1
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Krenz B, Lee J, Kannan T, Eilers M. Immune evasion: An imperative and consequence of MYC deregulation. Mol Oncol 2024. [PMID: 38957016 DOI: 10.1002/1878-0261.13695] [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: 02/07/2024] [Revised: 05/08/2024] [Accepted: 06/19/2024] [Indexed: 07/04/2024] Open
Abstract
MYC has been implicated in the pathogenesis of a wide range of human tumors and has been described for many years as a transcription factor that regulates genes with pleiotropic functions to promote tumorigenic growth. However, despite extensive efforts to identify specific target genes of MYC that alone could be responsible for promoting tumorigenesis, the field is yet to reach a consensus whether this is the crucial function of MYC. Recent work shifts the view on MYC's function from being a gene-specific transcription factor to an essential stress resilience factor. In highly proliferating cells, MYC preserves cell integrity by promoting DNA repair at core promoters, protecting stalled replication forks, and/or preventing transcription-replication conflicts. Furthermore, an increasing body of evidence demonstrates that MYC not only promotes tumorigenesis by driving cell-autonomous growth, but also enables tumors to evade the host's immune system. In this review, we summarize our current understanding of how MYC impairs antitumor immunity and why this function is evolutionarily hard-wired to the biology of the MYC protein family. We show why the cell-autonomous and immune evasive functions of MYC are mutually dependent and discuss ways to target MYC proteins in cancer therapy.
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Affiliation(s)
- Bastian Krenz
- Department of Biochemistry and Molecular Biology, Theodor Boveri Institute, Biocenter, University of Würzburg, Würzburg, Germany
- Mildred Scheel Early Career Center, Würzburg, Germany
| | - Jongkuen Lee
- Department of Biochemistry and Molecular Biology, Theodor Boveri Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - Toshitha Kannan
- Department of Biochemistry and Molecular Biology, Theodor Boveri Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - Martin Eilers
- Department of Biochemistry and Molecular Biology, Theodor Boveri Institute, Biocenter, University of Würzburg, Würzburg, Germany
- Comprehensive Cancer Center Mainfranken, Würzburg, Germany
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2
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Fain JS, Wangermez C, Loriot A, Denoue C, De Smet C. DNA Hypomethylation Underlies Epigenetic Swapping between AGO1 and AGO1-V2 Isoforms in Tumors. EPIGENOMES 2024; 8:24. [PMID: 39051182 PMCID: PMC11270204 DOI: 10.3390/epigenomes8030024] [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: 05/08/2024] [Revised: 06/10/2024] [Accepted: 06/18/2024] [Indexed: 07/27/2024] Open
Abstract
Human tumors progress in part by accumulating epigenetic alterations, which include gains and losses of DNA methylation in different parts of the cancer cell genome. Recent work has revealed a link between these two opposite alterations by showing that DNA hypomethylation in tumors can induce the expression of transcripts that overlap downstream gene promoters and thereby induce their hypermethylation. Preliminary in silico evidence prompted us to investigate if this mechanism applies to the locus harboring AGO1, a gene that plays a central role in miRNA biogenesis and RNA interference. Inspection of public RNA-Seq datasets and RT-qPCR experiments show that an alternative transcript starting 13.4 kb upstream of AGO1 (AGO1-V2) is expressed specifically in testicular germ cells, and becomes aberrantly activated in different types of tumors, particularly in tumors of the esophagus, stomach, and lung. This expression pattern classifies AGO1-V2 into the group of "Cancer-Germline" (CG) genes. Analysis of transcriptomic and methylomic datasets provided evidence that transcriptional activation of AGO1-V2 depends on DNA demethylation of its promoter region. Western blot experiments revealed that AGO1-V2 encodes a shortened isoform of AGO1, corresponding to a truncation of 75 aa in the N-terminal domain, and which we therefore referred to as "∆NAGO1". Interestingly, significant correlations between hypomethylation/activation of AGO1-V2 and hypermethylation/repression of AGO1 were observed upon examination of tumor cell lines and tissue datasets. Overall, our study reveals the existence of a process of interdependent epigenetic alterations in the AGO1 locus, which promotes swapping between two AGO1 protein-coding mRNA isoforms in tumors.
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Affiliation(s)
- Jean S. Fain
- Group of Genetics and Epigenetics, de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium; (J.S.F.); (C.W.)
| | - Camille Wangermez
- Group of Genetics and Epigenetics, de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium; (J.S.F.); (C.W.)
| | - Axelle Loriot
- Group of Computational Biology and Bioinformatics, de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium;
| | - Claudia Denoue
- Group of Genetics and Epigenetics, de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium; (J.S.F.); (C.W.)
| | - Charles De Smet
- Group of Genetics and Epigenetics, de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium; (J.S.F.); (C.W.)
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3
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Manjunath LE, Singh A, Devi Kumar S, Vasu K, Kar D, Sellamuthu K, Eswarappa SM. Transcript-specific induction of stop codon readthrough using a CRISPR-dCas13 system. EMBO Rep 2024; 25:2118-2143. [PMID: 38499809 PMCID: PMC11015002 DOI: 10.1038/s44319-024-00115-8] [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: 03/06/2023] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 03/20/2024] Open
Abstract
Stop codon readthrough (SCR) is the process where translation continues beyond a stop codon on an mRNA. Here, we describe a strategy to enhance or induce SCR in a transcript-selective manner using a CRISPR-dCas13 system. Using specific guide RNAs, we target dCas13 to the region downstream of canonical stop codons of mammalian AGO1 and VEGFA mRNAs, known to exhibit natural SCR. Readthrough assays reveal enhanced SCR of these mRNAs (both exogenous and endogenous) caused by the dCas13-gRNA complexes. This effect is associated with ribosomal pausing, which has been reported for several SCR events. Our data show that CRISPR-dCas13 can also induce SCR across premature termination codons (PTCs) in the mRNAs of green fluorescent protein and TP53. We demonstrate the utility of this strategy in the induction of readthrough across the thalassemia-causing PTC in HBB mRNA and hereditary spherocytosis-causing PTC in SPTA1 mRNA. Thus, CRISPR-dCas13 can be programmed to enhance or induce SCR in a transcript-selective and stop codon-specific manner.
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Affiliation(s)
- Lekha E Manjunath
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India
| | - Anumeha Singh
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Sangeetha Devi Kumar
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India
| | - Kirtana Vasu
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India
| | - Debaleena Kar
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India
| | - Karthi Sellamuthu
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India
- University of Texas Medical Branch, Galveston, TX, USA
| | - Sandeep M Eswarappa
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India.
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4
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Pandit M, Akhtar MN, Sundaram S, Sahoo S, Manjunath LE, Eswarappa SM. Termination codon readthrough of NNAT mRNA regulates calcium-mediated neuronal differentiation. J Biol Chem 2023; 299:105184. [PMID: 37611826 PMCID: PMC10506107 DOI: 10.1016/j.jbc.2023.105184] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 08/25/2023] Open
Abstract
Termination codon readthrough (TCR) is a process in which ribosomes continue to translate an mRNA beyond a stop codon generating a C-terminally extended protein isoform. Here, we demonstrate TCR in mammalian NNAT mRNA, which encodes NNAT, a proteolipid important for neuronal differentiation. This is a programmed event driven by cis-acting RNA sequences present immediately upstream and downstream of the canonical stop codon and is negatively regulated by NONO, an RNA-binding protein known to promote neuronal differentiation. Unlike the canonical isoform NNAT, we determined that the TCR product (NNATx) does not show detectable interaction with the sarco/endoplasmic reticulum Ca2+-ATPase isoform 2 Ca2+ pump, cannot increase cytoplasmic Ca2+ levels, and therefore does not enhance neuronal differentiation in Neuro-2a cells. Additionally, an antisense oligonucleotide that targets a region downstream of the canonical stop codon reduced TCR of NNAT and enhanced the differentiation of Neuro-2a cells to cholinergic neurons. Furthermore, NNATx-deficient Neuro-2a cells, generated using CRISPR-Cas9, showed increased cytoplasmic Ca2+ levels and enhanced neuronal differentiation. Overall, these results demonstrate regulation of neuronal differentiation by TCR of NNAT. Importantly, this process can be modulated using a synthetic antisense oligonucleotide.
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Affiliation(s)
- Madhuparna Pandit
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Md Noor Akhtar
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Susinder Sundaram
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Sarthak Sahoo
- Undergraduate Program, Indian Institute of Science, Bengaluru, India
| | - Lekha E Manjunath
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Sandeep M Eswarappa
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India.
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5
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Hsu CG, Li W, Sowden M, Chávez CL, Berk BC. Pnpt1 mediates NLRP3 inflammasome activation by MAVS and metabolic reprogramming in macrophages. Cell Mol Immunol 2023; 20:131-142. [PMID: 36596874 PMCID: PMC9886977 DOI: 10.1038/s41423-022-00962-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 11/13/2022] [Indexed: 01/05/2023] Open
Abstract
Polyribonucleotide nucleotidyltransferase 1 (Pnpt1) plays critical roles in mitochondrial homeostasis by controlling mitochondrial RNA (mt-RNA) processing, trafficking and degradation. Pnpt1 deficiency results in mitochondrial dysfunction that triggers a type I interferon response, suggesting a role in inflammation. However, the role of Pnpt1 in inflammasome activation remains largely unknown. In this study, we generated myeloid-specific Pnpt1-knockout mice and demonstrated that Pnpt1 depletion enhanced interleukin-1 beta (IL-1β) and interleukin-18 (IL-18) secretion in a mouse sepsis model. Using cultured peritoneal and bone marrow-derived macrophages, we demonstrated that Pnpt1 regulated NLRP3 inflammasome-dependent IL-1β release in response to lipopolysaccharide (LPS), followed by nigericin, ATP or poly (I:C) treatment. Pnpt1 deficiency in macrophages increased glycolysis after LPS administration and mt-reactive oxygen species (mt-ROS) after NLRP3 inflammasome activation. Pnpt1 activation of the inflammasome was dependent on increased glycolysis and the expression of mitochondrial antiviral-signaling protein (MAVS) but not NF-κB signaling. Collectively, these data suggest that Pnpt1 is an important mediator of inflammation, as shown by activation of the NLRP3 inflammasome in murine sepsis and cultured macrophages.
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Affiliation(s)
- Chia George Hsu
- Department of Medicine, Aab Cardiovascular Research Institute, University of Rochester, Rochester, NY, USA
| | - Wenjia Li
- Department of Medicine, Aab Cardiovascular Research Institute, University of Rochester, Rochester, NY, USA
- Department of Cardiovascular Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China
| | - Mark Sowden
- Department of Medicine, Aab Cardiovascular Research Institute, University of Rochester, Rochester, NY, USA
| | - Camila Lage Chávez
- Department of Medicine, Aab Cardiovascular Research Institute, University of Rochester, Rochester, NY, USA
| | - Bradford C Berk
- Department of Medicine, Aab Cardiovascular Research Institute, University of Rochester, Rochester, NY, USA.
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6
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Taylor S, Isobe S, Cao A, Contrepois K, Benayoun BA, Jiang L, Wang L, Melemenidis S, Ozen MO, Otsuki S, Shinohara T, Sweatt AJ, Kaplan J, Moonen JR, Marciano DP, Gu M, Miyagawa K, Hayes B, Sierra RG, Kupitz CJ, Del Rosario PA, Hsi A, Thompson AAR, Ariza ME, Demirci U, Zamanian RT, Haddad F, Nicolls MR, Snyder MP, Rabinovitch M. Endogenous Retroviral Elements Generate Pathologic Neutrophils in Pulmonary Arterial Hypertension. Am J Respir Crit Care Med 2022; 206:1019-1034. [PMID: 35696338 PMCID: PMC9801997 DOI: 10.1164/rccm.202102-0446oc] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Rationale: The role of neutrophils and their extracellular vesicles (EVs) in the pathogenesis of pulmonary arterial hypertension is unclear. Objectives: To relate functional abnormalities in pulmonary arterial hypertension neutrophils and their EVs to mechanisms uncovered by proteomic and transcriptomic profiling. Methods: Production of elastase, release of extracellular traps, adhesion, and migration were assessed in neutrophils from patients with pulmonary arterial hypertension and control subjects. Proteomic analyses were applied to explain functional perturbations, and transcriptomic data were used to find underlying mechanisms. CD66b-specific neutrophil EVs were isolated from plasma of patients with pulmonary arterial hypertension, and we determined whether they produce pulmonary hypertension in mice. Measurements and Main Results: Neutrophils from patients with pulmonary arterial hypertension produce and release increased neutrophil elastase, associated with enhanced extracellular traps. They exhibit reduced migration and increased adhesion attributed to elevated β1-integrin and vinculin identified by proteomic analysis and previously linked to an antiviral response. This was substantiated by a transcriptomic IFN signature that we related to an increase in human endogenous retrovirus K envelope protein. Transfection of human endogenous retrovirus K envelope in a neutrophil cell line (HL-60) increases neutrophil elastase and IFN genes, whereas vinculin is increased by human endogenous retrovirus K deoxyuridine triphosphate diphosphatase that is elevated in patient plasma. Neutrophil EVs from patient plasma contain increased neutrophil elastase and human endogenous retrovirus K envelope and induce pulmonary hypertension in mice, mitigated by elafin, an elastase inhibitor. Conclusions: Elevated human endogenous retroviral elements and elastase link a neutrophil innate immune response to pulmonary arterial hypertension.
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Affiliation(s)
- Shalina Taylor
- Vera Moulton Wall Center for Pulmonary Vascular Diseases,,Stanford Cardiovascular Institute,,Department of Pediatrics – Cardiology
| | - Sarasa Isobe
- Vera Moulton Wall Center for Pulmonary Vascular Diseases,,Stanford Cardiovascular Institute,,Department of Pediatrics – Cardiology
| | - Aiqin Cao
- Vera Moulton Wall Center for Pulmonary Vascular Diseases,,Stanford Cardiovascular Institute,,Department of Pediatrics – Cardiology
| | | | - Bérénice A. Benayoun
- Leonard Davis School of Gerontology and,Department of Molecular and Computational Biology, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, California
| | - Lihua Jiang
- Stanford Cardiovascular Institute,,Department of Genetics
| | - Lingli Wang
- Vera Moulton Wall Center for Pulmonary Vascular Diseases,,Stanford Cardiovascular Institute,,Department of Pediatrics – Cardiology
| | | | - Mehmet O. Ozen
- Department of Radiology Canary Center for Cancer Early Detection
| | - Shoichiro Otsuki
- Vera Moulton Wall Center for Pulmonary Vascular Diseases,,Stanford Cardiovascular Institute,,Department of Pediatrics – Cardiology
| | - Tsutomu Shinohara
- Vera Moulton Wall Center for Pulmonary Vascular Diseases,,Stanford Cardiovascular Institute,,Department of Pediatrics – Cardiology
| | - Andrew J. Sweatt
- Vera Moulton Wall Center for Pulmonary Vascular Diseases,,Department of Medicine – Pulmonary and Critical Care Medicine, and
| | - Jordan Kaplan
- Vera Moulton Wall Center for Pulmonary Vascular Diseases,,Stanford Cardiovascular Institute,,Department of Pediatrics – Cardiology
| | - Jan-Renier Moonen
- Vera Moulton Wall Center for Pulmonary Vascular Diseases,,Stanford Cardiovascular Institute,,Department of Pediatrics – Cardiology
| | | | - Mingxia Gu
- Vera Moulton Wall Center for Pulmonary Vascular Diseases,,Stanford Cardiovascular Institute,,Department of Pediatrics – Cardiology
| | - Kazuya Miyagawa
- Vera Moulton Wall Center for Pulmonary Vascular Diseases,,Stanford Cardiovascular Institute,,Department of Pediatrics – Cardiology
| | - Brandon Hayes
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California
| | - Raymond G. Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California
| | - Christopher J. Kupitz
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California
| | - Patricia A. Del Rosario
- Vera Moulton Wall Center for Pulmonary Vascular Diseases,,Department of Medicine – Pulmonary and Critical Care Medicine, and
| | - Andrew Hsi
- Vera Moulton Wall Center for Pulmonary Vascular Diseases
| | - A. A. Roger Thompson
- Vera Moulton Wall Center for Pulmonary Vascular Diseases,,Stanford Cardiovascular Institute,,Department of Pediatrics – Cardiology,,Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, United Kingdom; and
| | - Maria E. Ariza
- Department of Cancer Biology and Genetics and,Institute for Behavioral Medicine Research, The Ohio State University Wexner Medical Center, Columbus, Ohio
| | | | - Roham T. Zamanian
- Vera Moulton Wall Center for Pulmonary Vascular Diseases,,Department of Medicine – Pulmonary and Critical Care Medicine, and
| | - Francois Haddad
- Stanford Cardiovascular Institute,,Department of Medicine – Cardiovascular Medicine, Stanford University, Stanford, California
| | - Mark R. Nicolls
- Vera Moulton Wall Center for Pulmonary Vascular Diseases,,Stanford Cardiovascular Institute,,Department of Medicine – Pulmonary and Critical Care Medicine, and
| | | | - Marlene Rabinovitch
- Vera Moulton Wall Center for Pulmonary Vascular Diseases,,Stanford Cardiovascular Institute,,Department of Pediatrics – Cardiology
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7
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Baba H. [Introduction to Myelin Research]. YAKUGAKU ZASSHI 2022; 142:837-853. [PMID: 35908945 DOI: 10.1248/yakushi.21-00224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Myelin is a multilamellar membrane structure formed by oligodendrocytes in the central nervous system (CNS) and Schwann cells in the peripheral nervous system (PNS). It has been recognized as an insulator that is essential for the rapid and efficient propagation of action potentials by saltatory conduction. However, recently many studies have shown that myelin and myelin-forming cells interact with axons and regulate the nervous system far more actively than previously thought. For example, myelination changes axons dynamically and divides them into four distinct functional domains: node of Ranvier, paranode, juxtaparanode, and internode. Voltage-gated Na+ channels are clustered at the node, while K+ channels are at the juxtaparanode, and segregation of these channels by paranodal axoglial junction is necessary for proper axonal function. My research experience began at the neurology ward of the Niigata University Medical Hospital, where I saw a patient with peripheral neuropathy of unknown etiology more than 37 years ago. In the patient's serum, we found an autoantibody against a glycolipid enriched in the PNS. Since then, I have been interested in myelin because of its beautiful structure and unique roles in the nervous system. In this review, our recent studies related to CNS and PNS myelin are presented.
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Affiliation(s)
- Hiroko Baba
- Department of Molecular Neurobiology, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences
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8
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Nakanishi K. Anatomy of four human Argonaute proteins. Nucleic Acids Res 2022; 50:6618-6638. [PMID: 35736234 PMCID: PMC9262622 DOI: 10.1093/nar/gkac519] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/26/2022] [Accepted: 05/30/2022] [Indexed: 12/24/2022] Open
Abstract
MicroRNAs (miRNAs) bind to complementary target RNAs and regulate their gene expression post-transcriptionally. These non-coding regulatory RNAs become functional after loading into Argonaute (AGO) proteins to form the effector complexes. Humans have four AGO proteins, AGO1, AGO2, AGO3 and AGO4, which share a high sequence identity. Since most miRNAs are found across the four AGOs, it has been thought that they work redundantly, and AGO2 has been heavily studied as the exemplified human paralog. Nevertheless, an increasing number of studies have found that the other paralogs play unique roles in various biological processes and diseases. In the last decade, the structural study of the four AGOs has provided the field with solid structural bases. This review exploits the completed structural catalog to describe common features and differences in target specificity across the four AGOs.
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Affiliation(s)
- Kotaro Nakanishi
- To whom correspondence should be addressed. Tel: +1 614 688 2188;
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9
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Sahoo S, Singh D, Singh A, Pandit M, Vasu K, Som S, Pullagurla NJ, Laha D, Eswarappa SM. Identification and functional characterization of mRNAs that exhibit stop codon readthrough in Arabidopsis thaliana. J Biol Chem 2022; 298:102173. [PMID: 35752360 PMCID: PMC9293766 DOI: 10.1016/j.jbc.2022.102173] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 06/16/2022] [Accepted: 06/18/2022] [Indexed: 11/29/2022] Open
Abstract
Stop codon readthrough (SCR) is the process of continuation of translation beyond the stop codon, generating protein isoforms with C-terminal extensions. SCR has been observed in viruses, fungi, and multicellular organisms, including mammals. However, SCR is largely unexplored in plants. In this study, we have analyzed ribosome profiling datasets to identify mRNAs that exhibit SCR in Arabidopsis thaliana. Analyses of the ribosome density, ribosome coverage, and three-nucleotide periodicity of the ribosome profiling reads in the mRNA region downstream of the stop codon provided strong evidence for SCR in mRNAs of 144 genes. We show that SCR generated putative evolutionarily conserved nuclear localization signals, transmembrane helices, and intrinsically disordered regions in the C-terminal extensions of several of these proteins. Furthermore, gene ontology (GO) functional enrichment analysis revealed that these 144 genes belong to three major functional groups - translation, photosynthesis, and abiotic stress tolerance. Using a luminescence-based readthrough assay, we experimentally demonstrated SCR in representative mRNAs belonging to each of these functional classes. Finally, using microscopy, we show that the SCR product of one gene that contains a nuclear localization signal at the C-terminal extension, CURT1B, localizes to the nucleus as predicted. Based on these observations, we propose that SCR plays an important role in plant physiology by regulating protein localization and function.
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Affiliation(s)
- Sarthak Sahoo
- Undergraduate Program, Indian Institute of Science, Bengaluru, India; Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Divyoj Singh
- Undergraduate Program, Indian Institute of Science, Bengaluru, India
| | - Anumeha Singh
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Madhuparna Pandit
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Kirtana Vasu
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Saubhik Som
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | | | - Debabrata Laha
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
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10
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Ghosh S, Ataman M, Bak M, Börsch A, Schmidt A, Buczak K, Martin G, Dimitriades B, Herrmann CJ, Kanitz A, Zavolan M. CFIm-mediated alternative polyadenylation remodels cellular signaling and miRNA biogenesis. Nucleic Acids Res 2022; 50:3096-3114. [PMID: 35234914 PMCID: PMC8989530 DOI: 10.1093/nar/gkac114] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 01/31/2022] [Accepted: 02/04/2022] [Indexed: 12/13/2022] Open
Abstract
The mammalian cleavage factor I (CFIm) has been implicated in alternative polyadenylation (APA) in a broad range of contexts, from cancers to learning deficits and parasite infections. To determine how the CFIm expression levels are translated into these diverse phenotypes, we carried out a multi-omics analysis of cell lines in which the CFIm25 (NUDT21) or CFIm68 (CPSF6) subunits were either repressed by siRNA-mediated knockdown or over-expressed from stably integrated constructs. We established that >800 genes undergo coherent APA in response to changes in CFIm levels, and they cluster in distinct functional classes related to protein metabolism. The activity of the ERK pathway traces the CFIm concentration, and explains some of the fluctuations in cell growth and metabolism that are observed upon CFIm perturbations. Furthermore, multiple transcripts encoding proteins from the miRNA pathway are targets of CFIm-dependent APA. This leads to an increased biogenesis and repressive activity of miRNAs at the same time as some 3′ UTRs become shorter and presumably less sensitive to miRNA-mediated repression. Our study provides a first systematic assessment of a core set of APA targets that respond coherently to changes in CFIm protein subunit levels (CFIm25/CFIm68). We describe the elicited signaling pathways downstream of CFIm, which improve our understanding of the key role of CFIm in integrating RNA processing with other cellular activities.
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Affiliation(s)
- Souvik Ghosh
- Computational and Systems Biology, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Meric Ataman
- Computational and Systems Biology, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.,Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Maciej Bak
- Computational and Systems Biology, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.,Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Anastasiya Börsch
- Computational and Systems Biology, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.,Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Katarzyna Buczak
- Proteomics Core Facility, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Georges Martin
- Computational and Systems Biology, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Beatrice Dimitriades
- Computational and Systems Biology, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Christina J Herrmann
- Computational and Systems Biology, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.,Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Alexander Kanitz
- Computational and Systems Biology, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.,Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Mihaela Zavolan
- Computational and Systems Biology, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.,Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
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11
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Falchi FA, Pizzoccheri R, Briani F. Activity and Function in Human Cells of the Evolutionary Conserved Exonuclease Polynucleotide Phosphorylase. Int J Mol Sci 2022; 23:ijms23031652. [PMID: 35163574 PMCID: PMC8836086 DOI: 10.3390/ijms23031652] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 01/28/2022] [Accepted: 01/28/2022] [Indexed: 02/04/2023] Open
Abstract
Polynucleotide phosphorylase (PNPase) is a phosphorolytic RNA exonuclease highly conserved throughout evolution. Human PNPase (hPNPase) is located in mitochondria and is essential for mitochondrial function and homeostasis. Not surprisingly, mutations in the PNPT1 gene, encoding hPNPase, cause serious diseases. hPNPase has been implicated in a plethora of processes taking place in different cell compartments and involving other proteins, some of which physically interact with hPNPase. This paper reviews hPNPase RNA binding and catalytic activity in relation with the protein structure and in comparison, with the activity of bacterial PNPases. The functions ascribed to hPNPase in different cell compartments are discussed, highlighting the gaps that still need to be filled to understand the physiological role of this ancient protein in human cells.
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12
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Liang Y, Turcan S. Epigenetic Drugs and Their Immune Modulating Potential in Cancers. Biomedicines 2022; 10:biomedicines10020211. [PMID: 35203421 PMCID: PMC8868629 DOI: 10.3390/biomedicines10020211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/14/2022] [Accepted: 01/16/2022] [Indexed: 11/19/2022] Open
Abstract
Epigenetic drugs are used for the clinical treatment of hematologic malignancies; however, their therapeutic potential in solid tumors is still under investigation. Current evidence suggests that epigenetic drugs may lead to antitumor immunity by increasing antigen presentation and may enhance the therapeutic effect of immune checkpoint inhibitors. Here, we highlight their impact on the tumor epigenome and discuss the recent evidence that epigenetic agents may optimize the immune microenvironment and promote antiviral response.
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13
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Del Toro N, Lessard F, Bouchard J, Mobasheri N, Guillon J, Igelmann S, Tardif S, Buffard T, Bourdeau V, Brakier-Gingras L, Ferbeyre G. Cellular Senescence limits Translational Readthrough. Biol Open 2021; 10:272574. [PMID: 34676390 PMCID: PMC8649927 DOI: 10.1242/bio.058688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 10/14/2021] [Indexed: 11/20/2022] Open
Abstract
The origin and evolution of cancer cells is considered to be mainly fueled by DNA mutations. Although translation errors could also expand the cellular proteome, their role in cancer biology remains poorly understood. Tumor suppressors called caretakers block cancer initiation and progression by preventing DNA mutations and/or stimulating DNA repair. If translational errors contribute to tumorigenesis, then caretaker genes should prevent such errors in normal cells in response to oncogenic stimuli. Here, we show that the process of cellular senescence induced by oncogenes, tumor suppressors or chemotherapeutic drugs is associated with a reduction in translational readthrough (TR) measured using reporters containing termination codons withing the context of both normal translation termination or programmed TR. Senescence reduced both basal TR and TR stimulated by aminoglycosides. Mechanistically, the reduction of TR during senescence is controlled by the RB tumor suppressor pathway. Cells that escape from cellular senescence either induced by oncogenes or chemotherapy have an increased TR. Also, breast cancer cells that escape from therapy-induced senescence express high levels of AGO1x, a TR isoform of AGO1 linked to breast cancer progression. We propose that senescence and the RB pathway reduce TR limiting proteome diversity and the expression of TR proteins required for cancer cell proliferation. Summary: We report that senescence and the RB pathway reduce translational readthrough (TR) limiting proteome diversity and the expression of TR proteins such as Ago1X required for cancer cell proliferation.
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Affiliation(s)
- Neylen Del Toro
- Département de Biochimie et Médecine Moléculaire, Université de Montréal C.P. 6128, Succ. Centre-Ville, Montréal, Québec, H3C 3J7, Canada
| | - Frédéric Lessard
- Département de Biochimie et Médecine Moléculaire, Université de Montréal C.P. 6128, Succ. Centre-Ville, Montréal, Québec, H3C 3J7, Canada
| | - Jacob Bouchard
- Département de Biochimie et Médecine Moléculaire, Université de Montréal C.P. 6128, Succ. Centre-Ville, Montréal, Québec, H3C 3J7, Canada
| | - Nasrin Mobasheri
- Département de Biochimie et Médecine Moléculaire, Université de Montréal C.P. 6128, Succ. Centre-Ville, Montréal, Québec, H3C 3J7, Canada
| | - Jordan Guillon
- CRCHUM, 900 Saint-Denis, bureau R10.432, Montréal, Québec, H2X 0A9, Canada
| | - Sebastian Igelmann
- Département de Biochimie et Médecine Moléculaire, Université de Montréal C.P. 6128, Succ. Centre-Ville, Montréal, Québec, H3C 3J7, Canada.,CRCHUM, 900 Saint-Denis, bureau R10.432, Montréal, Québec, H2X 0A9, Canada
| | - Sarah Tardif
- Département de Biochimie et Médecine Moléculaire, Université de Montréal C.P. 6128, Succ. Centre-Ville, Montréal, Québec, H3C 3J7, Canada
| | - Tony Buffard
- Département de Biochimie et Médecine Moléculaire, Université de Montréal C.P. 6128, Succ. Centre-Ville, Montréal, Québec, H3C 3J7, Canada
| | - Véronique Bourdeau
- Département de Biochimie et Médecine Moléculaire, Université de Montréal C.P. 6128, Succ. Centre-Ville, Montréal, Québec, H3C 3J7, Canada
| | - Léa Brakier-Gingras
- Département de Biochimie et Médecine Moléculaire, Université de Montréal C.P. 6128, Succ. Centre-Ville, Montréal, Québec, H3C 3J7, Canada
| | - Gerardo Ferbeyre
- Département de Biochimie et Médecine Moléculaire, Université de Montréal C.P. 6128, Succ. Centre-Ville, Montréal, Québec, H3C 3J7, Canada.,CRCHUM, 900 Saint-Denis, bureau R10.432, Montréal, Québec, H2X 0A9, Canada
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14
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Alboushi L, Hackett AP, Naeli P, Bakhti M, Jafarnejad SM. Multifaceted control of mRNA translation machinery in cancer. Cell Signal 2021; 84:110037. [PMID: 33975011 DOI: 10.1016/j.cellsig.2021.110037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 05/06/2021] [Indexed: 12/15/2022]
Abstract
The mRNA translation machinery is tightly regulated through several, at times overlapping, mechanisms that modulate its efficiency and accuracy. Due to their fast rate of growth and metabolism, cancer cells require an excessive amount of mRNA translation and protein synthesis. However, unfavorable conditions, such as hypoxia, amino acid starvation, and oxidative stress, which are abundant in cancer, as well as many anti-cancer treatments inhibit mRNA translation. Cancer cells adapt to the various internal and environmental stresses by employing specialised transcript-specific translation to survive and gain a proliferative advantage. We will highlight the major signaling pathways and mechanisms of translation that regulate the global or mRNA-specific translation in response to the intra- or extra-cellular signals and stresses that are key components in the process of tumourigenesis.
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Affiliation(s)
- Lilas Alboushi
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Angela P Hackett
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Parisa Naeli
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Mostafa Bakhti
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Seyed Mehdi Jafarnejad
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK.
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15
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Ghosh S, Börsch A, Ghosh S, Zavolan M. The transcriptional landscape of a hepatoma cell line grown on scaffolds of extracellular matrix proteins. BMC Genomics 2021; 22:238. [PMID: 33823809 PMCID: PMC8025518 DOI: 10.1186/s12864-021-07532-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 03/14/2021] [Indexed: 11/10/2022] Open
Abstract
Background The behavior of cells in vivo is complex and highly dynamic, as it results from an interplay between intercellular matrix proteins with surface receptors and other microenvironmental cues. Although the effects of the cellular niche have been investigated for a number of cell types using different molecular approaches, comprehensive assessments of how the global transcriptome responds to 3D scaffolds composed of various extracellular matrix (ECM) constituents at different concentrations are still lacking. Results In this study, we explored the effects of two diverse extracellular matrix (ECM) components, Collagen I and Matrigel, on the transcriptional profile of cells in a cell culture system. Culturing Huh-7 cells on traditional cell culture plates (Control) or on the ECM components at different concentrations to modulate microenvironment properties, we have generated transcriptomics data that may be further explored to understand the differentiation and growth potential of this cell type for the development of 3D cultures. Our analysis infers transcription factors that are most responsible for the transcriptome response to the extracellular cues. Conclusion Our data indicates that the Collagen I substrate induces a robust transcriptional response in the Huh-7 cells, distinct from that induced by Matrigel. Enhanced hepatocyte markers (ALB and miR-122) reveal a potentially robust remodelling towards primary hepatocytes. Our results aid in defining the appropriate culture and transcription pathways while using hepatoma cell lines. As systems mimicking the in vivo structure and function of liver cells are still being developed, our study could potentially circumvent bottlenecks of limited availability of primary hepatocytes for preclinical studies of drug targets. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07532-2.
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Affiliation(s)
- Souvik Ghosh
- Biozentrum, University of Basel, Basel, Switzerland.
| | - Anastasiya Börsch
- Biozentrum, University of Basel, Basel, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Mihaela Zavolan
- Biozentrum, University of Basel, Basel, Switzerland. .,Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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16
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Nowak I, Sarshad AA. Argonaute Proteins Take Center Stage in Cancers. Cancers (Basel) 2021; 13:cancers13040788. [PMID: 33668654 PMCID: PMC7918559 DOI: 10.3390/cancers13040788] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary The dysregulation of RNA interference (RNAi) has often been observed in cancers, where the main focus of research has been on the small RNA molecules directing RNAi. In this review, we focus on the activity of Argonaute proteins, central components of RNAi, in tumorigenesis, and also highlight their potential applications in grading tumors and anti-cancer therapies. Abstract Argonaute proteins (AGOs) play crucial roles in RNA-induced silencing complex (RISC) formation and activity. AGOs loaded with small RNA molecules (miRNA or siRNA) either catalyze endoribonucleolytic cleavage of target RNAs or recruit factors responsible for translational silencing and target destabilization. miRNAs are well characterized and broadly studied in tumorigenesis; nevertheless, the functions of the AGOs in cancers have lagged behind. Here, we discuss the current state of knowledge on the role of AGOs in tumorigenesis, highlighting canonical and non-canonical functions of AGOs in cancer cells, as well as the biomarker potential of AGO expression in different of tumor types. Furthermore, we point to the possible application of the AGOs in development of novel therapeutic approaches.
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Affiliation(s)
- Iwona Nowak
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden;
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Aishe A. Sarshad
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden;
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Gothenburg, Sweden
- Correspondence:
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17
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Okude H, Ori D, Kawai T. Signaling Through Nucleic Acid Sensors and Their Roles in Inflammatory Diseases. Front Immunol 2021; 11:625833. [PMID: 33633744 PMCID: PMC7902034 DOI: 10.3389/fimmu.2020.625833] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 12/14/2020] [Indexed: 12/14/2022] Open
Abstract
Recognition of pathogen-derived nucleic acids by pattern-recognition receptors (PRRs) is essential for eliciting antiviral immune responses by inducing the production of type I interferons (IFNs) and proinflammatory cytokines. Such responses are a prerequisite for mounting innate and pathogen-specific adaptive immune responses. However, host cells also use nucleic acids as carriers of genetic information, and the aberrant recognition of self-nucleic acids by PRRs is associated with the onset of autoimmune or autoinflammatory diseases. In this review, we describe the mechanisms of nucleic acid sensing by PRRs, including Toll-like receptors, RIG-I-like receptors, and DNA sensor molecules, and their signaling pathways as well as the disorders caused by uncontrolled or unnecessary activation of these PRRs.
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Affiliation(s)
- Haruna Okude
- Laboratory of Molecular Immunobiology, Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), Ikoma, Japan
| | - Daisuke Ori
- Laboratory of Molecular Immunobiology, Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), Ikoma, Japan
| | - Taro Kawai
- Laboratory of Molecular Immunobiology, Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), Ikoma, Japan
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18
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Manjunath LE, Singh A, Sahoo S, Mishra A, Padmarajan J, Basavaraju CG, Eswarappa SM. Stop codon read-through of mammalian MTCH2 leading to an unstable isoform regulates mitochondrial membrane potential. J Biol Chem 2020; 295:17009-17026. [PMID: 33028634 PMCID: PMC7863902 DOI: 10.1074/jbc.ra120.014253] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 10/02/2020] [Indexed: 12/13/2022] Open
Abstract
Stop codon read-through (SCR) is a process of continuation of translation beyond a stop codon. This phenomenon, which occurs only in certain mRNAs under specific conditions, leads to a longer isoform with properties different from that of the canonical isoform. MTCH2, which encodes a mitochondrial protein that regulates mitochondrial metabolism, was selected as a potential read-through candidate based on evolutionary conservation observed in the proximal region of its 3' UTR. Here, we demonstrate translational read-through across two evolutionarily conserved, in-frame stop codons of MTCH2 using luminescence- and fluorescence-based assays, and by analyzing ribosome-profiling and mass spectrometry (MS) data. This phenomenon generates two isoforms, MTCH2x and MTCH2xx (single- and double-SCR products, respectively), in addition to the canonical isoform MTCH2, from the same mRNA. Our experiments revealed that a cis-acting 12-nucleotide sequence in the proximal 3' UTR of MTCH2 is the necessary signal for SCR. Functional characterization showed that MTCH2 and MTCH2x were localized to mitochondria with a long t1/2 (>36 h). However, MTCH2xx was found predominantly in the cytoplasm. This mislocalization and its unique C terminus led to increased degradation, as shown by greatly reduced t1/2 (<1 h). MTCH2 read-through-deficient cells, generated using CRISPR-Cas9, showed increased MTCH2 expression and, consistent with this, decreased mitochondrial membrane potential. Thus, double-SCR of MTCH2 regulates its own expression levels contributing toward the maintenance of normal mitochondrial membrane potential.
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Affiliation(s)
- Lekha E Manjunath
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Anumeha Singh
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Sarthak Sahoo
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Ashutosh Mishra
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Jinsha Padmarajan
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | | | - Sandeep M Eswarappa
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India.
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19
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Ghosh S, Guimaraes JC, Lanzafame M, Schmidt A, Syed AP, Dimitriades B, Börsch A, Ghosh S, Mittal N, Montavon T, Correia AL, Danner J, Meister G, Terracciano LM, Pfeffer S, Piscuoglio S, Zavolan M. Prevention of dsRNA-induced interferon signaling by AGO1x is linked to breast cancer cell proliferation. EMBO J 2020; 39:e103922. [PMID: 32812257 PMCID: PMC7507497 DOI: 10.15252/embj.2019103922] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 06/27/2020] [Accepted: 07/07/2020] [Indexed: 01/05/2023] Open
Abstract
Translational readthrough, i.e., elongation of polypeptide chains beyond the stop codon, was initially reported for viral RNA, but later found also on eukaryotic transcripts, resulting in proteome diversification and protein‐level modulation. Here, we report that AGO1x, an evolutionarily conserved translational readthrough isoform of Argonaute 1, is generated in highly proliferative breast cancer cells, where it curbs accumulation of double‐stranded RNAs (dsRNAs) and consequent induction of interferon responses and apoptosis. In contrast to other mammalian Argonaute protein family members with primarily cytoplasmic functions, AGO1x exhibits nuclear localization in the vicinity of nucleoli. We identify AGO1x interaction with the polyribonucleotide nucleotidyltransferase 1 (PNPT1) and show that the depletion of this protein further augments dsRNA accumulation. Our study thus uncovers a novel function of an Argonaute protein in buffering the endogenous dsRNA‐induced interferon responses, different than the canonical function of AGO proteins in the miRNA effector pathway. As AGO1x expression is tightly linked to breast cancer cell proliferation, our study thus suggests a new direction for limiting tumor growth.
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Affiliation(s)
- Souvik Ghosh
- Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Joao C Guimaraes
- Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Manuela Lanzafame
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Afzal Pasha Syed
- Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Beatrice Dimitriades
- Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Anastasiya Börsch
- Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Shreemoyee Ghosh
- Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Nitish Mittal
- Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Thomas Montavon
- Architecture et Réactivité de l'ARN, Institut de biologie moléculaire et cellulaire du CNRS, Université de Strasbourg, Strasbourg, France
| | - Ana Luisa Correia
- Department of Biomedicine, University of Basel/University Hospital Basel, Basel, Switzerland
| | - Johannes Danner
- Department of Biochemistry, Department of Biology and Preclinical Medicine, University of Regensburg, Regensburg, Germany
| | - Gunter Meister
- Department of Biochemistry, Department of Biology and Preclinical Medicine, University of Regensburg, Regensburg, Germany
| | | | - Sébastien Pfeffer
- Architecture et Réactivité de l'ARN, Institut de biologie moléculaire et cellulaire du CNRS, Université de Strasbourg, Strasbourg, France
| | - Salvatore Piscuoglio
- Institute of Pathology, University Hospital Basel, Basel, Switzerland.,Department of Biomedicine, University of Basel/University Hospital Basel, Basel, Switzerland
| | - Mihaela Zavolan
- Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland
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