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Wang WC, Hou TC, Kuo CY, Lai YC. Amplifications of EVX2 and HOXD9-HOXD13 on 2q31 in mature cystic teratomas of the ovary identified by array comparative genomic hybridization may explain teratoma characteristics in chondrogenesis and osteogenesis. J Ovarian Res 2024; 17:129. [PMID: 38907278 DOI: 10.1186/s13048-024-01458-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 06/16/2024] [Indexed: 06/23/2024] Open
Abstract
BACKGROUND Teratomas are a common type of germ cell tumor. However, only a few reports on their genomic constitution have been published. The study of teratomas may provide a better understanding of their stepwise differentiation processes and molecular bases, which could prove useful for the development of tissue-engineering technologies. METHODS In the present study, we analyzed the copy number aberrations of nine ovarian mature cystic teratomas using array comparative genomic hybridization in an attempt to reveal their genomic aberrations. RESULTS The many chromosomal aberrations observed on array comparative genomic hybridization analysis reveal the complex genetics of this tumor. Amplifications and deletions of large DNA fragments were observed in some samples, while amplifications of EVX2 and HOXD9-HOXD13 on 2q31.1, NDUFV1 on 11q13.2, and RPL10, SNORA70, DNASE1L1, TAZ, ATP6AP1, and GDI1 on Xq28 were found in all nine mature cystic teratomas. CONCLUSIONS Our results indicated that amplifications of these genes may play an important etiological role in teratoma formation. Moreover, amplifications of EVX2 and HOXD9-HOXD13 on 2q31.1, found on array comparative genomic hybridization, may help to explain the characteristics of teratomas in chondrogenesis and osteogenesis.
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Affiliation(s)
- Wen-Chung Wang
- Department of Obstetrics and Gynecology, Jen-Ai Hospital, Taichung, Taiwan
| | - Tai-Cheng Hou
- Department of Pathology, Jen-Ai Hospital, Taichung, Taiwan
| | - Chen-Yun Kuo
- Department of Pathology, Jen-Ai Hospital, Taichung, Taiwan
| | - Yen-Chein Lai
- Department of Medical Laboratory and Biotechnology, Chung Shan Medical University, No.110, Sec. 1, Chien Kuo N. Road, Taichung, 402, Taiwan, R.O.C..
- Clinical Laboratory, Chung Shan Medical University Hospital, Taichung, Taiwan.
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Tsang E, Han VX, Flutter C, Alshammery S, Keating BA, Williams T, Gloss BS, Graham ME, Aryamanesh N, Pang I, Wong M, Winlaw D, Cardamone M, Mohammad S, Gold W, Patel S, Dale RC. Ketogenic diet modifies ribosomal protein dysregulation in KMT2D Kabuki syndrome. EBioMedicine 2024; 104:105156. [PMID: 38768529 PMCID: PMC11134553 DOI: 10.1016/j.ebiom.2024.105156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 04/29/2024] [Accepted: 05/01/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND Kabuki syndrome (KS) is a genetic disorder caused by DNA mutations in KMT2D, a lysine methyltransferase that methylates histones and other proteins, and therefore modifies chromatin structure and subsequent gene expression. Ketones, derived from the ketogenic diet, are histone deacetylase inhibitors that can 'open' chromatin and encourage gene expression. Preclinical studies have shown that the ketogenic diet rescues hippocampal memory neurogenesis in mice with KS via the epigenetic effects of ketones. METHODS Single-cell RNA sequencing and mass spectrometry-based proteomics were used to explore molecular mechanisms of disease in individuals with KS (n = 4) versus controls (n = 4). FINDINGS Pathway enrichment analysis indicated that loss of function mutations in KMT2D are associated with ribosomal protein dysregulation at an RNA and protein level in individuals with KS (FDR <0.05). Cellular proteomics also identified immune dysregulation and increased abundance of other lysine modification and histone binding proteins, representing a potential compensatory mechanism. A 12-year-old boy with KS, suffering from recurrent episodes of cognitive decline, exhibited improved cognitive function and neuropsychological assessment performance after 12 months on the ketogenic diet, with concomitant improvement in transcriptomic ribosomal protein dysregulation. INTERPRETATION Our data reveals that lysine methyltransferase deficiency is associated with ribosomal protein dysfunction, with secondary immune dysregulation. Diet and the production of bioactive molecules such as ketone bodies serve as a significant environmental factor that can induce epigenetic changes and improve clinical outcomes. Integrating transcriptomic, proteomic, and clinical data can define mechanisms of disease and treatment effects in individuals with neurodevelopmental disorders. FUNDING This study was supported by the Dale NHMRC Investigator Grant (APP1193648) (R.D), Petre Foundation (R.D), and The Sydney Children's Hospital Foundation/Kids Research Early and Mid-Career Researcher Grant (E.T).
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Affiliation(s)
- Erica Tsang
- Kids Neuroscience Centre, The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, NSW, Australia; The Children's Hospital at Westmead Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Velda X Han
- Kids Neuroscience Centre, The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, NSW, Australia; Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore, Singapore; Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Chloe Flutter
- The Kabuki Syndrome Foundation - Volunteer, Northbrook, IL, USA
| | - Sarah Alshammery
- Kids Neuroscience Centre, The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, NSW, Australia; The Children's Hospital at Westmead Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Brooke A Keating
- Kids Neuroscience Centre, The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, NSW, Australia
| | - Tracey Williams
- Kids Rehab, The Children's Hospital at Westmead, Sydney, NSW, Australia
| | - Brian S Gloss
- Westmead Research Hub, Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Mark E Graham
- Biomedical Proteomics, Children's Medical Research Institute, The University of Sydney, Australia
| | - Nader Aryamanesh
- Bioinformatics Group, Children's Medical Research Institute, Westmead, Sydney, NSW, Australia; School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Ignatius Pang
- Bioinformatics Group, Children's Medical Research Institute, Westmead, Sydney, NSW, Australia
| | - Melanie Wong
- The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - David Winlaw
- Heart Centre, Ann and Robert H. Lurie Children's Hospital of Chicago and Feinberg School of Medicine, Northwestern University, USA
| | - Michael Cardamone
- Sydney Children's Hospital, Randwick, NSW, Australia; School of Clinical Medicine, University of New South Wales, NSW, Australia
| | - Shekeeb Mohammad
- Kids Neuroscience Centre, The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, NSW, Australia; The Children's Hospital at Westmead Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Wendy Gold
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, NSW, Australia; Molecular Neurobiology Research Laboratory, Kids Research, The Children's Hospital at Westmead & the Children's Medical Research Institute, NSW, Australia
| | - Shrujna Patel
- Kids Neuroscience Centre, The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, NSW, Australia; The Children's Hospital at Westmead Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Russell C Dale
- Kids Neuroscience Centre, The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, NSW, Australia; The Children's Hospital at Westmead Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia; The Brain and Mind Centre, The University of Sydney, Sydney, NSW, Australia.
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Yheskel M, Hatch HAM, Pedrosa E, Terry BK, Siebels AA, Zheng XY, Blok LER, Fencková M, Sidoli S, Schenck A, Zheng D, Lachman HM, Secombe J. KDM5-mediated transcriptional activation of ribosomal protein genes alters translation efficiency to regulate mitochondrial metabolism in neurons. Nucleic Acids Res 2024:gkae261. [PMID: 38597673 DOI: 10.1093/nar/gkae261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 03/20/2024] [Accepted: 03/31/2024] [Indexed: 04/11/2024] Open
Abstract
Genes encoding the KDM5 family of transcriptional regulators are disrupted in individuals with intellectual disability (ID). To understand the link between KDM5 and ID, we characterized five Drosophila strains harboring missense alleles analogous to those observed in patients. These alleles disrupted neuroanatomical development, cognition and other behaviors, and displayed a transcriptional signature characterized by the downregulation of many ribosomal protein genes. A similar transcriptional profile was observed in KDM5C knockout iPSC-induced human glutamatergic neurons, suggesting an evolutionarily conserved role for KDM5 proteins in regulating this class of gene. In Drosophila, reducing KDM5 changed neuronal ribosome composition, lowered the translation efficiency of mRNAs required for mitochondrial function, and altered mitochondrial metabolism. These data highlight the cellular consequences of altered KDM5-regulated transcriptional programs that could contribute to cognitive and behavioral phenotypes. Moreover, they suggest that KDM5 may be part of a broader network of proteins that influence cognition by regulating protein synthesis.
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Affiliation(s)
- Matanel Yheskel
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Hayden A M Hatch
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Erika Pedrosa
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Bethany K Terry
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Aubrey A Siebels
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Xiang Yu Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Laura E R Blok
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 Nijmegen, GA, The Netherlands
| | - Michaela Fencková
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 Nijmegen, GA, The Netherlands
- Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Ceske Budejovice 370 05, Czechia
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Annette Schenck
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 Nijmegen, GA, The Netherlands
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Neurology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
| | - Herbert M Lachman
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
| | - Julie Secombe
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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Yu W, Yuan R, Liu M, Liu K, Ding X, Hou Y. Effects of rpl1001 Gene Deletion on Cell Division of Fission Yeast and Its Molecular Mechanism. Curr Issues Mol Biol 2024; 46:2576-2597. [PMID: 38534780 DOI: 10.3390/cimb46030164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/27/2024] [Accepted: 03/12/2024] [Indexed: 03/28/2024] Open
Abstract
The rpl1001 gene encodes 60S ribosomal protein L10, which is involved in intracellular protein synthesis and cell growth. However, it is not yet known whether it is involved in the regulation of cell mitosis dynamics. This study focuses on the growth, spore production, cell morphology, the dynamics of microtubules, chromosomes, actin, myosin, and mitochondria of fission yeast (Schizosaccharomyces pombe) to investigate the impact of rpl1001 deletion on cell mitosis. RNA-Seq and bioinformatics analyses were also used to reveal key genes, such as hsp16, mfm1 and isp3, and proteasome pathways. The results showed that rpl1001 deletion resulted in slow cell growth, abnormal spore production, altered cell morphology, and abnormal microtubule number and length during interphase. The cell dynamics of the rpl1001Δ strain showed that the formation of a monopolar spindle leads to abnormal chromosome segregation with increased rate of spindle elongation in anaphase of mitosis, decreased total time of division, prolonged formation time of actin and myosin loops, and increased expression of mitochondrial proteins. Analysis of the RNA-Seq sequencing results showed that the proteasome pathway, up-regulation of isp3, and down-regulation of mfm1 and mfm2 in the rpl1001Δ strain were the main factors underpinning the increased number of spore production. Also, in the rpl1001Δ strain, down-regulation of dis1 caused the abnormal microtubule and chromosome dynamics, and down-regulation of hsp16 and pgk1 were the key genes affecting the delay of actin ring and myosin ring formation. This study reveals the effect and molecular mechanism of rpl1001 gene deletion on cell division, which provides the scientific basis for further clarifying the function of the Rpl1001 protein in cell division.
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Affiliation(s)
- Wen Yu
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong 637009, China
| | - Rongmei Yuan
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong 637009, China
| | - Mengnan Liu
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong 637009, China
| | - Ke Liu
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong 637009, China
| | - Xiang Ding
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China
| | - Yiling Hou
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong 637009, China
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Yang Q, Yu H, Li Q. Comparative Transcriptome Analysis Reveals the Role of Ribosome Reduction in Impeding Oogenesis in Female Triploid Crassostrea Gigas. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024; 26:125-135. [PMID: 38217752 DOI: 10.1007/s10126-024-10283-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 01/02/2024] [Indexed: 01/15/2024]
Abstract
The fecundity of triploid female Crassostrea gigas exhibited significant variation and was lower compared to diploid individuals. Previous studies categorized mature stage triploid female C. gigas into two groups: female α, characterized by a high number of oocytes, and female β, displaying few or no oocytes. To investigate the molecular mechanisms underlying irregular oogenesis and fecundity differences in triploid C. gigas, we performed a comparative analysis of gonad transcriptomes at different stages of gonadal development, including female α, female β, and diploids. During early oogenesis, functional enrichment analysis between female diploids and putative female β triploids revealed differently expressed genes (DEGs) in the ribosome and ribosome biogenesis pathways. Expression levels of DEGs in these pathways were significantly decreased in the putative female β triploid, suggesting a potential role of reduced ribosome levels in obstructing triploid oogenesis. Moreover, to identify regulatory pathways in gonad development, female oysters at the early and mature stages were compared. The DNA repair and recombination proteins pathways were enriched in female diploids and female α triploids but absent in female β triploids. Overall, we propose that decreased ribosome biogenesis in female triploids hinders the differentiation of germ stem cells, leading to the formation of a large number of abnormal germ cells and ultimately resulting in reduced fecundity. The variation in fertility among triploids appeared to be related to the degree of DNA damage repair during female gonad development. This study offers valuable insights into the oogenesis process in female triploid C. gigas.
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Affiliation(s)
- Qiong Yang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
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6
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Dharmadhikari AV, Abad MA, Khan S, Maroofian R, Sands TT, Ullah F, Samejima I, Wear MA, Moore KE, Kondakova E, Mitina N, Schaub T, Lee GK, Umandap CH, Berger SM, Iglesias AD, Popp B, Jamra RA, Gabriel H, Rentas S, Rippert AL, Izumi K, Conlin LK, Koboldt DC, Mosher TM, Hickey SE, Albert DVF, Norwood H, Lewanda AF, Dai H, Liu P, Mitani T, Marafi D, Pehlivan D, Posey JE, Lippa N, Vena N, Heinzen EL, Goldstein DB, Mignot C, de Sainte Agathe JM, Al-Sannaa NA, Zamani M, Sadeghian S, Azizimalamiri R, Seifia T, Zaki MS, Abdel-Salam GMH, Abdel-Hamid M, Alabdi L, Alkuraya FS, Dawoud H, Lofty A, Bauer P, Zifarelli G, Afzal E, Zafar F, Efthymiou S, Gossett D, Towne MC, Yeneabat R, Wontakal SN, Aggarwal VS, Rosenfeld JA, Tarabykin V, Ohta S, Lupski JR, Houlden H, Earnshaw WC, Davis EE, Jeyaprakash AA, Liao J. RNA methyltransferase SPOUT1/CENP-32 links mitotic spindle organization with the neurodevelopmental disorder SpADMiSS. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.09.23300329. [PMID: 38260255 PMCID: PMC10802637 DOI: 10.1101/2024.01.09.23300329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
SPOUT1/CENP-32 encodes a putative SPOUT RNA methyltransferase previously identified as a mitotic chromosome associated protein. SPOUT1/CENP-32 depletion leads to centrosome detachment from the spindle poles and chromosome misalignment. Aided by gene matching platforms, we identified 24 individuals with neurodevelopmental delays from 18 families with bi-allelic variants in SPOUT1/CENP-32 detected by exome/genome sequencing. Zebrafish spout1/cenp-32 mutants showed reduction in larval head size with concomitant apoptosis likely associated with altered cell cycle progression. In vivo complementation assays in zebrafish indicated that SPOUT1/CENP-32 missense variants identified in humans are pathogenic. Crystal structure analysis of SPOUT1/CENP-32 revealed that most disease-associated missense variants mapped to the catalytic domain. Additionally, SPOUT1/CENP-32 recurrent missense variants had reduced methyltransferase activity in vitro and compromised centrosome tethering to the spindle poles in human cells. Thus, SPOUT1/CENP-32 pathogenic variants cause an autosomal recessive neurodevelopmental disorder: SpADMiSS ( SPOUT1 Associated Development delay Microcephaly Seizures Short stature) underpinned by mitotic spindle organization defects and consequent chromosome segregation errors.
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7
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Di Vona C, Barba L, Ferrari R, de la Luna S. Loss of the DYRK1A Protein Kinase Results in the Reduction in Ribosomal Protein Gene Expression, Ribosome Mass and Reduced Translation. Biomolecules 2023; 14:31. [PMID: 38254631 PMCID: PMC10813206 DOI: 10.3390/biom14010031] [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: 11/17/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024] Open
Abstract
Ribosomal proteins (RPs) are evolutionary conserved proteins that are essential for protein translation. RP expression must be tightly regulated to ensure the appropriate assembly of ribosomes and to respond to the growth demands of cells. The elements regulating the transcription of RP genes (RPGs) have been characterized in yeast and Drosophila, yet how cells regulate the production of RPs in mammals is less well understood. Here, we show that a subset of RPG promoters is characterized by the presence of the palindromic TCTCGCGAGA motif and marked by the recruitment of the protein kinase DYRK1A. The presence of DYRK1A at these promoters is associated with the enhanced binding of the TATA-binding protein, TBP, and it is negatively correlated with the binding of the GABP transcription factor, establishing at least two clusters of RPGs that could be coordinately regulated. However, DYRK1A silencing leads to a global reduction in RPGs mRNAs, pointing at DYRK1A activities beyond those dependent on its chromatin association. Significantly, cells in which DYRK1A is depleted have reduced RP levels, fewer ribosomes, reduced global protein synthesis and a smaller size. We therefore propose a novel role for DYRK1A in coordinating the expression of genes encoding RPs, thereby controlling cell growth in mammals.
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Affiliation(s)
- Chiara Di Vona
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr Aiguader 88, 08003 Barcelona, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), 28029 Madrid, Spain
| | - Laura Barba
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr Aiguader 88, 08003 Barcelona, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), 28029 Madrid, Spain
| | - Roberto Ferrari
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Viale delle Scienze 23/A, 43124 Parma, Italy;
| | - Susana de la Luna
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr Aiguader 88, 08003 Barcelona, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), 28029 Madrid, Spain
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain
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Huang S, Zhang H, Chen W, Wang J, Wu Z, He M, Zhang J, Hu X, Xiang S. Screening of Tnfaip1-Interacting Proteins in Zebrafish Embryonic cDNA Libraries Using a Yeast Two-Hybrid System. Curr Issues Mol Biol 2023; 45:8215-8226. [PMID: 37886961 PMCID: PMC10605426 DOI: 10.3390/cimb45100518] [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: 09/18/2023] [Revised: 10/01/2023] [Accepted: 10/09/2023] [Indexed: 10/28/2023] Open
Abstract
TNFAIP1 regulates cellular biological functions, including DNA replication, DNA repair, and cell cycle, by binding to target proteins. Identification of Tnfaip1-interacting proteins contributes to the understanding of the molecular regulatory mechanisms of their biological functions. In this study, 48 hpf, 72 hpf, and 96 hpf wild-type zebrafish embryo mRNAs were used to construct yeast cDNA library. The library titer was 1.12 × 107 CFU/mL, the recombination rate was 100%, and the average length of the inserted fragments was greater than 1000 bp. A total of 43 potential interacting proteins of Tnfaip1 were identified using zebrafish Tnfaip1 as a bait protein. Utilizing GO functional annotation and KEGG signaling pathway analysis, we found that these interacting proteins are mainly involved in translation, protein catabolic process, ribosome assembly, cytoskeleton formation, amino acid metabolism, and PPAR signaling pathway. Further yeast spotting analyses identified four interacting proteins of Tnfaip1, namely, Ubxn7, Tubb4b, Rpl10, and Ybx1. The Tnfaip1-interacting proteins, screened from zebrafish embryo cDNA in this study, increased our understanding of the network of Tnfaip1-interacting proteins during the earliest embryo development and provided a molecular foundation for the future exploration of tnfaip1's biological functions.
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Affiliation(s)
- Shulan Huang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (S.H.); (H.Z.); (W.C.); (J.W.); (Z.W.); (M.H.); (J.Z.)
| | - Hongning Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (S.H.); (H.Z.); (W.C.); (J.W.); (Z.W.); (M.H.); (J.Z.)
| | - Wen Chen
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (S.H.); (H.Z.); (W.C.); (J.W.); (Z.W.); (M.H.); (J.Z.)
| | - Jiawei Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (S.H.); (H.Z.); (W.C.); (J.W.); (Z.W.); (M.H.); (J.Z.)
| | - Zhen Wu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (S.H.); (H.Z.); (W.C.); (J.W.); (Z.W.); (M.H.); (J.Z.)
| | - Meiqi He
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (S.H.); (H.Z.); (W.C.); (J.W.); (Z.W.); (M.H.); (J.Z.)
| | - Jian Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (S.H.); (H.Z.); (W.C.); (J.W.); (Z.W.); (M.H.); (J.Z.)
| | - Xiang Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (S.H.); (H.Z.); (W.C.); (J.W.); (Z.W.); (M.H.); (J.Z.)
| | - Shuanglin Xiang
- Engineering Research Center for Antibodies from Experimental Animals of Hunan Province, College of Life Sciences, Hunan Normal University, Changsha 410081, China
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Breznak SM, Peng Y, Deng L, Kotb NM, Flamholz Z, Rapisarda IT, Martin ET, LaBarge KA, Fabris D, Gavis ER, Rangan P. H/ACA snRNP-dependent ribosome biogenesis regulates translation of polyglutamine proteins. SCIENCE ADVANCES 2023; 9:eade5492. [PMID: 37343092 PMCID: PMC10284551 DOI: 10.1126/sciadv.ade5492] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 05/17/2023] [Indexed: 06/23/2023]
Abstract
Stem cells in many systems, including Drosophila germline stem cells (GSCs), increase ribosome biogenesis and translation during terminal differentiation. Here, we show that the H/ACA small nuclear ribonucleoprotein (snRNP) complex that promotes pseudouridylation of ribosomal RNA (rRNA) and ribosome biogenesis is required for oocyte specification. Reducing ribosome levels during differentiation decreased the translation of a subset of messenger RNAs that are enriched for CAG trinucleotide repeats and encode polyglutamine-containing proteins, including differentiation factors such as RNA-binding Fox protein 1. Moreover, ribosomes were enriched at CAG repeats within transcripts during oogenesis. Increasing target of rapamycin (TOR) activity to elevate ribosome levels in H/ACA snRNP complex-depleted germlines suppressed the GSC differentiation defects, whereas germlines treated with the TOR inhibitor rapamycin had reduced levels of polyglutamine-containing proteins. Thus, ribosome biogenesis and ribosome levels can control stem cell differentiation via selective translation of CAG repeat-containing transcripts.
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Affiliation(s)
- Shane M. Breznak
- Department of Biological Sciences, RNA Institute, University at Albany, 1400 Washington Avenue, LSRB 2033D, Albany, NY 12222, USA
| | - Yingshi Peng
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Limin Deng
- Department of Biological Sciences, RNA Institute, University at Albany, 1400 Washington Avenue, LSRB 2033D, Albany, NY 12222, USA
- Department of Chemistry, University of Connecticut, 55N Eagleville Rd, Storrs, CT 06269, USA
| | - Noor M. Kotb
- Department of Biological Sciences, RNA Institute, University at Albany, 1400 Washington Avenue, LSRB 2033D, Albany, NY 12222, USA
- Department of Biomedical Sciences, University at Albany School of Public Health, Albany, NY 12144, USA
| | - Zachary Flamholz
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Ian T. Rapisarda
- Department of Biological Sciences, RNA Institute, University at Albany, 1400 Washington Avenue, LSRB 2033D, Albany, NY 12222, USA
- Lake Erie College of Osteopathic Medicine, College of Medicine, 1858 W Grandview Blvd, Erie, PA 16509, USA
| | - Elliot T. Martin
- Department of Biological Sciences, RNA Institute, University at Albany, 1400 Washington Avenue, LSRB 2033D, Albany, NY 12222, USA
| | - Kara A. LaBarge
- Department of Biological Sciences, RNA Institute, University at Albany, 1400 Washington Avenue, LSRB 2033D, Albany, NY 12222, USA
| | - Dan Fabris
- Department of Biological Sciences, RNA Institute, University at Albany, 1400 Washington Avenue, LSRB 2033D, Albany, NY 12222, USA
- Department of Chemistry, University of Connecticut, 55N Eagleville Rd, Storrs, CT 06269, USA
| | - Elizabeth R. Gavis
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Prashanth Rangan
- Department of Biological Sciences, RNA Institute, University at Albany, 1400 Washington Avenue, LSRB 2033D, Albany, NY 12222, USA
- Black Family Stem Cell Institute, Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
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10
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Miller SC, MacDonald CC, Kellogg MK, Karamysheva ZN, Karamyshev AL. Specialized Ribosomes in Health and Disease. Int J Mol Sci 2023; 24:ijms24076334. [PMID: 37047306 PMCID: PMC10093926 DOI: 10.3390/ijms24076334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/21/2023] [Accepted: 03/23/2023] [Indexed: 03/30/2023] Open
Abstract
Ribosomal heterogeneity exists within cells and between different cell types, at specific developmental stages, and occurs in response to environmental stimuli. Mounting evidence supports the existence of specialized ribosomes, or specific changes to the ribosome that regulate the translation of a specific group of transcripts. These alterations have been shown to affect the affinity of ribosomes for certain mRNAs or change the cotranslational folding of nascent polypeptides at the exit tunnel. The identification of specialized ribosomes requires evidence of the incorporation of different ribosomal proteins or of modifications to rRNA and/or protein that lead(s) to physiologically relevant changes in translation. In this review, we summarize ribosomal heterogeneity and specialization in mammals and discuss their relevance to several human diseases.
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Affiliation(s)
- Sarah C. Miller
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Clinton C. MacDonald
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Morgana K. Kellogg
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | | | - Andrey L. Karamyshev
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Correspondence: ; Tel.: +1-806-743-4102
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11
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Breznak SM, Kotb NM, Rangan P. Dynamic regulation of ribosome levels and translation during development. Semin Cell Dev Biol 2023; 136:27-37. [PMID: 35725716 DOI: 10.1016/j.semcdb.2022.06.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/20/2022] [Accepted: 06/12/2022] [Indexed: 01/11/2023]
Abstract
The ability of ribosomes to translate mRNAs into proteins is the basis of all life. While ribosomes are essential for cell viability, reduction in levels of ribosomes can affect cell fate and developmental transitions in a tissue specific manner and can cause a plethora of related diseases called ribosomopathies. How dysregulated ribosomes homeostasis influences cell fate and developmental transitions is not fully understood. Model systems such as Drosophila and C. elegans oogenesis have been used to address these questions since defects in conserved steps in ribosome biogenesis result in stem cell differentiation and developmental defects. In this review, we first explore how ribosome levels affect stem cell differentiation. Second, we describe how ribosomal modifications and incorporation of ribosomal protein paralogs contribute to development. Third, we summarize how cells with perturbed ribosome biogenesis are sensed and eliminated during organismal growth.
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Affiliation(s)
- Shane M Breznak
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY, 12222, USA
| | - Noor M Kotb
- Department of Biomedical Sciences, The School of Public Health, University at Albany SUNY, 11 Albany, NY 12222, USA
| | - Prashanth Rangan
- Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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12
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Bacci L, Indio V, Rambaldelli G, Bugarin C, Magliocchetti F, Del Rio A, Pollutri D, Melchionda F, Pession A, Lanciotti M, Dufour C, Gaipa G, Montanaro L, Penzo M. Mutational analysis of ribosomal proteins in a cohort of pediatric patients with T-cell acute lymphoblastic leukemia reveals Q123R, a novel mutation in RPL10. Front Genet 2022; 13:1058468. [DOI: 10.3389/fgene.2022.1058468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/07/2022] [Indexed: 11/23/2022] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is a subtype of ALL involving the malignant expansion of T-cell progenitors. It is driven by a number of different possible genetic lesions, including mutations in genes encoding for ribosomal proteins (RPs). These are structural constituents of ribosomes, ubiquitous effectors of protein synthesis. Albeit the R98S mutation in RPL10, recurring with a higher frequency among RP mutations, has been extensively studied, less is known about the contribution of mutations occurring in other RPs. Alterations affecting translational machinery may not be well tolerated by cells, and there may be a selective pressure that determines the emergence of mutations with a compensatory effect. To explore this hypothesis, we sequenced the exomes of a cohort of 37 pediatric patients affected by T-ALL, and analyzed them to explore the co-occurrence of mutations in genes involved in ribosome biogenesis (including RPs) and translational control, and in known T-ALL driver genes. We found that some of the mutations in these sub-classes of genes tend to cluster together in different patients, indicating that their co-occurrence may confer some kind of advantage to leukemia cells. In addition, our sequencing highlighted the presence of a novel mutation in RPL10, namely the Q123R, which we found associated with a defect in protein synthesis. Our findings indicate that genetic alterations involving ribosome biogenesis and translational control should be carefully considered in the context of precision medicine in T-ALL.
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13
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Cappuccio G, De Bernardi ML, Morlando A, Peduto C, Scala I, Pinelli M, Bellacchio E, Gallo FG, Magli A, Plaitano C, Serrano M, Pías L, Català J, Bolasell M, Torella A, Nigro V, Zanni G, Brunetti‐Pierri N. Postnatal microcephaly and retinal involvement expand the phenotype of RPL10-related disorder. Am J Med Genet A 2022; 188:3032-3040. [PMID: 35876338 PMCID: PMC9545381 DOI: 10.1002/ajmg.a.62911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 05/16/2022] [Accepted: 07/07/2022] [Indexed: 01/31/2023]
Abstract
Hemizygous missense variants in the RPL10 gene encoding a ribosomal unit are responsible for an X-linked syndrome presenting with intellectual disability (ID), autism spectrum disorder, epilepsy, dysmorphic features, and multiple congenital anomalies. Among 15 individuals with RPL10-related disorder reported so far, only one patient had retinitis pigmentosa and microcephaly was observed in approximately half of the cases. By exome sequencing, three Italian and one Spanish male children, from three independent families, were found to carry the same hemizygous novel missense variant p.(Arg32Leu) in RPL10, inherited by their unaffected mother in all cases. The variant, not reported in gnomAD, is located in the 28S rRNA binding region, affecting an evolutionary conserved residue and predicted to disrupt the salt-bridge between Arg32 and Asp28. In addition to features consistent with RPL10-related disorder, all four boys had retinal degeneration and postnatal microcephaly. Pathogenic variants in genes responsible for inherited retinal degenerations were ruled out in all the probands. A novel missense RPL10 variant was detected in four probands with a recurrent phenotype including ID, dysmorphic features, progressive postnatal microcephaly, and retinal anomalies. The presented individuals suggest that retinopathy and postnatal microcephaly are clinical clues of RPL10-related disorder, and at least the retinal defect might be more specific for the p.(Arg32Leu) RPL10 variant, suggesting a specific genotype/phenotype correlation.
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Affiliation(s)
- Gerarda Cappuccio
- Department of Translational Medicine, Section of PediatricsFederico II UniversityNaplesItaly,Telethon Institute of Genetics and MedicineNaplesItaly,Present address:
Jan and Dan Duncan Neurological Research InstituteTexas Children's HospitalHoustonTexasUSA
| | | | - Alessia Morlando
- Department of Translational Medicine, Section of PediatricsFederico II UniversityNaplesItaly
| | - Cristina Peduto
- Department of Precision HealthUniversity of Campania 'Luigi Vanvitelli'NaplesItaly
| | - Iris Scala
- Department of Translational Medicine, Section of PediatricsFederico II UniversityNaplesItaly
| | - Michele Pinelli
- Department of Translational Medicine, Section of PediatricsFederico II UniversityNaplesItaly,Department of Molecular Medicine and Medical Biotechnology (DMMBM)Federico II UniversityNaplesItaly
| | - Emanuele Bellacchio
- Genetics and Rare Diseases Research DivisionBambino Gesù Children's HospitalRomeItaly
| | | | - Adriano Magli
- Department of Pediatric OphthalmologyUniversity of SalernoFiscianoItaly
| | - Carmen Plaitano
- Department of OphthalmologyA.O.U. San Giovanni Di Dio e Ruggi d'Aragona‐Scuola Medica SalernitanaSalernoItaly
| | - Mercedes Serrano
- Department of Ophthalmology and Department of Genetic and Molecular MedicineHospital Sant Joan de DéuBarcelonaSpain,U‐703 Centre for Biomedical Research on Rare Diseases (CIBER‐ER)Instituto de Salud Carlos IIIMadridSpain
| | - Leticia Pías
- Department of Ophthalmology and Department of Genetic and Molecular MedicineHospital Sant Joan de DéuBarcelonaSpain
| | - Jaume Català
- Department of Ophthalmology and Department of Genetic and Molecular MedicineHospital Sant Joan de DéuBarcelonaSpain
| | - Mercè Bolasell
- U‐703 Centre for Biomedical Research on Rare Diseases (CIBER‐ER)Instituto de Salud Carlos IIIMadridSpain
| | - Annalaura Torella
- Telethon Institute of Genetics and MedicineNaplesItaly,Department of Precision HealthUniversity of Campania 'Luigi Vanvitelli'NaplesItaly
| | - Vincenzo Nigro
- Telethon Institute of Genetics and MedicineNaplesItaly,Department of Precision HealthUniversity of Campania 'Luigi Vanvitelli'NaplesItaly
| | - Ginevra Zanni
- Unit of Muscular and Neurodegenerative Diseases, Department of NeurosciencesBambino Gesù Children's HospitalRomeItaly
| | - Nicola Brunetti‐Pierri
- Department of Translational Medicine, Section of PediatricsFederico II UniversityNaplesItaly,Telethon Institute of Genetics and MedicineNaplesItaly
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14
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Functions of block of proliferation 1 during anterior development in Xenopus laevis. PLoS One 2022; 17:e0273507. [PMID: 36007075 PMCID: PMC9409556 DOI: 10.1371/journal.pone.0273507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 08/09/2022] [Indexed: 11/19/2022] Open
Abstract
Block of proliferation 1 (Bop1) is a nucleolar protein known to be necessary for the assembly of the 60S subunit of ribosomes. Here, we show a specific bop1 expression in the developing anterior tissue of the South African clawed frog Xenopus laevis. Morpholino oligonucleotide-mediated knockdown approaches demonstrated that Bop1 is required for proper development of the cranial cartilage, brain, and the eyes. Furthermore, we show that bop1 knockdown leads to impaired retinal lamination with disorganized cell layers. Expression of neural crest-, brain-, and eye-specific marker genes was disturbed. Apoptotic and proliferative processes, which are known to be affected during ribosomal biogenesis defects, are not hindered upon bop1 knockdown. Because early Xenopus embryos contain a large store of maternal ribosomes, we considered if Bop1 might have a role independent of de novo ribosomal biogenesis. At early embryonic stages, pax6 expression was strongly reduced in bop1 morphants and synergy experiments indicate a common signaling pathway of the two molecules, Bop1 and Pax6. Our studies imply a novel function of Bop1 independent of ribosomal biogenesis.
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15
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Kumari A, Rahaman A, Zeng XA, Farooq MA, Huang Y, Yao R, Ali M, Ishrat R, Ali R. Temporal Cortex Microarray Analysis Revealed Impaired Ribosomal Biogenesis and Hyperactivity of the Glutamatergic System: An Early Signature of Asymptomatic Alzheimer's Disease. Front Neurosci 2022; 16:966877. [PMID: 35958988 PMCID: PMC9359077 DOI: 10.3389/fnins.2022.966877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 06/23/2022] [Indexed: 11/21/2022] Open
Abstract
Pathogenic aging is regarded as asymptomatic AD when there is no cognitive deficit except for neuropathology consistent with Alzheimer's disease. These individuals are highly susceptible to developing AD. Braak and Braak's theory specific to tau pathology illustrates that the brain's temporal cortex region is an initiation site for early AD progression. So, the hub gene analysis of this region may reveal early altered biological cascades that may be helpful to alleviate AD in an early stage. Meanwhile, cognitive processing also drags its attention because cognitive impairment is the ultimate result of AD. Therefore, this study aimed to explore changes in gene expression of aged control, asymptomatic AD (AsymAD), and symptomatic AD (symAD) in the temporal cortex region. We used microarray data sets to identify differentially expressed genes (DEGs) with the help of the R programming interface. Further, we constructed the protein-protein interaction (PPI) network by performing the STRING plugin in Cytoscape and determined the hub genes via the CytoHubba plugin. Furthermore, we conducted Gene Ontology (GO) enrichment analysis via Bioconductor's cluster profile package. Resultant, the AsymAD transcriptome revealed the early-stage changes of glutamatergic hyperexcitability. Whereas the connectivity of major hub genes in this network indicates a shift from initially reduced rRNA biosynthesis in the AsymAD group to impaired protein synthesis in the symAD group. Both share the phenomenon of breaking tight junctions and others. In conclusion, this study offers new understandings of the early biological vicissitudes that occur in the brain before the manifestation of symAD and gives new promising therapeutic targets for early AD intervention.
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Affiliation(s)
- Ankita Kumari
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Guangdong Key Laboratory of Food Intelligent Manufacturing, Foshan University, Foshan, China
- Overseas Expertise Introduction Centre for Discipline Innovation of Food Nutrition and Human Health (111 Centre), Guangzhou, China
| | - Abdul Rahaman
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Guangdong Key Laboratory of Food Intelligent Manufacturing, Foshan University, Foshan, China
- Overseas Expertise Introduction Centre for Discipline Innovation of Food Nutrition and Human Health (111 Centre), Guangzhou, China
- Abdul Rahaman
| | - Xin-An Zeng
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Guangdong Key Laboratory of Food Intelligent Manufacturing, Foshan University, Foshan, China
- Overseas Expertise Introduction Centre for Discipline Innovation of Food Nutrition and Human Health (111 Centre), Guangzhou, China
- *Correspondence: Xin-An Zeng
| | - Muhammad Adil Farooq
- Institute of Food Science and Technology, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
| | - Yanyan Huang
- Guangdong Key Laboratory of Food Intelligent Manufacturing, Foshan University, Foshan, China
| | - Runyu Yao
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Overseas Expertise Introduction Centre for Discipline Innovation of Food Nutrition and Human Health (111 Centre), Guangzhou, China
| | - Murtaza Ali
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Guangdong Key Laboratory of Food Intelligent Manufacturing, Foshan University, Foshan, China
- Overseas Expertise Introduction Centre for Discipline Innovation of Food Nutrition and Human Health (111 Centre), Guangzhou, China
| | - Romana Ishrat
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
- Romana Ishrat
| | - Rafat Ali
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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16
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Malone TJ, Kaczmarek LK. The role of altered translation in intellectual disability and epilepsy. Prog Neurobiol 2022; 213:102267. [PMID: 35364140 PMCID: PMC10583652 DOI: 10.1016/j.pneurobio.2022.102267] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 02/18/2022] [Accepted: 03/24/2022] [Indexed: 11/29/2022]
Abstract
A very high proportion of cases of intellectual disability are genetic in origin and are associated with the occurrence of epileptic seizures during childhood. These two disorders together effect more than 5% of the world's population. One feature linking the two diseases is that learning and memory require the synthesis of new synaptic components and ion channels, while maintenance of overall excitability also requires synthesis of similar proteins in response to altered neuronal stimulation. Many of these disorders result from mutations in proteins that regulate mRNA processing, translation initiation, translation elongation, mRNA stability or upstream translation modulators. One theme that emerges on reviewing this field is that mutations in proteins that regulate changes in translation following neuronal stimulation are more likely to result in epilepsy with intellectual disability than general translation regulators with no known role in activity-dependent changes. This is consistent with the notion that activity-dependent translation in neurons differs from that in other cells types in that the changes in local cellular composition, morphology and connectivity that occur generally in response to stimuli are directly coupled to local synaptic activity and persist for months or years after the original stimulus.
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Affiliation(s)
- Taylor J Malone
- Departments of Pharmacology, and of Cellular & Molecular Physiology, Yale University, 333 Cedar Street B-309, New Haven, CT 06520, USA
| | - Leonard K Kaczmarek
- Departments of Pharmacology, and of Cellular & Molecular Physiology, Yale University, 333 Cedar Street B-309, New Haven, CT 06520, USA.
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17
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Schreiner C, Kernl B, Dietmann P, Riegger RJ, Kühl M, Kühl SJ. The Ribosomal Protein L5 Functions During Xenopus Anterior Development Through Apoptotic Pathways. Front Cell Dev Biol 2022; 10:777121. [PMID: 35281111 PMCID: PMC8905602 DOI: 10.3389/fcell.2022.777121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 02/08/2022] [Indexed: 01/24/2023] Open
Abstract
Ribosomal biogenesis is a fundamental process necessary for cell growth and division. Ribosomal protein L5 (Rpl5) is part of the large ribosomal subunit. Mutations in this protein have been associated with the congenital disease Diamond Blackfan anemia (DBA), a so called ribosomopathy. Despite of the ubiquitous need of ribosomes, clinical manifestations of DBA include tissue-specific symptoms, e.g., craniofacial malformations, eye abnormalities, skin pigmentation failure, cardiac defects or liver cirrhosis. Here, we made use of the vertebrate model organism Xenopus laevis and showed a specific expression of rpl5 in the developing anterior tissue correlating with tissues affected in ribosomopathies. Upon Rpl5 knockdown using an antisense-based morpholino oligonucleotide approach, we showed different phenotypes affecting anterior tissue, i.e., defective cranial cartilage, malformed eyes, and microcephaly. Hence, the observed phenotypes in Xenopus laevis resemble the clinical manifestations of DBA. Analyses of the underlying molecular basis revealed that the expression of several marker genes of neural crest, eye, and brain are decreased during induction and differentiation of the respective tissue. Furthermore, Rpl5 knockdown led to decreased cell proliferation and increased cell apoptosis during early embryogenesis. Investigating the molecular mechanisms underlying Rpl5 function revealed a more than additive effect between either loss of function of Rpl5 and loss of function of c-Myc or loss of function of Rpl5 and gain of function of Tp53, suggesting a common signaling pathway of these proteins. The co-injection of the apoptosis blocking molecule Bcl2 resulted in a partial rescue of the eye phenotype, supporting the hypothesis that apoptosis is one main reason for the phenotypes occurring upon Rpl5 knockdown. With this study, we are able to shed more light on the still poorly understood molecular background of ribosomopathies.
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Affiliation(s)
- Corinna Schreiner
- Institute of Biochemistry and Molecular Biology, Ulm University, Ulm, Germany.,International Graduate School in Molecular Medicine Ulm, Ulm, Germany
| | - Bianka Kernl
- Institute of Biochemistry and Molecular Biology, Ulm University, Ulm, Germany.,International Graduate School in Molecular Medicine Ulm, Ulm, Germany
| | - Petra Dietmann
- Institute of Biochemistry and Molecular Biology, Ulm University, Ulm, Germany
| | - Ricarda J Riegger
- Institute of Biochemistry and Molecular Biology, Ulm University, Ulm, Germany
| | - Michael Kühl
- Institute of Biochemistry and Molecular Biology, Ulm University, Ulm, Germany
| | - Susanne J Kühl
- Institute of Biochemistry and Molecular Biology, Ulm University, Ulm, Germany
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18
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HEATR3 variants impair nuclear import of uL18 (RPL5) and drive Diamond-Blackfan anemia. Blood 2022; 139:3111-3126. [PMID: 35213692 PMCID: PMC9136880 DOI: 10.1182/blood.2021011846] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 02/03/2022] [Indexed: 11/21/2022] Open
Abstract
Biallelic variants in HEATR3 are associated with DBA and other clinical features in humans. HEATR3 variants destabilize the protein, resulting in a reduction of nuclear uL18 and impaired ribosome biogenesis.
The congenital bone marrow failure syndrome Diamond-Blackfan anemia (DBA) is typically associated with variants in ribosomal protein (RP) genes impairing erythroid cell development. Here we report multiple individuals with biallelic HEATR3 variants exhibiting bone marrow failure, short stature, facial and acromelic dysmorphic features, and intellectual disability. These variants destabilize a protein whose yeast homolog is known to synchronize the nuclear import of RPs uL5 (RPL11) and uL18 (RPL5), which are both critical for producing ribosomal subunits and for stabilizing the p53 tumor suppressor when ribosome biogenesis is compromised. Expression of HEATR3 variants or repression of HEATR3 expression in primary cells, cell lines of various origins, and yeast models impairs growth, differentiation, pre–ribosomal RNA processing, and ribosomal subunit formation reminiscent of DBA models of large subunit RP gene variants. Consistent with a role of HEATR3 in RP import, HEATR3-depleted cells or patient-derived fibroblasts display reduced nuclear accumulation of uL18. Hematopoietic progenitor cells expressing HEATR3 variants or small-hairpin RNAs knocking down HEATR3 synthesis reveal abnormal acceleration of erythrocyte maturation coupled to severe proliferation defects that are independent of p53 activation. Our study uncovers a new pathophysiological mechanism leading to DBA driven by biallelic HEATR3 variants and the destabilization of a nuclear import protein important for ribosome biogenesis.
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19
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Wiśniewska K, Gaffke L, Krzelowska K, Węgrzyn G, Pierzynowska K. Differences in gene expression patterns, revealed by RNA-seq analysis, between various Sanfilippo and Morquio disease subtypes. Gene 2021; 812:146090. [PMID: 34896230 DOI: 10.1016/j.gene.2021.146090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 10/11/2021] [Accepted: 11/16/2021] [Indexed: 11/04/2022]
Abstract
Mucopolysaccharidoses (MPS) are genetic disorders that affect up to 1 in 25,000 births. They are caused by dysfunctions of lysosomal hydrolases that degrade glycosaminoglycans (GAGs) which accumulate in cells, damaging their proper functioning. There are 7 types of MPS, distinguished by the kind of accumulated GAG and the defective enzyme, which differ significantly in the course of the disease. Despite the storage of the same GAGs, two of them (MPS III and IV) are divided into subtypes. While the course of MPS IV A and B is similar, the variability between MPS III A, B, C and D is high. This suggests that there are additional aspects that could influence the course of the disease. Therefore, the aim of this study was to determine differences of patterns of gene expression between all MPS III and IV subtypes. Transcriptomic studies, carried out with dermal fibroblasts from patients with all MPS III and IV subtypes, showed a significant variation in the gene expression pattern between individual MPS III subtypes, in contrast to MPS IV. Detailed analysis of transcripts with altered expression levels between MPS III subtypes indicated that these transcripts are mainly involved in maintaining the proper structure of connective tissue (COL4A1, COL4A2, COMP) and the structure of ribosomes (RPL10, RPL23, RPLP2). The results presented in this study indicate a significant role of genetic factors in the diversified course of MPS III subtypes.
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Affiliation(s)
- Karolina Wiśniewska
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Lidia Gaffke
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Karolina Krzelowska
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Karolina Pierzynowska
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland.
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20
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Regulation of mRNA translation in stem cells; links to brain disorders. Cell Signal 2021; 88:110166. [PMID: 34624487 DOI: 10.1016/j.cellsig.2021.110166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 08/09/2021] [Accepted: 09/29/2021] [Indexed: 11/22/2022]
Abstract
Translational control of gene expression is emerging as a cardinal step in the regulation of protein abundance. Especially for embryonic (ESC) and neuronal stem cells (NSC), regulation of mRNA translation is involved in the maintenance of pluripotency but also differentiation. For neuronal stem cells this regulation is linked to the various neuronal subtypes that arise in the developing brain and is linked to numerous brain disorders. Herein, we review translational control mechanisms in ESCs and NSCs during development and differentiation, and briefly discuss their link to brain disorders.
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21
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A proteome-wide atlas of lysine-reactive chemistry. Nat Chem 2021; 13:1081-1092. [PMID: 34504315 DOI: 10.1038/s41557-021-00765-4] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 07/05/2021] [Indexed: 01/24/2023]
Abstract
Recent advances in chemical proteomics have begun to characterize the reactivity and ligandability of lysines on a global scale. Yet, only a limited diversity of aminophilic electrophiles have been evaluated for interactions with the lysine proteome. Here, we report an in-depth profiling of >30 uncharted aminophilic chemotypes that greatly expands the content of ligandable lysines in human proteins. Aminophilic electrophiles showed disparate proteomic reactivities that range from selective interactions with a handful of lysines to, for a set of dicarboxaldehyde fragments, remarkably broad engagement of the covalent small-molecule-lysine interactions captured by the entire library. We used these latter 'scout' electrophiles to efficiently map ligandable lysines in primary human immune cells under stimulatory conditions. Finally, we show that aminophilic compounds perturb diverse biochemical functions through site-selective modification of lysines in proteins, including protein-RNA interactions implicated in innate immune responses. These findings support the broad potential of covalent chemistry for targeting functional lysines in the human proteome.
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22
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Kang J, Brajanovski N, Chan KT, Xuan J, Pearson RB, Sanij E. Ribosomal proteins and human diseases: molecular mechanisms and targeted therapy. Signal Transduct Target Ther 2021; 6:323. [PMID: 34462428 PMCID: PMC8405630 DOI: 10.1038/s41392-021-00728-8] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 07/12/2021] [Accepted: 07/30/2021] [Indexed: 02/07/2023] Open
Abstract
Ribosome biogenesis and protein synthesis are fundamental rate-limiting steps for cell growth and proliferation. The ribosomal proteins (RPs), comprising the structural parts of the ribosome, are essential for ribosome assembly and function. In addition to their canonical ribosomal functions, multiple RPs have extra-ribosomal functions including activation of p53-dependent or p53-independent pathways in response to stress, resulting in cell cycle arrest and apoptosis. Defects in ribosome biogenesis, translation, and the functions of individual RPs, including mutations in RPs have been linked to a diverse range of human congenital disorders termed ribosomopathies. Ribosomopathies are characterized by tissue-specific phenotypic abnormalities and higher cancer risk later in life. Recent discoveries of somatic mutations in RPs in multiple tumor types reinforce the connections between ribosomal defects and cancer. In this article, we review the most recent advances in understanding the molecular consequences of RP mutations and ribosomal defects in ribosomopathies and cancer. We particularly discuss the molecular basis of the transition from hypo- to hyper-proliferation in ribosomopathies with elevated cancer risk, a paradox termed "Dameshek's riddle." Furthermore, we review the current treatments for ribosomopathies and prospective therapies targeting ribosomal defects. We also highlight recent advances in ribosome stress-based cancer therapeutics. Importantly, insights into the mechanisms of resistance to therapies targeting ribosome biogenesis bring new perspectives into the molecular basis of cancer susceptibility in ribosomopathies and new clinical implications for cancer therapy.
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Affiliation(s)
- Jian Kang
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia
| | - Natalie Brajanovski
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia
| | - Keefe T. Chan
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia
| | - Jiachen Xuan
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia
| | - Richard B. Pearson
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia ,grid.1002.30000 0004 1936 7857Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, VIC Australia
| | - Elaine Sanij
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Clinical Pathology, University of Melbourne, Melbourne, VIC Australia ,grid.1073.50000 0004 0626 201XSt. Vincent’s Institute of Medical Research, Fitzroy, VIC Australia
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Neuditschko B, Leibetseder M, Brunmair J, Hagn G, Skos L, Gerner MC, Meier-Menches SM, Yotova I, Gerner C. Epithelial Cell Line Derived from Endometriotic Lesion Mimics Macrophage Nervous Mechanism of Pain Generation on Proteome and Metabolome Levels. Biomolecules 2021; 11:1230. [PMID: 34439896 PMCID: PMC8393596 DOI: 10.3390/biom11081230] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/09/2021] [Accepted: 08/13/2021] [Indexed: 02/07/2023] Open
Abstract
Endometriosis is a benign disease affecting one in ten women of reproductive age worldwide. Although the pain level is not correlated to the extent of the disease, it is still one of the cardinal symptoms strongly affecting the patients' quality of life. Yet, a molecular mechanism of this pathology, including the formation of pain, remains to be defined. Recent studies have indicated a close interaction between newly generated nerve cells and macrophages, leading to neurogenic inflammation in the pelvic area. In this context, the responsiveness of an endometriotic cell culture model was characterized upon inflammatory stimulation by employing a multi-omics approach, including proteomics, metabolomics and eicosanoid analysis. Differential proteomic profiling of the 12-Z endometriotic cell line treated with TNFα and IL1β unexpectedly showed that the inflammatory stimulation was able to induce a protein signature associated with neuroangiogenesis, specifically including neuropilins (NRP1/2). Untargeted metabolomic profiling in the same setup further revealed that the endometriotic cells were capable of the autonomous production of 7,8-dihydrobiopterin (BH2), 7,8-dihydroneopterin, normetanephrine and epinephrine. These metabolites are related to the development of neuropathic pain and the former three were found up-regulated upon inflammatory stimulation. Additionally, 12-Z cells were found to secrete the mono-oxygenated oxylipin 16-HETE, a known inhibitor of neutrophil aggregation and adhesion. Thus, inflammatory stimulation of endometriotic 12-Z cells led to specific protein and metabolite expression changes suggesting a direct involvement of these epithelial-like cells in endometriosis pain development.
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Affiliation(s)
- Benjamin Neuditschko
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Straße 38, 1090 Vienna, Austria; (B.N.); (M.L.); (J.B.); (G.H.); (L.S.); (S.M.M.-M.)
- Department of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Straße 42, 1090 Vienna, Austria
| | - Marlene Leibetseder
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Straße 38, 1090 Vienna, Austria; (B.N.); (M.L.); (J.B.); (G.H.); (L.S.); (S.M.M.-M.)
| | - Julia Brunmair
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Straße 38, 1090 Vienna, Austria; (B.N.); (M.L.); (J.B.); (G.H.); (L.S.); (S.M.M.-M.)
| | - Gerhard Hagn
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Straße 38, 1090 Vienna, Austria; (B.N.); (M.L.); (J.B.); (G.H.); (L.S.); (S.M.M.-M.)
| | - Lukas Skos
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Straße 38, 1090 Vienna, Austria; (B.N.); (M.L.); (J.B.); (G.H.); (L.S.); (S.M.M.-M.)
| | - Marlene C. Gerner
- Division of Biomedical Science, University of Applied Sciences, FH Campus Wien, Favoritenstraße 226, 1100 Vienna, Austria;
| | - Samuel M. Meier-Menches
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Straße 38, 1090 Vienna, Austria; (B.N.); (M.L.); (J.B.); (G.H.); (L.S.); (S.M.M.-M.)
- Department of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Straße 42, 1090 Vienna, Austria
- Joint Metabolome Facility, Faculty of Chemistry, University of Vienna, Waehringer Straße 38, 1090 Vienna, Austria
| | - Iveta Yotova
- Department of Obstetrics and Gynaecology, Medical University of Vienna, Spitalgasse 23, 1090 Vienna, Austria;
| | - Christopher Gerner
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Straße 38, 1090 Vienna, Austria; (B.N.); (M.L.); (J.B.); (G.H.); (L.S.); (S.M.M.-M.)
- Joint Metabolome Facility, Faculty of Chemistry, University of Vienna, Waehringer Straße 38, 1090 Vienna, Austria
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Norris K, Hopes T, Aspden JL. Ribosome heterogeneity and specialization in development. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 12:e1644. [PMID: 33565275 PMCID: PMC8647923 DOI: 10.1002/wrna.1644] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 12/13/2022]
Abstract
Regulation of protein synthesis is a vital step in controlling gene expression, especially during development. Over the last 10 years, it has become clear that rather than being homogeneous machines responsible for mRNA translation, ribosomes are highly heterogeneous and can play an active part in translational regulation. These "specialized ribosomes" comprise of specific protein and/or rRNA components, which are required for the translation of particular mRNAs. However, while there is extensive evidence for ribosome heterogeneity, support for specialized functions is limited. Recent work in a variety of developmental model organisms has shed some light on the biological relevance of ribosome heterogeneity. Tissue-specific expression of ribosomal components along with phenotypic analysis of ribosomal gene mutations indicate that ribosome heterogeneity and potentially specialization are common in key development processes like embryogenesis, spermatogenesis, oogenesis, body patterning, and neurogenesis. Several examples of ribosome specialization have now been proposed but strong links between ribosome heterogeneity, translation of specific mRNAs by defined mechanisms, and role of these translation events remain elusive. Furthermore, several studies have indicated that heterogeneous ribosome populations are a product of tissue-specific expression rather than specialized function and that ribosomal protein phenotypes are the result of extra-ribosomal function or overall reduced ribosome levels. Many important questions still need to be addressed in order to determine the functional importance of ribosome heterogeneity to development and disease, which is likely to vary across systems. It will be essential to dissect these issues to fully understand diseases caused by disruptions to ribosomal composition, such as ribosomopathies. This article is categorized under: Translation > Translation Regulation Translation > Ribosome Structure/Function RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Karl Norris
- Faculty of Biological Sciences, School of Molecular and Cellular BiologyUniversity of LeedsLeedsUK
- Leeds OmicsUniversity of LeedsLeedsUK
| | - Tayah Hopes
- Faculty of Biological Sciences, School of Molecular and Cellular BiologyUniversity of LeedsLeedsUK
- Leeds OmicsUniversity of LeedsLeedsUK
| | - Julie Louise Aspden
- Faculty of Biological Sciences, School of Molecular and Cellular BiologyUniversity of LeedsLeedsUK
- Leeds OmicsUniversity of LeedsLeedsUK
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Le Guen Y, Napolioni V, Belloy ME, Yu E, Krohn L, Ruskey JA, Gan-Or Z, Kennedy G, Eger SJ, Greicius MD. Common X-Chromosome Variants Are Associated with Parkinson Disease Risk. Ann Neurol 2021; 90:22-34. [PMID: 33583074 PMCID: PMC8601399 DOI: 10.1002/ana.26051] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 02/12/2021] [Accepted: 02/12/2021] [Indexed: 12/14/2022]
Abstract
OBJECTIVE The objective of this study was to identify genetic variants on the X-chromosome associated with Parkinson disease (PD) risk. METHODS We performed an X-chromosome-wide association study (XWAS) of PD risk by meta-analyzing results from sex-stratified analyses. To avoid spurious associations, we designed a specific harmonization pipeline for the X-chromosome and focused on a European ancestry sample. We included 11,142 cases, 280,164 controls, and 5,379 proxy cases, based on parental history of PD. Additionally, we tested the association of significant variants with (1) PD risk in an independent replication with 1,561 cases and 2,465 controls and (2) putamen volume in 33,360 individuals from the UK Biobank. RESULTS In the discovery meta-analysis, we identified rs7066890 (odds ratio [OR] = 1.10, 95% confidence interval [CI] = 1.06-1.14, p = 2.2 × 10-9 ), intron of GPM6B, and rs28602900 (OR = 1.10, 95% CI = 1.07-1.14, p = 1.6 × 10-8 ) in a high gene density region including RPL10, ATP6A1, FAM50A, and PLXNA3. The rs28602900 association with PD was replicated (OR = 1.16, 95% CI = 1.03-1.30, p = 0.016) and shown to colocalize with a significant expression quantitative locus (eQTL) regulating RPL10 expression in the putamen and other brain tissues in the Genotype-Tissue Expression Project. Additionally, the rs28602900 locus was found to be associated with reduced brain putamen volume. No results reached genome-wide significance in the sex-stratified analyses. INTERPRETATION We report the first XWAS of PD and identify 2 genome-wide significant loci. The rs28602900 association was replicated in an independent PD dataset and showed concordant effects in its association with putamen volume. Critically, rs26802900 is a significant eQTL of RPL10. These results support a role for ribosomal proteins in PD pathogenesis and show that the X-chromosome contributes to PD genetic risk. ANN NEUROL 2021;90:22-34.
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Affiliation(s)
- Yann Le Guen
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Valerio Napolioni
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Michael E Belloy
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Eric Yu
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada
| | - Lynne Krohn
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada
| | - Jennifer A Ruskey
- Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
| | - Ziv Gan-Or
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
| | - Gabriel Kennedy
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Sarah J Eger
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Michael D Greicius
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
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Recasens-Alvarez C, Alexandre C, Kirkpatrick J, Nojima H, Huels DJ, Snijders AP, Vincent JP. Ribosomopathy-associated mutations cause proteotoxic stress that is alleviated by TOR inhibition. Nat Cell Biol 2021; 23:127-135. [PMID: 33495632 PMCID: PMC7116740 DOI: 10.1038/s41556-020-00626-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 12/16/2020] [Indexed: 02/07/2023]
Abstract
Ribosomes are multicomponent molecular machines that synthesize all of the proteins of living cells. Most of the genes that encode the protein components of ribosomes are therefore essential. A reduction in gene dosage is often viable albeit deleterious and is associated with human syndromes, which are collectively known as ribosomopathies1-3. The cell biological basis of these pathologies has remained unclear. Here, we model human ribosomopathies in Drosophila and find widespread apoptosis and cellular stress in the resulting animals. This is not caused by insufficient protein synthesis, as reasonably expected. Instead, ribosomal protein deficiency elicits proteotoxic stress, which we suggest is caused by the accumulation of misfolded proteins that overwhelm the protein degradation machinery. We find that dampening the integrated stress response4 or autophagy increases the harm inflicted by ribosomal protein deficiency, suggesting that these activities could be cytoprotective. Inhibition of TOR activity-which decreases ribosomal protein production, slows down protein synthesis and stimulates autophagy5-reduces proteotoxic stress in our ribosomopathy model. Interventions that stimulate autophagy, combined with means of boosting protein quality control, could form the basis of a therapeutic strategy for this class of diseases.
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Affiliation(s)
| | | | | | - Hisashi Nojima
- The Francis Crick Institute, London, UK
- FUJIREBIO Inc, Tokyo, Japan
| | - David J Huels
- The Francis Crick Institute, London, UK
- Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, Academic Medical Center, Amsterdam, the Netherlands
- Academic Medical Center, Oncode Institute, Amsterdam, the Netherlands
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27
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Pollutri D, Penzo M. Ribosomal Protein L10: From Function to Dysfunction. Cells 2020; 9:cells9112503. [PMID: 33227977 PMCID: PMC7699173 DOI: 10.3390/cells9112503] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/13/2020] [Accepted: 11/16/2020] [Indexed: 12/18/2022] Open
Abstract
Eukaryotic cytoplasmic ribosomes are highly structured macromolecular complexes made up of four different ribosomal RNAs (rRNAs) and 80 ribosomal proteins (RPs), which play a central role in the decoding of genetic code for the synthesis of new proteins. Over the past 25 years, studies on yeast and human models have made it possible to identify RPL10 (ribosomal protein L10 gene), which is a constituent of the large subunit of the ribosome, as an important player in the final stages of ribosome biogenesis and in ribosome function. Here, we reviewed the literature to give an overview of the role of RPL10 in physiologic and pathologic processes, including inherited disease and cancer.
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Affiliation(s)
- Daniela Pollutri
- Department of Experimental, Diagnostic and Specialty Medicine Alma Mater Studiorum University of Bologna, Via Massarenti 9, 40138 Bologna, Italy;
- Center for Applied Biomedical Research (CRBA), Alma Mater Studiorum University of Bologna, Via Massarenti 9, 40138 Bologna, Italy
| | - Marianna Penzo
- Department of Experimental, Diagnostic and Specialty Medicine Alma Mater Studiorum University of Bologna, Via Massarenti 9, 40138 Bologna, Italy;
- Center for Applied Biomedical Research (CRBA), Alma Mater Studiorum University of Bologna, Via Massarenti 9, 40138 Bologna, Italy
- Correspondence: ; Tel.: +39-051-214-3521
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28
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Farooq M, Lindbæk L, Krogh N, Doganli C, Keller C, Mönnich M, Gonçalves AB, Sakthivel S, Mang Y, Fatima A, Andersen VS, Hussain MS, Eiberg H, Hansen L, Kjaer KW, Gopalakrishnan J, Pedersen LB, Møllgård K, Nielsen H, Baig SM, Tommerup N, Christensen ST, Larsen LA. RRP7A links primary microcephaly to dysfunction of ribosome biogenesis, resorption of primary cilia, and neurogenesis. Nat Commun 2020; 11:5816. [PMID: 33199730 PMCID: PMC7670429 DOI: 10.1038/s41467-020-19658-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 10/26/2020] [Indexed: 12/25/2022] Open
Abstract
Primary microcephaly (MCPH) is characterized by reduced brain size and intellectual disability. The exact pathophysiological mechanism underlying MCPH remains to be elucidated, but dysfunction of neuronal progenitors in the developing neocortex plays a major role. We identified a homozygous missense mutation (p.W155C) in Ribosomal RNA Processing 7 Homolog A, RRP7A, segregating with MCPH in a consanguineous family with 10 affected individuals. RRP7A is highly expressed in neural stem cells in developing human forebrain, and targeted mutation of Rrp7a leads to defects in neurogenesis and proliferation in a mouse stem cell model. RRP7A localizes to centrosomes, cilia and nucleoli, and patient-derived fibroblasts display defects in ribosomal RNA processing, primary cilia resorption, and cell cycle progression. Analysis of zebrafish embryos supported that the patient mutation in RRP7A causes reduced brain size, impaired neurogenesis and cell proliferation, and defective ribosomal RNA processing. These findings provide novel insight into human brain development and MCPH. The RRP7A a gene is involved in ribosome biogenesis. Here the authors report a homozygous missense mutation segregating with primary microcephaly, and show that this occurs via functional defects in both nucleoli and primary cilia disrupting cell proliferation and neurogenesis.
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Affiliation(s)
- Muhammad Farooq
- Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen, Denmark.,Department of Biochemistry and Biotechnology, The Islamia University of Bahawalpur, Baghdad ul Jadeed Campus, 63100, Bahawalpur, Punjab, Pakistan
| | - Louise Lindbæk
- Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen, Denmark
| | - Nicolai Krogh
- Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen, Denmark
| | - Canan Doganli
- Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen, Denmark
| | - Cecilie Keller
- Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen, Denmark
| | - Maren Mönnich
- Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen, Denmark
| | - André Brás Gonçalves
- Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen, Denmark
| | - Srinivasan Sakthivel
- Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen, Denmark
| | - Yuan Mang
- Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen, Denmark
| | - Ambrin Fatima
- Human Molecular Genetics Laboratory; Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering PIEAS, Jhang Road, 38000, Faisalabad, Punjab, Pakistan
| | - Vivi Søgaard Andersen
- Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen, Denmark
| | - Muhammad S Hussain
- Institute of Biochemistry I, University of Cologne, Joseph-Stelzmann-Strasse 52, D50931, Cologne, Germany.,Cologne Center for Genomics and Center for Molecular Medicine Cologne, University of Cologne, Robert-Koch-Strasse 21, D50931, Cologne, Germany
| | - Hans Eiberg
- Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen, Denmark
| | - Lars Hansen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen, Denmark
| | - Klaus Wilbrandt Kjaer
- Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen, Denmark
| | - Jay Gopalakrishnan
- Institute of Human Genetics, Universitätsstrasse 1, Heinrich-Heine-University, D-40225, Düsseldorf, Germany
| | - Lotte Bang Pedersen
- Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen, Denmark
| | - Kjeld Møllgård
- Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen, Denmark
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen, Denmark
| | - Shahid M Baig
- Human Molecular Genetics Laboratory; Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering PIEAS, Jhang Road, 38000, Faisalabad, Punjab, Pakistan
| | - Niels Tommerup
- Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen, Denmark
| | - Søren Tvorup Christensen
- Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen, Denmark.
| | - Lars Allan Larsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen, Denmark.
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Diofano F, Weinmann K, Schneider I, Thiessen KD, Rottbauer W, Just S. Genetic compensation prevents myopathy and heart failure in an in vivo model of Bag3 deficiency. PLoS Genet 2020; 16:e1009088. [PMID: 33137814 PMCID: PMC7605898 DOI: 10.1371/journal.pgen.1009088] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/31/2020] [Indexed: 12/15/2022] Open
Abstract
Mutations in the molecular co-chaperone Bcl2-associated athanogene 3 (BAG3) are found to cause dilated cardiomyopathy (DCM), resulting in systolic dysfunction and heart failure, as well as myofibrillar myopathy (MFM), which is characterized by protein aggregation and myofibrillar disintegration in skeletal muscle cells. Here, we generated a CRISPR/Cas9-induced Bag3 knockout zebrafish line and found the complete preservation of heart and skeletal muscle structure and function during embryonic development, in contrast to morpholino-mediated knockdown of Bag3. Intriguingly, genetic compensation, a process of transcriptional adaptation which acts independent of protein feedback loops, was found to prevent heart and skeletal muscle damage in our Bag3 knockout model. Proteomic profiling and quantitative real-time PCR analyses identified Bag2, another member of the Bag protein family, significantly upregulated on a transcript and protein level in bag3-/- mutants. This implied that the decay of bag3 mutant mRNA in homozygous bag3-/- embryos caused the transcriptional upregulation of bag2 expression. We further demonstrated that morpholino-mediated knockdown of Bag2 in bag3-/- embryos evoked severe functional and structural heart and skeletal muscle defects, which are similar to Bag3 morphants. However, Bag2 knockdown in bag3+/+ or bag3+/- embryos did not result in (cardio-)myopathy. Finally, we found that inhibition of the nonsense-mediated mRNA decay (NMD) machinery by knockdown of upf1, an essential NMD factor, caused severe heart and skeletal muscle defects in bag3-/- mutants due to the blockade of transcriptional adaptation of bag2 expression. Our findings provide evidence that genetic compensation might vitally influence the penetrance of disease-causing bag3 mutations in vivo. One form of genetic compensation is described as transcriptional adaptation of gene expression triggered by deleterious gene mutations. Although the precise molecular mechanism that induces genetic compensation needs to be defined, it represents a powerful biological phenomenon that warrants genetic robustness. We find that antisense-mediated knockdown of Bag3 in zebrafish embryos causes heart failure and myopathy. By contrast, CRISPR/Cas9-induced depletion of Bag3 does not result in the abrogation of heart and skeletal muscle function in zebrafish embryos. We find here that transcriptional activation of the Bag family member bag2 is capable of restoring heart and skeletal muscle function in bag3 mutant embryos, whereas this compensatory mechanism is not present in the bag3 morphants. Furthermore, we show that nonsense-mediated decay of bag3 mRNA is the molecular trigger for the compensatory upregulation of bag2. Our study provides evidence that genetic compensation via transcriptional adaptation is a vital modulator of disease peculiarity and penetrance in bag3 mutant zebrafish and that this biological phenomenon might also be active in certain human BAG3 mutation carriers.
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MESH Headings
- Adaptor Proteins, Signal Transducing/deficiency
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/metabolism
- Animals
- Apoptosis/genetics
- Apoptosis Regulatory Proteins/deficiency
- Apoptosis Regulatory Proteins/genetics
- Apoptosis Regulatory Proteins/metabolism
- Cardiomyopathies/genetics
- Cardiomyopathies/metabolism
- Cardiomyopathies/pathology
- Cardiomyopathy, Dilated/genetics
- Cardiomyopathy, Dilated/metabolism
- Cardiomyopathy, Dilated/pathology
- Disease Models, Animal
- Heart Failure/genetics
- Heart Failure/metabolism
- Heart Failure/pathology
- Molecular Chaperones/genetics
- Molecular Chaperones/metabolism
- Muscle Fibers, Skeletal/metabolism
- Muscular Diseases/genetics
- Muscular Diseases/metabolism
- Muscular Diseases/pathology
- Mutation
- Myocardium/metabolism
- Myopathies, Structural, Congenital/metabolism
- Phenotype
- Proteomics
- Zebrafish
- Zebrafish Proteins/deficiency
- Zebrafish Proteins/genetics
- Zebrafish Proteins/metabolism
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Affiliation(s)
- Federica Diofano
- Molecular Cardiology, Department of Internal Medicine II, University of Ulm, Ulm, Germany
| | - Karolina Weinmann
- Molecular Cardiology, Department of Internal Medicine II, University of Ulm, Ulm, Germany
- Department of Internal Medicine II, University of Ulm, Ulm, Germany
| | - Isabelle Schneider
- Molecular Cardiology, Department of Internal Medicine II, University of Ulm, Ulm, Germany
| | - Kevin D. Thiessen
- Molecular Cardiology, Department of Internal Medicine II, University of Ulm, Ulm, Germany
| | | | - Steffen Just
- Molecular Cardiology, Department of Internal Medicine II, University of Ulm, Ulm, Germany
- * E-mail:
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30
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Venturi G, Montanaro L. How Altered Ribosome Production Can Cause or Contribute to Human Disease: The Spectrum of Ribosomopathies. Cells 2020; 9:E2300. [PMID: 33076379 PMCID: PMC7602531 DOI: 10.3390/cells9102300] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/09/2020] [Accepted: 10/12/2020] [Indexed: 12/22/2022] Open
Abstract
A number of different defects in the process of ribosome production can lead to a diversified spectrum of disorders that are collectively identified as ribosomopathies. The specific factors involved may either play a role only in ribosome biogenesis or have additional extra-ribosomal functions, making it difficult to ascribe the pathogenesis of the disease specifically to an altered ribosome biogenesis, even if the latter is clearly affected. We reviewed the available literature in the field from this point of view with the aim of distinguishing, among ribosomopathies, the ones due to specific alterations in the process of ribosome production from those characterized by a multifactorial pathogenesis.
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Affiliation(s)
- Giulia Venturi
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Via Massarenti 9, 40138 Bologna, Italy;
- Center for Applied Biomedical Research, Alma Mater Studiorum-University of Bologna, Via Massarenti 9, 40138 Bologna, Italy
| | - Lorenzo Montanaro
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Via Massarenti 9, 40138 Bologna, Italy;
- Center for Applied Biomedical Research, Alma Mater Studiorum-University of Bologna, Via Massarenti 9, 40138 Bologna, Italy
- Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, 40138 Bologna, Italy
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31
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Skariah G, Todd PK. Translational control in aging and neurodegeneration. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1628. [PMID: 32954679 DOI: 10.1002/wrna.1628] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 08/19/2020] [Accepted: 09/07/2020] [Indexed: 12/13/2022]
Abstract
Protein metabolism plays central roles in age-related decline and neurodegeneration. While a large body of research has explored age-related changes in protein degradation, alterations in the efficiency and fidelity of protein synthesis with aging are less well understood. Age-associated changes occur in both the protein synthetic machinery (ribosomal proteins and rRNA) and within regulatory factors controlling translation. At the same time, many of the interventions that prolong lifespan do so in part by pre-emptively decreasing protein synthesis rates to allow better harmonization to age-related declines in protein catabolism. Here we review the roles of translation regulation in aging, with a specific focus on factors implicated in age-related neurodegeneration. We discuss how emerging technologies such as ribosome profiling and superior mass spectrometric approaches are illuminating age-dependent mRNA-specific changes in translation rates across tissues to reveal a critical interplay between catabolic and anabolic pathways that likely contribute to functional decline. These new findings point to nodes in posttranscriptional gene regulation that both contribute to aging and offer targets for therapy. This article is categorized under: Translation > Translation Regulation Translation > Ribosome Biogenesis Translation > Translation Mechanisms.
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Affiliation(s)
- Geena Skariah
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA
| | - Peter K Todd
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA
- Ann Arbor VA Healthcare System, Department of Veterans Affairs, Ann Arbor, Michigan, USA
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32
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Ribosomopathies: New Therapeutic Perspectives. Cells 2020; 9:cells9092080. [PMID: 32932838 PMCID: PMC7564184 DOI: 10.3390/cells9092080] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/03/2020] [Accepted: 09/08/2020] [Indexed: 12/13/2022] Open
Abstract
Ribosomopathies are a group of rare diseases in which genetic mutations cause defects in either ribosome biogenesis or function, given specific phenotypes. Ribosomal proteins, and multiple other factors that are necessary for ribosome biogenesis (rRNA processing, assembly of subunits, export to cytoplasm), can be affected in ribosomopathies. Despite the need for ribosomes in all cell types, these diseases result mainly in tissue-specific impairments. Depending on the type of ribosomopathy and its pathogenicity, there are many potential therapeutic targets. The present manuscript will review our knowledge of ribosomopathies, discuss current treatments, and introduce the new therapeutic perspectives based on recent research. Diamond–Blackfan anemia, currently treated with blood transfusion prior to steroids, could be managed with a range of new compounds, acting mainly on anemia, such as L-leucine. Treacher Collins syndrome could be managed by various treatments, but it has recently been shown that proteasomal inhibition by MG132 or Bortezomib may improve cranial skeleton malformations. Developmental defects resulting from ribosomopathies could be also treated pharmacologically after birth. It might thus be possible to treat certain ribosomopathies without using multiple treatments such as surgery and transplants. Ribosomopathies remain an open field in the search for new therapeutic approaches based on our recent understanding of the role of ribosomes and progress in gene therapy for curing genetic disorders.
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33
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34
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Cataloguing and Selection of mRNAs Localized to Dendrites in Neurons and Regulated by RNA-Binding Proteins in RNA Granules. Biomolecules 2020; 10:biom10020167. [PMID: 31978946 PMCID: PMC7072219 DOI: 10.3390/biom10020167] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/18/2020] [Accepted: 01/20/2020] [Indexed: 12/15/2022] Open
Abstract
Spatiotemporal translational regulation plays a key role in determining cell fate and function. Specifically, in neurons, local translation in dendrites is essential for synaptic plasticity and long-term memory formation. To achieve local translation, RNA-binding proteins in RNA granules regulate target mRNA stability, localization, and translation. To date, mRNAs localized to dendrites have been identified by comprehensive analyses. In addition, mRNAs associated with and regulated by RNA-binding proteins have been identified using various methods in many studies. However, the results obtained from these numerous studies have not been compiled together. In this review, we have catalogued mRNAs that are localized to dendrites and are associated with and regulated by the RNA-binding proteins fragile X mental retardation protein (FMRP), RNA granule protein 105 (RNG105, also known as Caprin1), Ras-GAP SH3 domain binding protein (G3BP), cytoplasmic polyadenylation element binding protein 1 (CPEB1), and staufen double-stranded RNA binding proteins 1 and 2 (Stau1 and Stau2) in RNA granules. This review provides comprehensive information on dendritic mRNAs, the neuronal functions of mRNA-encoded proteins, the association of dendritic mRNAs with RNA-binding proteins in RNA granules, and the effects of RNA-binding proteins on mRNA regulation. These findings provide insights into the mechanistic basis of protein-synthesis-dependent synaptic plasticity and memory formation and contribute to future efforts to understand the physiological implications of local regulation of dendritic mRNAs in neurons.
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35
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Blatt P, Martin ET, Breznak SM, Rangan P. Post-transcriptional gene regulation regulates germline stem cell to oocyte transition during Drosophila oogenesis. Curr Top Dev Biol 2019; 140:3-34. [PMID: 32591078 DOI: 10.1016/bs.ctdb.2019.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
During oogenesis, several developmental processes must be traversed to ensure effective completion of gametogenesis including, stem cell maintenance and asymmetric division, differentiation, mitosis and meiosis, and production of maternally contributed mRNAs, making the germline a salient model for understanding how cell fate transitions are mediated. Due to silencing of the genome during meiotic divisions, there is little instructive transcription, barring a few examples, to mediate these critical transitions. In Drosophila, several layers of post-transcriptional regulation ensure that the mRNAs required for these processes are expressed in a timely manner and as needed during germline differentiation. These layers of regulation include alternative splicing, RNA modification, ribosome production, and translational repression. Many of the molecules and pathways involved in these regulatory activities are conserved from Drosophila to humans making the Drosophila germline an elegant model for studying the role of post-transcriptional regulation during stem cell differentiation and meiosis.
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Affiliation(s)
- Patrick Blatt
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY, United States; University at Albany SUNY, Albany, NY, United States
| | - Elliot T Martin
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY, United States; University at Albany SUNY, Albany, NY, United States
| | - Shane M Breznak
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY, United States; University at Albany SUNY, Albany, NY, United States
| | - Prashanth Rangan
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY, United States; University at Albany SUNY, Albany, NY, United States.
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36
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Duerinckx S, Jacquemin V, Drunat S, Vial Y, Passemard S, Perazzolo C, Massart A, Soblet J, Racapé J, Desmyter L, Badoer C, Papadimitriou S, Le Borgne YA, Lefort A, Libert F, De Maertelaer V, Rooman M, Costagliola S, Verloes A, Lenaerts T, Pirson I, Abramowicz M. Digenic inheritance of human primary microcephaly delineates centrosomal and non-centrosomal pathways. Hum Mutat 2019; 41:512-524. [PMID: 31696992 PMCID: PMC7496698 DOI: 10.1002/humu.23948] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 11/01/2019] [Accepted: 11/03/2019] [Indexed: 12/30/2022]
Abstract
Primary microcephaly (PM) is characterized by a small head since birth and is vastly heterogeneous both genetically and phenotypically. While most cases are monogenic, genetic interactions between Aspm and Wdr62 have recently been described in a mouse model of PM. Here, we used two complementary, holistic in vivo approaches: high throughput DNA sequencing of multiple PM genes in human patients with PM, and genome‐edited zebrafish modeling for the digenic inheritance of PM. Exomes of patients with PM showed a significant burden of variants in 75 PM genes, that persisted after removing monogenic causes of PM (e.g., biallelic pathogenic variants in CEP152). This observation was replicated in an independent cohort of patients with PM, where a PM gene panel showed in addition that the burden was carried by six centrosomal genes. Allelic frequencies were consistent with digenic inheritance. In zebrafish, non‐centrosomal gene casc5 −/− produced a severe PM phenotype, that was not modified by centrosomal genes aspm or wdr62 invalidation. A digenic, quadriallelic PM phenotype was produced by aspm and wdr62. Our observations provide strong evidence for digenic inheritance of human PM, involving centrosomal genes. Absence of genetic interaction between casc5 and aspm or wdr62 further delineates centrosomal and non‐centrosomal pathways in PM.
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Affiliation(s)
- Sarah Duerinckx
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles, Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, Brussels, Belgium
| | - Valérie Jacquemin
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles, Brussels, Belgium
| | - Séverine Drunat
- Department of Genetics, Robert Debré University Hospital, APHP, Paris, France.,INSERM UMR 1141, Université de Paris Diderot, Paris, France
| | - Yoann Vial
- Department of Genetics, Robert Debré University Hospital, APHP, Paris, France.,INSERM UMR 1141, Université de Paris Diderot, Paris, France
| | - Sandrine Passemard
- Department of Genetics, Robert Debré University Hospital, APHP, Paris, France.,INSERM UMR 1141, Université de Paris Diderot, Paris, France
| | - Camille Perazzolo
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles, Brussels, Belgium
| | - Annick Massart
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles, Brussels, Belgium
| | - Julie Soblet
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, Brussels, Belgium.,Department of Genetics, ULB Center of Human Genetics, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium.,Department of Genetics, ULB Center of Human Genetics, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles, Brussels, Belgium
| | - Judith Racapé
- Faculty of Medicine, Université Libre de Bruxelles, Brussels, Belgium
| | - Laurence Desmyter
- Department of Genetics, ULB Center of Human Genetics, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Cindy Badoer
- Department of Genetics, ULB Center of Human Genetics, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Sofia Papadimitriou
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, Brussels, Belgium.,Machine Learning Group, Université Libre de Bruxelles, Brussels, Belgium.,Artificial Intelligence Lab, Vrije Universiteit Brussel, Brussels, Belgium
| | - Yann-Aël Le Borgne
- Machine Learning Group, Université Libre de Bruxelles, Brussels, Belgium
| | - Anne Lefort
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles, Brussels, Belgium
| | - Frédérick Libert
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles, Brussels, Belgium
| | - Viviane De Maertelaer
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles, Brussels, Belgium
| | - Marianne Rooman
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium
| | - Sabine Costagliola
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles, Brussels, Belgium
| | - Alain Verloes
- Department of Genetics, Robert Debré University Hospital, APHP, Paris, France.,INSERM UMR 1141, Université de Paris Diderot, Paris, France
| | - Tom Lenaerts
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, Brussels, Belgium.,Machine Learning Group, Université Libre de Bruxelles, Brussels, Belgium.,Artificial Intelligence Lab, Vrije Universiteit Brussel, Brussels, Belgium
| | - Isabelle Pirson
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles, Brussels, Belgium
| | - Marc Abramowicz
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles, Brussels, Belgium.,Present Address: Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
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37
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Farley-Barnes KI, Ogawa LM, Baserga SJ. Ribosomopathies: Old Concepts, New Controversies. Trends Genet 2019; 35:754-767. [PMID: 31376929 PMCID: PMC6852887 DOI: 10.1016/j.tig.2019.07.004] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/02/2019] [Accepted: 07/09/2019] [Indexed: 12/30/2022]
Abstract
Ribosomopathies are a diverse subset of diseases caused by reduced expression of, or mutations in, factors necessary for making ribosomes, the protein translation machinery in the cell. Despite the ubiquitous need for ribosomes in all cell types, ribosomopathies manifest with tissue-specific defects and sometimes increased cancer susceptibility, but few treatments target the underlying cause. By highlighting new research in the field, we review current hypotheses for the basis of this tissue specificity. Based on new work, we broaden our understanding of the role of ribosome biogenesis in diverse tissue types throughout embryonic development. We also pose the question of whether previously described human conditions such as aging can be at least partially attributed to defects in making ribosomes.
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Affiliation(s)
- Katherine I Farley-Barnes
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Lisa M Ogawa
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Susan J Baserga
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA.
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38
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Genuth NR, Barna M. Heterogeneity and specialized functions of translation machinery: from genes to organisms. Nat Rev Genet 2019; 19:431-452. [PMID: 29725087 DOI: 10.1038/s41576-018-0008-z] [Citation(s) in RCA: 141] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Regulation of mRNA translation offers the opportunity to diversify the expression and abundance of proteins made from individual gene products in cells, tissues and organisms. Emerging evidence has highlighted variation in the composition and activity of several large, highly conserved translation complexes as a means to differentially control gene expression. Heterogeneity and specialized functions of individual components of the ribosome and of the translation initiation factor complexes eIF3 and eIF4F, which are required for recruitment of the ribosome to the mRNA 5' untranslated region, have been identified. In this Review, we summarize the evidence for selective mRNA translation by components of these macromolecular complexes as a means to dynamically control the translation of the proteome in time and space. We further discuss the implications of this form of gene expression regulation for a growing number of human genetic disorders associated with mutations in the translation machinery.
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Affiliation(s)
- Naomi R Genuth
- Departments of Genetics and Developmental Biology, Stanford University, Stanford, CA, USA.,Department of Biology, Stanford University, Stanford, CA, USA
| | - Maria Barna
- Departments of Genetics and Developmental Biology, Stanford University, Stanford, CA, USA.
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39
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Sinibaldi L, Parisi V, Lanciotti S, Fontana P, Kuechler A, Baujat G, Torres B, Koetting J, Splendiani A, Postorivo D, Beygo J, Garaci FG, Malan V, Lüdecke H, Guida V, Krumbiegel M, Lonardo F, Novelli A, Albrecht B, Perria C, Scarano G, Spielmann M, Nardone AM, Battaglia A, Brancati F, Bernardini L. Delineation of
MidXq28‐duplication syndrome
distal to
MECP2
and proximal to
RAB39B
genes. Clin Genet 2019; 96:246-253. [PMID: 31090057 DOI: 10.1111/cge.13565] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/19/2019] [Accepted: 05/03/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Lorenzo Sinibaldi
- Medical Genetics UnitBambino Gesù Pediatric Hospital IRCCS Rome Italy
| | - Valentina Parisi
- Medical Genetics Unit, Casa Sollievo della Sofferenza IRCCSSan Giovanni Rotondo (FG) Italy
| | - Silvia Lanciotti
- Medical Genetics Residency ProgrammeTor Vergata University Rome Italy
| | - Paolo Fontana
- Medical Genetics UnitA.O.R.N. San Pio Benevento Italy
| | | | - Genevieve Baujat
- Department of GeneticsNecker‐Enfants Malades Hospital Paris France
| | - Barbara Torres
- Medical Genetics Unit, Casa Sollievo della Sofferenza IRCCSSan Giovanni Rotondo (FG) Italy
| | | | | | | | | | - Francesco G. Garaci
- Neuroradiology, Department of Biomedicine and PreventionTor Vergata University Rome Rome Italy
- San Raffaele Cassino Cassino Italy
| | - Valerie Malan
- Department of GeneticsNecker‐Enfants Malades Hospital Paris France
| | | | - Valentina Guida
- Medical Genetics Unit, Casa Sollievo della Sofferenza IRCCSSan Giovanni Rotondo (FG) Italy
| | - Mandy Krumbiegel
- Institute of Human GeneticsUniversity of Erlangen‐Nuremberg Erlangen Germany
| | | | - Antonio Novelli
- Medical Genetics LaboratoryBambino Gesù Pediatric Hospital IRCCS Rome Italy
| | | | - Chiara Perria
- Childhood and Adolescence Neuropsychiatry SectionUniversity of Sassari Sassari Italy
| | | | - Malte Spielmann
- Human Molecular Genomics GroupMax Planck Institute for Molecular Genetics Berlin Germany
| | | | - Agatino Battaglia
- Department of Developmental NeuroscienceIRCCS “Stella Maris Foundation” Pisa Italy
| | - Francesco Brancati
- Medical Genetics Residency ProgrammeTor Vergata University Rome Italy
- Human Genetics Institute, Life, Health, Environmental Sciences DepartmentUniversity of L'Aquila Italy
- Istituto Dermopatico dell'ImmacolataIRCCS Rome Italy
| | - Laura Bernardini
- Medical Genetics Unit, Casa Sollievo della Sofferenza IRCCSSan Giovanni Rotondo (FG) Italy
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40
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Ansar M, Ullah F, Paracha SA, Adams DJ, Lai A, Pais L, Iwaszkiewicz J, Millan F, Sarwar MT, Agha Z, Shah SF, Qaisar AA, Falconnet E, Zoete V, Ranza E, Makrythanasis P, Santoni FA, Ahmed J, Katsanis N, Walsh C, Davis EE, Antonarakis SE. Bi-allelic Variants in DYNC1I2 Cause Syndromic Microcephaly with Intellectual Disability, Cerebral Malformations, and Dysmorphic Facial Features. Am J Hum Genet 2019; 104:1073-1087. [PMID: 31079899 PMCID: PMC6556908 DOI: 10.1016/j.ajhg.2019.04.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 04/01/2019] [Indexed: 12/30/2022] Open
Abstract
Cargo transport along the cytoplasmic microtubular network is essential for neuronal function, and cytoplasmic dynein-1 is an established molecular motor that is critical for neurogenesis and homeostasis. We performed whole-exome sequencing, homozygosity mapping, and chromosomal microarray studies in five individuals from three independent pedigrees and identified likely-pathogenic variants in DYNC1I2 (Dynein Cytoplasmic 1 Intermediate Chain 2), encoding a component of the cytoplasmic dynein 1 complex. In a consanguineous Pakistani family with three affected individuals presenting with microcephaly, severe intellectual disability, simplification of cerebral gyration, corpus callosum hypoplasia, and dysmorphic facial features, we identified a homozygous splice donor site variant (GenBank: NM_001378.2:c.607+1G>A). We report two additional individuals who have similar neurodevelopmental deficits and craniofacial features and harbor deleterious variants; one individual bears a c.740A>G (p.Tyr247Cys) change in trans with a 374 kb deletion encompassing DYNC1I2, and an unrelated individual harbors the compound-heterozygous variants c.868C>T (p.Gln290∗) and c.740A>G (p.Tyr247Cys). Zebrafish larvae subjected to CRISPR-Cas9 gene disruption or transient suppression of dync1i2a displayed significantly altered craniofacial patterning with concomitant reduction in head size. We monitored cell death and cell cycle progression in dync1i2a zebrafish models and observed significantly increased apoptosis, likely due to prolonged mitosis caused by abnormal spindle morphology, and this finding offers initial insights into the cellular basis of microcephaly. Additionally, complementation studies in zebrafish demonstrate that p.Tyr247Cys attenuates gene function, consistent with protein structural analysis. Our genetic and functional data indicate that DYNC1I2 dysfunction probably causes an autosomal-recessive microcephaly syndrome and highlight further the critical roles of the dynein-1 complex in neurodevelopment.
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Affiliation(s)
- Muhammad Ansar
- Department of Genetic Medicine and Development, University of Geneva, 1206 Geneva, Switzerland
| | - Farid Ullah
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC 27701, USA; Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, 38000 Faisalabad, Pakistan; Pakistan Institute of Engineering and Applied Sciences, 45650 Islamabad, Pakistan
| | - Sohail A Paracha
- Institute of Basic Medical Sciences, Khyber Medical University, 25100 Peshawar, Pakistan
| | - Darius J Adams
- Atlantic Health System, Goryeb Children's Hospital, Morristown, NJ 07960, USA
| | - Abbe Lai
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Neurology and Pediatrics, Harvard Medical School, Center for Life Sciences, Blackfan Circle, Boston, MA 02115, USA
| | - Lynn Pais
- Medical and Population Genetics Program, Broad Institute of MIT, Cambridge, MA 02142, USA; Center for Mendelian Genomics, Harvard University, Cambridge, MA 02142, USA
| | - Justyna Iwaszkiewicz
- Swiss Institute of Bioinformatics, Molecular Modeling Group, Batiment Genopode, Unil Sorge, 1015 Lausanne, Switzerland
| | | | - Muhammad T Sarwar
- Institute of Basic Medical Sciences, Khyber Medical University, 25100 Peshawar, Pakistan
| | - Zehra Agha
- Department of Biosciences, COMSATS University, 45500 Islamabad, Pakistan
| | - Sayyed Fahim Shah
- Department of Medicine, KMU Institute of Medical Sciences, 26000 Kohat, Pakistan
| | - Azhar Ali Qaisar
- Radiology Department, Lady Reading Hospital, 25000 Peshawar, Pakistan
| | - Emilie Falconnet
- Department of Genetic Medicine and Development, University of Geneva, 1206 Geneva, Switzerland
| | - Vincent Zoete
- Swiss Institute of Bioinformatics, Molecular Modeling Group, Batiment Genopode, Unil Sorge, 1015 Lausanne, Switzerland; Department of Fundamental Oncology, Lausanne University, Ludwig Institute for Cancer Research, Route de la Corniche 9A, 1066 Epalinges, Switzerland
| | - Emmanuelle Ranza
- Department of Genetic Medicine and Development, University of Geneva, 1206 Geneva, Switzerland; Service of Genetic Medicine, University Hospitals of Geneva, 1205 Geneva, Switzerland
| | - Periklis Makrythanasis
- Department of Genetic Medicine and Development, University of Geneva, 1206 Geneva, Switzerland; Biomedical Research Foundation of the Academy of Athens, 115 27 Athens, Greece
| | - Federico A Santoni
- Department of Genetic Medicine and Development, University of Geneva, 1206 Geneva, Switzerland; Department of Endocrinology Diabetes and Metabolism, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - Jawad Ahmed
- Institute of Basic Medical Sciences, Khyber Medical University, 25100 Peshawar, Pakistan
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC 27701, USA
| | - Christopher Walsh
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Neurology and Pediatrics, Harvard Medical School, Center for Life Sciences, Blackfan Circle, Boston, MA 02115, USA; Medical and Population Genetics Program, Broad Institute of MIT, Cambridge, MA 02142, USA; Center for Mendelian Genomics, Harvard University, Cambridge, MA 02142, USA
| | - Erica E Davis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC 27701, USA.
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva, 1206 Geneva, Switzerland; Service of Genetic Medicine, University Hospitals of Geneva, 1205 Geneva, Switzerland; iGE3 Institute of Genetics and Genomics of Geneva, 1211 Geneva, Switzerland.
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41
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Emmott E, Jovanovic M, Slavov N. Ribosome Stoichiometry: From Form to Function. Trends Biochem Sci 2019; 44:95-109. [PMID: 30473427 PMCID: PMC6340777 DOI: 10.1016/j.tibs.2018.10.009] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/27/2018] [Accepted: 10/20/2018] [Indexed: 12/11/2022]
Abstract
The existence of eukaryotic ribosomes with distinct ribosomal protein (RP) stoichiometry and regulatory roles in protein synthesis has been speculated for over 60 years. Recent advances in mass spectrometry (MS) and high-throughput analysis have begun to identify and characterize distinct ribosome stoichiometry in yeast and mammalian systems. In addition to RP stoichiometry, ribosomes host a vast array of protein modifications, effectively expanding the number of human RPs from 80 to many thousands of distinct proteoforms. Is it possible that these proteoforms combine to function as a 'ribosome code' to tune protein synthesis? We outline the specific benefits that translational regulation by specialized ribosomes can offer and discuss the means and methodologies available to correlate and characterize RP stoichiometry with function. We highlight previous research with a focus on formulating hypotheses that can guide future experiments and crack the ribosome code.
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Affiliation(s)
- Edward Emmott
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Nikolai Slavov
- Department of Bioengineering, Northeastern University, Boston, MA, USA; Department of Biology, Northeastern University, Boston, MA, USA.
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Khan TN, Khan K, Sadeghpour A, Reynolds H, Perilla Y, McDonald MT, Gallentine WB, Baig SM, Davis EE, Katsanis N. Mutations in NCAPG2 Cause a Severe Neurodevelopmental Syndrome that Expands the Phenotypic Spectrum of Condensinopathies. Am J Hum Genet 2019; 104:94-111. [PMID: 30609410 PMCID: PMC6323578 DOI: 10.1016/j.ajhg.2018.11.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 11/26/2018] [Indexed: 01/29/2023] Open
Abstract
The use of whole-exome and whole-genome sequencing has been a catalyst for a genotype-first approach to diagnostics. Under this paradigm, we have implemented systematic sequencing of neonates and young children with a suspected genetic disorder. Here, we report on two families with recessive mutations in NCAPG2 and overlapping clinical phenotypes that include severe neurodevelopmental defects, failure to thrive, ocular abnormalities, and defects in urogenital and limb morphogenesis. NCAPG2 encodes a member of the condensin II complex, necessary for the condensation of chromosomes prior to cell division. Consistent with a causal role for NCAPG2, we found abnormal chromosome condensation, augmented anaphase chromatin-bridge formation, and micronuclei in daughter cells of proband skin fibroblasts. To test the functional relevance of the discovered variants, we generated an ncapg2 zebrafish model. Morphants displayed clinically relevant phenotypes, such as renal anomalies, microcephaly, and concomitant increases in apoptosis and altered mitotic progression. These could be rescued by wild-type but not mutant human NCAPG2 mRNA and were recapitulated in CRISPR-Cas9 F0 mutants. Finally, we noted that the individual with a complex urogenital defect also harbored a heterozygous NPHP1 deletion, a common contributor to nephronophthisis. To test whether sensitization at the NPHP1 locus might contribute to a more severe renal phenotype, we co-suppressed nphp1 and ncapg2, which resulted in significantly more dysplastic renal tubules in zebrafish larvae. Together, our data suggest that impaired function of NCAPG2 results in a severe condensinopathy, and they highlight the potential utility of examining candidate pathogenic lesions beyond the primary disease locus.
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Affiliation(s)
- Tahir N Khan
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA
| | - Kamal Khan
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA; Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Azita Sadeghpour
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA
| | - Hannah Reynolds
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA; Furman University, Greenville, SC 29613, USA
| | - Yezmin Perilla
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA
| | - Marie T McDonald
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, NC 27710, USA
| | - William B Gallentine
- Department of Pediatrics, Division of Pediatric Neurology, Duke University Medical Center, Durham, NC 27710, USA
| | - Shahid M Baig
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Erica E Davis
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA.
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA.
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Hetman M, Slomnicki LP. Ribosomal biogenesis as an emerging target of neurodevelopmental pathologies. J Neurochem 2018; 148:325-347. [PMID: 30144322 DOI: 10.1111/jnc.14576] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 08/15/2018] [Accepted: 08/21/2018] [Indexed: 12/17/2022]
Abstract
Development of the nervous system is carried out by complex gene expression programs that are regulated at both transcriptional and translational level. In addition, quality control mechanisms such as the TP53-mediated apoptosis or neuronal activity-stimulated survival ensure successful neurogenesis and formation of functional circuitries. In the nucleolus, production of ribosomes is essential for protein synthesis. In addition, it participates in chromatin organization and regulates the TP53 pathway via the ribosomal stress response. Its tight regulation is required for maintenance of genomic integrity. Mutations in several ribosomal components and trans-acting ribosomal biogenesis factors result in neurodevelopmental syndromes that present with microcephaly, autism, intellectual deficits and/or progressive neurodegeneration. Furthermore, ribosomal biogenesis is perturbed by exogenous factors that disrupt neurodevelopment including alcohol or Zika virus. In this review, we present recent literature that argues for a role of dysregulated ribosomal biogenesis in pathogenesis of various neurodevelopmental syndromes. We also discuss potential mechanisms through which such dysregulation may lead to cellular pathologies of the developing nervous system including insufficient proliferation and/or loss of neuroprogenitors cells, apoptosis of immature neurons, altered neuronal morphogenesis, and neurodegeneration.
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Affiliation(s)
- Michal Hetman
- Departments of Neurological Surgery, Kentucky Spinal Cord Injury Research Center, Louisville, Kentucky, USA.,Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky, USA
| | - Lukasz P Slomnicki
- Departments of Neurological Surgery, Kentucky Spinal Cord Injury Research Center, Louisville, Kentucky, USA
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44
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Aubert M, O'Donohue MF, Lebaron S, Gleizes PE. Pre-Ribosomal RNA Processing in Human Cells: From Mechanisms to Congenital Diseases. Biomolecules 2018; 8:biom8040123. [PMID: 30356013 PMCID: PMC6315592 DOI: 10.3390/biom8040123] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 10/19/2018] [Accepted: 10/19/2018] [Indexed: 12/15/2022] Open
Abstract
Ribosomal RNAs, the most abundant cellular RNA species, have evolved as the structural scaffold and the catalytic center of protein synthesis in every living organism. In eukaryotes, they are produced from a long primary transcript through an intricate sequence of processing steps that include RNA cleavage and folding and nucleotide modification. The mechanisms underlying this process in human cells have long been investigated, but technological advances have accelerated their study in the past decade. In addition, the association of congenital diseases to defects in ribosome synthesis has highlighted the central place of ribosomal RNA maturation in cell physiology regulation and broadened the interest in these mechanisms. Here, we give an overview of the current knowledge of pre-ribosomal RNA processing in human cells in light of recent progress and discuss how dysfunction of this pathway may contribute to the physiopathology of congenital diseases.
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Affiliation(s)
- Maxime Aubert
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France.
| | - Marie-Françoise O'Donohue
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France.
| | - Simon Lebaron
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France.
| | - Pierre-Emmanuel Gleizes
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France.
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45
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Small molecule inhibition of RAS/MAPK signaling ameliorates developmental pathologies of Kabuki Syndrome. Sci Rep 2018; 8:10779. [PMID: 30018450 PMCID: PMC6050262 DOI: 10.1038/s41598-018-28709-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 06/12/2018] [Indexed: 01/10/2023] Open
Abstract
Kabuki Syndrome (KS) is a rare disorder characterized by distinctive facial features, short stature, skeletal abnormalities, and neurodevelopmental deficits. Previously, we showed that loss of function of RAP1A, a RAF1 regulator, can activate the RAS/MAPK pathway and cause KS, an observation recapitulated in other genetic models of the disorder. These data suggested that suppression of this signaling cascade might be of therapeutic benefit for some features of KS. To pursue this possibility, we performed a focused small molecule screen of a series of RAS/MAPK pathway inhibitors, where we tested their ability to rescue disease-relevant phenotypes in a zebrafish model of the most common KS locus, kmt2d. Consistent with a pathway-driven screening paradigm, two of 27 compounds showed reproducible rescue of early developmental pathologies. Further analyses showed that one compound, desmethyl-Dabrafenib (dmDf), induced no overt pathologies in zebrafish embryos but could rescue MEK hyperactivation in vivo and, concomitantly, structural KS-relevant phenotypes in all KS zebrafish models (kmt2d, kmd6a and rap1). Mass spectrometry quantitation suggested that a 100 nM dose resulted in sub-nanomolar exposure of this inhibitor and was sufficient to rescue both mandibular and neurodevelopmental defects. Crucially, germline kmt2d mutants recapitulated the gastrulation movement defects, micrognathia and neurogenesis phenotypes of transient models; treatment with dmDf ameliorated all of them significantly. Taken together, our data reinforce a causal link between MEK hyperactivation and KS and suggest that chemical suppression of BRAF might be of potential clinical utility for some features of this disorder.
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46
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Angelova MT, Dimitrova DG, Dinges N, Lence T, Worpenberg L, Carré C, Roignant JY. The Emerging Field of Epitranscriptomics in Neurodevelopmental and Neuronal Disorders. Front Bioeng Biotechnol 2018; 6:46. [PMID: 29707539 PMCID: PMC5908907 DOI: 10.3389/fbioe.2018.00046] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 03/29/2018] [Indexed: 01/19/2023] Open
Abstract
Analogous to DNA methylation and histone modifications, RNA modifications represent a novel layer of regulation of gene expression. The dynamic nature and increasing number of RNA modifications offer new possibilities to rapidly alter gene expression upon specific environmental changes. Recent lines of evidence indicate that modified RNA molecules and associated complexes regulating and “reading” RNA modifications play key roles in the nervous system of several organisms, controlling both, its development and function. Mutations in several human genes that modify transfer RNA (tRNA) have been linked to neurological disorders, in particular to intellectual disability. Loss of RNA modifications alters the stability of tRNA, resulting in reduced translation efficiency and generation of tRNA fragments, which can interfere with neuronal functions. Modifications present on messenger RNAs (mRNAs) also play important roles during brain development. They contribute to neuronal growth and regeneration as well as to the local regulation of synaptic functions. Hence, potential combinatorial effects of RNA modifications on different classes of RNA may represent a novel code to dynamically fine tune gene expression during brain function. Here we discuss the recent findings demonstrating the impact of modified RNAs on neuronal processes and disorders.
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Affiliation(s)
- Margarita T Angelova
- Drosophila Genetics and Epigenetics, Sorbonne Université, Centre National de la Recherche Scientifique, Biologie du Développement-Institut de Biologie Paris Seine, Paris, France
| | - Dilyana G Dimitrova
- Drosophila Genetics and Epigenetics, Sorbonne Université, Centre National de la Recherche Scientifique, Biologie du Développement-Institut de Biologie Paris Seine, Paris, France
| | - Nadja Dinges
- Laboratory of RNA Epigenetics, Institute of Molecular Biology, Mainz, Germany
| | - Tina Lence
- Laboratory of RNA Epigenetics, Institute of Molecular Biology, Mainz, Germany
| | - Lina Worpenberg
- Laboratory of RNA Epigenetics, Institute of Molecular Biology, Mainz, Germany
| | - Clément Carré
- Drosophila Genetics and Epigenetics, Sorbonne Université, Centre National de la Recherche Scientifique, Biologie du Développement-Institut de Biologie Paris Seine, Paris, France
| | - Jean-Yves Roignant
- Laboratory of RNA Epigenetics, Institute of Molecular Biology, Mainz, Germany
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Khajuria RK, Munschauer M, Ulirsch JC, Fiorini C, Ludwig LS, McFarland SK, Abdulhay NJ, Specht H, Keshishian H, Mani DR, Jovanovic M, Ellis SR, Fulco CP, Engreitz JM, Schütz S, Lian J, Gripp KW, Weinberg OK, Pinkus GS, Gehrke L, Regev A, Lander ES, Gazda HT, Lee WY, Panse VG, Carr SA, Sankaran VG. Ribosome Levels Selectively Regulate Translation and Lineage Commitment in Human Hematopoiesis. Cell 2018; 173:90-103.e19. [PMID: 29551269 DOI: 10.1016/j.cell.2018.02.036] [Citation(s) in RCA: 257] [Impact Index Per Article: 42.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 11/28/2017] [Accepted: 02/15/2018] [Indexed: 01/17/2023]
Abstract
Blood cell formation is classically thought to occur through a hierarchical differentiation process, although recent studies have shown that lineage commitment may occur earlier in hematopoietic stem and progenitor cells (HSPCs). The relevance to human blood diseases and the underlying regulation of these refined models remain poorly understood. By studying a genetic blood disorder, Diamond-Blackfan anemia (DBA), where the majority of mutations affect ribosomal proteins and the erythroid lineage is selectively perturbed, we are able to gain mechanistic insight into how lineage commitment is programmed normally and disrupted in disease. We show that in DBA, the pool of available ribosomes is limited, while ribosome composition remains constant. Surprisingly, this global reduction in ribosome levels more profoundly alters translation of a select subset of transcripts. We show how the reduced translation of select transcripts in HSPCs can impair erythroid lineage commitment, illuminating a regulatory role for ribosome levels in cellular differentiation.
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Affiliation(s)
- Rajiv K Khajuria
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Berlin-Brandenburg School for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Berlin 13353, Germany
| | | | - Jacob C Ulirsch
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Claudia Fiorini
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Leif S Ludwig
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sean K McFarland
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nour J Abdulhay
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Harrison Specht
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - D R Mani
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Marko Jovanovic
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Steven R Ellis
- Department of Biochemistry and Molecular Biology, University of Louisville, Louisville, KY 40202, USA
| | - Charles P Fulco
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Sabina Schütz
- Institute of Medical Microbiology, Department of Medicine, University of Zurich, 8006 Zurich, Switzerland
| | - John Lian
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA; Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA
| | - Karen W Gripp
- Division of Medical Genetics, A. I. duPont Hospital for Children, Wilmington, DE 19803, USA
| | - Olga K Weinberg
- Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Geraldine S Pinkus
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Lee Gehrke
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA; Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Hanna T Gazda
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Winston Y Lee
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Vikram G Panse
- Institute of Medical Microbiology, Department of Medicine, University of Zurich, 8006 Zurich, Switzerland
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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Shi J, Zhang L, Zhou D, Zhang J, Lin Q, Guan W, Zhang J, Ren W, Xu G. Biological Function of Ribosomal Protein L10 on Cell Behavior in Human Epithelial Ovarian Cancer. J Cancer 2018; 9:745-756. [PMID: 29556332 PMCID: PMC5858496 DOI: 10.7150/jca.21614] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Accepted: 12/29/2017] [Indexed: 12/14/2022] Open
Abstract
Ribosomal protein L10 (RPL10) is one of large ribosomal proteins and plays a role in Wilms' tumor and premature ovarian failure. However, the function of RPL10 in human epithelial ovarian cancer (EOC) remains unknown. The purpose of this study was to examine the expression level and function of RPL10 in EOC. RPL10 protein expression was detected by immunohistochemistry and Western blot. The association RPL10 expression with clinical features was analyzed. Loss-of-function and gain-of-function approaches were applied in cellular assays, including cell viability, migration, invasion, and apoptosis. Our study demonstrated for the first time that RPL10 was upregulated in human EOC compared with normal ovarian tissues. Knockdown of RPL10 inhibited cell viability, migration, and invasion, and increased cell apoptosis. On the contrary, upregulation of RPL10 increased cell viability, migration, invasion, and decreased cell apoptosis. Furthermore, miR-143-3p regulated RPL10 expression. Our data indicate that RPL10 is a potential tissue biomarker of patients with EOC and may be a therapeutic target of ovarian cancer.
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Affiliation(s)
- Jimin Shi
- Center Laboratory, Jinshan Hospital, Fudan University, Shanghai 201508, China
| | - Lingyun Zhang
- Center Laboratory, Jinshan Hospital, Fudan University, Shanghai 201508, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Daibing Zhou
- Center Laboratory, Jinshan Hospital, Fudan University, Shanghai 201508, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Jinguo Zhang
- Center Laboratory, Jinshan Hospital, Fudan University, Shanghai 201508, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Qunbo Lin
- Center Laboratory, Jinshan Hospital, Fudan University, Shanghai 201508, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Wencai Guan
- Center Laboratory, Jinshan Hospital, Fudan University, Shanghai 201508, China
| | - Jihong Zhang
- Center Laboratory, Jinshan Hospital, Fudan University, Shanghai 201508, China
| | - Weimin Ren
- Center Laboratory, Jinshan Hospital, Fudan University, Shanghai 201508, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Guoxiong Xu
- Center Laboratory, Jinshan Hospital, Fudan University, Shanghai 201508, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
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49
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Kapur M, Ackerman SL. mRNA Translation Gone Awry: Translation Fidelity and Neurological Disease. Trends Genet 2018; 34:218-231. [PMID: 29352613 DOI: 10.1016/j.tig.2017.12.007] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 12/04/2017] [Accepted: 12/11/2017] [Indexed: 10/18/2022]
Abstract
Errors during mRNA translation can lead to a reduction in the levels of functional proteins and an increase in deleterious molecules. Advances in next-generation sequencing have led to the discovery of rare genetic disorders, many caused by mutations in genes encoding the mRNA translation machinery, as well as to a better understanding of translational dynamics through ribosome profiling. We discuss here multiple neurological disorders that are linked to errors in tRNA aminoacylation and ribosome decoding. We draw on studies from genetic models, including yeast and mice, to enhance our understanding of the translational defects observed in these diseases. Finally, we emphasize the importance of tRNA, their associated enzymes, and the inextricable link between accuracy and efficiency in the maintenance of translational fidelity.
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Affiliation(s)
- Mridu Kapur
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Section of Neurobiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Susan L Ackerman
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Section of Neurobiology, University of California, San Diego, La Jolla, CA 92093, USA.
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50
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Abstract
X-linked cerebellar ataxias (XLCA) are an expanding group of genetically heterogeneous and clinically variable conditions characterized by cerebellar dysgenesis (hypoplasia, atrophy, or dysplasia) caused by gene mutations or genomic imbalances on the X chromosome. The neurologic features of XLCA include hypotonia, developmental delay, intellectual disability, ataxia, and other cerebellar signs. Normal cognitive development has also been reported. Cerebellar defects may be isolated or associated with other brain malformations or extraneurologic involvement. More than 20 genes on the X chromosome, mainly encoding for proteins involved in brain development and synaptic function that have been constantly or occasionally associated with a pathologic cerebellar phenotype, and several families with X-linked inheritance have been reported. Given the excess of males with ataxia, this group of conditions is probably underestimated and families of patients with neuroradiologic and clinical evidence of a cerebellar disorder should be counseled for high risk of X-linked inheritance.
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Affiliation(s)
- Ginevra Zanni
- Unit of Neuromuscular and Neurodegenerative Disorders, Bambino Gesu' Children's Research Hospital, Rome, Italy.
| | - Enrico Bertini
- Unit of Neuromuscular and Neurodegenerative Disorders, Bambino Gesu' Children's Research Hospital, Rome, Italy
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