1
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Li Y, Perera L, He RS, Baptissart M, Petrovich RM, Morgan M. TENT5C functions as a corepressor in the ligand-bound glucocorticoid receptor and estrogen receptor α complexes. FEBS J 2025. [PMID: 40421654 DOI: 10.1111/febs.70137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2024] [Revised: 02/28/2025] [Accepted: 05/08/2025] [Indexed: 05/28/2025]
Abstract
Terminal nucleotidyltransferase 5C (TENT5C) is a noncanonical poly(A) polymerase that promotes cancer suppression. TENT5C has been proposed to mediate the susceptibility of multiple myeloma to treatment with dexamethasone, a steroid hormone analog that binds to the glucocorticoid receptor (GR). However, the relationship between TENT5C and nuclear receptor (NR) signaling remains unclear. In this study, we investigate the regulatory role of TENT5C in the GR and estrogen receptor α (ERα) ligand complexes. We find that TENT5C acts as a corepressor of both GR and ERα. Molecular dynamics simulations indicate that the third TENT5C LXXLL motif directly interacts with ERα, but not GR. The physical interaction of TENT5C and ERα is supported by co-immunoprecipitation assays. Reporter assays show that mutations to the third TENT5C LXXLL motif disrupt TENT5C-mediated repression of ERα but do not affect the repression of the GR complex. In addition, the disruption of TENT5C poly(A) polymerase activity does not appear to affect TENT5C repression of ERα in the cell lines studied. Taken together, our findings highlight a role of TENT5C as an NR corepressor, differentially modulating GR- and ERα-induced transcriptional activity.
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Affiliation(s)
- Yin Li
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Lalith Perera
- Genomic Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Rebecca S He
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Marine Baptissart
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Robert M Petrovich
- Genomic Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Marcos Morgan
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Durham, NC, USA
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2
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Wardaszka-Pianka P, Kuzniewska B, GumiNska N, Hojka-Osinska A, Puchalska M, Milek J, Stawikowska A, Krawczyk P, Pauzin FP, Wojtowicz T, Radwanska K, Bramham CR, Dziembowski A, Dziembowska M. Terminal nucleotidyltransferase Tent2 microRNA A-tailing enzyme regulates excitatory/inhibitory balance in the hippocampus. RNA (NEW YORK, N.Y.) 2025; 31:756-771. [PMID: 40101932 DOI: 10.1261/rna.080240.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2024] [Accepted: 02/25/2025] [Indexed: 03/20/2025]
Abstract
One of the posttranscriptional mechanisms regulating the stability of RNA molecules involves the addition of nontemplated nucleotides to their 3' ends, a process known as RNA tailing. To systematically investigate the physiological consequences of terminal nucleotidyltransferase TENT2 absence on RNA 3' end modifications in the mouse hippocampus, we developed a new Tent2 knockout mouse. Electrophysiological measurements revealed increased excitability in Tent2 KO hippocampal neurons, and behavioral analyses showed decreased anxiety and improved fear extinction in these mice. At the molecular level, we observed changes in miRNAs' monoadenylation in Tent2 KO mouse hippocampus, but found no effect of the TENT2 loss on the mRNAs' total poly(A) tail length, as measured by direct nanopore RNA sequencing. Moreover, differential expression analysis revealed transcripts related to synaptic transmission to be downregulated in the hippocampus of Tent2 knockout mice. These changes may explain the observed behavioral and electrophysiological alterations. Our data thus establish a link between TENT2-dependent miRNA tailing and the balance of inhibitory and excitatory neurotransmission.
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Affiliation(s)
| | - Bozena Kuzniewska
- Department of Animal Physiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
| | - Natalia GumiNska
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | - Anna Hojka-Osinska
- Bioinformatics Facility, International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | - Monika Puchalska
- Laboratory of Molecular Basis of Behavior, Nencki Institute of Experimental Biology, 02-093 Warsaw, Poland
| | - Jacek Milek
- Department of Animal Physiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
| | - Aleksandra Stawikowska
- Department of Animal Physiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
| | - Pawel Krawczyk
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | - Francois P Pauzin
- Department of Biomedicine, University of Bergen, 5007 Bergen, Norway
- Mohn Research Center for the Brain, University of Bergen, 5007 Bergen, Norway
| | - Tomasz Wojtowicz
- Laboratory of Cell Biophysics, Nencki Institute of Experimental Biology, 02-093 Warsaw, Poland
| | - Kasia Radwanska
- Laboratory of Molecular Basis of Behavior, Nencki Institute of Experimental Biology, 02-093 Warsaw, Poland
| | - Clive R Bramham
- Department of Biomedicine, University of Bergen, 5007 Bergen, Norway
- Mohn Research Center for the Brain, University of Bergen, 5007 Bergen, Norway
| | - Andrzej Dziembowski
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | - Magdalena Dziembowska
- Department of Animal Physiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
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3
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Krawczyk PS, Mazur M, Orzeł W, Gewartowska O, Jeleń S, Antczak W, Kasztelan K, Brouze A, Matylla-Kulińska K, Gumińska N, Tarkowski B, Owczarek EP, Affek K, Turowski P, Tudek A, Sroka M, Śpiewla T, Kusio-Kobiałka M, Wesołowska A, Nowis D, Golab J, Kowalska J, Jemielity J, Dziembowski A, Mroczek S. Re-adenylation by TENT5A enhances efficacy of SARS-CoV-2 mRNA vaccines. Nature 2025; 641:984-992. [PMID: 40240603 PMCID: PMC12095053 DOI: 10.1038/s41586-025-08842-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/26/2025] [Indexed: 04/18/2025]
Abstract
Despite the widespread use of mRNA vaccines against COVID-19, little is known about the metabolism of therapeutic RNAs. Here we use nanopore sequencing1-3 to analyse individual therapeutic mRNA molecules, focusing on their poly(A) tails. We show that the Moderna mRNA-1273 vaccine4 has a poly(A) tail of around 100 nucleotides, followed by an mΨCmΨAG sequence. In cell lines, mRNA-1273 undergoes rapid degradation initiated by mΨCmΨAG removal, followed by CCR4-NOT-mediated deadenylation. However, in medically relevant preclinical models, particularly in macrophages, mRNA-1273 poly(A) tails are extended to up to 200 nucleotides by the TENT5A poly(A) polymerase5-7, which is induced by the vaccine. Re-adenylation, which stabilizes target mRNAs, is consistently observed in synthetic mRNAs that encode proteins targeted to the endoplasmic reticulum, such as ovalbumin or antigens from Zika virus8 or the malaria parasite9. The extent of re-adenylation varies: the BioNTech-Pfizer BNT162b2 vaccine10 shows less potent re-adenylation than mRNA-1273, which correlates with a smaller proportion of membrane-associated BNT162b2. This highlights the crucial role of spatial accessibility to ER-resident TENT5A in determining re-adenylation efficiency. In vivo, TENT5A is expressed in immune cells that take up mRNA vaccine, and TENT5A deficiency reduces specific immunoglobulin production for mRNA vaccines after immunization in mice. Overall, our findings reveal a principle for enhancing the efficacy of therapeutic mRNAs, paving the way for improvement.
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Affiliation(s)
- Paweł S Krawczyk
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Michał Mazur
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Wiktoria Orzeł
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Olga Gewartowska
- Genome Engineering Facility, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Sebastian Jeleń
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Wiktor Antczak
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Karolina Kasztelan
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Aleksandra Brouze
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Katarzyna Matylla-Kulińska
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Natalia Gumińska
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Bartosz Tarkowski
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Ewelina P Owczarek
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Kamila Affek
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | | | | | - Małgorzata Sroka
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Tomasz Śpiewla
- Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Monika Kusio-Kobiałka
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | | | - Dominika Nowis
- Laboratory of Experimental Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Jakub Golab
- Department of Immunology, Medical University of Warsaw, Warsaw, Poland
| | | | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Andrzej Dziembowski
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland.
- Department of Embryology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| | - Seweryn Mroczek
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland.
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
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4
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Baptissart M, Gupta A, Poirot AC, Papas BN, Morgan M. TENT5C extends Odf1 poly(A) tail to sustain sperm morphogenesis and fertility. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.20.644152. [PMID: 40196629 PMCID: PMC11974682 DOI: 10.1101/2025.03.20.644152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2025]
Abstract
Changes in the poly(A) tail length of Odf1 and other transcripts critical for male fertility have been linked to translational activation during sperm formation 1-3. The mRNA poly(A) polymerase TENT5C is required for fastening the flagellum to the sperm head, but its role in shaping the poly(A) tail profile of the spermatid transcriptome remains limited 4,5. Here, we comprehensively document how changes in mRNA poly(A) tail length across the transcriptome reflect transcript metabolism in spermatids. In the absence of TENT5C polymerase activity, the poly(A) tail length of Odf1 transcripts is reduced, and the local distribution of ODF1 proteins in spermatids is disrupted. We show that mice expressing a catalytically inactive TENT5C produce headless spermatozoa with outer dense fibers detached from the axoneme, and other flagellar abnormalities associated with ODF1 deficiency 6. We propose that TENT5C poly(A) polymerase activity regulates the spatial translation of Odf1 mRNAs during spermiogenesis, a process critical for sperm morphogenesis and fertility. These findings highlight the power of poly(A) tail profiling to identify abnormal mRNA processing causative of infertility.
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Affiliation(s)
- Marine Baptissart
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina 27709, USA
| | - Ankit Gupta
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina 27709, USA
| | - Alexander C Poirot
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina 27709, USA
| | - Brian N Papas
- Integrative Bioinformatics, Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina 27709, USA
| | - Marcos Morgan
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina 27709, USA
- Corresponding and lead author
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5
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Gumińska N, Matylla-Kulińska K, Krawczyk PS, Maj M, Orzeł W, Mackiewicz Z, Brouze A, Mroczek S, Dziembowski A. Direct profiling of non-adenosines in poly(A) tails of endogenous and therapeutic mRNAs with Ninetails. Nat Commun 2025; 16:2664. [PMID: 40102414 PMCID: PMC11920217 DOI: 10.1038/s41467-025-57787-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 11/27/2024] [Indexed: 03/20/2025] Open
Abstract
Stability and translation of mRNAs, both endogenous and therapeutic, is determined by poly(A) tail. Direct RNA sequencing enables single-molecule measurements of poly(A) lengths, avoiding amplification bias. It also holds potential for observation of non-adenosines within poly(A), known to influence mRNA fate. However, there is no computational method to detect composite tails in Direct Sequencing data. To address this gap, we introduce the Ninetails, a neural network-based tool that accurately identifies and quantifies non-adenosines in poly(A) tails. Examination of different biological contexts revealed widespread non-adenosine decorations, with frequencies influenced by the origin of poly(A) tails differing by mRNA class, cell type, and species. Notably, substrates of cytoplasmic TENT5-polymerases and mitochondrially encoded mRNAs are enriched in composite tails. For mRNA therapeutics, we show that the composition of poly(A) tails in mRNA vaccines is dynamic during its cellular lifetime and that the manufacturing protocol of synthetic mRNAs affects the purity of poly(A) tails.
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Affiliation(s)
- Natalia Gumińska
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Katarzyna Matylla-Kulińska
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
- Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Paweł S Krawczyk
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | | | - Wiktoria Orzeł
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
- Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Zuzanna Mackiewicz
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Aleksandra Brouze
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Seweryn Mroczek
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
- Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Andrzej Dziembowski
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland.
- Faculty of Biology, University of Warsaw, Warsaw, Poland.
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6
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Czarnocka-Cieciura A, Brouze M, Gumińska N, Mroczek S, Gewartowska O, Krawczyk PS, Dziembowski A. Comprehensive analysis of poly(A) tails in mouse testes and ovaries using Nanopore Direct RNA Sequencing. Sci Data 2025; 12:43. [PMID: 39794363 PMCID: PMC11724052 DOI: 10.1038/s41597-024-04226-8] [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: 05/29/2024] [Accepted: 12/02/2024] [Indexed: 01/13/2025] Open
Abstract
Gametogenesis is a process in which dysfunctions lead to infertility, a growing health and social problem worldwide. In both spermatogenesis and oogenesis, post-transcriptional gene expression regulation is crucial. Essentially, all mRNAs possess non-templated poly(A) tails, whose composition and dynamics (elongation, shortening, and modifications) determine the fate of mRNA. Moreover, gametogenesis, especially oogenesis, represents a unique instance of the complexity of poly(A) tails metabolism, with oocyte-specific waves of cytoplasmic polyadenylation. In this context, we provide a comprehensive transcriptomic dataset focusing on mRNA poly(A) tail composition and dynamics in murine testes and ovaries. It consists of RNA samples isolated from wild-type and transgenic mice lacking TENT5 polymerases, which can extend poly(A) tails in the cytoplasm. TENT5 deficiencies have serious consequences. For instance, the defect of TENT5D causes infertility in humans. The data described here are generated mainly using the Oxford Nanopore Direct RNA Sequencing (DRS) method, which provides ground-truth information about mRNA molecules, including poly(A) tail length and nucleotide content. For instance, we show the prevalence of uridilated tails in testicular mRNAs.
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Affiliation(s)
| | - Michał Brouze
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
| | - Natalia Gumińska
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
| | - Seweryn Mroczek
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, 02-106, Poland
| | - Olga Gewartowska
- Genome Engineering Facility, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
| | - Paweł S Krawczyk
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
| | - Andrzej Dziembowski
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland.
- Department of Embryology, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Warsaw, 02-096, Poland.
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7
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Yamazaki H, Furuichi M, Katagiri M, Kajitani R, Itoh T, Chiba K. Recycling of Uridylated mRNAs in Starfish Embryos. Biomolecules 2024; 14:1610. [PMID: 39766317 PMCID: PMC11674185 DOI: 10.3390/biom14121610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2024] [Revised: 12/11/2024] [Accepted: 12/11/2024] [Indexed: 01/11/2025] Open
Abstract
In eukaryotes, mRNAs with long poly(A) tails are translationally active, but deadenylation and uridylation of these tails generally cause mRNA degradation. However, the fate of uridylated mRNAs that are not degraded quickly remains obscure. Here, using tail-seq and microinjection of the 3' region of mRNA, we report that some mRNAs in starfish are re-polyadenylated to be translationally active after deadenylation and uridylation. In oocytes, uridylated maternal cyclin B mRNAs are stable without decay, and they are polyadenylated to be translated after hormonal stimulation to resume meiosis, whereas they are deadenylated and re-uridylated at the blastula stage, followed by decay. Similarly, deadenylated and uridylated maternal ribosomal protein mRNAs, Rps29 and Rpl27a, were stable and inactive after hormonal stimulation, but they had been polyadenylated and active before hormonal stimulation. At the morula stage, uridylated maternal ribosomal protein mRNAs were re-polyadenylated, rendering them translationally active. These results indicate that uridylated mRNAs in starfish exist in a poised state, allowing them to be recycled or decayed.
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Affiliation(s)
- Haruka Yamazaki
- Department of Biological Sciences, Ochanomizu University, Bunkyo-ku, Tokyo 112-8610, Japan (M.K.)
| | - Megumi Furuichi
- Department of Biological Sciences, Ochanomizu University, Bunkyo-ku, Tokyo 112-8610, Japan (M.K.)
| | - Mikoto Katagiri
- Department of Biological Sciences, Ochanomizu University, Bunkyo-ku, Tokyo 112-8610, Japan (M.K.)
| | - Rei Kajitani
- School of Life Science and Technology, Institute of Science Tokyo, Meguro-ku, Tokyo 152-8550, Japan; (R.K.); (T.I.)
| | - Takehiko Itoh
- School of Life Science and Technology, Institute of Science Tokyo, Meguro-ku, Tokyo 152-8550, Japan; (R.K.); (T.I.)
| | - Kazuyoshi Chiba
- Department of Biological Sciences, Ochanomizu University, Bunkyo-ku, Tokyo 112-8610, Japan (M.K.)
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8
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Czarnocka-Cieciura A, Poznański J, Turtola M, Tomecki R, Krawczyk PS, Mroczek S, Orzeł W, Saha U, Jensen TH, Dziembowski A, Tudek A. Modeling of mRNA deadenylation rates reveal a complex relationship between mRNA deadenylation and decay. EMBO J 2024; 43:6525-6554. [PMID: 39394354 PMCID: PMC11649921 DOI: 10.1038/s44318-024-00258-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 09/11/2024] [Accepted: 09/19/2024] [Indexed: 10/13/2024] Open
Abstract
Complete cytoplasmic polyadenosine tail (polyA-tail) deadenylation is thought to be essential for initiating mRNA decapping and subsequent degradation. To investigate this prevalent model, we conducted direct RNA sequencing of S. cerevisiae mRNAs derived from chase experiments under steady-state and stress condition. Subsequently, we developed a numerical model based on a modified gamma distribution function, which estimated the transcriptomic deadenylation rate at 10 A/min. A simplified independent method, based on the delineation of quantile polyA-tail values, showed a correlation between the decay and deadenylation rates of individual mRNAs, which appeared consistent within functional transcript groups and associated with codon optimality. Notably, these rates varied during the stress response. Detailed analysis of ribosomal protein-coding mRNAs (RPG mRNAs), constituting 40% of the transcriptome, singled out this transcript group. While deadenylation and decay of RPG mRNAs accelerated under heat stress, their degradation could proceed even when deadenylation was blocked, depending entirely on ongoing nuclear export. Our findings support the general primary function of deadenylation in dictating the onset of decapping, while also demonstrating complex relations between these processes.
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Affiliation(s)
| | - Jarosław Poznański
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Adolfa Pawińskiego 5A, 02-106, Warsaw, Poland
| | - Matti Turtola
- Department of Life Technologies, University of Turku, Biocity, Tykistökatu 6, 205240, Turku, Finland
| | - Rafał Tomecki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Adolfa Pawińskiego 5A, 02-106, Warsaw, Poland
- University of Warsaw, Faculty of Biology, Miecznikowa 1, 02-089, Warsaw, Poland
| | - Paweł S Krawczyk
- International Institute of Molecular and Cell Biology, Księcia Trojdena 4, 02-109, Warsaw, Poland
| | - Seweryn Mroczek
- International Institute of Molecular and Cell Biology, Księcia Trojdena 4, 02-109, Warsaw, Poland
- University of Warsaw, Faculty of Biology, Miecznikowa 1, 02-089, Warsaw, Poland
| | - Wiktoria Orzeł
- International Institute of Molecular and Cell Biology, Księcia Trojdena 4, 02-109, Warsaw, Poland
| | - Upasana Saha
- Aarhus University, Department of Molecular Biology and Genetics-Universitetsbyen 81, 8000, Aarhus, Denmark
| | - Torben Heick Jensen
- Aarhus University, Department of Molecular Biology and Genetics-Universitetsbyen 81, 8000, Aarhus, Denmark
| | - Andrzej Dziembowski
- International Institute of Molecular and Cell Biology, Księcia Trojdena 4, 02-109, Warsaw, Poland.
- University of Warsaw, Faculty of Biology, Miecznikowa 1, 02-089, Warsaw, Poland.
| | - Agnieszka Tudek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Adolfa Pawińskiego 5A, 02-106, Warsaw, Poland.
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9
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Zhang J, Pan W, Wang Y, Zhang C, Wang C, Li S, Chen F, Zhu A. Enhancing vaccine efficacy: Evaluating the superiority of cationic liposome-embedded squalene adjuvant against PCV2 infection. Virology 2024; 600:110251. [PMID: 39362035 DOI: 10.1016/j.virol.2024.110251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2024] [Revised: 09/22/2024] [Accepted: 09/23/2024] [Indexed: 10/05/2024]
Abstract
Cationic liposome-embedded squalene (CLS) is a promising adjuvant that enhances antigen stability and mobility and improves immune response. This study compares the efficacy of a CLS-adjuvant porcine circovirus type 2 (PCV2) vaccine (CSV) with a conventional vaccine against PCV2. The CSV vaccine showed superior stability and was effective against PCV2-induced growth decline. It significantly increased serum immunoglobulin and cytokine levels, reduced serum PCV2 DNA, shortened the duration of viremia, and provided robust protection. CSV outperformed conventional vaccines, highlighting its potential for innovative vaccine development.
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Affiliation(s)
- Jiaqi Zhang
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, 430023, China.
| | - Wenjing Pan
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, 430023, China.
| | - You Wang
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, 430023, China.
| | - Chi Zhang
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, 430023, China.
| | - Chunwei Wang
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, 430023, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China.
| | - Shuang Li
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China.
| | - Fan Chen
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, 430023, China.
| | - Aixia Zhu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, 430023, China.
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10
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Brouze M, Czarnocka-Cieciura A, Gewartowska O, Kusio-Kobiałka M, Jachacy K, Szpila M, Tarkowski B, Gruchota J, Krawczyk P, Mroczek S, Borsuk E, Dziembowski A. TENT5-mediated polyadenylation of mRNAs encoding secreted proteins is essential for gametogenesis in mice. Nat Commun 2024; 15:5331. [PMID: 38909026 PMCID: PMC11193744 DOI: 10.1038/s41467-024-49479-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 05/31/2024] [Indexed: 06/24/2024] Open
Abstract
Cytoplasmic polyadenylation plays a vital role in gametogenesis; however, the participating enzymes and substrates in mammals remain unclear. Using knockout and knock-in mouse models, we describe the essential role of four TENT5 poly(A) polymerases in mouse fertility and gametogenesis. TENT5B and TENT5C play crucial yet redundant roles in oogenesis, with the double knockout of both genes leading to oocyte degeneration. Additionally, TENT5B-GFP knock-in females display a gain-of-function infertility effect, with multiple chromosomal aberrations in ovulated oocytes. TENT5C and TENT5D both regulate different stages of spermatogenesis, as shown by the sterility in males following the knockout of either gene. Finally, Tent5a knockout substantially lowers fertility, although the underlying mechanism is not directly related to gametogenesis. Through direct RNA sequencing, we discovered that TENT5s polyadenylate mRNAs encoding endoplasmic reticulum-targeted proteins essential for gametogenesis. Sequence motif analysis and reporter mRNA assays reveal that the presence of an endoplasmic reticulum-leader sequence represents the primary determinant of TENT5-mediated regulation.
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Affiliation(s)
- Michał Brouze
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, 02-106, Poland
| | | | - Olga Gewartowska
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
- Genome Engineering Facility, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, 02-106, Poland
| | - Monika Kusio-Kobiałka
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
| | - Kamil Jachacy
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, 02-106, Poland
| | - Marcin Szpila
- Genome Engineering Facility, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
- Laboratory of Embryology, Institute of Developmental Biology and Biomedical Research, Faculty of Biology, University of Warsaw, Warsaw, 02-096, Poland
| | - Bartosz Tarkowski
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, 02-106, Poland
| | - Jakub Gruchota
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, 02-106, Poland
| | - Paweł Krawczyk
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, 02-106, Poland
| | - Seweryn Mroczek
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, 02-106, Poland
| | - Ewa Borsuk
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
- Laboratory of Embryology, Institute of Developmental Biology and Biomedical Research, Faculty of Biology, University of Warsaw, Warsaw, 02-096, Poland
| | - Andrzej Dziembowski
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland.
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, 02-106, Poland.
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, 02-106, Poland.
- Laboratory of Embryology, Institute of Developmental Biology and Biomedical Research, Faculty of Biology, University of Warsaw, Warsaw, 02-096, Poland.
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11
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Resnati M, Pennacchio S, Viviani L, Perini T, Materozzi M, Orfanelli U, Bordini J, Molteni R, Nuvolone M, Da Vià M, Lazzaroni F, Bolli N, Cenci S, Milan E. TENT5C/FAM46C modulation in vivo reveals a trade-off between antibody secretion and tumor growth in multiple myeloma. Haematologica 2024; 109:1966-1972. [PMID: 38385303 PMCID: PMC11141651 DOI: 10.3324/haematol.2023.284299] [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: 09/18/2023] [Accepted: 02/13/2024] [Indexed: 02/23/2024] Open
Abstract
Not available.
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Affiliation(s)
- Massimo Resnati
- Age Related Diseases Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milano
| | - Sara Pennacchio
- Age Related Diseases Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milano
| | - Lisa Viviani
- Age Related Diseases Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milano
| | - Tommaso Perini
- Age Related Diseases Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milano, Italy; Hematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milano
| | - Maria Materozzi
- Age Related Diseases Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milano
| | - Ugo Orfanelli
- Age Related Diseases Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milano
| | - Jessica Bordini
- B-cell Neoplasia Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milano
| | - Raffaella Molteni
- Age Related Diseases Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milano
| | - Mario Nuvolone
- Department of Molecular Medicine, University of Pavia, Pavia, Italy; Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, Pavia
| | - Matteo Da Vià
- Hematology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano
| | - Francesca Lazzaroni
- Hematology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano
| | - Niccolò Bolli
- Hematology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy; Università degli Studi di Milano, Milano. Italy
| | - Simone Cenci
- Age Related Diseases Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milano, Italy; University Vita-Salute San Raffaele, Milano
| | - Enrico Milan
- Age Related Diseases Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milano, Italy; University Vita-Salute San Raffaele, Milano.
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12
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Yang K, Zhu T, Yin J, Zhang Q, Li J, Fan H, Han G, Xu W, Liu N, Lv X. The non-canonical poly(A) polymerase FAM46C promotes erythropoiesis. J Genet Genomics 2024; 51:594-607. [PMID: 38403115 DOI: 10.1016/j.jgg.2024.02.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 02/19/2024] [Accepted: 02/19/2024] [Indexed: 02/27/2024]
Abstract
The post-transcriptional regulation of mRNA is a crucial component of gene expression. The disruption of this process has detrimental effects on the normal development and gives rise to various diseases. Searching for novel post-transcriptional regulators and exploring their roles are essential for understanding development and disease. Through a multimodal analysis of red blood cell trait genome-wide association studies (GWAS) and transcriptomes of erythropoiesis, we identify FAM46C, a non-canonical RNA poly(A) polymerase, as a necessary factor for proper red blood cell development. FAM46C is highly expressed in the late stages of the erythroid lineage, and its developmental upregulation is controlled by an erythroid-specific enhancer. We demonstrate that FAM46C stabilizes mRNA and regulates erythroid differentiation in a polymerase activity-dependent manner. Furthermore, we identify transcripts of lysosome and mitochondria components as highly confident in vivo targets of FAM46C, which aligns with the need of maturing red blood cells for substantial clearance of organelles and maintenance of cellular redox homeostasis. In conclusion, our study unveils a unique role of FAM46C in positively regulating lysosome and mitochondria components, thereby promoting erythropoiesis.
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Affiliation(s)
- Ke Yang
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang 311121, China; Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang 311121, China; The State Key Laboratory for Complex, Severe, and Rare Diseases, Haihe Laboratory of Cell Ecosystem, Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China.
| | - Tianqi Zhu
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang 311121, China; Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang 311121, China
| | - Jiaying Yin
- The State Key Laboratory for Complex, Severe, and Rare Diseases, Haihe Laboratory of Cell Ecosystem, Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Qiaoli Zhang
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang 311121, China; Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang 311121, China
| | - Jing Li
- The State Key Laboratory for Complex, Severe, and Rare Diseases, Haihe Laboratory of Cell Ecosystem, Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Hong Fan
- The State Key Laboratory for Complex, Severe, and Rare Diseases, Haihe Laboratory of Cell Ecosystem, Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Gaijing Han
- The State Key Laboratory for Complex, Severe, and Rare Diseases, Haihe Laboratory of Cell Ecosystem, Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Weiyin Xu
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang 311121, China; Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang 311121, China
| | - Nan Liu
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang 311121, China; Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang 311121, China.
| | - Xiang Lv
- The State Key Laboratory for Complex, Severe, and Rare Diseases, Haihe Laboratory of Cell Ecosystem, Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China; Medical Epigenetics Research Center, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China.
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13
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Liu-Wei W, van der Toorn W, Bohn P, Hölzer M, Smyth RP, von Kleist M. Sequencing accuracy and systematic errors of nanopore direct RNA sequencing. BMC Genomics 2024; 25:528. [PMID: 38807060 PMCID: PMC11134706 DOI: 10.1186/s12864-024-10440-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 05/21/2024] [Indexed: 05/30/2024] Open
Abstract
BACKGROUND Direct RNA sequencing (dRNA-seq) on the Oxford Nanopore Technologies (ONT) platforms can produce reads covering up to full-length gene transcripts, while containing decipherable information about RNA base modifications and poly-A tail lengths. Although many published studies have been expanding the potential of dRNA-seq, its sequencing accuracy and error patterns remain understudied. RESULTS We present the first comprehensive evaluation of sequencing accuracy and characterisation of systematic errors in dRNA-seq data from diverse organisms and synthetic in vitro transcribed RNAs. We found that for sequencing kits SQK-RNA001 and SQK-RNA002, the median read accuracy ranged from 87% to 92% across species, and deletions significantly outnumbered mismatches and insertions. Due to their high abundance in the transcriptome, heteropolymers and short homopolymers were the major contributors to the overall sequencing errors. We also observed systematic biases across all species at the levels of single nucleotides and motifs. In general, cytosine/uracil-rich regions were more likely to be erroneous than guanines and adenines. By examining raw signal data, we identified the underlying signal-level features potentially associated with the error patterns and their dependency on sequence contexts. While read quality scores can be used to approximate error rates at base and read levels, failure to detect DNA adapters may be a source of errors and data loss. By comparing distinct basecallers, we reason that some sequencing errors are attributable to signal insufficiency rather than algorithmic (basecalling) artefacts. Lastly, we generated dRNA-seq data using the latest SQK-RNA004 sequencing kit released at the end of 2023 and found that although the overall read accuracy increased, the systematic errors remain largely identical compared to the previous kits. CONCLUSIONS As the first systematic investigation of dRNA-seq errors, this study offers a comprehensive overview of reproducible error patterns across diverse datasets, identifies potential signal-level insufficiency, and lays the foundation for error correction methods.
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Affiliation(s)
- Wang Liu-Wei
- Systems Medicine of Infectious Disease (P5), Robert Koch Institute, Berlin, Germany.
- International Max-Planck Research School 'Biology and Computation', Max-Planck Institute for Molecular Genetics, Berlin, Germany.
- Department of Mathematics and Computer Science, Freie Universität, Berlin, Germany.
| | - Wiep van der Toorn
- Systems Medicine of Infectious Disease (P5), Robert Koch Institute, Berlin, Germany
- Department of Mathematics and Computer Science, Freie Universität, Berlin, Germany
| | - Patrick Bohn
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Martin Hölzer
- Genome Competence Center (MF1), Robert Koch Institute, Berlin, Germany
| | - Redmond P Smyth
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
- Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Max von Kleist
- Systems Medicine of Infectious Disease (P5), Robert Koch Institute, Berlin, Germany.
- Department of Mathematics and Computer Science, Freie Universität, Berlin, Germany.
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14
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Ma WX, Wang SW, Fan QW, Wang YY, Chu CQ, Liu D, Guo Z, Tang JH, Wen JG. Mild hypothermia reduces lipopolysaccharide-induced microglial activation via down-regulation of Tent5c. Biochem Biophys Res Commun 2024; 706:149767. [PMID: 38484570 DOI: 10.1016/j.bbrc.2024.149767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 03/09/2024] [Indexed: 03/24/2024]
Abstract
Microglial activation is a critical factor in the pathogenesis and progression of neuroinflammatory diseases. Mild hypothermia, known for its neuroprotective properties, has been shown to alleviate microglial activation. In this study, we explore the differentially expressed (DE) mRNAs and long non-coding RNAs (lncRNAs) in BV-2 microglial cells under different conditions: normal temperature (CN), mild hypothermia (YT), normal temperature with lipopolysaccharide (LPS), and mild hypothermia with LPS (LPS + YT). Venn analysis revealed 119 DE mRNAs that were down-regulated in the LPS + YT vs LPS comparison but up-regulated in the CN vs LPS comparison, primarily enriched in Gene Ontology terms related to immune and inflammatory responses. Furthermore, through Venn analysis of YT vs CN and LPS + YT vs LPS comparisons, we identified 178 DE mRNAs and 432 DE lncRNAs. Among these transcripts, we validated the expression of Tent5c at the protein and mRNA levels. Additionally, siRNA-knockdown of Tent5c attenuated the expression of pro-inflammatory genes (TNF-α, IL-1β, Agrn, and Fpr2), cellular morphological changes, NLRP3 and p-P65 protein levels, immunofluorescence staining of p-P65 and number of cells with ASC-speck induced by LPS. Furthermore, Tent5c overexpression further potentiated the aforementioned indicators in the context of mild hypothermia with LPS treatment. Collectively, our findings highlight the significant role of Tent5c down-regulation in mediating the anti-inflammatory effects of mild hypothermia.
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Affiliation(s)
- Wen-Xian Ma
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Shao-Wen Wang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Qian-Wen Fan
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Yue-Yue Wang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Chao-Qun Chu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Dong Liu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Zhen Guo
- Hunan Provincial Key Laboratory of the Fundamental and Clinical Research on Functional Nucleic Acid, Changsha Medical University, Changsha, 410219, China
| | - Ji-Hui Tang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui, 230032, China.
| | - Jia-Gen Wen
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui, 230032, China.
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15
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Lai G, De Grossi F, Catusi I, Pesce E, Manfrini N. Dissecting the Puzzling Roles of FAM46C: A Multifaceted Pan-Cancer Tumour Suppressor with Increasing Clinical Relevance. Cancers (Basel) 2024; 16:1706. [PMID: 38730656 PMCID: PMC11083040 DOI: 10.3390/cancers16091706] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/23/2024] [Accepted: 04/25/2024] [Indexed: 05/13/2024] Open
Abstract
FAM46C is a well-established tumour suppressor with a role that is not completely defined or universally accepted. Although FAM46C expression is down-modulated in several tumours, significant mutations in the FAM46C gene are only found in multiple myeloma (MM). Consequently, its tumour suppressor activity has primarily been studied in the MM context. However, emerging evidence suggests that FAM46C is involved also in other cancer types, namely colorectal, prostate and gastric cancer and squamous cell and hepatocellular carcinoma, where FAM46C expression was found to be significantly reduced in tumoural versus non-tumoural tissues and where FAM46C was shown to possess anti-proliferative properties. Accordingly, FAM46C was recently proposed to function as a pan-cancer prognostic marker, bringing FAM46C under the spotlight and attracting growing interest from the scientific community in the pathways modulated by FAM46C and in its mechanistic activity. Here, we will provide the first comprehensive review regarding FAM46C by covering (1) the intracellular pathways regulated by FAM46C, namely the MAPK/ERK, PI3K/AKT, β-catenin and TGF-β/SMAD pathways; (2) the models regarding its mode of action, specifically the poly(A) polymerase, intracellular trafficking modulator and inhibitor of centriole duplication models, focusing on connections and interdependencies; (3) the regulation of FAM46C expression in different environments by interferons, IL-4, TLR engagement or transcriptional modulators; and, lastly, (4) how FAM46C expression levels associate with increased/decreased tumour cell sensitivity to anticancer agents, such as bortezomib, dexamethasone, lenalidomide, pomalidomide, doxorubicin, melphalan, SK1-I, docetaxel and norcantharidin.
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Affiliation(s)
- Giancarlo Lai
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, 20122 Milan, Italy; (G.L.); (F.D.G.); (E.P.)
- Department of Biosciences, University of Milan, 20133 Milan, Italy
| | - Federica De Grossi
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, 20122 Milan, Italy; (G.L.); (F.D.G.); (E.P.)
- Department of Biosciences, University of Milan, 20133 Milan, Italy
| | - Ilaria Catusi
- SC Clinical Pathology, SS Medical Genetics Laboratory, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy;
| | - Elisa Pesce
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, 20122 Milan, Italy; (G.L.); (F.D.G.); (E.P.)
- Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy
| | - Nicola Manfrini
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, 20122 Milan, Italy; (G.L.); (F.D.G.); (E.P.)
- Department of Biosciences, University of Milan, 20133 Milan, Italy
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16
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Krawczyk PS, Tudek A, Mroczek S, Dziembowski A. Transcriptome-Wide Analysis of mRNA Adenylation Status in Yeast Using Nanopore Sequencing. Methods Mol Biol 2024; 2723:193-214. [PMID: 37824072 DOI: 10.1007/978-1-0716-3481-3_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
There are multiple methods for studying deadenylation, either in vitro or in vivo, which allow for observation of mRNA abundance or poly(A) tail dynamics. However, direct RNA sequencing using the Oxford Nanopore Technologies (ONT) platform makes it possible to conduct transcriptome-wide analyses at the single-molecule level without the PCR bias introduced by other methods. In this chapter, we provide a protocol to measure both RNA levels and poly(A)-tail lengths in the yeast Saccharomyces cerevisiae using ONT.
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Affiliation(s)
- Pawel S Krawczyk
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | | | - Seweryn Mroczek
- International Institute of Molecular and Cell Biology, Warsaw, Poland
- Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Andrzej Dziembowski
- International Institute of Molecular and Cell Biology, Warsaw, Poland.
- Faculty of Biology, University of Warsaw, Warsaw, Poland.
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17
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Giraudo P, Simonnot Q, Pflieger D, Peter J, Gagliardi D, Zuber H. Nano3'RACE: A Method to Analyze Poly(A) Tail Length and Nucleotide Additions at the 3' Extremity of Selected mRNAs Using Nanopore Sequencing. Methods Mol Biol 2024; 2723:233-252. [PMID: 37824074 DOI: 10.1007/978-1-0716-3481-3_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Deadenylation is a major process that regulates gene expression by shaping the length of mRNA poly(A) tails. Deadenylation is controlled by factors in trans that recruit or impede deadenylases, by the incorporation of non-adenosines during poly(A) tail synthesis, and by the posttranscriptional addition of 3' nucleotides to poly(A) tails. Deciphering the regulation of poly(A) tail shortening requires both transcriptome-wide approaches and more targeted methodologies, allowing deep analyses of specific mRNAs. In this chapter, we present Nano3'RACE, a nanopore-based cDNA sequencing method that allows in-depth analysis to precisely measure poly(A) tail length and detect 3' terminal nucleotide addition, such as uridylation, for mRNAs of interest.
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Affiliation(s)
- Pietro Giraudo
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Quentin Simonnot
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - David Pflieger
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Jackson Peter
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Dominique Gagliardi
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Hélène Zuber
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France.
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18
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Liu S, Chen H, Yin Y, Lu D, Gao G, Li J, Bai XC, Zhang X. Inhibition of FAM46/TENT5 activity by BCCIPα adopting a unique fold. SCIENCE ADVANCES 2023; 9:eadf5583. [PMID: 37018411 PMCID: PMC10075960 DOI: 10.1126/sciadv.adf5583] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 03/07/2023] [Indexed: 06/19/2023]
Abstract
The FAM46 (also known as TENT5) proteins are noncanonical poly(A) polymerases (PAPs) implicated in regulating RNA stability. The regulatory mechanisms of FAM46 are poorly understood. Here, we report that the nuclear protein BCCIPα, but not the alternatively spliced isoform BCCIPβ, binds FAM46 and inhibits their PAP activity. Unexpectedly, our structures of the FAM46A/BCCIPα and FAM46C/BCCIPα complexes show that, despite sharing most of the sequence and differing only at the C-terminal portion, BCCIPα adopts a unique structure completely different from BCCIPβ. The distinct C-terminal segment of BCCIPα supports the adoption of the unique fold but does not directly interact with FAM46. The β sheets in BCCIPα and FAM46 pack side by side to form an extended β sheet. A helix-loop-helix segment in BCCIPα inserts into the active site cleft of FAM46, thereby inhibiting the PAP activity. Our results together show that the unique fold of BCCIPα underlies its interaction with and functional regulation of FAM46.
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Affiliation(s)
- Shun Liu
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hua Chen
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yan Yin
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Defen Lu
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Guoming Gao
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jie Li
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiao-Chen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xuewu Zhang
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
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19
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Wei ZY, Wang ZX, Li JH, Wen YS, Gao D, Xia SY, Li YN, Pan XB, Liu YS, Jin YY, Chen JH. Host A-to-I RNA editing signatures in intracellular bacterial and single-strand RNA viral infections. Front Immunol 2023; 14:1121096. [PMID: 37081881 PMCID: PMC10112020 DOI: 10.3389/fimmu.2023.1121096] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 03/13/2023] [Indexed: 04/07/2023] Open
Abstract
BackgroundMicrobial infection is accompanied by remodeling of the host transcriptome. Involvement of A-to-I RNA editing has been reported during viral infection but remains to be elucidated during intracellular bacterial infections.ResultsHerein we analyzed A-to-I RNA editing during intracellular bacterial infections based on 18 RNA-Seq datasets of 210 mouse samples involving 7 tissue types and 8 intracellular bacterial pathogens (IBPs), and identified a consensus signature of RNA editing for IBP infections, mainly involving neutrophil-mediated innate immunity and lipid metabolism. Further comparison of host RNA editing patterns revealed remarkable similarities between pneumonia caused by IBPs and single-strand RNA (ssRNA) viruses, such as altered editing enzyme expression, editing site numbers, and levels. In addition, functional enrichment analysis of genes with RNA editing highlighted that the Rab GTPase family played a common and vital role in the host immune response to IBP and ssRNA viral infections, which was indicated by the consistent up-regulated RNA editing of Ras-related protein Rab27a. Nevertheless, dramatic differences between IBP and viral infections were also observed, and clearly distinguished the two types of intracellular infections.ConclusionOur study showed transcriptome-wide host A-to-I RNA editing alteration during IBP and ssRNA viral infections. By identifying and comparing consensus signatures of host A-to-I RNA editing, our analysis implicates the importance of host A-to-I RNA editing during these infections and provides new insights into the diagnosis and treatment of infectious diseases.
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Affiliation(s)
- Zhi-Yuan Wei
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
| | - Zhi-Xin Wang
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
| | - Jia-Huan Li
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
| | - Yan-Shuo Wen
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
| | - Di Gao
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
| | - Shou-Yue Xia
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
| | - Yu-Ning Li
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
| | - Xu-Bin Pan
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
| | - Yan-Shan Liu
- Department of Pediatric Laboratory, Wuxi Children’s Hospital, Wuxi, Jiangsu, China
| | - Yun-Yun Jin
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
- *Correspondence: Jian-Huan Chen, ; Yun-Yun Jin,
| | - Jian-Huan Chen
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
- *Correspondence: Jian-Huan Chen, ; Yun-Yun Jin,
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20
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Ohguchi Y, Ohguchi H. DIS3: The Enigmatic Gene in Multiple Myeloma. Int J Mol Sci 2023; 24:ijms24044079. [PMID: 36835493 PMCID: PMC9958658 DOI: 10.3390/ijms24044079] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/01/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
Recent studies have revealed the genetic aberrations involved in the initiation and progression of various cancers, including multiple myeloma (MM), via next-generation sequencing analysis. Notably, DIS3 mutations have been identified in approximately 10% of patients with MM. Moreover, deletions of the long arm of chromosome 13, that includes DIS3, are present in approximately 40% of patients with MM. Regardless of the high incidence of DIS3 mutations and deletions, their contribution to the pathogenesis of MM has not yet been determined. Herein, we summarize the molecular and physiological functions of DIS3, focusing on hematopoiesis, and discuss the characteristics and potential roles of DIS3 mutations in MM. Recent findings highlight the essential roles of DIS3 in RNA homeostasis and normal hematopoiesis and suggest that the reduced activity of DIS3 may be involved in myelomagenesis by increasing genome instability.
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Affiliation(s)
- Yasuyo Ohguchi
- Division of Disease Epigenetics, Institute of Resource Development and Analysis, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
| | - Hiroto Ohguchi
- Division of Disease Epigenetics, Institute of Resource Development and Analysis, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
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21
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Brouze A, Krawczyk PS, Dziembowski A, Mroczek S. Measuring the tail: Methods for poly(A) tail profiling. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1737. [PMID: 35617484 PMCID: PMC10078590 DOI: 10.1002/wrna.1737] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/13/2022] [Accepted: 04/15/2022] [Indexed: 01/31/2023]
Abstract
The 3'-end poly(A) tail is an important and potent feature of most mRNA molecules that affects mRNA fate and translation efficiency. Polyadenylation is a posttranscriptional process that occurs in the nucleus by canonical poly(A) polymerases (PAPs). In some specific instances, the poly(A) tail can also be extended in the cytoplasm by noncanonical poly(A) polymerases (ncPAPs). This epitranscriptomic regulation of mRNA recently became one of the most interesting aspects in the field. Advances in RNA sequencing technologies and software development have allowed the precise measurement of poly(A) tails, identification of new ncPAPs, expansion of the function of known enzymes, discovery and a better understanding of the physiological role of tail heterogeneity, and recognition of a correlation between tail length and RNA translatability. Here, we summarize the development of polyadenylation research methods, including classic low-throughput approaches, Illumina-based genome-wide analysis, and advanced state-of-art techniques that utilize long-read third-generation sequencing with Pacific Biosciences and Oxford Nanopore Technologies platforms. A boost in technical opportunities over recent decades has allowed a better understanding of the regulation of gene expression at the mRNA level. This article is categorized under: RNA Methods > RNA Analyses In Vitro and In Silico.
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Affiliation(s)
- Aleksandra Brouze
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Paweł Szczepan Krawczyk
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Andrzej Dziembowski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland.,Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland.,Department of Embryology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Seweryn Mroczek
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland.,Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
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22
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Liudkovska V, Krawczyk PS, Brouze A, Gumińska N, Wegierski T, Cysewski D, Mackiewicz Z, Ewbank JJ, Drabikowski K, Mroczek S, Dziembowski A. TENT5 cytoplasmic noncanonical poly(A) polymerases regulate the innate immune response in animals. SCIENCE ADVANCES 2022; 8:eadd9468. [PMID: 36383655 PMCID: PMC9668313 DOI: 10.1126/sciadv.add9468] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Innate immunity is the first line of host defense against pathogens. Here, through global transcriptome and proteome analyses, we uncover that newly described cytoplasmic poly(A) polymerase TENT-5 (terminal nucleotidyltransferase 5) enhances the expression of secreted innate immunity effector proteins in Caenorhabditis elegans. Direct RNA sequencing revealed that multiple mRNAs with signal peptide-encoding sequences have shorter poly(A) tails in tent-5-deficient worms. Those mRNAs are translated at the endoplasmic reticulum where a fraction of TENT-5 is present, implying that they represent its direct substrates. Loss of tent-5 makes worms more susceptible to bacterial infection. Notably, the role of TENT-5 in innate immunity is evolutionarily conserved. Its orthologs, TENT5A and TENT5C, are expressed in macrophages and induced during their activation. Analysis of macrophages devoid of TENT5A/C revealed their role in the regulation of secreted proteins involved in defense response. In summary, our study reveals cytoplasmic polyadenylation to be a previously unknown component of the posttranscriptional regulation of innate immunity in animals.
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Affiliation(s)
- Vladyslava Liudkovska
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
- Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Paweł S Krawczyk
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Aleksandra Brouze
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
- Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Natalia Gumińska
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Tomasz Wegierski
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Dominik Cysewski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Zuzanna Mackiewicz
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Jonathan J Ewbank
- Aix Marseille University, INSERM, CNRS, CIML, Turing Centre for Living Systems, Marseille, France
| | - Krzysztof Drabikowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Seweryn Mroczek
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
- Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Andrzej Dziembowski
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
- Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
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23
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Nowacka M, Latoch P, Izert MA, Karolak NK, Tomecki R, Koper M, Tudek A, Starosta AL, Górna M. A cap 0-dependent mRNA capture method to analyze the yeast transcriptome. Nucleic Acids Res 2022; 50:e132. [PMID: 36259646 PMCID: PMC9825183 DOI: 10.1093/nar/gkac903] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/13/2022] [Accepted: 10/17/2022] [Indexed: 01/29/2023] Open
Abstract
Analysis of the protein coding transcriptome by the RNA sequencing requires either enrichment of the desired fraction of coding transcripts or depletion of the abundant non-coding fraction consisting mainly of rRNA. We propose an alternative mRNA enrichment strategy based on the RNA-binding properties of the human IFIT1, an antiviral protein recognizing cap 0 RNA. Here, we compare for Saccharomyces cerevisiae an IFIT1-based mRNA pull-down with yeast targeted rRNA depletion by the RiboMinus method. IFIT1-based RNA capture depletes rRNA more effectively, producing high quality RNA-seq data with an excellent coverage of the protein coding transcriptome, while depleting cap-less transcripts such as mitochondrial or some non-coding RNAs. We propose IFIT1 as a cost effective and versatile tool to prepare mRNA libraries for a variety of organisms with cap 0 mRNA ends, including diverse plants, fungi and eukaryotic microbes.
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Affiliation(s)
| | | | - Matylda A Izert
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Warsaw 02-093, Poland
| | - Natalia K Karolak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Warsaw 02-093, Poland,Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Warsaw 02-093, Poland
| | - Rafal Tomecki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Warsaw 02-106, Poland,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Warsaw 02-106, Poland
| | - Michał Koper
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Warsaw 02-106, Poland
| | - Agnieszka Tudek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Warsaw 02-106, Poland
| | - Agata L Starosta
- Correspondence may also be addressed to Agata L. Starosta. Tel: +48 22 592 33 41;
| | - Maria W Górna
- To whom correspondence should be addressed. Tel: +48 22 55 26 685;
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24
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Guegan F, Rajan KS, Bento F, Pinto-Neves D, Sequeira M, Gumińska N, Mroczek S, Dziembowski A, Cohen-Chalamish S, Doniger T, Galili B, Estévez AM, Notredame C, Michaeli S, Figueiredo LM. A long noncoding RNA promotes parasite differentiation in African trypanosomes. SCIENCE ADVANCES 2022; 8:eabn2706. [PMID: 35704590 PMCID: PMC9200285 DOI: 10.1126/sciadv.abn2706] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The parasite Trypanosoma brucei causes African sleeping sickness that is fatal to patients if untreated. Parasite differentiation from a replicative slender form into a quiescent stumpy form promotes host survival and parasite transmission. Long noncoding RNAs (lncRNAs) are known to regulate cell differentiation in other eukaryotes. To determine whether lncRNAs are also involved in parasite differentiation, we used RNA sequencing to survey the T. brucei genome, identifying 1428 previously uncharacterized lncRNA genes. We find that grumpy lncRNA is a key regulator that promotes parasite differentiation into the quiescent stumpy form. This function is promoted by a small nucleolar RNA encoded within the grumpy lncRNA. snoGRUMPY binds to messenger RNAs of at least two stumpy regulatory genes, promoting their expression. grumpy overexpression reduces parasitemia in infected mice. Our analyses suggest that T. brucei lncRNAs modulate parasite-host interactions and provide a mechanism by which grumpy regulates cell differentiation in trypanosomes.
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Affiliation(s)
- Fabien Guegan
- Instituto de Medicina Molecular–Joao Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Corresponding author. (F.G.); (L.M.F.)
| | - K. Shanmugha Rajan
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Fábio Bento
- Instituto de Medicina Molecular–Joao Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Daniel Pinto-Neves
- Instituto de Medicina Molecular–Joao Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Mariana Sequeira
- Instituto de Medicina Molecular–Joao Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Natalia Gumińska
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Seweryn Mroczek
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Andrzej Dziembowski
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Smadar Cohen-Chalamish
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Tirza Doniger
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Beathrice Galili
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Antonio M. Estévez
- Instituto de Parasitologia y Biomedicina ‘Lopez-Neyra,’ IPBLN-CSIC, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 17, 18016 Armilla, Granada, Spain
| | - Cedric Notredame
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Shulamit Michaeli
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Luisa M. Figueiredo
- Instituto de Medicina Molecular–Joao Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Corresponding author. (F.G.); (L.M.F.)
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25
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Vo DHT, McGleave G, Overton IM. Immune Cell Networks Uncover Candidate Biomarkers of Melanoma Immunotherapy Response. J Pers Med 2022; 12:jpm12060958. [PMID: 35743743 PMCID: PMC9225330 DOI: 10.3390/jpm12060958] [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: 04/04/2022] [Revised: 06/05/2022] [Accepted: 06/08/2022] [Indexed: 11/30/2022] Open
Abstract
The therapeutic activation of antitumour immunity by immune checkpoint inhibitors (ICIs) is a significant advance in cancer medicine, not least due to the prospect of long-term remission. However, many patients are unresponsive to ICI therapy and may experience serious side effects; companion biomarkers are urgently needed to help inform ICI prescribing decisions. We present the IMMUNETS networks of gene coregulation in five key immune cell types and their application to interrogate control of nivolumab response in advanced melanoma cohorts. The results evidence a role for each of the IMMUNETS cell types in ICI response and in driving tumour clearance with independent cohorts from TCGA. As expected, ‘immune hot’ status, including T cell proliferation, correlates with response to first-line ICI therapy. Genes regulated in NK, dendritic, and B cells are the most prominent discriminators of nivolumab response in patients that had previously progressed on another ICI. Multivariate analysis controlling for tumour stage and age highlights CIITA and IKZF3 as candidate prognostic biomarkers. IMMUNETS provide a resource for network biology, enabling context-specific analysis of immune components in orthogonal datasets. Overall, our results illuminate the relationship between the tumour microenvironment and clinical trajectories, with potential implications for precision medicine.
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Affiliation(s)
- Duong H. T. Vo
- The Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7AE, UK; (D.H.T.V.); (G.M.)
- Health Data Research Wales and Northern Ireland, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7AE, UK
| | - Gerard McGleave
- The Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7AE, UK; (D.H.T.V.); (G.M.)
- Health Data Research Wales and Northern Ireland, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7AE, UK
| | - Ian M. Overton
- The Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7AE, UK; (D.H.T.V.); (G.M.)
- Health Data Research Wales and Northern Ireland, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7AE, UK
- Correspondence:
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26
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Shin J, Paek KY, Chikhaoui L, Jung S, Ponny S, Suzuki Y, Padmanabhan K, Richter JD. Oppositional poly(A) tail length regulation by FMRP and CPEB1. RNA (NEW YORK, N.Y.) 2022; 28:756-765. [PMID: 35217597 PMCID: PMC9014880 DOI: 10.1261/rna.079050.121] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 02/09/2022] [Indexed: 05/03/2023]
Abstract
Poly(A) tail length is regulated in both the nucleus and cytoplasm. One factor that controls polyadenylation in the cytoplasm is CPEB1, an RNA binding protein that associates with specific mRNA 3'UTR sequences to tether enzymes that add and remove poly(A). Two of these enzymes, the noncanonical poly(A) polymerases GLD2 (TENT2, PAPD4, Wispy) and GLD4 (TENT4B, PAPD5, TRF4, TUT3), interact with CPEB1 to extend poly(A). To identify additional RNA binding proteins that might anchor GLD4 to RNA, we expressed double tagged GLD4 in U87MG cells, which was used for sequential immunoprecipitation and elution followed by mass spectrometry. We identified several RNA binding proteins that coprecipitated with GLD4, among which was FMRP. To assess whether FMRP regulates polyadenylation, we performed TAIL-seq from WT and FMRP-deficient HEK293 cells. Surprisingly, loss of FMRP resulted in an overall increase in poly(A), which was also observed for several specific mRNAs. Conversely, loss of CPEB1 elicited an expected decrease in poly(A), which was examined in cultured neurons. We also examined polyadenylation in wild type (WT) and FMRP-deficient mouse brain cortex by direct RNA nanopore sequencing, which identified RNAs with both increased and decreased poly(A). Our data show that FMRP has a role in mediating poly(A) tail length, which adds to its repertoire of RNA regulation.
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Affiliation(s)
- Jihae Shin
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Ki Young Paek
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Lies Chikhaoui
- Institut de Genomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, F-69364 Lyon, France
| | - Suna Jung
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - SitharaRaju Ponny
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Yutaka Suzuki
- University of Tokyo, Kashiwa II campus, Kashiwa-Shi 2770882, Japan
| | - Kiran Padmanabhan
- Institut de Genomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, F-69364 Lyon, France
| | - Joel D Richter
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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27
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Turner DJ, Saveliev A, Salerno F, Matheson LS, Screen M, Lawson H, Wotherspoon D, Kranc KR, Turner M. A functional screen of RNA binding proteins identifies genes that promote or limit the accumulation of CD138+ plasma cells. eLife 2022; 11:e72313. [PMID: 35451955 PMCID: PMC9106329 DOI: 10.7554/elife.72313] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 04/21/2022] [Indexed: 12/02/2022] Open
Abstract
To identify roles of RNA binding proteins (RBPs) in the differentiation or survival of antibody secreting plasma cells we performed a CRISPR/Cas9 knockout screen of 1213 mouse RBPs for their ability to affect proliferation and/or survival, and the abundance of differentiated CD138 + cells in vitro. We validated the binding partners CSDE1 and STRAP as well as the m6A binding protein YTHDF2 as promoting the accumulation of CD138 + cells in vitro. We validated the EIF3 subunits EIF3K and EIF3L and components of the CCR4-NOT complex as inhibitors of CD138 + cell accumulation in vitro. In chimeric mouse models YTHDF2-deficient plasma cells failed to accumulate.
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Affiliation(s)
- David J Turner
- Immunology Programme, The Babraham Institute,Babraham Research CampusCambridgeUnited Kingdom
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute (NCI)FrederickUnited States
| | - Alexander Saveliev
- Immunology Programme, The Babraham Institute,Babraham Research CampusCambridgeUnited Kingdom
| | - Fiamma Salerno
- Immunology Programme, The Babraham Institute,Babraham Research CampusCambridgeUnited Kingdom
| | - Louise S Matheson
- Immunology Programme, The Babraham Institute,Babraham Research CampusCambridgeUnited Kingdom
| | - Michael Screen
- Immunology Programme, The Babraham Institute,Babraham Research CampusCambridgeUnited Kingdom
| | - Hannah Lawson
- Laboratory of Haematopoietic Stem Cell and Leukaemia Biology, Queen Mary University of LondonLondonUnited Kingdom
| | - David Wotherspoon
- Laboratory of Haematopoietic Stem Cell and Leukaemia Biology, Queen Mary University of LondonLondonUnited Kingdom
| | - Kamil R Kranc
- Laboratory of Haematopoietic Stem Cell and Leukaemia Biology, Queen Mary University of LondonLondonUnited Kingdom
| | - Martin Turner
- Immunology Programme, The Babraham Institute,Babraham Research CampusCambridgeUnited Kingdom
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28
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Gleeson J, Leger A, Prawer YDJ, Lane TA, Harrison PJ, Haerty W, Clark MB. Accurate expression quantification from nanopore direct RNA sequencing with NanoCount. Nucleic Acids Res 2022; 50:e19. [PMID: 34850115 PMCID: PMC8886870 DOI: 10.1093/nar/gkab1129] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 10/23/2021] [Accepted: 10/27/2021] [Indexed: 11/13/2022] Open
Abstract
Accurately quantifying gene and isoform expression changes is essential to understanding cell functions, differentiation and disease. Sequencing full-length native RNAs using long-read direct RNA sequencing (DRS) has the potential to overcome many limitations of short and long-read sequencing methods that require RNA fragmentation, cDNA synthesis or PCR. However, there are a lack of tools specifically designed for DRS and its ability to identify differential expression in complex organisms is poorly characterised. We developed NanoCount for fast, accurate transcript isoform quantification in DRS and demonstrate it outperforms similar methods. Using synthetic controls and human SH-SY5Y cell differentiation into neuron-like cells, we show that DRS accurately quantifies RNA expression and identifies differential expression of genes and isoforms. Differential expression of 231 genes, 333 isoforms, plus 27 isoform switches were detected between undifferentiated and differentiated SH-SY5Y cells and samples clustered by differentiation state at the gene and isoform level. Genes upregulated in neuron-like cells were associated with neurogenesis. NanoCount quantification of thousands of novel isoforms discovered with DRS likewise enabled identification of their differential expression. Our results demonstrate enhanced DRS isoform quantification with NanoCount and establish the ability of DRS to identify biologically relevant differential expression of genes and isoforms.
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Affiliation(s)
- Josie Gleeson
- Centre for Stem Cell Systems, Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, Australia
| | - Adrien Leger
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Yair D J Prawer
- Centre for Stem Cell Systems, Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, Australia
| | - Tracy A Lane
- Department of Psychiatry, University of Oxford, Oxford, UK
| | - Paul J Harrison
- Department of Psychiatry, University of Oxford, Oxford, UK
- Oxford Health NHS Foundation Trust, Oxford, UK
| | - Wilfried Haerty
- The Earlham Institute, Norwich, UK
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Michael B Clark
- Centre for Stem Cell Systems, Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, Australia
- Department of Psychiatry, University of Oxford, Oxford, UK
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Beyond sequencing: machine learning algorithms extract biology hidden in Nanopore signal data. Trends Genet 2021; 38:246-257. [PMID: 34711425 DOI: 10.1016/j.tig.2021.09.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/01/2021] [Accepted: 09/01/2021] [Indexed: 11/24/2022]
Abstract
Nanopore sequencing provides signal data corresponding to the nucleotide motifs sequenced. Through machine learning-based methods, these signals are translated into long-read sequences that overcome the read size limit of short-read sequencing. However, analyzing the raw nanopore signal data provides many more opportunities beyond just sequencing genomes and transcriptomes: algorithms that use machine learning approaches to extract biological information from these signals allow the detection of DNA and RNA modifications, the estimation of poly(A) tail length, and the prediction of RNA secondary structures. In this review, we discuss how developments in machine learning methodologies contributed to more accurate basecalling and lower error rates, and how these methods enable new biological discoveries. We argue that direct nanopore sequencing of DNA and RNA provides a new dimensionality for genomics experiments and highlight challenges and future directions for computational approaches to extract the additional information provided by nanopore signal data.
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30
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Global view on the metabolism of RNA poly(A) tails in yeast Saccharomyces cerevisiae. Nat Commun 2021; 12:4951. [PMID: 34400637 PMCID: PMC8367983 DOI: 10.1038/s41467-021-25251-w] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 07/29/2021] [Indexed: 02/06/2023] Open
Abstract
The polyadenosine tail (poly[A]-tail) is a universal modification of eukaryotic messenger RNAs (mRNAs) and non-coding RNAs (ncRNAs). In budding yeast, Pap1-synthesized mRNA poly(A) tails enhance export and translation, whereas Trf4/5-mediated polyadenylation of ncRNAs facilitates degradation by the exosome. Using direct RNA sequencing, we decipher the extent of poly(A) tail dynamics in yeast defective in all relevant exonucleases, deadenylases, and poly(A) polymerases. Predominantly ncRNA poly(A) tails are 20-60 adenosines long. Poly(A) tails of newly transcribed mRNAs are 50 adenosine long on average, with an upper limit of 200. Exonucleolysis by Trf5-assisted nuclear exosome and cytoplasmic deadenylases trim the tails to 40 adenosines on average. Surprisingly, PAN2/3 and CCR4-NOT deadenylase complexes have a large pool of non-overlapping substrates mainly defined by expression level. Finally, we demonstrate that mRNA poly(A) tail length strongly responds to growth conditions, such as heat and nutrient deprivation.
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Perini T, Materozzi M, Milan E. The Immunity-malignancy equilibrium in multiple myeloma: lessons from oncogenic events in plasma cells. FEBS J 2021; 289:4383-4397. [PMID: 34117720 DOI: 10.1111/febs.16068] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/13/2021] [Accepted: 06/10/2021] [Indexed: 11/29/2022]
Abstract
Multiple myeloma (MM) is a malignancy of plasma cells (PC) that grow within the bone marrow and maintain massive immunoglobulin (Ig) production. Disease evolution is driven by genetic lesions, whose effects on cell biology and fitness underlie addictions and vulnerabilities of myeloma cells. Several genes mutated in myeloma are strictly involved in dictating PC identity and antibody factory function. Here, we evaluate the impact of mutations in IRF4, PRDM1, and XBP1, essential transcription factors driving the B to PC differentiation, on MM cell biology and homeostasis. These factors are highly specialized, with limited overlap in their downstream transcriptional programs. Indeed, IRF4 sustains metabolism, survival, and proliferation, while PRDM1 and XBP1 are mainly responsible for endoplasmic reticulum expansion and sustained Ig secretion. Interestingly, IRF4 undergoes activating mutations and translocations, while PRDM1 and XBP1 are hit by loss-of-function events, raising the hypothesis that containment of the secretory program, but not its complete extinction, may be beneficial to malignant PCs. Finally, recent studies unveiled that also the PRDM1 target, FAM46C/TENT5C, an onco-suppressor uniquely and frequently mutated or deleted in myeloma, is directly and potently involved in orchestrating ER homeostasis and secretory activity. Inactivating mutations found in this gene and its interactors strengthen the notion that reduced secretory capacity confers advantage to myeloma cells. We believe that dissection of the evolutionary pressure on genes driving PC-specific functions in myeloma will disclose the cellular strategies by which myeloma cells maintain an equilibrium between antibody production and survival, thus unveiling novel therapeutic targets.
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Affiliation(s)
- Tommaso Perini
- Age related Diseases Unit, Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milano, Italy.,University Vita-Salute San Raffaele, Milano, Italy.,Hematology and Bone Marrow Transplantation Unit, San Raffaele Scientific Institute, Milano, Italy
| | - Maria Materozzi
- Age related Diseases Unit, Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milano, Italy.,Department of Medicine, Surgery and Neurosciences, University of Siena, Italy
| | - Enrico Milan
- Age related Diseases Unit, Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milano, Italy.,University Vita-Salute San Raffaele, Milano, Italy
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Zhang H, Zhang SH, Hu JL, Wu YT, Ma XY, Chen Y, Yu B, Liao S, Huang H, Gao S. Structural and functional characterization of multiple myeloma associated cytoplasmic poly(A) polymerase FAM46C. Cancer Commun (Lond) 2021; 41:615-630. [PMID: 34048638 PMCID: PMC8286142 DOI: 10.1002/cac2.12163] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 03/28/2021] [Accepted: 04/29/2021] [Indexed: 12/11/2022] Open
Abstract
Background Multiple myeloma (MM) is a hematologic malignancy characterized by the accumulation of aberrant plasma cells within the bone marrow. The high frequent mutation of family with sequence similarity 46, member C (FAM46C) is closely related with the occurrence and progression of MM. Recently, FAM46C has been identified as a non‐canonical poly(A) polymerase (PAP) that functions as a tumor suppressor in MM. This study aimed to elucidate the structural features of this novel non‐canonical PAP and how MM‐related mutations affect the structural and biochemical properties of FAM46C, eventually advancing our understandings towards FAM46C mutation‐related MM occurrence. Methods We purified and crystallized a mammalian FAM46C construct, and solved its structure. Next, we characterized the property of FAM46C as a PAP through a combination of structural analysis, site‐directed mutagenesis and biochemical assays, and by comparison with its homolog FAM46B. Finally, we structurally analyzed MM‐related FAM46C mutations and tested the enzymatic activity of corresponding mutants. Results We determined the crystal structure of a mammalian FAM46C protein at 2.35 Å, and confirmed that FAM46C preferentially consumed adenosine triphosphate (ATP) and extended A‐rich RNA substrates. FAM46C showed a weaker PAP activity than its homolog FAM46B, and this difference was largely dependent on the residue variance at particular sites. Of them, residues at positions 77, 290, and 298 of mouse FAM46C were most important for the divergence in enzymatic activity. Among the MM‐associated FAM46C mutants, those residing at the catalytic site (D90G and D90H) or putative RNA‐binding site (I155L, S156F, D182Y, F184L, Y247V, and M270V) showed abolished or compromised PAP activity of FAM46C, while N72A and S248A did not severely affect the PAP activity. FAM46C mutants D90G, D90H, I155L, S156F, F184L, Y247V, and M270V had significantly lower inhibitory effect on apoptosis of RPMI‐8226 cells as compared to wild‐type FAM46C. Conclusions FAM46C is a prokaryotic‐like PAP with preference for A‐rich RNA substrates, and showed distinct enzymatic efficiency with its homolog FAM46B. The MM‐related missense mutations of FAM46C lead to various structural and biochemical outcomes to the protein.
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Affiliation(s)
- Hong Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China
| | - Shi-Hui Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China
| | - Jia-Li Hu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China.,Department of Oncology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, P. R. China
| | - Yu-Tong Wu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China
| | - Xiao-Yan Ma
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China
| | - Yang Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China
| | - Bing Yu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China
| | - Shuang Liao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China
| | - Huilin Huang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China
| | - Song Gao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, Guangdong, 510530, P. R. China
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The Interaction of the Tumor Suppressor FAM46C with p62 and FNDC3 Proteins Integrates Protein and Secretory Homeostasis. Cell Rep 2021; 32:108162. [PMID: 32966780 DOI: 10.1016/j.celrep.2020.108162] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 06/23/2020] [Accepted: 08/26/2020] [Indexed: 02/06/2023] Open
Abstract
FAM46C is a non-canonical poly(A) polymerase uniquely mutated in up to 20% of multiple myeloma (MM) patients, implying a tissue-specific tumor suppressor function. Here, we report that FAM46C selectively stabilizes mRNAs encoding endoplasmic reticulum (ER)-targeted proteins, thereby concertedly enhancing the expression of proteins that control ER protein import, folding, N-glycosylation, and trafficking and boosting protein secretion. This role requires the interaction with the ER membrane resident proteins FNDC3A and FNDC3B. In MM cells, FAM46C expression raises secretory capacity beyond sustainability, inducing ROS accumulation, ATP shortage, and cell death. FAM46C activity is regulated through rapid proteasomal degradation or the inhibitory interaction with the ZZ domain of the autophagic receptor p62 that hinders its association with FNDC3 proteins via sequestration in p62+ aggregates. Altogether, our data disclose a p62/FAM46C/FNDC3 circuit coordinating sustainable secretory activity and survival, providing an explanation for the MM-specific oncosuppressive role of FAM46C and uncovering potential therapeutic opportunities against cancer.
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Gewartowska O, Aranaz-Novaliches G, Krawczyk PS, Mroczek S, Kusio-Kobiałka M, Tarkowski B, Spoutil F, Benada O, Kofroňová O, Szwedziak P, Cysewski D, Gruchota J, Szpila M, Chlebowski A, Sedlacek R, Prochazka J, Dziembowski A. Cytoplasmic polyadenylation by TENT5A is required for proper bone formation. Cell Rep 2021; 35:109015. [PMID: 33882302 DOI: 10.1016/j.celrep.2021.109015] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 02/23/2021] [Accepted: 03/26/2021] [Indexed: 12/14/2022] Open
Abstract
Osteoblasts orchestrate bone formation through the secretion of type I collagen and other constituents of the matrix on which hydroxyapatite crystals mineralize. Here, we show that TENT5A, whose mutations were found in congenital bone disease osteogenesis imperfecta patients, is a cytoplasmic poly(A) polymerase playing a crucial role in regulating bone mineralization. Direct RNA sequencing revealed that TENT5A is induced during osteoblast differentiation and polyadenylates mRNAs encoding Col1α1, Col1α2, and other secreted proteins involved in osteogenesis, increasing their expression. We postulate that TENT5A, possibly together with its paralog TENT5C, is responsible for the wave of cytoplasmic polyadenylation of mRNAs encoding secreted proteins occurring during bone mineralization. Importantly, the Tent5a knockout (KO) mouse line displays bone fragility and skeletal hypomineralization phenotype resulting from quantitative and qualitative collagen defects. Thus, we report a biologically relevant posttranscriptional regulator of collagen production and, more generally, bone formation.
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Affiliation(s)
- Olga Gewartowska
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, 02-109 Warsaw, Poland; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Goretti Aranaz-Novaliches
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., 142 20 Prague 4, Czech Republic
| | - Paweł S Krawczyk
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, 02-109 Warsaw, Poland; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Seweryn Mroczek
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, 02-109 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Monika Kusio-Kobiałka
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, 02-109 Warsaw, Poland; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Bartosz Tarkowski
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, 02-109 Warsaw, Poland; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Frantisek Spoutil
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., 142 20 Prague 4, Czech Republic; Czech Centre for Phenogenomics, Institute of Molecular Genetics of the CAS, Prague, Czech Republic
| | - Oldrich Benada
- Institute of Microbiology of the Czech Academy of Sciences, v.v.i., 142 20 Prague 4, Czech Republic
| | - Olga Kofroňová
- Institute of Microbiology of the Czech Academy of Sciences, v.v.i., 142 20 Prague 4, Czech Republic
| | - Piotr Szwedziak
- Laboratory of Structural Cell Biology, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland; ReMedy-International Research Agenda Unit, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Dominik Cysewski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Jakub Gruchota
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, 02-109 Warsaw, Poland; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Marcin Szpila
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, 02-109 Warsaw, Poland; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Aleksander Chlebowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Radislav Sedlacek
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., 142 20 Prague 4, Czech Republic; Czech Centre for Phenogenomics, Institute of Molecular Genetics of the CAS, Prague, Czech Republic
| | - Jan Prochazka
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., 142 20 Prague 4, Czech Republic; Czech Centre for Phenogenomics, Institute of Molecular Genetics of the CAS, Prague, Czech Republic
| | - Andrzej Dziembowski
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, 02-109 Warsaw, Poland; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland.
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Scheer H, de Almeida C, Ferrier E, Simonnot Q, Poirier L, Pflieger D, Sement FM, Koechler S, Piermaria C, Krawczyk P, Mroczek S, Chicher J, Kuhn L, Dziembowski A, Hammann P, Zuber H, Gagliardi D. The TUTase URT1 connects decapping activators and prevents the accumulation of excessively deadenylated mRNAs to avoid siRNA biogenesis. Nat Commun 2021; 12:1298. [PMID: 33637717 PMCID: PMC7910438 DOI: 10.1038/s41467-021-21382-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 01/19/2021] [Indexed: 12/15/2022] Open
Abstract
Uridylation is a widespread modification destabilizing eukaryotic mRNAs. Yet, molecular mechanisms underlying TUTase-mediated mRNA degradation remain mostly unresolved. Here, we report that the Arabidopsis TUTase URT1 participates in a molecular network connecting several translational repressors/decapping activators. URT1 directly interacts with DECAPPING 5 (DCP5), the Arabidopsis ortholog of human LSM14 and yeast Scd6, and this interaction connects URT1 to additional decay factors like DDX6/Dhh1-like RNA helicases. Nanopore direct RNA sequencing reveals a global role of URT1 in shaping poly(A) tail length, notably by preventing the accumulation of excessively deadenylated mRNAs. Based on in vitro and in planta data, we propose a model that explains how URT1 could reduce the accumulation of oligo(A)-tailed mRNAs both by favoring their degradation and because 3' terminal uridines intrinsically hinder deadenylation. Importantly, preventing the accumulation of excessively deadenylated mRNAs avoids the biogenesis of illegitimate siRNAs that silence endogenous mRNAs and perturb Arabidopsis growth and development.
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Affiliation(s)
- Hélène Scheer
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Caroline de Almeida
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Emilie Ferrier
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Quentin Simonnot
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Laure Poirier
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - David Pflieger
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - François M Sement
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Sandrine Koechler
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Christina Piermaria
- Plateforme Protéomique Strasbourg Esplanade du CNRS, Université de Strasbourg, Strasbourg, France
| | - Paweł Krawczyk
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
| | - Seweryn Mroczek
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
| | - Johana Chicher
- Plateforme Protéomique Strasbourg Esplanade du CNRS, Université de Strasbourg, Strasbourg, France
| | - Lauriane Kuhn
- Plateforme Protéomique Strasbourg Esplanade du CNRS, Université de Strasbourg, Strasbourg, France
| | - Andrzej Dziembowski
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
| | - Philippe Hammann
- Plateforme Protéomique Strasbourg Esplanade du CNRS, Université de Strasbourg, Strasbourg, France
| | - Hélène Zuber
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France.
| | - Dominique Gagliardi
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France.
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Liu Q, Wang Y, Liu Y, Wang H, Li W, Tang P, Weng T, Zhou S, Liang L, Yuan J, Wang D, Wang L. Reduction chemistry-assisted nanopore determination method for immunoglobulin isotypes. NANOSCALE 2020; 12:19711-19718. [PMID: 32966507 DOI: 10.1039/d0nr04900j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Immunoglobulins can bind to an unlimited array of foreign antigens presented to the immune system. Among those isotypes, IgG and IgM play crucial roles in initial immune defense associated with innate immunity factors. Hence, the determination of IgG and IgM deficiencies or varying concentrations is widely used as a diagnostic indicator for immune deficiency disorders. Herein, we report a reduction chemistry-assisted nanopore method for IgG and IgM determination. TCEP (tris(2-carboxyethyl)phosphine) was used to cleave Ig proteins in fragments by means of disulfide bond reduction under different experimental conditions. This strategy enabled the observation of distinguishable current signals afforded by separated polypeptide fragments in an αHL nanopore. Together with molecular dynamics (MD) simulation results, highly effective electrostatic potentials and H-bonds, the dominant factors for these current signals, facilitated the capture of Ig fragments in an α-HL nanopore. More importantly, the signature signals were applicable for differentiating between IgG and IgM in blood serum without any problems of protein adsorption and clogging in the nanopore sensing. Furthermore, with comparative sensing sensitivity and selectivity, it is concluded that our method is a label-free single-molecule approach to measuring disease states that present as a result of the absence or over presence of immunoglobulin isotypes.
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Affiliation(s)
- Qianshan Liu
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China. and Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Yunjiao Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China. and Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Yaqing Liu
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China.
| | - Han Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China. and Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Wei Li
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China. and Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Peng Tang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China.
| | - Ting Weng
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China.
| | - Shuo Zhou
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China.
| | - Liyuan Liang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China. and Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Jiahu Yuan
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China. and Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Deqiang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China. and Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Liang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China. and Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
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Manfrini N, Mancino M, Miluzio A, Oliveto S, Balestra M, Calamita P, Alfieri R, Rossi RL, Sassoè-Pognetto M, Salio C, Cuomo A, Bonaldi T, Manfredi M, Marengo E, Ranzato E, Martinotti S, Cittaro D, Tonon G, Biffo S. FAM46C and FNDC3A Are Multiple Myeloma Tumor Suppressors That Act in Concert to Impair Clearing of Protein Aggregates and Autophagy. Cancer Res 2020; 80:4693-4706. [PMID: 32963011 DOI: 10.1158/0008-5472.can-20-1357] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 07/15/2020] [Accepted: 09/18/2020] [Indexed: 11/16/2022]
Abstract
Multiple myeloma is a plasma cell neoplasm characterized by the production of unfolded immunoglobulins, which cause endoplasmic reticulum (ER) stress and sensitivity to proteasome inhibition. The genomic landscape of multiple myeloma is characterized by the loss of several genes rarely mutated in other cancers that may underline specific weaknesses of multiple myeloma cells. One of these is FAM46C that is lost in more than 10% of patients with multiple myeloma. We show here that FAM46C is part of a new complex containing the ER-associated protein FNDC3A, which regulates trafficking and secretion and, by impairing autophagy, exacerbates proteostatic stress. Reconstitution of FAM46C in multiple myeloma cells that had lost it induced apoptosis and ER stress. Apoptosis was preceded by an increase of intracellular aggregates, which was not linked to increased translation of IgG mRNA, but rather to impairment of autophagy. Biochemical analysis showed that FAM46C requires interaction with ER bound protein FNDC3A to reside in the cytoplasmic side of the ER. FNDC3A was lost in some multiple myeloma cell lines. Importantly, depletion of FNDC3A increased the fitness of FAM46C-expressing cells and expression of FNDC3A in cells that had lost it recapitulated the effects of FAM46C, inducing aggregates and apoptosis. FAM46C and FNDC3A formed a complex that modulates secretion routes, increasing lysosome exocytosis. The cellular landscape generated by FAM46C/FNDC3A expression predicted sensitivity to sphingosine kinase inhibition. These results suggest that multiple myeloma cells remodel their trafficking machinery to cope with ER stress. SIGNIFICANCE: This study identifies a new multiple myeloma-specific tumor suppressor complex that regulates autophagy and unconventional secretion, highlighting the sensitivity of multiple myeloma cells to the accumulation of protein aggregates.
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Affiliation(s)
- Nicola Manfrini
- INGM, National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi," Milan, Italy.,Department of Biological Sciences, University of Milan, Milan, Italy
| | - Marilena Mancino
- INGM, National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi," Milan, Italy.,Department of Clinical Sciences and Community, University of Milan, Milan, Italy
| | - Annarita Miluzio
- INGM, National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi," Milan, Italy
| | - Stefania Oliveto
- INGM, National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi," Milan, Italy.,Department of Biological Sciences, University of Milan, Milan, Italy
| | - Matteo Balestra
- INGM, National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi," Milan, Italy
| | - Piera Calamita
- INGM, National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi," Milan, Italy.,Department of Biological Sciences, University of Milan, Milan, Italy
| | - Roberta Alfieri
- INGM, National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi," Milan, Italy
| | - Riccardo L Rossi
- INGM, National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi," Milan, Italy
| | - Marco Sassoè-Pognetto
- Department of Neuroscience "Rita Levi Montalcini," University of Turin, Torino, Italy
| | - Chiara Salio
- Department of Veterinary Sciences, University of Turin, Grugliasco, Torino, Italy
| | - Alessandro Cuomo
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Marcello Manfredi
- Center for Translational Research on Autoimmune and Allergic Diseases, University of Piemonte Orientale, Novara, Italy.,ISALIT, Novara, Italy.,Department of Translation Medicine, University of Piemonte Orientale, Novara, Italy
| | - Emilio Marengo
- Center for Translational Research on Autoimmune and Allergic Diseases, University of Piemonte Orientale, Novara, Italy.,ISALIT, Novara, Italy.,Department of Sciences and Technological Innovation, University of Piemonte Orientale, Alessandria, Italy
| | - Elia Ranzato
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Alessandria, Italy
| | - Simona Martinotti
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Alessandria, Italy
| | - Davide Cittaro
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giovanni Tonon
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy.,Functional Genomics of Cancer Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Stefano Biffo
- INGM, National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi," Milan, Italy. .,Department of Biological Sciences, University of Milan, Milan, Italy
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Liudkovska V, Dziembowski A. Functions and mechanisms of RNA tailing by metazoan terminal nucleotidyltransferases. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1622. [PMID: 33145994 PMCID: PMC7988573 DOI: 10.1002/wrna.1622] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 12/28/2022]
Abstract
Termini often determine the fate of RNA molecules. In recent years, 3' ends of almost all classes of RNA species have been shown to acquire nontemplated nucleotides that are added by terminal nucleotidyltransferases (TENTs). The best-described role of 3' tailing is the bulk polyadenylation of messenger RNAs in the cell nucleus that is catalyzed by canonical poly(A) polymerases (PAPs). However, many other enzymes that add adenosines, uridines, or even more complex combinations of nucleotides have recently been described. This review focuses on metazoan TENTs, which are either noncanonical PAPs or terminal uridylyltransferases with varying processivity. These enzymes regulate RNA stability and RNA functions and are crucial in early development, gamete production, and somatic tissues. TENTs regulate gene expression at the posttranscriptional level, participate in the maturation of many transcripts, and protect cells against viral invasion and the transposition of repetitive sequences. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Processing > 3' End Processing RNA Turnover and Surveillance > Regulation of RNA Stability.
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Affiliation(s)
- Vladyslava Liudkovska
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Andrzej Dziembowski
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland.,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
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