1
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Rehwinkel J, Mehdipour P. ADAR1: from basic mechanisms to inhibitors. Trends Cell Biol 2024:S0962-8924(24)00120-X. [PMID: 39030076 DOI: 10.1016/j.tcb.2024.06.006] [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: 02/13/2024] [Revised: 06/17/2024] [Accepted: 06/20/2024] [Indexed: 07/21/2024]
Abstract
Adenosine deaminase acting on RNA 1 (ADAR1) converts adenosine to inosine in double-stranded RNA (dsRNA) molecules, a process known as A-to-I editing. ADAR1 deficiency in humans and mice results in profound inflammatory diseases characterised by the spontaneous induction of innate immunity. In cells lacking ADAR1, unedited RNAs activate RNA sensors. These include melanoma differentiation-associated gene 5 (MDA5) that induces the expression of cytokines, particularly type I interferons (IFNs), protein kinase R (PKR), oligoadenylate synthase (OAS), and Z-DNA/RNA binding protein 1 (ZBP1). Immunogenic RNAs 'defused' by ADAR1 may include transcripts from repetitive elements and other long duplex RNAs. Here, we review these recent fundamental discoveries and discuss implications for human diseases. Some tumours depend on ADAR1 to escape immune surveillance, opening the possibility of unleashing anticancer therapies with ADAR1 inhibitors.
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Affiliation(s)
- Jan Rehwinkel
- Medical Research Council Translational Immune Discovery Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Parinaz Mehdipour
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford OX3 7DQ, UK.
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2
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Zhang H, Vandesompele J, Braeckmans K, De Smedt SC, Remaut K. Nucleic acid degradation as barrier to gene delivery: a guide to understand and overcome nuclease activity. Chem Soc Rev 2024; 53:317-360. [PMID: 38073448 DOI: 10.1039/d3cs00194f] [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] [Indexed: 01/03/2024]
Abstract
Gene therapy is on its way to revolutionize the treatment of both inherited and acquired diseases, by transferring nucleic acids to correct a disease-causing gene in the target cells of patients. In the fight against infectious diseases, mRNA-based therapeutics have proven to be a viable strategy in the recent Covid-19 pandemic. Although a growing number of gene therapies have been approved, the success rate is limited when compared to the large number of preclinical and clinical trials that have been/are being performed. In this review, we highlight some of the hurdles which gene therapies encounter after administration into the human body, with a focus on nucleic acid degradation by nucleases that are extremely abundant in mammalian organs, biological fluids as well as in subcellular compartments. We overview the available strategies to reduce the biodegradation of gene therapeutics after administration, including chemical modifications of the nucleic acids, encapsulation into vectors and co-administration with nuclease inhibitors and discuss which strategies are applied for clinically approved nucleic acid therapeutics. In the final part, we discuss the currently available methods and techniques to qualify and quantify the integrity of nucleic acids, with their own strengths and limitations.
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Affiliation(s)
- Heyang Zhang
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
| | - Jo Vandesompele
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Kevin Braeckmans
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Centre for Nano- and Biophotonics, Ghent University, 9000 Ghent, Belgium
| | - Stefaan C De Smedt
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Centre for Nano- and Biophotonics, Ghent University, 9000 Ghent, Belgium
| | - Katrien Remaut
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
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3
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Borgelt L, Wu P. Targeting Ribonucleases with Small Molecules and Bifunctional Molecules. ACS Chem Biol 2023; 18:2101-2113. [PMID: 37382390 PMCID: PMC10594538 DOI: 10.1021/acschembio.3c00191] [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: 03/30/2023] [Accepted: 06/06/2023] [Indexed: 06/30/2023]
Abstract
Ribonucleases (RNases) cleave and process RNAs, thereby regulating the biogenesis, metabolism, and degradation of coding and noncoding RNAs. Thus, small molecules targeting RNases have the potential to perturb RNA biology, and RNases have been studied as therapeutic targets of antibiotics, antivirals, and agents for autoimmune diseases and cancers. Additionally, the recent advances in chemically induced proximity approaches have led to the discovery of bifunctional molecules that target RNases to achieve RNA degradation or inhibit RNA processing. Here, we summarize the efforts that have been made to discover small-molecule inhibitors and activators targeting bacterial, viral, and human RNases. We also highlight the emerging examples of RNase-targeting bifunctional molecules and discuss the trends in developing such molecules for both biological and therapeutic applications.
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Affiliation(s)
- Lydia Borgelt
- Chemical Genomics Centre, Max
Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, Dortmund 44227, Germany
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, Dortmund 44227, Germany
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4
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Maria NI, Papoin J, Raparia C, Sun Z, Josselsohn R, Lu A, Katerji H, Syeda MM, Polsky D, Paulson R, Kalfa T, Barnes BJ, Zhang W, Blanc L, Davidson A. Human TLR8 induces inflammatory bone marrow erythromyeloblastic islands and anemia in SLE-prone mice. Life Sci Alliance 2023; 6:e202302241. [PMID: 37495396 PMCID: PMC10372407 DOI: 10.26508/lsa.202302241] [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: 06/27/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/28/2023] Open
Abstract
Anemia commonly occurs in systemic lupus erythematosus, a disease characterized by innate immune activation by nucleic acids. Overactivation of cytoplasmic sensors by self-DNA or RNA can cause erythroid cell death, while sparing other hematopoietic cell lineages. Whereas chronic inflammation is involved in this mechanism, less is known about the impact of systemic lupus erythematosus on the BM erythropoietic niche. We discovered that expression of the endosomal ssRNA sensor human TLR8 induces fatal anemia in Sle1.Yaa lupus mice. We observed that anemia was associated with a decrease in erythromyeloblastic islands and a block in differentiation at the CFU-E to proerythroblast transition in the BM. Single-cell RNAseq analyses of isolated BM erythromyeloblastic islands from human TLR8-expressing mice revealed that genes associated with essential central macrophage functions including adhesion and provision of nutrients were down-regulated. Although compensatory stress erythropoiesis occurred in the spleen, red blood cell half-life decreased because of hemophagocytosis. These data implicate the endosomal RNA sensor TLR8 as an additional innate receptor whose overactivation causes acquired failure of erythropoiesis via myeloid cell dysregulation.
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Affiliation(s)
- Naomi I Maria
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research, Manhasset, NY, USA
- Donald and Barbara Zucker School of Medicine at Northwell Health, Hempstead, NY, USA
| | - Julien Papoin
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research, Manhasset, NY, USA
- Donald and Barbara Zucker School of Medicine at Northwell Health, Hempstead, NY, USA
| | - Chirag Raparia
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research, Manhasset, NY, USA
- Donald and Barbara Zucker School of Medicine at Northwell Health, Hempstead, NY, USA
| | - Zeguo Sun
- Department of Medicine, Mount Sinai Medical Center, New York, NY, USA
| | - Rachel Josselsohn
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research, Manhasset, NY, USA
| | - Ailing Lu
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research, Manhasset, NY, USA
| | - Hani Katerji
- Department of Pathology, University of Rochester, Rochester, NY, USA
| | - Mahrukh M Syeda
- The Ronald O. Perelman Department of Dermatology, New York University Grossman School of Medicine, New York, NY, USA
| | - David Polsky
- The Ronald O. Perelman Department of Dermatology, New York University Grossman School of Medicine, New York, NY, USA
| | - Robert Paulson
- Department of Veterinary and Biomedical Sciences, Penn State College of Agricultural Sciences, University Park, PA, USA
| | - Theodosia Kalfa
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Betsy J Barnes
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research, Manhasset, NY, USA
- Donald and Barbara Zucker School of Medicine at Northwell Health, Hempstead, NY, USA
| | - Weijia Zhang
- Department of Medicine, Mount Sinai Medical Center, New York, NY, USA
| | - Lionel Blanc
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research, Manhasset, NY, USA
- Donald and Barbara Zucker School of Medicine at Northwell Health, Hempstead, NY, USA
| | - Anne Davidson
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research, Manhasset, NY, USA
- Donald and Barbara Zucker School of Medicine at Northwell Health, Hempstead, NY, USA
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5
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Springer NA, Meyer SM, Taghavi A, Benhamou RI, Tong Y, Childs-Disney JL, Disney MD. Methods for the study of ribonuclease targeting chimeras (RiboTACs). Methods Enzymol 2023; 692:249-298. [PMID: 37925183 PMCID: PMC10763923 DOI: 10.1016/bs.mie.2023.06.006] [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] [Indexed: 11/06/2023]
Abstract
Recently, a class of heterobifunctional small molecules called ribonuclease targeting chimeras (RiboTACs) have been developed that selectively induce degradation of RNAs in cells. These molecules function by recruiting latent ribonuclease (RNase L), an endoribonuclease involved in the innate immune response, to targeted RNA structures. The RiboTACs must activate RNase L in proximity to the RNA, resulting in cleavage of the RNA and downstream degradation. To develop and validate a new RiboTAC, several steps must be taken. First, small molecule activators that bind to RNase L must be identified. Next, since RNase L is only catalytically active upon ligand-induced homodimerization, the capability of identified small molecules to activate RNase L must be assessed. RNase L-activating small molecules should then be coupled to validated RNA-binding small molecules to construct the active RiboTAC. This RiboTAC can finally be assessed in cells for RNase L-dependent degradation of target RNAs. This chapter will provide several methods that are helpful to develop and assess RiboTACs throughout this process, including recombinant RNase L expression, methods to assess RNase L engagement in vitro such as saturation transfer difference nuclear magnetic resonance (STD NMR), an in vitro assay to assess activation of RNase L, and cellular methods to demonstrate RNase L-dependent cleavage.
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Affiliation(s)
- Noah A Springer
- The Scripps Research Institute & The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Department of Chemistry, Scripps Way, Jupiter, FL, United States
| | - Samantha M Meyer
- The Scripps Research Institute & The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Department of Chemistry, Scripps Way, Jupiter, FL, United States
| | - Amirhossein Taghavi
- The Scripps Research Institute & The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Department of Chemistry, Scripps Way, Jupiter, FL, United States
| | - Raphael I Benhamou
- Institute for Drug Research, The School of Pharmacy, The Hebrew University of Jerusalem, Hadassah-Ein Kerem, Jerusalem, Israel
| | - Yuquan Tong
- The Scripps Research Institute & The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Department of Chemistry, Scripps Way, Jupiter, FL, United States
| | - Jessica L Childs-Disney
- The Scripps Research Institute & The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Department of Chemistry, Scripps Way, Jupiter, FL, United States
| | - Matthew D Disney
- The Scripps Research Institute & The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Department of Chemistry, Scripps Way, Jupiter, FL, United States.
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6
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Hwang J, Haacke N, Borgelt L, Qiu X, Gasper R, Wu P. Rational design and evaluation of 2-((pyrrol-2-yl)methylene)thiophen-4-ones as RNase L inhibitors. Eur J Med Chem 2023; 256:115439. [PMID: 37201427 DOI: 10.1016/j.ejmech.2023.115439] [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: 02/08/2023] [Revised: 04/13/2023] [Accepted: 04/30/2023] [Indexed: 05/20/2023]
Abstract
Ribonuclease L (RNase L) plays a crucial role in an antiviral pathway of interferon-induced innate immunity by degrading RNAs to prevent viral replication. Modulating RNase L activity thus mediates the innate immune responses and inflammation. Although a few small molecule-based RNase L modulators have been reported, only limited molecules have been mechanistically investigated. This study explored the strategy of RNase L targeting by using a structure-based rational design approach and evaluated the RNase L-binding and inhibitory activities of the yielded 2-((pyrrol-2-yl)methylene)thiophen-4-ones, which exhibited improved inhibitory effect as determined by in vitro FRET and gel-based RNA cleavage assay. A further structural optimization study yielded selected thiophenones that showed >30-fold more potent inhibitory activity than that of sunitinib, the approved kinase inhibitor with reported RNase L inhibitory activity. The binding mode with RNase L for the resulting thiophenones was analyzed by using docking analysis. Furthermore, the obtained 2-((pyrrol-2-yl)methylene)thiophen-4-ones exhibited efficient inhibition of RNA degradation in cellular rRNA cleavage assay. The newly designed thiophenones are the most potent synthetic RNase L inhibitors reported to date and the results revealed in our study lay the foundation for the development of future RNase L-modulating small molecules with new scaffold and improved potency.
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Affiliation(s)
- Jimin Hwang
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Dortmund, 44227, Germany; Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, 44227, Germany; Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, 44227, Germany
| | - Neele Haacke
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Dortmund, 44227, Germany; Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, 44227, Germany; Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, 44227, Germany
| | - Lydia Borgelt
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Dortmund, 44227, Germany; Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, 44227, Germany; Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, 44227, Germany
| | - Xiaqiu Qiu
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Dortmund, 44227, Germany; Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, 44227, Germany; Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, 44227, Germany
| | - Raphael Gasper
- Crystallography and Biophysics Unit, Max Planck Institute of Molecular Physiology, Dortmund, 44227, Germany
| | - Peng Wu
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Dortmund, 44227, Germany; Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, 44227, Germany.
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7
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Langeberg CJ, Nichols PJ, Henen MA, Vicens Q, Vögeli B. Differential Structural Features of Two Mutant ADAR1p150 Zα Domains Associated with Aicardi-Goutières Syndrome. J Mol Biol 2023; 435:168040. [PMID: 36889460 PMCID: PMC10109538 DOI: 10.1016/j.jmb.2023.168040] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/08/2023]
Abstract
The Zα domain of ADARp150 is critical for proper Z-RNA substrate binding and is a key factor in the type-I interferon response pathway. Two point-mutations in this domain (N173S and P193A), which cause neurodegenerative disorders, are linked to decreased A-to-I editing in disease models. To understand this phenomenon at the molecular level, we biophysically and structurally characterized these two mutated domains, revealing that they bind Z-RNA with a decreased affinity. Less efficient binding to Z-RNA can be explained by structural changes in beta-wing, part of the Z-RNA-protein interface, and alteration of conformational dynamics of the proteins.
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Affiliation(s)
- Conner J Langeberg
- Department of Biochemistry and Molecular Genetics and RNA Bioscience Initiative, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA.
| | - Parker J Nichols
- Department of Biochemistry and Molecular Genetics and RNA Bioscience Initiative, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA.
| | - Morkos A Henen
- Department of Biochemistry and Molecular Genetics and RNA Bioscience Initiative, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA; Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt.
| | - Quentin Vicens
- Department of Biochemistry and Molecular Genetics and RNA Bioscience Initiative, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA; RNA Bioscience Initiative, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA.
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics and RNA Bioscience Initiative, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA; RNA Bioscience Initiative, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA.
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8
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RBP-RNA interactions in the control of autoimmunity and autoinflammation. Cell Res 2023; 33:97-115. [PMID: 36599968 PMCID: PMC9892603 DOI: 10.1038/s41422-022-00752-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 11/07/2022] [Indexed: 01/06/2023] Open
Abstract
Autoimmunity and autoinflammation arise from aberrant immunological and inflammatory responses toward self-components, contributing to various autoimmune diseases and autoinflammatory diseases. RNA-binding proteins (RBPs) are essential for immune cell development and function, mainly via exerting post-transcriptional regulation of RNA metabolism and function. Functional dysregulation of RBPs and abnormities in RNA metabolism are closely associated with multiple autoimmune or autoinflammatory disorders. Distinct RBPs play critical roles in aberrant autoreactive inflammatory responses via orchestrating a complex regulatory network consisting of DNAs, RNAs and proteins within immune cells. In-depth characterizations of RBP-RNA interactomes during autoimmunity and autoinflammation will lead to a better understanding of autoimmune pathogenesis and facilitate the development of effective therapeutic strategies. In this review, we summarize and discuss the functions of RBP-RNA interactions in controlling aberrant autoimmune inflammation and their potential as biomarkers and therapeutic targets.
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9
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Lightfoot HL, Smith GF. Targeting RNA with small molecules-A safety perspective. Br J Pharmacol 2023. [PMID: 36631428 DOI: 10.1111/bph.16027] [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: 02/24/2022] [Revised: 06/30/2022] [Accepted: 12/20/2022] [Indexed: 01/13/2023] Open
Abstract
RNA is a major player in cellular function, and consequently can drive a number of disease pathologies. Over the past several years, small molecule-RNA targeting (smRNA targeting) has developed into a promising drug discovery approach. Numerous techniques, tools, and assays have been developed to support this field, and significant investments have been made by pharmaceutical and biotechnology companies. To date, the focus has been on identifying disease validated primary targets for smRNA drug development, yet RNA as a secondary (off) target for all small molecule drug programs largely has been unexplored. In this perspective, we discuss structure, target, and mechanism-driven safety aspects of smRNAs and highlight how these parameters can be evaluated in drug discovery programs to produce potentially safer drugs.
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Affiliation(s)
- Helen L Lightfoot
- Safety and Mechanistic Pharmacology, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Graham F Smith
- Data Science and AI, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
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10
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Liu S, Won H, Clarke D, Matoba N, Khullar S, Mu Y, Wang D, Gerstein M. Illuminating links between cis-regulators and trans-acting variants in the human prefrontal cortex. Genome Med 2022; 14:133. [PMID: 36424644 PMCID: PMC9685876 DOI: 10.1186/s13073-022-01133-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 10/25/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Neuropsychiatric disorders afflict a large portion of the global population and constitute a significant source of disability worldwide. Although Genome-wide Association Studies (GWAS) have identified many disorder-associated variants, the underlying regulatory mechanisms linking them to disorders remain elusive, especially those involving distant genomic elements. Expression quantitative trait loci (eQTLs) constitute a powerful means of providing this missing link. However, most eQTL studies in human brains have focused exclusively on cis-eQTLs, which link variants to nearby genes (i.e., those within 1 Mb of a variant). A complete understanding of disease etiology requires a clearer understanding of trans-regulatory mechanisms, which, in turn, entails a detailed analysis of the relationships between variants and expression changes in distant genes. METHODS By leveraging large datasets from the PsychENCODE consortium, we conducted a genome-wide survey of trans-eQTLs in the human dorsolateral prefrontal cortex. We also performed colocalization and mediation analyses to identify mediators in trans-regulation and use trans-eQTLs to link GWAS loci to schizophrenia risk genes. RESULTS We identified ~80,000 candidate trans-eQTLs (at FDR<0.25) that influence the expression of ~10K target genes (i.e., "trans-eGenes"). We found that many variants associated with these candidate trans-eQTLs overlap with known cis-eQTLs. Moreover, for >60% of these variants (by colocalization), the cis-eQTL's target gene acts as a mediator for the trans-eQTL SNP's effect on the trans-eGene, highlighting examples of cis-mediation as essential for trans-regulation. Furthermore, many of these colocalized variants fall into a discernable pattern wherein cis-eQTL's target is a transcription factor or RNA-binding protein, which, in turn, targets the gene associated with the candidate trans-eQTL. Finally, we show that trans-regulatory mechanisms provide valuable insights into psychiatric disorders: beyond what had been possible using only cis-eQTLs, we link an additional 23 GWAS loci and 90 risk genes (using colocalization between candidate trans-eQTLs and schizophrenia GWAS loci). CONCLUSIONS We demonstrate that the transcriptional architecture of the human brain is orchestrated by both cis- and trans-regulatory variants and found that trans-eQTLs provide insights into brain-disease biology.
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Affiliation(s)
- Shuang Liu
- Waisman Center, University of Wisconsin - Madison, Madison, WI, 53705, USA
| | - Hyejung Won
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Declan Clarke
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Nana Matoba
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Saniya Khullar
- Waisman Center, University of Wisconsin - Madison, Madison, WI, 53705, USA.,Department of Biostatistics and Medical Informatics, University of Wisconsin - Madison, Madison, WI, 53706, USA
| | - Yudi Mu
- Department of Statistics, University of Wisconsin - Madison, Madison, WI, 53706, USA
| | - Daifeng Wang
- Waisman Center, University of Wisconsin - Madison, Madison, WI, 53705, USA. .,Department of Biostatistics and Medical Informatics, University of Wisconsin - Madison, Madison, WI, 53706, USA. .,Department of Computer Sciences, University of Wisconsin - Madison, Madison, WI, 53706, USA.
| | - Mark Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA. .,Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA. .,Department of Computer Science, Yale University, New Haven, CT, 06520, USA. .,Department of Statistics and Data Science, Yale University, New Haven, CT, 06520, USA.
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11
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Meyer SM, Tanaka T, Zanon PRA, Baisden JT, Abegg D, Yang X, Akahori Y, Alshakarchi Z, Cameron MD, Adibekian A, Disney MD. DNA-Encoded Library Screening To Inform Design of a Ribonuclease Targeting Chimera (RiboTAC). J Am Chem Soc 2022; 144:21096-21102. [PMID: 36342850 PMCID: PMC10786349 DOI: 10.1021/jacs.2c07217] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Ribonuclease targeting chimeras (RiboTACs) induce degradation of an RNA target by facilitating an interaction between an RNA and a ribonuclease (RNase). We describe the screening of a DNA-encoded library (DEL) to identify binders of monomeric RNase L to provide a compound that induced dimerization of RNase L, activating its ribonuclease activity. This compound was incorporated into the design of a next-generation RiboTAC that targeted the microRNA-21 (miR-21) precursor and alleviated a miR-21-associated cellular phenotype in triple-negative breast cancer cells. The RNA-binding module in the RiboTAC is Dovitinib, a known receptor tyrosine kinase (RTK) inhibitor, which was previously identified to bind miR-21 as an off-target. Conversion of Dovitinib into this RiboTAC reprograms the known drug to selectively affect the RNA target. This work demonstrates that DEL can be used to identify compounds that bind and recruit proteins with effector functions in heterobifunctional compounds.
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Affiliation(s)
- Samantha M. Meyer
- The Scripps Research Institute & UF Scripps Biomedical Research, Department of Chemistry, Jupiter, FL 33458
| | - Toru Tanaka
- The Scripps Research Institute & UF Scripps Biomedical Research, Department of Chemistry, Jupiter, FL 33458
| | - Patrick R. A. Zanon
- The Scripps Research Institute & UF Scripps Biomedical Research, Department of Chemistry, Jupiter, FL 33458
| | - Jared T. Baisden
- The Scripps Research Institute & UF Scripps Biomedical Research, Department of Chemistry, Jupiter, FL 33458
| | - Daniel Abegg
- The Scripps Research Institute & UF Scripps Biomedical Research, Department of Chemistry, Jupiter, FL 33458
| | - Xueyi Yang
- The Scripps Research Institute & UF Scripps Biomedical Research, Department of Chemistry, Jupiter, FL 33458
| | - Yoshihiro Akahori
- The Scripps Research Institute & UF Scripps Biomedical Research, Department of Chemistry, Jupiter, FL 33458
| | - Zainab Alshakarchi
- The Scripps Research Institute & UF Scripps Biomedical Research, Department of Chemistry, Jupiter, FL 33458
| | - Michael D. Cameron
- The Scripps Research Institute & UF Scripps Biomedical Research, Department of Chemistry, Jupiter, FL 33458
| | - Alexander Adibekian
- The Scripps Research Institute & UF Scripps Biomedical Research, Department of Chemistry, Jupiter, FL 33458
| | - Matthew D. Disney
- The Scripps Research Institute & UF Scripps Biomedical Research, Department of Chemistry, Jupiter, FL 33458
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12
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Li Y, Ruan GX, Chen W, Huang H, Zhang R, Wang J, Li Y, Xu S, Ou X. RNA-Editing Enzyme ADAR1 p150 Isoform Is Critical for Germinal Center B Cell Response. THE JOURNAL OF IMMUNOLOGY 2022; 209:1071-1082. [DOI: 10.4049/jimmunol.2200149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 07/11/2022] [Indexed: 01/04/2023]
Abstract
Abstract
Adenosine deaminase acting on RNA (ADAR)1 is the principal enzyme for adenosine-to-inosine editing, an RNA modification–avoiding cytosolic nucleic acid sensor’s activation triggered by endogenous dsRNAs. Two ADAR1 isoforms exist in mammals, a longer IFN-inducible and mainly cytoplasm-localized p150 isoform and a shorter constitutively expressed and primarily nucleus-localized p110 isoform. Studies of ADAR1 mutant mice have demonstrated that ADAR1 is essential for multiple physiological processes, including embryonic development, innate immune response, and B and T lymphocyte development. However, it remained unknown whether ADAR1 plays a role in the humoral immune response. In this study, we conditionally delete Adar1 in activated B cells and show that ADAR1-deficient mice have a defective T cell–dependent Ab response and diminished germinal center (GC) B cells. Using various double mutant mice concurrently deficient in ADAR1 and different downstream dsRNA sensors, we demonstrate that ADAR1 regulates the GC response by preventing hyperactivation of the melanoma differentiation-associated protein 5 (MDA5) but not the protein kinase R or RNase L pathway. We also show that p150 is exclusively responsible for ADAR1’s function in the GC response, and the p110 isoform cannot substitute for the p150’s role, even when p110 is constitutively expressed in the cytoplasm. We further demonstrated that the dsRNA-binding but not the RNA-editing activity is required for ADAR1’s function in the GC response. Thus, our data suggest that the ADAR1 p150 isoform plays a crucial role in regulating the GC B cell response.
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Affiliation(s)
- Yuxing Li
- *Harbin Institute of Technology, Harbin, China
- †Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Gui-Xin Ruan
- †Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Wenjing Chen
- †Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Hengjun Huang
- †Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Rui Zhang
- †Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Jing Wang
- †Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yan Li
- †Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Shengli Xu
- ‡Singapore Immunology Network, Agency for Science, Technology and Research, Singapore; and
- §Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Xijun Ou
- †Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
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13
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Borgelt L, Haacke N, Lampe P, Qiu X, Gasper R, Schiller D, Hwang J, Sievers S, Wu P. Small-molecule screening of ribonuclease L binders for RNA degradation. Biomed Pharmacother 2022; 154:113589. [PMID: 36029542 DOI: 10.1016/j.biopha.2022.113589] [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: 07/07/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 11/15/2022] Open
Abstract
Small molecules targeting the ubiquitous latent ribonuclease (RNase L), which has limited sequence specificity toward single-stranded RNA substrates, hold great potential to be developed as broad-spectrum antiviral drugs by modulating the RNase L-mediated innate immune responses. The recent development of proximity-inducing bifunctional molecules, as described in the strategy of ribonuclease targeting chimeras, demonstrated that small-molecule RNase L activators can function as the essential RNase L-recruiting component to design bifunctional molecules for targeted RNA degradation. However, only a single screening study on small-molecule RNase L activators with poor potency has been reported to date. Herein, we established a FRET assay and conducted a screening of 240,000 small molecules to identify new RNase L activators with improved potency. The extremely low hit rate of less than 0.03% demonstrated the challenging nature of RNase L activation by small molecules available from current screening collections. A few hit compounds induced enhanced thermal stability of RNase L upon binding, although validation assays did not lead to the identification of compounds with significantly improved RNase L activating potency. The sulfonamide compound 17 induced a thermal shift of ~ 0.9 °C upon binding to RNase L, induced significant apoptosis in cancer cells, and showed single-digit micromolar inhibitory activity against cancer cell proliferation. This study paves the way for future structural optimization for the development of small-molecule RNase L binders.
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Affiliation(s)
- Lydia Borgelt
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany; Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany; Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund 44227, Germany
| | - Neele Haacke
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany; Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany; Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund 44227, Germany
| | - Philipp Lampe
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany; Compound Management and Screening Center, Dortmund 44227, Germany
| | - Xiaqiu Qiu
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany; Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany; Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund 44227, Germany
| | - Raphael Gasper
- Crystallography and Biophysics Unit, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany
| | - Damian Schiller
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund 44227, Germany
| | - Jimin Hwang
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany; Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany; Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund 44227, Germany
| | - Sonja Sievers
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany; Compound Management and Screening Center, Dortmund 44227, Germany
| | - Peng Wu
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany; Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany.
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14
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Tang J, Dong B, Liu M, Liu S, Niu X, Gaughan C, Asthana A, Zhou H, Xu Z, Zhang G, Silverman RH, Huang H. Identification of Small Molecule Inhibitors of RNase L by Fragment-Based Drug Discovery. J Med Chem 2022; 65:1445-1457. [PMID: 34841869 PMCID: PMC10620946 DOI: 10.1021/acs.jmedchem.1c01156] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The pseudokinase-endoribonuclease RNase L plays important roles in antiviral innate immunity and is also implicated in many other cellular activities. The inhibition of RNase L showed therapeutic potential for Aicardi-Goutières syndrome (AGS). Thus, RNase L is a promising drug target. In this study, using an enzyme assay and NMR screening, we discovered 13 inhibitory fragments against RNase L. Cocrystal structures of RNase L separately complexed with two different fragments were determined in which both fragments bound to the ATP-binding pocket of the pseudokinase domain. Myricetin, vitexin, and hyperoside, three natural products sharing similar scaffolds with the fragment AC40357, demonstrated a potent inhibitory activity in vitro. In addition, myricetin has a promising cellular inhibitory activity. A cocrystal structure of RNase L with myricetin provided a structural basis for inhibitor design by allosterically modulating the ribonuclease activity. Our findings demonstrate that fragment screening can lead to the discovery of natural product inhibitors of RNase L.
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Affiliation(s)
- Jinle Tang
- State Key Laboratory of Chemical Oncogenomics, Laboratory of Structural Biology and Drug Discovery, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Beihua Dong
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Ming Liu
- State Key Laboratory of Chemical Oncogenomics, Laboratory of Structural Biology and Drug Discovery, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Shuyan Liu
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People’s Hospital, Southern University of Science and Technology, Shenzhen 518112, China
| | - Xiaogang Niu
- College of Chemistry and Molecular Engineering, Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China
| | - Christina Gaughan
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Abhishek Asthana
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Huan Zhou
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
| | - Zhengshuang Xu
- State Key Laboratory of Chemical Oncogenomics, Laboratory of Structural Biology and Drug Discovery, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Guoliang Zhang
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People’s Hospital, Southern University of Science and Technology, Shenzhen 518112, China
| | - Robert H. Silverman
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Hao Huang
- State Key Laboratory of Chemical Oncogenomics, Laboratory of Structural Biology and Drug Discovery, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
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15
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Maurano M, Snyder JM, Connelly C, Henao-Mejia J, Sidrauski C, Stetson DB. Protein kinase R and the integrated stress response drive immunopathology caused by mutations in the RNA deaminase ADAR1. Immunity 2021; 54:1948-1960.e5. [PMID: 34343497 DOI: 10.1016/j.immuni.2021.07.001] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 03/18/2021] [Accepted: 06/30/2021] [Indexed: 10/20/2022]
Abstract
The RNA deaminase ADAR1 is an essential negative regulator of the RNA sensor MDA5, and loss of ADAR1 function triggers inappropriate activation of MDA5 by self-RNAs. Mutations in ADAR, the gene that encodes ADAR1, cause human immune diseases, including Aicardi-Goutières syndrome (AGS). However, the mechanisms of MDA5-dependent disease pathogenesis in vivo remain unknown. Here we generated mice with a single amino acid change in ADAR1 that models the most common human ADAR AGS mutation. These Adar mutant mice developed lethal disease that required MDA5, the RIG-I-like receptor LGP2, type I interferons, and the eIF2α kinase PKR. A small-molecule inhibitor of the integrated stress response (ISR) that acts downstream of eIF2α phosphorylation prevented immunopathology and rescued the mice from mortality. These findings place PKR and the ISR as central components of immunopathology in vivo and identify therapeutic targets for treatment of human diseases associated with the ADAR1-MDA5 axis.
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Affiliation(s)
- Megan Maurano
- Department of Immunology, University of Washington School of Medicine, Seattle, WA 98195, USA; Medical Scientist Training Program, University of Washington School of Medicine, Seattle, WA 98195, USA; Molecular and Cellular Biology Graduate Program, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Jessica M Snyder
- Department of Comparative Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | | | - Jorge Henao-Mejia
- Department of Pathology and Laboratory Medicine, Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; Division of Protective Immunity, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | | | - Daniel B Stetson
- Department of Immunology, University of Washington School of Medicine, Seattle, WA 98195, USA.
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