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Yadav P, Tamilselvan R, Mani H, Singh KK. MicroRNA-mediated regulation of nonsense-mediated mRNA decay factors: Insights into microRNA prediction tools and profiling techniques. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195022. [PMID: 38437914 DOI: 10.1016/j.bbagrm.2024.195022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 02/28/2024] [Accepted: 03/01/2024] [Indexed: 03/06/2024]
Abstract
Nonsense-mediated mRNA decay (NMD) stands out as a prominent RNA surveillance mechanism within eukaryotes, meticulously overseeing both RNA abundance and integrity by eliminating aberrant transcripts. These defective transcripts are discerned through the concerted efforts of translating ribosomes, eukaryotic release factors (eRFs), and trans-acting NMD factors, with Up-Frameshift 3 (UPF3) serving as a noteworthy component. Remarkably, in humans, UPF3 exists in two paralogous forms, UPF3A (UPF3) and UPF3B (UPF3X). Beyond its role in quality control, UPF3 wields significant influence over critical cellular processes, including neural development, synaptic plasticity, and axon guidance. However, the precise regulatory mechanisms governing UPF3 remain elusive. MicroRNAs (miRNAs) emerge as pivotal post-transcriptional gene regulators, exerting substantial impact on diverse pathological and physiological pathways. This comprehensive review encapsulates our current understanding of the intricate regulatory nexus between NMD and miRNAs, with particular emphasis on the essential role played by UPF3B in neurodevelopment. Additionally, we bring out the significance of the 3'-untranslated region (3'-UTR) as the molecular bridge connecting NMD and miRNA-mediated gene regulation. Furthermore, we provide an in-depth exploration of diverse computational tools tailored for the prediction of potential miRNA targets. To complement these computational approaches, we delineate experimental techniques designed to validate predicted miRNA-mRNA interactions, empowering readers with the knowledge necessary to select the most appropriate methodology for their specific research objectives.
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Affiliation(s)
- Priyanka Yadav
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Raja Tamilselvan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Harita Mani
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Kusum Kumari Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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Lai S, Shiraishi H, Sebastian WA, Shimizu N, Umeda R, Ikeuchi M, Kiyota K, Takeno T, Miyazaki S, Yano S, Shimada T, Yoshimura A, Hanada R, Hanada T. Effect of nonsense-mediated mRNA decay factor SMG9 deficiency on premature aging in zebrafish. Commun Biol 2024; 7:654. [PMID: 38806677 PMCID: PMC11133409 DOI: 10.1038/s42003-024-06356-6] [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: 06/20/2023] [Accepted: 05/20/2024] [Indexed: 05/30/2024] Open
Abstract
SMG9 is an essential component of the nonsense-mediated mRNA decay (NMD) machinery, a quality control mechanism that selectively degrades aberrant transcripts. Mutations in SMG9 are associated with heart and brain malformation syndrome (HBMS). However, the molecular mechanism underlying HBMS remains unclear. We generated smg9 mutant zebrafish (smg9oi7/oi7) that have a lifespan of approximately 6 months or longer, allowing for analysis of the in vivo function of Smg9 in adults in more detail. smg9oi7/oi7 zebrafish display congenital brain abnormalities and reduced cardiac contraction. Additionally, smg9oi7/oi7 zebrafish exhibit a premature aging phenotype. Analysis of NMD target mRNAs shows a trend toward increased mRNA levels in smg9oi7/oi7 zebrafish. Spermidine oxidase (Smox) is increased in smg9oi7/oi7 zebrafish, resulting in the accumulation of byproducts, reactive oxygen species, and acrolein. The accumulation of smox mRNA due to NMD dysregulation caused by Smg9 deficiency leads to increased oxidative stress, resulting in premature aging.
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Affiliation(s)
- Shaohong Lai
- Department of Cell Biology, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Hiroshi Shiraishi
- Department of Cell Biology, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | | | - Nobuyuki Shimizu
- Department of Cell Biology, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Ryohei Umeda
- Department of Neurophysiology, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Mayo Ikeuchi
- Department of Cell Biology, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Kyoko Kiyota
- Department of Cell Biology, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Takashi Takeno
- Department of Cell Biology, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Shuya Miyazaki
- Department of Cell Biology, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Shinji Yano
- Institute for Research Management, Oita University, Yufu, Oita, Japan
| | - Tatsuo Shimada
- Oita Medical Technology School, Japan College of Judo-Therapy, Acupuncture & Moxibustion Therapy, Oita, Japan
| | - Akihiko Yoshimura
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Reiko Hanada
- Department of Neurophysiology, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Toshikatsu Hanada
- Department of Cell Biology, Oita University Faculty of Medicine, Yufu, Oita, Japan.
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Ma Z, Sharma R, Rogers AN. Physiological Consequences of Nonsense-Mediated Decay and Its Role in Adaptive Responses. Biomedicines 2024; 12:1110. [PMID: 38791071 PMCID: PMC11117581 DOI: 10.3390/biomedicines12051110] [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: 04/07/2024] [Revised: 04/30/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
The evolutionarily conserved nonsense-mediated mRNA decay (NMD) pathway is a quality control mechanism that degrades aberrant mRNA containing one or more premature termination codons (PTCs). Recent discoveries indicate that NMD also differentially regulates mRNA from wild-type protein-coding genes despite lacking PTCs. Together with studies showing that NMD is involved in development and adaptive responses that influence health and longevity, these findings point to an expanded role of NMD that adds a new layer of complexity in the post-transcriptional regulation of gene expression. However, the extent of its control, whether different types of NMD play different roles, and the resulting physiological outcomes remain unclear and need further elucidation. Here, we review different branches of NMD and what is known of the physiological outcomes associated with this type of regulation. We identify significant gaps in the understanding of this process and the utility of genetic tools in accelerating progress in this area.
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Affiliation(s)
- Zhengxin Ma
- MDI Biological Laboratory, Bar Harbor, ME 04609, USA
| | - Ratna Sharma
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA;
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Hossain MN, Gao Y, Hatfield MJ, de Avila JM, McClure MC, Du M. Cold exposure impacts DNA methylation patterns in cattle sperm. Front Genet 2024; 15:1346150. [PMID: 38444759 PMCID: PMC10912962 DOI: 10.3389/fgene.2024.1346150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 01/23/2024] [Indexed: 03/07/2024] Open
Abstract
DNA methylation is influenced by various exogenous factors such as nutrition, temperature, toxicants, and stress. Bulls from the Pacific Northwest region of the United States and other northern areas are exposed to extreme cold temperatures during winter. However, the effects of cold exposure on the methylation patterns of bovine sperm remain unclear. To address, DNA methylation profiles of sperm collected during late spring and winter from the same bulls were analyzed using whole genome bisulfite sequencing (WGBS). Bismark (0.22.3) were used for mapping the WGBS reads and R Bioconductor package DSS was used for differential methylation analysis. Cold exposure induced 3,163 differentially methylated cytosines (DMCs) with methylation difference ≥10% and a q-value < 0.05. We identified 438 differentially methylated regions (DMRs) with q-value < 0.05, which overlapped with 186 unique genes. We also identified eight unique differentially methylated genes (DMGs) (Pax6, Macf1, Mest, Ubqln1, Smg9, Ctnnb1, Lsm4, and Peg10) involved in embryonic development, and nine unique DMGs (Prmt6, Nipal1, C21h15orf40, Slc37a3, Fam210a, Raly, Rgs3, Lmbr1, and Gan) involved in osteogenesis. Peg10 and Mest, two paternally expressed imprinted genes, exhibited >50% higher methylation. The differential methylation patterns of six distinct DMRs: Peg10, Smg9 and Mest related to embryonic development and Lmbr1, C21h15orf40 and Prtm6 related to osteogenesis, were assessed by methylation-specific PCR (MS-PCR), which confirmed the existence of variable methylation patterns in those locations across the two seasons. In summary, cold exposure induces differential DNA methylation patterns in genes that appear to affect embryonic development and osteogenesis in the offspring. Our findings suggest the importance of replicating the results of the current study with a larger sample size and exploring the potential of these changes in affecting offspring development.
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Affiliation(s)
- Md Nazmul Hossain
- Nutrigenomics and Growth Biology Laboratory, Department of Animal Sciences, Washington State University, Pullman, WA, United States
- Department of Livestock Production and Management, Faculty of Veterinary, Animal, and Biomedical Sciences, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Yao Gao
- Nutrigenomics and Growth Biology Laboratory, Department of Animal Sciences, Washington State University, Pullman, WA, United States
| | - Michael J. Hatfield
- Nutrigenomics and Growth Biology Laboratory, Department of Animal Sciences, Washington State University, Pullman, WA, United States
| | - Jeanene M. de Avila
- Nutrigenomics and Growth Biology Laboratory, Department of Animal Sciences, Washington State University, Pullman, WA, United States
| | | | - Min Du
- Nutrigenomics and Growth Biology Laboratory, Department of Animal Sciences, Washington State University, Pullman, WA, United States
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Saleh Alanazi SH, Farooq Khan M, Alazami AM, Baabbad A, Ahmed Wadaan M. Calotropis procera: A double edged sword against glioblastoma, inhibiting glioblastoma cell line growth by targeting histone deacetylases (HDAC) and angiogenesis. Heliyon 2024; 10:e24406. [PMID: 38304784 PMCID: PMC10831610 DOI: 10.1016/j.heliyon.2024.e24406] [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: 08/17/2023] [Revised: 12/16/2023] [Accepted: 01/08/2024] [Indexed: 02/03/2024] Open
Abstract
Despite substantial investments in anti-glioblastoma (GBM) drug discovery over the last decade, progress is limited to preclinical stages, with clinical studies frequently encountering obstacles. Angiogenic and histone deacetylase inhibitors (HDACi) have shown profound results in pre-clinical studies. Investigating a multicomponent anti-cancer remedy that disrupts the tumor angiogenic blood vessels and simultaneously disrupts HDACs, while inducing minimal side effects, is critically needed. The crude extracts derived from medicinal plants serve as a renewable reservoir of anti-tumor drugs, exhibiting reduced toxicity compared to chemically synthesized formulations. Calotropis procera is a traditional medicinal plant, and its anticancer potential against many cancer cell lines has been reported, however its antiangiogenic and HDAC inhibitory action is largely unknown. The anticancer activity of methanol leaf extract of C. procera was tested in three types of human glioblastoma cell lines. Wild-type and transgenic zebrafish embryos were used to evaluate developmental toxicity and angiogenic activity. A human angiogenic antibody array was used to profile angiogenic proteins in the U251 GM cell line. A real-time reverse transcriptase polymerase chain reaction (RT PCR) assay was used to detect the differential expression of eleven HDAC genes in U251 cells treated with C. procera extract. The extract significantly reduced the proliferation of all three types of GBM cell lines and the cytotoxicity was found to be more pronounced in U251 GM cells, with an IC50 value of 2.63 ± 0.23 μg/ml, possibly by arresting the cell cycle at the G2/M transition. The extract did not exhibit toxic effects in zebrafish embryos, even at concentrations as high as 1000 μg/ml. The extract also inhibited angiogenic blood vessel formation in the transgenic zebrafish model in a dose-dependent manner. The results from the angiogenic antibody array have suggested novel angiogenesis targets that can be utilized to treat GBM. Real-time RT PCR analysis has shown that C. procrea extract caused an upregulation of HDAC5, 7, and 10, while the mRNA of HDAC1, 2, 3 and 8 (Class I HDACs), and HDAC4, 6, and 9 (Class II) were downregulated in U251 GM cells. The cytotoxicity of the C. procera extract on GBM cell lines could be due to its dual action by regulation of both tumor angiogenesis and histone deacetylases enzymes. Through this study, the C. procera leaf extract has been suggested as an effective remedy to treat GBM with minimal toxicity. In addition, various novel angiogenic and HDAC targets has been identified which could be helpful in designing better therapeutic strategies to manage glioblastoma multiforme in human patients.
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Affiliation(s)
- Shamsa Hilal Saleh Alanazi
- Bioproducts Research Chair, Department of Zoology, College of Science, King Saud University, P.O Box 2455 Riyadh 11451, Kingdom of Saudi Arabia
| | - Muhammad Farooq Khan
- Bioproducts Research Chair, Department of Zoology, College of Science, King Saud University, P.O Box 2455 Riyadh 11451, Kingdom of Saudi Arabia
| | - Anas M. Alazami
- Translational Genomics Department, Centre for Genomic Medicine, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Almohannad Baabbad
- Bioproducts Research Chair, Department of Zoology, College of Science, King Saud University, P.O Box 2455 Riyadh 11451, Kingdom of Saudi Arabia
| | - Mohammad Ahmed Wadaan
- Bioproducts Research Chair, Department of Zoology, College of Science, King Saud University, P.O Box 2455 Riyadh 11451, Kingdom of Saudi Arabia
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Patro I, Sahoo A, Nayak BR, Das R, Majumder S, Panigrahi GK. Nonsense-Mediated mRNA Decay: Mechanistic Insights and Physiological Significance. Mol Biotechnol 2023:10.1007/s12033-023-00927-4. [PMID: 37930508 DOI: 10.1007/s12033-023-00927-4] [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: 07/12/2023] [Accepted: 09/28/2023] [Indexed: 11/07/2023]
Abstract
Nonsense-mediated mRNA decay (NMD) is an evolutionarily conserved surveillance mechanism across eukaryotes and also regulates the expression of physiological transcripts, thus involved in gene regulation. It essentially ensures recognition and removal of aberrant transcripts. Therefore, the NMD protects the cellular system by restricting the synthesis of truncated proteins, potentially by eliminating the faulty mRNAs. NMD is an evolutionarily conserved surveillance mechanism across eukaryotes and also regulates the expression of physiological transcripts, thus involved in gene regulation as well. Primarily, the NMD machinery scans and differentiates the aberrant and non-aberrant transcripts. A myriad of cellular dysfunctions arise due to production of truncated proteins, so the NMD core proteins, the up-frameshift factors (UPFs) recognizes the faulty mRNAs and further recruits factors resulting in the mRNA degradation. NMD exhibits astounding variability in its ability in regulating cellular mechanisms including both pathological and physiological events. But, the detailed underlying molecular mechanisms in NMD remains blurred and require extensive investigation to gain insights on cellular homeostasis. The complexity in understanding of NMD pathway arises due to the involvement of numerous proteins, molecular interactions and their functioning in different steps of this process. Moreover methods such as alternative splicing generates numerous isoforms of mRNA, so it makes difficulties in understanding the impact of alternative splicing on the efficiency of NMD functioning. Role of NMD in cancer development is very complex. Studies have shown that in some cases cancer cells use NMD pathway as a tool to exploit the NMD mechanism to maintain tumor microenvironment. A greater level of understanding about the intricate mechanism of how tumor used NMD pathway for their benefits, a strategy can be developed for targeting and inhibiting NMD factors involved in pro-tumor activity. There are very little amount of information available about the NMD pathway, how it discriminate mRNAs that are targeted by NMD from those that are not. This review highlights our current understanding of NMD, specifically the regulatory mechanisms and attempts to outline less explored questions that warrant further investigations. Taken as a whole, a detailed molecular understanding of the NMD mechanism could lead to wide-ranging applications for improving cellular homeostasis and paving out strategies in combating pathological disorders leaping forward toward achieving United Nations sustainable development goals (SDG 3: Good health and well-being).
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Affiliation(s)
- Ipsita Patro
- School of Applied Sciences, Centurion University of Technology and Management, Bhubaneswar, Odisha, India
| | - Annapurna Sahoo
- School of Applied Sciences, Centurion University of Technology and Management, Bhubaneswar, Odisha, India.
| | - Bilash Ranjan Nayak
- School of Applied Sciences, Centurion University of Technology and Management, Bhubaneswar, Odisha, India
| | - Rutupurna Das
- School of Applied Sciences, Centurion University of Technology and Management, Bhubaneswar, Odisha, India
| | - Sanjoy Majumder
- School of Applied Sciences, Centurion University of Technology and Management, Bhubaneswar, Odisha, India
| | - Gagan Kumar Panigrahi
- School of Applied Sciences, Centurion University of Technology and Management, Bhubaneswar, Odisha, India.
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Monaghan L, Longman D, Cáceres JF. Translation-coupled mRNA quality control mechanisms. EMBO J 2023; 42:e114378. [PMID: 37605642 PMCID: PMC10548175 DOI: 10.15252/embj.2023114378] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/24/2023] [Accepted: 08/01/2023] [Indexed: 08/23/2023] Open
Abstract
mRNA surveillance pathways are essential for accurate gene expression and to maintain translation homeostasis, ensuring the production of fully functional proteins. Future insights into mRNA quality control pathways will enable us to understand how cellular mRNA levels are controlled, how defective or unwanted mRNAs can be eliminated, and how dysregulation of these can contribute to human disease. Here we review translation-coupled mRNA quality control mechanisms, including the non-stop and no-go mRNA decay pathways, describing their mechanisms, shared trans-acting factors, and differences. We also describe advances in our understanding of the nonsense-mediated mRNA decay (NMD) pathway, highlighting recent mechanistic findings, the discovery of novel factors, as well as the role of NMD in cellular physiology and its impact on human disease.
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Affiliation(s)
- Laura Monaghan
- MRC Human Genetics Unit, Institute of Genetics and CancerUniversity of EdinburghEdinburghUK
| | - Dasa Longman
- MRC Human Genetics Unit, Institute of Genetics and CancerUniversity of EdinburghEdinburghUK
| | - Javier F Cáceres
- MRC Human Genetics Unit, Institute of Genetics and CancerUniversity of EdinburghEdinburghUK
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Wang F, Zha Z, He Y, Li J, Zhong Z, Xiao Q, Tan Z. Genome-Wide Re-Sequencing Data Reveals the Population Structure and Selection Signatures of Tunchang Pigs in China. Animals (Basel) 2023; 13:1835. [PMID: 37889708 PMCID: PMC10252034 DOI: 10.3390/ani13111835] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/26/2023] [Accepted: 05/30/2023] [Indexed: 09/29/2023] Open
Abstract
Tunchang pig is one population of Hainan pig in the Hainan Province of China, with the characteristics of delicious meat, strong adaptability, and high resistance to diseases. To explore the genetic diversity and population structure of Tunchang pigs and uncover their germplasm characteristics, 10 unrelated Tunchang pigs were re-sequenced using the Illumina NovaSeq 150 bp paired-end platform with an average depth of 10×. Sequencing data from 36 individuals of 7 other pig breeds (including 4 local Chinese pig breeds (5 Jinhua, 5 Meishan, 5 Rongchang, and 6 Wuzhishan), and 3 commonly used commercial pig breeds (5 Duorc, 5 Landrace, and 5 Large White)) were downloaded from the NCBI public database. After analysis of genetic diversity and population structure, it has been found that compared to commercial pigs, Tunchang pigs have higher genetic diversity and are genetically close to native Chinese breeds. Three methods, FST, θπ, and XP-EHH, were used to detect selection signals for three breeds of pigs: Tunchang, Duroc, and Landrace. A total of 2117 significantly selected regions and 201 candidate genes were screened. Gene enrichment analysis showed that candidate genes were mainly associated with good adaptability, disease resistance, and lipid metabolism traits. Finally, further screening was conducted to identify potential candidate genes related to phenotypic traits, including meat quality (SELENOV, CBR4, TNNT1, TNNT3, VPS13A, PLD3, SRFBP1, and SSPN), immune regulation (CD48, FBL, PTPRH, GNA14, LOX, SLAMF6, CALCOCO1, IRGC, and ZNF667), growth and development (SYT5, PRX, PPP1R12C, and SMG9), reproduction (LGALS13 and EPG5), vision (SLC9A8 and KCNV2), energy metabolism (ATP5G2), cell migration (EPS8L1), and olfaction (GRK3). In summary, our research results provide a genomic overview of the genetic variation, genetic diversity, and population structure of the Tunchang pig population, which will be valuable for breeding and conservation of Tunchang pigs in the future.
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Affiliation(s)
| | | | | | | | | | - Qian Xiao
- School of Animal Science and Technology, Hainan University, Haikou 570228, China; (F.W.)
| | - Zhen Tan
- School of Animal Science and Technology, Hainan University, Haikou 570228, China; (F.W.)
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Hsieh MC, Lai CY, Yeh CM, Yang PS, Cheng JK, Wang HH, Lin KH, Nie ST, Lin TB, Peng HY. Phosphorylated Upstream Frameshift 1-dependent Nonsense-mediated μ-Opioid Receptor mRNA Decay in the Spinal Cord Contributes to the Development of Neuropathic Allodynia-like Behavior in Rats. Anesthesiology 2023; 138:634-655. [PMID: 36867667 DOI: 10.1097/aln.0000000000004550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
BACKGROUND Nonsense-mediated messenger RNA (mRNA) decay increases targeted mRNA degradation and has been implicated in the regulation of gene expression in neurons. The authors hypothesized that nonsense-mediated μ-opioid receptor mRNA decay in the spinal cord is involved in the development of neuropathic allodynia-like behavior in rats. METHODS Adult Sprague-Dawley rats of both sexes received spinal nerve ligation to induce neuropathic allodynia-like behavior. The mRNA and protein expression contents in the dorsal horn of animals were measured by biochemical analyses. Nociceptive behaviors were evaluated by the von Frey test and the burrow test. RESULTS On Day 7, spinal nerve ligation significantly increased phosphorylated upstream frameshift 1 (UPF1) expression in the dorsal horn (mean ± SD; 0.34 ± 0.19 in the sham ipsilateral group vs. 0.88 ± 0.15 in the nerve ligation ipsilateral group; P < 0.001; data in arbitrary units) and drove allodynia-like behaviors in rats (10.58 ± 1.72 g in the sham ipsilateral group vs. 1.19 ± 0.31 g in the nerve ligation ipsilateral group, P < 0.001). No sex-based differences were found in either Western blotting or behavior tests in rats. Eukaryotic translation initiation factor 4A3 (eIF4A3) triggered SMG1 kinase (0.06 ± 0.02 in the sham group vs. 0.20 ± 0.08 in the nerve ligation group, P = 0.005, data in arbitrary units)-mediated UPF1 phosphorylation, leading to increased nonsense-mediated mRNA decay factor SMG7 binding and µ-opioid receptor mRNA degradation (0.87 ± 0.11-fold in the sham group vs. 0.50 ± 0.11-fold in the nerve ligation group, P = 0.002) in the dorsal horn of the spinal cord after spinal nerve ligation. Pharmacologic or genetic inhibition of this signaling pathway in vivo ameliorated allodynia-like behaviors after spinal nerve ligation. CONCLUSIONS This study suggests that phosphorylated UPF1-dependent nonsense-mediated μ-opioid receptor mRNA decay is involved in the pathogenesis of neuropathic pain. EDITOR’S PERSPECTIVE
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Affiliation(s)
- Ming-Chun Hsieh
- Department of Medicine, Mackay Medical College, New Taipei, Taiwan
| | - Cheng-Yuan Lai
- Institute of Biomedical Sciences, MacKay Medical College, New Taipei City, Taiwan
| | - Chou-Ming Yeh
- Division of Thoracic Surgery, Department of Health, Taichung Hospital, Executive Yuan, Taichung, Taiwan; Central Taiwan University of Science and Technology, Taichung, Taiwan
| | - Po-Sheng Yang
- Department of Medicine, Mackay Medical College, New Taipei, Taiwan; Department of Surgery, Mackay Memorial Hospital, Taipei, Taiwan
| | - Jen-Kun Cheng
- Department of Medicine, Mackay Medical College, New Taipei, Taiwan; Department of Anesthesiology, Mackay Memorial Hospital, Taipei, Taiwan
| | - Hsueh-Hsiao Wang
- Department of Medicine, Mackay Medical College, New Taipei, Taiwan
| | - Kuan-Hung Lin
- Institute of Biomedical Sciences, MacKay Medical College, New Taipei City, Taiwan; Traditional Herbal Medicine Research Center, Taipei Medical University Hospital, Taipei, Taiwan; Department of Pharmacology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Siao-Tong Nie
- Department of Medicine, Mackay Medical College, New Taipei, Taiwan
| | - Tzer-Bin Lin
- Department of Physiology, School of Medicine, College of Medicine, Taipei Medical University, Taipei City, Taiwan; Institute of New Drug Development, College of Medicine, China Medical University, Taichung, Taiwan
| | - Hsien-Yu Peng
- Department of Medicine, Mackay Medical College, New Taipei, Taiwan; Institute of Biomedical Sciences, MacKay Medical College, New Taipei City, Taiwan
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Kadife E, Harper A, Chien K, Lino TK, Brownfoot FC. Novel genes associated with a placental phenotype in knockout mice also respond to cellular stressors in primary human trophoblasts. Placenta 2023; 139:68-74. [PMID: 37331027 DOI: 10.1016/j.placenta.2023.05.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 04/17/2023] [Accepted: 05/17/2023] [Indexed: 06/20/2023]
Abstract
INTRODUCTION Placental insufficiency is a leading cause of intrauterine growth restriction, contributing to perinatal morbidity and mortality. The molecular regulation of placental development and what causes placental insufficiency is poorly understood. Recently, a panel of genes were found to cause significant placental dysmorphologies in mice with severely growth restricted off-spring. We aimed to assess whether these genes were also implicated in human intrauterine growth restriction. METHODS We explored the expression of nine genes in primary cytotrophoblast cells in hypoxic (n = 6) and glucose starvation (n = 5) conditions in vitro. We also explored whether the genes were dysregulated in intrauterine growth restricted human placental samples (n = 11), with (n = 20) or without preeclampsia compared to gestationally matched controls (<34 weeks gestation) (n = 17). RESULTS Hypoxic stress significantly upregulated the expressions of BRD2 (p = 0.0313), SMG9 (p = 0.0313) genes. In contrast, glucose starvation significantly suppressed Kif1bp (p = 0.0089) in primary cytotrophoblasts. The FRYL, NEK9, CHTOP, PSPH, ATP11A, HM13 genes did not change under hypoxia or glucose starvation conditions. The expression of these genes was not altered in placenta from patients with intrauterine growth restriction, compared to gestationally matched controls. DISCUSSION We demonstrate that some of the genes that cause a placental phenotype in mice, respond to hypoxic and glucose mediated stress in human cytotrophoblast isolations. Despite this, they are unchanged in placenta from patients with intrauterine growth restriction. Therefore, dysregulation of these genes is less likely to contribute to preterm intrauterine growth restriction in humans.
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Affiliation(s)
- Elif Kadife
- Obstetric Diagnostics and Therapeutics Group, Department of Obstetrics and Gynaecology, University of Melbourne, Mercy Hospital for Women, 163 Studley Road, Heidelberg, 3084, Victoria, Australia; Mercy Perinatal, Mercy Hospital for Women Heidelberg, 163 Studley Road, Heidelberg, 3084, Victoria, Australia
| | - Alesia Harper
- Obstetric Diagnostics and Therapeutics Group, Department of Obstetrics and Gynaecology, University of Melbourne, Mercy Hospital for Women, 163 Studley Road, Heidelberg, 3084, Victoria, Australia; Mercy Perinatal, Mercy Hospital for Women Heidelberg, 163 Studley Road, Heidelberg, 3084, Victoria, Australia
| | - Keegan Chien
- Obstetric Diagnostics and Therapeutics Group, Department of Obstetrics and Gynaecology, University of Melbourne, Mercy Hospital for Women, 163 Studley Road, Heidelberg, 3084, Victoria, Australia; Mercy Perinatal, Mercy Hospital for Women Heidelberg, 163 Studley Road, Heidelberg, 3084, Victoria, Australia
| | - Tu'uhevaha Kaitu'u Lino
- Diagnostics Discovery and Reverse Translation in Pregnancy, Department of Obstetrics and Gynaecology, University of Melbourne, Mercy Hospital for Women, 163 Studley Road, Heidelberg, 3084, Victoria, Australia
| | - Fiona C Brownfoot
- Obstetric Diagnostics and Therapeutics Group, Department of Obstetrics and Gynaecology, University of Melbourne, Mercy Hospital for Women, 163 Studley Road, Heidelberg, 3084, Victoria, Australia; Mercy Perinatal, Mercy Hospital for Women Heidelberg, 163 Studley Road, Heidelberg, 3084, Victoria, Australia.
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11
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Radford BN, Zhao X, Glazer T, Eaton M, Blackwell D, Mohammad S, Lo Vercio LD, Devine J, Shalom-Barak T, Hallgrimsson B, Cross JC, Sucov HM, Barak Y, Dean W, Hemberger M. Defects in placental syncytiotrophoblast cells are a common cause of developmental heart disease. Nat Commun 2023; 14:1174. [PMID: 36859534 PMCID: PMC9978031 DOI: 10.1038/s41467-023-36740-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 02/15/2023] [Indexed: 03/03/2023] Open
Abstract
Placental abnormalities have been sporadically implicated as a source of developmental heart defects. Yet it remains unknown how often the placenta is at the root of congenital heart defects (CHDs), and what the cellular mechanisms are that underpin this connection. Here, we selected three mouse mutant lines, Atp11a, Smg9 and Ssr2, that presented with placental and heart defects in a recent phenotyping screen, resulting in embryonic lethality. To dissect phenotype causality, we generated embryo- and trophoblast-specific conditional knockouts for each of these lines. This was facilitated by the establishment of a new transgenic mouse, Sox2-Flp, that enables the efficient generation of trophoblast-specific conditional knockouts. We demonstrate a strictly trophoblast-driven cause of the CHD and embryonic lethality in one of the three lines (Atp11a) and a significant contribution of the placenta to the embryonic phenotypes in another line (Smg9). Importantly, our data reveal defects in the maternal blood-facing syncytiotrophoblast layer as a shared pathology in placentally induced CHD models. This study highlights the placenta as a significant source of developmental heart disorders, insights that will transform our understanding of the vast number of unexplained congenital heart defects.
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Affiliation(s)
- Bethany N Radford
- Dept. of Biochemistry and Molecular Biology, Cumming School of Medicine, Alberta Children's Hospital Research Institute, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada
| | - Xiang Zhao
- Dept. of Cell Biology and Anatomy, Cumming School of Medicine, Alberta Children's Hospital Research Institute, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada
| | - Tali Glazer
- Dept. of Biochemistry and Molecular Biology, Cumming School of Medicine, Alberta Children's Hospital Research Institute, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada
| | - Malcolm Eaton
- Dept. of Biochemistry and Molecular Biology, Cumming School of Medicine, Alberta Children's Hospital Research Institute, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada
| | - Danielle Blackwell
- Dept. of Biochemistry and Molecular Biology, Cumming School of Medicine, Alberta Children's Hospital Research Institute, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada
| | - Shuhiba Mohammad
- Dept. of Biochemistry and Molecular Biology, Cumming School of Medicine, Alberta Children's Hospital Research Institute, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada
| | - Lucas Daniel Lo Vercio
- Dept. of Cell Biology and Anatomy, Cumming School of Medicine, Alberta Children's Hospital Research Institute, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada
| | - Jay Devine
- Dept. of Cell Biology and Anatomy, Cumming School of Medicine, Alberta Children's Hospital Research Institute, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada
| | - Tali Shalom-Barak
- Magee-Women's Research Institute, Dept. of Obstetrics/Gynecology and Reproductive Sciences, University of Pittsburgh, 204 Craft Ave., Pittsburgh, PA, 15213, USA
| | - Benedikt Hallgrimsson
- Dept. of Cell Biology and Anatomy, Cumming School of Medicine, Alberta Children's Hospital Research Institute, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada
| | - James C Cross
- Dept. of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, Alberta Children's Hospital Research Institute, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada
| | - Henry M Sucov
- Dept. of Regenerative Medicine and Cell Biology, Division of Cardiology, Dept. of Medicine, Medical University of South Carolina, 173 Ashley Ave., Charleston, SC, 29403, USA
| | - Yaacov Barak
- Magee-Women's Research Institute, Dept. of Obstetrics/Gynecology and Reproductive Sciences, University of Pittsburgh, 204 Craft Ave., Pittsburgh, PA, 15213, USA
| | - Wendy Dean
- Dept. of Cell Biology and Anatomy, Cumming School of Medicine, Alberta Children's Hospital Research Institute, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada.
| | - Myriam Hemberger
- Dept. of Biochemistry and Molecular Biology, Cumming School of Medicine, Alberta Children's Hospital Research Institute, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada.
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12
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Llorca-Cardenosa MJ, Aronson LI, Krastev DB, Nieminuszczy J, Alexander J, Song F, Dylewska M, Broderick R, Brough R, Zimmermann A, Zenke FT, Gurel B, Riisnaes R, Ferreira A, Roumeliotis T, Choudhary J, Pettitt SJ, de Bono J, Cervantes A, Haider S, Niedzwiedz W, Lord CJ, Chong IY. SMG8/SMG9 Heterodimer Loss Modulates SMG1 Kinase to Drive ATR Inhibitor Resistance. Cancer Res 2022; 82:3962-3973. [PMID: 36273494 PMCID: PMC9627126 DOI: 10.1158/0008-5472.can-21-4339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 07/19/2022] [Accepted: 08/26/2022] [Indexed: 01/07/2023]
Abstract
Gastric cancer represents the third leading cause of global cancer mortality and an area of unmet clinical need. Drugs that target the DNA damage response, including ATR inhibitors (ATRi), have been proposed as novel targeted agents in gastric cancer. Here, we sought to evaluate the efficacy of ATRi in preclinical models of gastric cancer and to understand how ATRi resistance might emerge as a means to identify predictors of ATRi response. A positive selection genome-wide CRISPR-Cas9 screen identified candidate regulators of ATRi resistance in gastric cancer. Loss-of-function mutations in either SMG8 or SMG9 caused ATRi resistance by an SMG1-mediated mechanism. Although ATRi still impaired ATR/CHK1 signaling in SMG8/9-defective cells, other characteristic responses to ATRi exposure were not seen, such as changes in ATM/CHK2, γH2AX, phospho-RPA, or 53BP1 status or changes in the proportions of cells in S- or G2-M-phases of the cell cycle. Transcription/replication conflicts (TRC) elicited by ATRi exposure are a likely cause of ATRi sensitivity, and SMG8/9-defective cells exhibited a reduced level of ATRi-induced TRCs, which could contribute to ATRi resistance. These observations suggest ATRi elicits antitumor efficacy in gastric cancer but that drug resistance could emerge via alterations in the SMG8/9/1 pathway. SIGNIFICANCE These findings reveal how cancer cells acquire resistance to ATRi and identify pathways that could be targeted to enhance the overall effectiveness of these inhibitors.
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Affiliation(s)
| | | | - Dragomir B. Krastev
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
- Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | | | - John Alexander
- The Institute of Cancer Research, London, United Kingdom
| | - Feifei Song
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
- Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | | | | | - Rachel Brough
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
- Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Astrid Zimmermann
- The healthcare business of Merck KGaA, Biopharma R&D, Translational Innovation Platform Oncology, Darmstadt, Germany
| | - Frank T. Zenke
- The healthcare business of Merck KGaA, Biopharma R&D, Translational Innovation Platform Oncology, Darmstadt, Germany
| | - Bora Gurel
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden Hospital NHS Foundation Trust, London, United Kingdom
| | - Ruth Riisnaes
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden Hospital NHS Foundation Trust, London, United Kingdom
| | - Ana Ferreira
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden Hospital NHS Foundation Trust, London, United Kingdom
| | | | | | - Stephen J. Pettitt
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
- Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Johann de Bono
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden Hospital NHS Foundation Trust, London, United Kingdom
| | - Andres Cervantes
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia, 46010, Spain
- CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - Syed Haider
- Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | | | - Christopher J. Lord
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
- Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Irene Y. Chong
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden Hospital NHS Foundation Trust, London, United Kingdom
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13
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Rahikkala E, Urpa L, Ghimire B, Topa H, Kurki MI, Koskela M, Airavaara M, Hämäläinen E, Pylkäs K, Körkkö J, Savolainen H, Suoranta A, Bertoli-Avella A, Rolfs A, Mattila P, Daly M, Palotie A, Pietiläinen O, Moilanen J, Kuismin O. A novel variant in SMG9 causes intellectual disability, confirming a role for nonsense-mediated decay components in neurocognitive development. Eur J Hum Genet 2022; 30:619-627. [PMID: 35087184 PMCID: PMC9090808 DOI: 10.1038/s41431-022-01046-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 12/04/2021] [Accepted: 01/11/2022] [Indexed: 12/13/2022] Open
Abstract
Biallelic loss-of-function variants in the SMG9 gene, encoding a regulatory subunit of the mRNA nonsense-mediated decay (NMD) machinery, are reported to cause heart and brain malformation syndrome. Here we report five patients from three unrelated families with intellectual disability (ID) and a novel pathogenic SMG9 c.551 T > C p.(Val184Ala) homozygous missense variant, identified using exome sequencing. Sanger sequencing confirmed recessive segregation in each family. SMG9 c.551T > C p.(Val184Ala) is most likely an autozygous variant identical by descent. Characteristic clinical findings in patients were mild to moderate ID, intention tremor, pyramidal signs, dyspraxia, and ocular manifestations. We used RNA sequencing of patients and age- and sex-matched healthy controls to assess the effect of the variant. RNA sequencing revealed that the SMG9 c.551T > C variant did not affect the splicing or expression level of SMG9 gene products, and allele-specific expression analysis did not provide evidence that the nonsense mRNA-induced NMD was affected. Differential gene expression analysis identified prevalent upregulation of genes in patients, including the genes SMOX, OSBP2, GPX3, and ZNF155. These findings suggest that normal SMG9 function may be involved in transcriptional regulation without affecting nonsense mRNA-induced NMD. In conclusion, we demonstrate that the SMG9 c.551T > C missense variant causes a neurodevelopmental disorder and impacts gene expression. NMD components have roles beyond aberrant mRNA degradation that are crucial for neurocognitive development.
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Affiliation(s)
- Elisa Rahikkala
- Department of Clinical Genetics, PEDEGO Research Unit and Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland.
- Institute of Biomedicine, University of Turku, Turku, Finland.
| | - Lea Urpa
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Bishwa Ghimire
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Hande Topa
- Neuroscience Center, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Mitja I Kurki
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Psychiatric & Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- The Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Maryna Koskela
- Neuroscience Center, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Mikko Airavaara
- Neuroscience Center, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Eija Hämäläinen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Katri Pylkäs
- Cancer and Translational Medicine Research Unit and Biocenter Oulu, University of Oulu, NordLab Oulu, Oulu, Finland
| | - Jarmo Körkkö
- Center for Intellectual Disability Care, Oulu University Hospital, Oulu, Finland
| | - Helena Savolainen
- Center for Intellectual Disability Care, Oulu University Hospital, Oulu, Finland
| | - Anu Suoranta
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | | | - Arndt Rolfs
- Centogene GmbH, 18055, Rostock, Germany
- Medical Faculty, University of Rostock, Rostock, Germany
| | - Pirkko Mattila
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Mark Daly
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Psychiatric & Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- The Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Psychiatric & Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- The Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Olli Pietiläinen
- Neuroscience Center, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- The Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jukka Moilanen
- Department of Clinical Genetics, PEDEGO Research Unit and Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Outi Kuismin
- Department of Clinical Genetics, PEDEGO Research Unit and Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
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14
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Yang Q, Qin Z, Zhang Q, Yi S, Yi S, Luo J. Identification of a novel compound heterozygous SMG9 variants in a Chinese family with heart and brain malformation syndrome using whole exome sequencing. BMC Med Genomics 2022; 15:67. [PMID: 35321723 PMCID: PMC8943999 DOI: 10.1186/s12920-022-01217-9] [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: 01/18/2022] [Accepted: 03/17/2022] [Indexed: 11/13/2022] Open
Abstract
SMG9-deficiency syndrome, also known as heart and brain malformation syndrome, is a very rare congenital genetic disorder mainly characterized by brain, heart, and growth and developmental abnormalities. This syndrome is an autosomal recessive disease resulting from mutations in the SMG9 gene, which encodes a critical component of nonsense-mediated mRNA decay. Thus far, only twelve SMG9 deficiency patients have been reported with five novel homozygous SMG9 mutations. The most frequent characteristic features of these patients are facial dysmorphism, severe global developmental delay, intellectual disability, congenital heart disease, growth restriction, microcephaly, and brain abnormalities. Herein, whole exome sequencing was performed to identify novel compound heterozygous SMG9 variants (NM_019108.3: c.1318_1319delAG (p.Ser440*) and c.947A>G (p.His316Arg)) in the proband, who exhibited syndromic intellectual disability. Mutations were confirmed as segregating in his affected sister and other unaffected family members by Sanger sequencing. The patients we describe here have a similar dysmorphology profile associated with SMG9-deficiency syndrome. Comparing the phenotype with that of patients in published reports, our patients can walk independently and their growth parameters are normal. In addition, short stature, failure to thrive, and microcephaly were not observed. Possible residual function of the H316R SMG9 variant could explain the milder phenotype observed in our patients. Our report is the first description of a non-consanguineous Chinese pedigree with novel compound heterozygous variants in the SMG9 gene. The molecular confirmation of the patient expands the genetic spectrum of SMG9-deficiency syndrome, and the manifestation of SMG9-deficiency syndrome in the patient provides additional clinical information regarding this syndrome.
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Affiliation(s)
- Qi Yang
- Guangxi Key Laboratory of Birth Defects Research and Prevention, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, No. 59, Xiangzhu Road, Nanning, China.,Department of Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Zailong Qin
- Guangxi Key Laboratory of Birth Defects Research and Prevention, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, No. 59, Xiangzhu Road, Nanning, China.,Department of Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Qinle Zhang
- Guangxi Key Laboratory of Birth Defects Research and Prevention, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, No. 59, Xiangzhu Road, Nanning, China.,Department of Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Shang Yi
- Guangxi Key Laboratory of Birth Defects Research and Prevention, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, No. 59, Xiangzhu Road, Nanning, China.,Department of Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Sheng Yi
- Guangxi Key Laboratory of Birth Defects Research and Prevention, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, No. 59, Xiangzhu Road, Nanning, China.,Department of Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Jingsi Luo
- Guangxi Key Laboratory of Birth Defects Research and Prevention, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, No. 59, Xiangzhu Road, Nanning, China. .,Department of Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China.
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15
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Lejeune F. Nonsense-Mediated mRNA Decay, a Finely Regulated Mechanism. Biomedicines 2022; 10:biomedicines10010141. [PMID: 35052820 PMCID: PMC8773229 DOI: 10.3390/biomedicines10010141] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 02/01/2023] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is both a mechanism for rapidly eliminating mRNAs carrying a premature termination codon and a pathway that regulates many genes. This implies that NMD must be subject to regulation in order to allow, under certain physiological conditions, the expression of genes that are normally repressed by NMD. Therapeutically, it might be interesting to express certain NMD-repressed genes or to allow the synthesis of functional truncated proteins. Developing such approaches will require a good understanding of NMD regulation. This review describes the different levels of this regulation in human cells.
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Affiliation(s)
- Fabrice Lejeune
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277—CANTHER—Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France;
- Unité Tumorigenèse et Résistance aux Traitements, Institut Pasteur de Lille, F-59000 Lille, France
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16
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Lai HC, Ho UY, James A, De Souza P, Roberts TL. RNA metabolism and links to inflammatory regulation and disease. Cell Mol Life Sci 2021; 79:21. [PMID: 34971439 PMCID: PMC11072290 DOI: 10.1007/s00018-021-04073-5] [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: 01/13/2021] [Revised: 09/29/2021] [Accepted: 10/22/2021] [Indexed: 11/29/2022]
Abstract
Inflammation is vital to protect the host against foreign organism invasion and cellular damage. It requires tight and concise gene expression for regulation of pro- and anti-inflammatory gene expression in immune cells. Dysregulated immune responses caused by gene mutations and errors in post-transcriptional regulation can lead to chronic inflammatory diseases and cancer. The mechanisms underlying post-transcriptional gene expression regulation include mRNA splicing, mRNA export, mRNA localisation, mRNA stability, RNA/protein interaction, and post-translational events such as protein stability and modification. The majority of studies to date have focused on transcriptional control pathways. However, post-transcriptional regulation of mRNA in eukaryotes is equally important and related information is lacking. In this review, we will focus on the mechanisms involved in the pre-mRNA splicing events, mRNA surveillance, RNA degradation pathways, disorders or symptoms caused by mutations or errors in post-transcriptional regulation during innate immunity especially toll-like receptor mediated pathways.
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Affiliation(s)
- Hui-Chi Lai
- Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia.
- South West Sydney Clinical School, UNSW Australia, Liverpool, NSW, Australia.
| | - Uda Y Ho
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - Alexander James
- Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia
| | - Paul De Souza
- Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia
- School of Medicine, University of Wollongong, Wollongong, NSW, Australia
- School of Medicine, Western Sydney University, Macarthur, NSW, Australia
| | - Tara L Roberts
- Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia
- South West Sydney Clinical School, UNSW Australia, Liverpool, NSW, Australia
- School of Medicine, Western Sydney University, Macarthur, NSW, Australia
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17
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Cell Type-Specific Role of RNA Nuclease SMG6 in Neurogenesis. Cells 2021; 10:cells10123365. [PMID: 34943873 PMCID: PMC8699217 DOI: 10.3390/cells10123365] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/22/2021] [Accepted: 11/26/2021] [Indexed: 12/11/2022] Open
Abstract
SMG6 is an endonuclease, which cleaves mRNAs during nonsense-mediated mRNA decay (NMD), thereby regulating gene expression and controling mRNA quality. SMG6 has been shown as a differentiation license factor of totipotent embryonic stem cells. To investigate whether it controls the differentiation of lineage-specific pluripotent progenitor cells, we inactivated Smg6 in murine embryonic neural stem cells. Nestin-Cre-mediated deletion of Smg6 in mouse neuroprogenitor cells (NPCs) caused perinatal lethality. Mutant mice brains showed normal structure at E14.5 but great reduction of the cortical NPCs and late-born cortical neurons during later stages of neurogenesis (i.e., E18.5). Smg6 inactivation led to dramatic cell death in ganglionic eminence (GE) and a reduction of interneurons at E14.5. Interestingly, neurosphere assays showed self-renewal defects specifically in interneuron progenitors but not in cortical NPCs. RT-qPCR analysis revealed that the interneuron differentiation regulators Dlx1 and Dlx2 were reduced after Smg6 deletion. Intriguingly, when Smg6 was deleted specifically in cortical and hippocampal progenitors, the mutant mice were viable and showed normal size and architecture of the cortex at E18.5. Thus, SMG6 regulates cell fate in a cell type-specific manner and is more important for neuroprogenitors originating from the GE than for progenitors from the cortex.
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18
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Abdel-Salam GMH, Duan R, Abdel-Hamid MS, Sayed ISM, Jhangiani SN, Khan Z, Du H, Gibbs RA, Posey JE, Marafi D, Lupski JR. Expanding the phenotypic and allelic spectrum of SMG8: Clinical observations reveal overlap with SMG9-associated disease trait. Am J Med Genet A 2021; 188:648-657. [PMID: 34761517 DOI: 10.1002/ajmg.a.62561] [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: 07/23/2021] [Revised: 10/03/2021] [Accepted: 10/22/2021] [Indexed: 11/06/2022]
Abstract
SMG8 (MIM *617315) is a regulatory subunit involved in nonsense-mediated mRNA decay (NMD), a cellular protective pathway that regulates mRNA transcription, transcript stability, and degrades transcripts containing premature stop codons. SMG8 binds SMG9 and SMG1 to form the SMG1C complex and inhibit the kinase activity of SMG1. Biallelic deleterious variants in SMG9 are known to cause a heart and brain malformation syndrome (HBMS; MIM #616920), whereas biallelic deleterious variants in SMG8 were recently described to cause a novel neurodevelopmental disorder (NDD) with dysmorphic facies and cataracts, now defined as Alzahrani-Kuwahara syndrome (ALKUS: MIM #619268). Only eight subjects from four families with ALKUS have been described to date. Through research reanalysis of a nondiagnostic clinical exome, we identified a subject from a fifth unrelated family with a homozygous deleterious variant in SMG8 and features consistent with ALKUS. Interestingly, the subject also had unilateral microphthalmia, a clinical feature that has been described in SMG9-related disorder. Our study expands the phenotypic spectrum of SMG8-related disorder, demonstrates an overlapping phenotype between SMG8- and SMG9-related rare disease traits, provides further evidence for the SMG8 and SMG9 protein interactions, and highlights the importance of revisiting nondiagnostic exome data to identify and affirm emerging novel genes for rare disease traits.
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Affiliation(s)
- Ghada M H Abdel-Salam
- Clinical Genetics Department, Human Genetics and Genome Research Division, National ResearchCentre, Cairo, Egypt
| | - Ruizhi Duan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Mohamed S Abdel-Hamid
- Medical Molecular Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Inas S M Sayed
- Orodental Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Ziad Khan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Department of Pediatrics, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA.,Texas Children's Hospital, Houston, Texas, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
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19
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Langer LM, Bonneau F, Gat Y, Conti E. Cryo-EM reconstructions of inhibitor-bound SMG1 kinase reveal an autoinhibitory state dependent on SMG8. eLife 2021; 10:72353. [PMID: 34698635 PMCID: PMC8592573 DOI: 10.7554/elife.72353] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/25/2021] [Indexed: 12/31/2022] Open
Abstract
The PI3K-related kinase (PIKK) SMG1 monitors the progression of metazoan nonsense-mediated mRNA decay (NMD) by phosphorylating the RNA helicase UPF1. Previous work has shown that the activity of SMG1 is impaired by small molecule inhibitors, is reduced by the SMG1 interactors SMG8 and SMG9, and is downregulated by the so-called SMG1 insertion domain. However, the molecular basis for this complex regulatory network has remained elusive. Here, we present cryo-electron microscopy reconstructions of human SMG1-9 and SMG1-8-9 complexes bound to either a SMG1 inhibitor or a non-hydrolyzable ATP analog at overall resolutions ranging from 2.8 to 3.6 Å. These structures reveal the basis with which a small molecule inhibitor preferentially targets SMG1 over other PIKKs. By comparison with our previously reported substrate-bound structure (Langer et al.,2020), we show that the SMG1 insertion domain can exert an autoinhibitory function by directly blocking the substrate-binding path as well as overall access to the SMG1 kinase active site. Together with biochemical analysis, our data indicate that SMG1 autoinhibition is stabilized by the presence of SMG8. Our results explain the specific inhibition of SMG1 by an ATP-competitive small molecule, provide insights into regulation of its kinase activity within the NMD pathway, and expand the understanding of PIKK regulatory mechanisms in general.
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Affiliation(s)
- Lukas M Langer
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Fabien Bonneau
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Yair Gat
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Elena Conti
- Max Planck Institute of Biochemistry, Martinsried, Germany
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20
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Jin X, Yin J, Zhu H, Li W, Yu K, Liu M, Zhang X, Lu M, Wan Z, Huang X. SMG9 Serves as an Oncogene to Promote the Tumor Progression via EMT and Wnt/β-Catenin Signaling Pathway in Hepatocellular Carcinoma. Front Pharmacol 2021; 12:701454. [PMID: 34456727 PMCID: PMC8397484 DOI: 10.3389/fphar.2021.701454] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 08/03/2021] [Indexed: 01/02/2023] Open
Abstract
Background/Aims: SMG9 participates in the nonsense-mediated mRNA decay process that degrades mRNA harboring nonsense mutations introduced either at the level of transcription or RNA processing. However, little is known about the role of SMG9 in hepatocellular carcinoma (HCC). The objective of this research was to clarify the effects of SMG9 expression on HCC progression. Methods: Microarray data were acquired from NCBI Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) database to bioinformatically analyze the differential expression of SMG9 between HCC patients and normal controls. SMG9 mRNA level was measured in sixteen sets of fresh tumor tissues and adjacent non-cancerous liver tissues (ANLTs) via reverse transcription-quantitative polymerase chain reaction (RT-qPCR). SMG9 protein expression was analyzed in ninety-five sets of paired formalin-fixed and paraffin-embedded tissue specimens by immunohistochemistry (IHC). In addition, clinicopathological features of SMG9 in HCC were checked. For in vitro studies, small interfering RNA (siRNA) was used to silence SMG9 expression for exploring biological functions and underlying mechanisms of SMG9 in SMMC-7721 and HepG2. Results: We found that SMG9 was upregulated in HCC tissues and SMG9 levels were closely related to TNM stage, tumor number and tumor size. Cox regression and Kaplan–Meier proportional hazards analyses showed that high expression of SMG9 was associated with poor patient survival. Furthermore, proliferation, apoptosis resistance, migration and invasion of both SMMC-7721 and HepG2 cells were suppressed by SMG9 inhibition. In addition, EMT and the Wnt/β-catenin signaling pathway were involved in SMG9-mediated HCC progression. Conclusions: SMG9 may serve as a potential novel prognostic biomarker and therapeutic target in HCC patients.
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Affiliation(s)
- Xing Jin
- Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jie Yin
- Department of Nuclear Medicine, The Affiliated Hospital of Yangzhou University, Yangzhou, China
| | - Hongling Zhu
- Department of Gynecology, Shanghai Armed Police Corps Hospital, Shanghai, China
| | - Weikang Li
- Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Kewei Yu
- Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Miao Liu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiujuan Zhang
- Department of Liver Disease, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Miaolian Lu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zemin Wan
- Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xianzhang Huang
- Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
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21
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Feng YL, Li ND. Duplication of 19q (13.2-13.31) associated with comitant esotropia: A case report. World J Clin Cases 2021; 9:5526-5534. [PMID: 34307605 PMCID: PMC8281424 DOI: 10.12998/wjcc.v9.i20.5526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 12/23/2020] [Accepted: 03/11/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Comitant esotropia is the most common form of strabismus. It is caused by heterogeneous environmental and genetic risk factors. The pure duplication of the long arm of chromosome 19 is a rare abnormality. Only 8 patients with partial trisomy of the long arm of chromosome 19q have been reported to date. Here, we describe a girl with pure duplication of 19q, who was diagnosed with congenital esotropia, microcephaly, and gallbladder agenesis.
CASE SUMMARY The patient was diagnosed with esotropia when she was 1-year-old. The Krimsky method showed +50 prism diopters in the primary gaze position. No additional abnormal findings were observed following slit lamp and fundus examination, but the features of the full-field electroretinogram showed a decreased amplitude and increased implicit times. Magnetic resonance imaging showed ventriculomegaly with thinning of the corpus callosum and splenium in her brain. A 4.42 Mb mosaic duplication within 19q13.2-q13.31 region (chr19:39,343,725 to 43,762,586) was detected by microarray comparative genomic hybridization.
CONCLUSION Strabismus is reported in many live borns with pure duplication of 19q. This important clinical characteristic indicates that the candidate genes fundamental for this phenotype may be narrowed to genes within the 19q13.3-q13.31 region. There were two candidate genes observed that may contribute to the comitant esotropia phenotype, namely XRCC1 (19:43,543,311) and SMG9 (19:43,727,991).
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Affiliation(s)
- Yue-Lan Feng
- Department of Ophthalmology, National Center for Children's Health, Beijing Children’s Hospital, Capital Medical University, Beijing 100045, China
- Department of Ophthalmology, First Hospital Affiliated to Baotou Medical College, Baotou 014010, Inner Mongolia Autonomous Region, China
| | - Ning-Dong Li
- Department of Ophthalmology, National Center for Children's Health, Beijing Children’s Hospital, Capital Medical University, Beijing 100045, China
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22
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Nogueira G, Fernandes R, García-Moreno JF, Romão L. Nonsense-mediated RNA decay and its bipolar function in cancer. Mol Cancer 2021; 20:72. [PMID: 33926465 PMCID: PMC8082775 DOI: 10.1186/s12943-021-01364-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 04/19/2021] [Indexed: 12/17/2022] Open
Abstract
Nonsense-mediated decay (NMD) was first described as a quality-control mechanism that targets and rapidly degrades aberrant mRNAs carrying premature termination codons (PTCs). However, it was found that NMD also degrades a significant number of normal transcripts, thus arising as a mechanism of gene expression regulation. Based on these important functions, NMD regulates several biological processes and is involved in the pathophysiology of a plethora of human genetic diseases, including cancer. The present review aims to discuss the paradoxical, pro- and anti-tumorigenic roles of NMD, and how cancer cells have exploited both functions to potentiate the disease. Considering recent genetic and bioinformatic studies, we also provide a comprehensive overview of the present knowledge of the advantages and disadvantages of different NMD modulation-based approaches in cancer therapy, reflecting on the challenges imposed by the complexity of this disease. Furthermore, we discuss significant advances in the recent years providing new perspectives on the implications of aberrant NMD-escaping frameshifted transcripts in personalized immunotherapy design and predictive biomarker optimization. A better understanding of how NMD differentially impacts tumor cells according to their own genetic identity will certainly allow for the application of novel and more effective personalized treatments in the near future.
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Affiliation(s)
- Gonçalo Nogueira
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016, Lisbon, Portugal.,BioISI - Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisbon, Portugal
| | - Rafael Fernandes
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016, Lisbon, Portugal.,BioISI - Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisbon, Portugal
| | - Juan F García-Moreno
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016, Lisbon, Portugal.,BioISI - Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisbon, Portugal
| | - Luísa Romão
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016, Lisbon, Portugal. .,BioISI - Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisbon, Portugal.
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23
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Lee PJ, Yang S, Sun Y, Guo JU. Regulation of nonsense-mediated mRNA decay in neural development and disease. J Mol Cell Biol 2021; 13:269-281. [PMID: 33783512 PMCID: PMC8339359 DOI: 10.1093/jmcb/mjab022] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 01/27/2021] [Accepted: 02/05/2021] [Indexed: 11/26/2022] Open
Abstract
Eukaryotes have evolved a variety of mRNA surveillance mechanisms to detect and degrade aberrant mRNAs with potential deleterious outcomes. Among them, nonsense-mediated mRNA decay (NMD) functions not only as a quality control mechanism targeting aberrant mRNAs containing a premature termination codon but also as a posttranscriptional gene regulation mechanism targeting numerous physiological mRNAs. Despite its well-characterized molecular basis, the regulatory scope and biological functions of NMD at an organismal level are incompletely understood. In humans, mutations in genes encoding core NMD factors cause specific developmental and neurological syndromes, suggesting a critical role of NMD in the central nervous system. Here, we review the accumulating biochemical and genetic evidence on the developmental regulation and physiological functions of NMD as well as an emerging role of NMD dysregulation in neurodegenerative diseases.
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Affiliation(s)
- Paul Jongseo Lee
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA.,Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06520, USA
| | - Suzhou Yang
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA.,Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06520, USA
| | - Yu Sun
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Junjie U Guo
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA.,Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06520, USA
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24
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Altuwaijri N, Abdelbaky M, Alhashem A, Alrakaf M, Hashem M, Alzahrani F, Alkuraya FS. Further delineation of SMG9-related heart and brain malformation syndrome. Am J Med Genet A 2021; 185:1624-1630. [PMID: 33609422 DOI: 10.1002/ajmg.a.62139] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/08/2021] [Accepted: 02/08/2021] [Indexed: 11/05/2022]
Affiliation(s)
- Norah Altuwaijri
- Department of Translational Genomics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mona Abdelbaky
- Department of Pediatrics, Prince Sultan Medical Military City, Riyadh, Saudi Arabia
| | - Amal Alhashem
- Department of Pediatrics, Prince Sultan Medical Military City, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Maha Alrakaf
- Department of Obstetrics and Gynecology, Maternal fetal Medicine Division, Prince Sultan Medical Military City, Riyadh, Saudi Arabia
| | - Mais Hashem
- Department of Translational Genomics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fatema Alzahrani
- Department of Translational Genomics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Department of Pediatrics, Prince Sultan Medical Military City, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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25
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Harding P, Cunha DL, Moosajee M. Animal and cellular models of microphthalmia. THERAPEUTIC ADVANCES IN RARE DISEASE 2021; 2:2633004021997447. [PMID: 37181112 PMCID: PMC10032472 DOI: 10.1177/2633004021997447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 02/02/2021] [Indexed: 05/16/2023]
Abstract
Microphthalmia is a rare developmental eye disorder affecting 1 in 7000 births. It is defined as a small (axial length ⩾2 standard deviations below the age-adjusted mean) underdeveloped eye, caused by disruption of ocular development through genetic or environmental factors in the first trimester of pregnancy. Clinical phenotypic heterogeneity exists amongst patients with varying levels of severity, and associated ocular and systemic features. Up to 11% of blind children are reported to have microphthalmia, yet currently no treatments are available. By identifying the aetiology of microphthalmia and understanding how the mechanisms of eye development are disrupted, we can gain a better understanding of the pathogenesis. Animal models, mainly mouse, zebrafish and Xenopus, have provided extensive information on the genetic regulation of oculogenesis, and how perturbation of these pathways leads to microphthalmia. However, differences exist between species, hence cellular models, such as patient-derived induced pluripotent stem cell (iPSC) optic vesicles, are now being used to provide greater insights into the human disease process. Progress in 3D cellular modelling techniques has enhanced the ability of researchers to study interactions of different cell types during eye development. Through improved molecular knowledge of microphthalmia, preventative or postnatal therapies may be developed, together with establishing genotype-phenotype correlations in order to provide patients with the appropriate prognosis, multidisciplinary care and informed genetic counselling. This review summarises some key discoveries from animal and cellular models of microphthalmia and discusses how innovative new models can be used to further our understanding in the future. Plain language summary Animal and Cellular Models of the Eye Disorder, Microphthalmia (Small Eye) Microphthalmia, meaning a small, underdeveloped eye, is a rare disorder that children are born with. Genetic changes or variations in the environment during the first 3 months of pregnancy can disrupt early development of the eye, resulting in microphthalmia. Up to 11% of blind children have microphthalmia, yet currently no treatments are available. By understanding the genes necessary for eye development, we can determine how disruption by genetic changes or environmental factors can cause this condition. This helps us understand why microphthalmia occurs, and ensure patients are provided with the appropriate clinical care and genetic counselling advice. Additionally, by understanding the causes of microphthalmia, researchers can develop treatments to prevent or reduce the severity of this condition. Animal models, particularly mice, zebrafish and frogs, which can also develop small eyes due to the same genetic/environmental changes, have helped us understand the genes which are important for eye development and can cause birth eye defects when disrupted. Studying a patient's own cells grown in the laboratory can further help researchers understand how changes in genes affect their function. Both animal and cellular models can be used to develop and test new drugs, which could provide treatment options for patients living with microphthalmia. This review summarises the key discoveries from animal and cellular models of microphthalmia and discusses how innovative new models can be used to further our understanding in the future.
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Affiliation(s)
| | | | - Mariya Moosajee
- UCL Institute of Ophthalmology, 11-43 Bath
Street, London, EC1V 9EL, UK
- Moorfields Eye Hospital NHS Foundation Trust,
London, UK
- Great Ormond Street Hospital for Children NHS
Foundation Trust, London, UK
- The Francis Crick Institute, London, UK
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26
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Alzahrani F, Kuwahara H, Long Y, Al-Owain M, Tohary M, AlSayed M, Mahnashi M, Fathi L, Alnemer M, Al-Hamed MH, Lemire G, Boycott KM, Hashem M, Han W, Al-Maawali A, Al Mahrizi F, Al-Thihli K, Gao X, Alkuraya FS. Recessive, Deleterious Variants in SMG8 Expand the Role of Nonsense-Mediated Decay in Developmental Disorders in Humans. Am J Hum Genet 2020; 107:1178-1185. [PMID: 33242396 DOI: 10.1016/j.ajhg.2020.11.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 11/04/2020] [Indexed: 12/16/2022] Open
Abstract
We have previously described a heart-, eye-, and brain-malformation syndrome caused by homozygous loss-of-function variants in SMG9, which encodes a critical component of the nonsense-mediated decay (NMD) machinery. Here, we describe four consanguineous families with four different likely deleterious homozygous variants in SMG8, encoding a binding partner of SMG9. The observed phenotype greatly resembles that linked to SMG9 and comprises severe global developmental delay, microcephaly, facial dysmorphism, and variable congenital heart and eye malformations. RNA-seq analysis revealed a general increase in mRNA expression levels with significant overrepresentation of core NMD substrates. We also identified increased phosphorylation of UPF1, a key SMG1-dependent step in NMD, which most likely represents the loss of SMG8--mediated inhibition of SMG1 kinase activity. Our data show that SMG8 and SMG9 deficiency results in overlapping developmental disorders that most likely converge mechanistically on impaired NMD.
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27
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Lemire G, MacDonald SK, Boycott KM. SMG9-deficiency syndrome caused by a homozygous missense variant: Expanding the genotypic and phenotypic spectrum of this developmental disorder. Am J Med Genet A 2020; 182:1829-1831. [PMID: 32412169 DOI: 10.1002/ajmg.a.61616] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/20/2020] [Accepted: 04/22/2020] [Indexed: 01/01/2023]
Affiliation(s)
- Gabrielle Lemire
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Stella K MacDonald
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
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28
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Harding P, Moosajee M. The Molecular Basis of Human Anophthalmia and Microphthalmia. J Dev Biol 2019; 7:jdb7030016. [PMID: 31416264 PMCID: PMC6787759 DOI: 10.3390/jdb7030016] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 08/08/2019] [Accepted: 08/08/2019] [Indexed: 12/16/2022] Open
Abstract
Human eye development is coordinated through an extensive network of genetic signalling pathways. Disruption of key regulatory genes in the early stages of eye development can result in aborted eye formation, resulting in an absent eye (anophthalmia) or a small underdeveloped eye (microphthalmia) phenotype. Anophthalmia and microphthalmia (AM) are part of the same clinical spectrum and have high genetic heterogeneity, with >90 identified associated genes. By understanding the roles of these genes in development, including their temporal expression, the phenotypic variation associated with AM can be better understood, improving diagnosis and management. This review describes the genetic and structural basis of eye development, focusing on the function of key genes known to be associated with AM. In addition, we highlight some promising avenues of research involving multiomic approaches and disease modelling with induced pluripotent stem cell (iPSC) technology, which will aid in developing novel therapies.
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Affiliation(s)
| | - Mariya Moosajee
- UCL Institute of Ophthalmology, London EC1V 9EL, UK.
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK.
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK.
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29
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Lecoquierre F, Bonnevalle A, Chadie A, Gayet C, Dumant‐Forest C, Renaux‐Petel M, Leca J, Hazelzet T, Brasseur‐Daudruy M, Louillet F, Muraine M, Coutant S, Quenez O, Boland A, Deleuze J, Frebourg T, Goldenberg A, Saugier‐Veber P, Guerrot A, Nicolas G. Confirmation and further delineation of the SMG9‐deficiency syndrome, a rare and severe developmental disorder. Am J Med Genet A 2019; 179:2257-2262. [DOI: 10.1002/ajmg.a.61317] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 07/22/2019] [Indexed: 11/06/2022]
Affiliation(s)
- François Lecoquierre
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized MedicineNormandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital Rouen France
| | - Antoine Bonnevalle
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized MedicineNormandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital Rouen France
| | - Alexandra Chadie
- Department of Neonatal Pediatrics and Intensive Care—NeuropediatricsRouen University Hospital Rouen France
| | - Claire Gayet
- Department of PediatricsRouen University Hospital Rouen France
| | | | | | | | | | | | | | - Marc Muraine
- Department of OphthalmologyRouen University Hospital Rouen France
| | - Sophie Coutant
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized MedicineNormandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital Rouen France
| | - Olivier Quenez
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized MedicineNormandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital Rouen France
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine (CNRGH)Institut de Biologie François Jacob, CEA, Université Paris‐Saclay Evry France
| | - Jean‐François Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH)Institut de Biologie François Jacob, CEA, Université Paris‐Saclay Evry France
| | - Thierry Frebourg
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized MedicineNormandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital Rouen France
| | - Alice Goldenberg
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized MedicineNormandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital Rouen France
| | - Pascale Saugier‐Veber
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized MedicineNormandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital Rouen France
| | - Anne‐Marie Guerrot
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized MedicineNormandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital Rouen France
| | - Gaël Nicolas
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized MedicineNormandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital Rouen France
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30
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Han X, Wei Y, Wang H, Wang F, Ju Z, Li T. Nonsense-mediated mRNA decay: a 'nonsense' pathway makes sense in stem cell biology. Nucleic Acids Res 2019; 46:1038-1051. [PMID: 29272451 PMCID: PMC5814811 DOI: 10.1093/nar/gkx1272] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 12/09/2017] [Indexed: 01/04/2023] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a highly conserved post-transcriptional regulatory mechanism of gene expression in eukaryotes. Originally, NMD was identified as an RNA surveillance machinery in degrading 'aberrant' mRNA species with premature termination codons. Recent studies indicate that NMD regulates the stability of natural gene transcripts that play significant roles in cell functions. Although components and action modes of the NMD machinery in degrading its RNA targets have been extensively studied with biochemical and structural approaches, the biological roles of NMD remain to be defined. Stem cells are rare cell populations, which play essential roles in tissue homeostasis and hold great promises in regenerative medicine. Stem cells self-renew to maintain the cellular identity and differentiate into somatic lineages with specialized functions to sustain tissue integrity. Transcriptional regulations and epigenetic modulations have been extensively implicated in stem cell biology. However, post-transcriptional regulatory mechanisms, such as NMD, in stem cell regulation are largely unknown. In this paper, we summarize the recent findings on biological roles of NMD factors in embryonic and tissue-specific stem cells. Furthermore, we discuss the possible mechanisms of NMD in regulating stem cell fates.
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Affiliation(s)
- Xin Han
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Yanling Wei
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Hua Wang
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Feilong Wang
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Zhenyu Ju
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Tangliang Li
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
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Monies D, Abouelhoda M, Assoum M, Moghrabi N, Rafiullah R, Almontashiri N, Alowain M, Alzaidan H, Alsayed M, Subhani S, Cupler E, Faden M, Alhashem A, Qari A, Chedrawi A, Aldhalaan H, Kurdi W, Khan S, Rahbeeni Z, Alotaibi M, Goljan E, Elbardisy H, ElKalioby M, Shah Z, Alruwaili H, Jaafar A, Albar R, Akilan A, Tayeb H, Tahir A, Fawzy M, Nasr M, Makki S, Alfaifi A, Akleh H, Yamani S, Bubshait D, Mahnashi M, Basha T, Alsagheir A, Abu Khaled M, Alsaleem K, Almugbel M, Badawi M, Bashiri F, Bohlega S, Sulaiman R, Tous E, Ahmed S, Algoufi T, Al-Mousa H, Alaki E, Alhumaidi S, Alghamdi H, Alghamdi M, Sahly A, Nahrir S, Al-Ahmari A, Alkuraya H, Almehaidib A, Abanemai M, Alsohaibaini F, Alsaud B, Arnaout R, Abdel-Salam GMH, Aldhekri H, AlKhater S, Alqadi K, Alsabban E, Alshareef T, Awartani K, Banjar H, Alsahan N, Abosoudah I, Alashwal A, Aldekhail W, Alhajjar S, Al-Mayouf S, Alsemari A, Alshuaibi W, Altala S, Altalhi A, Baz S, Hamad M, Abalkhail T, Alenazi B, Alkaff A, Almohareb F, Al Mutairi F, Alsaleh M, Alsonbul A, Alzelaye S, Bahzad S, Manee AB, Jarrad O, Meriki N, Albeirouti B, Alqasmi A, AlBalwi M, Makhseed N, Hassan S, Salih I, Salih MA, Shaheen M, Sermin S, Shahrukh S, Hashmi S, Shawli A, Tajuddin A, Tamim A, Alnahari A, Ghemlas I, Hussein M, Wali S, Murad H, Meyer BF, Alkuraya FS. Lessons Learned from Large-Scale, First-Tier Clinical Exome Sequencing in a Highly Consanguineous Population. Am J Hum Genet 2019; 104:1182-1201. [PMID: 31130284 DOI: 10.1016/j.ajhg.2019.04.011] [Citation(s) in RCA: 142] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 04/11/2019] [Indexed: 12/16/2022] Open
Abstract
We report the results of clinical exome sequencing (CES) on >2,200 previously unpublished Saudi families as a first-tier test. The predominance of autosomal-recessive causes allowed us to make several key observations. We highlight 155 genes that we propose to be recessive, disease-related candidates. We report additional mutational events in 64 previously reported candidates (40 recessive), and these events support their candidacy. We report recessive forms of genes that were previously associated only with dominant disorders and that have phenotypes ranging from consistent with to conspicuously distinct from the known dominant phenotypes. We also report homozygous loss-of-function events that can inform the genetics of complex diseases. We were also able to deduce the likely causal variant in most couples who presented after the loss of one or more children, but we lack samples from those children. Although a similar pattern of mostly recessive causes was observed in the prenatal setting, the higher proportion of loss-of-function events in these cases was notable. The allelic series presented by the wealth of recessive variants greatly expanded the phenotypic expression of the respective genes. We also make important observations about dominant disorders; these observations include the pattern of de novo variants, the identification of 74 candidate dominant, disease-related genes, and the potential confirmation of 21 previously reported candidates. Finally, we describe the influence of a predominantly autosomal-recessive landscape on the clinical utility of rapid sequencing (Flash Exome). Our cohort's genotypic and phenotypic data represent a unique resource that can contribute to improved variant interpretation through data sharing.
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Affiliation(s)
- Dorota Monies
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh 12354, Saudi Arabia; Saudi Diagnostic Laboratories, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Mohammed Abouelhoda
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh 12354, Saudi Arabia; Saudi Diagnostic Laboratories, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Mirna Assoum
- Saudi Diagnostic Laboratories, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Nabil Moghrabi
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh 12354, Saudi Arabia; Saudi Diagnostic Laboratories, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Rafiullah Rafiullah
- Saudi Diagnostic Laboratories, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Naif Almontashiri
- Clinical Molecular and Biochemical Genetics, Taibah University, Madinah 42353, Saudi Arabia
| | - Mohammed Alowain
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Hamad Alzaidan
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Moeen Alsayed
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Shazia Subhani
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh 12354, Saudi Arabia; Saudi Diagnostic Laboratories, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Edward Cupler
- Neurosciences Department, King Faisal Specialist Hospital and Research Centre, Jeddah 23433, Saudi Arabia
| | - Maha Faden
- Genetics and Metabolism, King Saud Medical Complex, Riyadh 12746, Saudi Arabia
| | - Amal Alhashem
- Pediatrics Department, Prince Sultan Military Medical Complex, Riyadh 12233, Saudi Arabia
| | - Alya Qari
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Aziza Chedrawi
- Neurosciences Department, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Hisham Aldhalaan
- Neurosciences Department, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Wesam Kurdi
- Obstetrics and Gynecology Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Sameena Khan
- Neurosciences Department, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Zuhair Rahbeeni
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Maha Alotaibi
- Genetics and Metabolism, King Saud Medical Complex, Riyadh 12746, Saudi Arabia
| | - Ewa Goljan
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh 12354, Saudi Arabia; Saudi Diagnostic Laboratories, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Hadeel Elbardisy
- Saudi Diagnostic Laboratories, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Mohamed ElKalioby
- Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh 12354, Saudi Arabia; Saudi Diagnostic Laboratories, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Zeeshan Shah
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh 12354, Saudi Arabia; Saudi Diagnostic Laboratories, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Hibah Alruwaili
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh 12354, Saudi Arabia; Saudi Diagnostic Laboratories, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Amal Jaafar
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh 12354, Saudi Arabia; Saudi Diagnostic Laboratories, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Ranad Albar
- Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh 12354, Saudi Arabia
| | - Asma Akilan
- Saudi Diagnostic Laboratories, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Hamsa Tayeb
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh 12354, Saudi Arabia; Saudi Diagnostic Laboratories, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Asma Tahir
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh 12354, Saudi Arabia; Saudi Diagnostic Laboratories, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Mohammed Fawzy
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh 12354, Saudi Arabia; Saudi Diagnostic Laboratories, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Mohammed Nasr
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh 12354, Saudi Arabia; Saudi Diagnostic Laboratories, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Shaza Makki
- Saudi Diagnostic Laboratories, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Abdullah Alfaifi
- Pediatrics Department, Security Forces Hospital, Riyadh 11481, Saudi Arabia
| | - Hanna Akleh
- Academic and Training Affairs, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Suad Yamani
- Neurosciences Department, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Dalal Bubshait
- Pediatrics Department, King Fahad Hospital of the University, Al-Khobar 31952, Saudi Arabia
| | - Mohammed Mahnashi
- Genetics and Medicine, King Fahd Central Hospital, Gizan 82666, Saudi Arabia
| | - Talal Basha
- Pediatrics Department, King Faisal Specialist Hospital and Research Centre, Jeddah 23433, Saudi Arabia
| | - Afaf Alsagheir
- Pediatrics Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Musad Abu Khaled
- Neurosciences Department, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Khalid Alsaleem
- Pediatrics Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Maisoon Almugbel
- Obstetrics and Gynecology Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Manal Badawi
- Neurosciences Department, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Fahad Bashiri
- Department of Pediatrics, College of Medicine and King Khalid University Hospital, King Saud University, Riyadh 11461, Saudi Arabia
| | - Saeed Bohlega
- Neurosciences Department, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Raashida Sulaiman
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Ehab Tous
- Neurosciences Department, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Syed Ahmed
- Pediatric Hematology and Oncology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Talal Algoufi
- Pediatric Hematology and Oncology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Hamoud Al-Mousa
- Allergy - Immunology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Emadia Alaki
- Allergy - Immunology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Susan Alhumaidi
- Pediatrics Department, King Saud Medical City, Riyadh 12746, Saudi Arabia
| | - Hadeel Alghamdi
- Pediatrics Department, King Faisal Specialist Hospital and Research Centre, Jeddah 23433, Saudi Arabia
| | - Malak Alghamdi
- Pediatrics Department, King Saud Medical City, Riyadh 12746, Saudi Arabia
| | - Ahmed Sahly
- Pediatrics Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Shapar Nahrir
- Pediatrics Department, King Saud Medical City, Riyadh 12746, Saudi Arabia
| | - Ali Al-Ahmari
- Pediatric Hematology and Oncology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Hisham Alkuraya
- Vitreoretinal Surgery, Specialized Medical Centre, Riyadh 11564, Saudi Arabia
| | - Ali Almehaidib
- Gastroenterology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Mohammed Abanemai
- Gastroenterology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Fahad Alsohaibaini
- Gastroenterology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Bandar Alsaud
- Allergy - Immunology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Rand Arnaout
- Allergy - Immunology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | | | - Hasan Aldhekri
- Pediatrics Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Suzan AlKhater
- Pediatrics Department, King Fahad Hospital of the University, Al-Khobar 31952, Saudi Arabia; Department of Pediatrics, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 34221, Saudi Arabia
| | - Khalid Alqadi
- Neurosciences Department, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Essam Alsabban
- Pediatrics Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Turki Alshareef
- Pediatric Nephrology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Khalid Awartani
- Obstetrics and Gynecology Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Hanaa Banjar
- Pediatric Pulmonology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Nada Alsahan
- Obstetrics and Gynecology Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Ibraheem Abosoudah
- Pediatric Hematology and Oncology, King Faisal Specialist Hospital and Research Centre, Jeddah 23433, Saudi Arabia
| | - Abdullah Alashwal
- Pediatric Endocrine and Metabolism, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Wajeeh Aldekhail
- Gastroenterology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Sami Alhajjar
- Pediatric Infectious Diseases, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Sulaiman Al-Mayouf
- Pediatrics Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Abdulaziz Alsemari
- Neurosciences Department, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Walaa Alshuaibi
- Pediatrics Department, King Khalid University Hospital, Riyadh 12372, Saudi Arabia
| | - Saeed Altala
- Pediatrics Department, Armed Forces Hospital, Khamis Mushait 62451, Saudi Arabia
| | - Abdulhadi Altalhi
- Pediatric Nephrology, King Saud Medical City, Riyadh 12746, Saudi Arabia
| | - Salah Baz
- Neurosciences Department, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Muddathir Hamad
- Pediatrics Department, King Khalid University Hospital, Riyadh 12372, Saudi Arabia
| | - Tariq Abalkhail
- Neurosciences Department, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Badi Alenazi
- Pediatrics Department, Alyamama Hospital, Riyadh 14222, Saudi Arabia
| | - Alya Alkaff
- Obstetrics and Gynecology Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Fahad Almohareb
- Oncology Center, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Fuad Al Mutairi
- King Abdullah International Medical Research Centre, King Saud Bin Abdulaziz University for Health Sciences, Riyadh 11564, Saudi Arabia; Medical Genetic Division, Department of Pediatrics, King Abdulaziz Medical City, Riyadh 14611, Saudi Arabia
| | - Mona Alsaleh
- Pediatric Hematology and Oncology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Abdullah Alsonbul
- Pediatric Rheumatology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Somaya Alzelaye
- Pediatric Endocrine and Diabetes, Al Qunfudah General Hospital, Al Qunfudhah 28821, Saudi Arabia
| | - Shakir Bahzad
- Kuwait Medical Genetics Center, Kuwait City 65000, Kuwait
| | - Abdulaziz Bin Manee
- Pediatrics Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Ola Jarrad
- Pediatrics Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Neama Meriki
- Maternal and Fetal Medicine, King Khalid University Hospital, Riyadh 12372, Saudi Arabia
| | - Bassem Albeirouti
- Hematology and Oncology, King Faisal Specialist Hospital and Research Centre, Jeddah 23433, Saudi Arabia
| | - Amal Alqasmi
- Pediatrics Department, King Saud Medical City, Riyadh 12746, Saudi Arabia
| | - Mohammed AlBalwi
- Department of Pathology and Laboratory Medicine, King Saud bin Abdulaziz University for Health Sciences, King Abdullah International Medical Research Center, King Abdulaziz Medical City, Riyadh 11426, Saudi Arabia
| | - Nawal Makhseed
- Pediatrics Department, Alsoor Clinic, Kuwait City 65000, Kuwait
| | - Saeed Hassan
- Pediatrics Department, King Khalid University Hospital, Riyadh 12372, Saudi Arabia
| | - Isam Salih
- Hepatic-Pancreatic Surgery, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Mustafa A Salih
- Department of Pediatrics, College of Medicine and King Khalid University Hospital, King Saud University, Riyadh 11461, Saudi Arabia
| | - Marwan Shaheen
- Hematology and Bone Marrow Transplant, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Saadeh Sermin
- Pediatric Nephrology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Shamsad Shahrukh
- Neurosciences Department, King Faisal Specialist Hospital and Research Centre, Jeddah 23433, Saudi Arabia
| | - Shahrukh Hashmi
- Hematology and Bone Marrow Transplant, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Ayman Shawli
- Department of Pediatrics, King Abdulaziz Medical City, Jeddah 9515, Saudi Arabia
| | - Ameen Tajuddin
- Neurology, King Fahad Hospital, Medina 59046, Saudi Arabia
| | - Abdullah Tamim
- Pediatrics Neurology, King Faisal Specialist Hospital and Research Centre, Jeddah 23433, Saudi Arabia
| | - Ahmed Alnahari
- Pediatric Department, King Fahad Central Hospital, Gizan, 82666, Saudi Arabia
| | - Ibrahim Ghemlas
- Pediatric Hematology and Oncology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Maged Hussein
- Nephrology Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Sami Wali
- Pediatrics Department, Prince Sultan Military Medical Complex, Riyadh 12233, Saudi Arabia
| | - Hatem Murad
- Neurosciences Department, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Brian F Meyer
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh 12354, Saudi Arabia; Saudi Diagnostic Laboratories, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh 12354, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia.
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Tan Y, Ma Z, Jin Y, Zong R, Wu J, Ren Z. MicroRNA 4651 regulates nonsense-mediated mRNA decay by targeting SMG9 mRNA. Gene 2019; 701:65-71. [PMID: 30902786 DOI: 10.1016/j.gene.2019.03.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 03/11/2019] [Accepted: 03/17/2019] [Indexed: 02/07/2023]
Abstract
Nonsense-mediated mRNA decay (NMD) is originally identified as a conserved RNA surveillance mechanism that rapidly degrades aberrant mRNA containing premature termination codons (PTCs). However, the molecular regulation mechanisms by which microRNAs inhibit NMD has not been well understood. Here we identified that miR-4651 participated in the NMD pathway by downregulating expression levels of SMG9. We provided evidences that (1) Overexpression of miR-4651 mimic significantly inhibited the expression of SMG9 (P < 0.05); (2) NMD substrates genes, TBL2 and GADD45B were both increased at mRNA and protein expression levels when SMG9 was suppressed by siRNA, whereas decreased by SMG9 overexpression; (3) Expression of SMG9 was significantly increased but TBL2, GADD45B were significantly decreased when cells transfected with miR-4651 inhibitor (P < 0.05). These results indicated that miR-4651 regulated NMD by targeting SMG9 mRNA. Our study highlights that miR-4651 represses NMD. miR-4651 targets SMG9 and represses the expression levels of SMG9. NMD activity is decreased additionally when SMG9 is inhibited. The present study provides evidence for microRNA/NMD regulatory mechanism.
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Affiliation(s)
- Yanjie Tan
- Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Zhenfa Ma
- Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Yi Jin
- Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Ruojun Zong
- Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Jian Wu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China.
| | - Zhuqing Ren
- Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China; The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China.
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Iwama K, Mizuguchi T, Takeshita E, Nakagawa E, Okazaki T, Nomura Y, Iijima Y, Kajiura I, Sugai K, Saito T, Sasaki M, Yuge K, Saikusa T, Okamoto N, Takahashi S, Amamoto M, Tomita I, Kumada S, Anzai Y, Hoshino K, Fattal-Valevski A, Shiroma N, Ohfu M, Moroto M, Tanda K, Nakagawa T, Sakakibara T, Nabatame S, Matsuo M, Yamamoto A, Yukishita S, Inoue K, Waga C, Nakamura Y, Watanabe S, Ohba C, Sengoku T, Fujita A, Mitsuhashi S, Miyatake S, Takata A, Miyake N, Ogata K, Ito S, Saitsu H, Matsuishi T, Goto YI, Matsumoto N. Genetic landscape of Rett syndrome-like phenotypes revealed by whole exome sequencing. J Med Genet 2019; 56:396-407. [DOI: 10.1136/jmedgenet-2018-105775] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 01/17/2019] [Accepted: 01/21/2019] [Indexed: 11/03/2022]
Abstract
BackgroundRett syndrome (RTT) is a characteristic neurological disease presenting with regressive loss of neurodevelopmental milestones. Typical RTT is generally caused by abnormality of methyl-CpG binding protein 2 (MECP2). Our objective to investigate the genetic landscape of MECP2-negative typical/atypical RTT and RTT-like phenotypes using whole exome sequencing (WES).MethodsWe performed WES on 77 MECP2-negative patients either with typical RTT (n=11), atypical RTT (n=22) or RTT-like phenotypes (n=44) incompatible with the RTT criteria.ResultsPathogenic or likely pathogenic single-nucleotide variants in 28 known genes were found in 39 of 77 (50.6%) patients. WES-based CNV analysis revealed pathogenic deletions involving six known genes (including MECP2) in 8 of 77 (10.4%) patients. Overall, diagnostic yield was 47 of 77 (61.0 %). Furthermore, strong candidate variants were found in four novel genes: a de novo variant in each of ATPase H+ transporting V0 subunit A1 (ATP6V0A1), ubiquitin-specific peptidase 8 (USP8) and microtubule-associated serine/threonine kinase 3 (MAST3), as well as biallelic variants in nuclear receptor corepressor 2 (NCOR2).ConclusionsOur study provides a new landscape including additional genetic variants contributing to RTT-like phenotypes, highlighting the importance of comprehensive genetic analysis.
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Fernandes R, Nogueira G, da Costa PJ, Pinto F, Romão L. Nonsense-Mediated mRNA Decay in Development, Stress and Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1157:41-83. [DOI: 10.1007/978-3-030-19966-1_3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Stephen J, Maddirevula S, Nampoothiri S, Burke JD, Herzog M, Shukla A, Steindl K, Eskin A, Patil SJ, Joset P, Lee H, Garrett LJ, Yokoyama T, Balanda N, Bodine SP, Tolman NJ, Zerfas PM, Zheng A, Ramantani G, Girisha KM, Rivas C, Suresh PV, Elkahloun A, Alsaif HS, Wakil SM, Mahmoud L, Ali R, Prochazkova M, Kulkarni AB, Ben-Omran T, Colak D, Morris HD, Rauch A, Martinez-Agosto JA, Nelson SF, Alkuraya FS, Gahl WA, Malicdan MCV, Malicdan MCV. Bi-allelic TMEM94 Truncating Variants Are Associated with Neurodevelopmental Delay, Congenital Heart Defects, and Distinct Facial Dysmorphism. Am J Hum Genet 2018; 103:948-967. [PMID: 30526868 DOI: 10.1016/j.ajhg.2018.11.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 11/02/2018] [Indexed: 02/06/2023] Open
Abstract
Neurodevelopmental disorders (NDD) are genetically and phenotypically heterogeneous conditions due to defects in genes involved in development and function of the nervous system. Individuals with NDD, in addition to their primary neurodevelopmental phenotype, may also have accompanying syndromic features that can be very helpful diagnostically especially those with recognizable facial appearance. In this study, we describe ten similarly affected individuals from six unrelated families of different ethnic origins having bi-allelic truncating variants in TMEM94, which encodes for an uncharacterized transmembrane nuclear protein that is highly conserved across mammals. The affected individuals manifested with global developmental delay/intellectual disability, and dysmorphic facial features including triangular face, deep set eyes, broad nasal root and tip and anteverted nostrils, thick arched eye brows, hypertrichosis, pointed chin, and hypertelorism. Birthweight in the upper normal range was observed in most, and all but one had congenital heart defects (CHD). Gene expression analysis in available cells from affected individuals showed reduced expression of TMEM94. Global transcriptome profiling using microarray and RNA sequencing revealed several dysregulated genes essential for cell growth, proliferation and survival that are predicted to have an impact on cardiotoxicity hematological system and neurodevelopment. Loss of Tmem94 in mouse model generated by CRISPR/Cas9 was embryonic lethal and led to craniofacial and cardiac abnormalities and abnormal neuronal migration pattern, suggesting that this gene is important in craniofacial, cardiovascular, and nervous system development. Our study suggests the genetic etiology of a recognizable dysmorphic syndrome with NDD and CHD and highlights the role of TMEM94 in early development.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - May Christine V Malicdan
- Section of Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; NIH Undiagnosed Diseases Program, NHGRI and the Common Fund, National Institutes of Health, Bethesda, MD 20892, USA; Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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36
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Karamyshev AL, Karamysheva ZN. Lost in Translation: Ribosome-Associated mRNA and Protein Quality Controls. Front Genet 2018; 9:431. [PMID: 30337940 PMCID: PMC6180196 DOI: 10.3389/fgene.2018.00431] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 09/11/2018] [Indexed: 12/15/2022] Open
Abstract
Aberrant, misfolded, and mislocalized proteins are often toxic to cells and result in many human diseases. All proteins and their mRNA templates are subject to quality control. There are several distinct mechanisms that control the quality of mRNAs and proteins during translation at the ribosome. mRNA quality control systems, nonsense-mediated decay, non-stop decay, and no-go decay detect premature stop codons, the absence of a natural stop codon, and stalled ribosomes in translation, respectively, and degrade their mRNAs. Defective truncated polypeptide nascent chains generated from faulty mRNAs are degraded by ribosome-associated protein quality control pathways. Regulation of aberrant protein production, a novel pathway, senses aberrant proteins by monitoring the status of nascent chain interactions during translation and triggers degradation of their mRNA. Here, we review the current progress in understanding of the molecular mechanisms of mRNA and protein quality controls at the ribosome during translation.
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Affiliation(s)
- Andrey L Karamyshev
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - Zemfira N Karamysheva
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
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37
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Gupta MK, De Jesus DF, Kahraman S, Valdez IA, Shamsi F, Yi L, Swensen AC, Tseng YH, Qian WJ, Kulkarni RN. Insulin receptor-mediated signaling regulates pluripotency markers and lineage differentiation. Mol Metab 2018; 18:153-163. [PMID: 30316806 PMCID: PMC6308035 DOI: 10.1016/j.molmet.2018.09.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 09/07/2018] [Accepted: 09/11/2018] [Indexed: 12/30/2022] Open
Abstract
Objectives Insulin receptor (IR)-mediated signaling is involved in the regulation of pluripotent stem cells; however, its direct effects on regulating the maintenance of pluripotency and lineage development are not fully understood. The main objective of this study is to understand the role of IR signaling in pluripotency and lineage development. Methods To explore the role of IR signaling, we generated IR knock-out (IRKO) mouse induced pluripotent stem cells (miPSCs) from E14.5 mouse embryonic fibroblasts (MEFs) of global IRKO mice using a cocktail of four reprogramming factors: Oct4, Sox2, Klf4, cMyc. We performed pluripotency characterization and directed the differentiation of control and IRKO iPSCs into neural progenitors (ectoderm), adipocyte progenitors (mesoderm), and pancreatic beta-like cells (endoderm). We mechanistically confirmed these findings via phosphoproteomics analyses of control and IRKO iPSCs. Results Interestingly, expression of pluripotency markers including Klf4, Lin28a, Tbx3, and cMyc were upregulated, while abundance of Oct4 and Nanog were enhanced by 4-fold and 3-fold, respectively, in IRKO iPSCs. Analyses of signaling pathways demonstrated downregulation of phospho-STAT3, p-mTor and p-Erk and an increase in the total mTor and Erk proteins in IRKO iPSCs in the basal unstimulated state. Stimulation with leukemia inhibitory factor (LIF) showed a ∼33% decrease of phospho-ERK in IRKO iPSCs. On the contrary, Erk phosphorylation was increased during in vitro spontaneous differentiation of iPSCs lacking IRs. Lineage-specific directed differentiation of the iPSCs revealed that cells lacking IR showed enhanced expression of neuronal lineage markers (Pax6, Tubb3, Ascl1 and Oligo2) while exhibiting a decrease in adipocyte (Fas, Acc, Pparγ, Fabp4, C/ebpα, and Fsp27) and pancreatic beta cell markers (Ngn3, Isl1, and Sox9). Further molecular characterization by phosphoproteomics confirmed the novel IR-mediated regulation of the global pluripotency network including several key proteins involved in diverse aspects of growth and embryonic development. Conclusion We report, for the first time to our knowledge, the phosphoproteome of insulin, IGF1, and LIF stimulation in mouse iPSCs to reveal the importance of insulin receptor signaling for the maintenance of pluripotency and lineage determination. Insulin receptor signaling regulates expression of key pluripotency genes including Oct4 and Nanog. IRKO iPSCs show upregulation of neuronal markers during differentiation. Adipocyte and pancreatic beta cell differentiation are perturbed in IRKO iPSCs. Phosphoproteomics analyses confirmed the role of IR in regulation of pluripotency and developmental proteins.
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Affiliation(s)
- Manoj K Gupta
- Islet Cell and Regenerative Biology, Joslin Diabetes Center, Department of Medicine, Brigham and Women's Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Dario F De Jesus
- Islet Cell and Regenerative Biology, Joslin Diabetes Center, Department of Medicine, Brigham and Women's Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02215, USA; Graduate Program in Areas of Basic and Applied Biology (GABBA), Abel Salazar Biomedical Sciences Institute, University of Porto, 5000 Porto, Portugal
| | - Sevim Kahraman
- Islet Cell and Regenerative Biology, Joslin Diabetes Center, Department of Medicine, Brigham and Women's Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Ivan A Valdez
- Islet Cell and Regenerative Biology, Joslin Diabetes Center, Department of Medicine, Brigham and Women's Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Farnaz Shamsi
- Section of Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA
| | - Lian Yi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Adam C Swensen
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Yu-Hua Tseng
- Section of Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Rohit N Kulkarni
- Islet Cell and Regenerative Biology, Joslin Diabetes Center, Department of Medicine, Brigham and Women's Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02215, USA.
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Liu B, Pjanic M, Wang T, Nguyen T, Gloudemans M, Rao A, Castano VG, Nurnberg S, Rader DJ, Elwyn S, Ingelsson E, Montgomery SB, Miller CL, Quertermous T. Genetic Regulatory Mechanisms of Smooth Muscle Cells Map to Coronary Artery Disease Risk Loci. Am J Hum Genet 2018; 103:377-388. [PMID: 30146127 PMCID: PMC6128252 DOI: 10.1016/j.ajhg.2018.08.001] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Accepted: 08/01/2018] [Indexed: 12/30/2022] Open
Abstract
Coronary artery disease (CAD) is the leading cause of death globally. Genome-wide association studies (GWASs) have identified more than 95 independent loci that influence CAD risk, most of which reside in non-coding regions of the genome. To interpret these loci, we generated transcriptome and whole-genome datasets using human coronary artery smooth muscle cells (HCASMCs) from 52 unrelated donors, as well as epigenomic datasets using ATAC-seq on a subset of 8 donors. Through systematic comparison with publicly available datasets from GTEx and ENCODE projects, we identified transcriptomic, epigenetic, and genetic regulatory mechanisms specific to HCASMCs. We assessed the relevance of HCASMCs to CAD risk using transcriptomic and epigenomic level analyses. By jointly modeling eQTL and GWAS datasets, we identified five genes (SIPA1, TCF21, SMAD3, FES, and PDGFRA) that may modulate CAD risk through HCASMCs, all of which have relevant functional roles in vascular remodeling. Comparison with GTEx data suggests that SIPA1 and PDGFRA influence CAD risk predominantly through HCASMCs, while other annotated genes may have multiple cell and tissue targets. Together, these results provide tissue-specific and mechanistic insights into the regulation of a critical vascular cell type associated with CAD in human populations.
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Affiliation(s)
- Boxiang Liu
- Department of Biology, School of Humanities and Sciences, Stanford University, Stanford, CA 94305, USA; Cardiovascular Institute, Stanford School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA
| | - Milos Pjanic
- Cardiovascular Institute, Stanford School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA; Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Ting Wang
- Cardiovascular Institute, Stanford School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Trieu Nguyen
- Cardiovascular Institute, Stanford School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA; Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Michael Gloudemans
- Biomedical Informatics Training Program, Stanford School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA
| | - Abhiram Rao
- Cardiovascular Institute, Stanford School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Victor G Castano
- Cardiovascular Institute, Stanford School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA; Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Sylvia Nurnberg
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Daniel J Rader
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Susannah Elwyn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Erik Ingelsson
- Cardiovascular Institute, Stanford School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA; Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Stephen B Montgomery
- Cardiovascular Institute, Stanford School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Clint L Miller
- Center for Public Health Genomics, Department of Public Health Sciences, Biochemistry and Genetics, and Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
| | - Thomas Quertermous
- Cardiovascular Institute, Stanford School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA; Department of Medicine, Stanford University, Stanford, CA 94305, USA.
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Maddirevula S, Alsahli S, Alhabeeb L, Patel N, Alzahrani F, Shamseldin HE, Anazi S, Ewida N, Alsaif HS, Mohamed JY, Alazami AM, Ibrahim N, Abdulwahab F, Hashem M, Abouelhoda M, Monies D, Al Tassan N, Alshammari M, Alsagheir A, Seidahmed MZ, Sogati S, Aglan MS, Hamad MH, Salih MA, Hamed AA, Alhashmi N, Nabil A, Alfadli F, Abdel-Salam GMH, Alkuraya H, Peitee WO, Keng WT, Qasem A, Mushiba AM, Zaki MS, Fassad MR, Alfadhel M, Alexander S, Sabr Y, Temtamy S, Ekbote AV, Ismail S, Hosny GA, Otaify GA, Amr K, Al Tala S, Khan AO, Rizk T, Alaqeel A, Alsiddiky A, Singh A, Kapoor S, Alhashem A, Faqeih E, Shaheen R, Alkuraya FS. Expanding the phenome and variome of skeletal dysplasia. Genet Med 2018; 20:1609-1616. [PMID: 29620724 DOI: 10.1038/gim.2018.50] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 02/13/2018] [Indexed: 12/15/2022] Open
Abstract
PURPOSE To describe our experience with a large cohort (411 patients from 288 families) of various forms of skeletal dysplasia who were molecularly characterized. METHODS Detailed phenotyping and next-generation sequencing (panel and exome). RESULTS Our analysis revealed 224 pathogenic/likely pathogenic variants (54 (24%) of which are novel) in 123 genes with established or tentative links to skeletal dysplasia. In addition, we propose 5 genes as candidate disease genes with suggestive biological links (WNT3A, SUCO, RIN1, DIP2C, and PAN2). Phenotypically, we note that our cohort spans 36 established phenotypic categories by the International Skeletal Dysplasia Nosology, as well as 18 novel skeletal dysplasia phenotypes that could not be classified under these categories, e.g., the novel C3orf17-related skeletal dysplasia. We also describe novel phenotypic aspects of well-known disease genes, e.g., PGAP3-related Toriello-Carey syndrome-like phenotype. We note a strong founder effect for many genes in our cohort, which allowed us to calculate a minimum disease burden for the autosomal recessive forms of skeletal dysplasia in our population (7.16E-04), which is much higher than the global average. CONCLUSION By expanding the phenotypic, allelic, and locus heterogeneity of skeletal dysplasia in humans, we hope our study will improve the diagnostic rate of patients with these conditions.
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Affiliation(s)
- Sateesh Maddirevula
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Saud Alsahli
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Lamees Alhabeeb
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nisha Patel
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fatema Alzahrani
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hanan E Shamseldin
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Shams Anazi
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nour Ewida
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hessa S Alsaif
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Jawahir Y Mohamed
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Anas M Alazami
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Niema Ibrahim
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mais Hashem
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mohamed Abouelhoda
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Dorota Monies
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Nada Al Tassan
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Muneera Alshammari
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Afaf Alsagheir
- Department of Pediatrics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | | | - Samira Sogati
- Department of Medical Genetics, King Fahad General Hospital, Jeddah, Saudi Arabia
| | - Mona S Aglan
- Clinical Genetics Department, Human Genetics & Genome Research Division, Center of Excellence of Human Genetics, National Research Centre, Cairo, Egypt
| | - Muddathir H Hamad
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Mustafa A Salih
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Ahlam A Hamed
- Department of Pediatrics and Child Health, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | | | - Amira Nabil
- Human Genetics Department, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Fatima Alfadli
- Department of Pediatrics, Maternity and Children's Hospital, Medina, Saudi Arabia
| | - Ghada M H Abdel-Salam
- Clinical Genetics Department, Human Genetics & Genome Research Division, Center of Excellence of Human Genetics, National Research Centre, Cairo, Egypt
| | - Hisham Alkuraya
- Global Eye Care, Specialized Medical Center Hospital, Riyadh, Saudi Arabia
| | | | - W T Keng
- Clinical Genetics, Hospital Kuala Lumpur, Kuala Lumpur, Malaysia
| | - Abdullah Qasem
- Department of Pediatric, Prince Sultan Medical Military City, Riyadh, Saudi Arabia
| | - Aziza M Mushiba
- Department of Pediatric Subspecialties, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics & Genome Research Division, Center of Excellence of Human Genetics, National Research Centre, Cairo, Egypt
| | - Mahmoud R Fassad
- The Human Genetics Department, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Majid Alfadhel
- King Abdullah International Medical Research Centre, King Saud bin Abdulaziz University for Health Sciences, Genetics Division, Department of Pediatrics, King Abdulaziz Medical City, MNGHA, Riyadh, Saudi Arabia
| | - Saji Alexander
- Department of Paediatric Endocrinology and Diabetes, Chelsea and Westminster Hospital NHS Foundation Trust, London, UK
| | - Yasser Sabr
- Department of Obstetrics and Gynecology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Samia Temtamy
- Clinical Genetics Department, Human Genetics & Genome Research Division, Center of Excellence of Human Genetics, National Research Centre, Cairo, Egypt
| | - Alka V Ekbote
- Clinical Genetics Unit, Christian Medical College, Vellore, India
| | - Samira Ismail
- Clinical Genetics Department, Human Genetics & Genome Research Division, Center of Excellence of Human Genetics, National Research Centre, Cairo, Egypt
| | | | - Ghada A Otaify
- Clinical Genetics Department, Human Genetics & Genome Research Division, Center of Excellence of Human Genetics, National Research Centre, Cairo, Egypt
| | - Khalda Amr
- Clinical Genetics Department, Human Genetics & Genome Research Division, Center of Excellence of Human Genetics, National Research Centre, Cairo, Egypt
| | - Saeed Al Tala
- Department of Pediatrics, Armed Forces Hospital Program Southwest Region, Khamis Mushait, Saudi Arabia
| | - Arif O Khan
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Eye Institute, Cleveland Clinic Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Tamer Rizk
- Department of Pediatric Neurology, Dr. Sulaiman Al Habib Hospital, Riyadh, Saudi Arabia
| | - Aida Alaqeel
- Department of Pediatric, Prince Sultan Medical Military City, Riyadh, Saudi Arabia
| | - Abdulmonem Alsiddiky
- Department of Orthopedics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Ankur Singh
- Department of Pediatrics, Genetic Clinic, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Seema Kapoor
- Department of Pediatrics, Maulana Azad Medical College, New Delhi, India
| | - Amal Alhashem
- Department of Pediatric, Prince Sultan Medical Military City, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Eissa Faqeih
- Department of Pediatric Subspecialties, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Ranad Shaheen
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia. .,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia. .,Department of Pediatric, Prince Sultan Medical Military City, Riyadh, Saudi Arabia. .,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.
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40
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Beyond quality control: The role of nonsense-mediated mRNA decay (NMD) in regulating gene expression. Semin Cell Dev Biol 2018; 75:78-87. [DOI: 10.1016/j.semcdb.2017.08.053] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 08/25/2017] [Accepted: 08/28/2017] [Indexed: 11/23/2022]
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41
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Gupta P, Li YR. Upf proteins: highly conserved factors involved in nonsense mRNA mediated decay. Mol Biol Rep 2017; 45:39-55. [PMID: 29282598 DOI: 10.1007/s11033-017-4139-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 12/14/2017] [Indexed: 11/28/2022]
Abstract
Over 10% of genetic diseases are caused by mutations that introduce a premature termination codon in protein-coding mRNA. Nonsense-mediated mRNA decay (NMD) is an essential cellular pathway that degrades these mRNAs to prevent the accumulation of harmful partial protein products. NMD machinery is also increasingly appreciated to play a role in other essential cellular functions, including telomere homeostasis and the regulation of normal mRNA turnover, and is misregulated in numerous cancers. Hence, understanding and designing therapeutics targeting NMD is an important goal in biomedical science. The central regulator of NMD, the Upf1 protein, interacts with translation termination factors and contextual factors to initiate NMD specifically on mRNAs containing PTCs. The molecular details of how these contextual factors affect Upf1 function remain poorly understood. Here, we review plausible models for the NMD pathway and the evidence for the variety of roles NMD machinery may play in different cellular processes.
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Affiliation(s)
- Puneet Gupta
- Harvard College, Harvard University, Cambridge, MA, 02138, USA.,School of Arts and Sciences, St. Bonaventure University, St. Bonaventure, NY, 14778, USA
| | - Yan-Ruide Li
- Harvard Medical School, Harvard University, Boston, MA, 02115, USA. .,College of Life Sciences, Zhejiang University, 866 Yu Hang Tang Road, Hangzhou, 310058, China.
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Qiao XH, Wang F, Zhang XL, Huang RT, Xue S, Wang J, Qiu XB, Liu XY, Yang YQ. MEF2C loss-of-function mutation contributes to congenital heart defects. Int J Med Sci 2017; 14:1143-1153. [PMID: 29104469 PMCID: PMC5666546 DOI: 10.7150/ijms.21353] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 08/22/2017] [Indexed: 12/19/2022] Open
Abstract
Congenital heart disease (CHD) is the most common type of developmental abnormality in humans, and is a leading cause for substantially increased morbidity and mortality in affected individuals. Increasing studies demonstrates a pivotal role of genetic defects in the pathogenesis of CHD, and presently mutations in more than 60 genes have been associated with CHD. Nevertheless, CHD is of pronounced genetic heterogeneity, and the genetic basis underpinning CHD in a large proportion of patients remains unclear. In the present study, the whole coding exons and splicing donors/acceptors of the MEF2C gene, which codes for a transcription factor essential for normal cardiovascular development, were sequenced in 200 unrelated patients affected with CHD, and a novel heterozygous missense mutation, p.L38P, was identified in an index patient with patent ductus arteriosus (PDA) and ventricular septal defect (VSD). Genetic scan of the mutation carrier's family members available showed that the mutation was present in all affected family members but absent in unaffected family members. Analysis of the proband's pedigree revealed that the mutation co-segregated with PDA, which was transmitted as an autosomal dominant trait with complete penetrance. The mutation changed the amino acid that was completely conserved evolutionarily, and did not exist in 300 unrelated, ethnically-matched healthy individuals used as controls. Functional deciphers by using a dual-luciferase reporter assay system unveiled that the mutant MEF2C protein had a significantly reduced transcriptional activity. Furthermore, the mutation significantly diminished the synergistic activation between MEF2C and GATA4, another cardiac core transcription factor that has been causally linked to CHD. In conclusion, this is the first report on the association of a MEF2C loss-of-function mutation with an increased vulnerability to CHD in humans, which provides novel insight into the molecular mechanisms underlying CHD, implying potential implications for early diagnosis and timely prophylaxis of CHD.
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Affiliation(s)
- Xiao-Hui Qiao
- Department of Pediatric Internal Medicine, Ningbo Women & Children's Hospital, 339 Liuding Street, Ningbo 315012, China
| | - Fei Wang
- Department of Neurosurgery, Tongji Hospital, Tongji University School of Medicine, 389 Xincun Road, Shanghai 200065, China
| | - Xian-Ling Zhang
- Department of Cardiology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, 301 Middle Yanchang Road, Shanghai 200072, China
| | - Ri-Tai Huang
- Department of Cardiovascular Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 1630 Dongfang Road, Shanghai 200127, China
| | - Song Xue
- Department of Cardiovascular Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 1630 Dongfang Road, Shanghai 200127, China
| | - Juan Wang
- Department of Cardiovascular Medicine, East Hospital, Tongji University School of Medicine, 150 Jimo Road, Shanghai 200120, China
| | - Xing-Biao Qiu
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, 241 West Huaihai Road, Shanghai 200030, China
| | - Xing-Yuan Liu
- Department of Pediatrics, Tongji Hospital, Tongji University School of Medicine, 389 Xincun Road, Shanghai 200065, China
| | - Yi-Qing Yang
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, 241 West Huaihai Road, Shanghai 200030, China
- Department of Cardiovascular Research Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University, 241 West Huaihai Road, Shanghai 200030, China
- Department of Central Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University, 241 West Huaihai Road, Shanghai 200030, China
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43
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da Costa PJ, Menezes J, Romão L. The role of alternative splicing coupled to nonsense-mediated mRNA decay in human disease. Int J Biochem Cell Biol 2017; 91:168-175. [PMID: 28743674 DOI: 10.1016/j.biocel.2017.07.013] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 07/15/2017] [Accepted: 07/18/2017] [Indexed: 12/29/2022]
Abstract
Alternative pre-mRNA splicing (AS) affects gene expression as it generates proteome diversity. Nonsense-mediated mRNA decay (NMD) is a surveillance pathway that recognizes and selectively degrades mRNAs carrying premature translation-termination codons (PTCs), preventing the production of truncated proteins that could result in disease. Several studies have also implicated NMD in the regulation of steady-state levels of physiological mRNAs. In addition, it is known that several regulated AS events do not lead to generation of protein products, as they lead to transcripts that carry PTCs and thus, they are committed to NMD. Indeed, an estimated one-third of naturally occurring, alternatively spliced mRNAs is targeted for NMD, being AS coupled to NMD (AS-NMD) an efficient strategy to regulate gene expression. In this review, we will focus on how AS mechanism operates and how can be coupled to NMD to fine-tune gene expression levels. Furthermore, we will demonstrate the physiological significance of the interplay among AS and NMD in human disease, such as cancer and neurological disorders. The understanding of how AS-NMD orchestrates expression of vital genes is of utmost importance for the advance in diagnosis, prognosis and treatment of many human disorders.
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Affiliation(s)
- Paulo J da Costa
- Department of Human Genetics, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Juliane Menezes
- Department of Human Genetics, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Luísa Romão
- Department of Human Genetics, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal.
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44
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Li L, Lingaraju M, Basquin C, Basquin J, Conti E. Structure of a SMG8-SMG9 complex identifies a G-domain heterodimer in the NMD effector proteins. RNA (NEW YORK, N.Y.) 2017; 23:1028-1034. [PMID: 28389433 PMCID: PMC5473137 DOI: 10.1261/rna.061200.117] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 04/04/2017] [Indexed: 06/07/2023]
Abstract
Nonsense-mediated mRNA decay (NMD) is a eukaryotic mRNA degradation pathway involved in surveillance and post-transcriptional regulation, and executed by the concerted action of several trans-acting factors. The SMG1 kinase is an essential NMD factor in metazoans and is associated with two recently identified and yet poorly characterized proteins, SMG8 and SMG9. We determined the 2.5 Å resolution crystal structure of a SMG8-SMG9 core complex from C. elegans We found that SMG8-SMG9 is a G-domain heterodimer with architectural similarities to the dynamin-like family of GTPases such as Atlastin and GBP1. The SMG8-SMG9 heterodimer forms in the absence of nucleotides, with interactions conserved from worms to humans. Nucleotide binding occurs at the G domain of SMG9 but not of SMG8. Fitting the GDP-bound SMG8-SMG9 structure in EM densities of the human SMG1-SMG8-SMG9 complex raises the possibility that the nucleotide site of SMG9 faces SMG1 and could impact the kinase conformation and/or regulation.
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Affiliation(s)
- Liang Li
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, D-82152 Martinsried, Germany
| | - Mahesh Lingaraju
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, D-82152 Martinsried, Germany
| | - Claire Basquin
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, D-82152 Martinsried, Germany
| | - Jérome Basquin
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, D-82152 Martinsried, Germany
| | - Elena Conti
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, D-82152 Martinsried, Germany
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45
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Knowlton MN, Smith CL. Naming CRISPR alleles: endonuclease-mediated mutation nomenclature across species. Mamm Genome 2017; 28:367-376. [PMID: 28589392 PMCID: PMC5569137 DOI: 10.1007/s00335-017-9698-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 05/27/2017] [Indexed: 12/29/2022]
Abstract
The widespread use of CRISPR/Cas and other targeted endonuclease technologies in many species has led to an explosion in the generation of new mutations and alleles. The ability to generate many different mutations from the same target sequence either by homology-directed repair with a donor sequence or non-homologous end joining-induced insertions and deletions necessitates a means for representing these mutations in literature and databases. Standardized nomenclature can be used to generate unambiguous, concise, and specific symbols to represent mutations and alleles. The research communities of a variety of species using CRISPR/Cas and other endonuclease-mediated mutation technologies have developed different approaches to naming and identifying such alleles and mutations. While some organism-specific research communities have developed allele nomenclature that incorporates the method of generation within the official allele or mutant symbol, others use metadata tags that include method of generation or mutagen. Organism-specific research community databases together with organism-specific nomenclature committees are leading the way in providing standardized nomenclature and metadata to facilitate the integration of data from alleles and mutations generated using CRISPR/Cas and other targeted endonucleases.
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Affiliation(s)
| | - Cynthia L Smith
- Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, 04609, USA
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Patel N, Shamseldin HE, Sakati N, Khan AO, Softa A, Al-Fadhli FM, Hashem M, Abdulwahab FM, Alshidi T, Alomar R, Alobeid E, Wakil SM, Colak D, Alkuraya FS. GZF1 Mutations Expand the Genetic Heterogeneity of Larsen Syndrome. Am J Hum Genet 2017; 100:831-836. [PMID: 28475863 DOI: 10.1016/j.ajhg.2017.04.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 04/11/2017] [Indexed: 10/19/2022] Open
Abstract
Larsen syndrome is characterized by the dislocation of large joints and other less consistent clinical findings. Heterozygous FLNB mutations account for the majority of Larsen syndrome cases, but biallelic mutations in CHST3 and B4GALT7 have been more recently described, thus confirming the existence of recessive forms of the disease. In a multiplex consanguineous Saudi family affected by severe and recurrent large joint dislocation and severe myopia, we identified a homozygous truncating variant in GZF1 through a combined autozygome and exome approach. Independently, the same approach identified a second homozygous truncating GZF1 variant in another multiplex consanguineous family affected by severe myopia, retinal detachment, and milder skeletal involvement. GZF1 encodes GDNF-inducible zinc finger protein 1, a transcription factor of unknown developmental function, which we found to be expressed in the eyes and limbs of developing mice. Global transcriptional profiling of cells from affected individuals revealed a shared pattern of gene dysregulation and significant enrichment of genes encoding matrix proteins, including P3H2, which hints at a potential disease mechanism. Our results suggest that GZF1 mutations cause a phenotype of severe myopia and significant articular involvement not previously described in Larsen syndrome.
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Abstract
As the most prevalent form of birth defect in humans worldwide, congenital heart disease (CHD) is responsible for substantial morbidity and is still the leading cause of birth defect-related demises. Increasing evidence demonstrates that genetic defects play an important role in the pathogenesis of CHD, and mutations in multiple genes, especially in those coding for cardiac core transcription factors, have been causally linked to various CHDs. Nevertheless, CHD is a genetically heterogeneous disease and the genetic determinants underpinning CHD in an overwhelming majority of patients remain elusive. In the current study, genomic DNA was extracted from venous blood samples of 165 unrelated patients with CHD, and the coding exons and splicing junction sites of the HAND1 gene, which encodes a basic helix-loop-helix transcription factor essential for cardiovascular development, were sequenced. As a result, a novel heterozygous mutation, p.R118C, was identified in a patient with tetralogy of Fallot (TOF). The missense mutation, which was absent in 600 referential chromosomes, altered the amino acid that was completely conserved evolutionarily. Biological assays with a dual-luciferase reporter assay system revealed that the R118C-mutant HAND1 protein had significantly reduced transcriptional activity when compared with its wild-type counterpart. Furthermore, the mutation significantly decreased the synergistic activation of a downstream target gene between HAND1 and GATA4, another cardiac core transcription factor associated with TOF. To our knowledge, this is the first report on the association of a HAND1 loss-of-function mutation with enhanced susceptibility to TOF in humans. The findings provide novel insight into the molecular etiology underlying TOF, suggesting potential implications for the improved prophylactic and therapeutic strategies for TOF.
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48
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Lara-Pezzi E, Desco M, Gatto A, Gómez-Gaviro MV. Neurogenesis: Regulation by Alternative Splicing and Related Posttranscriptional Processes. Neuroscientist 2016; 23:466-477. [PMID: 27837180 DOI: 10.1177/1073858416678604] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The complexity of the mammalian brain requires highly specialized protein function and diversity. As neurons differentiate and the neuronal circuitry is established, several mRNAs undergo alternative splicing and other posttranscriptional changes that expand the variety of protein isoforms produced. Recent advances are beginning to shed light on the molecular mechanisms that regulate isoform switching during neurogenesis and the role played by specific RNA binding proteins in this process. Neurogenesis and neuronal wiring were recently shown to also be regulated by RNA degradation through nonsense-mediated decay. An additional layer of regulatory complexity in these biological processes is the interplay between alternative splicing and long noncoding RNAs. Dysregulation of posttranscriptional regulation results in defective neuronal differentiation and/or synaptic connections that lead to neurodevelopmental and psychiatric disorders.
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Affiliation(s)
- Enrique Lara-Pezzi
- 1 Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain.,2 National Heart and Lung Institute, Imperial College London, London, UK
| | - Manuel Desco
- 3 Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III, Madrid, Spain.,4 Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Alberto Gatto
- 1 Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
| | - María Victoria Gómez-Gaviro
- 3 Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III, Madrid, Spain.,4 Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
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Kato T, Takada S. In vivoandin vitrodisease modeling with CRISPR/Cas9. Brief Funct Genomics 2016; 16:13-24. [DOI: 10.1093/bfgp/elw031] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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