han
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wu Jiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China
| | - Yin-Na Su
- National Institute of Biological Sciences, Beijing, 102206, China
| | - He Zhao
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yang Zhou
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wu-Qiang Cao
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xun Zhang
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Wei
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wan-Ke Zhang
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qing-Xin Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Biao Ma
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Shou-Yi Chen
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jian-Jun Tao
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Cui-Cui Yin
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jin-Song Zhang
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
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15
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Sun Y, Hu T, Zhang M, Song J, Qin Z, Liu M, Ji J, Li Z, Qiu Z, Bian J. Structure-Guided Discovery of Potent and Selective CLK2 Inhibitors for the Treatment of Knee Osteoarthritis. J Med Chem 2024. [PMID: 38500250 DOI: 10.1021/acs.jmedchem.3c02092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Osteoarthritis is the most common joint disorder. However, there are no disease-modifying drugs approved for OA treatment. CDC2-like kinase 2 (CLK2) could modulate Wnt signaling via alternative splicing of Wnt target genes and further affect bone differentiation, chondrocyte function, and inflammation, making CLK2 an attractive target for OA therapy. In this study, we designed and synthesized a series of highly potent CLK2 inhibitors based on Indazole 1. Among them, compound LQ23 showed more elevated inhibitory activity against CLK2 than the lead compound (IC50, 1.4 nM) with high CLK2/CLK3 selectivity (>70-fold). Furthermore, LQ23 showed outstanding antiosteoarthritis effects in vitro and in vivo, with the roles specific in decreased inflammatory cytokines, downregulated cartilage degradative enzymes, and increased joint cartilage via suppressing CLK2/Wnt signaling pathway. Overall, these data support LQ23 as a potential candidate for intra-articular knee OA therapy, leveraging its unique mechanism of action for targeted treatment.
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Affiliation(s)
- Yongqiang Sun
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Tianxing Hu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Mengdi Zhang
- School of Basic Medical Sciences and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Jiaxing Song
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Zhen Qin
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Mai Liu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Jinliang Ji
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Zhiyu Li
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Zhixia Qiu
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Jinlei Bian
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
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16
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Chen W, Geng D, Chen J, Han X, Xie Q, Guo G, Chen X, Zhang W, Tang S, Zhong X. Roles and mechanisms of aberrant alternative splicing in melanoma - implications for targeted therapy and immunotherapy resistance. Cancer Cell Int 2024; 24:101. [PMID: 38462618 PMCID: PMC10926661 DOI: 10.1186/s12935-024-03280-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 02/22/2024] [Indexed: 03/12/2024] Open
Abstract
BACKGROUND Despite advances in therapeutic strategies, resistance to immunotherapy and the off-target effects of targeted therapy have significantly weakened the benefits for patients with melanoma. MAIN BODY Alternative splicing plays a crucial role in transcriptional reprogramming during melanoma development. In particular, aberrant alternative splicing is involved in the efficacy of immunotherapy, targeted therapy, and melanoma metastasis. Abnormal expression of splicing factors and variants may serve as biomarkers or therapeutic targets for the diagnosis and prognosis of melanoma. Therefore, comprehensively integrating their roles and related mechanisms is essential. This review provides the first detailed summary of the splicing process in melanoma and the changes occurring in this pathway. CONCLUSION The focus of this review is to provide strategies for developing novel diagnostic biomarkers and summarize their potential to alter resistance to targeted therapies and immunotherapy.
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Affiliation(s)
- Wanxian Chen
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Deyi Geng
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Jiasheng Chen
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Xiaosha Han
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Qihu Xie
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Genghong Guo
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Xuefen Chen
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Wancong Zhang
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Shijie Tang
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Xiaoping Zhong
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China.
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China.
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17
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Alhabsi A, Butt H, Kirschner GK, Blilou I, Mahfouz MM. SCR106 splicing factor modulates abiotic stress responses by maintaining RNA splicing in rice. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:802-818. [PMID: 37924151 PMCID: PMC10837019 DOI: 10.1093/jxb/erad433] [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: 10/01/2023] [Accepted: 10/29/2023] [Indexed: 11/06/2023]
Abstract
Plants employ sophisticated molecular machinery to fine-tune their responses to growth, developmental, and stress cues. Gene expression influences plant cellular responses through regulatory processes such as transcription and splicing. Pre-mRNA is alternatively spliced to increase the genome coding potential and further regulate expression. Serine/arginine-rich (SR) proteins, a family of pre-mRNA splicing factors, recognize splicing cis-elements and regulate both constitutive and alternative splicing. Several studies have reported SR protein genes in the rice genome, subdivided into six subfamilies based on their domain structures. Here, we identified a new splicing factor in rice with an RNA recognition motif (RRM) and SR-dipeptides, which is related to the SR proteins, subfamily SC. OsSCR106 regulates pre-mRNA splicing under abiotic stress conditions. It localizes to the nuclear speckles, a major site for pre-mRNA splicing in the cell. The loss-of-function scr106 mutant is hypersensitive to salt, abscisic acid, and low-temperature stress, and harbors a developmental abnormality indicated by the shorter length of the shoot and root. The hypersensitivity to stress phenotype was rescued by complementation using OsSCR106 fused behind its endogenous promoter. Global gene expression and genome-wide splicing analysis in wild-type and scr106 seedlings revealed that OsSCR106 regulates its targets, presumably through regulating the alternative 3'-splice site. Under salt stress conditions, we identified multiple splice isoforms regulated by OsSCR106. Collectively, our results suggest that OsSCR106 is an important splicing factor that plays a crucial role in accurate pre-mRNA splicing and regulates abiotic stress responses in plants.
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Affiliation(s)
- Abdulrahman Alhabsi
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Haroon Butt
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Gwendolyn K Kirschner
- Laboratory of Plant Cell and Developmental Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Ikram Blilou
- Laboratory of Plant Cell and Developmental Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
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18
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Granados AA, Kanrar N, Elowitz MB. Combinatorial expression motifs in signaling pathways. CELL GENOMICS 2024; 4:100463. [PMID: 38216284 PMCID: PMC10794782 DOI: 10.1016/j.xgen.2023.100463] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 08/02/2023] [Accepted: 11/15/2023] [Indexed: 01/14/2024]
Abstract
In animal cells, molecular pathways often comprise families of variant components, such as ligands or receptors. These pathway components are differentially expressed by different cell types, potentially tailoring pathway function to cell context. However, it has remained unclear how pathway expression profiles are distributed across cell types and whether similar profiles can occur in dissimilar cell types. Here, using single-cell gene expression datasets, we identified pathway expression motifs, defined as recurrent expression profiles that are broadly distributed across diverse cell types. Motifs appeared in core pathways, including TGF-β, Notch, Wnt, and the SRSF splice factors, and involved combinatorial co-expression of multiple components. Motif usage was weakly correlated between pathways in adult cell types and during dynamic developmental transitions. Together, these results suggest a mosaic view of cell type organization, in which different cell types operate many of the same pathways in distinct modes.
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Affiliation(s)
- Alejandro A Granados
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute and Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA
| | - Nivedita Kanrar
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute and Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute and Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA.
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19
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Yao ZL, Fang QF, Li JY, Zhou M, Du S, Chen HJ, Wang H, Jiang SJ, Wang X, Zhao Y, Ji XS. Alternative splicing of histone demethylase Kdm6bb mediates temperature-induced sex reversal in the Nile tilapia. Curr Biol 2023; 33:5057-5070.e5. [PMID: 37995698 DOI: 10.1016/j.cub.2023.10.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 09/05/2023] [Accepted: 10/23/2023] [Indexed: 11/25/2023]
Abstract
Sex determination in many fish species is remarkably plastic and temperature sensitive. Nile tilapia display a genetic sex-determination system (XX/XY). However, high-temperature treatment during critical thermosensitive periods can induce XX females into XXm pseudo-males, and this phenomenon is termed temperature-induced sex reversal (TISR). To investigate the molecular mechanism of TISR in Nile tilapia, we performed Iso-seq analysis and found a dramatic effect of high temperature on gene alternative splicing (AS). Kdm6bb histone demethylase showed a novel AS at intron 5 that generates Kdm6bb_tv1 transcripts without intron 5 and Kdm6bb_tv2 with intron 5. Kdm6bb_tv1 encodes a full-length protein while Kdm6bb_tv2 encodes a truncated protein. Expression analysis revealed that intron 5 splicing of Kdm6bb is male and gonad biased at larval stage, and only gonad biased at adult stage. High-temperature treatment induced intron 5 splicing in the gonads of XX and XY fish, resulting in increased Kdm6bb_tv1 expression. To directly test the role of Kdm6bb_tv1 in Nile tilapia TISR, we knocked out expression of Kdm6bb_tv1. However, Kdm6bb_tv1-/- homozygous mutants showed embryonic lethality. Overexpression of Kdm6bb_tv1, but not Kdm6bb_tv2, induced sex reversal of XX females into pseudo-males. Overexpression of Kdm6bb_tv1, as with high-temperature treatment, modified the promotor region of Gsdf and Dmrt1 by demethylating the trimethylated lysine 27 of histone 3 (H3K27me3), thereby increasing expression. Collectively, these studies demonstrate that AS of Kdm6bb intron 5 increases the expression of Kdm6bb_tv1, which acts as a direct link between high temperature and activation of Gsdf and Dmrt1 expression, leading to male sex determination.
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Affiliation(s)
- Zhi Lei Yao
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian 271018, Shandong, China; Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Taian 271018, Shandong, China
| | - Qing Feng Fang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian 271018, Shandong, China; Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Taian 271018, Shandong, China
| | - Jia Yue Li
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian 271018, Shandong, China; Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Taian 271018, Shandong, China
| | - Min Zhou
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian 271018, Shandong, China; Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Taian 271018, Shandong, China
| | - Shaojun Du
- Department of Biochemistry and Molecular Biology, Institute of Marine and Environmental Technology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Hong Ju Chen
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian 271018, Shandong, China; Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Taian 271018, Shandong, China
| | - Hui Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian 271018, Shandong, China; Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Taian 271018, Shandong, China
| | - Shi-Jin Jiang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian 271018, Shandong, China; Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Taian 271018, Shandong, China
| | - Xiao Wang
- Library, Shandong Agricultural University, Taian 271018, Shandong, China
| | - Yan Zhao
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian 271018, Shandong, China; Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Taian 271018, Shandong, China.
| | - Xiang Shan Ji
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian 271018, Shandong, China; Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Taian 271018, Shandong, China.
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20
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DePew AT, Bruckner JJ, O’Connor-Giles KM, Mosca TJ. Neuronal LRP4 directs the development, maturation, and cytoskeletal organization of peripheral synapses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.03.564481. [PMID: 37961323 PMCID: PMC10635100 DOI: 10.1101/2023.11.03.564481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Synapse development requires multiple signaling pathways to accomplish the myriad of steps needed to ensure a successful connection. Transmembrane receptors on the cell surface are optimally positioned to facilitate communication between the synapse and the rest of the neuron and often function as synaptic organizers to synchronize downstream signaling events. One such organizer, the LDL receptor-related protein LRP4, is a cell surface receptor most well-studied postsynaptically at mammalian neuromuscular junctions. Recent work, however, has identified emerging roles for LRP4 as a presynaptic molecule, but how LRP4 acts as a presynaptic organizer, what roles LRP4 plays in organizing presynaptic biology, and the downstream mechanisms of LRP4 are not well understood. Here we show that LRP4 functions presynaptically at Drosophila neuromuscular synapses, acting in motor neurons to instruct multiple aspects of pre- and postsynaptic development. Loss of presynaptic LRP4 results in a range of developmental defects, impairing active zone organization, synapse growth, physiological function, microtubule organization, synaptic ultrastructure, and synapse maturation. We further demonstrate that LRP4 promotes most aspects of presynaptic development via a downstream SR-protein kinase, SRPK79D. SRPK79D overexpression suppresses synaptic defects associated with loss of lrp4. These data demonstrate a function for LRP4 as a peripheral synaptic organizer acting presynaptically, highlight a downstream mechanism conserved with its CNS function, and indicate previously unappreciated roles for LRP4 in cytoskeletal organization, synapse maturation, and active zone organization, underscoring its developmental importance.
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Affiliation(s)
- Alison T. DePew
- Dept. of Neuroscience, Vickie and Jack Farber Institute of Neuroscience, Thomas Jefferson University, Philadelphia, PA 19107 USA
| | - Joseph J. Bruckner
- Cell and Molecular Biology Training Program, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Kate M. O’Connor-Giles
- Department of Neuroscience, Brown University, Providence, RI 02912 USA
- Carney Institute for Brain Science, Brown University, Providence, RI 02912, USA
| | - Timothy J. Mosca
- Dept. of Neuroscience, Vickie and Jack Farber Institute of Neuroscience, Thomas Jefferson University, Philadelphia, PA 19107 USA
- Lead Contact
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21
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Dahal S, Clayton K, Cabral T, Cheng R, Jahanshahi S, Ahmed C, Koirala A, Villasmil Ocando A, Malty R, Been T, Hernandez J, Mangos M, Shen D, Babu M, Calarco J, Chabot B, Attisano L, Houry WA, Cochrane A. On a path toward a broad-spectrum anti-viral: inhibition of HIV-1 and coronavirus replication by SR kinase inhibitor harmine. J Virol 2023; 97:e0039623. [PMID: 37706687 PMCID: PMC10617549 DOI: 10.1128/jvi.00396-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/14/2023] [Indexed: 09/15/2023] Open
Abstract
IMPORTANCE This study highlights the crucial role RNA processing plays in regulating viral gene expression and replication. By targeting SR kinases, we identified harmine as a potent inhibitor of HIV-1 as well as coronavirus (HCoV-229E and multiple SARS-CoV-2 variants) replication. Harmine inhibits HIV-1 protein expression and reduces accumulation of HIV-1 RNAs in both cell lines and primary CD4+ T cells. Harmine also suppresses coronavirus replication post-viral entry by preferentially reducing coronavirus sub-genomic RNA accumulation. By focusing on host factors rather than viral targets, our study offers a novel approach to combating viral infections that is effective against a range of unrelated viruses. Moreover, at doses required to inhibit virus replication, harmine had limited toxicity and minimal effect on the host transcriptome. These findings support the viability of targeting host cellular processes as a means of developing broad-spectrum anti-virals.
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Affiliation(s)
- Subha Dahal
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Kiera Clayton
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Tyler Cabral
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Ran Cheng
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Shahrzad Jahanshahi
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Choudhary Ahmed
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Amrit Koirala
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
- Dan L. Duncan Cancer Comprehensive Center, Baylor College of Medicine, Houston, Texas, USA
| | | | - Ramy Malty
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Research and Innovation Centre, Department of Biochemistry, University of Regina, Regina, Saskatchewan, Canada
| | - Terek Been
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Javier Hernandez
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Maria Mangos
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - David Shen
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Mohan Babu
- Research and Innovation Centre, Department of Biochemistry, University of Regina, Regina, Saskatchewan, Canada
| | - John Calarco
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Benoit Chabot
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Liliana Attisano
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Walid A. Houry
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Alan Cochrane
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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22
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Kurosawa R, Iida K, Ajiro M, Awaya T, Yamada M, Kosaki K, Hagiwara M. PDIVAS: Pathogenicity predictor for Deep-Intronic Variants causing Aberrant Splicing. BMC Genomics 2023; 24:601. [PMID: 37817060 PMCID: PMC10563346 DOI: 10.1186/s12864-023-09645-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 09/01/2023] [Indexed: 10/12/2023] Open
Abstract
BACKGROUND Deep-intronic variants that alter RNA splicing were ineffectively evaluated in the search for the cause of genetic diseases. Determination of such pathogenic variants from a vast number of deep-intronic variants (approximately 1,500,000 variants per individual) represents a technical challenge to researchers. Thus, we developed a Pathogenicity predictor for Deep-Intronic Variants causing Aberrant Splicing (PDIVAS) to easily detect pathogenic deep-intronic variants. RESULTS PDIVAS was trained on an ensemble machine-learning algorithm to classify pathogenic and benign variants in a curated dataset. The dataset consists of manually curated pathogenic splice-altering variants (SAVs) and commonly observed benign variants within deep introns. Splicing features and a splicing constraint metric were used to maximize the predictive sensitivity and specificity, respectively. PDIVAS showed an average precision of 0.92 and a maximum MCC of 0.88 in classifying these variants, which were the best of the previous predictors. When PDIVAS was applied to genome sequencing analysis on a threshold with 95% sensitivity for reported pathogenic SAVs, an average of 27 pathogenic candidates were extracted per individual. Furthermore, the causative variants in simulated patient genomes were more efficiently prioritized than the previous predictors. CONCLUSION Incorporating PDIVAS into variant interpretation pipelines will enable efficient detection of disease-causing deep-intronic SAVs and contribute to improving the diagnostic yield. PDIVAS is publicly available at https://github.com/shiro-kur/PDIVAS .
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Affiliation(s)
- Ryo Kurosawa
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan.
| | - Kei Iida
- Faculty of Science and Engineering, Kindai University, 3-4-1 Kowakae, Higashi-osaka, Osaka, 577-8502, Japan
- Medical Research Support Center, Graduate School of Medicine, Kyoto University, Yoshida- Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Masahiko Ajiro
- Division of Cancer RNA Research, National Cancer Center Research Institute, Tokyo, 104- 0045, Japan
- Department of Drug Discovery Medicine, Graduate School of Medicine, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Tomonari Awaya
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
- Laboratory of Tumor Microenvironment and Immunity, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Mamiko Yamada
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Masatoshi Hagiwara
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan.
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23
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Vorobeva MA, Skvortsov DA, Pervouchine DD. Cooperation and Competition of RNA Secondary Structure and RNA-Protein Interactions in the Regulation of Alternative Splicing. Acta Naturae 2023; 15:23-31. [PMID: 38234601 PMCID: PMC10790352 DOI: 10.32607/actanaturae.26826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 10/31/2023] [Indexed: 01/19/2024] Open
Abstract
The regulation of alternative splicing in eukaryotic cells is carried out through the coordinated action of a large number of factors, including RNA-binding proteins and RNA structure. The RNA structure influences alternative splicing by blocking cis-regulatory elements, or bringing them closer or farther apart. In combination with RNA-binding proteins, it generates transcript conformations that help to achieve the necessary splicing outcome. However, the binding of regulatory proteins depends on RNA structure and, vice versa, the formation of RNA structure depends on the interaction with regulators. Therefore, RNA structure and RNA-binding proteins are inseparable components of common regulatory mechanisms. This review highlights examples of alternative splicing regulation by RNA-binding proteins, the regulation through local and long-range RNA structures, as well as how these elements work together, cooperate, and compete.
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Affiliation(s)
- M. A. Vorobeva
- M.V. Lomonosov Moscow State University, Moscow, 119192 Russian Federation
| | - D. A. Skvortsov
- M.V. Lomonosov Moscow State University, Moscow, 119192 Russian Federation
| | - D. D. Pervouchine
- Skolkovo Institute of Science and Technology, Moscow, 121205 Russian Federation
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24
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Jiang T, Wang L, Tang L, Zeb A, Hou Y. Identification of two short peptide motifs from serine/arginine-rich protein ribonucleic acid recognition motif-1 domain acting as splicing regulators. PeerJ 2023; 11:e16103. [PMID: 37744237 PMCID: PMC10512959 DOI: 10.7717/peerj.16103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 08/25/2023] [Indexed: 09/26/2023] Open
Abstract
Background Serine/arginine-rich (SR) proteins regulate pre-mRNA splicing. However, structurally similar proteins often behave differently in splicing regulation and the underlying mechanisms are largely unknown. Here, using SMN1/2 minigenes we extensively analyzed four SR proteins, SRSF1/5/6/9. Methods In this study, the effects of these proteins on SMN1/2 exon 7 splicing when tethered at either intron 6 or 7 were evaluated using an MS2-tethering assay. Deletion analysis in four SR proteins and co-overexpression analysis were performed. Results Splicing outcomes varied among all four SR proteins, SRSF1 and SRSF5 function the same at the two sites, acting as repressor and stimulator, respectively; while SRSF6 and SRSF9 promote exon 7 inclusion at only one site. Further, the key domains of each SR proteins were investigated, which identified a potent inhibitory nonapeptide in the C-terminus of SRSF1/9 ribonucleic acid recognition motif-1 (RRM1) and a potent stimulatory heptapeptide at the N-terminus of SRSF5/6 RRM1. Conclusion The insight of the four SR proteins and their domains in affecting SMN gene splicing brings a new perspective on the modes of action of SR proteins; and the functional peptides obtained here offers new ideas for developing splice switching-related therapies.
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Affiliation(s)
- Tao Jiang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, NanJing, China
- Department of Rehabilitation, Southwest Hospital, Third Military Medical University Army Medical University, Chongqing, China
| | - Li Wang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, NanJing, China
| | - Liang Tang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, NanJing, China
| | - Azhar Zeb
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, NanJing, China
| | - Yanjun Hou
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, NanJing, China
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25
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Rodriguez Gallo MC, Uhrig RG. Phosphorylation mediated regulation of RNA splicing in plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1249057. [PMID: 37780493 PMCID: PMC10539000 DOI: 10.3389/fpls.2023.1249057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 08/22/2023] [Indexed: 10/03/2023]
Abstract
For the past two decades, the study of alternative splicing (AS) and its involvement in plant development and stress response has grown in popularity. Only recently however, has the focus shifted to the study of how AS regulation (or lack-thereof) affects downstream mRNA and protein landscapes and how these AS regulatory events impact plant development and stress tolerance. In humans, protein phosphorylation represents one of the predominant mechanisms by which AS is regulated and thus the protein kinases governing these phosphorylation events are of interest for further study. Large-scale phosphoproteomic studies in plants have consistently found that RNA splicing-related proteins are extensively phosphorylated, however, the signaling pathways involved in AS regulation have not been resolved. In this mini-review, we summarize our current knowledge of the three major splicing-related protein kinase families in plants that are suggested to mediate AS phospho-regulation and draw comparisons to their metazoan orthologs. We also summarize and contextualize the phosphorylation events identified as occurring on splicing-related protein families to illustrate the high degree to which splicing-related proteins are modified, placing a new focus on elucidating the impacts of AS at the protein and PTM-level.
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Affiliation(s)
| | - R. Glen Uhrig
- University of Alberta, Department of Biological Sciences, Edmonton, AB, Canada
- University of Alberta, Department of Biochemistry, Edmonton, AB, Canada
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26
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Cho S, Chun Y, He L, Ramirez CB, Ganesh KS, Jeong K, Song J, Cheong JG, Li Z, Choi J, Kim J, Koundouros N, Ding F, Dephoure N, Jang C, Blenis J, Lee G. FAM120A couples SREBP-dependent transcription and splicing of lipogenesis enzymes downstream of mTORC1. Mol Cell 2023; 83:3010-3026.e8. [PMID: 37595559 PMCID: PMC10494788 DOI: 10.1016/j.molcel.2023.07.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 05/23/2023] [Accepted: 07/15/2023] [Indexed: 08/20/2023]
Abstract
The mechanistic target of rapamycin complex 1 (mTORC1) is a master regulator of cell growth that stimulates macromolecule synthesis through transcription, RNA processing, and post-translational modification of metabolic enzymes. However, the mechanisms of how mTORC1 orchestrates multiple steps of gene expression programs remain unclear. Here, we identify family with sequence similarity 120A (FAM120A) as a transcription co-activator that couples transcription and splicing of de novo lipid synthesis enzymes downstream of mTORC1-serine/arginine-rich protein kinase 2 (SRPK2) signaling. The mTORC1-activated SRPK2 phosphorylates splicing factor serine/arginine-rich splicing factor 1 (SRSF1), enhancing its binding to FAM120A. FAM120A directly interacts with a lipogenic transcription factor SREBP1 at active promoters, thereby bridging the newly transcribed lipogenic genes from RNA polymerase II to the SRSF1 and U1-70K-containing RNA-splicing machinery. This mTORC1-regulated, multi-protein complex promotes efficient splicing and stability of lipogenic transcripts, resulting in fatty acid synthesis and cancer cell proliferation. These results elucidate FAM120A as a critical transcription co-factor that connects mTORC1-dependent gene regulation programs for anabolic cell growth.
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Affiliation(s)
- Sungyun Cho
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Yujin Chun
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Long He
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Cuauhtemoc B Ramirez
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California Irvine, Irvine, CA, USA; Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Kripa S Ganesh
- Department of Biochemistry, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Kyungjo Jeong
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul, South Korea
| | - Junho Song
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul, South Korea
| | - Jin Gyu Cheong
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Zhongchi Li
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Jungmin Choi
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul, South Korea; Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Joohwan Kim
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Nikos Koundouros
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, USA; Meyer Cancer Center, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Fangyuan Ding
- Department of Biomedical Engineering, Department of Developmental and Cell Biology, Department of Pharmaceutical Sciences, Center for Synthetic Biology, and Center for Neural Circuit Mapping, University of California Irvine, Irvine, CA, USA; Center for Complex Biological Systems and Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Noah Dephoure
- Meyer Cancer Center, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Cholsoon Jang
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA; Center for Complex Biological Systems and Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA; Center for Epigenetics and Metabolism, University of California Irvine, Irvine, CA, USA
| | - John Blenis
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, USA; Meyer Cancer Center, Weill Cornell Medicine, Cornell University, New York, NY, USA.
| | - Gina Lee
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California Irvine, Irvine, CA, USA; Center for Complex Biological Systems and Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA; Center for Epigenetics and Metabolism, University of California Irvine, Irvine, CA, USA.
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27
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Morales ML, García-Vicente R, Rodríguez-García A, Reyes-Palomares A, Vincelle-Nieto Á, Álvarez N, Ortiz-Ruiz A, Garrido-García V, Giménez A, Carreño-Tarragona G, Sánchez R, Ayala R, Martínez-López J, Linares M. Posttranslational splicing modifications as a key mechanism in cytarabine resistance in acute myeloid leukemia. Leukemia 2023; 37:1649-1659. [PMID: 37422594 PMCID: PMC10400425 DOI: 10.1038/s41375-023-01963-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 06/14/2023] [Accepted: 06/29/2023] [Indexed: 07/10/2023]
Abstract
Despite the approval of several drugs for AML, cytarabine is still widely used as a therapeutic approach. However, 85% of patients show resistance and only 10% overcome the disease. Using RNA-seq and phosphoproteomics, we show that RNA splicing and serine-arginine-rich (SR) proteins phosphorylation were altered during cytarabine resistance. Moreover, phosphorylation of SR proteins at diagnosis were significantly lower in responder than non-responder patients, pointing to their utility to predict response. These changes correlated with altered transcriptomic profiles of SR protein target genes. Notably, splicing inhibitors were therapeutically effective in treating sensitive and resistant AML cells as monotherapy or combination with other approved drugs. H3B-8800 and venetoclax combination showed the best efficacy in vitro, demonstrating synergistic effects in patient samples and no toxicity in healthy hematopoietic progenitors. Our results establish that RNA splicing inhibition, alone or combined with venetoclax, could be useful for the treatment of newly diagnosed or relapsed/refractory AML.
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Affiliation(s)
- María Luz Morales
- Department of Translational Hematology, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, Hospital 12 de Octubre - Centro Nacional de Investigaciones Oncológicas, CIBERONC, ES 28041, Madrid, Spain.
| | - Roberto García-Vicente
- Department of Translational Hematology, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, Hospital 12 de Octubre - Centro Nacional de Investigaciones Oncológicas, CIBERONC, ES 28041, Madrid, Spain
| | - Alba Rodríguez-García
- Department of Translational Hematology, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, Hospital 12 de Octubre - Centro Nacional de Investigaciones Oncológicas, CIBERONC, ES 28041, Madrid, Spain
| | - Armando Reyes-Palomares
- Department of Biochemistry and Molecular Biology, Veterinary School, Universidad Complutense de Madrid, ES 28040, Madrid, Spain
| | - África Vincelle-Nieto
- Department of Biochemistry and Molecular Biology, Veterinary School, Universidad Complutense de Madrid, ES 28040, Madrid, Spain
| | - Noemí Álvarez
- Department of Translational Hematology, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, Hospital 12 de Octubre - Centro Nacional de Investigaciones Oncológicas, CIBERONC, ES 28041, Madrid, Spain
| | - Alejandra Ortiz-Ruiz
- Department of Translational Hematology, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, Hospital 12 de Octubre - Centro Nacional de Investigaciones Oncológicas, CIBERONC, ES 28041, Madrid, Spain
| | - Vanesa Garrido-García
- Department of Translational Hematology, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, Hospital 12 de Octubre - Centro Nacional de Investigaciones Oncológicas, CIBERONC, ES 28041, Madrid, Spain
| | - Alicia Giménez
- Department of Translational Hematology, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, Hospital 12 de Octubre - Centro Nacional de Investigaciones Oncológicas, CIBERONC, ES 28041, Madrid, Spain
| | - Gonzalo Carreño-Tarragona
- Department of Translational Hematology, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, Hospital 12 de Octubre - Centro Nacional de Investigaciones Oncológicas, CIBERONC, ES 28041, Madrid, Spain
| | - Ricardo Sánchez
- Department of Translational Hematology, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, Hospital 12 de Octubre - Centro Nacional de Investigaciones Oncológicas, CIBERONC, ES 28041, Madrid, Spain
| | - Rosa Ayala
- Department of Translational Hematology, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, Hospital 12 de Octubre - Centro Nacional de Investigaciones Oncológicas, CIBERONC, ES 28041, Madrid, Spain
- Department of Medicine, Medicine School, Universidad Complutense de Madrid, ES 28040, Madrid, Spain
| | - Joaquín Martínez-López
- Department of Translational Hematology, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, Hospital 12 de Octubre - Centro Nacional de Investigaciones Oncológicas, CIBERONC, ES 28041, Madrid, Spain
- Department of Medicine, Medicine School, Universidad Complutense de Madrid, ES 28040, Madrid, Spain
| | - María Linares
- Department of Translational Hematology, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, Hospital 12 de Octubre - Centro Nacional de Investigaciones Oncológicas, CIBERONC, ES 28041, Madrid, Spain.
- Department of Biochemistry and Molecular Biology, Pharmacy School, Universidad Complutense de Madrid, ES 28040, Madrid, Spain.
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Covello G, Siva K, Adami V, Denti MA. HCS-Splice: A High-Content Screening Method to Advance the Discovery of RNA Splicing-Modulating Therapeutics. Cells 2023; 12:1959. [PMID: 37566038 PMCID: PMC10417277 DOI: 10.3390/cells12151959] [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: 06/25/2023] [Revised: 07/10/2023] [Accepted: 07/13/2023] [Indexed: 08/12/2023] Open
Abstract
Nucleic acid therapeutics have demonstrated an impressive acceleration in recent years. They work through multiple mechanisms of action, including the downregulation of gene expression and the modulation of RNA splicing. While several drugs based on the former mechanism have been approved, few target the latter, despite the promise of RNA splicing modulation. To improve our ability to discover novel RNA splicing-modulating therapies, we developed HCS-Splice, a robust cell-based High-Content Screening (HCS) assay. By implementing the use of a two-colour (GFP/RFP) fluorescent splicing reporter plasmid, we developed a versatile, effective, rapid, and robust high-throughput strategy for the identification of potent splicing-modulating molecules. The HCS-Splice strategy can also be used to functionally confirm splicing mutations in human genetic disorders or to screen drug candidates. As a proof-of-concept, we introduced a dementia-related splice-switching mutation in the Microtubule-Associated Protein Tau (MAPT) exon 10 splicing reporter. We applied HCS-Splice to the wild-type and mutant reporters and measured the functional change in exon 10 inclusion. To demonstrate the applicability of the method in cell-based drug discovery, HCS-Splice was used to evaluate the efficacy of an exon 10-targeting siRNA, which was able to restore the correct alternative splicing balance.
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Affiliation(s)
- Giuseppina Covello
- RNA Biology and Biotechnology Laboratory, Department of Cellular, Computational and Integrative Biology—CIBIO, University of Trento, 38123 Trento, Italy;
| | - Kavitha Siva
- RNA Biology and Biotechnology Laboratory, Department of Cellular, Computational and Integrative Biology—CIBIO, University of Trento, 38123 Trento, Italy;
| | - Valentina Adami
- High Throughput Screening and Validation Core Facility (HTS), Department of Cellular, Computational and Integrative Biology—CIBIO, University of Trento, 38123 Trento, Italy;
| | - Michela Alessandra Denti
- RNA Biology and Biotechnology Laboratory, Department of Cellular, Computational and Integrative Biology—CIBIO, University of Trento, 38123 Trento, Italy;
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29
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Scott HM, Smith MH, Coleman AK, Apostalo SL, Wagner AR, Watson RO, Patrick KL. Serine arginine-rich splicing factor (SRSF7) cooperates with the histone methyltransferase KMT5a to promote the type I interferon response via transcriptional activation of IRF7. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.09.540055. [PMID: 37503164 PMCID: PMC10369877 DOI: 10.1101/2023.05.09.540055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Tight regulation of macrophage immune gene expression is required to fight infection without risking harmful inflammation. The contribution of RNA binding proteins (RBPs) to shaping the macrophage response to pathogens remains poorly understood. Transcriptomic analysis revealed that a member of the serine/arginine-rich (SR) family of mRNA processing factors, SRSF7, is required for optimal expression of a cohort of interferon stimulated genes (ISGs) in macrophages. Using genetic and biochemical assays, we discovered that in addition to its canonical role in regulating alternative splicing, SRSF7 drives transcription of interferon regulatory transcription factor 7 (IRF7) to promote antiviral immunity. At the Irf7 promoter, SRSF7 maximizes STAT1 transcription factor binding and RNA polymerase II elongation via cooperation with the H4K20me1 histone methyltransferase KMT5a (SET8). These studies define an unorthodox role for an SR protein in activating transcription and reveal an unappreciated RNA binding protein-chromatin network that orchestrates macrophage antiviral gene expression.
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30
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Laloum T, Carvalho SD, Martín G, Richardson DN, Cruz TMD, Carvalho RF, Stecca KL, Kinney AJ, Zeidler M, Barbosa ICR, Duque P. The SCL30a SR protein regulates ABA-dependent seed traits and germination under stress. PLANT, CELL & ENVIRONMENT 2023; 46:2112-2127. [PMID: 37098235 DOI: 10.1111/pce.14593] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/03/2023] [Accepted: 04/10/2023] [Indexed: 05/23/2023]
Abstract
SR proteins are conserved RNA-binding proteins best known as splicing regulators that have also been implicated in other steps of gene expression. Despite mounting evidence for a role in plant development and stress responses, the molecular pathways underlying SR protein regulation of these processes remain poorly understood. Here we show that the plant-specific SCL30a SR protein negatively regulates ABA signaling to control seed traits and stress responses during germination in Arabidopsis. Transcriptome-wide analyses revealed that loss of SCL30a function barely affects splicing, but largely induces ABA-responsive gene expression and genes repressed during germination. Accordingly, scl30a mutant seeds display delayed germination and hypersensitivity to ABA and high salinity, while transgenic plants overexpressing SCL30a exhibit reduced ABA and salt stress sensitivity. An ABA biosynthesis inhibitor rescues the enhanced mutant seed stress sensitivity, and epistatic analyses confirm that this hypersensitivity requires a functional ABA pathway. Finally, seed ABA levels are unchanged by altered SCL30a expression, indicating that the gene promotes seed germination under stress by reducing sensitivity to the phytohormone. Our results reveal a new player in ABA-mediated control of early development and stress response.
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Affiliation(s)
- Tom Laloum
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | | | | | | | | | - Kevin L Stecca
- Crop Genetics Research and Development, DuPont Experimental Station, Wilmington, Delaware, USA
| | - Anthony J Kinney
- Crop Genetics Research and Development, DuPont Experimental Station, Wilmington, Delaware, USA
| | - Mathias Zeidler
- Institute of Plant Physiology, Justus-Liebig-University Gießen, Gießen, Germany
| | | | - Paula Duque
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
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31
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Titus MB, Chang AW, Popitsch N, Ebmeier CC, Bono JM, Olesnicky EC. The identification of protein and RNA interactors of the splicing factor Caper in the adult Drosophila nervous system. Front Mol Neurosci 2023; 16:1114857. [PMID: 37435576 PMCID: PMC10332324 DOI: 10.3389/fnmol.2023.1114857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 05/19/2023] [Indexed: 07/13/2023] Open
Abstract
Post-transcriptional gene regulation is a fundamental mechanism that helps regulate the development and healthy aging of the nervous system. Mutations that disrupt the function of RNA-binding proteins (RBPs), which regulate post-transcriptional gene regulation, have increasingly been implicated in neurological disorders including amyotrophic lateral sclerosis, Fragile X Syndrome, and spinal muscular atrophy. Interestingly, although the majority of RBPs are expressed widely within diverse tissue types, the nervous system is often particularly sensitive to their dysfunction. It is therefore critical to elucidate how aberrant RNA regulation that results from the dysfunction of ubiquitously expressed RBPs leads to tissue specific pathologies that underlie neurological diseases. The highly conserved RBP and alternative splicing factor Caper is widely expressed throughout development and is required for the development of Drosophila sensory and motor neurons. Furthermore, caper dysfunction results in larval and adult locomotor deficits. Nonetheless, little is known about which proteins interact with Caper, and which RNAs are regulated by Caper. Here we identify proteins that interact with Caper in both neural and muscle tissue, along with neural specific Caper target RNAs. Furthermore, we show that a subset of these Caper-interacting proteins and RNAs genetically interact with caper to regulate Drosophila gravitaxis behavior.
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Affiliation(s)
- M. Brandon Titus
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, United States
| | - Adeline W. Chang
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, United States
| | - Niko Popitsch
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | | | - Jeremy M. Bono
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, United States
| | - Eugenia C. Olesnicky
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, United States
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32
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Bouligny IM, Maher KR, Grant S. Secondary-Type Mutations in Acute Myeloid Leukemia: Updates from ELN 2022. Cancers (Basel) 2023; 15:3292. [PMID: 37444402 DOI: 10.3390/cancers15133292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/15/2023] [Accepted: 06/17/2023] [Indexed: 07/15/2023] Open
Abstract
The characterization of the molecular landscape and the advent of targeted therapies have defined a new era in the prognostication and treatment of acute myeloid leukemia. Recent revisions in the European LeukemiaNet 2022 guidelines have refined the molecular, cytogenetic, and treatment-related boundaries between myelodysplastic neoplasms (MDS) and AML. This review details the molecular mechanisms and cellular pathways of myeloid maturation aberrancies contributing to dysplasia and leukemogenesis, focusing on recent molecular categories introduced in ELN 2022. We provide insights into novel and rational therapeutic combination strategies that exploit mechanisms of leukemogenesis, highlighting the underpinnings of splicing factors, the cohesin complex, and chromatin remodeling. Areas of interest for future research are summarized, and we emphasize approaches designed to advance existing treatment strategies.
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Affiliation(s)
- Ian M Bouligny
- Division of Hematology and Oncology, Department of Internal Medicine, Virginia Commonwealth University Massey Cancer Center, Richmond, VA 23298, USA
| | - Keri R Maher
- Division of Hematology and Oncology, Department of Internal Medicine, Virginia Commonwealth University Massey Cancer Center, Richmond, VA 23298, USA
| | - Steven Grant
- Division of Hematology and Oncology, Department of Internal Medicine, Virginia Commonwealth University Massey Cancer Center, Richmond, VA 23298, USA
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33
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Martinez BA, Gill MS. The SR protein RSP-2 influences expression of the truncated insulin receptor DAF-2B in Caenorhabditis elegans. G3 (BETHESDA, MD.) 2023; 13:jkad064. [PMID: 36966398 PMCID: PMC10234397 DOI: 10.1093/g3journal/jkad064] [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: 12/01/2022] [Revised: 02/24/2023] [Accepted: 02/26/2023] [Indexed: 03/27/2023]
Abstract
The alternatively spliced daf-2b transcript in Caenorhabditis elegans encodes a truncated isoform of the nematode insulin receptor that retains the extracellular ligand binding domain but lacks the intracellular signaling domain and is therefore unable to transduce a signal. To identify factors that influence expression of daf-2b, we performed a targeted RNA interference screen of rsp genes, which encode splicing factors from the serine/arginine protein family. Loss of rsp-2 significantly increased the expression of a fluorescent daf-2b splicing reporter, as well as increasing expression of endogenous daf-2b transcripts. Correspondingly, rsp-2 mutants exhibited similar phenotypes to those previously observed with DAF-2B overexpression, namely suppression of pheromone-induced dauer formation, enhancement of dauer entry in insulin signaling mutants, inhibition of dauer recovery, and increased lifespan. However, the epistatic relationship between rsp-2 and daf-2b varied according to the experimental context. Increased dauer entry and delayed dauer exit of rsp-2 mutants in an insulin signaling mutant background were partially dependent on daf-2b. Conversely, suppression of pheromone-induced dauer formation and increased lifespan in rsp-2 mutants were independent of daf-2b. These data demonstrate that C. elegans RSP-2, an ortholog of human splicing factor protein SRSF5/SRp40, is involved in regulating the expression of the truncated DAF-2B isoform. However, we also find that RSP-2 can influence dauer formation and lifespan independently of DAF-2B.
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Affiliation(s)
- Bryan A Martinez
- Institute on the Biology of Aging and Metabolism and the Department of Genetics, Cell Biology and Development, University of Minnesota, 4-114 Nils Hasselmo Hall, 312 Church Street SE, Minneapolis, MN 55455, USA
| | - Matthew S Gill
- Institute on the Biology of Aging and Metabolism and the Department of Genetics, Cell Biology and Development, University of Minnesota, 4-114 Nils Hasselmo Hall, 312 Church Street SE, Minneapolis, MN 55455, USA
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34
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Zheng K, Ren Z, Wang Y. Serine-arginine protein kinases and their targets in viral infection and their inhibition. Cell Mol Life Sci 2023; 80:153. [PMID: 37198350 PMCID: PMC10191411 DOI: 10.1007/s00018-023-04808-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/10/2023] [Accepted: 05/12/2023] [Indexed: 05/19/2023]
Abstract
Accumulating evidence has consolidated the interaction between viral infection and host alternative splicing. Serine-arginine (SR) proteins are a class of highly conserved splicing factors critical for the spliceosome maturation, alternative splicing and RNA metabolism. Serine-arginine protein kinases (SRPKs) are important kinases that specifically phosphorylate SR proteins to regulate their distribution and activities in the central pre-mRNA splicing and other cellular processes. In addition to the predominant SR proteins, other cytoplasmic proteins containing a serine-arginine repeat domain, including viral proteins, have been identified as substrates of SRPKs. Viral infection triggers a myriad of cellular events in the host and it is therefore not surprising that viruses explore SRPKs-mediated phosphorylation as an important regulatory node in virus-host interactions. In this review, we briefly summarize the regulation and biological function of SRPKs, highlighting their involvement in the infection process of several viruses, such as viral replication, transcription and capsid assembly. In addition, we review the structure-function relationships of currently available inhibitors of SRPKs and discuss their putative use as antivirals against well-characterized viruses or newly emerging viruses. We also highlight the viral proteins and cellular substrates targeted by SRPKs as potential antiviral therapeutic candidates.
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Affiliation(s)
- Kai Zheng
- School of Pharmacy, Shenzhen University Medical School, Shenzhen, 518055, China.
| | - Zhe Ren
- Institute of Biomedicine, College of Life Science and Technology, Guangdong Province Key Laboratory of Bioengineering Medicine, Key Laboratory of Innovative Technology Research On Natural Products and Cosmetics Raw Materials, Jinan University, Guangzhou, 510632, China
| | - Yifei Wang
- Institute of Biomedicine, College of Life Science and Technology, Guangdong Province Key Laboratory of Bioengineering Medicine, Key Laboratory of Innovative Technology Research On Natural Products and Cosmetics Raw Materials, Jinan University, Guangzhou, 510632, China
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35
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Lim WF, Rinaldi C. RNA Transcript Diversity in Neuromuscular Research. J Neuromuscul Dis 2023:JND221601. [PMID: 37182892 DOI: 10.3233/jnd-221601] [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: 05/16/2023]
Abstract
Three decades since the Human Genome Project began, scientists have now identified more then 25,000 protein coding genes in the human genome. The vast majority of the protein coding genes (> 90%) are multi-exonic, with the coding DNA being interrupted by intronic sequences, which are removed from the pre-mRNA transcripts before being translated into proteins, a process called splicing maturation. Variations in this process, i.e. by exon skipping, intron retention, alternative 5' splice site (5'ss), 3' splice site (3'ss), or polyadenylation usage, lead to remarkable transcriptome and proteome diversity in human tissues. Given its critical biological importance, alternative splicing is tightly regulated in a tissue- and developmental stage-specific manner. The central nervous system and skeletal muscle are amongst the tissues with the highest number of differentially expressed alternative exons, revealing a remarkable degree of transcriptome complexity. It is therefore not surprising that splicing mis-regulation is causally associated with a myriad of neuromuscular diseases, including but not limited to amyotrophic lateral sclerosis (ALS), spinal muscular atrophy (SMA), Duchenne muscular dystrophy (DMD), and myotonic dystrophy type 1 and 2 (DM1, DM2). A gene's transcript diversity has since become an integral and an important consideration for drug design, development and therapy. In this review, we will discuss transcript diversity in the context of neuromuscular diseases and current approaches to address splicing mis-regulation.
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Affiliation(s)
- Wooi Fang Lim
- Department of Paediatrics and Institute of Developmental and Regenerative Medicine, University of Oxford, Oxford, UK
| | - Carlo Rinaldi
- Department of Paediatrics and Institute of Developmental and Regenerative Medicine, University of Oxford, Oxford, UK
- MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford, UK
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36
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He S, Valkov E, Cheloufi S, Murn J. The nexus between RNA-binding proteins and their effectors. Nat Rev Genet 2023; 24:276-294. [PMID: 36418462 DOI: 10.1038/s41576-022-00550-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2022] [Indexed: 11/25/2022]
Abstract
RNA-binding proteins (RBPs) regulate essentially every event in the lifetime of an RNA molecule, from its production to its destruction. Whereas much has been learned about RNA sequence specificity and general functions of individual RBPs, the ways in which numerous RBPs instruct a much smaller number of effector molecules, that is, the core engines of RNA processing, as to where, when and how to act remain largely speculative. Here, we survey the known modes of communication between RBPs and their effectors with a particular focus on converging RBP-effector interactions and their roles in reducing the complexity of RNA networks. We discern the emerging unifying principles and discuss their utility in our understanding of RBP function, regulation of biological processes and contribution to human disease.
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Affiliation(s)
- Shiyang He
- Department of Biochemistry, University of California, Riverside, CA, USA
- Center for RNA Biology and Medicine, Riverside, CA, USA
| | - Eugene Valkov
- RNA Biology Laboratory & Center for Structural Biology, Center for Cancer Research, National Cancer Institute (NCI), Frederick, MD, USA
| | - Sihem Cheloufi
- Department of Biochemistry, University of California, Riverside, CA, USA.
- Center for RNA Biology and Medicine, Riverside, CA, USA.
- Stem Cell Center, University of California, Riverside, CA, USA.
| | - Jernej Murn
- Department of Biochemistry, University of California, Riverside, CA, USA.
- Center for RNA Biology and Medicine, Riverside, CA, USA.
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37
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Kumar K, Sinha SK, Maity U, Kirti PB, Kumar KRR. Insights into established and emerging roles of SR protein family in plants and animals. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1763. [PMID: 36131558 DOI: 10.1002/wrna.1763] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 08/11/2022] [Accepted: 08/22/2022] [Indexed: 05/13/2023]
Abstract
Splicing of pre-mRNA is an essential part of eukaryotic gene expression. Serine-/arginine-rich (SR) proteins are highly conserved RNA-binding proteins present in all metazoans and plants. SR proteins are involved in constitutive and alternative splicing, thereby regulating the transcriptome and proteome diversity in the organism. In addition to their role in splicing, SR proteins are also involved in mRNA export, nonsense-mediated mRNA decay, mRNA stability, and translation. Due to their pivotal roles in mRNA metabolism, SR proteins play essential roles in normal growth and development. Hence, any misregulation of this set of proteins causes developmental defects in both plants and animals. SR proteins from the animal kingdom are extensively studied for their canonical and noncanonical functions. Compared with the animal kingdom, plant genomes harbor more SR protein-encoding genes and greater diversity of SR proteins, which are probably evolved for plant-specific functions. Evidence from both plants and animals confirms the essential role of SR proteins as regulators of gene expression influencing cellular processes, developmental stages, and disease conditions. This article is categorized under: RNA Processing > Splicing Mechanisms RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Kundan Kumar
- Department of Biotechnology, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
| | - Shubham Kumar Sinha
- Department of Biotechnology, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
| | - Upasana Maity
- Department of Biotechnology, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
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38
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Wang R, Kumar B, Bhat-Nakshatri P, Khatpe AS, Murphy MP, Wanczyk KE, Simpson E, Chen D, Gao H, Liu Y, Doud EH, Mosley AL, Nakshatri H. A human skeletal muscle stem/myotube model reveals multiple signaling targets of cancer secretome in skeletal muscle. iScience 2023; 26:106541. [PMID: 37102148 PMCID: PMC10123345 DOI: 10.1016/j.isci.2023.106541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 12/16/2022] [Accepted: 03/24/2023] [Indexed: 04/03/2023] Open
Abstract
Skeletal muscle dysfunction or reprogramming due to the effects of the cancer secretome is observed in multiple malignancies. Although mouse models are routinely used to study skeletal muscle defects in cancer, because of species specificity of certain cytokines/chemokines in the secretome, a human model system is required. Here, we establish simplified multiple skeletal muscle stem cell lines (hMuSCs), which can be differentiated into myotubes. Using single nuclei ATAC-seq (snATAC-seq) and RNA-seq (snRNA-seq), we document chromatin accessibility and transcriptomic changes associated with the transition of hMuSCs to myotubes. Cancer secretome accelerated stem to myotube differentiation, altered the alternative splicing machinery and increased inflammatory, glucocorticoid receptor, and wound healing pathways in hMuSCs. Additionally, cancer secretome reduced metabolic and survival pathway associated miR-486, AKT, and p53 signaling in hMuSCs. hMuSCs underwent myotube differentiation when engrafted into NSG mice and thus providing a humanized in vivo skeletal muscle model system to study cancer cachexia.
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Affiliation(s)
- Ruizhong Wang
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Brijesh Kumar
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | | | - Aditi S. Khatpe
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Michael P. Murphy
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- VA Roudebush Medical Center, Indianapolis, IN 46202, USA
| | - Kristen E. Wanczyk
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- VA Roudebush Medical Center, Indianapolis, IN 46202, USA
| | - Edward Simpson
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Duojiao Chen
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Hongyu Gao
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Yunlong Liu
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Emma H. Doud
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Amber L. Mosley
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Harikrishna Nakshatri
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- VA Roudebush Medical Center, Indianapolis, IN 46202, USA
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39
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Song M, Pang L, Zhang M, Qu Y, Laster KV, Dong Z. Cdc2-like kinases: structure, biological function, and therapeutic targets for diseases. Signal Transduct Target Ther 2023; 8:148. [PMID: 37029108 PMCID: PMC10082069 DOI: 10.1038/s41392-023-01409-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 03/15/2023] [Accepted: 03/20/2023] [Indexed: 04/09/2023] Open
Abstract
The CLKs (Cdc2-like kinases) belong to the dual-specificity protein kinase family and play crucial roles in regulating transcript splicing via the phosphorylation of SR proteins (SRSF1-12), catalyzing spliceosome molecular machinery, and modulating the activities or expression of non-splicing proteins. The dysregulation of these processes is linked with various diseases, including neurodegenerative diseases, Duchenne muscular dystrophy, inflammatory diseases, viral replication, and cancer. Thus, CLKs have been considered as potential therapeutic targets, and significant efforts have been exerted to discover potent CLKs inhibitors. In particular, clinical trials aiming to assess the activities of the small molecules Lorecivivint on knee Osteoarthritis patients, and Cirtuvivint and Silmitasertib in different advanced tumors have been investigated for therapeutic usage. In this review, we comprehensively documented the structure and biological functions of CLKs in various human diseases and summarized the significance of related inhibitors in therapeutics. Our discussion highlights the most recent CLKs research, paving the way for the clinical treatment of various human diseases.
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Affiliation(s)
- Mengqiu Song
- Department of Pathophysiology, School of Basic Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China
- China-US (Henan) Hormel Cancer Institute, No.127, Dongming Road, Jinshui District, Zhengzhou, Henan, 450008, China
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, Henan, China
| | - Luping Pang
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, Henan, China
- Academy of Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China
- Research Center of Basic Medicine, Academy of Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China
| | - Mengmeng Zhang
- Department of Pathophysiology, School of Basic Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China
- Academy of Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China
| | - Yingzi Qu
- Department of Pathophysiology, School of Basic Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China
- Academy of Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China
| | - Kyle Vaughn Laster
- China-US (Henan) Hormel Cancer Institute, No.127, Dongming Road, Jinshui District, Zhengzhou, Henan, 450008, China
| | - Zigang Dong
- Department of Pathophysiology, School of Basic Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China.
- China-US (Henan) Hormel Cancer Institute, No.127, Dongming Road, Jinshui District, Zhengzhou, Henan, 450008, China.
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, Henan, China.
- Academy of Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China.
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40
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Luther CH, Brandt P, Vylkova S, Dandekar T, Müller T, Dittrich M. Integrated analysis of SR-like protein kinases Sky1 and Sky2 links signaling networks with transcriptional regulation in Candida albicans. Front Cell Infect Microbiol 2023; 13:1108235. [PMID: 37082713 PMCID: PMC10111165 DOI: 10.3389/fcimb.2023.1108235] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 03/01/2023] [Indexed: 04/07/2023] Open
Abstract
Fungal infections are a major global health burden where Candida albicans is among the most common fungal pathogen in humans and is a common cause of invasive candidiasis. Fungal phenotypes, such as those related to morphology, proliferation and virulence are mainly driven by gene expression, which is primarily regulated by kinase signaling cascades. Serine-arginine (SR) protein kinases are highly conserved among eukaryotes and are involved in major transcriptional processes in human and S. cerevisiae. Candida albicans harbors two SR protein kinases, while Sky2 is important for metabolic adaptation, Sky1 has similar functions as in S. cerevisiae. To investigate the role of these SR kinases for the regulation of transcriptional responses in C. albicans, we performed RNA sequencing of sky1Δ and sky2Δ and integrated a comprehensive phosphoproteome dataset of these mutants. Using a Systems Biology approach, we study transcriptional regulation in the context of kinase signaling networks. Transcriptomic enrichment analysis indicates that pathways involved in the regulation of gene expression are downregulated and mitochondrial processes are upregulated in sky1Δ. In sky2Δ, primarily metabolic processes are affected, especially for arginine, and we observed that arginine-induced hyphae formation is impaired in sky2Δ. In addition, our analysis identifies several transcription factors as potential drivers of the transcriptional response. Among these, a core set is shared between both kinase knockouts, but it appears to regulate different subsets of target genes. To elucidate these diverse regulatory patterns, we created network modules by integrating the data of site-specific protein phosphorylation and gene expression with kinase-substrate predictions and protein-protein interactions. These integrated signaling modules reveal shared parts but also highlight specific patterns characteristic for each kinase. Interestingly, the modules contain many proteins involved in fungal morphogenesis and stress response. Accordingly, experimental phenotyping shows a higher resistance to Hygromycin B for sky1Δ. Thus, our study demonstrates that a combination of computational approaches with integration of experimental data can offer a new systems biological perspective on the complex network of signaling and transcription. With that, the investigation of the interface between signaling and transcriptional regulation in C. albicans provides a deeper insight into how cellular mechanisms can shape the phenotype.
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Affiliation(s)
- Christian H. Luther
- University of Würzburg, Department of Bioinformatics, Biocenter/Am Hubland 97074, Würzburg, Germany
| | - Philipp Brandt
- Septomics Research Center, Friedrich Schiller University and Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
| | - Slavena Vylkova
- Septomics Research Center, Friedrich Schiller University and Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
| | - Thomas Dandekar
- University of Würzburg, Department of Bioinformatics, Biocenter/Am Hubland 97074, Würzburg, Germany
| | - Tobias Müller
- University of Würzburg, Department of Bioinformatics, Biocenter/Am Hubland 97074, Würzburg, Germany
| | - Marcus Dittrich
- University of Würzburg, Department of Bioinformatics, Biocenter/Am Hubland 97074, Würzburg, Germany
- University of Würzburg, Institut of Human Genetics, Biocenter/Am Hubland 97074, Würzburg, Germany
- *Correspondence: Marcus Dittrich,
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Ong HW, Adderley J, Tobin AB, Drewry DH, Doerig C. Parasite and host kinases as targets for antimalarials. Expert Opin Ther Targets 2023; 27:151-169. [PMID: 36942408 DOI: 10.1080/14728222.2023.2185511] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
INTRODUCTION The deployment of Artemisinin-based combination therapies and transmission control measures led to a decrease in the global malaria burden over the recent decades. Unfortunately, this trend is now reversing, in part due to resistance against available treatments, calling for the development of new drugs against untapped targets to prevent cross-resistance. AREAS COVERED In view of their demonstrated druggability in noninfectious diseases, protein kinases represent attractive targets. Kinase-focussed antimalarial drug discovery is facilitated by the availability of kinase-targeting scaffolds and large libraries of inhibitors, as well as high-throughput phenotypic and biochemical assays. We present an overview of validated Plasmodium kinase targets and their inhibitors, and briefly discuss the potential of host cell kinases as targets for host-directed therapy. EXPERT OPINION We propose priority research areas, including (i) diversification of Plasmodium kinase targets (at present most efforts focus on a very small number of targets); (ii) polypharmacology as an avenue to limit resistance (kinase inhibitors are highly suitable in this respect); and (iii) preemptive limitation of resistance through host-directed therapy (targeting host cell kinases that are required for parasite survival) and transmission-blocking through targeting sexual stage-specific kinases as a strategy to protect curative drugs from the spread of resistance.
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Affiliation(s)
- Han Wee Ong
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC USA
| | - Jack Adderley
- Department of Laboratory Medicine, School of Health and Biomedical Sciences, Rmit University, Bundoora VIC Australia
| | - Andrew B Tobin
- Advanced Research Centre, University of Glasgow, Glasgow, UK
| | - David H Drewry
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC USA
| | - Christian Doerig
- Department of Laboratory Medicine, School of Health and Biomedical Sciences, Rmit University, Bundoora VIC Australia
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The Antidepressant Sertraline Affects Cell Signaling and Metabolism in Trichophyton rubrum. J Fungi (Basel) 2023; 9:jof9020275. [PMID: 36836389 PMCID: PMC9961077 DOI: 10.3390/jof9020275] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 01/24/2023] [Accepted: 02/08/2023] [Indexed: 02/22/2023] Open
Abstract
The dermatophyte Trichophyton rubrum is responsible for most human cutaneous infections. Its treatment is complex, mainly because there are only a few structural classes of fungal inhibitors. Therefore, new strategies addressing these problems are essential. The development of new drugs is time-consuming and expensive. The repositioning of drugs already used in medical practice has emerged as an alternative to discovering new drugs. The antidepressant sertraline (SRT) kills several important fungal pathogens. Accordingly, we investigated the inhibitory mechanism of SRT in T. rubrum to broaden the knowledge of its impact on eukaryotic microorganisms and to assess its potential for future use in dermatophytosis treatments. We performed next-generation sequencing (RNA-seq) to identify the genes responding to SRT at the transcript level. We identified that a major effect of SRT was to alter expression for genes involved in maintaining fungal cell wall and plasma membrane stability, including ergosterol biosynthetic genes. SRT also altered the expression of genes encoding enzymes related to fungal energy metabolism, cellular detoxification, and defense against oxidative stress. Our findings provide insights into a specific molecular network interaction that maintains metabolic stability and is perturbed by SRT, showing potential targets for its strategic use in dermatophytosis.
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Pimentel DC, Leopoldo JR, Teixeira LF, Barros MVDA, de Souza APM, Onofre TS, de Carvalho RL, Machado SA, Messias IG, Pinto CCDS, Poleto MD, Diogo MA, Mariotini-Moura C, Bressan GC, Teixeira RR, Fietto JLR, Vasconcellos RDS. First evidence of a serine arginine protein kinase (SRPK) in leishmania braziliensis and its potential as therapeutic target. Acta Trop 2023; 238:106801. [PMID: 36563831 DOI: 10.1016/j.actatropica.2022.106801] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/17/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
Leishmaniasis is a parasitic disease found in tropical and subtropical regions around the world, caused by parasites of the genus Leishmania. The disease is a public health concern and presents clinical manifestations that can cause death, disability, and mutilation. The parasite has promastigote (vector) and amastigote (vertebrate host) forms and kinase enzymes are involved in this differentiation process. In the present investigation, we show, for the first time, evidence of a serine/arginine protein kinase in Leshmania braziliensis (LbSRPK). Our results show that amastigotes express more LbSRPK than promastigotes. Analogues of SRPIN340 (a known inhibitor of SRPK) were evaluated for their leishmanicidal activity and two of them, namely SRVIC22 and SRVIC32 showed important leishmanicidal activity in vitro. SRVIC22 and SRVIC32 were able to reduce the infection rate in macrophages and the number of intracellular amastigotes by 55 and 60%, respectively. Bioinformatics analysis revealed the existence of two different amino acid residues in the active site of LbSRPK compared to their human homologue (Tyr/Leu-and Ser/Tyr), which could explain the absence of leishmanicidal activity of SRPIN340 on infected macrophages. In order to enhance leishmanicidal activity of the analogues, optimizations were proposed in the structures of the ligands, suggesting strong interactions with the catalytic site of LbSRPK. Although the evidence on the action of inhibitors upon LbSRPK is only indirect, our studies not only reveal, for the first time, evidence of a SRPK in Leishmania, but also shed light on a new therapeutic target for drug development.
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Affiliation(s)
- Débora Cristina Pimentel
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Campus Universitário, CEP, Viçosa, MG 36570-900, Brazil
| | - Juliana Rodrigues Leopoldo
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Campus Universitário, CEP, Viçosa, MG 36570-900, Brazil
| | - Leilane Ferreira Teixeira
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Campus Universitário, CEP, Viçosa, MG 36570-900, Brazil
| | - Marcus Vinícius de Andrade Barros
- Departamento de Química, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Campus Universitário, CEP, Viçosa, MG 36570-900, Brazil
| | - Ana Paula Martins de Souza
- Departamento de Química, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Campus Universitário, CEP, Viçosa, MG 36570-900, Brazil
| | - Thiago Souza Onofre
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Rayane Luiza de Carvalho
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Campus Universitário, CEP, Viçosa, MG 36570-900, Brazil
| | - Sara Andrade Machado
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Campus Universitário, CEP, Viçosa, MG 36570-900, Brazil
| | - Isabelly Gonçalves Messias
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Campus Universitário, CEP, Viçosa, MG 36570-900, Brazil
| | - Carla Cristina de Souza Pinto
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Campus Universitário, CEP, Viçosa, MG 36570-900, Brazil
| | - Marcelo Depolo Poleto
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Campus Universitário, CEP, Viçosa, MG 36570-900, Brazil
| | - Marcel Arruda Diogo
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Campus Universitário, CEP, Viçosa, MG 36570-900, Brazil
| | - Christiane Mariotini-Moura
- FAMINAS Muriaé, Bairro Universitário Muriaé, Av. Cristiano Ferreira Varella, 655, CEP, MG 36888-233, Brazil
| | - Gustavo Costa Bressan
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Campus Universitário, CEP, Viçosa, MG 36570-900, Brazil
| | - Robson Ricardo Teixeira
- Departamento de Química, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Campus Universitário, CEP, Viçosa, MG 36570-900, Brazil
| | - Juliana Lopes Rangel Fietto
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Campus Universitário, CEP, Viçosa, MG 36570-900, Brazil
| | - Raphael de Souza Vasconcellos
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Campus Universitário, CEP, Viçosa, MG 36570-900, Brazil.
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Vital T, Wali A, Butler KV, Xiong Y, Foster JP, Marcel SS, McFadden AW, Nguyen VU, Bailey BM, Lamb KN, James LI, Frye SV, Mosely AL, Jin J, Pattenden SG, Davis IJ. MS0621, a novel small-molecule modulator of Ewing sarcoma chromatin accessibility, interacts with an RNA-associated macromolecular complex and influences RNA splicing. Front Oncol 2023; 13:1099550. [PMID: 36793594 PMCID: PMC9924231 DOI: 10.3389/fonc.2023.1099550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 01/11/2023] [Indexed: 01/31/2023] Open
Abstract
Ewing sarcoma is a cancer of children and young adults characterized by the critical translocation-associated fusion oncoprotein EWSR1::FLI1. EWSR1::FLI1 targets characteristic genetic loci where it mediates aberrant chromatin and the establishment of de novo enhancers. Ewing sarcoma thus provides a model to interrogate mechanisms underlying chromatin dysregulation in tumorigenesis. Previously, we developed a high-throughput chromatin-based screening platform based on the de novo enhancers and demonstrated its utility in identifying small molecules capable of altering chromatin accessibility. Here, we report the identification of MS0621, a molecule with previously uncharacterized mechanism of action, as a small molecule modulator of chromatin state at sites of aberrant chromatin accessibility at EWSR1::FLI1-bound loci. MS0621 suppresses cellular proliferation of Ewing sarcoma cell lines by cell cycle arrest. Proteomic studies demonstrate that MS0621 associates with EWSR1::FLI1, RNA binding and splicing proteins, as well as chromatin regulatory proteins. Surprisingly, interactions with chromatin and many RNA-binding proteins, including EWSR1::FLI1 and its known interactors, were RNA-independent. Our findings suggest that MS0621 affects EWSR1::FLI1-mediated chromatin activity by interacting with and altering the activity of RNA splicing machinery and chromatin modulating factors. Genetic modulation of these proteins similarly inhibits proliferation and alters chromatin in Ewing sarcoma cells. The use of an oncogene-associated chromatin signature as a target allows for a direct approach to screen for unrecognized modulators of epigenetic machinery and provides a framework for using chromatin-based assays for future therapeutic discovery efforts.
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Affiliation(s)
- Tamara Vital
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Aminah Wali
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Kyle V. Butler
- Mount Sinai Center for Therapeutics Discovery, Department of Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Mount Sinai Center for Therapeutics Discovery, Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Mount Sinai Center for Therapeutics Discovery, Department of Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Yan Xiong
- Mount Sinai Center for Therapeutics Discovery, Department of Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Mount Sinai Center for Therapeutics Discovery, Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Mount Sinai Center for Therapeutics Discovery, Department of Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Joseph P. Foster
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Shelsa S. Marcel
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Andrew W. McFadden
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Valerie U. Nguyen
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Benton M. Bailey
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Kelsey N. Lamb
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Lindsey I. James
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Stephen V. Frye
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Amber L. Mosely
- Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Department of Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Mount Sinai Center for Therapeutics Discovery, Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Mount Sinai Center for Therapeutics Discovery, Department of Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Samantha G. Pattenden
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Ian J. Davis
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Pediatrics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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Nishanth MJ, Jha S. Genome-wide landscape of RNA-binding protein (RBP) networks as potential molecular regulators of psychiatric co-morbidities: a computational analysis. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2023. [DOI: 10.1186/s43042-022-00382-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Abstract
Background
Psychiatric disorders are a major burden on global health. These illnesses manifest as co-morbid conditions, further complicating the treatment. There is a limited understanding of the molecular and regulatory basis of psychiatric co-morbidities. The existing research in this regard has largely focused on epigenetic modulators, non-coding RNAs, and transcription factors. RNA-binding proteins (RBPs) functioning as multi-protein complexes are now known to be predominant controllers of multiple gene regulatory processes. However, their involvement in gene expression dysregulation in psychiatric co-morbidities is yet to be understood.
Results
Ten RBPs (QKI, ELAVL2, EIF2S1, SRSF3, IGF2BP2, EIF4B, SNRNP70, FMR1, DAZAP1, and MBNL1) were identified to be associated with psychiatric disorders such as schizophrenia, major depression, and bipolar disorders. Analysis of transcriptomic changes in response to individual depletion of these RBPs showed the potential influence of a large number of RBPs driving differential gene expression, suggesting functional cross-talk giving rise to multi-protein networks. Subsequent transcriptome analysis of post-mortem human brain samples from diseased and control individuals also suggested the involvement of ~ 100 RBPs influencing gene expression changes. These RBPs were found to regulate various processes including transcript splicing, mRNA transport, localization, stability, and translation. They were also found to form an extensive interactive network. Further, hnRNP, SRSF, and PCBP family RBPs, Matrin3, U2AF2, KHDRBS1, PTBP1, and also PABPN1 were found to be the hub proteins of the RBP network.
Conclusions
Extensive RBP networks involving a few hub proteins could result in transcriptome-wide dysregulation of post-transcriptional modifications, potentially driving multiple psychiatric disorders. Understanding the functional involvement of RBP networks in psychiatric disorders would provide insights into the molecular basis of psychiatric co-morbidities.
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Chu Y, Bao L, Teng Y, Yuan B, Ma L, Liu Y, Kang H. The Fibrotic Effects of LINC00663 in Human Hepatic Stellate LX-2 Cells and in Bile Duct-Ligated Cholestasis Mice Are Mediated through the Splicing Factor 2-Fibronectin. Cells 2023; 12:cells12020215. [PMID: 36672150 PMCID: PMC9857260 DOI: 10.3390/cells12020215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 12/25/2022] [Accepted: 12/30/2022] [Indexed: 01/06/2023] Open
Abstract
Hepatic fibrosis can develop into cirrhosis or even cancer without active therapy at an early stage. Long non-coding RNAs (lncRNAs) have been shown to be involved in the regulation of a wide variety of important biological processes. However, lncRNA mechanism(s) involved in cholestatic liver fibrosis remain unclear. RNA sequence data of hepatic stellate cells from bile duct ligation (BDL) mice or controls were analyzed by weighted gene co-expression network analysis (WGCNA). Based on WGCNA analysis, a competing endogenous RNA network was constructed. We identified LINC00663 and evaluated its function using a panel of assays, including a wound healing assay, a dual-luciferase reporter assay, RNA binding protein immunoprecipitation and chromatin immunoprecipitation. Functional research showed that LINC00663 promoted the activation, migration and epithelial-mesenchymal transition (EMT) of LX-2 cells and liver fibrosis in BDL mice. Mechanistically, LINC00663 regulated splicing factor 2 (SF2)-fibronectin (FN) alternative splicing through the sponging of hsa-miR-3916. Moreover, forkhead box A1 (FOXA1) specifically interacted with the promoter of LINC00663. In summary, we elaborated the fibrotic effects of LINC00663 in human hepatic stellate LX-2 cells and in bile duct-ligated cholestasis mice. We established a FOXA1/LINC00663/hsa-miR-3916/SF2-FN axis that provided a potential target for the diagnosis and targeted therapy of cholestatic liver fibrosis.
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Affiliation(s)
- Yang Chu
- Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang 110001, China
| | - Linan Bao
- Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang 110001, China
| | - Yun Teng
- Department of Laboratory Medicine, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Bo Yuan
- Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang 110001, China
| | - Lijie Ma
- Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang 110001, China
| | - Ying Liu
- Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang 110001, China
| | - Hui Kang
- Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang 110001, China
- Correspondence:
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Kim GN, Yu KL, Kim HI, You JC. Investigation of the effect of SRSF9 overexpression on HIV-1 production. BMB Rep 2022; 55:639-644. [PMID: 36330710 PMCID: PMC9813430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Indexed: 12/29/2022] Open
Abstract
Serine-arginine-rich splicing factors (SRSFs) are members of RNA processing proteins in the serine-arginine-rich (SR) family that could regulate the alternative splicing of the human immunodeficiency virus-1 (HIV-1). Whether SRSF9 has any effect on HIV-1 regulation requires elucidation. Here, we report for the first time the effects and mechanisms of SRSF9 on HIV-1 regulation. The overexpression of SRSF9 inhibits viral production and infectivity in both HEK293T and MT-4 cells. Deletion analysis of SRSF9 determined that the RNA regulation motif domain of SRSF9 is important for anti-HIV-1 effects. Furthermore, overexpression of SRSF9 increases multiple spliced forms of viral mRNA, such as Vpr mRNA. These data suggest that SRSF9 overexpression inhibits HIV-1 production by inducing the imbalanced HIV-1 mRNA splicing that could be exploited further for a novel HIV-1 therapeutic molecule. [BMB Reports 2022; 55(12): 639-644].
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Affiliation(s)
- Ga-Na Kim
- Department of Pathology, National Research Laboratory for Molecular Virology, College of Medicine, The Catholic University of Korea, Seoul 05505, Korea
| | - Kyung-Lee Yu
- Department of Pathology, National Research Laboratory for Molecular Virology, College of Medicine, The Catholic University of Korea, Seoul 05505, Korea
| | - Hae-In Kim
- Department of Pathology, National Research Laboratory for Molecular Virology, College of Medicine, The Catholic University of Korea, Seoul 05505, Korea
| | - Ji Chang You
- Department of Pathology, National Research Laboratory for Molecular Virology, College of Medicine, The Catholic University of Korea, Seoul 05505, Korea,Corresponding author. Tel: +82-2-3147-8734; Fax: +82-2-3147-9282; E-mail:
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Lo A, McSharry M, Berger AH. Oncogenic KRAS alters splicing factor phosphorylation and alternative splicing in lung cancer. BMC Cancer 2022; 22:1315. [PMID: 36522653 PMCID: PMC9756471 DOI: 10.1186/s12885-022-10311-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 11/10/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Alternative RNA splicing is widely dysregulated in cancers including lung adenocarcinoma, where aberrant splicing events are frequently caused by somatic splice site mutations or somatic mutations of splicing factor genes. However, the majority of mis-splicing in cancers is unexplained by these known mechanisms. We hypothesize that the aberrant Ras signaling characteristic of lung cancers plays a role in promoting the alternative splicing observed in tumors. METHODS We recently performed transcriptome and proteome profiling of human lung epithelial cells ectopically expressing oncogenic KRAS and another cancer-associated Ras GTPase, RIT1. Unbiased analysis of phosphoproteome data identified altered splicing factor phosphorylation in KRAS-mutant cells, so we performed differential alternative splicing analysis using rMATS to identify significantly altered isoforms in lung epithelial cells. To determine whether these isoforms were uniquely regulated by KRAS, we performed a large-scale splicing screen in which we generated over 300 unique RNA sequencing profiles of isogenic A549 lung adenocarcinoma cells ectopically expressing 75 different wild-type or variant alleles across 28 genes implicated in lung cancer. RESULTS Mass spectrometry data showed widespread downregulation of splicing factor phosphorylation in lung epithelial cells expressing mutant KRAS compared to cells expressing wild-type KRAS. We observed alternative splicing in the same cells, with 2196 and 2416 skipped exon events in KRASG12V and KRASQ61H cells, respectively, 997 of which were shared (p < 0.001 by hypergeometric test). In the high-throughput splicing screen, mutant KRAS induced the greatest number of differential alternative splicing events, second only to the RNA binding protein RBM45 and its variant RBM45M126I. We identified ten high confidence cassette exon events across multiple KRAS variants and cell lines. These included differential splicing of the Myc Associated Zinc Finger (MAZ). As MAZ regulates expression of KRAS, this splice variant may be a mechanism for the cell to modulate wild-type KRAS levels in the presence of oncogenic KRAS. CONCLUSION Proteomic and transcriptomic profiling of lung epithelial cells uncovered splicing factor phosphorylation and mRNA splicing events regulated by oncogenic KRAS. These data suggest that in addition to widespread transcriptional changes, the Ras signaling pathway can promote post-transcriptional splicing changes that may contribute to oncogenic processes.
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Affiliation(s)
- April Lo
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Maria McSharry
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Alice H Berger
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Herbold Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
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Lee FFY, Alper S. Alternative pre-mRNA splicing as a mechanism for terminating Toll-like Receptor signaling. Front Immunol 2022; 13:1023567. [PMID: 36531997 PMCID: PMC9755862 DOI: 10.3389/fimmu.2022.1023567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 11/11/2022] [Indexed: 12/03/2022] Open
Abstract
While inflammation induced by Toll-like receptor (TLR) signaling is required to combat infection, persistent inflammation can damage host tissues and contribute to a myriad of acute and chronic inflammatory disorders. Thus, it is essential not only that TLR signaling be activated in the presence of pathogens but that TLR signaling is ultimately terminated. One mechanism that limits persistent TLR signaling is alternative pre-mRNA splicing. In addition to encoding the canonical mRNAs that produce proteins that promote inflammation, many genes in the TLR signaling pathway also encode alternative mRNAs that produce proteins that are dominant negative inhibitors of signaling. Many of these negative regulators are induced by immune challenge, so production of these alternative isoforms represents a negative feedback loop that limits persistent inflammation. While these alternative splicing events have been investigated on a gene by gene basis, there has been limited systemic analysis of this mechanism that terminates TLR signaling. Here we review what is known about the production of negatively acting alternative isoforms in the TLR signaling pathway including how these inhibitors function, how they are produced, and what role they may play in inflammatory disease.
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Affiliation(s)
- Frank Fang Yao Lee
- Department of Immunology and Genomic Medicine and Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, United States,Department of Immunology and Microbiology, University of Colorado School of Medicine, Anschutz, CO, United States
| | - Scott Alper
- Department of Immunology and Genomic Medicine and Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, United States,Department of Immunology and Microbiology, University of Colorado School of Medicine, Anschutz, CO, United States,*Correspondence: Scott Alper,
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De Silva NIU, Fargason T, Zhang Z, Wang T, Zhang J. Inter-domain Flexibility of Human Ser/Arg-Rich Splicing Factor 1 Allows Variable Spacer Length in Cognate RNA’s Bipartite Motifs. Biochemistry 2022; 61:2922-2932. [DOI: 10.1021/acs.biochem.2c00565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- Naiduwadura Ivon Upekala De Silva
- Department of Chemistry, College of Arts and Sciences, University of Alabama at Birmingham, CH266, 901 14th Street South, Birmingham, Alabama35294-1240, United States
| | - Talia Fargason
- Department of Chemistry, College of Arts and Sciences, University of Alabama at Birmingham, CH266, 901 14th Street South, Birmingham, Alabama35294-1240, United States
| | - Zihan Zhang
- Department of Chemistry, College of Arts and Sciences, University of Alabama at Birmingham, CH266, 901 14th Street South, Birmingham, Alabama35294-1240, United States
| | - Ting Wang
- Department of Chemistry, College of Arts and Sciences, University of Alabama at Birmingham, CH266, 901 14th Street South, Birmingham, Alabama35294-1240, United States
| | - Jun Zhang
- Department of Chemistry, College of Arts and Sciences, University of Alabama at Birmingham, CH266, 901 14th Street South, Birmingham, Alabama35294-1240, United States
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