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DDX3X Is Hijacked by Snakehead Vesiculovirus Phosphoprotein To Facilitate Virus Replication via Stabilization of the Phosphoprotein. J Virol 2023; 97:e0003523. [PMID: 36744958 PMCID: PMC9972964 DOI: 10.1128/jvi.00035-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Asp-Glu-Ala-Asp (DEAD) box helicase 3 X-linked (DDX3X) plays important regulatory roles in the replication of many viruses. However, the role of DDX3X in rhabdovirus replication has seldomly been investigated. In this study, snakehead vesiculovirus (SHVV), a kind of fish rhabdovirus, was used to study the role of DDX3X in rhabdovirus replication. DDX3X was identified as an interacting partner of SHVV phosphoprotein (P). The expression level of DDX3X was increased at an early stage of SHVV infection and then decreased to a normal level at a later infection stage. Overexpression of DDX3X promoted, while knockdown of DDX3X using specific small interfering RNAs (siRNAs) suppressed, SHVV replication, indicating that DDX3X was a proviral factor for SHVV replication. The N-terminal and core domains of DDX3X (DDX3X-N and DDX3X-Core) were determined to be the regions responsible for its interaction with SHVV P. Overexpression of DDX3X-Core suppressed SHVV replication by competitively disrupting the interaction between full-length DDX3X and SHVV P, suggesting that full-length DDX3X-P interaction was required for SHVV replication. Mechanistically, DDX3X-mediated promotion of SHVV replication was due not to inhibition of interferon expression but to maintenance of the stability of SHVV P to avoid autophagy-lysosome-dependent degradation. Collectively, our data suggest that DDX3X is hijacked by SHVV P to ensure effective replication of SHVV, which suggests an important anti-SHVV target. This study will help elucidate the role of DDX3X in regulating the replication of rhabdoviruses. IMPORTANCE Growing evidence has suggested that DDX3X plays important roles in virus replication. In one respect, DDX3X inhibits the replication of viruses, including hepatitis B virus, influenza A virus, Newcastle disease virus, duck Tembusu virus, and red-spotted grouper nervous necrosis virus. In another respect, DDX3X is required for the replication of viruses, including hepatitis C virus, Japanese encephalitis virus, West Nile virus, murine norovirus, herpes simplex virus, and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Because DDX3X has rarely been investigated in rhabdovirus replication, this study aimed at investigating the role of DDX3X in rhabdovirus replication by using the fish rhabdovirus SHVV as a model. We found that DDX3X was required for SHVV replication, with the mechanism that DDX3X interacts with and maintains the stability of SHVV phosphoprotein. Our data provide novel insights into the role of DDX3X in virus replication and will facilitate the design of antiviral drugs against rhabdovirus infection.
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Cabrera Zapata LE, Garcia-Segura LM, Cambiasso MJ, Arevalo MA. Genetics and Epigenetics of the X and Y Chromosomes in the Sexual Differentiation of the Brain. Int J Mol Sci 2022; 23:ijms232012288. [PMID: 36293143 PMCID: PMC9603441 DOI: 10.3390/ijms232012288] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 11/27/2022] Open
Abstract
For many decades to date, neuroendocrinologists have delved into the key contribution of gonadal hormones to the generation of sex differences in the developing brain and the expression of sex-specific physiological and behavioral phenotypes in adulthood. However, it was not until recent years that the role of sex chromosomes in the matter started to be seriously explored and unveiled beyond gonadal determination. Now we know that the divergent evolutionary process suffered by X and Y chromosomes has determined that they now encode mostly dissimilar genetic information and are subject to different epigenetic regulations, characteristics that together contribute to generate sex differences between XX and XY cells/individuals from the zygote throughout life. Here we will review and discuss relevant data showing how particular X- and Y-linked genes and epigenetic mechanisms controlling their expression and inheritance are involved, along with or independently of gonadal hormones, in the generation of sex differences in the brain.
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Affiliation(s)
- Lucas E. Cabrera Zapata
- Instituto de Investigación Médica Mercedes y Martín Ferreyra (INIMEC), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Córdoba, Córdoba 5016, Argentina
- Instituto Cajal (IC), Consejo Superior de Investigaciones Científicas (CSIC), 28002 Madrid, Spain
| | | | - María Julia Cambiasso
- Instituto de Investigación Médica Mercedes y Martín Ferreyra (INIMEC), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Córdoba, Córdoba 5016, Argentina
- Cátedra de Biología Celular, Facultad de Odontología, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
- Correspondence: (M.J.C.); (M.A.A.)
| | - Maria Angeles Arevalo
- Instituto Cajal (IC), Consejo Superior de Investigaciones Científicas (CSIC), 28002 Madrid, Spain
- Centro de Investigación Biomédica en Red de Fragilidad y Envejecimiento Saludable (CIBERFES), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Correspondence: (M.J.C.); (M.A.A.)
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Ng-Cordell E, Kolesnik-Taylor A, O'Brien S, Astle D, Scerif G, Baker K. Social and emotional characteristics of girls and young women with DDX3X-associated intellectual disability: a descriptive and comparative study. J Autism Dev Disord 2022:10.1007/s10803-022-05527-w. [PMID: 35536379 PMCID: PMC9087164 DOI: 10.1007/s10803-022-05527-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2022] [Indexed: 11/30/2022]
Abstract
DDX3X variants are a common cause of intellectual disability (ID) in females, and have been associated with autism spectrum disorder and emotional-behavioural difficulties. In this study, we compared phenotypic data for 23 females with DDX3X variants, to 23 females with ID and other genetic diagnoses. We found a wide range of adaptive, social and emotional function within the DDX3X group. Autism characteristics did not differ between DDX3X and comparison groups, while levels of anxiety and self-injurious behaviour (SIB) were significantly higher in the DDX3X group. Within the DDX3X group, adaptive function, autism characteristics, anxiety and SIB scores were positively correlated, with evidence for group-specific associations with SIB. Future work is warranted to explore the multilevel mechanisms contributing to social and emotional development in individuals with DDX3X variants.
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Affiliation(s)
- Elise Ng-Cordell
- Department of Psychology, University of British Columbia, Vancouver, Canada.,MRC Cognition and Brain Sciences Unit, University of Cambridge, Cambridge, United Kingdom
| | - Anna Kolesnik-Taylor
- MRC Cognition and Brain Sciences Unit, University of Cambridge, Cambridge, United Kingdom
| | - Sinéad O'Brien
- MRC Cognition and Brain Sciences Unit, University of Cambridge, Cambridge, United Kingdom
| | - Duncan Astle
- MRC Cognition and Brain Sciences Unit, University of Cambridge, Cambridge, United Kingdom
| | - Gaia Scerif
- Department of Experimental Psychology, University of Oxford, Oxford, United Kingdom
| | - Kate Baker
- MRC Cognition and Brain Sciences Unit, University of Cambridge, Cambridge, United Kingdom. .,Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom.
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Dai Y, Yang Z, Guo J, Li H, Gong J, Xie Y, Xiao B, Wang H, Long L. Expansion of Clinical and Genetic Spectrum of DDX3X Neurodevelopmental Disorder in 23 Chinese Patients. Front Mol Neurosci 2022; 15:793001. [PMID: 35392274 PMCID: PMC8981727 DOI: 10.3389/fnmol.2022.793001] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 02/02/2022] [Indexed: 01/12/2023] Open
Abstract
AimDe novo DDX3X variants account for 1–3% of unexplained intellectual disability cases in females and very rarely in males. Yet, the clinical and genetic features of DDX3X neurodevelopmental disorder in the Chinese cohort have not been characterized.MethodA total of 23 Chinese patients (i.e., 22 female and 1 male) with 22 de novo DDX3X deleterious variants were detected among 2,317 probands with unexplained intellectual disability (ID) undertaking whole exome sequencing (WES). The age, sex, genetic data, feeding situation, growth, developmental conditions, and auxiliary examinations of the cohort were collected. The Chinese version of the Gesell Development Diagnosis Scale (GDDS-C) was used to evaluate neurodevelopment of DDX3X patients. The Social Communication Questionnaire (SCQ)-Lifetime version was applied as a primary screener to assess risk for autism spectrum disorder (ASD).ResultA total of 17 DDX3X variants were novel and 22 were de novo. Missense variants overall were only slightly more common than loss-of-function variants and were mainly located in two functional subdomains. The average age of this cohort was 2.67 (±1.42) years old. The overlapping phenotypic spectrum between this cohort and previously described reports includes intellectual disability (23/23, 100%) with varying degrees of severity, muscle tone abnormalities (17/23, 73.9%), feeding difficulties (13/23, 56.5%), ophthalmologic problems (11/23, 47.8%), and seizures (6/23, 26.1%). A total of 15 individuals had notable brain anatomical disruption (15/23, 65.2%), including lateral ventricle enlargement, corpus callosum abnormalities, and delayed myelination. Furthermore, 9 patients showed abnormal electroencephalogram results (9/23, 39.1%). Hypothyroidism was first noted as a novel clinical feature (6/23, 26.1%). The five primary neurodevelopmental domains of GDDS-C in 21 patients were impaired severely, and 13 individuals were above the “at-risk” threshold for ASD.InterpretationAlthough a certain degree of phenotypic overlap with previously reported cohorts, our study described the phenotypic and variation spectrum of 23 additional individuals carrying DDX3X variants in the Chinese population, adding hypothyroidism as a novel finding. We confirmed the importance of DDX3X as a pathogenic gene in unexplained intellectual disability, supporting the necessity of the application of WES in patients with unexplained intellectual disability.
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Affiliation(s)
- Yuwei Dai
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Zhuanyi Yang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Jialing Guo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Haoyu Li
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- The Institute of Skull Base Surgery and Neurooncology at Hunan Province, Changsha, China
| | - Jiaoe Gong
- Department of Neurology, Hunan Children’s Hospital, Changsha, China
| | - Yuanyuan Xie
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Bo Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Hua Wang
- Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
- NHC Key Laboratory of Birth Defects Research, Prevention and Treatment (Hunan Provincial Maternal and Child Health Care Hospital), Changsha, China
- *Correspondence: Lili Long,
| | - Lili Long
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- NHC Key Laboratory of Birth Defects Research, Prevention and Treatment (Hunan Provincial Maternal and Child Health Care Hospital), Changsha, China
- Hua Wang,
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X-linked histone H3K27 demethylase Kdm6a regulates sexually dimorphic differentiation of hypothalamic neurons. Cell Mol Life Sci 2021; 78:7043-7060. [PMID: 34633482 PMCID: PMC8558156 DOI: 10.1007/s00018-021-03945-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/26/2021] [Accepted: 09/17/2021] [Indexed: 12/26/2022]
Abstract
Several X-linked genes are involved in neuronal differentiation and may contribute to the generation of sex dimorphisms in the brain. Previous results showed that XX hypothalamic neurons grow faster, have longer axons, and exhibit higher expression of the neuritogenic gene neurogenin 3 (Ngn3) than XY before perinatal masculinization. Here we evaluated the participation of candidate X-linked genes in the development of these sex differences, focusing mainly on Kdm6a, a gene encoding for an H3K27 demethylase with functions controlling gene expression genome-wide. We established hypothalamic neuronal cultures from wild-type or transgenic Four Core Genotypes mice, a model that allows evaluating the effect of sex chromosomes independently of gonadal type. X-linked genes Kdm6a, Eif2s3x and Ddx3x showed higher expression in XX compared to XY neurons, regardless of gonadal sex. Moreover, Kdm6a expression pattern with higher mRNA levels in XX than XY did not change with age at E14, P0, and P60 in hypothalamus or under 17β-estradiol treatment in culture. Kdm6a pharmacological blockade by GSK-J4 reduced axonal length only in female neurons and decreased the expression of neuritogenic genes Neurod1, Neurod2 and Cdk5r1 in both sexes equally, while a sex-specific effect was observed in Ngn3. Finally, Kdm6a downregulation using siRNA reduced axonal length and Ngn3 expression only in female neurons, abolishing the sex differences observed in control conditions. Altogether, these results point to Kdm6a as a key mediator of the higher axogenesis and Ngn3 expression observed in XX neurons before the critical period of brain masculinization.
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Hansen CL, Pelegri F. Primordial Germ Cell Specification in Vertebrate Embryos: Phylogenetic Distribution and Conserved Molecular Features of Preformation and Induction. Front Cell Dev Biol 2021; 9:730332. [PMID: 34604230 PMCID: PMC8481613 DOI: 10.3389/fcell.2021.730332] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/25/2021] [Indexed: 11/24/2022] Open
Abstract
The differentiation of primordial germ cells (PGCs) occurs during early embryonic development and is critical for the survival and fitness of sexually reproducing species. Here, we review the two main mechanisms of PGC specification, induction, and preformation, in the context of four model vertebrate species: mouse, axolotl, Xenopus frogs, and zebrafish. We additionally discuss some notable molecular characteristics shared across PGC specification pathways, including the shared expression of products from three conserved germline gene families, DAZ (Deleted in Azoospermia) genes, nanos-related genes, and DEAD-box RNA helicases. Then, we summarize the current state of knowledge of the distribution of germ cell determination systems across kingdom Animalia, with particular attention to vertebrate species, but include several categories of invertebrates - ranging from the "proto-vertebrate" cephalochordates to arthropods, cnidarians, and ctenophores. We also briefly highlight ongoing investigations and potential lines of inquiry that aim to understand the evolutionary relationships between these modes of specification.
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Affiliation(s)
| | - Francisco Pelegri
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, United States
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Xu J, Cai Y, Ma Z, Jiang B, Liu W, Cheng J, Jin H, Li Y. DEAD/DEAH-box helicase 5 is hijacked by an avian oncogenic herpesvirus to inhibit interferon beta production and promote viral replication. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 119:104048. [PMID: 33609615 DOI: 10.1016/j.dci.2021.104048] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 02/11/2021] [Accepted: 02/14/2021] [Indexed: 06/12/2023]
Abstract
DEAD-box helicase 5 (DDX5) plays a significant role in tumorigenesis and regulates viral replication of several viruses. An avian oncogenic herpesvirus, Marek's disease virus (MDV), is widely known to cause immunosuppression and lymphoma in chickens. However, the underlying mechanisms of how DDX5 plays a role in viral replication remain unclear. In this study, we show that MDV inhibits the production of interferon beta (IFN-β) in chicken embryo fibroblasts (CEFs) by increasing the expression level and promoting the nuclear aggregation of DDX5. We further reveal how DDX5 down-regulates melanoma differentiation-associated gene 5/toll-like receptor 3 signaling through the fundamental transcription factor, interferon regulatory factor 1. MDV replication is suppressed, and the production of IFN-β is promoted in the DDX5 absented CEFs. Taken together, our investigations demonstrate that MDV inhibits IFN-β production by targeting DDX5-mediated signaling to facilitate viral replication, which offers a novel insight into the mechanism by which an avian oncogenic herpesvirus replicates in chicken cells.
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Affiliation(s)
- Jian Xu
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, PR China
| | - Yunhong Cai
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, PR China
| | - Zhenbang Ma
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, PR China
| | - Bo Jiang
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, PR China
| | - Wenxiao Liu
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, PR China
| | - Jing Cheng
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, PR China
| | - Huan Jin
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, PR China
| | - Yongqing Li
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, PR China.
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Fontenla S, Rinaldi G, Tort JF. Lost and Found: Piwi and Argonaute Pathways in Flatworms. Front Cell Infect Microbiol 2021; 11:653695. [PMID: 34123869 PMCID: PMC8191739 DOI: 10.3389/fcimb.2021.653695] [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: 01/15/2021] [Accepted: 05/10/2021] [Indexed: 11/13/2022] Open
Abstract
Platyhelminthes comprise one of the major phyla of invertebrate animals, inhabiting a wide range of ecosystems, and one of the most successful in adapting to parasitic life. Small non-coding RNAs have been implicated in regulating complex developmental transitions in model parasitic species. Notably, parasitic flatworms have lost Piwi RNA pathways but gained a novel Argonaute gene. Herein, we analyzed, contrasted and compared the conservation of small RNA pathways among several free-living species (a paraphyletic group traditionally known as ‘turbellarians’) and parasitic species (organized in the monophyletic clade Neodermata) to disentangle possible adaptations during the transition to parasitism. Our findings showed that complete miRNA and RNAi pathways are present in all analyzed free-living flatworms. Remarkably, whilst all ‘turbellarians’ have Piwi proteins, these were lost in parasitic Neodermantans. Moreover, two clusters of Piwi class Argonaute genes are present in all ‘turbellarians’. Interestingly, we identified a divergent Piwi class Argonaute in free living flatworms exclusively, which we named ‘Fliwi’. In addition, other key proteins of the Piwi pathways were conserved in ‘turbellarians’, while none of them were detected in Neodermatans. Besides Piwi and the canonical Argonaute proteins, a flatworm-specific class of Argonautes (FL-Ago) was identified in the analyzed species confirming its ancestrallity to all Platyhelminthes. Remarkably, this clade was expanded in parasitic Neodermatans, but not in free-living species. These phyla-specific Argonautes showed lower sequence conservation compared to other Argonaute proteins, suggesting that they might have been subjected to high evolutionary rates. However, key residues involved in the interaction with the small RNA and mRNA cleavage in the canonical Argonautes were more conserved in the FL-Agos than in the Piwi Argonautes. Whether this is related to specialized functions and adaptations to parasitism in Neodermatans remains unclear. In conclusion, differences detected in gene conservation, sequence and structure of the Argonaute family suggest tentative biological and evolutionary diversifications that are unique to Platyhelminthes. The remarkable divergencies in the small RNA pathways between free-living and parasitic flatworms indicate that they may have been involved in the adaptation to parasitism of Neodermatans.
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Affiliation(s)
- Santiago Fontenla
- Departamento de Genética, Facultad de Medicina, Universidad de la República (UDELAR), Montevideo, Uruguay
| | | | - Jose F Tort
- Departamento de Genética, Facultad de Medicina, Universidad de la República (UDELAR), Montevideo, Uruguay
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Wei Q, Geng J, Chen Y, Lin H, Wang J, Fang Z, Wang F, Zhang Z. Structure and function of DEAH-box helicase 32 and its role in cancer. Oncol Lett 2021; 21:382. [PMID: 33777205 PMCID: PMC7988694 DOI: 10.3892/ol.2021.12643] [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: 08/16/2020] [Accepted: 12/23/2020] [Indexed: 11/06/2022] Open
Abstract
DEAH-box helicase 32 (DHX32) is an RNA helicase with unique structural characteristics that is involved in numerous biological processes associated with RNA, including ribosome biosynthesis, transcription, mRNA splicing and translation. Increasing evidence suggests that abnormal DHX32 expression contributes to cancer initiation and development, due to dysregulated cell proliferation, differentiation, apoptosis and other processes. In the current review, the discovery, structure and function of DHX32, as well as the association between abnormal DHX32 expression and tumors are discussed. DHX32 expression is downregulated in acute lymphoblastic leukemia, but upregulated in solid tumors, including colorectal and breast cancer. Furthermore, DHX32 expression levels are associated with the pathological and clinical features of the cancer. Therefore, DHX32 may serve as a novel liquid biopsy marker for auxiliary diagnosis and prognosis screening, as well as a possible target for cancer therapy. The molecular mechanism underlying the contribution of DHX32 towards the initiation and development of cancer requires further investigation for the development of anticancer treatments based on manipulating DHX32 expression and function.
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Affiliation(s)
- Qingchun Wei
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, Fujian 361102, P.R. China
| | - Jinting Geng
- Xiamen Key Laboratory of Biomarker Translational Medicine, Center of Medical Laboratory of Xiamen Humanity Hospital, Fujian Medical University, Xiamen, Fujian 361009, P.R. China
| | - Yongquan Chen
- Xiamen Key Laboratory of Biomarker Translational Medicine, Center of Medical Laboratory of Xiamen Humanity Hospital, Fujian Medical University, Xiamen, Fujian 361009, P.R. China
| | - Huayue Lin
- Center of Clinical Laboratory, Xiamen University Affiliated Zhongshan Hospital, Xiamen, Fujian 361104, P.R. China
| | - Jiajia Wang
- Center of Clinical Laboratory, Xiamen University Affiliated Zhongshan Hospital, Xiamen, Fujian 361104, P.R. China
| | - Zanxi Fang
- Center of Clinical Laboratory, Xiamen University Affiliated Zhongshan Hospital, Xiamen, Fujian 361104, P.R. China
| | - Fen Wang
- Center for Cancer and Stem Cell Biology, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX 77030, USA
| | - Zhongying Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, Fujian 361102, P.R. China
- Xiamen Key Laboratory of Biomarker Translational Medicine, Center of Medical Laboratory of Xiamen Humanity Hospital, Fujian Medical University, Xiamen, Fujian 361009, P.R. China
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Temporomandibular Disorders Slow Down the Regeneration Process of Masticatory Muscles: Transcriptomic Analysis. ACTA ACUST UNITED AC 2021; 57:medicina57040354. [PMID: 33916982 PMCID: PMC8067552 DOI: 10.3390/medicina57040354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/31/2021] [Accepted: 04/06/2021] [Indexed: 11/17/2022]
Abstract
Background and Objectives: Musculoskeletal injuries represent a pathological condition due to limited joint motility and morphological and functional alterations of the muscles. Temporomandibular disorders (TMDs) are pathological conditions due to alterations in the musculoskeletal system. TMDs mainly cause temporomandibular joint and masticatory muscle dysfunctions following trauma, along with various pathologies and inflammatory processes. TMD affects approximately 15% of the population and causes malocclusion problems and common symptoms such as myofascial pain and migraine. The aim of this work was to provide a transcriptomic profile of masticatory muscles obtained from TMD migraine patients compared to control. Materials and Methods: We used Next Generation Sequencing (NGS) technology to evaluate transcriptomes in masseter and temporalis muscle samples. Results: The transcriptomic analysis showed a prevalent downregulation of the genes involved in the myogenesis process. Conclusions: In conclusion, our findings suggest that the muscle regeneration process in TMD migraine patients may be slowed, therefore therapeutic interventions are needed to restore temporomandibular joint function and promote healing processes.
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Mokdadi M, Abdelkrim YZ, Banroques J, Huvelle E, Oualha R, Yeter-Alat H, Guizani I, Barhoumi M, Tanner NK. The In Silico Identification of Potential Members of the Ded1/DDX3 Subfamily of DEAD-Box RNA Helicases from the Protozoan Parasite Leishmania infantum and Their Analyses in Yeast. Genes (Basel) 2021; 12:212. [PMID: 33535521 PMCID: PMC7912733 DOI: 10.3390/genes12020212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/27/2021] [Accepted: 01/29/2021] [Indexed: 12/14/2022] Open
Abstract
DEAD-box RNA helicases are ubiquitous proteins found in all kingdoms of life and that are associated with all processes involving RNA. Their central roles in biology make these proteins potential targets for therapeutic or prophylactic drugs. The Ded1/DDX3 subfamily of DEAD-box proteins is of particular interest because of their important role(s) in translation. In this paper, we identified and aligned the protein sequences of 28 different DEAD-box proteins from the kinetoplast-protozoan parasite Leishmania infantum, which is the cause of the visceral form of leishmaniasis that is often lethal if left untreated, and compared them with the consensus sequence derived from DEAD-box proteins in general, and from the Ded1/DDX3 subfamily in particular, from a wide variety of other organisms. We identified three potential homologs of the Ded1/DDX3 subfamily and the equivalent proteins from the related protozoan parasite Trypanosoma brucei, which is the causative agent of sleeping sickness. We subsequently tested these proteins for their ability to complement a yeast strain deleted for the essential DED1 gene. We found that the DEAD-box proteins from Trypanosomatids are highly divergent from other eukaryotes, and consequently they are suitable targets for protein-specific drugs.
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Affiliation(s)
- Molka Mokdadi
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France; (M.M.); (Y.Z.A.); (J.B.); (E.H.); (H.Y.-A.)
- PSL Research University, 75005 Paris, France
- Laboratory of Molecular Epidemiology and Experimental Pathology (LR16IPT04), Institut Pasteur de Tunis, Université de Tunis El Manar, 13 Place Pasteur, BP74 Tunis-Belvédère 1002, Tunisia; (R.O.); (I.G.)
- Institut National des Sciences Appliquées et Technologies, Université de Carthage, CEDEX, Tunis 1080, Tunisia
| | - Yosser Zina Abdelkrim
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France; (M.M.); (Y.Z.A.); (J.B.); (E.H.); (H.Y.-A.)
- Laboratory of Molecular Epidemiology and Experimental Pathology (LR16IPT04), Institut Pasteur de Tunis, Université de Tunis El Manar, 13 Place Pasteur, BP74 Tunis-Belvédère 1002, Tunisia; (R.O.); (I.G.)
| | - Josette Banroques
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France; (M.M.); (Y.Z.A.); (J.B.); (E.H.); (H.Y.-A.)
- PSL Research University, 75005 Paris, France
| | - Emmeline Huvelle
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France; (M.M.); (Y.Z.A.); (J.B.); (E.H.); (H.Y.-A.)
- PSL Research University, 75005 Paris, France
| | - Rafeh Oualha
- Laboratory of Molecular Epidemiology and Experimental Pathology (LR16IPT04), Institut Pasteur de Tunis, Université de Tunis El Manar, 13 Place Pasteur, BP74 Tunis-Belvédère 1002, Tunisia; (R.O.); (I.G.)
| | - Hilal Yeter-Alat
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France; (M.M.); (Y.Z.A.); (J.B.); (E.H.); (H.Y.-A.)
- PSL Research University, 75005 Paris, France
| | - Ikram Guizani
- Laboratory of Molecular Epidemiology and Experimental Pathology (LR16IPT04), Institut Pasteur de Tunis, Université de Tunis El Manar, 13 Place Pasteur, BP74 Tunis-Belvédère 1002, Tunisia; (R.O.); (I.G.)
| | - Mourad Barhoumi
- Laboratory of Molecular Epidemiology and Experimental Pathology (LR16IPT04), Institut Pasteur de Tunis, Université de Tunis El Manar, 13 Place Pasteur, BP74 Tunis-Belvédère 1002, Tunisia; (R.O.); (I.G.)
| | - N. Kyle Tanner
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France; (M.M.); (Y.Z.A.); (J.B.); (E.H.); (H.Y.-A.)
- PSL Research University, 75005 Paris, France
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12
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You H, Zhou Y, Yan J. Using Magnetic Tweezers to Unravel the Mechanism of the G-quadruplex Binding and Unwinding Activities of DHX36 Helicase. Methods Mol Biol 2021; 2209:175-191. [PMID: 33201470 DOI: 10.1007/978-1-0716-0935-4_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Single-molecule manipulation methods are useful techniques to probe the interactions of proteins and nucleic acid structures. Here, we describe the magnetic tweezers-based single-molecule investigation of the binding of helicases to G-quadruplex structures and their ATP-dependent unwinding activity, using DHX36 (also known as RHAU and G4R1) helicase and a DNA G-quadruplex structure for an example. We specifically emphasize on the principle and method to probe the interactions between DHX36 and the DNA G-quadruplex in different intermediate states during an ATPase cycle of DHX36, based on detecting the DHX36-induced changes in the lifetime of the DNA G-quadruplex under tension. The principle of the measurement can be broadly extended to the studies of other DNA or RNA G-quadruplex helicases.
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Affiliation(s)
- Huijuan You
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Zhou
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Jie Yan
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore.
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13
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Wang J, Liu J, Ye M, Liu F, Wu S, Huang J, Shi G. Ddx56 maintains proliferation of mouse embryonic stem cells via ribosome assembly and interaction with the Oct4/Sox2 complex. Stem Cell Res Ther 2020; 11:314. [PMID: 32703285 PMCID: PMC7376950 DOI: 10.1186/s13287-020-01800-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/07/2020] [Accepted: 07/01/2020] [Indexed: 12/17/2022] Open
Abstract
Background Embryonic stem cells (ESCs) are important source of clinical stem cells for therapy, so dissecting the functional gene regulatory network involved in their self-renewal and proliferation is an urgent task. We previously reported that Ddx56 interacts with the core transcriptional factor Oct4 by mass spectrometry analysis in ESCs. However, the exact function of Ddx56 in ESCs remains unclear. Methods We investigated the role of Ddx56 in mouse ESCs (mESCs) through both gain- and loss-of-function strategies. The effect of Ddx56 on mESCs was determined based on morphological changes, involvement in the network of pluripotency markers (Nanog, Oct4, Sox2), and altered lineage marker expression. In addition, the role of Ddx56 in mESCs was evaluated by polysome fractionation, qRT-PCR, and co-immunoprecipitation (co-IP). Finally, RNA sequencing was applied to explore potential network regulation by Ddx56 in mESCs. Result We found that Ddx56 participated in ribosome assembly, as knockout or RNAi knockdown of Ddx56 led to ribosome dysfunction and cell lethality. Surprisingly, exogenous expression of C-terminal domain truncated Ddx56 (Ddx56 ΔC-ter) did not affect ribosome assembly, but decreased mESC proliferation by downregulation of proliferation-related genes and cell cycle changing. In terms of mechanism, Ddx56 interacted with the Oct4 and Sox2 complex by binding to Sox2, whereas Ddx56 ΔC-ter showed weaker interaction with Sox2 and led to retardation of mESC proliferation. Conclusions Ddx56 maintains ESC proliferation by conventional regulation of ribosome assembly and interaction with the Oct4 and Sox2 complex.
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Affiliation(s)
- Jingwen Wang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Jiahui Liu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Miaoman Ye
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Feng Liu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Su Wu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Junjiu Huang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.,Key Laboratory of Reproductive Medicine of Guangdong Province, The First Affiliated Hospital and School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Guang Shi
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
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14
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Hu L, Xin X, Lin S, Luo M, Chen J, Qiu H, Ma L, Huang J. A child with a novel DDX3X variant mimicking cerebral palsy: a case report. Ital J Pediatr 2020; 46:88. [PMID: 32600431 PMCID: PMC7325255 DOI: 10.1186/s13052-020-00850-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 06/15/2020] [Indexed: 11/21/2022] Open
Abstract
Background Cerebral palsy (CP) is a non-progressive disorder of movement and posture due to a static insult to the brain. In CP, the depth of investigation is guided by the patients’ medical history and their clinical examination. Magnetic resonance imaging (MRI) has a high yield and is widely used for investigation in CP. Case presentation In this paper, we report a novel DDX3X variant in a girl afflicted with the X-linked mental retardation-102 (MRX102). The girl had been misdiagnosed with CP in her early life based on a comprehensive clinical evaluation and associated clinical features, such as developmental delay, reduced activities of the arms and legs, and abnormal brain MRI. Subsequently, whole-exome sequencing was applied to better distinguish between CP and actual MRX102 with similar characteristics. Conclusions We report on a de novo heterozygous DDX3X variant mimicking cerebral palsy and suggest a thorough and conscientious review during diagnosis of CP.
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Affiliation(s)
- Liqin Hu
- Department of Gynaecology and Obstetrics, Ganzhou Maternal and Child Health Hospital, Ganzhou, 341000, Jiangxi Province, China
| | - Xiaoqin Xin
- Department of Clinical Laboratory, Ganzhou People's Hospital, Ganzhou, 341000, Jiangxi Province, China
| | - Shaobin Lin
- Fetal Medicine Centre, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong Province, China
| | - Min Luo
- Department of Pediatric Neurorehabilitation, Ganzhou Maternal and Child Health Hospital, Ganzhou, 341000, Jiangxi Province, China
| | - Junkun Chen
- Department of Medical Genetics, Ganzhou Maternal and Child Health Hospital, Ganzhou, 341000, Jiangxi Province, China
| | - Hongsheng Qiu
- Neonatology Department, Ganzhou Maternal and Child Health Hospital, Ganzhou, 341000, Jiangxi Province, China
| | - Li Ma
- Department of Gynaecology and Obstetrics, Ganzhou Maternal and Child Health Hospital, Ganzhou, 341000, Jiangxi Province, China
| | - Jungao Huang
- Department of Medical Genetics, Ganzhou Maternal and Child Health Hospital, Ganzhou, 341000, Jiangxi Province, China.
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15
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A Computational Approach with Biological Evaluation: Combinatorial Treatment of Curcumin and Exemestane Synergistically Regulates DDX3 Expression in Cancer Cell Lines. Biomolecules 2020; 10:biom10060857. [PMID: 32512851 PMCID: PMC7355417 DOI: 10.3390/biom10060857] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/15/2020] [Accepted: 05/20/2020] [Indexed: 01/07/2023] Open
Abstract
DDX3 belongs to RNA helicase family that demonstrates oncogenic properties and has gained wider attention due to its role in cancer progression, proliferation and transformation. Mounting reports have evidenced the role of DDX3 in cancers making it a promising target to abrogate DDX3 triggered cancers. Dual pharmacophore models were generated and were subsequently validated. They were used as 3D queries to screen the InterBioScreen database, resulting in the selection of curcumin that was escalated to molecular dynamics simulation studies. In vitro anti-cancer analysis was conducted on three cell lines such as MCF-7, MDA-MB-231 and HeLa, which were evaluated along with exemestane. Curcumin was docked into the active site of the protein target (PDB code 2I4I) to estimate the binding affinity. The compound has interacted with two key residues and has displayed stable molecular dynamics simulation results. In vitro analysis has demonstrated that both the candidate compounds have reduced the expression of DDX3 in three cell lines. However, upon combinatorial treatment of curcumin (10 and 20 μM) and exemestane (50 μM) a synergism was exhibited, strikingly downregulating the DDX3 expression and has enhanced apoptosis in three cell lines. The obtained results illuminate the use of curcumin as an alternative DDX3 inhibitor and can serve as a chemical scaffold to design new small molecules.
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16
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Chucair-Elliott AJ, Ocanas SR, Stanford DR, Hadad N, Wronowski B, Otalora L, Stout MB, Freeman WM. Tamoxifen induction of Cre recombinase does not cause long-lasting or sexually divergent responses in the CNS epigenome or transcriptome: implications for the design of aging studies. GeroScience 2019; 41:691-708. [PMID: 31493147 PMCID: PMC6885072 DOI: 10.1007/s11357-019-00090-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 08/01/2019] [Indexed: 12/27/2022] Open
Abstract
The systemic delivery of tamoxifen (Tam) to activate inducible CreERT2-loxP transgenic mouse systems is now widely used in neuroscience studies. This critical technological advancement allows temporal control of DNA-cre recombination, avoidance of embryonically lethal phenotypes, and minimization of residual cell labeling encountered in constitutively active drivers. Despite its advantages, the use of Tam has the potential to cause long-lasting, uncharacterized side effects on the transcriptome and epigenome in the CNS, given its mixed estrogen receptor (ER) agonist/antagonist actions. With the welcome focus on including both sexes in biomedical studies and efforts to understand sex differences, Tam administration could also cause sexually divergent responses that would confound studies. To examine these issues, epigenetic and transcriptomic profiles were compared in C57BL/6 J female and male hippocampus, cortex, and retina 1 month after a 5-day Tam treatment typical for cre induction, or vehicle control (sunflower seed oil). Cytosine methylation and hydroxymethylation levels, in both CG and non-CG contexts, were unchanged as determined by oxidative bisulfite sequencing. Long-lasting Tam transcriptomic effects were also not evident/minimal. Furthermore, there is no evidence of sexually divergent responses with Tam administration and Tam did not alter sex differences evident in controls. Combined with recently reported data that Tam alone does not cause long-lasting changes in behavior and neurogenesis, our findings provide confidence that Tam can be used as a cre-recombinase inducer without introducing significant confounds in transcriptomic and epigenomic neuroscience studies, particularly those focused on genomic and transcriptomic aspects of the aging brain.
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Affiliation(s)
- Ana J Chucair-Elliott
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Physiology, University of Oklahoma Health Sciences Center, 975 NE 10th Street, Oklahoma City, OK, 73104, USA
| | - Sarah R Ocanas
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Physiology, University of Oklahoma Health Sciences Center, 975 NE 10th Street, Oklahoma City, OK, 73104, USA
| | - David R Stanford
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Physiology, University of Oklahoma Health Sciences Center, 975 NE 10th Street, Oklahoma City, OK, 73104, USA
| | - Niran Hadad
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Oklahoma Nathan Shock Center for Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Benjamin Wronowski
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Laura Otalora
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Physiology, University of Oklahoma Health Sciences Center, 975 NE 10th Street, Oklahoma City, OK, 73104, USA
| | - Michael B Stout
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Nutritional Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Willard M Freeman
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Department of Physiology, University of Oklahoma Health Sciences Center, 975 NE 10th Street, Oklahoma City, OK, 73104, USA.
- Oklahoma Nathan Shock Center for Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Oklahoma City Veterans Affairs Medical Center, Oklahoma City, OK, USA.
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17
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Dong MB, Wang G, Chow RD, Ye L, Zhu L, Dai X, Park JJ, Kim HR, Errami Y, Guzman CD, Zhou X, Chen KY, Renauer PA, Du Y, Shen J, Lam SZ, Zhou JJ, Lannin DR, Herbst RS, Chen S. Systematic Immunotherapy Target Discovery Using Genome-Scale In Vivo CRISPR Screens in CD8 T Cells. Cell 2019; 178:1189-1204.e23. [PMID: 31442407 PMCID: PMC6719679 DOI: 10.1016/j.cell.2019.07.044] [Citation(s) in RCA: 173] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 05/17/2019] [Accepted: 07/24/2019] [Indexed: 12/12/2022]
Abstract
CD8 T cells play essential roles in anti-tumor immune responses. Here, we performed genome-scale CRISPR screens in CD8 T cells directly under cancer immunotherapy settings and identified regulators of tumor infiltration and degranulation. The in vivo screen robustly re-identified canonical immunotherapy targets such as PD-1 and Tim-3, along with genes that have not been characterized in T cells. The infiltration and degranulation screens converged on an RNA helicase Dhx37. Dhx37 knockout enhanced the efficacy of antigen-specific CD8 T cells against triple-negative breast cancer in vivo. Immunological characterization in mouse and human CD8 T cells revealed that DHX37 suppresses effector functions, cytokine production, and T cell activation. Transcriptomic profiling and biochemical interrogation revealed a role for DHX37 in modulating NF-κB. These data demonstrate high-throughput in vivo genetic screens for immunotherapy target discovery and establishes DHX37 as a functional regulator of CD8 T cells.
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Affiliation(s)
- Matthew B Dong
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; System Biology Institute, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Yale MD-PhD Program, Yale University School of Medicine, New Haven, CT 06510, USA; Immunobiology Program, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Guangchuan Wang
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; System Biology Institute, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA
| | - Ryan D Chow
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; System Biology Institute, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Yale MD-PhD Program, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Lupeng Ye
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; System Biology Institute, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA
| | - Lvyun Zhu
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; System Biology Institute, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA
| | - Xiaoyun Dai
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; System Biology Institute, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA
| | - Jonathan J Park
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; System Biology Institute, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Yale MD-PhD Program, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Hyunu R Kim
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; System Biology Institute, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA
| | - Youssef Errami
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; System Biology Institute, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA
| | - Christopher D Guzman
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; System Biology Institute, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Immunobiology Program, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA; Combined Program in the Biological and Biomedical Sciences, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Xiaoyu Zhou
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; System Biology Institute, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA
| | - Krista Y Chen
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; System Biology Institute, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; The College, Yale University, New Haven, CT 06520, USA
| | - Paul A Renauer
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; System Biology Institute, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Combined Program in the Biological and Biomedical Sciences, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Yaying Du
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; System Biology Institute, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA
| | - Johanna Shen
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; System Biology Institute, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; The College, Yale University, New Haven, CT 06520, USA
| | - Stanley Z Lam
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; System Biology Institute, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; The College, Yale University, New Haven, CT 06520, USA
| | - Jingjia J Zhou
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; System Biology Institute, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; The College, Yale University, New Haven, CT 06520, USA
| | - Donald R Lannin
- Department of Surgery, Yale University School of Medicine, New Haven, CT 06510, USA; Breast Cancer Program, Yale University School of Medicine, New Haven, CT06510, USA; Smilow Cancer Hospital, 35 Park Street, New Haven, CT 06510; Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Roy S Herbst
- Department of Medicine, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06510, USA; Smilow Cancer Hospital, 35 Park Street, New Haven, CT 06510; Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Sidi Chen
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; System Biology Institute, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Yale MD-PhD Program, Yale University School of Medicine, New Haven, CT 06510, USA; Immunobiology Program, Yale University School of Medicine, New Haven, CT 06510, USA; Combined Program in the Biological and Biomedical Sciences, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Liver Center, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Center for Biomedical Data Science, Yale University School of Medicine, New Haven, CT 06510, USA.
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18
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Nicola P, Blackburn PR, Rasmussen KJ, Bertsch NL, Klee EW, Hasadsri L, Pichurin PN, Rankin J, Raymond FL, Clayton-Smith J. De novo DDX3X missense variants in males appear viable and contribute to syndromic intellectual disability. Am J Med Genet A 2019; 179:570-578. [PMID: 30734472 DOI: 10.1002/ajmg.a.61061] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 12/12/2018] [Accepted: 01/04/2019] [Indexed: 12/23/2022]
Abstract
DDX3X (Xp11.4) encodes a DEAD-box RNA helicase that escapes X chromosome inactivation. Pathogenic variants in DDX3X have been shown to cause X-linked intellectual disability (ID) (MRX102, MIM: 300958). The phenotypes associated with DDX3X variants are heterogeneous and include brain and behavioral abnormalities, microcephaly, hypotonia, and movement disorders and/or spasticity. The majority of DDX3X variants described are de novo mutations in females with ID. In contrast, most male DDX3X variants are inherited from an unaffected mother, with one documented exception being a recently identified de novo splice site variant. It has been suggested, therefore, that DDX3X exerts its effects through haploinsufficiency in females, and that affected males carry hypomorphic alleles that retain partial function. Given the lack of male de novo DDX3X variants, loss-of-function variants in this gene are suspected to be male lethal. Through whole-exome sequencing, we identified three unrelated males with hemizygous missense DDX3X variants and ID. All three variants were confirmed by Sanger sequencing, with two established as de novo. In silico analyses were supportive of pathogenicity. We report the male phenotypes and compare them to phenotypes observed in previously reported male and female patients. In conclusion, we propose that de novo DDX3X variants are not necessarily male lethal and should be considered as a cause of syndromic ID in both males and females.
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Affiliation(s)
- Pantelis Nicola
- University Hospital of South Manchester NHS Foundation Trust, Manchester, United Kingdom.,Manchester Centre for Genomic Medicine, Manchester, United Kingdom
| | - Patrick R Blackburn
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota.,Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Kristen J Rasmussen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Nicole L Bertsch
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota.,Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota
| | - Linda Hasadsri
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Pavel N Pichurin
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota
| | - Julia Rankin
- Clinical Genetics Department, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - F Lucy Raymond
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
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- Deciphering Developmental Disorders Study (DDD), Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Jill Clayton-Smith
- Manchester Centre for Genomic Medicine, Manchester, United Kingdom.,Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
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19
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Roles of DDX5 in the tumorigenesis, proliferation, differentiation, metastasis and pathway regulation of human malignancies. Biochim Biophys Acta Rev Cancer 2019; 1871:85-98. [DOI: 10.1016/j.bbcan.2018.11.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 11/02/2018] [Accepted: 11/03/2018] [Indexed: 02/07/2023]
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20
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Tapia-Morales S, López-Landavery EA, Giffard-Mena I, Ramírez-Álvarez N, Gómez-Reyes RJE, Díaz F, Galindo-Sánchez CE. Transcriptomic response of the Crassostrea virginica gonad after exposure to a water-accommodation fraction of hydrocarbons and the potential implications in reproduction. Mar Genomics 2018; 43:9-18. [PMID: 30409725 DOI: 10.1016/j.margen.2018.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 10/06/2018] [Accepted: 10/20/2018] [Indexed: 11/26/2022]
Abstract
The Crassostrea virginica oyster has biological and economic importance in the Gulf of Mexico, an area with a high extraction and production of hydrocarbons. Exposure to hydrocarbons affects the reproductive processes in bivalves. In C. virginica, the effect of hydrocarbons on the gonad of the undifferentiated organism has not been evaluated to determine the possible damage during the maturation process. To evaluate this effect, RNA-seq data was generated from C. virginica gonads exposed to a 200 μg/L of hydrocarbons at different exposure times (7, 14 and 21 days) and a control treatment (without hydrocarbons). The analysis of the gonad transcriptome showed the negative effect of hydrocarbons on maturation, with a sub-expression of 22 genes involved in different stages of this process. Additionally, genes in the immune system were down-regulated, which may indicate that exposure to hydrocarbons causes immunosuppression in bivalves. A group of oxidative stress genes was also reduced. These data contribute to a better understanding of the effect of hydrocarbons on the reproductive process in bivalves and, at the same time, allow us to identify possible biomarkers associated with hydrocarbon contamination in the gonad of C. virginica.
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Affiliation(s)
- S Tapia-Morales
- Centro de Investigación Científica y Educación Superior de Ensenada, Laboratorio de Genómica Marina, Carretera Ensenada-Tijuana, C.P. 22860 Ensenada, B. C., Mexico; Universidad Autónoma de Baja California, Facultad de Ciencias Marinas, Laboratorio de Patología Experimental Acuícola, Carretera Ensenada-Tijuana No. 3917, C.P. 22860 Ensenada, B. C., Mexico
| | - E A López-Landavery
- Centro de Investigación Científica y Educación Superior de Ensenada, Laboratorio de Genómica Marina, Carretera Ensenada-Tijuana, C.P. 22860 Ensenada, B. C., Mexico
| | - I Giffard-Mena
- Universidad Autónoma de Baja California, Facultad de Ciencias Marinas, Laboratorio de Patología Experimental Acuícola, Carretera Ensenada-Tijuana No. 3917, C.P. 22860 Ensenada, B. C., Mexico
| | - N Ramírez-Álvarez
- Universidad Autónoma de Baja California, Instituto de Investigaciones Oceanológicas, Carretera Ensenada-Tijuana No. 3917, C.P. 22860 Ensenada, B. C., Mexico
| | - R J E Gómez-Reyes
- Centro de Investigación Científica y Educación Superior de Ensenada, Laboratorio de Genómica Marina, Carretera Ensenada-Tijuana, C.P. 22860 Ensenada, B. C., Mexico
| | - F Díaz
- Centro de Investigación Científica y Educación Superior de Ensenada, Laboratorio de Genómica Marina, Carretera Ensenada-Tijuana, C.P. 22860 Ensenada, B. C., Mexico
| | - C E Galindo-Sánchez
- Centro de Investigación Científica y Educación Superior de Ensenada, Laboratorio de Genómica Marina, Carretera Ensenada-Tijuana, C.P. 22860 Ensenada, B. C., Mexico.
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21
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X-chromosomale Entwicklungsstörungen im weiblichen Geschlecht. MED GENET-BERLIN 2018. [DOI: 10.1007/s11825-018-0199-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Zusammenfassung
In den letzten Jahren wurden Mutationen in einer wachsenden Zahl von X‑chromosomalen Genen als Ursache für Entwicklungsstörungen bei Mädchen identifiziert. Dies führt zu einer Aufweichung der traditionellen Abgrenzung von X‑chromosomal-rezessiven und X‑chromosomal-dominanten Erbgängen. Für viele X‑chromosomale, mit Entwicklungsstörungen assoziierte Gene zeichnet sich nun ein phänotypisches Spektrum ab, welches beide Geschlechter umfasst. Die Mechanismen, die zu einer oft variablen Krankheitsausprägung zwischen den Geschlechtern aber auch innerhalb des weiblichen Geschlechts führen, sind bisher noch sehr unvollständig verstanden. Verschiedene Faktoren wie Art, Lokalisation und „Schwere“ der jeweiligen Mutation sowie insbesondere die X‑Inaktivierung spielen dabei eine Rolle. Dieser Artikel gibt einen Überblick über den derzeitigen Kenntnisstand (ohne Anspruch auf Vollständigkeit) X‑chromosomaler Entwicklungsstörungen bei Mädchen. Exemplarisch werden zudem einige neue Krankheitsbilder bei Mädchen beschrieben und diskutiert, die durch De-novo-Mutationen in X‑chromosomalen Genen verursacht werden.
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22
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Wang X, Posey JE, Rosenfeld JA, Bacino CA, Scaglia F, Immken L, Harris JM, Hickey SE, Mosher TM, Slavotinek A, Zhang J, Beuten J, Leduc MS, He W, Vetrini F, Walkiewicz MA, Bi W, Xiao R, Liu P, Shao Y, Gezdirici A, Gulec EY, Jiang Y, Darilek SA, Hansen AW, Khayat MM, Pehlivan D, Piard J, Muzny DM, Hanchard N, Belmont JW, Van Maldergem L, Gibbs RA, Eldomery MK, Akdemir ZC, Adesina AM, Chen S, Lee YC, Lee B, Lupski JR, Eng CM, Xia F, Yang Y, Graham BH, Moretti P. Phenotypic expansion in DDX3X - a common cause of intellectual disability in females. Ann Clin Transl Neurol 2018; 5:1277-1285. [PMID: 30349862 PMCID: PMC6186933 DOI: 10.1002/acn3.622] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 06/21/2018] [Accepted: 06/24/2018] [Indexed: 12/14/2022] Open
Abstract
De novo variants in DDX3X account for 1–3% of unexplained intellectual disability (ID) cases and are amongst the most common causes of ID especially in females. Forty‐seven patients (44 females, 3 males) have been described. We identified 31 additional individuals carrying 29 unique DDX3X variants, including 30 postnatal individuals with complex clinical presentations of developmental delay or ID, and one fetus with abnormal ultrasound findings. Rare or novel phenotypes observed include respiratory problems, congenital heart disease, skeletal muscle mitochondrial DNA depletion, and late‐onset neurologic decline. Our findings expand the spectrum of DNA variants and phenotypes associated with DDX3X disorders.
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Affiliation(s)
- Xia Wang
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Baylor Genetics Houston Texas
| | - Jennifer E Posey
- Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | - Jill A Rosenfeld
- Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | - Carlos A Bacino
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Texas Children's Hospital Houston Texas
| | - Fernando Scaglia
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Texas Children's Hospital Houston Texas
| | | | | | - Scott E Hickey
- Clinical Pediatrics The Ohio State University Columbus Ohio.,Division of Molecular & Human Genetics Nationwide Children's Hospital Columbus Ohio
| | - Theresa M Mosher
- Division of Molecular & Human Genetics Nationwide Children's Hospital Columbus Ohio
| | - Anne Slavotinek
- Department of Pediatrics Division of Genetics University of California San Francisco California
| | | | | | - Magalie S Leduc
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Baylor Genetics Houston Texas
| | | | | | - Magdalena A Walkiewicz
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Baylor Genetics Houston Texas
| | - Weimin Bi
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Baylor Genetics Houston Texas
| | - Rui Xiao
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Baylor Genetics Houston Texas
| | - Pengfei Liu
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Baylor Genetics Houston Texas
| | - Yunru Shao
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Texas Children's Hospital Houston Texas
| | - Alper Gezdirici
- Department of Genetics Kanuni Sultan Suleyman Training and Research Hospital Instanbul Turkey
| | - Elif Y Gulec
- Department of Genetics Kanuni Sultan Suleyman Training and Research Hospital Instanbul Turkey
| | - Yunyun Jiang
- Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | - Sandra A Darilek
- Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | - Adam W Hansen
- Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | - Michael M Khayat
- Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | - Davut Pehlivan
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Section of Neurology Department of Pediatrics Baylor College of Medicine Houston Texas
| | - Juliette Piard
- Centre de Génétique Humaine Université de Franche-Comté Besançon France
| | - Donna M Muzny
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Human Genome Sequencing Center Baylor College of Medicine Houston Texas
| | - Neil Hanchard
- Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | - John W Belmont
- Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | | | - Richard A Gibbs
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Human Genome Sequencing Center Baylor College of Medicine Houston Texas
| | | | - Zeynep C Akdemir
- Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | - Adekunle M Adesina
- Texas Children's Hospital Houston Texas.,Pathology Baylor College of Medicine Houston Texas
| | - Shan Chen
- Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | - Yi-Chien Lee
- Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | | | - Brendan Lee
- Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | - James R Lupski
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Texas Children's Hospital Houston Texas.,Human Genome Sequencing Center Baylor College of Medicine Houston Texas
| | - Christine M Eng
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Baylor Genetics Houston Texas
| | - Fan Xia
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Baylor Genetics Houston Texas
| | - Yaping Yang
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Baylor Genetics Houston Texas
| | - Brett H Graham
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Texas Children's Hospital Houston Texas.,Medical and Molecular Genetics Indiana University School of Medicine Indianapolis Indiana
| | - Paolo Moretti
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Neurology Baylor College of Medicine and Michael E. DeBakey VA Medical Center Houston Texas.,Neurology University of Utah and George E. Wahlen VA Medical Center Salt Lake City Utah
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23
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Shirokikh NE, Preiss T. Translation initiation by cap-dependent ribosome recruitment: Recent insights and open questions. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1473. [PMID: 29624880 DOI: 10.1002/wrna.1473] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 02/02/2018] [Accepted: 02/14/2018] [Indexed: 12/14/2022]
Abstract
Gene expression universally relies on protein synthesis, where ribosomes recognize and decode the messenger RNA template by cycling through translation initiation, elongation, and termination phases. All aspects of translation have been studied for decades using the tools of biochemistry and molecular biology available at the time. Here, we focus on the mechanism of translation initiation in eukaryotes, which is remarkably more complex than prokaryotic initiation and is the target of multiple types of regulatory intervention. The "consensus" model, featuring cap-dependent ribosome entry and scanning of mRNA leader sequences, represents the predominantly utilized initiation pathway across eukaryotes, although several variations of the model and alternative initiation mechanisms are also known. Recent advances in structural biology techniques have enabled remarkable molecular-level insights into the functional states of eukaryotic ribosomes, including a range of ribosomal complexes with different combinations of translation initiation factors that are thought to represent bona fide intermediates of the initiation process. Similarly, high-throughput sequencing-based ribosome profiling or "footprinting" approaches have allowed much progress in understanding the elongation phase of translation, and variants of them are beginning to reveal the remaining mysteries of initiation, as well as aspects of translation termination and ribosomal recycling. A current view on the eukaryotic initiation mechanism is presented here with an emphasis on how recent structural and footprinting results underpin axioms of the consensus model. Along the way, we further outline some contested mechanistic issues and major open questions still to be addressed. This article is categorized under: Translation > Translation Mechanisms Translation > Translation Regulation RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Nikolay E Shirokikh
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia
| | - Thomas Preiss
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia
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24
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Li MY, Liu JQ, Chen DP, Li ZY, Qi B, Yin WJ, He L. p68 prompts the epithelial-mesenchymal transition in cervical cancer cells by transcriptionally activating the TGF-β1 signaling pathway. Oncol Lett 2017; 15:2111-2116. [PMID: 29434913 PMCID: PMC5777103 DOI: 10.3892/ol.2017.7552] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 09/28/2017] [Indexed: 11/16/2022] Open
Abstract
Overexpression of p68 has been reported in various types of cancer. However, little study has been conducted on the expression and role of p68 in cervical cancer. Therefore, the present study focuses on the role of p68 in cervical cancer cells, which may elucidate its potential mechanism of cervical cancer progression and shed light on the precision medical treatment of cervical cancer. Firstly, the expression of p68 was analyzed using reverse transcription-quantitative polymerase chain reaction and western blot analysis. The changes to cell morphology were observed using an inverted microscope (XDS-500D; Shanghai Caikon Optical Instrument Co., Ltd., Shanghai, China). Cell migration was determined using an in vitro scratch assay. The present study demonstrated that the mRNA and protein levels of p68 were significantly enhanced in cervical cancer CaSki, HeLa [human papillomavirus (HPV)-18-positive], SiHa (HPV-16-positive) and C-33A (HPV-negative) cell lines compared with the human keratinocyte HaCaT cell line. Overexpression of p68 induced an elongated and spindle-shaped morphology in CaSki cells. Upregulation of p68 increased the expression of α-smooth muscle actin, vimentin and fibronectin however, epithelial marker E-cadherin was significantly decreased. Furthermore, the in vitro scratch assay demonstrated that overexpression of p68 markedly enhanced CaSki cell migration capacity at 24 and 48 h. Knockdown of p68 partially reversed transforming growth factor-β1 (TGF-β1)-induced changes in epithelial-mesenchymal transition (EMT) markers and cell morphological changes. In summary, the present study demonstrated that p68 transcriptionally activated the expression of TGF-β1, thereby prompting EMT in cervical cancer cells.
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Affiliation(s)
- Ming-Yi Li
- The 5th Ward of The Radiotherapy Department, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, Guangdong 510095, P.R. China
| | - Jin-Quan Liu
- The 5th Ward of The Radiotherapy Department, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, Guangdong 510095, P.R. China
| | - Dong-Ping Chen
- The 5th Ward of The Radiotherapy Department, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, Guangdong 510095, P.R. China
| | - Zhou-Yu Li
- The 5th Ward of The Radiotherapy Department, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, Guangdong 510095, P.R. China
| | - Bin Qi
- The 5th Ward of The Radiotherapy Department, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, Guangdong 510095, P.R. China
| | - Wen-Jing Yin
- The 5th Ward of The Radiotherapy Department, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, Guangdong 510095, P.R. China
| | - Lu He
- The 5th Ward of The Radiotherapy Department, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, Guangdong 510095, P.R. China
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25
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von Kopylow K, Spiess AN. Human spermatogonial markers. Stem Cell Res 2017; 25:300-309. [PMID: 29239848 DOI: 10.1016/j.scr.2017.11.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 11/06/2017] [Accepted: 11/13/2017] [Indexed: 12/22/2022] Open
Abstract
In this review, we provide an up-to-date compilation of published human spermatogonial markers, with focus on the three nuclear subtypes Adark, Apale and B. In addition, we have extended our recently published list of putative spermatogonial markers with protein expression and RNA-sequencing data from the Human Protein Atlas and supported these by literature evidence. Most importantly, we have put substantial effort in acquiring a comprehensive list of new and potentially interesting markers by refiltering the raw data of 15 published germ cell expression datasets (four human, eleven rodent) and subsequent building of intersections to acquire a robust, cross-species set of spermatogonia-enriched or -specific transcripts.
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Affiliation(s)
- Kathrein von Kopylow
- Department of Andrology, University Hospital Hamburg-Eppendorf, Hamburg, Germany.
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26
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Xing Z, Wang S, Tran EJ. Characterization of the mammalian DEAD-box protein DDX5 reveals functional conservation with S. cerevisiae ortholog Dbp2 in transcriptional control and glucose metabolism. RNA (NEW YORK, N.Y.) 2017; 23:1125-1138. [PMID: 28411202 PMCID: PMC5473146 DOI: 10.1261/rna.060335.116] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 04/10/2017] [Indexed: 05/09/2023]
Abstract
DEAD-box proteins are a class of nonprocessive RNA helicases that dynamically modulate the structure of RNA and ribonucleoprotein complexes (RNPs). However, the precise roles of individual members are not well understood. Work from our laboratory revealed that the DEAD-box protein Dbp2 in Saccharomyces cerevisiae is an active RNA helicase in vitro that functions in transcription by promoting mRNP assembly, repressing cryptic transcription initiation, and regulating long noncoding RNA activity. Interestingly, Dbp2 is also linked to glucose sensing and hexose transporter gene expression. DDX5 is the mammalian ortholog of Dbp2 that has been implicated in cancer and metabolic syndrome, suggesting that the role of Dbp2 and DDX5 in glucose metabolic regulation is conserved. Herein, we present a refined biochemical and biological comparison of yeast Dbp2 and human DDX5 enzymes. We find that human DDX5 possesses a 10-fold higher unwinding activity than Dbp2, which is partially due to the presence of a mammalian/avian specific C-terminal extension. Interestingly, ectopic expression of DDX5 rescues the cold sensitivity, cryptic initiation defects, and impaired glucose import in dbp2Δ cells, suggesting functional conservation. Consistently, we show that DDX5 promotes glucose uptake and glycolysis in mouse AML12 hepatocyte cells, suggesting that mammalian DDX5 and S. cerevisiae Dbp2 share conserved roles in cellular metabolism.
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Affiliation(s)
- Zheng Xing
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47906, USA
| | - Siwen Wang
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47906, USA
| | - Elizabeth J Tran
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47906, USA
- Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana 47906, USA
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27
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Yoneyama-Hirozane M, Kondo M, Matsumoto SI, Morikawa-Oki A, Morishita D, Nakanishi A, Kawamoto T, Nakayama M. High-Throughput Screening to Identify Inhibitors of DEAD Box Helicase DDX41. SLAS DISCOVERY 2017; 22:1084-1092. [PMID: 28426938 DOI: 10.1177/2472555217705952] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The human DEAD (Asp-Glu-Ala-Asp) box protein DDX41, a member of the DEXDc helicase family, has nucleic acid-dependent ATPase and RNA and DNA translocase and unwinding activities. DDX41 is affected by somatic mutations in sporadic cases of myeloid neoplasms as well as in a biallelic fashion in 50% of patients with germline DDX41 mutations. The R525H mutation in DDX41 is thought to play important roles in the development of hereditary myelodysplastic syndrome and acute myelocytic leukemia. In this study, human DDX41 and its R525H mutant (R525H) were expressed in Escherichia coli and purified. The ATPase activities of the recombinant DDX41 and R525H proteins were dependent on both ATP and double-stranded DNA (dsDNA), such as poly(dG-dC) and poly(dA-dT). High-throughput screening was performed with a dsDNA-dependent ATPase assay using the human R525H proteins. After hit confirmation and counterscreening, several small-molecule inhibitors were successfully identified. These compounds show DDX41-selective inhibitory activities.
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Affiliation(s)
- Mariko Yoneyama-Hirozane
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
| | - Mitsuyo Kondo
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
| | - Shin-Ichi Matsumoto
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
| | - Akiko Morikawa-Oki
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
| | - Daisuke Morishita
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
| | - Atsushi Nakanishi
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
| | - Tomohiro Kawamoto
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
| | - Masaharu Nakayama
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
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28
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Eldomery MK, Coban-Akdemir Z, Harel T, Rosenfeld JA, Gambin T, Stray-Pedersen A, Küry S, Mercier S, Lessel D, Denecke J, Wiszniewski W, Penney S, Liu P, Bi W, Lalani SR, Schaaf CP, Wangler MF, Bacino CA, Lewis RA, Potocki L, Graham BH, Belmont JW, Scaglia F, Orange JS, Jhangiani SN, Chiang T, Doddapaneni H, Hu J, Muzny DM, Xia F, Beaudet AL, Boerwinkle E, Eng CM, Plon SE, Sutton VR, Gibbs RA, Posey JE, Yang Y, Lupski JR. Lessons learned from additional research analyses of unsolved clinical exome cases. Genome Med 2017; 9:26. [PMID: 28327206 PMCID: PMC5361813 DOI: 10.1186/s13073-017-0412-6] [Citation(s) in RCA: 162] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 02/08/2017] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Given the rarity of most single-gene Mendelian disorders, concerted efforts of data exchange between clinical and scientific communities are critical to optimize molecular diagnosis and novel disease gene discovery. METHODS We designed and implemented protocols for the study of cases for which a plausible molecular diagnosis was not achieved in a clinical genomics diagnostic laboratory (i.e. unsolved clinical exomes). Such cases were recruited to a research laboratory for further analyses, in order to potentially: (1) accelerate novel disease gene discovery; (2) increase the molecular diagnostic yield of whole exome sequencing (WES); and (3) gain insight into the genetic mechanisms of disease. Pilot project data included 74 families, consisting mostly of parent-offspring trios. Analyses performed on a research basis employed both WES from additional family members and complementary bioinformatics approaches and protocols. RESULTS Analysis of all possible modes of Mendelian inheritance, focusing on both single nucleotide variants (SNV) and copy number variant (CNV) alleles, yielded a likely contributory variant in 36% (27/74) of cases. If one includes candidate genes with variants identified within a single family, a potential contributory variant was identified in a total of ~51% (38/74) of cases enrolled in this pilot study. The molecular diagnosis was achieved in 30/63 trios (47.6%). Besides this, the analysis workflow yielded evidence for pathogenic variants in disease-associated genes in 4/6 singleton cases (66.6%), 1/1 multiplex family involving three affected siblings, and 3/4 (75%) quartet families. Both the analytical pipeline and the collaborative efforts between the diagnostic and research laboratories provided insights that allowed recent disease gene discoveries (PURA, TANGO2, EMC1, GNB5, ATAD3A, and MIPEP) and increased the number of novel genes, defined in this study as genes identified in more than one family (DHX30 and EBF3). CONCLUSION An efficient genomics pipeline in which clinical sequencing in a diagnostic laboratory is followed by the detailed reanalysis of unsolved cases in a research environment, supplemented with WES data from additional family members, and subject to adjuvant bioinformatics analyses including relaxed variant filtering parameters in informatics pipelines, can enhance the molecular diagnostic yield and provide mechanistic insights into Mendelian disorders. Implementing these approaches requires collaborative clinical molecular diagnostic and research efforts.
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Affiliation(s)
- Mohammad K. Eldomery
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Present Address: Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, 350 W. 11th Street, Indianapolis, IN 46202 USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Tamar Harel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Institute of Computer Science, Warsaw University of Technology, 00-665 Warsaw, Poland
| | - Asbjørg Stray-Pedersen
- Norwegian National Unit for Newborn Screening, Women and Children’s Division, Oslo University Hospital, 0424 Oslo, Norway
| | - Sébastien Küry
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes, CEDEX 1 France
| | - Sandra Mercier
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes, CEDEX 1 France
- Atlantic Gene Therapies, UMR1089, Nantes, France
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Jonas Denecke
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Wojciech Wiszniewski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Samantha Penney
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Baylor Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Baylor Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Seema R. Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Christian P. Schaaf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030 USA
| | - Michael F. Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Carlos A. Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Richard Alan Lewis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030 USA
| | - Lorraine Potocki
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Brett H. Graham
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - John W. Belmont
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Fernando Scaglia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Jordan S. Orange
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital Center for Human Immuno-Biology, Houston, TX USA
| | - Shalini N. Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Theodore Chiang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Jianhong Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Baylor Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Arthur L. Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Baylor Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Christine M. Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Baylor Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Sharon E. Plon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Cancer Center, Texas Children’s Hospital, Houston, TX 7703 USA
| | - V. Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
- Baylor-Hopkins Center for Mendelian Genomics, Baltimore, MD USA
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Baylor Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030 USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, TX 77030-3498 USA
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The multiple functions of RNA helicases as drivers and regulators of gene expression. Nat Rev Mol Cell Biol 2016; 17:426-38. [PMID: 27251421 DOI: 10.1038/nrm.2016.50] [Citation(s) in RCA: 178] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
RNA helicases comprise the largest family of enzymes involved in the metabolism of mRNAs, the processing and fate of which rely on their packaging into messenger ribonucleoprotein particles (mRNPs). In this Review, we describe how the capacity of some RNA helicases to either remodel or lock the composition of mRNP complexes underlies their pleiotropic functions at different steps of the gene expression process. We illustrate the roles of RNA helicases in coordinating gene expression steps and programmes, and propose that RNA helicases function as molecular drivers and guides of the progression of their mRNA substrates from one RNA-processing factory to another, to a productive mRNA pool that leads to protein synthesis or to unproductive mRNA pools that are stored or degraded.
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Bol GM, Xie M, Raman V. DDX3, a potential target for cancer treatment. Mol Cancer 2015; 14:188. [PMID: 26541825 PMCID: PMC4636063 DOI: 10.1186/s12943-015-0461-7] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 10/22/2015] [Indexed: 12/27/2022] Open
Abstract
RNA helicases are a large family of proteins with a distinct motif, referred to as the DEAD/H (Asp-Glu-Ala-Asp/His). The exact functions of all the human DEAD/H box proteins are unknown. However, it has been consistently demonstrated that these proteins are associated with several aspects of energy-dependent RNA metabolism, including translation, ribosome biogenesis, and pre-mRNA splicing. In addition, DEAD/H box proteins participate in nuclear-cytoplasmic transport and organellar gene expression. A member of this RNA helicase family, DDX3, has been identified in a variety of cellular biogenesis processes, including cell-cycle regulation, cellular differentiation, cell survival, and apoptosis. In cancer, DDX3 expression has been evaluated in patient samples of breast, lung, colon, oral, and liver cancer. Both tumor suppressor and oncogenic functions have been attributed to DDX3 and are discussed in this review. In general, there is concordance with in vitro evidence to support the hypothesis that DDX3 is associated with an aggressive phenotype in human malignancies. Interestingly, very few cancer types harbor mutations in DDX3, which result in altered protein function rather than a loss of function. Efficacy of drugs to curtail cancer growth is hindered by adaptive responses that promote drug resistance, eventually leading to treatment failure. One way to circumvent development of resistant disease is to develop novel drugs that target over-expressed proteins involved in this adaptive response. Moreover, if the target gene is developmentally regulated, there is less of a possibility to abruptly accumulate mutations leading to drug resistance. In this regard, DDX3 could be a druggable target for cancer treatment. We present an overview of DDX3 biology and the currently available DDX3 inhibitors for cancer treatment.
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Affiliation(s)
- Guus Martinus Bol
- Department of Pathology, University Medical Center Utrecht Cancer Center, 3508 GA, Utrecht, The Netherlands.,Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, 720 Rutland Ave, Traylor 340, Baltimore, MD, 21205, USA
| | - Min Xie
- Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, 720 Rutland Ave, Traylor 340, Baltimore, MD, 21205, USA
| | - Venu Raman
- Department of Pathology, University Medical Center Utrecht Cancer Center, 3508 GA, Utrecht, The Netherlands. .,Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, 720 Rutland Ave, Traylor 340, Baltimore, MD, 21205, USA. .,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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Sun J, Wen X, Jin F, Li Y, Hu J, Sun Y. Bioinformatics analyses of differentially expressed genes associated with bisphosphonate-related osteonecrosis of the jaw in patients with multiple myeloma. Onco Targets Ther 2015; 8:2681-8. [PMID: 26445550 PMCID: PMC4590669 DOI: 10.2147/ott.s88463] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
PURPOSE This study aimed to explore the molecular mechanisms associated with bisphosphonate (BP)-related osteonecrosis of the jaw (ONJ) in patients with multiple myeloma (MM). METHODS The gene expression profile GSE7116 was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) from eleven patients with ONJ resulting from MM treated with BPs (ONJBPs) and ten MM patients without ONJ treated with BPs (MMBPs) were analyzed. Gene ontology (GO) and pathway enrichment analyses of DEGs were performed, followed by functional annotation and protein-protein interaction network construction. Finally, sub-network modules were constructed and analyzed. RESULTS A total of 166 up- and 473 down-regulated DEGs were identified. The up-regulated DEGs were enriched in pathways related to cancer, and the down-regulated DEGs were enriched in pathways related to the immune system. Moreover, the GO terms enriched by the up-regulated DEGs were associated with misfolded proteins, and the down-regulated DEGs were associated with immune responses. After functional annotation, 16 transcription factors were identified, including X-box binding protein 1 (XBP1). In protein-protein interaction network analysis, tumor necrosis factor (TNF) and interleukin 1, beta (IL1B) had higher connectivity degrees. Among the constructed sub-network modules, module 1 was the best one, and DEAD (Asp-Glu-Ala-Asp) box helicase 5 (DDX5) was a hub gene. The DEGs in module 1 were mainly enriched in GO terms related to RNA splicing. CONCLUSION DEGs of ONJ were mainly enriched in pathways related to the immune system and RNA splicing. DEGs such as TNF, ILB1, DDX5, and XBP1 may be the potential targets of ONJ treatment.
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Affiliation(s)
- Jingnan Sun
- Stem Cell and Cancer Center, First Affiliated Hospital, Jilin University, Changchun, Jilin, People's Republic of China
| | - Xue Wen
- Stem Cell and Cancer Center, First Affiliated Hospital, Jilin University, Changchun, Jilin, People's Republic of China
| | - Fengyan Jin
- Stem Cell and Cancer Center, First Affiliated Hospital, Jilin University, Changchun, Jilin, People's Republic of China
| | - Yuying Li
- Stem Cell and Cancer Center, First Affiliated Hospital, Jilin University, Changchun, Jilin, People's Republic of China
| | - Jifan Hu
- Stanford University Medical School, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA
| | - Yunpeng Sun
- Cardiovascular Surgery Department, First Affiliated Hospital, Jilin University, Changchun, Jilin, People's Republic of China
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ATP Binding Cassette Transporter Mediates Both Heme and Pesticide Detoxification in Tick Midgut Cells. PLoS One 2015; 10:e0134779. [PMID: 26258982 PMCID: PMC4530934 DOI: 10.1371/journal.pone.0134779] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 07/14/2015] [Indexed: 11/23/2022] Open
Abstract
In ticks, the digestion of blood occurs intracellularly and proteolytic digestion of hemoglobin takes place in a dedicated type of lysosome, the digest vesicle, followed by transfer of the heme moiety of hemoglobin to a specialized organelle that accumulates large heme aggregates, called hemosomes. In the present work, we studied the uptake of fluorescent metalloporphyrins, used as heme analogs, and amitraz, one of the most regularly used acaricides to control cattle tick infestations, by Rhipicephalus (Boophilus) microplus midgut cells. Both compounds were taken up by midgut cells in vitro and accumulated inside the hemosomes. Transport of both molecules was sensitive to cyclosporine A (CsA), a well-known inhibitor of ATP binding cassette (ABC) transporters. Rhodamine 123, a fluorescent probe that is also a recognized ABC substrate, was similarly directed to the hemosome in a CsA-sensitive manner. Using an antibody against conserved domain of PgP-1-type ABC transporter, we were able to immunolocalize PgP-1 in the digest vesicle membranes. Comparison between two R. microplus strains that were resistant and susceptible to amitraz revealed that the resistant strain detoxified both amitraz and Sn-Pp IX more efficiently than the susceptible strain, a process that was also sensitive to CsA. A transcript containing an ABC transporter signature exhibited 2.5-fold increased expression in the amitraz-resistant strain when compared with the susceptible strain. RNAi-induced down-regulation of this ABC transporter led to the accumulation of metalloporphyrin in the digestive vacuole, interrupting heme traffic to the hemosome. This evidence further confirms that this transcript codes for a heme transporter. This is the first report of heme transport in a blood-feeding organism. While the primary physiological function of the hemosome is to detoxify heme and attenuate its toxicity, we suggest that the use of this acaricide detoxification pathway by ticks may represent a new molecular mechanism of resistance to pesticides.
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Snijders Blok L, Madsen E, Juusola J, Gilissen C, Baralle D, Reijnders M, Venselaar H, Helsmoortel C, Cho M, Hoischen A, Vissers LE, Koemans T, Wissink-Lindhout W, Eichler E, Romano C, Van Esch H, Stumpel C, Vreeburg M, Smeets E, Oberndorff K, van Bon B, Shaw M, Gecz J, Haan E, Bienek M, Jensen C, Loeys B, Van Dijck A, Innes A, Racher H, Vermeer S, Di Donato N, Rump A, Tatton-Brown K, Parker M, Henderson A, Lynch S, Fryer A, Ross A, Vasudevan P, Kini U, Newbury-Ecob R, Chandler K, Male A, Dijkstra S, Schieving J, Giltay J, van Gassen K, Schuurs-Hoeijmakers J, Tan P, Pediaditakis I, Haas S, Retterer K, Reed P, Monaghan K, Haverfield E, Natowicz M, Myers A, Kruer M, Stein Q, Strauss K, Brigatti K, Keating K, Burton B, Kim K, Charrow J, Norman J, Foster-Barber A, Kline A, Kimball A, Zackai E, Harr M, Fox J, McLaughlin J, Lindstrom K, Haude K, van Roozendaal K, Brunner H, Chung W, Kooy R, Pfundt R, Kalscheuer V, Mehta S, Katsanis N, Kleefstra T, Kleefstra T. Mutations in DDX3X Are a Common Cause of Unexplained Intellectual Disability with Gender-Specific Effects on Wnt Signaling. Am J Hum Genet 2015; 97:343-52. [PMID: 26235985 DOI: 10.1016/j.ajhg.2015.07.004] [Citation(s) in RCA: 185] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 07/13/2015] [Indexed: 12/22/2022] Open
Abstract
Intellectual disability (ID) affects approximately 1%-3% of humans with a gender bias toward males. Previous studies have identified mutations in more than 100 genes on the X chromosome in males with ID, but there is less evidence for de novo mutations on the X chromosome causing ID in females. In this study we present 35 unique deleterious de novo mutations in DDX3X identified by whole exome sequencing in 38 females with ID and various other features including hypotonia, movement disorders, behavior problems, corpus callosum hypoplasia, and epilepsy. Based on our findings, mutations in DDX3X are one of the more common causes of ID, accounting for 1%-3% of unexplained ID in females. Although no de novo DDX3X mutations were identified in males, we present three families with segregating missense mutations in DDX3X, suggestive of an X-linked recessive inheritance pattern. In these families, all males with the DDX3X variant had ID, whereas carrier females were unaffected. To explore the pathogenic mechanisms accounting for the differences in disease transmission and phenotype between affected females and affected males with DDX3X missense variants, we used canonical Wnt defects in zebrafish as a surrogate measure of DDX3X function in vivo. We demonstrate a consistent loss-of-function effect of all tested de novo mutations on the Wnt pathway, and we further show a differential effect by gender. The differential activity possibly reflects a dose-dependent effect of DDX3X expression in the context of functional mosaic females versus one-copy males, which reflects the complex biological nature of DDX3X mutations.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Tjitske Kleefstra
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands.
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Proteomic Analysis of Immature Fraxinus mandshurica Cotyledon Tissues during Somatic Embryogenesis: Effects of Explant Browning on Somatic Embryogenesis. Int J Mol Sci 2015; 16:13692-713. [PMID: 26084048 PMCID: PMC4490518 DOI: 10.3390/ijms160613692] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 06/10/2015] [Indexed: 11/30/2022] Open
Abstract
Manchurian ash (Fraxinus mandshurica Rupr.) is a valuable hardwood species in Northeast China. In cultures of F. mandshurica, somatic embryos were produced mainly on browned explants. Therefore, we studied the mechanism of explant browning and its relationship with somatic embryogenesis (SE). We used explants derived from F. mandshurica immature zygotic embryo cotyledons as materials. Proteins were extracted from browned embryogenic explants, browned non-embryogenic explants, and non-brown explants, and then separated by 2-dimensional electrophoresis. Differentially and specifically expressed proteins were analyzed by mass spectrometry to identify proteins involved in the browning of explants and SE. Some stress response and defense proteins such as chitinases, peroxidases, aspartic proteinases, and an osmotin-like protein played important roles during SE of F. mandshurica. Our results indicated that explant browning might not be caused by the accumulation and oxidation of polyphenols only, but also by some stress-related processes, which were involved in programmed cell death (PCD), and then induced SE.
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Eggers S, DeBoer KD, van den Bergen J, Gordon L, White SJ, Jamsai D, McLachlan RI, Sinclair AH, O'Bryan MK. Copy number variation associated with meiotic arrest in idiopathic male infertility. Fertil Steril 2015; 103:214-9. [DOI: 10.1016/j.fertnstert.2014.09.030] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Revised: 09/23/2014] [Accepted: 09/23/2014] [Indexed: 12/15/2022]
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Guturi KKN, Sarkar M, Bhowmik A, Das N, Ghosh MK. DEAD-box protein p68 is regulated by β-catenin/transcription factor 4 to maintain a positive feedback loop in control of breast cancer progression. Breast Cancer Res 2014; 16:496. [PMID: 25499975 PMCID: PMC4308923 DOI: 10.1186/s13058-014-0496-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 12/04/2014] [Indexed: 01/28/2023] Open
Abstract
INTRODUCTION Nuclear accumulation of β-catenin is important for cancer development and it is found to overlap with p68 (DDX5) immunoreactivity in most breast cancers, as indicated by both clinical investigations and studies in cell lines. In this study, we aim to investigate the regulation of p68 gene expression through β-catenin/transcription factor 4 (TCF4) signaling in breast cancer. METHODS Formalin-fixed paraffin-embedded sections derived from normal human breast and breast cancer samples were used for immunohistochemical analysis. Protein and mRNA expressions were determined by immunoblotting and quantitative RT-PCR respectively. Promoter activity of p68 was checked using luciferase assay. Occupancy of several factors on the p68 promoter was evaluated using chromatin immunoprecipitation. Finally, a syngeneic mouse model of breast cancer was used to assess physiological significance. RESULTS We demonstrated that β-catenin can directly induce transcription of p68 promoter or indirectly through regulation of c-Myc in both human and mouse breast cancer cells. Moreover, by chromatin immunoprecipitation assay, we have found that both β-catenin and TCF4 occupy the endogenous p68 promoter, which is further enhanced by Wnt signaling. Furthermore, we have also established a positive feedback regulation for the expression of TCF4 by p68. To the best of our knowledge, this is the first report on β-catenin/TCF4-mediated p68 gene regulation, which plays an important role in epithelial to mesenchymal transition, as shown in vitro in breast cancer cell lines and in vivo in an animal breast tumour model. CONCLUSIONS Our findings indicate that Wnt/β-catenin signaling plays an important role in breast cancer progression through p68 upregulation.
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Affiliation(s)
- Kiran Kumar Naidu Guturi
- Signal Transduction in Cancer and Stem Cells Laboratory, Cancer Biology and Inflammatory Disorder Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology (CSIR-IICB), 4 Raja S C Mullick Road, Jadavpur, Kolkata, 700032, India.
| | - Moumita Sarkar
- Signal Transduction in Cancer and Stem Cells Laboratory, Cancer Biology and Inflammatory Disorder Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology (CSIR-IICB), 4 Raja S C Mullick Road, Jadavpur, Kolkata, 700032, India.
| | - Arijit Bhowmik
- Signal Transduction in Cancer and Stem Cells Laboratory, Cancer Biology and Inflammatory Disorder Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology (CSIR-IICB), 4 Raja S C Mullick Road, Jadavpur, Kolkata, 700032, India.
| | - Nilanjana Das
- Signal Transduction in Cancer and Stem Cells Laboratory, Cancer Biology and Inflammatory Disorder Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology (CSIR-IICB), 4 Raja S C Mullick Road, Jadavpur, Kolkata, 700032, India.
| | - Mrinal Kanti Ghosh
- Signal Transduction in Cancer and Stem Cells Laboratory, Cancer Biology and Inflammatory Disorder Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology (CSIR-IICB), 4 Raja S C Mullick Road, Jadavpur, Kolkata, 700032, India.
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Umate P, Tuteja N, Tuteja R. Genome-wide comprehensive analysis of human helicases. Commun Integr Biol 2014. [DOI: 10.4161/cib.13844] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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Nozaki K, Kagamu H, Shoji S, Igarashi N, Ohtsubo A, Okajima M, Miura S, Watanabe S, Yoshizawa H, Narita I. DDX3X induces primary EGFR-TKI resistance based on intratumor heterogeneity in lung cancer cells harboring EGFR-activating mutations. PLoS One 2014; 9:e111019. [PMID: 25343452 PMCID: PMC4208809 DOI: 10.1371/journal.pone.0111019] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 09/26/2014] [Indexed: 11/19/2022] Open
Abstract
The specific mechanisms how lung cancer cells harboring epidermal growth factor receptor (EGFR) activating mutations can survive treatment with EGFR-tyrosine kinase inhibitors (TKIs) until they eventually acquire treatment-resistance genetic mutations are unclear. The phenotypic diversity of cancer cells caused by genetic or epigenetic alterations (intratumor heterogeneity) confers treatment failure and may foster tumor evolution through Darwinian selection. Recently, we found DDX3X as the protein that was preferentially expressed in murine melanoma with cancer stem cell (CSC)-like phenotypes by proteome analysis. In this study, we transfected PC9, human lung cancer cells harboring EGFR exon19 deletion, with cDNA encoding DDX3X and found that DDX3X, an ATP-dependent RNA helicase, induced CSC-like phenotypes and the epithelial-mesenchymal transition (EMT) accompanied with loss of sensitivity to EGFR-TKI. DDX3X expression was associated with upregulation of Sox2 and increase of cancer cells exhibiting CSC-like phenotypes, such as anchorage-independent proliferation, strong expression of CD44, and aldehyde dehydrogenase (ALDH). The EMT with switching from E-cadherin to N-cadherin was also facilitated by DDX3X. Either ligand-independent or ligand-induced EGFR phosphorylation was inhibited in lung cancer cells that strongly expressed DDX3X. Lack of EGFR signal addiction resulted in resistance to EGFR-TKI. Moreover, we found a small nonadherent subpopulation that strongly expressed DDX3X accompanied by the same stem cell-like properties and the EMT in parental PC9 cells. The unique subpopulation lacked EGFR signaling and was highly resistant to EGFR-TKI. In conclusion, our data indicate that DDX3X may play a critical role for inducing phenotypic diversity, and that treatment targeting DDX3X may overcome primary resistance to EGFR-TKI resulting from intratumor heterogeneity.
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Affiliation(s)
- Koichiro Nozaki
- Division of Respiratory Medicine, Department of Homeostatic Regulation and Development, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Hiroshi Kagamu
- Division of Respiratory Medicine, Department of Homeostatic Regulation and Development, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
- * E-mail:
| | - Satoshi Shoji
- Division of Respiratory Medicine, Department of Homeostatic Regulation and Development, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Natsue Igarashi
- Division of Respiratory Medicine, Department of Homeostatic Regulation and Development, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Aya Ohtsubo
- Division of Respiratory Medicine, Department of Homeostatic Regulation and Development, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Masaaki Okajima
- Division of Respiratory Medicine, Department of Homeostatic Regulation and Development, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Satoru Miura
- Division of Respiratory Medicine, Department of Homeostatic Regulation and Development, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Satoshi Watanabe
- Bioscience Medical Research Center, Niigata University Medical and Dental Hospital, Niigata, Japan
| | - Hirohisa Yoshizawa
- Bioscience Medical Research Center, Niigata University Medical and Dental Hospital, Niigata, Japan
| | - Ichiei Narita
- Division of Respiratory Medicine, Department of Homeostatic Regulation and Development, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
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Youn JH, Hayashida K, Koizumi N, Ohnishi M, Sugimoto C. Comparative genomic analysis of eight Leptospira strains from Japan and the Philippines revealing the existence of four putative novel genomic islands/islets in L. interrogans serovar Lai strain 56601. Comp Immunol Microbiol Infect Dis 2014; 37:289-97. [PMID: 25449997 DOI: 10.1016/j.cimid.2014.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 07/22/2014] [Accepted: 09/25/2014] [Indexed: 11/15/2022]
Abstract
Leptospirosis is one of the most widespread zoonotic diseases worldwide and can be considered an emerging health problem to both human and animal. Despite the importance of the disease, complete genome sequences are currently available for only three Leptospira interrogans strains: 56601, Fiocruz L1-130, and IPAV. Therefore, intra- and inter-species comparative genomic analyses of Leptospira are limited. Here, to advance current knowledge of the genomic differences within Leptospira species, next-generation sequencing technology was used to examine the genomes of eight L. interrogans strains belonging to six different serogroups isolated from humans and dogs in Japan and the Philippines. The genomic sequences were mapped to that of the reference strain, L. interrogans serovar Lai strain 56601. The results revealed the presence of four novel genomic islands/islets (GIs) in strain 56601. This study provides a deeper insight into the molecular basis and evolutionary perspective of the virulence of leptospires.
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Affiliation(s)
- Jung-Ho Youn
- Division of Collaboration and Education, Research Center for Zoonosis Control, Hokkaido University, Kita-20, Nishi-10, Kita-ku, Sapporo 001-0020, Hokkaido, Japan.
| | - Kyoko Hayashida
- National Research Center for Protozoan Diseases, Obihiro University, Nishi-2-13, Inada-cho, Obihiro 080-8555, Hokkaido, Japan
| | - Nobuo Koizumi
- Department of Bacteriology, National Institute of Infectious Disease, 1-23-1 Toyama, Shinju-ku 162-8640, Tokyo, Japan
| | - Makoto Ohnishi
- Department of Bacteriology, National Institute of Infectious Disease, 1-23-1 Toyama, Shinju-ku 162-8640, Tokyo, Japan
| | - Chihiro Sugimoto
- Division of Collaboration and Education, Research Center for Zoonosis Control, Hokkaido University, Kita-20, Nishi-10, Kita-ku, Sapporo 001-0020, Hokkaido, Japan.
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Snijders Blok C, Corsten-Janssen N, FitzPatrick DR, Romano C, Fichera M, Vitello GA, Willemsen MH, Schoots J, Pfundt R, van Ravenswaaij-Arts CM, Hoefsloot L, Kleefstra T. Definition of 5q11.2 microdeletion syndrome reveals overlap with CHARGE syndrome and 22q11 deletion syndrome phenotypes. Am J Med Genet A 2014; 164A:2843-8. [DOI: 10.1002/ajmg.a.36680] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 06/12/2014] [Indexed: 11/10/2022]
Affiliation(s)
| | - Nicole Corsten-Janssen
- Department of Genetics; University of Groningen, University Medical Center Groningen; Groningen The Netherlands
| | - David R. FitzPatrick
- MRC Human Genetics Unit, MRC IGMM; University of Edinburgh; Edinburgh United Kingdom
| | - Corrado Romano
- I.R.C.C.S. Associazione Oasi Maria Santissima; Troina Italy
| | - Marco Fichera
- I.R.C.C.S. Associazione Oasi Maria Santissima; Troina Italy
- Medical Genetics; University of Catania; Catania Italy
| | | | - Marjolein H. Willemsen
- Department of Human Genetics; Radboud University Medical Center; Nijmegen The Netherlands
| | - Jeroen Schoots
- Department of Human Genetics; Radboud University Medical Center; Nijmegen The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics; Radboud University Medical Center; Nijmegen The Netherlands
| | | | - Lies Hoefsloot
- Clinical Genetics, Erasmus MC; University Medical Center Rotterdam; Rotterdam The Netherlands
| | - Tjitske Kleefstra
- Department of Human Genetics; Radboud University Medical Center; Nijmegen The Netherlands
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41
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Proteomic analysis of metacyclogenesis in Leishmania infantum wild-type and PTR1 null mutant. EUPA OPEN PROTEOMICS 2014. [DOI: 10.1016/j.euprot.2014.07.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Gokulakrishnan P, Kumar RR, Sharma BD, Mendiratta SK, Malav O, Sharma D. Determination of sex origin of meat and meat products on the DNA basis: a review. Crit Rev Food Sci Nutr 2014; 55:1303-14. [PMID: 24915321 DOI: 10.1080/10408398.2012.690095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Sex determination of domestic animal's meat is of potential value in meat authentication and quality control studies. Methods aiming at determining the sex origin of meat may be based either on the analysis of hormone or on the analysis of nucleic acids. At the present time, sex determination of meat and meat products based on hormone analysis employ gas chromatography-mass spectrometry (GC-MS), high-performance liquid chromatography-mass spectrometry/mass spectrometry (HPLC-MS/MS), and enzyme-linked immunosorbent assay (ELISA). Most of the hormone-based methods proved to be highly specific and sensitive but were not performed on a regular basis for meat sexing due to the technical limitations or the expensive equipments required. On the other hand, the most common methodology to determine the sex of meat is unquestionably traditional polymerase chain reaction (PCR) that involves gel electrophoresis of DNA amplicons. This review is intended to provide an overview of the DNA-based methods for sex determination of meat and meat products.
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Affiliation(s)
- Palanisamy Gokulakrishnan
- a Division of Livestock Products Technology , Indian Veterinary Research Institute , Izatnagar, Bareilly , Uttar Pradesh , India
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43
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Identification of sexually dimorphic genes in the neonatal mouse cortex and hippocampus. Brain Res 2014; 1562:23-38. [PMID: 24661915 DOI: 10.1016/j.brainres.2014.03.017] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 03/08/2014] [Accepted: 03/15/2014] [Indexed: 01/01/2023]
Abstract
The cerebral cortex and hippocampus are important for the control of cognitive functions and social behaviors, many of which are sexually dimorphic and tightly regulated by gonadal steroid hormones via activation of their respective nuclear receptors. As different levels of sex steroid hormones are present between the sexes during early development and their receptors act as transcription factors to regulate gene expression, we hypothesize that sexually dimorphic gene expression in the developing mouse cortex and hippocampus might result in sex differences in brain structures and neural circuits governing distinct behaviors between the sexes as adults. To test our hypothesis, we used gene expression microarrays to identify 90 candidate genes differentially expressed in the neonatal cortex/hippocampus between male and female mice, including 55 male-biased and 35 female-biased genes. Among these genes, sexually dimorphic expression of eight sex chromosome genes was confirmed by reverse transcription with quantitative PCR (RT-qPCR), including three located on the X chromosome (Xist, Eif2s3x, and Kdm6a), three on the Y chromosome (Ddx3y, Eif2s3y, and Kdm5d), and two in the pseudoautosomal region of the X and Y chromosomes (Erdr1 and Mid1). In addition, five autosomal genes (Cd151, Dab2, Klk8, Meg3, and Prkdc) were also validated for their sexually dimorphic expression in the neonatal mouse cortex/hippocampus. Gene Ontology annotation analysis suggests that many of these sexually dimorphic genes are involved in histone modifications, cell proliferation/death, androgen/estrogen signaling pathways, and synaptic organization, and these biological processes have been implicated in differential neural development, cognitive function, and neurological diseases between the sexes.
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Affiliation(s)
- Shaochun Yuan
- State Key Laboratory of Biocontrol, National Engineering Center of South China Sea for Marine Biotechnology, Department of Biochemistry, College of Life Sciences, Sun Yat-sen (Zhongshan) University, Guangzhou 510275, People's Republic of China; , , , ,
| | - Xin Tao
- State Key Laboratory of Biocontrol, National Engineering Center of South China Sea for Marine Biotechnology, Department of Biochemistry, College of Life Sciences, Sun Yat-sen (Zhongshan) University, Guangzhou 510275, People's Republic of China; , , , ,
| | - Shengfeng Huang
- State Key Laboratory of Biocontrol, National Engineering Center of South China Sea for Marine Biotechnology, Department of Biochemistry, College of Life Sciences, Sun Yat-sen (Zhongshan) University, Guangzhou 510275, People's Republic of China; , , , ,
| | - Shangwu Chen
- State Key Laboratory of Biocontrol, National Engineering Center of South China Sea for Marine Biotechnology, Department of Biochemistry, College of Life Sciences, Sun Yat-sen (Zhongshan) University, Guangzhou 510275, People's Republic of China; , , , ,
| | - Anlong Xu
- State Key Laboratory of Biocontrol, National Engineering Center of South China Sea for Marine Biotechnology, Department of Biochemistry, College of Life Sciences, Sun Yat-sen (Zhongshan) University, Guangzhou 510275, People's Republic of China; , , , ,
- Center of Scientific Research, Beijing University of Chinese Medicine, Beijing 100029, People’s Republic of China
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45
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Evolutionary conservation and expression of human RNA-binding proteins and their role in human genetic disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 825:1-55. [PMID: 25201102 DOI: 10.1007/978-1-4939-1221-6_1] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
RNA-binding proteins (RBPs) are effectors and regulators of posttranscriptional gene regulation (PTGR). RBPs regulate stability, maturation, and turnover of all RNAs, often binding thousands of targets at many sites. The importance of RBPs is underscored by their dysregulation or mutations causing a variety of developmental and neurological diseases. This chapter globally discusses human RBPs and provides a brief introduction to their identification and RNA targets. We review RBPs based on common structural RNA-binding domains, study their evolutionary conservation and expression, and summarize disease associations of different RBP classes.
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The variable N-terminal region of DDX5 contains structural elements and auto-inhibits its interaction with NS5B of hepatitis C virus. Biochem J 2012; 446:37-46. [PMID: 22640416 DOI: 10.1042/bj20120001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
RNA helicases of the DEAD (Asp-Glu-Ala-Asp)-box family of proteins are involved in many aspects of RNA metabolism from transcription to RNA decay, but most of them have also been shown to be multifunctional. The DEAD-box helicase DDX5 of host cells has been shown to interact with the RNA-dependent RNA polymerase (NS5B) of HCV (hepatitis C virus). In the present study, we report the presence of two independent NS5B-binding sites in DDX5, one located at the N-terminus and another at the C-terminus. The N-terminal fragment of DDX5, which consists of the first 305 amino acids and shall be referred as DDX5-N, was expressed and crystallized. The crystal structure shows that domain 1 (residues 79-303) of DDX5 contains the typical features found in the structures of other DEAD-box helicases. DDX5-N also contains the highly variable NTR (N-terminal region) of unknown function and the crystal structure reveals structural elements in part of the NTR, namely residues 52-78. This region forms an extensive loop and an α-helix. From co-immunoprecipitation experiments, the NTR of DDX5-N was observed to auto-inhibit its interaction with NS5B. Interestingly, the α-helix in NTR is essential for this auto-inhibition and seems to mediate the interaction between the highly flexible 1-51 residues in NTR and the NS5B-binding site in DDX5-N. Furthermore, NMR investigations reveal that there is a direct interaction between DDX5 and NS5B in vitro.
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47
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The presence of the Y-chromosome, not the absence of the second X-chromosome, alters the mRNA levels stored in the fully grown XY mouse oocyte. PLoS One 2012; 7:e40481. [PMID: 22792347 PMCID: PMC3391287 DOI: 10.1371/journal.pone.0040481] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 06/08/2012] [Indexed: 12/23/2022] Open
Abstract
The oocytes of B6.YTIR sex-reversed female mouse mature in culture but fail to develop after fertilization because of their cytoplasmic defects. To identify the defective components, we compared the gene expression profiles between the fully-grown oocytes of B6.YTIR (XY) females and those of their XX littermates by cDNA microarray. 173 genes were found to be higher and 485 genes were lower in XY oocytes than in XX oocytes by at least 2-fold. We compared the transcript levels of selected genes by RT-PCR in XY and XX oocytes, as well as in XO oocytes missing paternal X-chromosomes. All genes tested showed comparable transcript levels between XX and XO oocytes, indicating that mRNA accumulation is well adjusted in XO oocytes. By contrast, in addition to Y-encoded genes, many genes showed significantly different transcript levels in XY oocytes. We speculate that the presence of the Y-chromosome, rather than the absence of the second X-chromosome, caused dramatic changes in the gene expression profile in the XY fully-grown oocyte.
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48
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Gokulakrishnan P, Kumar RR, Sharma BD, Mendiratta SK, Sharma D. Sex Determination of Cattle Meat by Polymerase Chain Reaction Amplification of the DEAD Box Protein (DDX3X/DDX3Y) Gene. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2012; 25:733-7. [PMID: 25049620 PMCID: PMC4093110 DOI: 10.5713/ajas.2012.12003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2012] [Revised: 03/17/2012] [Accepted: 02/21/2012] [Indexed: 11/27/2022]
Abstract
Determination of sex origin of cattle meat by fast and reliable molecular methods is an important measure to ensure correct allocation of export refunds particularly in European countries and also female cattle (cow) slaughter is legally banned in India because of religious beliefs. Based on the DEAD box protein gene located on the X and Y chromosomes, 2 pair of primers were designed and the system of PCR was optimized. Upon PCR amplification, male tissue showed 2 bands, while female tissue resulted in only one band. The accuracy and specificity of the primers was assessed using DNA template extracted from cattle meat of known sex. The protocol was subjected to a blind test and showed 100% concordance, proving its accuracy and reliability.
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Affiliation(s)
- P Gokulakrishnan
- Genome Mapping Laboratory, Central Avian Research Institute, Izatnagar, Bareilly (U.P.) 243 122, India
| | - R R Kumar
- Genome Mapping Laboratory, Central Avian Research Institute, Izatnagar, Bareilly (U.P.) 243 122, India
| | - B D Sharma
- Genome Mapping Laboratory, Central Avian Research Institute, Izatnagar, Bareilly (U.P.) 243 122, India
| | - S K Mendiratta
- Genome Mapping Laboratory, Central Avian Research Institute, Izatnagar, Bareilly (U.P.) 243 122, India
| | - D Sharma
- Genome Mapping Laboratory, Central Avian Research Institute, Izatnagar, Bareilly (U.P.) 243 122, India
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Singh M, Singh PK, Misra-Bhattacharya S. RNAi mediated silencing of ATPase RNA helicase gene in adult filarial parasite Brugia malayi impairs in vitro microfilaria release and adult parasite viability. J Biotechnol 2011; 157:351-8. [PMID: 22192512 DOI: 10.1016/j.jbiotec.2011.12.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2011] [Revised: 12/02/2011] [Accepted: 12/06/2011] [Indexed: 02/05/2023]
Abstract
The DExD/H box families of RNA helicases are a multifunctional group of proteins involved in unwinding of inter- and intra-molecular base-paired regions. Successful knockdown of DEAD box RNA helicase gene (BmL3-Helicase) of human lymphatic filarial parasite Brugia malayi was done with specifically designed and chemically synthesized siRNA of <20bp to observe the role of enzyme in parasite biology and its worth as an antifilarial drug target. We made efforts to deliver siRNA into parasite by both electroporation and soaking that resulted into diminished helicase gene expression associated with decreased parasite motility, viability (97%) and release of microfilariae (81.0% reduction) from adult females in vitro. The specific gene knockdown also resulted into death of adult male worms in addition to phenotypic deformities in female worm intrauterine stages. RT-PCR of siRNA treated worms revealed a complete knockdown of BmL3-Helicase transcription within 16h. The present findings thus illustrate that targeting helicase gene of B. malayi would not only interfere with embryogenesis and microfilarial production but also result into decreased motility and viability of microfilariae and adult parasites. The B. malayi helicase enzyme thus represents a possible antifilarial drug target.
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Affiliation(s)
- Meghna Singh
- Division of Parasitology, Central Drug Research Institute, CSIR, M.G. Marg, Lucknow 226001 (U.P.), India
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50
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Bruns AM, Horvath CM. Activation of RIG-I-like receptor signal transduction. Crit Rev Biochem Mol Biol 2011; 47:194-206. [PMID: 22066529 DOI: 10.3109/10409238.2011.630974] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mammalian cells have the ability to recognize virus infection and mount a powerful antiviral response. Pattern recognition receptor proteins detect molecular signatures of virus infection and activate antiviral signaling cascades. The RIG-I-like receptors are cytoplasmic DExD/H box proteins that can specifically recognize virus-derived RNA species as a molecular feature discriminating the pathogen from the host. The RIG-I-like receptor family is composed of three homologous proteins, RIG-I, MDA5, and LGP2. All of these proteins can bind double-stranded RNA species with varying affinities via their conserved DExD/H box RNA helicase domains and C-terminal regulatory domains. The recognition of foreign RNA by the RLRs activates enzymatic functions and initiates signal transduction pathways resulting in the production of antiviral cytokines and the establishment of a broadly effective cellular antiviral state that protects neighboring cells from infection and triggers innate and adaptive immune systems. The propagation of this signal via the interferon antiviral system has been studied extensively, while the precise roles for enzymatic activities of the RNA helicase domain in antiviral responses are only beginning to be elucidated. Here, current models for RLR ligand recognition and signaling are reviewed.
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Affiliation(s)
- Annie M Bruns
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
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