1
|
Hase N, Misiak D, Taubert H, Hüttelmaier S, Gekle M, Köhn M. APOBEC3C-mediated NF-κB activation enhances clear cell renal cell carcinoma progression. Mol Oncol 2024. [PMID: 39183666 DOI: 10.1002/1878-0261.13721] [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: 11/28/2023] [Revised: 07/01/2024] [Accepted: 08/01/2024] [Indexed: 08/27/2024] Open
Abstract
Renowned as the predominant form of kidney cancer, clear cell renal cell carcinoma (ccRCC) exhibits susceptibility to immunotherapies due to its specific expression profile as well as notable immune cell infiltration. Despite this, effectively treating metastatic ccRCC remains a significant challenge, necessitating a more profound comprehension of the underlying molecular mechanisms governing its progression. Here, we unveil that the enhanced expression of the RNA-binding protein DNA dC → dU-editing enzyme APOBEC-3C (APOBEC3C; also known as A3C) in ccRCC tissue and ccRCC-derived cell lines serves as a catalyst for tumor growth by amplifying nuclear factor-kappa B (NF-κB) activity. By employing RNA-sequencing and cell-based assays in ccRCC-derived cell lines, we determined that A3C is a stress-responsive factor and crucial for cell survival. Furthermore, we identified that A3C binds and potentially stabilizes messenger RNAs (mRNAs) encoding positive regulators of the NF-κB pathway. Upon A3C depletion, essential subunits of the NF-κB family are abnormally restrained in the cytoplasm, leading to deregulation of NF-κB target genes. Our study illuminates the pivotal role of A3C in promoting ccRCC tumor development, positioning it as a prospective target for future therapeutic strategies.
Collapse
Affiliation(s)
- Nora Hase
- Junior Group 'Non-Coding RNAs and RBPs in Human Diseases', Medical Faculty, Martin Luther University Halle/Wittenberg, Germany
| | - Danny Misiak
- Section for Molecular Cell Biology, Institute of Molecular Medicine, Martin Luther University Halle/Wittenberg, Germany
| | - Helge Taubert
- Department of Urology and Pediatric Urology, University Hospital Erlangen, Friedrich Alexander University Erlangen/Nürnberg, Germany
| | - Stefan Hüttelmaier
- Section for Molecular Cell Biology, Institute of Molecular Medicine, Martin Luther University Halle/Wittenberg, Germany
| | - Michael Gekle
- Julius-Bernstein-Institute of Physiology, Martin Luther University Halle/Wittenberg, Germany
| | - Marcel Köhn
- Junior Group 'Non-Coding RNAs and RBPs in Human Diseases', Medical Faculty, Martin Luther University Halle/Wittenberg, Germany
| |
Collapse
|
2
|
Kamakura T, Kameda K, Manabe M, Torii K, Sugiura Y, Ito S, Nakayama S, Shimizu T, Nagashima E, Kamiya K, Oka M, Tanaka M, Otsuka M, Ohtsuka M, Kotani A. PTBP1 protects Y RNA from cleavage leading to its apoptosis-specific degradation. Cell Death Discov 2024; 10:322. [PMID: 38997262 PMCID: PMC11245482 DOI: 10.1038/s41420-024-02080-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 06/12/2024] [Accepted: 06/19/2024] [Indexed: 07/14/2024] Open
Abstract
Some RNAs such as 28S rRNA, U1 small nuclear RNA (snRNA), and Y RNAs are known to be cleaved during apoptosis. The underlying mechanism, functions, and biological significance of RNA degradation in apoptosis remain elusive. Y RNAs are non-coding RNAs widely conserved from bacteria to mammals, and are major components of Ro ribonucleoprotein (RNP) complexes which contain the 60 kDa Ro protein (SS-A) and the 50 kDa La protein (SS-B). The autoantigenic Ro and La proteins were identified by autoantibodies present in the sera from patients with Systemic lupus erythematosus (SLE) and Sjögren's syndrome (SjS). We previously identified novel, functional small RNAs named AGO-taxis small RNAs (ASRs) that are specifically bound to Argonaute protein 1 (AGO1), which are processed from Y RNAs. Cell-free analysis combined with fractionation methods revealed that the apoptosis-specific biogenesis of ASRs or cleavage of Y RNA was induced by truncation of polypyrimidine tract-binding protein 1 (PTBP1), which is an endoribonuclease inhibitor of Y RNAs by caspase 3. Caspase 3-resistant PTBP1 mutant protected cleavage of Y RNAs in apoptosis induced by staurosporine. Furthermore, caspase 3-resistant PTBP1 mutant knock-in mice showed elevated cytokines, dysregulation of the germinal center formation compared to the wild-type mice at LPS stimulation, and high positivity of antinuclear antibody. Those results suggest that cleavage of Y RNAs or biogenesis of ASR during apoptosis has critical biological functions and their deregulation result in immune dysregulation and the formation of autoantibody, possibly leading to the development of autoimmune diseases.
Collapse
Affiliation(s)
- Takeshi Kamakura
- Department of Regulation of Infectious Cancer, Research Institute of Microbiological Disease, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Kazuaki Kameda
- Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, 06519, USA
| | - Masahiko Manabe
- Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan
| | - Kan Torii
- Department of Regulation of Infectious Cancer, Research Institute of Microbiological Disease, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Yuki Sugiura
- Multi-Omics Platform, Center for Cancer Immunotherapy and Immunobiology, Kyoto University, Kyoto, 606-8501, Japan
| | - Seiko Ito
- Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan
| | - Shunya Nakayama
- Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan
- Laboratory of Veterinary Physiology, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, 252-0880, Japan
| | - Takanobu Shimizu
- Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan
| | - Etsuko Nagashima
- Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan
| | - Kosuke Kamiya
- Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan
| | - Masahiro Oka
- Department of Regulation of Infectious Cancer, Research Institute of Microbiological Disease, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Masafumi Tanaka
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan
| | - Motoyuki Otsuka
- Department of Gastroenterology and Hepatology, Academic Field of Medicine, Density and Pharmaceutical Sciences, Okayama University, Okayama, 700-8558, Japan
| | - Masato Ohtsuka
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan
| | - Ai Kotani
- Department of Regulation of Infectious Cancer, Research Institute of Microbiological Disease, Osaka University, Suita, Osaka, 565-0871, Japan.
| |
Collapse
|
3
|
Szakats S, McAtamney A, Wilson MJ. Identification of novel microRNAs in the embryonic mouse brain using deep sequencing. Mol Cell Biochem 2024; 479:297-311. [PMID: 37059894 PMCID: PMC10890980 DOI: 10.1007/s11010-023-04730-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 04/04/2023] [Indexed: 04/16/2023]
Abstract
Many advances in small RNA-seq technology and bioinformatics pipelines have been made recently, permitting the discovery of novel miRNAs in the embryonic day 15.5 (E15.5) mouse brain. We aimed to improve miRNA discovery in this tissue to expand our knowledge of the regulatory networks that underpin normal neurodevelopment, find new candidates for neurodevelopmental disorder aetiology, and deepen our understanding of non-coding RNA evolution. A high-quality small RNA-seq dataset of 458 M reads was generated. An unbiased miRNA discovery pipeline identified fifty putative novel miRNAs, six of which were selected for further validation. A combination of conservation analysis and target functional prediction was used to determine the authenticity of novel miRNA candidates. These findings demonstrate that miRNAs remain to be discovered, particularly if they have the features of other small RNA species.
Collapse
Affiliation(s)
- Susanna Szakats
- Developmental Genomics Laboratory, Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
| | - Alice McAtamney
- Developmental Genomics Laboratory, Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
| | - Megan J Wilson
- Developmental Genomics Laboratory, Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
| |
Collapse
|
4
|
Shin HC, Bochkov YA, Kim K, Gern JE, Jarjour NN, Esnault S. A motif in the 5'untranslated region of messenger RNAs regulates protein synthesis in a S6 kinase-dependent manner. Adv Biol Regul 2023; 89:100975. [PMID: 37302177 PMCID: PMC10735251 DOI: 10.1016/j.jbior.2023.100975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/05/2023] [Indexed: 06/13/2023]
Abstract
The 5' untranslated regions (UTRs) in messenger RNAs (mRNAs) play an important role in the regulation of protein synthesis. We had previously identified a group of mRNAs that includes human semaphorin 7A (SEMA7A) whose translation is upregulated by the Erk/p90S6K pathway in human eosinophils, with a potential negative impact in asthma and airway inflammation. In the current study, we aimed to find a common 5'UTR regulatory cis-element, and determine its impact on protein synthesis. We identified a common and conserved 5'UTR motif GGCTG-[(C/G)T(C/G)]n-GCC that was present in this group of mRNAs. Mutations of the first two GG bases in this motif in SEMA7A 5'UTR led to a complete loss of S6K activity dependence for maximal translation. In conclusion, the newly identified 5'UTR motif present in SEMA7A has a critical role in regulating S6K-dependent protein synthesis.
Collapse
Affiliation(s)
- Hyun-Chul Shin
- Department of Chemistry Education, Korea National University of Education, Cheongju-si, Chungcheonbuk-do, Republic of Korea
| | - Yury A Bochkov
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
| | - Kangsan Kim
- Department of Chemistry Education, Korea National University of Education, Cheongju-si, Chungcheonbuk-do, Republic of Korea
| | - James E Gern
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA; Department of Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
| | - Nizar N Jarjour
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
| | - Stephane Esnault
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA.
| |
Collapse
|
5
|
Lima DDS, Amichi LJA, Fernandez MA, Constantino AA, Seixas FAV. NCYPred: A Bidirectional LSTM Network With Attention for Y RNA and Short Non-Coding RNA Classification. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:557-565. [PMID: 34826297 DOI: 10.1109/tcbb.2021.3131136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Short non-coding RNAs (sncRNAs) are involved in multiple cellular processes and can be divided into dozens of classes. Among such classes, Y RNAs have been gaining attention, being essential factors for the initiation of DNA replication on vertebrates, as well as potential tumor biomarkers. Homologs have also been described in nematodes and insects, as well as related sequences in bacteria. Methods capable of accurately predicting Y RNA transcripts are lacking. In this work, we developed an attention-based LSTM network and built a classification model able to classify sncRNAs (including Y RNA) directly from nucleotide sequences. A dataset consisting of 45,447 sncRNA sequences, from a wide range of organisms, obtained from Rfam 14.3 was built. Performance evaluation demonstrated that our proposed method, NCYPred (Non-Coding/Y RNA Prediction), can accurately predict Y RNA sequences and their homologs, as well as 11 additional classes, achieving results comparable with state-of-the-art methods. We also demonstrate that applying t-SNE on learned sequence representations could be useful for sequence analysis. Our model is freely available as a web-server (https://www.gpea.uem.br/ncypred/).
Collapse
|
6
|
Schrimpf A, Knappe O, Qvartskhava N, Poschmann G, Stühler K, Bidmon HJ, Luedde T, Häussinger D, Görg B. Hyperammonemia-induced changes in the cerebral transcriptome and proteome. Anal Biochem 2022; 641:114548. [DOI: 10.1016/j.ab.2022.114548] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 10/10/2021] [Accepted: 01/06/2022] [Indexed: 02/07/2023]
|
7
|
Schena GJ, Murray EK, Hildebrand AN, Headrick AL, Yang Y, Koch KA, Kubo H, Eaton D, Johnson J, Berretta R, Mohsin S, Kishore R, McKinsey TA, Elrod JW, Houser SR. Cortical bone stem cell-derived exosomes' therapeutic effect on myocardial ischemia-reperfusion and cardiac remodeling. Am J Physiol Heart Circ Physiol 2021; 321:H1014-H1029. [PMID: 34623184 PMCID: PMC8793944 DOI: 10.1152/ajpheart.00197.2021] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 09/27/2021] [Accepted: 09/27/2021] [Indexed: 12/20/2022]
Abstract
Heart failure is the one of the leading causes of death in the United States. Heart failure is a complex syndrome caused by numerous diseases, including severe myocardial infarction (MI). MI occurs after an occlusion of a cardiac artery causing downstream ischemia. MI is followed by cardiac remodeling involving extensive remodeling and fibrosis, which, if the original insult is severe or prolonged, can ultimately progress into heart failure. There is no "cure" for heart failure because therapies to regenerate dead tissue are not yet available. Previous studies have shown that in both post-MI and post-ischemia-reperfusion (I/R) models of heart failure, administration of cortical bone stem cell (CBSC) treatment leads to a reduction in scar size and improved cardiac function. Our first study investigated the ability of mouse CBSC-derived exosomes (mCBSC-dEXO) to recapitulate mouse CBSCs (mCBSC) therapeutic effects in a 24-h post-I/R model. This study showed that injection of mCBSCs and mCBSC-dEXOs into the ischemic region of an infarct had a protective effect against I/R injury. mCBSC-dEXOs recapitulated the effects of CBSC treatment post-I/R, indicating exosomes are partly responsible for CBSC's beneficial effects. To examine if exosomes decrease fibrotic activation, adult rat ventricular fibroblasts (ARVFs) and adult human cardiac fibroblasts (NHCFs) were treated with transforming growth factor β (TGFβ) to activate fibrotic signaling before treatment with mCBSC- and human CBSC (hCBSC)-dEXOs. hCBSC-dEXOs caused a 100-fold decrease in human fibroblast activation. To further understand the signaling mechanisms regulating the protective decrease in fibrosis, we performed RNA sequencing on the NHCFs after hCBSC-dEXO treatment. The group treated with both TGFβ and exosomes showed a decrease in small nucleolar RNA (snoRNA), known to be involved with ribosome stability.NEW & NOTEWORTHY Our work is noteworthy due to the identification of factors within stem cell-derived exosomes (dEXOs) that alter fibroblast activation through the hereto-unknown mechanism of decreasing small nucleolar RNA (snoRNA) signaling within cardiac fibroblasts. The study also shows that the injection of stem cells or a stem-cell-derived exosome therapy at the onset of reperfusion elicits cardioprotection, emphasizing the importance of early treatment in the post-ischemia-reperfusion (I/R) wounded heart.
Collapse
Affiliation(s)
- Giana J Schena
- Cardiovascular Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania
| | - Emma K Murray
- Center for Translational Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania
| | - Alycia N Hildebrand
- Center for Translational Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania
| | - Alaina L Headrick
- Division of Cardiology & Consortium for Fibrosis Research and Translation, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Yijun Yang
- Cardiovascular Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania
| | - Keith A Koch
- Division of Cardiology & Consortium for Fibrosis Research and Translation, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Hajime Kubo
- Cardiovascular Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania
| | - Deborah Eaton
- Cardiovascular Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania
| | - Jaslyn Johnson
- Cardiovascular Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania
| | - Remus Berretta
- Cardiovascular Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania
| | - Sadia Mohsin
- Cardiovascular Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania
| | - Raj Kishore
- Center for Translational Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania
| | - Timothy A McKinsey
- Division of Cardiology & Consortium for Fibrosis Research and Translation, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - John W Elrod
- Center for Translational Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania
| | - Steven R Houser
- Cardiovascular Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania
| |
Collapse
|
8
|
Kaucsár T, Róka B, Tod P, Do PT, Hegedűs Z, Szénási G, Hamar P. Divergent regulation of lncRNA expression by ischemia in adult and aging mice. GeroScience 2021; 44:429-445. [PMID: 34697716 PMCID: PMC8811094 DOI: 10.1007/s11357-021-00460-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 09/11/2021] [Indexed: 12/24/2022] Open
Abstract
Elderly patients have increased susceptibility to acute kidney injury (AKI). Long noncoding RNAs (lncRNA) are key regulators of cellular processes, and have been implicated in both aging and AKI. Our aim was to study the effects of aging and ischemia-reperfusion injury (IRI) on the renal expression of lncRNAs. Adult and old (10- and 26-30-month-old) C57BL/6 N mice were subjected to unilateral IRI followed by 7 days of reperfusion. Renal expression of 90 lncRNAs and mRNA expression of injury, regeneration, and fibrosis markers was measured by qPCR in the injured and contralateral control kidneys. Tubular injury, regeneration, and fibrosis were assessed by histology. Urinary lipocalin-2 excretion was increased in old mice prior to IRI, but plasma urea was similar. In the control kidneys of old mice tubular cell necrosis and apoptosis, mRNA expression of kidney injury molecule-1, fibronectin-1, p16, and p21 was elevated. IRI increased plasma urea concentration only in old mice, but injury, regeneration, and fibrosis scores and their mRNA markers were similar in both age groups. AK082072 and Y lncRNAs were upregulated, while H19 and RepA transcript were downregulated in the control kidneys of old mice. IRI upregulated Miat, Igf2as, SNHG5, SNHG6, RNCR3, Malat1, Air, Linc1633, and Neat1 v1, while downregulated Linc1242. LncRNAs H19, AK082072, RepA transcript, and Six3os were influenced by both aging and IRI. Our results indicate that both aging and IRI alter renal lncRNA expression suggesting that lncRNAs have a versatile and complex role in aging and kidney injury. An Ingenuity Pathway Analysis highlighted that the most downregulated H19 may be linked to aging/senescence through p53.
Collapse
Affiliation(s)
- Tamás Kaucsár
- Institute of Translational Medicine, Semmelweis University, Budapest, Hungary
| | - Beáta Róka
- Institute of Translational Medicine, Semmelweis University, Budapest, Hungary
| | - Pál Tod
- Institute of Translational Medicine, Semmelweis University, Budapest, Hungary
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Phuong Thanh Do
- Institute of Translational Medicine, Semmelweis University, Budapest, Hungary
| | - Zoltán Hegedűs
- Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
- Department of Biochemistry and Medical Chemistry, Medical School, University of Pécs, Pécs, Hungary
| | - Gábor Szénási
- Institute of Translational Medicine, Semmelweis University, Budapest, Hungary
| | - Péter Hamar
- Institute of Translational Medicine, Semmelweis University, Budapest, Hungary.
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary.
| |
Collapse
|
9
|
Mosbach ML, Pfafenrot C, von Strandmann EP, Bindereif A, Preußer C. Molecular Determinants for RNA Release into Extracellular Vesicles. Cells 2021; 10:2674. [PMID: 34685656 PMCID: PMC8534350 DOI: 10.3390/cells10102674] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 01/05/2023] Open
Abstract
Extracellular vesicles (EVs) are important for intercellular communication and act as vehicles for biological material, such as various classes of coding and non-coding RNAs, a few of which were shown to selectively target into vesicles. However, protein factors, mechanisms, and sequence elements contributing to this specificity remain largely elusive. Here, we use a reporter system that results in different types of modified transcripts to decipher the specificity determinants of RNAs released into EVs. First, we found that small RNAs are more efficiently packaged into EVs than large ones, and second, we determined absolute quantities for several endogenous RNA transcripts in EVs (U6 snRNA, U1 snRNA, Y1 RNA, and GAPDH mRNA). We show that RNA polymerase III (pol III) transcripts are more efficiently secreted into EVs compared to pol II-derived transcripts. Surprisingly, our quantitative analysis revealed no RNA accumulation in the vesicles relative to the total cellular levels, based on both overexpressed reporter transcripts and endogenous RNAs. RNA appears to be EV-associated only at low copy numbers, ranging between 0.02 and 1 molecule per EV. This RNA association may reflect internal EV encapsulation or a less tightly bound state at the vesicle surface.
Collapse
Affiliation(s)
- Marie-Luise Mosbach
- Institute of Biochemistry, Justus Liebig University of Gießen, 35392 Gießen, Germany; (M.-L.M.); (C.P.)
| | - Christina Pfafenrot
- Institute of Biochemistry, Justus Liebig University of Gießen, 35392 Gießen, Germany; (M.-L.M.); (C.P.)
| | - Elke Pogge von Strandmann
- Institute for Tumor Immunology, Center for Tumor Biology and Immunology (ZTI), Philipps University of Marburg, 35043 Marburg, Germany;
| | - Albrecht Bindereif
- Institute of Biochemistry, Justus Liebig University of Gießen, 35392 Gießen, Germany; (M.-L.M.); (C.P.)
| | - Christian Preußer
- Institute for Tumor Immunology, Center for Tumor Biology and Immunology (ZTI), Philipps University of Marburg, 35043 Marburg, Germany;
| |
Collapse
|
10
|
Flynn RA, Pedram K, Malaker SA, Batista PJ, Smith BAH, Johnson AG, George BM, Majzoub K, Villalta PW, Carette JE, Bertozzi CR. Small RNAs are modified with N-glycans and displayed on the surface of living cells. Cell 2021; 184:3109-3124.e22. [PMID: 34004145 DOI: 10.1016/j.cell.2021.04.023] [Citation(s) in RCA: 235] [Impact Index Per Article: 78.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/18/2020] [Accepted: 04/14/2021] [Indexed: 12/20/2022]
Abstract
Glycans modify lipids and proteins to mediate inter- and intramolecular interactions across all domains of life. RNA is not thought to be a major target of glycosylation. Here, we challenge this view with evidence that mammals use RNA as a third scaffold for glycosylation. Using a battery of chemical and biochemical approaches, we found that conserved small noncoding RNAs bear sialylated glycans. These "glycoRNAs" were present in multiple cell types and mammalian species, in cultured cells, and in vivo. GlycoRNA assembly depends on canonical N-glycan biosynthetic machinery and results in structures enriched in sialic acid and fucose. Analysis of living cells revealed that the majority of glycoRNAs were present on the cell surface and can interact with anti-dsRNA antibodies and members of the Siglec receptor family. Collectively, these findings suggest the existence of a direct interface between RNA biology and glycobiology, and an expanded role for RNA in extracellular biology.
Collapse
Affiliation(s)
- Ryan A Flynn
- Department of Chemistry, Stanford University, Stanford, CA, USA.
| | - Kayvon Pedram
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Stacy A Malaker
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Pedro J Batista
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Benjamin A H Smith
- Department of Chemical and Systems Biology and ChEM-H, Stanford University, Stanford, CA, USA
| | - Alex G Johnson
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Benson M George
- Department of Cancer Biology, Stanford University, Stanford, CA, USA
| | - Karim Majzoub
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA; IGMM, CNRS, University of Montpellier, Montpellier, France
| | - Peter W Villalta
- Masonic Cancer Center and Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Jan E Carette
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
| |
Collapse
|
11
|
Zorn P, Misiak D, Gekle M, Köhn M. Identification and initial characterization of POLIII-driven transcripts by msRNA-sequencing. RNA Biol 2021; 18:1807-1817. [PMID: 33404286 PMCID: PMC8583065 DOI: 10.1080/15476286.2020.1871216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Non-coding RNAs (ncRNAs) are powerful regulators of gene expression but medium-sized (50–300 nts in length) ncRNAs (msRNAs) are barely picked-up precisely by RNA-sequencing. Here we describe msRNA-sequencing (msRNAseq), a modified protocol that associated with a computational analyses pipeline identified about ~1800 msRNA loci, including over 300 putatively novel msRNAs, in human and murine cells. We focused on the identification and initial characterization of three POLIII-derived transcripts. The validation of these uncharacterized msRNAs identified an ncRNA in antisense orientation from the POLR3E locus transcribed by POLIII. This msRNA, termed POLAR (POLR3E Antisense RNA), has a strikingly short half-life, localizes to paraspeckles (PSPs) and associates with PSP-associated proteins indicating that msRNAseq identifies functional msRNAs. Thus, our analyses will pave the way for analysing the roles of msRNAs in cells, development and diseases.
Collapse
Affiliation(s)
| | - Danny Misiak
- Institute of Molecular Medicine, University of Halle-Wittenberg, Halle (Saale), Germany
| | - Michael Gekle
- Julius-Bernstein-Institute of Physiology, University of Halle-Wittenberg, Germany
| | | |
Collapse
|
12
|
Täuber H, Hüttelmaier S, Köhn M. POLIII-derived non-coding RNAs acting as scaffolds and decoys. J Mol Cell Biol 2020; 11:880-885. [PMID: 31152666 PMCID: PMC6884708 DOI: 10.1093/jmcb/mjz049] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 03/11/2019] [Accepted: 04/14/2019] [Indexed: 12/17/2022] Open
Abstract
A large variety of eukaryotic small structured POLIII-derived non-coding RNAs (ncRNAs) have been described in the past. However, for only few, e.g. 7SL and H1/MRP families, cellular functions are well understood. For the vast majority of these transcripts, cellular functions remain unknown. Recent findings on the role of Y RNAs and other POLIII-derived ncRNAs suggest an evolutionarily conserved function of these ncRNAs in the assembly and function of ribonucleoprotein complexes (RNPs). These RNPs provide cellular `machineries’, which are essential for guiding the fate and function of a variety of RNAs. In this review, we summarize current knowledge on the role of POLIII-derived ncRNAs in the assembly and function of RNPs. We propose that these ncRNAs serve as scaffolding factors that `chaperone’ RNA-binding proteins (RBPs) to form functional RNPs. In addition or associated with this role, some small ncRNAs act as molecular decoys impairing the RBP-guided control of RNA fate by competing with other RNA substrates. This suggests that POLIII-derived ncRNAs serve essential and conserved roles in the assembly of larger RNPs and thus the control of gene expression by indirectly guiding the fate of mRNAs and lncRNAs.
Collapse
Affiliation(s)
- Hendrik Täuber
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, Charles Tanford Protein Centre, Kurt-Mothes-Str. 3a, 06120 Halle, Germany
| | - Stefan Hüttelmaier
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, Charles Tanford Protein Centre, Kurt-Mothes-Str. 3a, 06120 Halle, Germany
| | - Marcel Köhn
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, Charles Tanford Protein Centre, Kurt-Mothes-Str. 3a, 06120 Halle, Germany.,Julius Bernstein Institute of Physiology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, Charles Tanford Protein Centre, Kurt-Mothes-Str. 3a, 06120 Halle, Germany
| |
Collapse
|
13
|
Abramowicz A, Story MD. The Long and Short of It: The Emerging Roles of Non-Coding RNA in Small Extracellular Vesicles. Cancers (Basel) 2020; 12:cancers12061445. [PMID: 32498257 PMCID: PMC7352322 DOI: 10.3390/cancers12061445] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 12/21/2022] Open
Abstract
Small extracellular vesicles (EVs) play a significant role in intercellular communication through their non-coding RNA (ncRNA) cargo. While the initial examination of EV cargo identified both mRNA and miRNA, later studies revealed a wealth of other types of EV-related non-randomly packed ncRNAs, including tRNA and tRNA fragments, Y RNA, piRNA, rRNA, and lncRNA. A number of potential roles for these ncRNA species were suggested, with strong evidence provided in some cases, whereas the role for other ncRNA is more speculative. For example, long non-coding RNA might be used as a potential diagnostic tool but might also mediate resistance to certain cancer-specific chemotherapy agents. piRNAs, on the other hand, have a significant role in genome integrity, however, no role has yet been defined for the piRNAs found in EVs. While our knowledgebase for the function of ncRNA-containing EVs is still modest, the potential role that these EV-ensconced ncRNA might play is promising. This review summarizes the ncRNA content of EVs and describes the function where known, or the potential utility of EVs that harbor specific types of ncRNA.
Collapse
Affiliation(s)
- Agata Abramowicz
- Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-102 Gliwice, Poland;
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Michael D Story
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Correspondence:
| |
Collapse
|
14
|
Y RNA: An Overview of Their Role as Potential Biomarkers and Molecular Targets in Human Cancers. Cancers (Basel) 2020; 12:cancers12051238. [PMID: 32423154 PMCID: PMC7281143 DOI: 10.3390/cancers12051238] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/03/2020] [Accepted: 05/07/2020] [Indexed: 12/12/2022] Open
Abstract
Y RNA are a class of small non-coding RNA that are largely conserved. Although their discovery was almost 40 years ago, their function is still under investigation. This is evident in cancer biology, where their role was first studied just a dozen years ago. Since then, only a few contributions were published, mostly scattered across different tumor types and, in some cases, also suffering from methodological limitations. Nonetheless, these sparse data may be used to make some estimations and suggest routes to better understand the role of Y RNA in cancer formation and characterization. Here we summarize the current knowledge about Y RNA in multiple types of cancer, also including a paragraph about tumors that might be included in this list in the future, if more evidence becomes available. The picture arising indicates that Y RNA might be useful in tumor characterization, also relying on non-invasive methods, such as the analysis of the content of extracellular vesicles (EV) that are retrieved from blood plasma and other bodily fluids. Due to the established role of Y RNA in DNA replication, it is possible to hypothesize their therapeutic targeting to inhibit cell proliferation in oncological patients.
Collapse
|
15
|
Valkov N, Das S. Y RNAs: Biogenesis, Function and Implications for the Cardiovascular System. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1229:327-342. [PMID: 32285422 DOI: 10.1007/978-981-15-1671-9_20] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In recent years, progress in the field of high-throughput sequencing technology and its application to a wide variety of biological specimens has greatly advanced the discovery and cataloging of a diverse set of non-coding RNAs (ncRNAs) that have been found to have unexpected biological functions. Y RNAs are an emerging class of highly conserved, small ncRNAs. There is a growing number of reports in the literature demonstrating that Y RNAs and their fragments are not just random degradation products but are themselves bioactive molecules. This review will outline what is currently known about Y RNA including biogenesis, structure and functional roles. In addition, we will provide an overview of studies reporting the presence and functions attributed to Y RNAs in the cardiovascular system.
Collapse
Affiliation(s)
- Nedyalka Valkov
- Cardiovascular Research Center of Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Saumya Das
- Cardiovascular Research Center of Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
16
|
Seki T, Yamagata H, Uchida S, Chen C, Kobayashi A, Kobayashi M, Harada K, Matsuo K, Watanabe Y, Nakagawa S. Altered expression of long noncoding RNAs in patients with major depressive disorder. J Psychiatr Res 2019; 117:92-99. [PMID: 31351391 DOI: 10.1016/j.jpsychires.2019.07.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 07/10/2019] [Accepted: 07/18/2019] [Indexed: 02/06/2023]
Abstract
Although major depressive disorder (MDD) is a leading cause of disability worldwide, its pathophysiology is poorly understood. Increasing evidence suggests that aberrant regulation of transcription plays a key role in the pathophysiology of MDD. Recently, long noncoding RNAs (lncRNAs) have been recognized for their important functions in chromatin structure, gene expression, and the subsequent manifestation of various biological processes in the central nervous system. However, it is unclear whether the aberrant expression and function of lncRNAs are associated with the pathophysiology of MDD. In this study, we sought to evaluate the expression of lncRNAs in peripheral blood leukocytes as potential biomarkers for MDD. We measured the expression levels of 83 lncRNAs in the peripheral blood leukocytes of 29 MDD patients and 29 age- and gender-matched healthy controls using quantitative reverse transcription PCR (RT-qPCR) analysis. We found that MDD patients exhibited distinct expression signatures. Specifically, the expression level of one lncRNA (RMRP) was lower while the levels of four (Y5, MER11C, PCAT1, and PCAT29) were higher in MDD patients compared to healthy controls. The expression level of RMRP was correlated with depression severity as measured by the Hamilton Depression Rating Scale (HAM-D). Moreover, RMRP expression was lower in a mouse model of depression, corroborating the observation from MDD patients. Taken together, our data suggest that lower RMRP levels may serve as a potential biomarker for MDD.
Collapse
Affiliation(s)
- Tomoe Seki
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Hirotaka Yamagata
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.
| | - Shusaku Uchida
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Chong Chen
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan
| | - Ayumi Kobayashi
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan
| | - Masaaki Kobayashi
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan
| | - Kenichiro Harada
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan
| | - Koji Matsuo
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan
| | - Yoshifumi Watanabe
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan
| | - Shin Nakagawa
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan
| |
Collapse
|
17
|
Gyuris A, Navarrete-Perea J, Jo A, Cristea S, Zhou S, Fraser K, Wei Z, Krichevsky AM, Weissleder R, Lee H, Gygi SP, Charest A. Physical and Molecular Landscapes of Mouse Glioma Extracellular Vesicles Define Heterogeneity. Cell Rep 2019; 27:3972-3987.e6. [PMID: 31242427 PMCID: PMC6604862 DOI: 10.1016/j.celrep.2019.05.089] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 04/15/2019] [Accepted: 05/22/2019] [Indexed: 12/21/2022] Open
Abstract
Cancer extracellular vesicles (EVs) are highly heterogeneous, which impedes our understanding of their function as intercellular communication agents and biomarkers. To deconstruct this heterogeneity, we analyzed extracellular RNAs (exRNAs) and extracellular proteins (exPTNs) from size fractionation of large, medium, and small EVs and ribonucleoprotein complexes (RNPs) from mouse glioblastoma cells by RNA sequencing and quantitative proteomics. mRNA from medium-sized EVs most closely reflects the cellular transcriptome, whereas small EV exRNA is enriched in small non-coding RNAs and RNPs contain precisely processed tRNA fragments. The exPTN composition of EVs and RNPs reveals that they are closely related by vesicle type, independent of their cellular origin, and single EV analysis reveals that small EVs are less heterogeneous in their protein content than larger ones. We provide a foundation for better understanding of segregation of macromolecules in glioma EVs through a catalog of diverse exRNAs and exPTNs.
Collapse
Affiliation(s)
- Aron Gyuris
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | | | - Ala Jo
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Simona Cristea
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Shuang Zhou
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Kyle Fraser
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Zhiyun Wei
- Department of Neurology, Ann Romney Center for Neurologic Diseases, Initiative for RNA Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Anna M Krichevsky
- Department of Neurology, Ann Romney Center for Neurologic Diseases, Initiative for RNA Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Hakho Lee
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Steve P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02215, USA
| | - Al Charest
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA.
| |
Collapse
|
18
|
Sole C, Arnaiz E, Manterola L, Otaegui D, Lawrie CH. The circulating transcriptome as a source of cancer liquid biopsy biomarkers. Semin Cancer Biol 2019; 58:100-108. [PMID: 30684535 DOI: 10.1016/j.semcancer.2019.01.003] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 01/16/2019] [Accepted: 01/22/2019] [Indexed: 02/07/2023]
Abstract
Non-invasive biomarkers or liquid biopsies have the potential to revolutionise cancer patient management as repeated sampling allows real-time monitoring of disease progression and response to treatment. This allows for earlier intervention and dynamic treatment management; both cornerstones of personalised medicine. The circulating transcriptome represents a rich source of potential cancer biomarkers that includes many classes of RNA, both coding and non-coding, that are only now beginning to be explored. In particular the increasing power and availability of RNAseq techniques have pushed studies beyond circulating miRNAs, to other classes of RNA including mRNA, snRNA, snoRNA, piRNA, YRNA, lncRNA and circRNA. In this review we focus on the emerging potential for these different classes of RNA as cancer biomarkers, and in particular the barriers and limitations that remain to be overcome if these molecules are to become part of routine clinical practice.
Collapse
Affiliation(s)
- Carla Sole
- Molecular Oncology Group, Biodonostia Research Institute, Paseo Doctor Begiristain, s/n, San Sebastián, 20014, Spain
| | - Esther Arnaiz
- Molecular Oncology Group, Biodonostia Research Institute, Paseo Doctor Begiristain, s/n, San Sebastián, 20014, Spain
| | - Lorea Manterola
- Molecular Oncology Group, Biodonostia Research Institute, Paseo Doctor Begiristain, s/n, San Sebastián, 20014, Spain
| | - David Otaegui
- Multiple Sclerosis Group, Biodonostia Research Institute, Paseo Doctor Begiristain, s/n, San Sebastián, 20014, Spain
| | - Charles H Lawrie
- Molecular Oncology Group, Biodonostia Research Institute, Paseo Doctor Begiristain, s/n, San Sebastián, 20014, Spain; Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, United Kingdom; IKERBASQUE, Basque Foundation for Science, María Díaz Haroko Kalea, 3, 48013, Bilbao, Spain.
| |
Collapse
|
19
|
Driedonks TAP, Nolte-'t Hoen ENM. Circulating Y-RNAs in Extracellular Vesicles and Ribonucleoprotein Complexes; Implications for the Immune System. Front Immunol 2019; 9:3164. [PMID: 30697216 PMCID: PMC6340977 DOI: 10.3389/fimmu.2018.03164] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 12/21/2018] [Indexed: 12/25/2022] Open
Abstract
The exchange of extracellular vesicles (EV) between immune cells plays a role in various immune regulatory processes. EV are nano-sized lipid bilayer-enclosed structures that contain a multitude of proteins and small non-coding RNA molecules. Of the various RNA classes present in EV, miRNAs have been most intensively studied because of their known gene-regulatory functions. These miRNAs constitute only a minor part of all EV-enclosed RNA, whereas other 20–200 nt sized non-coding RNAs were shown to be abundantly present in EV. Several of these mid-sized RNAs perform basic functions in cells, but their function in EV remains elusive. One prominent class of mid-sized extracellular RNAs associated with EV are the Y-RNAs. This family of highly conserved non-coding RNAs was initially discovered as RNA component of circulating ribonucleoprotein autoantigens in serum from Systemic Lupus Erythematosus and Sjögren's Syndrome patients. Y-RNA has been implicated in cellular processes such as DNA replication and RNA quality control. In recent years, Y-RNA has been abundantly detected in EV from multiple different cell lines and biofluids, and also in murine and human retroviruses. Accumulating evidence suggests that EV-associated Y-RNA may be involved in a range of immune-related processes, including inflammation, immune suppression, and establishment of the tumor microenvironment. Moreover, changes in plasma levels of extracellular Y-RNA have been associated with various diseases. Recent studies have aimed to address the mechanisms underlying their release and function. We for example showed that the levels of EV-associated Y-RNA released by immune cells can be regulated by Toll-like receptor (TLR) signaling. Combined, these data have triggered increased interest in extracellular Y-RNAs. In this review, we provide an overview of studies reporting the occurrence of extracellular Y-RNAs, as well as signaling properties and immune-related functions attributed to these RNAs. We list RNA-binding proteins currently known to interact with Y-RNAs and evaluate their occurrence in EV. In parallel, we discuss technical challenges in assessing whether extracellular Y-RNAs are contained in ribonucleoprotein complexes or EV. By integrating the current knowledge on extracellular Y-RNA we further reflect on the biomarker potential of Y-RNA and their role in immune cell communication and immunopathology.
Collapse
Affiliation(s)
- Tom A P Driedonks
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Esther N M Nolte-'t Hoen
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| |
Collapse
|
20
|
Tebaldi T, Zuccotti P, Peroni D, Köhn M, Gasperini L, Potrich V, Bonazza V, Dudnakova T, Rossi A, Sanguinetti G, Conti L, Macchi P, D'Agostino V, Viero G, Tollervey D, Hüttelmaier S, Quattrone A. HuD Is a Neural Translation Enhancer Acting on mTORC1-Responsive Genes and Counteracted by the Y3 Small Non-coding RNA. Mol Cell 2018; 71:256-270.e10. [PMID: 30029004 PMCID: PMC6060611 DOI: 10.1016/j.molcel.2018.06.032] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 04/24/2018] [Accepted: 06/21/2018] [Indexed: 01/19/2023]
Abstract
The RNA-binding protein HuD promotes neurogenesis and favors recovery from peripheral axon injury. HuD interacts with many mRNAs, altering both stability and translation efficiency. We generated a nucleotide resolution map of the HuD RNA interactome in motor neuron-like cells, identifying HuD target sites in 1,304 mRNAs, almost exclusively in the 3' UTR. HuD binds many mRNAs encoding mTORC1-responsive ribosomal proteins and translation factors. Altered HuD expression correlates with the translation efficiency of these mRNAs and overall protein synthesis, in a mTORC1-independent fashion. The predominant HuD target is the abundant, small non-coding RNA Y3, amounting to 70% of the HuD interaction signal. Y3 functions as a molecular sponge for HuD, dynamically limiting its recruitment to polysomes and its activity as a translation and neuron differentiation enhancer. These findings uncover an alternative route to the mTORC1 pathway for translational control in motor neurons that is tunable by a small non-coding RNA.
Collapse
Affiliation(s)
- Toma Tebaldi
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento 38123, Italy
| | - Paola Zuccotti
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento 38123, Italy
| | - Daniele Peroni
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento 38123, Italy
| | - Marcel Köhn
- Institute of Molecular Medicine, Martin-Luther-University Halle-Wittenberg, Halle 06120, Germany; Julius-Bernstein-Institute of Physiology, Martin-Luther-University Halle-Wittenberg, Halle 06097, Germany
| | - Lisa Gasperini
- Laboratory of Molecular and Cellular Neurobiology, Centre for Integrative Biology, University of Trento, Trento 38123, Italy
| | - Valentina Potrich
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento 38123, Italy
| | - Veronica Bonazza
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento 38123, Italy
| | - Tatiana Dudnakova
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Annalisa Rossi
- Laboratory of Molecular and Cellular Neurobiology, Centre for Integrative Biology, University of Trento, Trento 38123, Italy
| | - Guido Sanguinetti
- School of Informatics, University of Edinburgh, Edinburgh EH8 9AB, UK
| | - Luciano Conti
- Laboratory of Stem Cell Biology, Centre for Integrative Biology, University of Trento, Trento 38123, Italy
| | - Paolo Macchi
- Laboratory of Molecular and Cellular Neurobiology, Centre for Integrative Biology, University of Trento, Trento 38123, Italy
| | - Vito D'Agostino
- Centre for Integrative Biology, University of Trento, Trento 38123, Italy
| | - Gabriella Viero
- Institute of Biophysics, CNR Unit at Trento, Trento 38123, Italy
| | - David Tollervey
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Stefan Hüttelmaier
- Institute of Molecular Medicine, Martin-Luther-University Halle-Wittenberg, Halle 06120, Germany
| | - Alessandro Quattrone
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento 38123, Italy.
| |
Collapse
|
21
|
Irimie AI, Zimta AA, Ciocan C, Mehterov N, Dudea D, Braicu C, Berindan-Neagoe I. The Unforeseen Non-Coding RNAs in Head and Neck Cancer. Genes (Basel) 2018; 9:genes9030134. [PMID: 29494516 PMCID: PMC5867855 DOI: 10.3390/genes9030134] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 02/21/2018] [Accepted: 02/22/2018] [Indexed: 12/18/2022] Open
Abstract
Previously ignored non-coding RNAs (ncRNAs) have become the subject of many studies. However, there is an imbalance in the amount of consideration that ncRNAs are receiving. Some transcripts such as microRNAs (miRNAs) or small interfering RNAs (siRNAs) have gained much attention, but it is necessary to investigate other “pieces of the RNA puzzle”. These can offer a more complete view over normal and pathological cell behavior. The other ncRNA species are less studied, either due to their recent discovery, such as stable intronic sequence RNA (sisRNA), YRNA, miRNA-offset RNAs (moRNA), telomerase RNA component (TERC), natural antisense transcript (NAT), transcribed ultraconserved regions (T-UCR), and pseudogene transcript, or because they are still largely seen as non-coding transcripts with no relevance to pathogenesis. Moreover, some are still considered housekeeping RNAs, for instance small nucleolar RNAs (snoRNAs) and TERC. Our review summarizes the biogenesis, mechanism of action and potential role of less known ncRNAs in head and neck cancer, with a particular focus on the installment and progress for this particular cancer type.
Collapse
Affiliation(s)
- Alexandra Iulia Irimie
- Department of Prosthetic Dentistry and Dental Materials, Division Dental Propaedeutic, Aesthetic, "IuliuHatieganu" University of Medicine and Pharmacy, Cluj-Napoca, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Alina-Andreea Zimta
- MEDFUTURE-Research Center for Advanced Medicine, University of Medicine and Pharmacy Iuliu-Hatieganu, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Cristina Ciocan
- MEDFUTURE-Research Center for Advanced Medicine, University of Medicine and Pharmacy Iuliu-Hatieganu, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Nikolay Mehterov
- Department of Medical Biology, Medical University Plovdiv, BulVasilAprilov 15-А, Plovdiv 4002, Bulgaria.
- Technological Center for Emergency Medicine, BulVasilAprilov 15-А, Plovdiv 4002, Bulgaria.
| | - Diana Dudea
- Department of Prosthetic Dentistry and Dental Materials, Division Dental Propaedeutic, Aesthetic, "IuliuHatieganu" University of Medicine and Pharmacy, Cluj-Napoca, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Cornelia Braicu
- Research Center for Functional Genomics and Translational Medicine, "IuliuHatieganu" University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Ioana Berindan-Neagoe
- MEDFUTURE-Research Center for Advanced Medicine, University of Medicine and Pharmacy Iuliu-Hatieganu, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
- Research Center for Functional Genomics and Translational Medicine, "IuliuHatieganu" University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
- Department of Functional Genomics and Experimental Pathology, The Oncology Institute "Prof. Dr. Ion Chiricuta", Republicii 34 Street, 400015 Cluj-Napoca, Romania.
| |
Collapse
|
22
|
Abstract
INTRODUCTION Osteoarthritis (OA), a chronic, debilitating and degenerative disease of the joints, is the most common form of arthritis. The seriousness of this prevalent and chronic disease is often overlooked. Disease modifying OA drug development is hindered by the lack of soluble biomarkers to detect OA early. The objective of OA biomarker research is to identify early OA prior to the appearance of radiographic signs and the development of pain. Areas covered: This review has focused on extracellular genomic material that could serve as biomarkers of OA. Recent studies have examined the expression of extracellular genomic material such as miRNA, lncRNA, snoRNA, mRNA and cell-free DNA, which are aberrantly expressed in the body fluids of OA patients. Changes in genomic content of peripheral blood mononuclear cells in OA could also function as biomarkers of OA. Expert commentary: There is an unmet need for soluble biomarkers for detecting and then monitoring OA disease progression. Extracellular genomic material research may also reveal more about the underlying pathophysiology of OA. Minimally-invasive liquid biopsies such as synovial fluid and blood sampling of genomic material may be more sensitive over radiography in the detection, diagnosis and monitoring of OA in the future.
Collapse
Affiliation(s)
- Emma Budd
- a The D-BOARD European Consortium for Biomarker Discovery, School of Veterinary Medicine , University of Surrey , Guildford , UK.,b Department of Veterinary Pre-Clinical Sciences, School of Veterinary Medicine, Faculty of Health and Medical Sciences , University of Surrey , Guildford , UK
| | - Giovanna Nalesso
- b Department of Veterinary Pre-Clinical Sciences, School of Veterinary Medicine, Faculty of Health and Medical Sciences , University of Surrey , Guildford , UK
| | - Ali Mobasheri
- a The D-BOARD European Consortium for Biomarker Discovery, School of Veterinary Medicine , University of Surrey , Guildford , UK.,b Department of Veterinary Pre-Clinical Sciences, School of Veterinary Medicine, Faculty of Health and Medical Sciences , University of Surrey , Guildford , UK.,c Arthritis Research UK Centre for Sport, Exercise and Osteoarthritis , Queen's Medical Centre , Nottingham , UK
| |
Collapse
|
23
|
Kabeerdoss J, Sandhya P, Danda D. Y RNA derived small RNAs in Sjögren's syndrome: Candidate biomarkers? Int J Rheum Dis 2017; 20:1763-1766. [PMID: 29152879 DOI: 10.1111/1756-185x.13229] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Anti-Ro and anti-La antibodies are important in pathogenesis and diagnosis of Sjögren's syndrome (SS). Ro60, Ro52 and La are RNA binding proteins of Y RNA, which were discovered more than three decades ago. Significance of Y RNA is not appreciated as much as Ro and La in SS. It can be hypothesised that 5'-YsRNA, short fragment derived from Y RNA may be recognized by TLR7 in pDC, which induces type I interferon signature in SS. New genomics tools, namely RNA seq, enables assay of 5'-YsRNA in blood. 5'-YsRNA has the potential to be a novel biomarker of SS.
Collapse
Affiliation(s)
- Jayakanthan Kabeerdoss
- Department of Immunology and Rheumatology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Pulukool Sandhya
- Department of Immunology and Rheumatology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Debashish Danda
- Department of Immunology and Rheumatology, Christian Medical College, Vellore, Tamil Nadu, India
| |
Collapse
|
24
|
Wei Z, Batagov AO, Schinelli S, Wang J, Wang Y, El Fatimy R, Rabinovsky R, Balaj L, Chen CC, Hochberg F, Carter B, Breakefield XO, Krichevsky AM. Coding and noncoding landscape of extracellular RNA released by human glioma stem cells. Nat Commun 2017; 8:1145. [PMID: 29074968 PMCID: PMC5658400 DOI: 10.1038/s41467-017-01196-x] [Citation(s) in RCA: 351] [Impact Index Per Article: 50.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 08/25/2017] [Indexed: 02/07/2023] Open
Abstract
Tumor-released RNA may mediate intercellular communication and serve as biomarkers. Here we develop a protocol enabling quantitative, minimally biased analysis of extracellular RNAs (exRNAs) associated with microvesicles, exosomes (collectively called EVs), and ribonucleoproteins (RNPs). The exRNA complexes isolated from patient-derived glioma stem-like cultures exhibit distinct compositions, with microvesicles most closely reflecting cellular transcriptome. exRNA is enriched in small ncRNAs, such as miRNAs in exosomes, and precisely processed tRNA and Y RNA fragments in EVs and exRNPs. EV-enclosed mRNAs are mostly fragmented, and UTRs enriched; nevertheless, some full-length mRNAs are present. Overall, there is less than one copy of non-rRNA per EV. Our results suggest that massive EV/exRNA uptake would be required to ensure functional impact of transferred RNA on brain recipient cells and predict the most impactful miRNAs in such conditions. This study also provides a catalog of diverse exRNAs useful for biomarker discovery and validates its feasibility on cerebrospinal fluid. While circulating DNA has been extensively explored as a potential cancer biomarker, RNA potential has been overlooked so far. Here the authors present a comprehensive analysis of extracellular RNA secreted by glioblastoma cells that could prove a valuable resource for biomarker discovery and a means of intercellular communication.
Collapse
Affiliation(s)
- Zhiyun Wei
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, HMS Initiative for RNA Medicine, Boston, MA, 02115, USA
| | - Arsen O Batagov
- Vishuo Biomedical, #3-33 Teletech Park, 20 Science Park Road, Singapore, 117674, Singapore
| | - Sergio Schinelli
- Department of Drug Sciences, University of Pavia, Pavia, 27100, Italy
| | - Jintu Wang
- Beijing Genomics Institute, Shenzhen, 518083, China
| | - Yang Wang
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, HMS Initiative for RNA Medicine, Boston, MA, 02115, USA
| | - Rachid El Fatimy
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, HMS Initiative for RNA Medicine, Boston, MA, 02115, USA
| | - Rosalia Rabinovsky
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, HMS Initiative for RNA Medicine, Boston, MA, 02115, USA
| | - Leonora Balaj
- Department of Neurology and Radiology, Massachusetts General Hospital and Program in Neuroscience, Harvard Medical School, Charlestown, MA, 02129, USA
| | - Clark C Chen
- Neurosurgery Department, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Fred Hochberg
- Department of Neurosurgery, University of California, La Jolla, San Diego, CA, 92093, USA.,Scintillon Institute, San Diego, CA, 92121, USA
| | - Bob Carter
- Department of Neurosurgery, University of California, La Jolla, San Diego, CA, 92093, USA
| | - Xandra O Breakefield
- Department of Neurology and Radiology, Massachusetts General Hospital and Program in Neuroscience, Harvard Medical School, Charlestown, MA, 02129, USA
| | - Anna M Krichevsky
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, HMS Initiative for RNA Medicine, Boston, MA, 02115, USA.
| |
Collapse
|
25
|
PARN Modulates Y RNA Stability and Its 3'-End Formation. Mol Cell Biol 2017; 37:MCB.00264-17. [PMID: 28760775 DOI: 10.1128/mcb.00264-17] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 07/24/2017] [Indexed: 11/20/2022] Open
Abstract
Loss-of-function mutations in 3'-to-5' exoribonucleases have been implicated in hereditary human diseases. For example, PARN mutations cause a severe form of dyskeratosis congenita (DC), wherein PARN deficiency leads to human telomerase RNA instability. Since the DC phenotype in PARN patients is even more severe than that of loss-of-function alleles in telomerase components, we hypothesized that PARN would also be required for the stability of other RNAs. Here, we show that PARN depletion reduces the levels of abundant human Y RNAs, which might contribute to the severe phenotype of DC observed in patients. Depletion of PAPD5 or the cytoplasmic exonuclease DIS3L rescues the effect of PARN depletion on Y RNA levels, suggesting that PARN stabilizes Y RNAs by removing oligoadenylated tails added by PAPD5, which would otherwise recruit DIS3L for Y RNA degradation. Through deep sequencing of 3' ends, we provide evidence that PARN can also deadenylate the U6 and RMRP RNAs without affecting their levels. Moreover, we observed widespread posttranscriptional oligoadenylation, uridylation, and guanylation of U6 and Y RNA 3' ends, suggesting that in mammalian cells, the formation of a 3' end for noncoding RNAs can be a complex process governed by the activities of various 3'-end polymerases and exonucleases.
Collapse
|
26
|
Haderk F, Schulz R, Iskar M, Cid LL, Worst T, Willmund KV, Schulz A, Warnken U, Seiler J, Benner A, Nessling M, Zenz T, Göbel M, Dürig J, Diederichs S, Paggetti J, Moussay E, Stilgenbauer S, Zapatka M, Lichter P, Seiffert M. Tumor-derived exosomes modulate PD-L1 expression in monocytes. Sci Immunol 2017; 2:2/13/eaah5509. [PMID: 28754746 DOI: 10.1126/sciimmunol.aah5509] [Citation(s) in RCA: 213] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 03/23/2017] [Accepted: 06/12/2017] [Indexed: 12/14/2022]
Abstract
In chronic lymphocytic leukemia (CLL), monocytes and macrophages are skewed toward protumorigenic phenotypes, including the release of tumor-supportive cytokines and the expression of immunosuppressive molecules such as programmed cell death 1 ligand 1 (PD-L1). To understand the mechanism driving protumorigenic skewing in CLL, we evaluated the role of tumor cell-derived exosomes in the cross-talk with monocytes. We carried out RNA sequencing and proteome analyses of CLL-derived exosomes and identified noncoding Y RNA hY4 as a highly abundant RNA species that is enriched in exosomes from plasma of CLL patients compared with healthy donor samples. Transfer of CLL-derived exosomes or hY4 alone to monocytes resulted in key CLL-associated phenotypes, including the release of cytokines, such as C-C motif chemokine ligand 2 (CCL2), CCL4, and interleukin-6, and the expression of PD-L1. These responses were abolished in Toll-like receptor 7 (TLR7)-deficient monocytes, suggesting exosomal hY4 as a driver of TLR7 signaling. Pharmacologic inhibition of endosomal TLR signaling resulted in a substantially reduced activation of monocytes in vitro and attenuated CLL development in vivo. Our results indicate that exosome-mediated transfer of noncoding RNAs to monocytes contributes to cancer-related inflammation and concurrent immune escape via PD-L1 expression.
Collapse
Affiliation(s)
- Franziska Haderk
- Department of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ralph Schulz
- Department of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Murat Iskar
- Department of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Laura Llaó Cid
- Department of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas Worst
- Division of Signaling and Functional Genomics, DKFZ, Heidelberg, Germany
| | - Karolin V Willmund
- Department of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Angela Schulz
- Department of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Genomics and Proteomics Core Facility, DKFZ, Heidelberg, Germany
| | - Uwe Warnken
- Genomics and Proteomics Core Facility, DKFZ, Heidelberg, Germany
| | - Jana Seiler
- Division of RNA Biology and Cancer (B150), DKFZ, Heidelberg, Germany
| | - Axel Benner
- Division of Biostatistics, DKFZ, Heidelberg, Germany
| | | | - Thorsten Zenz
- Department of Molecular Therapy in Hematology and Oncology and Department of Translational Oncology, National Center for Tumor Diseases (NCT); DKFZ; and Department of Medicine V, University Hospital Heidelberg, Heidelberg, Germany
| | - Maria Göbel
- Department of Hematology, Essen University Hospital, Essen, Germany
| | - Jan Dürig
- Department of Hematology, Essen University Hospital, Essen, Germany
| | - Sven Diederichs
- Division of RNA Biology and Cancer (B150), DKFZ, Heidelberg, Germany.,Division of Cancer Research, Department of Thoracic Surgery, Medical Center-Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK), Freiburg, Germany
| | - Jérôme Paggetti
- Laboratory of Experimental Cancer Research, Luxembourg Institute of Health, Luxembourg City, Luxembourg
| | - Etienne Moussay
- Laboratory of Experimental Cancer Research, Luxembourg Institute of Health, Luxembourg City, Luxembourg
| | | | - Marc Zapatka
- Department of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Peter Lichter
- Department of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martina Seiffert
- Department of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| |
Collapse
|
27
|
Rollinson S, Young K, Bennion-Callister J, Pickering-Brown SM. Identification of biological pathways regulated by PGRN and GRN peptide treatments using transcriptome analysis. Eur J Neurosci 2016; 44:2214-25. [PMID: 27307215 DOI: 10.1111/ejn.13297] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 06/14/2016] [Indexed: 01/06/2023]
Abstract
Mutations in progranulin (PGRN) have been linked to two neurodegenerative disorders, heterozygote mutations with frontotemporal lobar degeneration (FTLD) and homozygote mutations with neuronal ceroid lipofuscinosis (NCL). Human PGRN is 593aa secreted growth factor, made up of seven and a half repeats of a highly conserved granulin motif that is cleaved to produce the granulin peptides A-G and paragranulin. While it is thought that PGRN protects against neurodegeneration through its role in inflammation and tissue repair, the role of PGRN and granulins in the nervous system is currently unclear. To better understand this, we prepared recombinant PGRN, granulin A-F and paragranulin, and used these to treat differentiated neuronal SH-SY5Y cells. Using RNA sequencing and bioinformatics techniques we investigated the functional effects of PGRN and the individual granulins upon the transcriptome. For PGRN treatment we show that the main effect of short-duration treatments is the down-regulation of transcripts, supporting that signalling pathway induction appears to be dominant effect. Gene ontology analysis, however, also supports the regulation of biological processes such as the spliceosome and proteasome in response to PGRN treatment, as well as the lysosomal pathway constituents such as CHMP1A, further supporting the role of PGRN in lysosomal function. We also show that the response to granulin treatments involves the regulation of numerous non-coding RNA's, and the granulins cluster into groups of similar activity on the basis of expression profile with paragranulin and PGRN having similar expression profiles, while granulins B, D, E and G appear more similar.
Collapse
Affiliation(s)
- Sara Rollinson
- Institute of Brain Behaviour and Mental Health, University of Manchester, AV Hill Building, Ackers Street, Manchester, M13 9PT, UK
| | - Kate Young
- Institute of Brain Behaviour and Mental Health, University of Manchester, AV Hill Building, Ackers Street, Manchester, M13 9PT, UK
| | - Janis Bennion-Callister
- Institute of Brain Behaviour and Mental Health, University of Manchester, AV Hill Building, Ackers Street, Manchester, M13 9PT, UK
| | - Stuart M Pickering-Brown
- Institute of Brain Behaviour and Mental Health, University of Manchester, AV Hill Building, Ackers Street, Manchester, M13 9PT, UK
| |
Collapse
|
28
|
Coll-Bonfill N, de la Cruz-Thea B, Pisano MV, Musri MM. Noncoding RNAs in smooth muscle cell homeostasis: implications in phenotypic switch and vascular disorders. Pflugers Arch 2016; 468:1071-87. [PMID: 27109570 DOI: 10.1007/s00424-016-1821-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 04/04/2016] [Indexed: 12/16/2022]
Abstract
Vascular smooth muscle cells (SMC) are a highly specialized cell type that exhibit extraordinary plasticity in adult animals in response to a number of environmental cues. Upon vascular injury, SMC undergo phenotypic switch from a contractile-differentiated to a proliferative/migratory-dedifferentiated phenotype. This process plays a major role in vascular lesion formation and during the development of vascular remodeling. Vascular remodeling comprises the accumulation of dedifferentiated SMC in the intima of arteries and is central to a number of vascular diseases such as arteriosclerosis, chronic obstructive pulmonary disease or pulmonary hypertension. Therefore, it is critical to understand the molecular mechanisms that govern SMC phenotype. In the last decade, a number of new classes of noncoding RNAs have been described. These molecules have emerged as key factors controlling tissue homeostasis during physiological and pathological conditions. In this review, we will discuss the role of noncoding RNAs, including microRNAs and long noncoding RNAs, in the regulation of SMC plasticity.
Collapse
Affiliation(s)
- N Coll-Bonfill
- Department of Pulmonary Medicine Hospital Clínic-Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Barcelona, Spain
| | - B de la Cruz-Thea
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, INIMEC-CONICET, Universidad Nacional de Córdoba, Friuli 2434, 5016, Córdoba, Argentina
| | - M V Pisano
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, INIMEC-CONICET, Universidad Nacional de Córdoba, Friuli 2434, 5016, Córdoba, Argentina
| | - M M Musri
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, INIMEC-CONICET, Universidad Nacional de Córdoba, Friuli 2434, 5016, Córdoba, Argentina.
| |
Collapse
|
29
|
Busch B, Bley N, Müller S, Glaß M, Misiak D, Lederer M, Vetter M, Strauß HG, Thomssen C, Hüttelmaier S. The oncogenic triangle of HMGA2, LIN28B and IGF2BP1 antagonizes tumor-suppressive actions of the let-7 family. Nucleic Acids Res 2016; 44:3845-64. [PMID: 26917013 PMCID: PMC4856984 DOI: 10.1093/nar/gkw099] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Accepted: 02/11/2016] [Indexed: 12/22/2022] Open
Abstract
The tumor-suppressive let-7 microRNA family targets various oncogene-encoding mRNAs. We identify the let-7 targets HMGA2, LIN28B and IGF2BP1 to form a let-7 antagonizing self-promoting oncogenic triangle. Surprisingly, 3′-end processing of IGF2BP1 mRNAs is unaltered in aggressive cancers and tumor-derived cells although IGF2BP1 synthesis was proposed to escape let-7 attack by APA-dependent (alternative polyadenylation) 3′ UTR shortening. However, the expression of the triangle factors is inversely correlated with let-7 levels and promoted by LIN28B impairing let-7 biogenesis. Moreover, IGF2BP1 enhances the expression of all triangle factors by recruiting the respective mRNAs in mRNPs lacking AGO proteins and let-7 miRNAs. This indicates that the downregulation of let-7, largely facilitated by LIN28B upregulation, and the protection of let-7 target mRNAs by IGF2BP1-directed shielding in mRNPs synergize in enhancing the expression of triangle factors. The oncogenic potential of this triangle was confirmed in ovarian cancer (OC)-derived ES-2 cells transduced with let-7 targeting decoys. In these, the depletion of HMGA2 only diminishes tumor cell growth under permissive conditions. The depletion of LIN28B and more prominently IGF2BP1 severely impairs tumor cell viability, self-renewal and 2D as well as 3D migration. In conclusion, this suggests the targeting of the HMGA2-LIN28B-IGF2BP1 triangle as a promising strategy in cancer treatment.
Collapse
Affiliation(s)
- Bianca Busch
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin-Luther-University Halle Wittenberg, ZAMED, Heinrich-Damerow-Str.1, 06120 Halle, Germany
| | - Nadine Bley
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin-Luther-University Halle Wittenberg, ZAMED, Heinrich-Damerow-Str.1, 06120 Halle, Germany
| | - Simon Müller
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin-Luther-University Halle Wittenberg, ZAMED, Heinrich-Damerow-Str.1, 06120 Halle, Germany
| | - Markus Glaß
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin-Luther-University Halle Wittenberg, ZAMED, Heinrich-Damerow-Str.1, 06120 Halle, Germany
| | - Danny Misiak
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin-Luther-University Halle Wittenberg, ZAMED, Heinrich-Damerow-Str.1, 06120 Halle, Germany
| | - Marcell Lederer
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin-Luther-University Halle Wittenberg, ZAMED, Heinrich-Damerow-Str.1, 06120 Halle, Germany
| | - Martina Vetter
- Clinic of Gynecology, Faculty of Medicine, Martin-Luther-University Halle Wittenberg, Ernst-Grube-Straße 40, 06120 Halle, Germany
| | - Hans-Georg Strauß
- Clinic of Gynecology, Faculty of Medicine, Martin-Luther-University Halle Wittenberg, Ernst-Grube-Straße 40, 06120 Halle, Germany
| | - Christoph Thomssen
- Clinic of Gynecology, Faculty of Medicine, Martin-Luther-University Halle Wittenberg, Ernst-Grube-Straße 40, 06120 Halle, Germany
| | - Stefan Hüttelmaier
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin-Luther-University Halle Wittenberg, ZAMED, Heinrich-Damerow-Str.1, 06120 Halle, Germany
| |
Collapse
|
30
|
Abstract
In metazoan the 3′-end processing of histone mRNAs is a conserved process involving the concerted action of many protein factors and the non-coding U7 snRNA. Recently, we identified that the processing of histone pre-mRNAs is promoted by an additional ncRNA, the Y3-derived Y3** RNA. U7 modulates the association of the U7 snRNP whereas Y3** promotes recruitment of CPSF (cleavage and polyadenylation specific factor) proteins to nascent histone transcripts at histone locus bodies (HLBs) in mammals. This enhances the 3′-end cleavage of nascent histone pre-mRNAs and modulates HLB assembly. Here we discuss new insights in the role of ncRNAs in the spatiotemporal control of histone synthesis. We propose that ncRNAs scaffold the formation of functional protein-RNA complexes and their sequential deposition on nascent histone pre-mRNAs at HLBs. These findings add to the multiple roles of ncRNAs in controlling gene expression and may provide new avenues for targeting histone synthesis in cancer.
Collapse
Affiliation(s)
- Marcel Köhn
- a Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin-Luther-University Halle Wittenberg, ZAMED , Halle , Germany
| | - Stefan Hüttelmaier
- a Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin-Luther-University Halle Wittenberg, ZAMED , Halle , Germany
| |
Collapse
|
31
|
Köhn M, Ihling C, Sinz A, Krohn K, Hüttelmaier S. The Y3** ncRNA promotes the 3' end processing of histone mRNAs. Genes Dev 2016; 29:1998-2003. [PMID: 26443846 PMCID: PMC4604341 DOI: 10.1101/gad.266486.115] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
In this study, Köhn et al. investigated how the cleavage and polyadenylation specificity factor (CPSF) is recruited to nascent histone pre-mRNAs during 3′ end processing of canonical histone mRNAs. They showed that the noncoding Y3/Y3** RNAs modulate the 3′ end processing of canonical histone mRNAs by binding to CPSF, thereby delineating a novel mechanism involved in the regulation of histone pre-mRNA processing. We demonstrate that the Y3/Y3** noncoding RNAs (ncRNAs) bind to the CPSF (cleavage and polyadenylation specificity factor) and that Y3** associates with the 3′ untranslated region (UTR) of histone pre-mRNAs. The depletion of Y3** impairs the 3′ end processing of histone pre-mRNAs as well as the formation and protein dynamics of histone locus bodies (HLBs), the site of histone mRNA synthesis and processing. HLB morphology is also disturbed by knockdown of the CPSF but not the U7-snRNP components. In conclusion, we propose that the Y3** ncRNA promotes the 3′ end processing of histone pre-mRNAs by enhancing the recruitment of the CPSF to histone pre-mRNAs at HLBs.
Collapse
Affiliation(s)
- Marcel Köhn
- Institute of Molecular Medicine, Martin-Luther-University Halle-Wittenberg, Saxony-Anhalt 06120, Germany
| | - Christian Ihling
- Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Saxony-Anhalt 06120, Germany
| | - Andrea Sinz
- Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Saxony-Anhalt 06120, Germany
| | - Knut Krohn
- Interdisziplinäres Zentrum für Klinische Forschung, Core Unit DNA-Technologies, University Leipzig, Saxony 04103, Germany
| | - Stefan Hüttelmaier
- Institute of Molecular Medicine, Martin-Luther-University Halle-Wittenberg, Saxony-Anhalt 06120, Germany
| |
Collapse
|
32
|
Kowalski MP, Krude T. Functional roles of non-coding Y RNAs. Int J Biochem Cell Biol 2015; 66:20-9. [PMID: 26159929 PMCID: PMC4726728 DOI: 10.1016/j.biocel.2015.07.003] [Citation(s) in RCA: 151] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 07/03/2015] [Accepted: 07/04/2015] [Indexed: 12/20/2022]
Abstract
Non-coding RNAs are involved in a multitude of cellular processes but the biochemical function of many small non-coding RNAs remains unclear. The family of small non-coding Y RNAs is conserved in vertebrates and related RNAs are present in some prokaryotic species. Y RNAs are also homologous to the newly identified family of non-coding stem-bulge RNAs (sbRNAs) in nematodes, for which potential physiological functions are only now emerging. Y RNAs are essential for the initiation of chromosomal DNA replication in vertebrates and, when bound to the Ro60 protein, they are involved in RNA stability and cellular responses to stress in several eukaryotic and prokaryotic species. Additionally, short fragments of Y RNAs have recently been identified as abundant components in the blood and tissues of humans and other mammals, with potential diagnostic value. While the number of functional roles of Y RNAs is growing, it is becoming increasingly clear that the conserved structural domains of Y RNAs are essential for distinct cellular functions. Here, we review the biochemical functions associated with these structural RNA domains, as well as the functional conservation of Y RNAs in different species. The existing biochemical and structural evidence supports a domain model for these small non-coding RNAs that has direct implications for the modular evolution of functional non-coding RNAs.
Collapse
Affiliation(s)
- Madzia P Kowalski
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, United Kingdom
| | - Torsten Krude
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, United Kingdom.
| |
Collapse
|
33
|
Duarte Junior FF, de Lima Neto QA, Rando FDS, de Freitas DVB, Pattaro Júnior JR, Polizelli LG, Munhoz REF, Seixas FAV, Fernandez MA. Identification and molecular structure analysis of a new noncoding RNA, a sbRNA homolog, in the silkworm Bombyx mori genome. MOLECULAR BIOSYSTEMS 2014; 11:801-8. [PMID: 25521575 DOI: 10.1039/c4mb00595c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The small noncoding group of RNAs called stem-bulge RNAs (sbRNAs), first reported in Caenorhabditis elegans, is described as molecules homologous to the Y RNAs, a specific class of noncoding RNAs that is present in vertebrates. This homology indicates the possibility of the existence of sbRNAs in other invertebrate organisms. In this work, we used bioinformatic tools and conserved sequences of sbRNAs from C. Elegans and Y RNAs to search for homologous sbRNA sequences in the Bombyx mori genome. This analysis led to the discovery of one noncoding gene, which was translated into RNA segments and comparatively analysed with segments from human and hamster Y RNAs and C. elegans sbRNAs in molecular dynamic simulations. This gene represents the first evidence for a new sbRNA-like noncoding RNA, the BmsbRNA gene, in this Lepidoptera genome.
Collapse
Affiliation(s)
- Francisco Ferreira Duarte Junior
- Departamento de Biotecnologia, Genética e Biologia Celular, Universidade Estadual de Maringá, Av. Colombo, 5790, 87020-900, Maringá, Paraná, Brasil.
| | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Chen X, Sim S, Wurtmann EJ, Feke A, Wolin SL. Bacterial noncoding Y RNAs are widespread and mimic tRNAs. RNA (NEW YORK, N.Y.) 2014; 20:1715-1724. [PMID: 25232022 PMCID: PMC4201824 DOI: 10.1261/rna.047241.114] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 07/30/2014] [Indexed: 05/30/2023]
Abstract
Many bacteria encode an ortholog of the Ro60 autoantigen, a ring-shaped protein that is bound in animal cells to noncoding RNAs (ncRNAs) called Y RNAs. Studies in Deinococcus radiodurans revealed that Y RNA tethers Ro60 to polynucleotide phosphorylase, specializing this exoribonuclease for structured RNA degradation. Although Ro60 orthologs are present in a wide range of bacteria, Y RNAs have been detected in only two species, making it unclear whether these ncRNAs are common Ro60 partners in bacteria. In this study, we report that likely Y RNAs are encoded near Ro60 in >250 bacterial and phage species. By comparing conserved features, we discovered that at least one Y RNA in each species contains a domain resembling tRNA. We show that these RNAs contain nucleotide modifications characteristic of tRNA and are substrates for several enzymes that recognize tRNAs. Our studies confirm the importance of Y RNAs in bacterial physiology and identify a new class of ncRNAs that mimic tRNA.
Collapse
Affiliation(s)
- Xinguo Chen
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, USA
| | - Soyeong Sim
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, USA
| | - Elisabeth J Wurtmann
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, USA
| | - Ann Feke
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, USA
| | - Sandra L Wolin
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, USA Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, USA
| |
Collapse
|
35
|
Beatty M, Guduric-Fuchs J, Brown E, Bridgett S, Chakravarthy U, Hogg RE, Simpson DA. Small RNAs from plants, bacteria and fungi within the order Hypocreales are ubiquitous in human plasma. BMC Genomics 2014; 15:933. [PMID: 25344700 PMCID: PMC4230795 DOI: 10.1186/1471-2164-15-933] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 10/16/2014] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND The human microbiome plays a significant role in maintaining normal physiology. Changes in its composition have been associated with bowel disease, metabolic disorders and atherosclerosis. Sequences of microbial origin have been observed within small RNA sequencing data obtained from blood samples. The aim of this study was to characterise the microbiome from which these sequences are derived. RESULTS Abundant non-human small RNA sequences were identified in plasma and plasma exosomal samples. Assembly of these short sequences into longer contigs was the pivotal novel step in ascertaining their origin by BLAST searches. Most reads mapped to rRNA sequences. The taxonomic profiles of the microbes detected were very consistent between individuals but distinct from microbiomes reported at other sites. The majority of bacterial reads were from the phylum Proteobacteria, whilst for 5 of 6 individuals over 90% of the more abundant fungal reads were from the phylum Ascomycota; of these over 90% were from the order Hypocreales. Many contigs were from plants, presumably of dietary origin. In addition, extremely abundant small RNAs derived from human Y RNAs were detected. CONCLUSIONS A characteristic profile of a subset of the human microbiome can be obtained by sequencing small RNAs present in the blood. The source and functions of these molecules remain to be determined, but the specific profiles are likely to reflect health status. The potential to provide biomarkers of diet and for the diagnosis and prognosis of human disease is immense.
Collapse
Affiliation(s)
| | | | | | | | | | | | - David Arthur Simpson
- Centre for Experimental Medicine, Queen's University Belfast, Belfast, Northern Ireland, UK.
| |
Collapse
|
36
|
Evolutionary conservation and expression of human RNA-binding proteins and their role in human genetic disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 825:1-55. [PMID: 25201102 DOI: 10.1007/978-1-4939-1221-6_1] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
RNA-binding proteins (RBPs) are effectors and regulators of posttranscriptional gene regulation (PTGR). RBPs regulate stability, maturation, and turnover of all RNAs, often binding thousands of targets at many sites. The importance of RBPs is underscored by their dysregulation or mutations causing a variety of developmental and neurological diseases. This chapter globally discusses human RBPs and provides a brief introduction to their identification and RNA targets. We review RBPs based on common structural RNA-binding domains, study their evolutionary conservation and expression, and summarize disease associations of different RBP classes.
Collapse
|