1
|
Husain RA, Jiao X, Hennings JC, Giesecke J, Palsule G, Beck-Wödl S, Osmanović D, Bjørgo K, Mir A, Ilyas M, Abbasi SM, Efthymiou S, Dominik N, Maroofian R, Houlden H, Rankin J, Pagnamenta AT, Nashabat M, Altwaijri W, Alfadhel M, Umair M, Khouj E, Reardon W, El-Hattab AW, Mekki M, Houge G, Beetz C, Bauer P, Putoux A, Lesca G, Sanlaville D, Alkuraya FS, Taylor RW, Mentzel HJ, Hübner CA, Huppke P, Hart RP, Haack TB, Kiledjian M, Rubio I. Biallelic NUDT2 variants defective in mRNA decapping cause a neurodevelopmental disease. Brain 2024; 147:1197-1205. [PMID: 38141063 PMCID: PMC10994549 DOI: 10.1093/brain/awad434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 11/08/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
Dysfunctional RNA processing caused by genetic defects in RNA processing enzymes has a profound impact on the nervous system, resulting in neurodevelopmental conditions. We characterized a recessive neurological disorder in 18 children and young adults from 10 independent families typified by intellectual disability, motor developmental delay and gait disturbance. In some patients peripheral neuropathy, corpus callosum abnormalities and progressive basal ganglia deposits were present. The disorder is associated with rare variants in NUDT2, a mRNA decapping and Ap4A hydrolysing enzyme, including novel missense and in-frame deletion variants. We show that these NUDT2 variants lead to a marked loss of enzymatic activity, strongly implicating loss of NUDT2 function as the cause of the disorder. NUDT2-deficient patient fibroblasts exhibit a markedly altered transcriptome, accompanied by changes in mRNA half-life and stability. Amongst the most up-regulated mRNAs in NUDT2-deficient cells, we identified host response and interferon-responsive genes. Importantly, add-back experiments using an Ap4A hydrolase defective in mRNA decapping highlighted loss of NUDT2 decapping as the activity implicated in altered mRNA homeostasis. Our results confirm that reduction or loss of NUDT2 hydrolase activity is associated with a neurological disease, highlighting the importance of a physiologically balanced mRNA processing machinery for neuronal development and homeostasis.
Collapse
Affiliation(s)
- Ralf A Husain
- Department of Neuropediatrics, Jena University Hospital, 07747 Jena, Germany
- Center for Rare Diseases, Jena University Hospital, 07747 Jena, Germany
| | - Xinfu Jiao
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA
| | | | - Jan Giesecke
- Department of Anaesthesiology and Intensive Care Medicine, Jena University Hospital, Member of the Leibniz Center for Photonics in Infection Research (LPI), 07747 Jena, Germany
| | - Geeta Palsule
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA
| | - Stefanie Beck-Wödl
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Dina Osmanović
- Institute of Human Genetics, Jena University Hospital, 07747 Jena, Germany
| | - Kathrine Bjørgo
- Department of Medical Genetics, Oslo University Hospital, 0424 Oslo, Norway
| | - Asif Mir
- Department of Biological Sciences, Faculty of Sciences, International Islamic University, Islamabad 44000, Pakistan
| | - Muhammad Ilyas
- Department of Biological Sciences, Faculty of Sciences, International Islamic University, Islamabad 44000, Pakistan
| | - Saad M Abbasi
- Department of Biological Sciences, Faculty of Sciences, International Islamic University, Islamabad 44000, Pakistan
| | - Stephanie Efthymiou
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Natalia Dominik
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Reza Maroofian
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Julia Rankin
- Department of Clinical Genetics, Royal Devon University Hospital, Exeter, EX1 2ED, UK
| | - Alistair T Pagnamenta
- Oxford NIHR Biomedical Research Centre, Wellcome Centre for Human Genetics, Oxford, OX3 7BN, UK
| | - Marwan Nashabat
- Medical Genomics Research Department, King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs, Riyadh 11426, Saudi Arabia
| | - Waleed Altwaijri
- Department of Pediatrics, Neurology Division, King Abdullah Specialist Children’s Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh 11426, Saudi Arabia
| | - Majid Alfadhel
- Medical Genomics Research Department, King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs, Riyadh 11426, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh 11426, Saudi Arabia
- Genetics and Precision Medicine Department, King Abdullah Specialized Children's Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh 11426, Saudi Arabia
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs, Riyadh 11426, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh 11426, Saudi Arabia
| | - Ebtissal Khouj
- Department of Translational Genomics, Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | | | - Ayman W El-Hattab
- Department of Clinical Sciences, College of Medicine, University of Sharjah, 27272, Sharjah, United Arab Emirates
- Department of Pediatrics, University Hospital Sharjah, 72772, Sharjah, United Arab Emirates
| | - Mohammed Mekki
- Department of Pediatrics, University Hospital Sharjah, 72772, Sharjah, United Arab Emirates
| | - Gunnar Houge
- Department of Medical Genetics, Haukeland University Hospital, 5021 Bergen, Norway
| | | | | | - Audrey Putoux
- Groupement Hospitalier Est, Hospices Civils de Lyon, Service de Génétique, Centre de Référence Anomalies du Développement, 69677 Bron Cedex, France
- Équipe GENDEV, Centre de Recherche en Neurosciences de Lyon, Univ Lyon, Univ Lyon 1, INSERM U1028 CNRS UMR5292, 69008 Lyon, France
| | - Gaetan Lesca
- Groupement Hospitalier Est, Hospices Civils de Lyon, Service de Génétique, Centre de Référence Anomalies du Développement, 69677 Bron Cedex, France
- Physiopathologie et Génétique du Neurone et du Muscle, Univ Lyon, Univ Lyon 1, CNRS, INSERM, UMR5261, U1315, Institut NeuroMyoGène, 69008 Lyon, France
| | - Damien Sanlaville
- Groupement Hospitalier Est, Hospices Civils de Lyon, Service de Génétique, Centre de Référence Anomalies du Développement, 69677 Bron Cedex, France
- Physiopathologie et Génétique du Neurone et du Muscle, Univ Lyon, Univ Lyon 1, CNRS, INSERM, UMR5261, U1315, Institut NeuroMyoGène, 69008 Lyon, France
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE1 4LP, UK
| | - Hans-Joachim Mentzel
- Center for Rare Diseases, Jena University Hospital, 07747 Jena, Germany
- Section of Pediatric Radiology, Department of Radiology, Jena University Hospital, 07747 Jena, Germany
| | - Christian A Hübner
- Center for Rare Diseases, Jena University Hospital, 07747 Jena, Germany
- Institute of Human Genetics, Jena University Hospital, 07747 Jena, Germany
| | - Peter Huppke
- Department of Neuropediatrics, Jena University Hospital, 07747 Jena, Germany
- Center for Rare Diseases, Jena University Hospital, 07747 Jena, Germany
| | - Ronald P Hart
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Megerditch Kiledjian
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA
| | - Ignacio Rubio
- Department of Anaesthesiology and Intensive Care Medicine, Jena University Hospital, Member of the Leibniz Center for Photonics in Infection Research (LPI), 07747 Jena, Germany
- Center for Sepsis Control and Care, Jena University Hospital, 07747 Jena, Germany
| |
Collapse
|
2
|
Katahira J, Ohmae T, Yasugi M, Sasaki R, Itoh Y, Kohda T, Hieda M, Yokota Hirai M, Okamoto T, Miyamoto Y. Nsp14 of SARS-CoV-2 inhibits mRNA processing and nuclear export by targeting the nuclear cap-binding complex. Nucleic Acids Res 2023; 51:7602-7618. [PMID: 37260089 PMCID: PMC10415132 DOI: 10.1093/nar/gkad483] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/12/2023] [Accepted: 05/21/2023] [Indexed: 06/02/2023] Open
Abstract
To facilitate selfish replication, viruses halt host gene expression in various ways. The nuclear export of mRNA is one such process targeted by many viruses. SARS-CoV-2, the etiological agent of severe acute respiratory syndrome, also prevents mRNA nuclear export. In this study, Nsp14, a bifunctional viral replicase subunit, was identified as a novel inhibitor of mRNA nuclear export. Nsp14 induces poly(A)+ RNA nuclear accumulation and the dissolution/coalescence of nuclear speckles. Genome-wide gene expression analysis revealed the global dysregulation of splicing and 3'-end processing defects of replication-dependent histone mRNAs by Nsp14. These abnormalities were also observed in SARS-CoV-2-infected cells. A mutation introduced at the guanine-N7-methyltransferase active site of Nsp14 diminished these inhibitory activities. Targeted capillary electrophoresis-mass spectrometry analysis (CE-MS) unveiled the production of N7-methyl-GTP in Nsp14-expressing cells. Association of the nuclear cap-binding complex (NCBC) with the mRNA cap and subsequent recruitment of U1 snRNP and the stem-loop binding protein (SLBP) were impaired by Nsp14. These data suggest that the defects in mRNA processing and export arise from the compromise of NCBC function by N7-methyl-GTP, thus exemplifying a novel viral strategy to block host gene expression.
Collapse
Affiliation(s)
- Jun Katahira
- Laboratory of Cellular Molecular Biology, Graduate School of Veterinary Sciences, Osaka Metropolitan University, 1-58 Rinku-Orai-kita, Izumisano, Osaka 598-8531, Japan
| | - Tatsuya Ohmae
- Laboratory of Cellular Molecular Biology, Graduate School of Veterinary Sciences, Osaka Metropolitan University, 1-58 Rinku-Orai-kita, Izumisano, Osaka 598-8531, Japan
| | - Mayo Yasugi
- Laboratory of Veterinary Public Health, Graduate School of Veterinary Sciences, Osaka Metropolitan University, 1-58 Rinku-Orai-kita, Izumisano, Osaka 598-8531, Japan
| | - Ryosuke Sasaki
- RIKEN Center for Sustainable Resource Science, Mass Spectrometry and Microscopy Unit, 1-7-22 Suehiro. Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Yumi Itoh
- Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tomoko Kohda
- Laboratory of Veterinary Epidemiology, Graduate School of Veterinary Sciences, Osaka Metropolitan University, 1-58 Rinku-Orai-kita, Izumisano, Osaka 598-8531, Japan
| | - Miki Hieda
- Department of Medical Technology, Ehime Prefectural University of Health Sciences, 543 Tobe-Cho Takaoda, Iyo, Ehime791-2102, Japan
| | - Masami Yokota Hirai
- RIKEN Center for Sustainable Resource Science, Mass Spectrometry and Microscopy Unit, 1-7-22 Suehiro. Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Toru Okamoto
- Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yoichi Miyamoto
- Laboratory of Nuclear Transport Dynamics, National Institutes of Biomedical Innovation, Health, and Nutrition (NIBIOHN), 7-6-8 Saito Asagi, Ibaraki, Osaka 567-0085, Japan
| |
Collapse
|
3
|
Wu S, Ballah AK, Che W, Wang X. M7G-related LncRNAs: A comprehensive analysis of the prognosis and immunity in glioma. Front Genet 2022; 13:961278. [DOI: 10.3389/fgene.2022.961278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 11/02/2022] [Indexed: 11/17/2022] Open
Abstract
Today, numerous international researchers have demonstrated that N7-methylguanosine (m7G) related long non-coding RNAs (m7G-related lncRNAs) are closely linked to the happenings and developments of various human beings’ cancers. However, the connection between m7G-related lncRNAs and glioma prognosis has not been investigated. We did this study to look for new potential biomarkers and construct an m7G-related lncRNA prognostic signature for glioma. We identified those lncRNAs associated with DEGs from glioma tissue sequences as m7G-related lncRNAs. First, we used Pearson’s correlation analysis to identify 28 DEGs by glioma and normal brain tissue gene sequences and predicated 657 m7G-related lncRNAs. Then, eight lncRNAs associated with prognosis were obtained and used to construct the m7G risk score model by lasso and Cox regression analysis methods. Furthermore, we used Kaplan-Meier analysis, time-dependent ROC, principal component analysis, clinical variables, independent prognostic analysis, nomograms, calibration curves, and expression levels of lncRNAs to determine the model’s accuracy. Importantly, we validated the model with external and internal validation methods and found it has strong predictive power. Finally, we performed functional enrichment analysis (GSEA, aaGSEA enrichment analyses) and analyzed immune checkpoints, associated pathways, and drug sensitivity based on predictors. In conclusion, we successfully constructed the formula of m7G-related lncRNAs with powerful predictive functions. Our study provides instructional value for analyzing glioma pathogenesis and offers potential research targets for glioma treatment and scientific research.
Collapse
|
4
|
Ma X, Yang B, Yang Y, Wu G, Ma X, Yu X, Li Y, Wang Y, Guo Q. Identification of N7-methylguanosine-related IncRNA signature as a potential predictive biomarker for colon adenocarcinoma. Front Genet 2022; 13:946845. [PMID: 36105111 PMCID: PMC9465161 DOI: 10.3389/fgene.2022.946845] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 07/21/2022] [Indexed: 11/16/2022] Open
Abstract
N7-Methylguanosine (m7G) is an RNA modification serving as a key part of colon cancer development. Thus, a comprehensive analysis was executed to explore prognostic roles and associations with the immune status of the m7G-related lncRNA (m7G-RNAs) in colon adenocarcinoma (COAD). Identification of m7G-RNAs was achieved via Pearson’s correlation analysis of lncRNAs in the TCGA-COAD dataset and m7G regulators. A prognostic signature was developed via LASSO analyses. ESTIMATE, CIBERSORT, and ssGSEA algorithms were utilized to assess immune infiltration between different risk groups. Survival analysis suggested the high-risk group possesses poor outcomes compared with the low-risk group. According to the ROC curves, the m7G-RNAs signature exhibited a reliable capability of prediction (AUCs at 1, 3, and 5 years were 0.770, 0.766, and 0.849, respectively). Multivariate hazard analysis proved that the signature was an independent predictive indicator for OS. Moreover, the risk score was related to infiltration levels of naïve B cells, CD4+ memory T cells, and resting NK cells. The result revealed the prognostic value of m7G modification in COAD and provided a novel perspective on personalized immunotherapy strategies.
Collapse
Affiliation(s)
- Xiaomei Ma
- The First Clinical Medical College, Lanzhou University, Lanzhou, China
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China
- Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Baoshun Yang
- General Surgery Ward 5, First Hospital of Lanzhou University, Lanzhou, China
- *Correspondence: Qinghong Guo, ; Baoshun Yang,
| | - Yuan Yang
- The First Clinical Medical College, Lanzhou University, Lanzhou, China
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China
- Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Guozhi Wu
- The First Clinical Medical College, Lanzhou University, Lanzhou, China
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China
- Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Xiaoli Ma
- The First Clinical Medical College, Lanzhou University, Lanzhou, China
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China
- Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Xiao Yu
- The First Clinical Medical College, Lanzhou University, Lanzhou, China
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China
- Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Yingwen Li
- The First Clinical Medical College, Lanzhou University, Lanzhou, China
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China
- Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Yuping Wang
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China
- Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Qinghong Guo
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China
- Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
- *Correspondence: Qinghong Guo, ; Baoshun Yang,
| |
Collapse
|
5
|
Swartzel JC, Bond MJ, Pintado-Urbanc AP, Daftary M, Krone MW, Douglas T, Carder EJ, Zimmer JT, Maeda T, Simon MD, Crews CM. Targeted Degradation of mRNA Decapping Enzyme DcpS by a VHL-Recruiting PROTAC. ACS Chem Biol 2022; 17:1789-1798. [PMID: 35749470 PMCID: PMC10367122 DOI: 10.1021/acschembio.2c00145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The RNA decapping scavenger protein, DcpS, has recently been identified as a dependency in acute myeloid leukemia (AML). The potent DcpS inhibitor RG3039 attenuates AML cell viability, and shRNA knockdown of DcpS is also antiproliferative. Importantly, DcpS was found to be non-essential in normal human hematopoietic cells, which opens a therapeutic window for AML treatment by DcpS modulation. Considering this strong DcpS dependence in AML cell lines, we explored PROTAC-mediated degradation as an alternative strategy to modulate DcpS activity. Herein, we report the development of JCS-1, a PROTAC exhibiting effective degradation of DcpS at nanomolar concentrations. JCS-1 non-covalently binds DcpS with a RG3039-based warhead and recruits the E3 ligase VHL, which induces potent, rapid, and sustained DcpS degradation in several AML cell lines. JCS-1 serves as a chemical biology tool to interrogate DcpS degradation and associated changes in RNA processes in different cellular contexts, which may be an attractive strategy for the treatment of AML and other DcpS-dependent genetic disorders.
Collapse
Affiliation(s)
- Jake C Swartzel
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Michael J Bond
- Department of Pharmacology, Yale University, New Haven, Connecticut 06511, United States
| | - Andreas P Pintado-Urbanc
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States.,Institute for Biomolecular Design and Discovery, Yale University, West Haven, Connecticut 06516, United States
| | - Mehana Daftary
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Mackenzie W Krone
- Department of Molecular, Cellular, and Developmental Biology, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Todd Douglas
- Department of Molecular, Cellular, and Developmental Biology, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Evan J Carder
- Department of Molecular, Cellular, and Developmental Biology, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Joshua T Zimmer
- Institute for Biomolecular Design and Discovery, Yale University, West Haven, Connecticut 06516, United States.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Takahiro Maeda
- Division of Precision Medicine, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Matthew D Simon
- Institute for Biomolecular Design and Discovery, Yale University, West Haven, Connecticut 06516, United States.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Craig M Crews
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States.,Department of Pharmacology, Yale University, New Haven, Connecticut 06511, United States.,Department of Molecular, Cellular, and Developmental Biology, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06511, United States
| |
Collapse
|
6
|
Li H, Hu Y, Liu D, Wang J, Han P, Zhang N, Li Y. Bioinformatic Characterization of Whole Blood Neutrophils in Pelvic Inflammatory Disease: A Potential Prognostic Indicator for Transumbilical Single-Port Laparoscopic Pelvic Abscess Surgery. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:2555603. [PMID: 35401780 PMCID: PMC8993565 DOI: 10.1155/2022/2555603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/31/2021] [Accepted: 01/11/2022] [Indexed: 12/19/2022]
Abstract
The purpose of this research is to determine the prognosis of patients treated with transumbilical single-port laparoscopic surgery for acute pelvic inflammatory illness. Postoperative data on 129 patients treated with laparoscopic surgery for acute pelvic inflammatory illness were obtained retrospectively. It was observed that the shorter the time required for postoperative leukocyte recovery to normal, the shorter the time required for postoperative pain and diet recovery, as well as hospital stay, in such individuals. CIBERSORT was used to examine patient data from GEO. The most significant difference between the normal and pelvic inflammatory groups was in neutrophil content. Association study found a substantial positive correlation between the quantity of neutrophils infiltrating the immune system and the abundance of monocyte M0 infiltrating the immune system. Neutrophil immune infiltration was strongly inversely linked with plasma cells, activated CD8+ Tm cells, and active CD4+ Tm cells. Four mRNAs linked with pelvic inflammatory illness were revealed to be strongly associated with neutrophil immune infiltration, notably CALML4, COQ10B, DCPS, and PPP2R1A. The ROC revealed that CALML4 (area under the curve (AUC): 0.769, 95% confidence interval (CI): 0.638-0.881), COQ10B (AUC: 0.742, 95% CI: 0.587-0.881), PPP2R1A (AUC: 0.733 95% CI: 0.593-0.857), and DCPS (AUC: 0.745, 95% CI: 0.571-0.900) were potential markers for predicting pelvic inflammatory disease. CALML4, COQ10B, PPP2R1A, and DCPS may be critical determinants determining the amount of preoperative neutrophil infiltration and the time required for leukocyte recovery after single-port laparoscopy in acute pelvic inflammatory illness.
Collapse
Affiliation(s)
- Haining Li
- General Hospital of Ningxia Medical University, China
| | | | - Dan Liu
- General Hospital of Ningxia Medical University, China
| | | | | | | | - Yan Li
- General Hospital of Ningxia Medical University, China
| |
Collapse
|
7
|
Salamon I, Palsule G, Luo X, Roque A, Tucai S, Khosla I, Volk N, Liu W, Cui H, Pozzo VD, Zalamea P, Jiao X, D’Arcangelo G, Hart RP, Rasin MR, Kiledjian M. mRNA-Decapping Associated DcpS Enzyme Controls Critical Steps of Neuronal Development. Cereb Cortex 2022; 32:1494-1507. [PMID: 34467373 PMCID: PMC8971079 DOI: 10.1093/cercor/bhab302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/08/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
Homozygous mutations in the gene encoding the scavenger mRNA-decapping enzyme, DcpS, have been shown to underlie developmental delay and intellectual disability. Intellectual disability is associated with both abnormal neocortical development and mRNA metabolism. However, the role of DcpS and its scavenger decapping activity in neuronal development is unknown. Here, we show that human neurons derived from patients with a DcpS mutation have compromised differentiation and neurite outgrowth. Moreover, in the developing mouse neocortex, DcpS is required for the radial migration, polarity, neurite outgrowth, and identity of developing glutamatergic neurons. Collectively, these findings demonstrate that the scavenger mRNA decapping activity contributes to multiple pivotal roles in neural development and further corroborate that mRNA metabolism and neocortical pathologies are associated with intellectual disability.
Collapse
Affiliation(s)
- Iva Salamon
- Department of Neuroscience and Cell Biology, Rutgers, Robert Wood Johnson Medical School, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Geeta Palsule
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Xiaobing Luo
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Alfonso Roque
- Department of Neuroscience and Cell Biology, Rutgers, Robert Wood Johnson Medical School, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Shawn Tucai
- Department of Neuroscience and Cell Biology, Rutgers, Robert Wood Johnson Medical School, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Ishan Khosla
- Department of Neuroscience and Cell Biology, Rutgers, Robert Wood Johnson Medical School, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Nicole Volk
- Department of Neuroscience and Cell Biology, Rutgers, Robert Wood Johnson Medical School, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Wendy Liu
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Huijuan Cui
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Valentina Dal Pozzo
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Petronio Zalamea
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Xinfu Jiao
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Gabriella D’Arcangelo
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Ronald P Hart
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Mladen-Roko Rasin
- Department of Neuroscience and Cell Biology, Rutgers, Robert Wood Johnson Medical School, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Megerditch Kiledjian
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| |
Collapse
|
8
|
Evaluation of carboxyfluorescein-labeled 7-methylguanine nucleotides as probes for studying cap-binding proteins by fluorescence anisotropy. Sci Rep 2021; 11:7687. [PMID: 33833335 PMCID: PMC8032668 DOI: 10.1038/s41598-021-87306-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/26/2021] [Indexed: 11/17/2022] Open
Abstract
Fluorescence anisotropy (FA) is a powerful technique for the discovery of protein inhibitors in a high-throughput manner. In this study, we sought to develop new universal FA-based assays for the evaluation of compounds targeting mRNA 5′ cap-binding proteins of therapeutic interest, including eukaryotic translation initiation factor 4E and scavenger decapping enzyme. For this purpose, a library of 19 carboxyfluorescein probes based on 7-methylguanine nucleotides was evaluated as FA probes for these proteins. Optimal probe:protein systems were further investigated in competitive binding experiments and adapted for high-throughput screening. Using a small in-house library of compounds, we verified and confirmed the accuracy of the developed FA assay to study cap-binding protein binders. The applications of the most promising probes were then extended to include evaluation of allosteric inhibitors as well as RNA ligands. From this analysis, we confirmed the utility of the method to study small molecule ligands and evaluate differently 5′ capped RNAs.
Collapse
|
9
|
Zhang S, Zhang X, Purmann C, Ma S, Shrestha A, Davis KN, Ho M, Huang Y, Pattni R, Hung Wong W, Bernstein JA, Hallmayer J, Urban AE. Network Effects of the 15q13.3 Microdeletion on the Transcriptome and Epigenome in Human-Induced Neurons. Biol Psychiatry 2021; 89:497-509. [PMID: 32919612 PMCID: PMC9359316 DOI: 10.1016/j.biopsych.2020.06.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 06/16/2020] [Accepted: 06/16/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND The 15q13.3 microdeletion is associated with several neuropsychiatric disorders, including autism and schizophrenia. Previous association and functional studies have investigated the potential role of several genes within the deletion in neuronal dysfunction, but the molecular effects of the deletion as a whole remain largely unknown. METHODS Induced pluripotent stem cells, from 3 patients with the 15q13.3 microdeletion and 3 control subjects, were generated and converted into induced neurons. We analyzed the effects of the 15q13.3 microdeletion on genome-wide gene expression, DNA methylation, chromatin accessibility, and sensitivity to cisplatin-induced DNA damage. Furthermore, we measured gene expression changes in induced neurons with CRISPR (clustered regularly interspaced short palindromic repeats) knockouts of individual 15q13.3 microdeletion genes. RESULTS In both induced pluripotent stem cells and induced neurons, gene copy number change within the 15q13.3 microdeletion was accompanied by significantly decreased gene expression and no compensatory changes in DNA methylation or chromatin accessibility, supporting the model that haploinsufficiency of genes within the deleted region drives the disorder. Furthermore, we observed global effects of the microdeletion on the transcriptome and epigenome, with disruptions in several neuropsychiatric disorder-associated pathways and gene families, including Wnt signaling, ribosome function, DNA binding, and clustered protocadherins. Individual gene knockouts mirrored many of the observed changes in an overlapping fashion between knockouts. CONCLUSIONS Our multiomics analysis of the 15q13.3 microdeletion revealed downstream effects in pathways previously associated with neuropsychiatric disorders and indications of interactions between genes within the deletion. This molecular systems analysis can be applied to other chromosomal aberrations to further our etiological understanding of neuropsychiatric disorders.
Collapse
Affiliation(s)
- Siming Zhang
- Department of Genetics, School of Humanities and Science, Stanford University, Stanford, California
| | - Xianglong Zhang
- Department of Psychiatry and Behavioral Sciences, School of Humanities and Science, Stanford University, Stanford, California
| | - Carolin Purmann
- Department of Psychiatry and Behavioral Sciences, School of Humanities and Science, Stanford University, Stanford, California
| | - Shining Ma
- Department of Pediatrics, School of Humanities and Sciences, Stanford University, Stanford, California
| | - Anima Shrestha
- School of Medicine, Stanford University, and Department of Statistics, School of Humanities and Sciences, Stanford University, Stanford, California
| | - Kasey N Davis
- Department of Psychiatry and Behavioral Sciences, School of Humanities and Science, Stanford University, Stanford, California
| | - Marcus Ho
- Department of Psychiatry and Behavioral Sciences, School of Humanities and Science, Stanford University, Stanford, California
| | - Yiling Huang
- Department of Psychiatry and Behavioral Sciences, School of Humanities and Science, Stanford University, Stanford, California
| | - Reenal Pattni
- Department of Psychiatry and Behavioral Sciences, School of Humanities and Science, Stanford University, Stanford, California
| | - Wing Hung Wong
- Department of Pediatrics, School of Humanities and Sciences, Stanford University, Stanford, California
| | - Jonathan A Bernstein
- Department of Human Biology, School of Humanities and Science, Stanford University, Stanford, California
| | - Joachim Hallmayer
- Department of Psychiatry and Behavioral Sciences, School of Humanities and Science, Stanford University, Stanford, California
| | - Alexander E Urban
- Department of Genetics, School of Humanities and Science, Stanford University, Stanford, California; Department of Psychiatry and Behavioral Sciences, School of Humanities and Science, Stanford University, Stanford, California.
| |
Collapse
|
10
|
Mutations in genes encoding regulators of mRNA decapping and translation initiation: links to intellectual disability. Biochem Soc Trans 2021; 48:1199-1211. [PMID: 32412080 PMCID: PMC7329352 DOI: 10.1042/bst20200109] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/08/2020] [Accepted: 04/14/2020] [Indexed: 12/12/2022]
Abstract
Intellectual disability (ID) affects at least 1% of the population, and typically presents in the first few years of life. ID is characterized by impairments in cognition and adaptive behavior and is often accompanied by further delays in language and motor skills, as seen in many neurodevelopmental disorders (NDD). Recent widespread high-throughput approaches that utilize whole-exome sequencing or whole-genome sequencing have allowed for a considerable increase in the identification of these pathogenic variants in monogenic forms of ID. Notwithstanding this progress, the molecular and cellular consequences of the identified mutations remain mostly unknown. This is particularly important as the associated protein dysfunctions are the prerequisite to the identification of targets for novel drugs of these rare disorders. Recent Next-Generation sequencing-based studies have further established that mutations in genes encoding proteins involved in RNA metabolism are a major cause of NDD. Here, we review recent studies linking germline mutations in genes encoding factors mediating mRNA decay and regulators of translation, namely DCPS, EDC3, DDX6 helicase and ID. These RNA-binding proteins have well-established roles in mRNA decapping and/or translational repression, and the mutations abrogate their ability to remove 5′ caps from mRNA, diminish their interactions with cofactors and stabilize sub-sets of transcripts. Additional genes encoding RNA helicases with roles in translation including DDX3X and DHX30 have also been linked to NDD. Given the speed in the acquisition, analysis and sharing of sequencing data, and the importance of post-transcriptional regulation for brain development, we anticipate mutations in more such factors being identified and functionally characterized.
Collapse
|
11
|
Pelletier J, Schmeing TM, Sonenberg N. The multifaceted eukaryotic cap structure. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1636. [PMID: 33300197 DOI: 10.1002/wrna.1636] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/16/2020] [Accepted: 11/03/2020] [Indexed: 12/13/2022]
Abstract
The 5' cap structure is added onto RNA polymerase II transcripts soon after initiation of transcription and modulates several post-transcriptional regulatory events involved in RNA maturation. It is also required for stimulating translation initiation of many cytoplasmic mRNAs and serves to protect mRNAs from degradation. These functional properties of the cap are mediated by several cap binding proteins (CBPs) involved in nuclear and cytoplasmic gene expression steps. The role that CBPs play in gene regulation, as well as the biophysical nature by which they recognize the cap, is quite intricate. Differences in mechanisms of capping as well as nuances in cap recognition speak to the potential of targeting these processes for drug development. In this review, we focus on recent findings concerning the cap epitranscriptome, our understanding of cap binding by different CBPs, and explore therapeutic targeting of CBP-cap interaction. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Processing > Capping and 5' End Modifications Translation > Translation Mechanisms.
Collapse
Affiliation(s)
- Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Department of Oncology, McGill University, Montreal, Quebec, Canada.,Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada.,Centre de Recherche en Biologie Structurale, McGill University, Montreal, Quebec, Canada
| | - T Martin Schmeing
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Centre de Recherche en Biologie Structurale, McGill University, Montreal, Quebec, Canada
| | - Nahum Sonenberg
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| |
Collapse
|
12
|
Grozdanov PN, Masoumzadeh E, Kalscheuer VM, Bienvenu T, Billuart P, Delrue MA, Latham MP, MacDonald CC. A missense mutation in the CSTF2 gene that impairs the function of the RNA recognition motif and causes defects in 3' end processing is associated with intellectual disability in humans. Nucleic Acids Res 2020; 48:9804-9821. [PMID: 32816001 PMCID: PMC7515730 DOI: 10.1093/nar/gkaa689] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 08/03/2020] [Accepted: 08/18/2020] [Indexed: 11/25/2022] Open
Abstract
CSTF2 encodes an RNA-binding protein that is essential for mRNA cleavage and polyadenylation (C/P). No disease-associated mutations have been described for this gene. Here, we report a mutation in the RNA recognition motif (RRM) of CSTF2 that changes an aspartic acid at position 50 to alanine (p.D50A), resulting in intellectual disability in male patients. In mice, this mutation was sufficient to alter polyadenylation sites in over 1300 genes critical for brain development. Using a reporter gene assay, we demonstrated that C/P efficiency of CSTF2D50A was lower than wild type. To account for this, we determined that p.D50A changed locations of amino acid side chains altering RNA binding sites in the RRM. The changes modified the electrostatic potential of the RRM leading to a greater affinity for RNA. These results highlight the significance of 3′ end mRNA processing in expression of genes important for brain plasticity and neuronal development.
Collapse
Affiliation(s)
- Petar N Grozdanov
- Department of Cell Biology & Biochemistry, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430-6540, USA
| | - Elahe Masoumzadeh
- Department of Chemistry & Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA
| | - Vera M Kalscheuer
- Max Planck Institute for Molecular Genetics, Research Group Development and Disease, Ihnestr. 63-73, D-14195 Berlin, Germany
| | - Thierry Bienvenu
- Institut de Psychiatrie et de Neurosciences de Paris, Inserm U1266, 102 rue de la Santé, 75014 Paris, France
| | - Pierre Billuart
- Institut de Psychiatrie et de Neurosciences de Paris, Inserm U1266, 102 rue de la Santé, 75014 Paris, France
| | - Marie-Ange Delrue
- Département de Génétique Médicale, CHU Sainte Justine, Montréal, Canada
| | - Michael P Latham
- Department of Chemistry & Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA
| | - Clinton C MacDonald
- Department of Cell Biology & Biochemistry, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430-6540, USA
| |
Collapse
|
13
|
Masoudi M, Bereshneh AH, Rasoulinezhad M, Ashrafi MR, Garshasbi M, Tavasoli AR. Leukoencephalopathy in Al-Raqad syndrome: Expanding the clinical and neuroimaging features caused by a biallelic novel missense variant in DCPS. Am J Med Genet A 2020; 182:2391-2398. [PMID: 32770650 DOI: 10.1002/ajmg.a.61776] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 05/05/2020] [Accepted: 05/07/2020] [Indexed: 11/11/2022]
Abstract
Al-Raqad syndrome (ARS) is a rare autosomal recessive congenital disorder, associated mainly with developmental delay, and intellectual disability. This syndrome is caused by mutations in DCPS, encoding scavenger mRNA decapping enzyme, which plays a role in the 3-prime-end mRNA decay pathway. Whole-exome sequencing was performed on an offspring of a consanguineous family presenting with developmental delay, intellectual disability, growth retardation, mild craniofacial abnormalities, cerebral and cerebellar atrophy, and white matter diffuse hypomyelination pattern. A novel biallelic missense variant, c.918G>C p. (Glu306Asp), in the DCPS gene was identified which was confirmed by sanger sequencing and segregation analysis subsequently. Few cases of ARS have been described up to now, and this study represents a 7-years-old boy presenting with central and peripheral nervous system impaired myelination in addition to ocular and dental manifestation, therefore outstretch both neuroimaging and clinical findings of this ultra-rare syndrome.
Collapse
Affiliation(s)
- Maryam Masoudi
- Myelin Disorders Clinic, Pediatric Neurology Division, Children's Medical Center, Pediatrics Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Hosseini Bereshneh
- Prenatal Diagnosis and Genetic Research Center, Dastgheib Hospital, Shiraz University of Medical Sciences, Shiraz, Iran.,Department of Medical Genetics, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Maryam Rasoulinezhad
- Myelin Disorders Clinic, Pediatric Neurology Division, Children's Medical Center, Pediatrics Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahmoud Reza Ashrafi
- Myelin Disorders Clinic, Pediatric Neurology Division, Children's Medical Center, Pediatrics Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran
| | - Masoud Garshasbi
- Faculty of Medical Sciences, Department of Medical Genetics, Tarbiat Modares University, Tehran, Iran
| | - Ali Reza Tavasoli
- Myelin Disorders Clinic, Pediatric Neurology Division, Children's Medical Center, Pediatrics Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
14
|
Ferenc-Mrozek A, Bojarska E, Stepinski J, Darzynkiewicz E, Lukaszewicz M. Effect of the His-Tag Location on Decapping Scavenger Enzymes and Their Hydrolytic Activity toward Cap Analogs. ACS OMEGA 2020; 5:10759-10766. [PMID: 32455195 PMCID: PMC7240826 DOI: 10.1021/acsomega.0c00304] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 04/08/2020] [Indexed: 05/11/2023]
Abstract
Decapping scavenger enzymes (DcpSs) are important players in mRNA degradation machinery and conserved in eukaryotes. Importantly, human DcpS is the recognized target for spinal muscular atrophy (SMA) and acute myeloid leukemia (AML) therapy, and has recently been connected to development of intellectual disability. Most recombinant DcpSs used in biochemical and biophysical studies are prepared as tagged proteins, with polyhistidine (His-tag) at the N-terminus or C-terminus. Our work is the first report on the parallel characterization of three versions of DcpSs (native and N- or C-terminally tagged) of three species (humans, Caenorhabditis elegans , and Ascaris suum). The native forms of all three enzymes were prepared by N-(His)10 tag cleavage. Protein thermal stability, measured by differential scanning fluorimetry (DSF), was unaffected in the case of native and tagged versions of human and A. suum DcpS; however, the melting temperature (T m) of C. elagans DcpS of was significantly influenced by the presence of the additional N- or C-tag. To investigate the impact of the tag positioning on the catalytic properties of DcpS, we tested the hydrolytic activity of native DcpS and their His-tagged counterparts toward cap dinucleotides (m7GpppG and m3 2,2,7GpppG) and m7GDP. The kinetic data indicate that dinucleotide substrates are hydrolyzed with comparable efficiency by native human and A. suum DcpS and their His-tagged forms. In contrast, both His-tagged C. elegans DcpSs exhibited higher activity toward m7GpppG than the native enzyme. m7GDP is resistant to enzymatic cleavage by all three forms of human and nematode DcpS.
Collapse
Affiliation(s)
- Aleksandra Ferenc-Mrozek
- Division
of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland
- Centre
of New Technologies, University of Warsaw, 02-093 Warsaw, Poland
| | - Elzbieta Bojarska
- Centre
of New Technologies, University of Warsaw, 02-093 Warsaw, Poland
| | - Janusz Stepinski
- Division
of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland
| | - Edward Darzynkiewicz
- Division
of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland
- Centre
of New Technologies, University of Warsaw, 02-093 Warsaw, Poland
| | - Maciej Lukaszewicz
- Division
of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland
| |
Collapse
|
15
|
Charenton C, Graille M. mRNA decapping: finding the right structures. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2018.0164. [PMID: 30397101 DOI: 10.1098/rstb.2018.0164] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2018] [Indexed: 12/14/2022] Open
Abstract
In eukaryotes, the elimination of the m7GpppN mRNA cap, a process known as decapping, is a critical, largely irreversible and highly regulated step of mRNA decay that withdraws the targeted mRNAs from the pool of translatable templates. The decapping reaction is catalysed by a multi-protein complex formed by the Dcp2 catalytic subunit and its Dcp1 cofactor, a holoenzyme that is poorly active on its own and needs several accessory proteins (Lsm1-7 complex, Pat1, Edc1-2, Edc3 and/or EDC4) to be fully efficient. Here, we discuss the several crystal structures of Dcp2 domains bound to various partners (proteins or small molecules) determined in the last couple of years that have considerably improved our current understanding of how Dcp2, assisted by its various activators, is recruited to its mRNA targets and adopts its active conformation upon substrate recognition. We also describe how, over the years, elegant integrative structural biology approaches combined to biochemistry and genetics led to the identification of the correct structure of the active Dcp1-Dcp2 holoenzyme among the many available conformations trapped by X-ray crystallography.This article is part of the theme issue '5' and 3' modifications controlling RNA degradation'.
Collapse
Affiliation(s)
- Clément Charenton
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, F-91128 Palaiseau cedex, France
| | - Marc Graille
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, F-91128 Palaiseau cedex, France
| |
Collapse
|
16
|
Alesi V, Capolino R, Genovesea S, Capriati T, Loddo S, Calvieri G, Calacci C, Diociaiuti A, Diamanti A, Novelli A, Dallapiccola B. An additional patient with a homozygous mutation in DCPS contributes to the delination of Al-Raqad syndrome. Am J Med Genet A 2018; 176:2781-2786. [PMID: 30289615 DOI: 10.1002/ajmg.a.40488] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 07/03/2018] [Accepted: 07/05/2018] [Indexed: 11/07/2022]
Abstract
DCPS gene encodes for a protein involved in gene expression regulation through promoting cap degradation during mRNA decapping processes. Mutations altering the DCPS function have been associated to a distinct disorder, Al-Raqad syndrome, so far described only in two families. We report on a patient harboring a novel homozygous missense mutation in DCPS, presenting with growth retardation, craniofacial anomalies, skin dyschromia, and neuromuscular defects. This case study explains the molecular spectrum of DCPS mutations and might contribute to the phenotypic delineation of this rare condition.
Collapse
Affiliation(s)
- Viola Alesi
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Rossella Capolino
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Silvia Genovesea
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Teresa Capriati
- Artificial Nutrition Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Sara Loddo
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Giusy Calvieri
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Chiara Calacci
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Andrea Diociaiuti
- Dermatology Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Antonella Diamanti
- Artificial Nutrition Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Antonio Novelli
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Bruno Dallapiccola
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| |
Collapse
|
17
|
Corbett AH. Post-transcriptional regulation of gene expression and human disease. Curr Opin Cell Biol 2018; 52:96-104. [PMID: 29518673 PMCID: PMC5988930 DOI: 10.1016/j.ceb.2018.02.011] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 02/08/2018] [Accepted: 02/15/2018] [Indexed: 12/18/2022]
Abstract
A large number of mutations in genes that encode RNA binding proteins cause human disease. Many of these RNA binding proteins mediate key steps in post-transcriptional regulation of gene expression from mRNA processing to eventual decay in the cytoplasm. Surprisingly, these RNA binding proteins, which are ubiquitously expressed and play fundamental roles in gene expression, are often altered in tissue-specific disease. Mutations linked to disease impact nearly every post-transcriptional processing step and cause diverse disease phenotypes in a variety of specific tissues. This review summarizes steps in post-transcriptional regulation of gene expression that have been linked to disease providing specific examples of some of the many genes affected. Finally, recent advances that hold promise for treatment of some of these diseases are presented.
Collapse
Affiliation(s)
- Anita H Corbett
- Department of Biology, RRC 1021, Emory University, 1510 Clifton Road, NE, Atlanta 30322, GA, United States.
| |
Collapse
|
18
|
Heck AM, Wilusz J. The Interplay between the RNA Decay and Translation Machinery in Eukaryotes. Cold Spring Harb Perspect Biol 2018; 10:a032839. [PMID: 29311343 PMCID: PMC5932591 DOI: 10.1101/cshperspect.a032839] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
RNA decay plays a major role in regulating gene expression and is tightly networked with other aspects of gene expression to effectively coordinate post-transcriptional regulation. The goal of this work is to provide an overview of the major factors and pathways of general messenger RNA (mRNA) decay in eukaryotic cells, and then discuss the effective interplay of this cytoplasmic process with the protein synthesis machinery. Given the transcript-specific and fluid nature of mRNA stability in response to changing cellular conditions, understanding the fundamental networking between RNA decay and translation will provide a foundation for a complete mechanistic understanding of this important aspect of cell biology.
Collapse
Affiliation(s)
- Adam M Heck
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80525
- Program in Cell & Molecular Biology, Colorado State University, Fort Collins, Colorado 80525
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80525
- Program in Cell & Molecular Biology, Colorado State University, Fort Collins, Colorado 80525
| |
Collapse
|
19
|
Scheller U, Pfisterer K, Uebe S, Ekici AB, Reis A, Jamra R, Ferrazzi F. Integrative bioinformatics analysis characterizing the role of EDC3 in mRNA decay and its association to intellectual disability. BMC Med Genomics 2018; 11:41. [PMID: 29685133 PMCID: PMC5914069 DOI: 10.1186/s12920-018-0358-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 04/04/2018] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Decapping of mRNA is an important step in the regulation of mRNA turnover and therefore of gene expression, which is a key process controlling development and homeostasis of all organisms. It has been shown that EDC3 plays a role in mRNA decapping, however its function is not well understood. Previously, we have associated a homozygous variant in EDC3 with autosomal recessive intellectual disability. Here, we investigate the functional role of EDC3. METHODS We performed transcriptome analyses in patients' samples. In addition, we established an EDC3 loss-of-function model using siRNA-based knockdown in the human neuroblastoma cell line SKNBE and carried out RNA sequencing. Integrative bioinformatics analyses were performed to identify EDC3-dependent candidate genes and/or pathways. RESULTS Our analyses revealed that 235 genes were differentially expressed in patients versus controls. In addition, AU-rich element (ARE)-containing mRNAs, whose degradation in humans has been suggested to involve EDC3, had higher fold changes than non-ARE-containing genes. The analysis of RNA sequencing data from the EDC3 in vitro loss-of-function model confirmed the higher fold changes of ARE-containing mRNAs compared to non-ARE-containing mRNAs and further showed an upregulation of long non-coding and coding RNAs. In total, 764 genes were differentially expressed. Integrative bioinformatics analyses of these genes identified dysregulated candidate pathways, including pathways related to synapses/coated vesicles and DNA replication/cell cycle. CONCLUSION Our data support the involvement of EDC3 in mRNA decay, including ARE-containing mRNAs, and suggest that EDC3 might be preferentially involved in the degradation of long coding and non-coding RNAs. Furthermore, our results associate ECD3 loss-of-function with synapses-related pathways. Collectively, our data provide novel information that might help elucidate the molecular mechanisms underlying the association of intellectual disability with the dysregulation of mRNA degradation.
Collapse
Affiliation(s)
- Ute Scheller
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Schwabachanlage 10, 91054 Erlangen, Germany
| | - Kathrin Pfisterer
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Schwabachanlage 10, 91054 Erlangen, Germany
| | - Steffen Uebe
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Schwabachanlage 10, 91054 Erlangen, Germany
| | - Arif B. Ekici
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Schwabachanlage 10, 91054 Erlangen, Germany
| | - André Reis
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Schwabachanlage 10, 91054 Erlangen, Germany
| | - Rami Jamra
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Schwabachanlage 10, 91054 Erlangen, Germany
- Institute of Human Genetics, University of Leipzig, Philipp-Rosenthal-Straße 55, 04103 Leipzig, Germany
| | - Fulvia Ferrazzi
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Schwabachanlage 10, 91054 Erlangen, Germany
| |
Collapse
|
20
|
Yamauchi T, Masuda T, Canver MC, Seiler M, Semba Y, Shboul M, Al-Raqad M, Maeda M, Schoonenberg VAC, Cole MA, Macias-Trevino C, Ishikawa Y, Yao Q, Nakano M, Arai F, Orkin SH, Reversade B, Buonamici S, Pinello L, Akashi K, Bauer DE, Maeda T. Genome-wide CRISPR-Cas9 Screen Identifies Leukemia-Specific Dependence on a Pre-mRNA Metabolic Pathway Regulated by DCPS. Cancer Cell 2018; 33:386-400.e5. [PMID: 29478914 PMCID: PMC5849534 DOI: 10.1016/j.ccell.2018.01.012] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 11/23/2017] [Accepted: 01/19/2018] [Indexed: 12/26/2022]
Abstract
To identify novel targets for acute myeloid leukemia (AML) therapy, we performed genome-wide CRISPR-Cas9 screening using AML cell lines, followed by a second screen in vivo. Here, we show that the mRNA decapping enzyme scavenger (DCPS) gene is essential for AML cell survival. The DCPS enzyme interacted with components of pre-mRNA metabolic pathways, including spliceosomes, as revealed by mass spectrometry. RG3039, a DCPS inhibitor originally developed to treat spinal muscular atrophy, exhibited anti-leukemic activity via inducing pre-mRNA mis-splicing. Humans harboring germline biallelic DCPS loss-of-function mutations do not exhibit aberrant hematologic phenotypes, indicating that DCPS is dispensable for human hematopoiesis. Our findings shed light on a pre-mRNA metabolic pathway and identify DCPS as a target for AML therapy.
Collapse
Affiliation(s)
- Takuji Yamauchi
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan; Department of Stem Cell Biology and Medicine, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Takeshi Masuda
- Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan
| | - Matthew C Canver
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | | | - Yuichiro Semba
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Mohammad Shboul
- Institute of Medical Biology, A∗STAR, 8A Biomedical Grove, Singapore 138648, Singapore
| | - Mohammed Al-Raqad
- Institute of Medical Biology, A∗STAR, 8A Biomedical Grove, Singapore 138648, Singapore; Al-Balqa Applied University, Faculty of Science, Al-Salt, Salt 19117, Jordan
| | - Manami Maeda
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Vivien A C Schoonenberg
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Mitchel A Cole
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Claudio Macias-Trevino
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Yuichi Ishikawa
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Qiuming Yao
- Department of Pathology & Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Michitaka Nakano
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Fumio Arai
- Department of Stem Cell Biology and Medicine, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Stuart H Orkin
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Bruno Reversade
- Institute of Medical Biology, A∗STAR, 8A Biomedical Grove, Singapore 138648, Singapore
| | | | - Luca Pinello
- Department of Pathology & Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Koichi Akashi
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan; Center for Cellular and Molecular Medicine, Kyushu University Hospital, Fukuoka 812-8582, Japan
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Takahiro Maeda
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Center for Cellular and Molecular Medicine, Kyushu University Hospital, Fukuoka 812-8582, Japan.
| |
Collapse
|
21
|
Lennox AL, Mao H, Silver DL. RNA on the brain: emerging layers of post-transcriptional regulation in cerebral cortex development. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2017; 7. [PMID: 28837264 DOI: 10.1002/wdev.290] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 07/19/2017] [Accepted: 07/20/2017] [Indexed: 12/11/2022]
Abstract
Embryonic development is a critical period during which neurons of the brain are generated and organized. In the developing cerebral cortex, this requires complex processes of neural progenitor proliferation, neuronal differentiation, and migration. Each step relies upon highly regulated control of gene expression. In particular, RNA splicing, stability, localization, and translation have emerged as key post-transcriptional regulatory nodes of mouse corticogenesis. Trans-regulators of RNA metabolism, including microRNAs (miRs) and RNA-binding proteins (RBPs), orchestrate diverse steps of cortical development. These trans-factors function either individually or cooperatively to influence RNAs, often of similar classes, termed RNA regulons. New technological advances raise the potential for an increasingly sophisticated understanding of post-transcriptional control in the developing neocortex. Many RNA-binding factors are also implicated in neurodevelopmental diseases of the cortex. Therefore, elucidating how RBPs and miRs converge to influence mRNA expression in progenitors and neurons will give valuable insights into mechanisms of cortical development and disease. WIREs Dev Biol 2018, 7:e290. doi: 10.1002/wdev.290 This article is categorized under: Gene Expression and Transcriptional Hierarchies > Regulatory RNA Nervous System Development > Vertebrates: Regional Development Adult Stem Cells, Tissue Renewal, and Regeneration > Stem Cells and Disease.
Collapse
Affiliation(s)
- Ashley L Lennox
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Hanqian Mao
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA.,Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, USA
| | - Debra L Silver
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA.,Department of Cell Biology, Duke University Medical Center, Durham, NC, USA.,Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
| |
Collapse
|
22
|
Kasprzyk R, Kowalska J, Wieczorek Z, Szabelski M, Stolarski R, Jemielity J. Acetylpyrene-labelled 7-methylguanine nucleotides: unusual fluorescence properties and application to decapping scavenger activity monitoring. Org Biomol Chem 2016; 14:3863-8. [PMID: 26975842 DOI: 10.1039/c6ob00419a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
7-Methylguanosine (m(7)G) nucleotides labelled with acetylpyrene (AcPy) were synthesized as fluorescent mRNA 5' end (cap) analogues. The unique fluorescent properties of m(7)G-AcPy conjugates, different from G-AcPy, can be applied to studying various mRNA cap-related processes including the evaluation of putative inhibitors of DcpS enzyme-a therapeutic target in neuromuscular diseases.
Collapse
Affiliation(s)
- Renata Kasprzyk
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland.
| | | | | | | | | | | |
Collapse
|
23
|
Kumar R, Corbett MA, van Bon BWM, Woenig JA, Weir L, Douglas E, Friend KL, Gardner A, Shaw M, Jolly LA, Tan C, Hunter MF, Hackett A, Field M, Palmer EE, Leffler M, Rogers C, Boyle J, Bienek M, Jensen C, Van Buggenhout G, Van Esch H, Hoffmann K, Raynaud M, Zhao H, Reed R, Hu H, Haas SA, Haan E, Kalscheuer VM, Gecz J. THOC2 Mutations Implicate mRNA-Export Pathway in X-Linked Intellectual Disability. Am J Hum Genet 2015; 97:302-10. [PMID: 26166480 DOI: 10.1016/j.ajhg.2015.05.021] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 05/27/2015] [Indexed: 11/30/2022] Open
Abstract
Export of mRNA from the cell nucleus to the cytoplasm is essential for protein synthesis, a process vital to all living eukaryotic cells. mRNA export is highly conserved and ubiquitous. Mutations affecting mRNA and mRNA processing or export factors, which cause aberrant retention of mRNAs in the nucleus, are thus emerging as contributors to an important class of human genetic disorders. Here, we report that variants in THOC2, which encodes a subunit of the highly conserved TREX mRNA-export complex, cause syndromic intellectual disability (ID). Affected individuals presented with variable degrees of ID and commonly observed features included speech delay, elevated BMI, short stature, seizure disorders, gait disturbance, and tremors. X chromosome exome sequencing revealed four missense variants in THOC2 in four families, including family MRX12, first ascertained in 1971. We show that two variants lead to decreased stability of THOC2 and its TREX-complex partners in cells derived from the affected individuals. Protein structural modeling showed that the altered amino acids are located in the RNA-binding domains of two complex THOC2 structures, potentially representing two different intermediate RNA-binding states of THOC2 during RNA transport. Our results show that disturbance of the canonical molecular pathway of mRNA export is compatible with life but results in altered neuronal development with other comorbidities.
Collapse
MESH Headings
- Active Transport, Cell Nucleus/genetics
- Amino Acid Sequence
- Base Sequence
- Chromosomes, Human, X/genetics
- Humans
- Mental Retardation, X-Linked/genetics
- Mental Retardation, X-Linked/pathology
- Models, Molecular
- Molecular Sequence Data
- Mutation, Missense/genetics
- Pedigree
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/genetics
- Sequence Analysis, DNA
- Syndrome
Collapse
Affiliation(s)
- Raman Kumar
- School of Paediatrics and Reproductive Health, Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia
| | - Mark A Corbett
- School of Paediatrics and Reproductive Health, Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia
| | - Bregje W M van Bon
- School of Paediatrics and Reproductive Health, Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia; Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Joshua A Woenig
- School of Paediatrics and Reproductive Health, Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia
| | - Lloyd Weir
- School of Paediatrics and Reproductive Health, Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia
| | - Evelyn Douglas
- Genetics and Molecular Pathology, SA Pathology, North Adelaide, SA 5006, Australia
| | - Kathryn L Friend
- Genetics and Molecular Pathology, SA Pathology, North Adelaide, SA 5006, Australia
| | - Alison Gardner
- School of Paediatrics and Reproductive Health, Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia
| | - Marie Shaw
- School of Paediatrics and Reproductive Health, Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia
| | - Lachlan A Jolly
- School of Paediatrics and Reproductive Health, Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia
| | - Chuan Tan
- School of Paediatrics and Reproductive Health, Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia
| | - Matthew F Hunter
- Monash Genetics, Monash Medical Centre, Clayton, VIC 3168, Australia; Department of Paediatrics, Monash University, Clayton, VIC 3168, Australia
| | - Anna Hackett
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW 2298, Australia
| | - Michael Field
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW 2298, Australia
| | - Elizabeth E Palmer
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW 2298, Australia
| | - Melanie Leffler
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW 2298, Australia
| | - Carolyn Rogers
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW 2298, Australia
| | - Jackie Boyle
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW 2298, Australia
| | - Melanie Bienek
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Corinna Jensen
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | | | - Hilde Van Esch
- Center for Human Genetics, University Hospitals Leuven, Leuven 3000, Belgium
| | - Katrin Hoffmann
- Institute of Human Genetics, Martin Luther University Halle-Wittenberg, Magdeburger Strasse 2, 06112 Halle (Saale), Germany
| | - Martine Raynaud
- INSERM U930, Imaging and Brain, François-Rabelais University, 37000 Tours, France; INSERM U930, Service de Génétique, Centre Hospitalier Régional Universitaire, 37000 Tours, France
| | - Huiying Zhao
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4029, Australia
| | - Robin Reed
- Department of Cell Biology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | - Hao Hu
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Stefan A Haas
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Eric Haan
- School of Paediatrics and Reproductive Health, Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia; South Australian Clinical Genetics Service, SA Pathology, North Adelaide, SA 5006, Australia
| | - Vera M Kalscheuer
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Jozef Gecz
- School of Paediatrics and Reproductive Health, Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia; School of Molecular and Biomedical Sciences, University of Adelaide, Adelaide, SA 5005, Australia.
| |
Collapse
|
24
|
Zhou M, Bail S, Plasterer HL, Rusche J, Kiledjian M. DcpS is a transcript-specific modulator of RNA in mammalian cells. RNA (NEW YORK, N.Y.) 2015; 21:1306-1312. [PMID: 26001796 PMCID: PMC4478349 DOI: 10.1261/rna.051573.115] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 04/09/2015] [Indexed: 06/04/2023]
Abstract
The scavenger decapping enzyme DcpS is a multifunctional protein initially identified by its property to hydrolyze the resulting cap structure following 3' end mRNA decay. In Saccharomyces cerevisiae, the DcpS homolog Dcs1 is an obligate cofactor for the 5'-3' exoribonuclease Xrn1 while the Caenorhabditis elegans homolog Dcs-1, facilitates Xrn1 mediated microRNA turnover. In both cases, this function is independent of the decapping activity. Whether DcpS and its decapping activity can affect mRNA steady state or stability in mammalian cells remains unknown. We sought to determine DcpS target genes in mammalian cells using a cell-permeable DcpS inhibitor compound, RG3039 initially developed for therapeutic treatment of spinal muscular atrophy. Global mRNA levels were examined following DcpS decapping inhibition with RG3039. The steady-state levels of 222 RNAs were altered upon RG3039 treatment. Of a subset selected for validation, two transcripts that appear to be long noncoding RNAs HS370762 and BC011766, were dependent on DcpS and its scavenger decapping catalytic activity and referred to as DcpS-responsive noncoding transcripts (DRNT) 1 and 2, respectively. Interestingly, only the increase in DRNT1 transcript was accompanied with an increase of its RNA stability and this increase was dependent on both DcpS and Xrn1. Importantly, unlike in yeast where the DcpS homolog is an obligate cofactor for Xrn1, stability of additional Xrn1 dependent RNAs were not altered by a reduction in DcpS levels. Collectively, our data demonstrate that DcpS in conjunction with Xrn1 has the potential to regulate RNA stability in a transcript-selective manner in mammalian cells.
Collapse
Affiliation(s)
- Mi Zhou
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Sophie Bail
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey 08854, USA
| | | | - James Rusche
- Repligen Corporation, Waltham, Massachusetts 02453, USA
| | - Megerditch Kiledjian
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey 08854, USA
| |
Collapse
|