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Huang C, Mantlo E, Paessler S. Lassa virus NP DEDDh 3'-5' exoribonuclease activity is required for optimal viral RNA replication and mutation control. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.12.536665. [PMID: 37090668 PMCID: PMC10120729 DOI: 10.1101/2023.04.12.536665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Lassa virus (LASV), a mammarenavirus from Arenaviridae, is the causative agent of Lassa fever (LF) endemic in West Africa. Currently, there are no vaccines or antivirals approved for LF. The RNA-dependent RNA polymerases (RdRp) of RNA viruses are error-prone. As a negative-sense RNA virus, how LASV copes with errors in RNA synthesis and ensures optimal RNA replication are not well elucidated. LASV nucleoprotein (NP) contains a DEDDH 3'-to-5' exoribonuclease motif (ExoN), which is known to be essential for LASV evasion of the interferon response via its ability to degrade virus-derived double-stranded RNA. Herein, we present evidence that LASV NP ExoN has an additional function important for viral RNA replication. We rescued an ExoN-deficient LASV mutant (ExoN- rLASV) by using a reverse genetics system. Our data indicated that abrogation of NP ExoN led to impaired LASV growth and RNA replication in interferon-deficient cells as compared with wild-type rLASV. By utilizing PacBio Single Molecule, Real-Time (SMRT) long-read sequencing technology, we found that rLASV lacking ExoN activity was prone to producing aberrant viral genomic RNA with structural variations. In addition, NP ExoN deficiency enhanced LASV sensitivity to mutagenic nucleoside analogues in virus titration assay. Next-generation deep sequencing analysis showed increased single nucleotide substitution in ExoN- LASV RNA following mutagenic 5-flurouracil treatment. In conclusion, our study revealed that LASV NP ExoN is required for efficient viral RNA replication and mutation control. Among negative-sense RNA viruses, LASV NP is the first example that a viral protein, other than the RdRp, contributes to reduce errors in RNA replication and maintain genomic RNA integrity. These new findings promote our understanding of the basics of LASV infection and inform antiviral and vaccine development.
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Affiliation(s)
- Cheng Huang
- Department of Pathology, Galveston National Laboratory and
Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston,
TX, USA
| | - Emily Mantlo
- Department of Pathology, Galveston National Laboratory and
Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston,
TX, USA
- Current address: Department of Microbiology & Immunology,
Upstate Medical University, Syracuse, NY, USA
| | - Slobodan Paessler
- Department of Pathology, Galveston National Laboratory and
Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston,
TX, USA
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Akhtar F, Ruiz JH, Liu YG, Resendez RG, Feliers D, Morales LD, Diaz-Badillo A, Lehman DM, Arya R, Lopez-Alvarenga JC, Blangero J, Duggirala R, Mummidi S. Functional characterization of the disease-associated CCL2 rs1024611G-rs13900T haplotype: The role of the RNA-binding protein HuR. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.31.564937. [PMID: 37961304 PMCID: PMC10635030 DOI: 10.1101/2023.10.31.564937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
CC-chemokine ligand 2 (CCL2) is involved in the pathogenesis of several diseases associated with monocyte/macrophage recruitment, such as HIV-associated neurocognitive disorder (HAND), tuberculosis, and atherosclerosis. The rs1024611 (alleles:A>G; G is the risk allele) polymorphism in the CCL2 cis-regulatory region is associated with increased CCL2 expression in vitro and ex vivo, leukocyte mobilization in vivo, and deleterious disease outcomes. However, the molecular basis for the rs1024611-associated differential CCL2 expression remains poorly characterized. It is conceivable that genetic variant(s) in linkage disequilibrium (LD) with rs1024611 could mediate such effects. Previously, we used rs13900 (alleles:_C>T) in the CCL2 3' untranslated region (3' UTR) that is in perfect LD with rs1024611 to demonstrate allelic expression imbalance (AEI) of CCL2 in heterozygous individuals. Here we tested the hypothesis that the rs13900 could modulate CCL2 expression by altering mRNA turnover and/or translatability. The rs13900 T allele conferred greater stability to the CCL2 transcript when compared to the rs13900 C allele. The rs13900 T allele also had increased binding to Human Antigen R (HuR), an RNA-binding protein, in vitro and ex vivo. The rs13900 alleles imparted differential activity to reporter vectors and influenced the translatability of the reporter transcript. We further demonstrated a role for HuR in mediating allele-specific effects on CCL2 expression in overexpression and silencing studies. The presence of the rs1024611G-rs13900T conferred a distinct transcriptomic signature related to inflammation and immunity. Our studies suggest that the differential interactions of HuR with rs13900 could modulate CCL2 expression and explain the interindividual differences in CCL2-mediated disease susceptibility.
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Affiliation(s)
- Feroz Akhtar
- Department of Health and Behavioral Sciences, Texas A&M University- San Antonio, Texas, USA
| | - Joselin Hernandez Ruiz
- Utah Center for Genetic Discovery, Department of Human Genetics, University of Utah, Salt Lake City, Utah, USA
| | - Ya-Guang Liu
- Department of Pathology, School of Medicine, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Roy G. Resendez
- Department of Health and Behavioral Sciences, Texas A&M University- San Antonio, Texas, USA
| | - Denis Feliers
- Department of Medicine, School of Medicine, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Liza D. Morales
- South Texas Diabetes and Obesity Institute, Department of Genetics, School of Medicine, University of Texas Rio Grane Valley, Brownsville, USA
| | - Alvaro Diaz-Badillo
- Department of Health and Behavioral Sciences, Texas A&M University- San Antonio, Texas, USA
| | - Donna M. Lehman
- Department of Health and Behavioral Sciences, Texas A&M University- San Antonio, Texas, USA
| | - Rector Arya
- Department of Health and Behavioral Sciences, Texas A&M University- San Antonio, Texas, USA
| | - Juan Carlos Lopez-Alvarenga
- Department of Population Health and Biostatistics, School of Medicine, University of Texas Rio Grande Valley, Harlingen, Texas, USA
| | - John Blangero
- South Texas Diabetes and Obesity Institute, Department of Genetics, School of Medicine, University of Texas Rio Grane Valley, Brownsville, USA
| | - Ravindranath Duggirala
- Department of Health and Behavioral Sciences, Texas A&M University- San Antonio, Texas, USA
| | - Srinivas Mummidi
- Department of Health and Behavioral Sciences, Texas A&M University- San Antonio, Texas, USA
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Strizova Z, Smetanova J, Bartunkova J, Milota T. Principles and Challenges in anti-COVID-19 Vaccine Development. Int Arch Allergy Immunol 2021; 182:339-349. [PMID: 33524979 PMCID: PMC7900461 DOI: 10.1159/000514225] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 12/30/2020] [Indexed: 12/05/2022] Open
Abstract
The number of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected patients keeps rising in most of the European countries despite the pandemic precaution measures. The current antiviral and anti-inflammatory therapeutic approaches are only supportive, have limited efficacy, and the prevention in reducing the transmission of SARS-CoV-2 virus is the best hope for public health. It is presumed that an effective vaccination against SARS-CoV-2 infection could mobilize the innate and adaptive immune responses and provide a protection against severe forms of coronavirus disease 2019 (COVID-19) disease. As the race for the effective and safe vaccine has begun, different strategies were introduced. To date, viral vector-based vaccines, genetic vaccines, attenuated vaccines, and protein-based vaccines are the major vaccine types tested in the clinical trials. Over 80 clinical trials have been initiated; however, only 18 vaccines have reached the clinical phase II/III or III, and 4 vaccine candidates are under consideration or have been approved for the use so far. In addition, the protective effect of the off-target vaccines, such as Bacillus Calmette-Guérin and measles vaccine, is being explored in randomized prospective clinical trials with SARS-CoV-2-infected patients. In this review, we discuss the most promising anti-COVID-19 vaccine clinical trials and different vaccination strategies in order to provide more clarity into the ongoing clinical trials.
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Affiliation(s)
- Zuzana Strizova
- Department of Immunology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czechia
| | - Jitka Smetanova
- Department of Immunology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czechia
| | - Jirina Bartunkova
- Department of Immunology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czechia
| | - Tomas Milota
- Department of Immunology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czechia,
- Department of Paediatric and Adult Rheumatology, University Hospital Motol, Prague, Czechia,
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4
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Sebastian-delaCruz M, Gonzalez-Moro I, Olazagoitia-Garmendia A, Castellanos-Rubio A, Santin I. The Role of lncRNAs in Gene Expression Regulation through mRNA Stabilization. Noncoding RNA 2021; 7:ncrna7010003. [PMID: 33466464 PMCID: PMC7839045 DOI: 10.3390/ncrna7010003] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 12/28/2020] [Accepted: 12/30/2020] [Indexed: 12/12/2022] Open
Abstract
mRNA stability influences gene expression and translation in almost all living organisms, and the levels of mRNA molecules in the cell are determined by a balance between production and decay. Maintaining an accurate balance is crucial for the correct function of a wide variety of biological processes and to maintain an appropriate cellular homeostasis. Long non-coding RNAs (lncRNAs) have been shown to participate in the regulation of gene expression through different molecular mechanisms, including mRNA stabilization. In this review we provide an overview on the molecular mechanisms by which lncRNAs modulate mRNA stability and decay. We focus on how lncRNAs interact with RNA binding proteins and microRNAs to avoid mRNA degradation, and also on how lncRNAs modulate epitranscriptomic marks that directly impact on mRNA stability.
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Affiliation(s)
- Maialen Sebastian-delaCruz
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, 48940 Leioa, Spain; (M.S.-d.); (A.O.-G.); (A.C.-R.)
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain;
| | - Itziar Gonzalez-Moro
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain;
- Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940 Leioa, Spain
| | - Ane Olazagoitia-Garmendia
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, 48940 Leioa, Spain; (M.S.-d.); (A.O.-G.); (A.C.-R.)
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain;
| | - Ainara Castellanos-Rubio
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, 48940 Leioa, Spain; (M.S.-d.); (A.O.-G.); (A.C.-R.)
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain;
- Ikerbasque, Basque Foundation for Science, 48009 Bilbao, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Izortze Santin
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain;
- Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940 Leioa, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Correspondence: ; Tel.: +34-94-601-32-09
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5
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Basu S, Mallik S, Hait S, Kundu S. Genome-scale molecular principles of mRNA half-life regulation in yeast. FEBS J 2020; 288:3428-3447. [PMID: 33319437 DOI: 10.1111/febs.15670] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 11/07/2020] [Accepted: 12/11/2020] [Indexed: 12/22/2022]
Abstract
Precise control of protein and messenger RNA (mRNA) degradation is essential for cellular metabolism and homeostasis. Controlled and specific degradation of both molecular species necessitates their engagements with the respective degradation machineries; this engagement involves a disordered/unstructured segment of the substrate traversing the degradation tunnel of the machinery and accessing the catalytic sites. However, while molecular factors influencing protein degradation have been extensively explored on a genome scale, and in multiple organisms, such a comprehensive understanding remains missing for mRNAs. Here, we analyzed multiple genome-scale experimental yeast mRNA half-life data in light of experimentally derived mRNA secondary structures and protein binding data, along with high-resolution X-ray crystallographic structures of the RNase machines. Results unraveled a consistent genome-scale trend that mRNAs comprising longer terminal and/or internal unstructured segments have significantly shorter half-lives; the lengths of the 5'-terminal, 3'-terminal, and internal unstructured segments that affect mRNA half-life are compatible with molecular structures of the 5' exo-, 3' exo-, and endoribonuclease machineries. Sequestration into ribonucleoprotein complexes elongates mRNA half-life, presumably by burying ribonuclease engagement sites under oligomeric interfaces. After gene duplication, differences in terminal unstructured lengths, proportions of internal unstructured segments, and oligomerization modes result in significantly altered half-lives of paralogous mRNAs. Side-by-side comparison of molecular principles underlying controlled protein and mRNA degradation in yeast unravels their remarkable mechanistic similarities and suggests how the intrinsic structural features of the two molecular species, at two different levels of the central dogma, regulate their half-lives on genome scale.
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Affiliation(s)
- Sudipto Basu
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India.,Center of Excellence in Systems Biology and Biomedical Engineering (TEQIP Phase-III), University of Calcutta, Kolkata, India
| | - Saurav Mallik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Suman Hait
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India
| | - Sudip Kundu
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India.,Center of Excellence in Systems Biology and Biomedical Engineering (TEQIP Phase-III), University of Calcutta, Kolkata, India
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6
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Wolfe MB, Schagat TL, Paulsen MT, Magnuson B, Ljungman M, Park D, Zhang C, Campbell ZT, Goldstrohm AC, Freddolino PL. Principles of mRNA control by human PUM proteins elucidated from multimodal experiments and integrative data analysis. RNA (NEW YORK, N.Y.) 2020; 26:1680-1703. [PMID: 32753408 PMCID: PMC7566576 DOI: 10.1261/rna.077362.120] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 07/30/2020] [Indexed: 05/27/2023]
Abstract
The human PUF-family proteins, PUM1 and PUM2, posttranscriptionally regulate gene expression by binding to a PUM recognition element (PRE) in the 3'-UTR of target mRNAs. Hundreds of PUM1/2 targets have been identified from changes in steady-state RNA levels; however, prior studies could not differentiate between the contributions of changes in transcription and RNA decay rates. We applied metabolic labeling to measure changes in RNA turnover in response to depletion of PUM1/2, showing that human PUM proteins regulate expression almost exclusively by changing RNA stability. We also applied an in vitro selection workflow to precisely identify the binding preferences of PUM1 and PUM2. By integrating our results with prior knowledge, we developed a "rulebook" of key contextual features that differentiate functional versus nonfunctional PREs, allowing us to train machine learning models that accurately predict the functional regulation of RNA targets by the human PUM proteins.
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Affiliation(s)
- Michael B Wolfe
- Department of Biological Chemistry and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | - Michelle T Paulsen
- Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Brian Magnuson
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Mats Ljungman
- Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan 48109, USA
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Daeyoon Park
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Chi Zhang
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas 75080, USA
| | - Zachary T Campbell
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas 75080, USA
| | - Aaron C Goldstrohm
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Peter L Freddolino
- Department of Biological Chemistry and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
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7
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Zeng X, Lee HK, Wang C, Achikeh P, Liu C, Hennighausen L. The interdependence of mammary-specific super-enhancers and their native promoters facilitates gene activation during pregnancy. Exp Mol Med 2020; 52:682-690. [PMID: 32321991 PMCID: PMC7210877 DOI: 10.1038/s12276-020-0425-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 03/08/2020] [Accepted: 03/16/2020] [Indexed: 11/09/2022] Open
Abstract
Lineage-specific genetic programs rely on cell-restricted super-enhancers, which are platforms for high-density transcription factor occupation. It is not known whether super-enhancers synergize specifically with their native promoters or provide autonomous and independent regulatory platforms. Here, we investigated the ability of the mammary Wap super-enhancer to activate the promoter of the juxtaposed and ubiquitously expressed Tbrg4 gene in the mouse mammary gland. The Wap super-enhancer was fused, alone or in combination with the Wap promoter, to the Tbrg4 gene. While the super-enhancer increased the expression of the Tbrg4 promoter five-fold, the combination of the super-enhancer and promoter resulted in 80-fold gene upregulation, demonstrating lineage-specific promoter-enhancer synergy. Employing ChIP-seq profiling to determine transcription factor binding and identify activating histone marks, we uncovered a chromatin platform that enables the high-level expression of the native promoter-enhancer but not the heterologous promoter. Taken together, our data reveal that lineage-specific enhancer-promoter synergy is critical for mammary gene regulation during pregnancy and lactation.
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Affiliation(s)
- Xianke Zeng
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Hye Kyung Lee
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Chaochen Wang
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Precious Achikeh
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Chengyu Liu
- Transgenic Core, National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, MD, 20892, USA
| | - Lothar Hennighausen
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
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8
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Mandel J, Avula R, Prochownik EV. Sequential analysis of transcript expression patterns improves survival prediction in multiple cancers. BMC Cancer 2020; 20:297. [PMID: 32264880 PMCID: PMC7140376 DOI: 10.1186/s12885-020-06756-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 03/13/2020] [Indexed: 02/08/2023] Open
Abstract
Background Long-term survival in numerous cancers often correlates with specific whole transcriptome profiles or the expression patterns of smaller numbers of transcripts. In some instances, these are better predictors of survival than are standard classification methods such as clinical stage or hormone receptor status in breast cancer. Here, we have used the method of “t-distributed stochastic neighbor embedding” (t-SNE) to show that, collectively, the expression patterns of small numbers of functionally-related transcripts from fifteen cancer pathways correlate with long-term survival in the vast majority of tumor types from The Cancer Genome Atlas (TCGA). We then ask whether the sequential application of t-SNE using the transcripts from a second pathway improves predictive capability or whether t-SNE can be used to refine the initial predictive power of whole transcriptome profiling. Methods RNAseq data from 10,227 tumors in TCGA were previously analyzed using t-SNE-based clustering of 362 transcripts comprising 15 distinct cancer-related pathways. After showing that certain clusters were associated with differential survival, each relevant cluster was re-analyzed by t-SNE with a second pathway’s transcripts. Alternatively, groups with differential survival identified by whole transcriptome profiling were subject to a second, t-SNE-based analysis. Results Sequential analyses employing either t-SNE➔t-SNE or whole transcriptome profiling➔t-SNE analyses were in many cases superior to either individual method at predicting long-term survival. We developed a dynamic and intuitive R Shiny web application to explore the t-SNE based transcriptome clustering and survival analysis across all TCGA cancers and all 15 cancer-related pathways in this analysis. This application provides a simple interface to select specific t-SNE clusters and analyze survival predictability using both individual or sequential approaches. The user can recreate the relationships described in this analysis and further explore many different cancer, pathway, and cluster combinations. Non-R users can access the application on the web at https://chpupsom19.shinyapps.io/Survival_Analysis_tsne_umap_TCGA. The application, R scripts performing survival analysis, and t-SNE clustering results of TCGA expression data can be accessed on GitHub enabling users to download and run the application locally with ease (https://github.com/RavulaPitt/Sequential-t-SNE/). Conclusions The long-term survival of patients correlated with expression patterns of 362 transcripts from 15 cancer-related pathways. In numerous cases, however, survival could be further improved when the cohorts were re-analyzed using iterative t-SNE clustering or when t-SNE clustering was applied to cohorts initially segregated by whole transcriptome-based hierarchical clustering.
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Affiliation(s)
- Jordan Mandel
- The Division of Hematology/Oncology, Children's Hospital of Pittsburgh of UPMC, Rangos Research Center, Room, 5124, 4401 Penn Ave, Pittsburgh, PA, 15224, USA.
| | - Raghunandan Avula
- The Division of Hematology/Oncology, Children's Hospital of Pittsburgh of UPMC, Rangos Research Center, Room, 5124, 4401 Penn Ave, Pittsburgh, PA, 15224, USA
| | - Edward V Prochownik
- The Division of Hematology/Oncology, Children's Hospital of Pittsburgh of UPMC, Rangos Research Center, Room, 5124, 4401 Penn Ave, Pittsburgh, PA, 15224, USA. .,The Hillman Cancer Center of The University of Pittsburgh Medical Center, UPMC, 5150 Centre Ave, Pittsburgh, PA, 15232, USA. .,The Pittsburgh Liver Research Center, S414 Biomedical Science Tower, 200 Lothrop Street, Pittsburgh, USA. .,The Department of Microbiology and Molecular Genetics, 450 Technology Dr, Pittsburgh, PA, 15219, USA.
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Serum lipids, retinoic acid and phenol red differentially regulate expression of keratins K1, K10 and K2 in cultured keratinocytes. Sci Rep 2020; 10:4829. [PMID: 32179842 PMCID: PMC7076045 DOI: 10.1038/s41598-020-61640-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 02/27/2020] [Indexed: 01/30/2023] Open
Abstract
Abnormal keratinocyte differentiation is fundamental to pathologies such as skin cancer and mucosal inflammatory diseases. The ability to grow keratinocytes in vitro allows the study of differentiation however any translational value is limited if keratinocytes get altered by the culture method. Although serum lipids (SLPs) and phenol red (PR) are ubiquitous components of culture media their effect on differentiation is largely unknown. We show for the first time that PR and SLP themselves suppress expression of differentiation-specific keratins K1, K10 and K2 in normal human epidermal keratinocytes (NHEK) and two important cell lines, HaCaT and N/TERT-1. Removal of SLP increased expression of K1, K10 and K2 in 2D and 3D cultures, which was further enhanced in the absence of PR. The effect was reversed for K1 and K10 by adding all-trans retinoic acid (ATRA) but increased for K2 in the absence of PR. Furthermore, retinoid regulation of differentiation-specific keratins involves post-transcriptional mechanisms as we show KRT2 mRNA is stabilised whilst KRT1 and KRT10 mRNAs are destabilised in the presence of ATRA. Taken together, our results indicate that the presence of PR and SLP in cell culture media may significantly impact in vitro studies of keratinocyte differentiation.
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10
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Yang DC, Eldredge AC, Hickey JC, Muradyan H, Guan Z. Multivalent Peptide-Functionalized Bioreducible Polymers for Cellular Delivery of Various RNAs. Biomacromolecules 2020; 21:1613-1624. [DOI: 10.1021/acs.biomac.0c00211] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Dong-Chu Yang
- Department of Chemistry, University of California, 1102 Natural
Sciences 2, Irvine, California 92697-2025, United States
| | - Alexander C. Eldredge
- Department of Chemistry, University of California, 1102 Natural
Sciences 2, Irvine, California 92697-2025, United States
| | - James C. Hickey
- Department of Chemistry, University of California, 1102 Natural
Sciences 2, Irvine, California 92697-2025, United States
| | - Hurik Muradyan
- Department of Chemistry, University of California, 1102 Natural
Sciences 2, Irvine, California 92697-2025, United States
| | - Zhibin Guan
- Department of Chemistry, University of California, 1102 Natural
Sciences 2, Irvine, California 92697-2025, United States
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11
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Herzog VA, Fasching N, Ameres SL. Determining mRNA Stability by Metabolic RNA Labeling and Chemical Nucleoside Conversion. Methods Mol Biol 2020; 2062:169-189. [PMID: 31768977 PMCID: PMC7611866 DOI: 10.1007/978-1-4939-9822-7_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
The varying rates at which mRNAs decay are tightly coordinated with transcriptional changes to shape gene expression during development and disease. But currently available RNA sequencing approaches lack the temporal information to determine the relative contribution of RNA biogenesis, processing and turnover to the establishment of steady-state gene expression profiles.Here, we describe a protocol that combines metabolic RNA labeling with chemical nucleoside conversion by thiol-linked alkylation of 4-thiouridine to determine RNA stability in cultured cells (SLAMseq). When coupled to cost-effective mRNA 3' end sequencing approaches, SLAMseq determines the half-life of polyadenylated transcripts in a global and transcript-specific manner using untargeted or targeted cDNA library preparation protocols.We provide a step-by-step instruction for time-resolved mRNA 3' end sequencing, which augments traditional RNA-seq approaches to acquire the temporal resolution necessary to study the molecular principles that control gene expression.
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Affiliation(s)
- Veronika A Herzog
- IMBA-Institute of Molecular Biotechnology, Vienna Biocenter (VBC), Vienna, Austria
| | - Nina Fasching
- IMBA-Institute of Molecular Biotechnology, Vienna Biocenter (VBC), Vienna, Austria
| | - Stefan L Ameres
- IMBA-Institute of Molecular Biotechnology, Vienna Biocenter (VBC), Vienna, Austria.
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Liu L, Weiss E, Panas MD, Götte B, Sellberg S, Thaa B, McInerney GM. RNA processing bodies are disassembled during Old World alphavirus infection. J Gen Virol 2019; 100:1375-1389. [DOI: 10.1099/jgv.0.001310] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
RNA processing bodies (P-bodies) are non-membranous cytoplasmic aggregates of mRNA and proteins involved in mRNA decay and translation repression. P-bodies actively respond to environmental stresses, associated with another type of RNA granules, known as stress granules (SGs). Alphaviruses were previously shown to block SG induction at late stages of infection, which is important for efficient viral growth. In this study, we found that P-bodies were disassembled or reduced in number very early in infection with Semliki Forest virus (SFV) or chikungunya virus (CHIKV) in a panel of cell lines. Similar to SGs, reinduction of P-bodies by a second stress (sodium arsenite) was also blocked in infected cells. The disassembly of P-bodies still occurred in non-phosphorylatable eIF2α mouse embryonal fibroblasts (MEFs) that are impaired in SG assembly. Studies of translation status by ribopuromycylation showed that P-body disassembly is independent of host translation shutoff, which requires the phosphorylation of eIF2α in the SFV- or CHIKV-infected cells. Labelling of newly synthesized RNA with bromo-UTP showed that host transcription shutoff correlated with P-body disassembly at the same early stage (3–4 h) after infection. However, inhibition of global transcription with actinomycin D (ActD) failed to disassemble P-bodies as effectively as the viruses did. Interestingly, blocking nuclear import with importazole led to an efficient P-bodies loss. Our data reveal that P-bodies are disassembled independently from SG formation at early stages of Old World alphavirus infection and that nuclear import is involved in the dynamic of P-bodies.
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Affiliation(s)
- Lifeng Liu
- Department of Microbiology, Tumor and Cell Biology, Biomedicum, Karolinska Institutet, Solnavägen 1, 171 77 Solna, Sweden
| | - Eva Weiss
- Department of Microbiology, Tumor and Cell Biology, Biomedicum, Karolinska Institutet, Solnavägen 1, 171 77 Solna, Sweden
| | - Marc D. Panas
- Department of Microbiology, Tumor and Cell Biology, Biomedicum, Karolinska Institutet, Solnavägen 1, 171 77 Solna, Sweden
| | - Benjamin Götte
- Department of Microbiology, Tumor and Cell Biology, Biomedicum, Karolinska Institutet, Solnavägen 1, 171 77 Solna, Sweden
| | - Stina Sellberg
- Department of Microbiology, Tumor and Cell Biology, Biomedicum, Karolinska Institutet, Solnavägen 1, 171 77 Solna, Sweden
| | - Bastian Thaa
- Department of Microbiology, Tumor and Cell Biology, Biomedicum, Karolinska Institutet, Solnavägen 1, 171 77 Solna, Sweden
| | - Gerald M. McInerney
- Department of Microbiology, Tumor and Cell Biology, Biomedicum, Karolinska Institutet, Solnavägen 1, 171 77 Solna, Sweden
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Feng Y, Liu M, Wang Z, Zhao X, Han B, Xing Y, Wang M, Yang Y. A 4-bp deletion in the 5'UTR of TaAFP-B is associated with seed dormancy in common wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2019; 19:349. [PMID: 31399044 PMCID: PMC6688260 DOI: 10.1186/s12870-019-1950-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 07/29/2019] [Indexed: 05/06/2023]
Abstract
BACKGROUND AFP is a negative regulator of ABA signaling that promotes ABI5 protein degradation and weakens regulation of ABA signaling by targeting upstream genes of ABI5, and TaABI5 gene was seed-specific, and accumulated during wheat grain maturation and dormancy acquisition, which played an important role in seed dormancy; TaAFP has a conserved domain with AFP, so TaAFP may also play an important role in seed dormancy in wheat. RESULTS Two allelic variants of TaAFP were identified on chromosome 2BS in common wheat, and designated as TaAFP-B1a and TaAFP-B1b. Sequence analysis showed a 4-bp deletion in the 5'UTR region of TaAFP-B1b compared with TaAFP-B1a. Based on the 4-bp deletion, a co-dominant functional marker of TaAFP-B was developed and designated as AFPB. The genotype generating a 203-bp fragment (TaAFP-B1b) was more resistant to pre-harvest sprouting than the genotype producing a 207-bp fragment (TaAFP-B1a) in a test of 91 white-grained Chinese wheat cultivars and advanced lines. The average germination index(GI) values of TaAFP-B1a and that of TaAFP-B1b were 45.18 and 30.72%, respectively, indicating a significant difference (P < 0.001). Moreover, the 4-bp deletion located in the 5'UTR not only affected the transcription level of TaAFP-B but also affected the mRNA decay, reduced the translation level of GUS and tdTomatoER and GUS activity in wheat leaves of transient expression. The transcript expression and the mRNA half-life value of TaAFP-B1a in developing seeds and mature seeds were much higher than those of TaAFP-B1b. CONCLUSION We identified a 4-bp InDel in the 5'UTR of TaAFP-B, which affected the mRNA transcription level, mRNA decay, translation levels of GUS and tdTomatoER, GUS activity, and was significantly associated with seed dormancy in common wheat. A functional marker was developed and validated based on this InDel.
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Affiliation(s)
- Yumei Feng
- College of Life Sciences, Inner Mongolia Agricultural University, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Erdos Road, Hohhot, 010018 Inner Mongolia China
| | - Meng Liu
- College of Life Sciences, Inner Mongolia Agricultural University, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Erdos Road, Hohhot, 010018 Inner Mongolia China
| | - Zeng Wang
- College of Life Sciences, Inner Mongolia Agricultural University, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Erdos Road, Hohhot, 010018 Inner Mongolia China
| | - Xianlin Zhao
- Wheat Research Institute, Henan Academy of Agricultural Sciences, Henan Key Laboratory of Wheat Biology, National Engineering Laboratory for Wheat, Key Laboratory of Wheat Biology and Genetic Breeding in Central Huang-Huai Region, Ministry of Agriculture, Zhengzhou, 450002 China
| | - Bing Han
- College of Life Sciences, Inner Mongolia Agricultural University, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Erdos Road, Hohhot, 010018 Inner Mongolia China
| | - Yanping Xing
- College of Life Sciences, Inner Mongolia Agricultural University, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Erdos Road, Hohhot, 010018 Inner Mongolia China
| | - Maoyan Wang
- College of Life Sciences, Inner Mongolia Agricultural University, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Erdos Road, Hohhot, 010018 Inner Mongolia China
| | - Yan Yang
- College of Life Sciences, Inner Mongolia Agricultural University, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Erdos Road, Hohhot, 010018 Inner Mongolia China
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Mandel J, Wang H, Normolle DP, Chen W, Yan Q, Lucas PC, Benos PV, Prochownik EV. Expression patterns of small numbers of transcripts from functionally-related pathways predict survival in multiple cancers. BMC Cancer 2019; 19:686. [PMID: 31299925 PMCID: PMC6626418 DOI: 10.1186/s12885-019-5851-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 06/18/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Genetic profiling of cancers for variations in copy number, structure or expression of certain genes has improved diagnosis, risk-stratification and therapeutic decision-making. However the tumor-restricted nature of these changes limits their application to certain cancer types or sub-types. Tests with broader prognostic capabilities are lacking. METHODS Using RNAseq data from 10,227 tumors in The Cancer Genome Atlas (TCGA), we evaluated 212 protein-coding transcripts from 12 cancer-related pathways. We employed t-distributed stochastic neighbor embedding (t-SNE) to identify expression pattern difference among each pathway's transcripts. We have previously used t-SNE to show that survival in some cancers correlates with expression patterns of transcripts encoding ribosomal proteins and enzymes for cholesterol biosynthesis and fatty acid oxidation. RESULTS Using the above 212 transcripts, t-SNE-assisted transcript pattern profiling identified patient cohorts with significant survival differences in 30 of 34 different cancer types comprising 9350 tumors (91.4% of all TCGA cases). Small subsets of each pathway's transcripts, comprising no more than 50-60 from the original group, played particularly prominent roles in determining overall t-SNE patterns. In several cases, further refinements in long-term survival could be achieved by sequential t-SNE profiling with two pathways' transcripts, by a combination of t-SNE plus whole transcriptome profiling or by employing t-SNE on immuno-histochemically defined breast cancer subtypes. In two cancer types, individuals with Stage IV disease at presentation could be readily subdivided into groups with highly significant survival differences based on t-SNE-based tumor sub-classification. CONCLUSIONS t-SNE-assisted profiling of a small number of transcripts allows the prediction of long-term survival across multiple cancer types.
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Affiliation(s)
- Jordan Mandel
- The Division of Hematology/Oncology, Children’s Hospital of Pittsburgh of UPMC, Children’s Hospital of Pittsburgh of UPMC, Rangos Research Center, Fl. 5, Bay 8, 4401 Penn Ave, Pittsburgh, PA 15224 USA
| | - Huabo Wang
- The Division of Hematology/Oncology, Children’s Hospital of Pittsburgh of UPMC, Children’s Hospital of Pittsburgh of UPMC, Rangos Research Center, Fl. 5, Bay 8, 4401 Penn Ave, Pittsburgh, PA 15224 USA
| | - Daniel P. Normolle
- The Department of Biostatistics and The University of Pittsburgh Graduate School of Public Health, 130 De Soto Street, Pittsburgh, PA 15261 USA
- The Hillman Cancer Center of The University of Pittsburgh Medical Center, UPMC, 5150 Centre Ave, Pittsburgh, PA 15232 USA
| | - Wei Chen
- The Division of Pulmonary Medicine, Allergy and Immunology, Children’s Hospital of Pittsburgh of UPMC, 4401 Penn Ave, Pittsburgh, PA 15224 USA
| | - Qi Yan
- The Division of Pulmonary Medicine, Allergy and Immunology, Children’s Hospital of Pittsburgh of UPMC, 4401 Penn Ave, Pittsburgh, PA 15224 USA
| | - Peter C. Lucas
- The Division of Hematology/Oncology, Children’s Hospital of Pittsburgh of UPMC, Children’s Hospital of Pittsburgh of UPMC, Rangos Research Center, Fl. 5, Bay 8, 4401 Penn Ave, Pittsburgh, PA 15224 USA
- The Hillman Cancer Center of The University of Pittsburgh Medical Center, UPMC, 5150 Centre Ave, Pittsburgh, PA 15232 USA
- The Department of Pathology, The University of Pittsburgh Medical Center, S-417 BST 200 Lothrop Street, Pittsburgh, PA 15261 USA
| | - Panayiotis V. Benos
- The Department of Computational and Systems Biology, The University of Pittsburgh Medical Center, 3501 Fifth Avenue, 3064 BST3, Pittsburgh, PA 15260 USA
- Department of Biomedical Informatics, The University of Pittsburgh Medical Center, 5607 Baum Blvd, Pittsburgh, PA 15206 USA
- The Joint Carnegie Mellon-University of Pittsburgh Program in Computational Biology, 3501 Fifth Ave, Pittsburgh, PA 15213 USA
- The Pittsburgh Liver Research Center, S414 Biomedical Science Tower, 200 Lothrop Street, Pittsburgh, PA 15224 USA
| | - Edward V. Prochownik
- The Division of Hematology/Oncology, Children’s Hospital of Pittsburgh of UPMC, Children’s Hospital of Pittsburgh of UPMC, Rangos Research Center, Fl. 5, Bay 8, 4401 Penn Ave, Pittsburgh, PA 15224 USA
- The Hillman Cancer Center of The University of Pittsburgh Medical Center, UPMC, 5150 Centre Ave, Pittsburgh, PA 15232 USA
- The Pittsburgh Liver Research Center, S414 Biomedical Science Tower, 200 Lothrop Street, Pittsburgh, PA 15224 USA
- The Department of Microbiology and Molecular Genetics, 450 Technology Dr. Pittsburgh, Pittsburgh, PA 15219 USA
- Division of Hematology/Oncology, Children’s Hospital of Pittsburgh of UPMC, Rangos Research Center, 4401 Penn Ave, Pittsburgh, PA 15224 USA
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15
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Omar N, Lokanathan Y, Mohd Razi ZR, Bt Haji Idrus R. The effects of Centella asiatica (L.) Urban on neural differentiation of human mesenchymal stem cells in vitro. Altern Ther Health Med 2019; 19:167. [PMID: 31286956 PMCID: PMC6615117 DOI: 10.1186/s12906-019-2581-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 06/27/2019] [Indexed: 01/17/2023]
Abstract
Background Centella asiatica (L.) Urban, known as Indian Pennywort, is a tropical medicinal plant from Apiaceae family native to Southeast Asian countries. It has been widely used as a nerve tonic in Ayuverdic medicine since ancient times. However, whether it can substitute for neurotrophic factors to induce human mesenchymal stem cell (hMSCs) differentiation into the neural lineage remains unknown. This study aimed to investigate the effect of a raw extract of C. asiatica (L.) (RECA) on the neural differentiation of hMSCs in vitro. Methods The hMSCs derived from human Wharton’s jelly umbilical cord (hWJMSCs; n = 6) were treated with RECA at different concentrations; 400, 800, 1200, 1600, 2000 and 2400 μg/ml. The cytotoxicity of RECA was evaluated via the MTT (3-(4, 5-dimethylthiazolyl-2)-2, 5-diphenyltetrazolium bromide) and cell proliferation assays. The hWJMSCs were then induced to neural lineage for 9 days either with RECA alone or RECA in combination with neurotrophic factors (NF). Cell morphological changes were observed under an inverted microscope, while the expression of the neural markers S100β, p75 NGFR, MBP, GFAP and MOG was analyzed by quantitative polymerase chain reaction and immunocytochemistry. The cell cycle profile of differentiated and undifferentiated hWJMSCs was investigated through cell cycle analysis. Results RECA exerted effects on both proliferation and neural differentiation of hWJMSCs in a dose-dependent manner. RECA reduced the proliferation of hWJMSCs and was cytotoxic to cells above 1600 μg/ml, with IC50 value, 1875 ± 55.67 μg/ml. In parallel with the reduction in cell viability, cell enlargement was also observed at the end of the induction. Cells treated with RECA alone had more obvious protein expression of the neural markers compared to the other groups. Meanwhile, gene expression of the aforementioned markers was detected at low levels across the experimental groups. The supplementation of hWJMSCs with RECA did not change the normal life cycle of the cells. Conclusions Although RECA reduced the proliferation of hWJMSCs, a low dose of RECA (400 μg/ml), alone or in combination of neurotrophic factors (NF + RECA 400 μg/ml), has the potential to differentiate hWJMSCs into Schwann cells and other neural lineage cells. Electronic supplementary material The online version of this article (10.1186/s12906-019-2581-x) contains supplementary material, which is available to authorized users.
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Koh WS, Porter JR, Batchelor E. Tuning of mRNA stability through altering 3'-UTR sequences generates distinct output expression in a synthetic circuit driven by p53 oscillations. Sci Rep 2019; 9:5976. [PMID: 30979970 PMCID: PMC6461691 DOI: 10.1038/s41598-019-42509-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 02/28/2019] [Indexed: 11/29/2022] Open
Abstract
Synthetic biological circuits that can generate outputs with distinct expression dynamics are useful for a variety of biomedical and industrial applications. We present a method to control output dynamics by altering output mRNA decay rates. Using oscillatory expression of the transcription factor p53 as the circuit regulator, we use two approaches for controlling target gene transcript degradation rates based on the output gene's 3'-untranslated region (3'-UTR): introduction of copies of destabilizing AU-rich elements into the 3'-UTR or swapping in naturally occurring 3'-UTRs conferring different transcript stabilities. As a proof of principle, we apply both methods to control the expression dynamics of a fluorescent protein and visualize the circuit output dynamics in single living cells. We then use the naturally occurring 3'-UTR approach to restore apoptosis in a tunable manner in a cancer cell line deficient for caspase-3 expression. Our method can be readily adapted to regulate multiple outputs each with different expression dynamics under the control of a single naturally occurring or synthetically constructed biological oscillator.
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Affiliation(s)
- Woo Seuk Koh
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Joshua R Porter
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Eric Batchelor
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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Zhang C, Maruggi G, Shan H, Li J. Advances in mRNA Vaccines for Infectious Diseases. Front Immunol 2019; 10:594. [PMID: 30972078 PMCID: PMC6446947 DOI: 10.3389/fimmu.2019.00594] [Citation(s) in RCA: 397] [Impact Index Per Article: 79.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 03/05/2019] [Indexed: 12/19/2022] Open
Abstract
During the last two decades, there has been broad interest in RNA-based technologies for the development of prophylactic and therapeutic vaccines. Preclinical and clinical trials have shown that mRNA vaccines provide a safe and long-lasting immune response in animal models and humans. In this review, we summarize current research progress on mRNA vaccines, which have the potential to be quick-manufactured and to become powerful tools against infectious disease and we highlight the bright future of their design and applications.
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Affiliation(s)
- Cuiling Zhang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | | | - Hu Shan
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Junwei Li
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
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Exploring the Involvement of NLRP3 and IL-1 β in Osteoarthritis of the Hand: Results from a Pilot Study. Mediators Inflamm 2019; 2019:2363460. [PMID: 30983879 PMCID: PMC6431515 DOI: 10.1155/2019/2363460] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 12/04/2018] [Accepted: 12/19/2018] [Indexed: 12/27/2022] Open
Abstract
Hand osteoarthritis (HOA) includes different subsets; a particular and uncommon form is erosive HOA (EHOA). Interleukin- (IL-) 1β plays a crucial role in the pathogenesis of osteoarthritis (OA); it is synthesized as an inactive precursor which requires the intervention of a cytosolic multiprotein complex, named inflammasome, for its activation. The aim of this study was to investigate the involvement of IL-1β and the NOD-like receptor pyrin domain containing 3 (NLRP3) inflammasome in patients with EHOA and nonerosive HOA (NEHOA) compared to healthy controls. In particular, we evaluated the gene expression of IL-1β and NLRP3, the serum levels of IL-1β, IL-6, IL-17, and tumor necrosis factor- (TNF-) α, and the protein levels of IL-1β and NLRP3. We also assessed the relationships between IL-1β and NLRP3 and clinical, laboratory, and radiological findings. Fifty-four patients with HOA (25 EHOA and 29 NEHOA) and 20 healthy subjects were included in the study. Peripheral blood mononuclear cell (PBMC) gene and protein expressions of IL-1β and NLRP3 were quantified by quantitative real-time PCR and western blot. IL-1β, IL-6, IL-17, and TNF-α serum levels were determined by ELISA. IL-1β gene expression was significantly reduced (p = 0.0208) in EHOA compared to healthy controls. NLRP3 protein levels were significantly increased in the NEHOA group versus the control (p = 0.0063) and EHOA groups (p = 0.0038). IL-1β serum levels were not significantly different across the groups; IL-6, IL-17, and TNF-α were not detectable in any sample. IL-1β concentrations were negatively correlated with the Kellgren-Lawrence score in the whole population (r = −0.446; p = 0.0008) and in NEHOA (r = −0.608; p = 0.004), while IL-1β gene expression was positively correlated with the number of joint swellings in the EHOA group (r = 0.512; p = 0.011). Taken together, our results, showing poorly detectable IL-1β concentrations and minimal inflammasome activity in the PBMCs of HOA patients, suggest a low grade of systemic inflammation in HOA. This evidence does not preclude a possible involvement of these factors at the local level.
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Matveeva EA, Mathbout LF, Fondufe-Mittendorf YN. PARP1 is a versatile factor in the regulation of mRNA stability and decay. Sci Rep 2019; 9:3722. [PMID: 30842529 PMCID: PMC6403249 DOI: 10.1038/s41598-019-39969-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 02/01/2019] [Indexed: 12/30/2022] Open
Abstract
PARP1 is an abundant nuclear protein with many pleiotropic functions involved in epigenetic and transcriptional controls. Abundance of mRNA depends on the balance between synthesis and decay of a particular transcript. PARP1 binds RNA and its depletion results in increased expression of genes involved in nonsense-mediated decay, suggesting that PARP1 might be involved in mRNA stability. This is of interest considering RNA binding proteins play key roles in post-transcriptional processes in all eukaryotes. We tested the direct impact of PARP1 and PARylation on mRNA stability and decay. By measuring the half-lives of two PARP1-mRNA targets we found that the half-lives were significantly decreased in PARP1-depleted cells. PARP1 depletion impacted both the synthesis of nascent mRNA and the stability of mature mRNAs. PARylation impacted the production of nascent mRNA and the stability of mature mRNA, albeit to a lesser extent than PARP1 KD. PARylation enhanced the impact of PARP1 depletion. These studies provide the first direct comparative role of PARP1 and PARylation in RNA stability and decay, adding a new dimension as to how PARP1 regulates gene expression. These studies present a platform to begin to tease out the influence of PARP1 at each step of RNA biogenesis and decay to fine-tune gene expression.
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Affiliation(s)
- Elena A Matveeva
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Lein F Mathbout
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
- College of Medicine, Alfaisal University, Al Maather', Riyadh, Saudi Arabia
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mRNA as a Transformative Technology for Vaccine Development to Control Infectious Diseases. Mol Ther 2019; 27:757-772. [PMID: 30803823 DOI: 10.1016/j.ymthe.2019.01.020] [Citation(s) in RCA: 290] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 01/30/2019] [Accepted: 01/30/2019] [Indexed: 02/07/2023] Open
Abstract
In the last two decades, there has been growing interest in mRNA-based technology for the development of prophylactic vaccines against infectious diseases. Technological advancements in RNA biology, chemistry, stability, and delivery systems have accelerated the development of fully synthetic mRNA vaccines. Potent, long-lasting, and safe immune responses observed in animal models, as well as encouraging data from early human clinical trials, make mRNA-based vaccination an attractive alternative to conventional vaccine approaches. Thanks to these data, together with the potential for generic, low-cost manufacturing processes and the completely synthetic nature, the prospects for mRNA vaccines are very promising. In addition, mRNA vaccines have the potential to streamline vaccine discovery and development, and facilitate a rapid response to emerging infectious diseases. In this review, we overview the unique attributes of mRNA vaccine approaches, review the data of mRNA vaccines against infectious diseases, discuss the current challenges, and highlight perspectives about the future of this promising technology.
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21
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GAPDH as a model non-canonical AU-rich RNA binding protein. Semin Cell Dev Biol 2019; 86:162-173. [DOI: 10.1016/j.semcdb.2018.03.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 02/13/2018] [Accepted: 03/20/2018] [Indexed: 02/06/2023]
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Global analysis of RNA metabolism using bio-orthogonal labeling coupled with next-generation RNA sequencing. Methods 2018; 155:88-103. [PMID: 30529548 DOI: 10.1016/j.ymeth.2018.12.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 11/30/2018] [Accepted: 12/03/2018] [Indexed: 11/21/2022] Open
Abstract
Many open questions in RNA biology relate to the kinetics of gene expression and the impact of RNA binding regulatory factors on processing or decay rates of particular transcripts. Steady state measurements of RNA abundance obtained from RNA-seq approaches are not able to separate the effects of transcription from those of RNA decay in the overall abundance of any given transcript, instead only giving information on the (presumed steady-state) abundances of transcripts. Through the combination of metabolic labeling and high-throughput sequencing, several groups have been able to measure both transcription rates and decay rates of the entire transcriptome of an organism in a single experiment. This review focuses on the methodology used to specifically measure RNA decay at a global level. By comparing and contrasting approaches and describing the experimental protocols in a modular manner, we intend to provide both experienced and new researchers to the field the ability to combine aspects of various protocols to fit the unique needs of biological questions not addressed by current methods.
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23
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Lino CA, Harper JC, Carney JP, Timlin JA. Delivering CRISPR: a review of the challenges and approaches. Drug Deliv 2018; 25:1234-1257. [PMID: 29801422 PMCID: PMC6058482 DOI: 10.1080/10717544.2018.1474964] [Citation(s) in RCA: 632] [Impact Index Per Article: 105.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 05/03/2018] [Accepted: 05/07/2018] [Indexed: 12/13/2022] Open
Abstract
Gene therapy has long held promise to correct a variety of human diseases and defects. Discovery of the Clustered Regularly-Interspaced Short Palindromic Repeats (CRISPR), the mechanism of the CRISPR-based prokaryotic adaptive immune system (CRISPR-associated system, Cas), and its repurposing into a potent gene editing tool has revolutionized the field of molecular biology and generated excitement for new and improved gene therapies. Additionally, the simplicity and flexibility of the CRISPR/Cas9 site-specific nuclease system has led to its widespread use in many biological research areas including development of model cell lines, discovering mechanisms of disease, identifying disease targets, development of transgene animals and plants, and transcriptional modulation. In this review, we present the brief history and basic mechanisms of the CRISPR/Cas9 system and its predecessors (ZFNs and TALENs), lessons learned from past human gene therapy efforts, and recent modifications of CRISPR/Cas9 to provide functions beyond gene editing. We introduce several factors that influence CRISPR/Cas9 efficacy which must be addressed before effective in vivo human gene therapy can be realized. The focus then turns to the most difficult barrier to potential in vivo use of CRISPR/Cas9, delivery. We detail the various cargos and delivery vehicles reported for CRISPR/Cas9, including physical delivery methods (e.g. microinjection; electroporation), viral delivery methods (e.g. adeno-associated virus (AAV); full-sized adenovirus and lentivirus), and non-viral delivery methods (e.g. liposomes; polyplexes; gold particles), and discuss their relative merits. We also examine several technologies that, while not currently reported for CRISPR/Cas9 delivery, appear to have promise in this field. The therapeutic potential of CRISPR/Cas9 is vast and will only increase as the technology and its delivery improves.
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Affiliation(s)
- Christopher A. Lino
- Bioenergy and Defense Technologies, Sandia National Laboratories, Albuquerque, NM, USA
| | - Jason C. Harper
- Bioenergy and Defense Technologies, Sandia National Laboratories, Albuquerque, NM, USA
| | - James P. Carney
- Bioenergy and Defense Technologies, Sandia National Laboratories, Albuquerque, NM, USA
| | - Jerilyn A. Timlin
- Bioenergy and Defense Technologies, Sandia National Laboratories, Albuquerque, NM, USA
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Fortenbery GW, Sarathy B, Carraway KR, Mansfield KD. Hypoxic stabilization of mRNA is HIF-independent but requires mtROS. Cell Mol Biol Lett 2018; 23:48. [PMID: 30305827 PMCID: PMC6172842 DOI: 10.1186/s11658-018-0112-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 09/25/2018] [Indexed: 01/09/2023] Open
Abstract
Background Tissue ischemia can arise in response to numerous physiologic and pathologic conditions. The cellular response to decreased perfusion, most notably a decrease in glucose and oxygen, is important for cellular survival. In response to oxygen deprivation or hypoxia, one of the key response elements is hypoxia inducible factor (HIF) and a key protein induced by hypoxia is vascular endothelial growth factor (VEGF). Under hypoxia, we and others have reported an increase in the half-life of VEGF and other hypoxia related mRNAs including MYC and CYR61; however, the mediator of this response has yet to be identified. For this study, we sought to determine if HIF-mediated transcriptional activity is involved in the mRNA stabilization induced by hypoxia. Methods HEK293T or C6 cells were cultured in either normoxic or hypoxic (1% oxygen) conditions in the presence of 1 g/L glucose for all experiments. Pharmacological treatments were used to mimic hypoxia (desferroxamine, dimethyloxaloglutamate, CoCl2), inhibit mitochondrial respiration (rotenone, myxothiazol), scavenge reactive oxygen species (ROS; ebselen), or generate mitochondrial ROS (antimycin A). siRNAs were used to knock down components of the HIF transcriptional apparatus. mRNA half-life was determined via actinomycin D decay and real time PCR and western blotting was used to determine mRNA and protein levels respectively. Results Treatment of HEK293T or C6 cells with hypoxic mimetics, desferroxamine, dimethyloxaloglutamate, or CoCl2 showed similar induction of HIF compared to hypoxia treatment, however, in contrast to hypoxia, the mimetics caused no significant increase in VEGF, MYC or CYR61 mRNA half-life. Knockdown of HIF-alpha or ARNT via siRNA also had no effect on hypoxic mRNA stabilization. Interestingly, treatment of HEK293T cells with the mitochondrial inhibitors rotenone and myxothiazol, or the glutathione peroxidase mimetic ebselen did prevent the hypoxic stabilization of VEGF, MYC, and CYR61, suggesting a role for mtROS in the process. Additionally, treatment with antimycin A, which has been shown to generate mtROS, was able to drive the normoxic stabilization of these mRNAs. Conclusion Overall these data suggest that hypoxic mRNA stabilization is independent of HIF transcriptional activity but requires mtROS.
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Affiliation(s)
- Grey W Fortenbery
- 1Brody School of Medicine, East Carolina University, Greenville, NC 27834 USA
| | - Brinda Sarathy
- 2Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, NC 27834 USA
| | - Kristen R Carraway
- 2Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, NC 27834 USA
| | - Kyle D Mansfield
- 2Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, NC 27834 USA
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Astakhova AA, Chistyakov DV, Sergeeva MG, Reiser G. Regulation of the ARE-binding proteins, TTP (tristetraprolin) and HuR (human antigen R), in inflammatory response in astrocytes. Neurochem Int 2018; 118:82-90. [DOI: 10.1016/j.neuint.2018.04.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 04/20/2018] [Accepted: 04/23/2018] [Indexed: 01/06/2023]
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Beta RAA, Balatsos NAA. Tales around the clock: Poly(A) tails in circadian gene expression. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1484. [PMID: 29911349 DOI: 10.1002/wrna.1484] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 04/15/2018] [Accepted: 04/20/2018] [Indexed: 11/07/2022]
Abstract
Circadian rhythms are ubiquitous time-keeping processes in eukaryotes with a period of ~24 hr. Light is perhaps the main environmental cue (zeitgeber) that affects several aspects of physiology and behaviour, such as sleep/wake cycles, orientation of birds and bees, and leaf movements in plants. Temperature can serve as the main zeitgeber in the absence of light cycles, even though it does not lead to rhythmicity through the same mechanism as light. Additional cues include feeding patterns, humidity, and social rhythms. At the molecular level, a master oscillator orchestrates circadian rhythms and organizes molecular clocks located in most cells. The generation of the 24 hr molecular clock is based on transcriptional regulation, as it drives intrinsic rhythmic changes based on interlocked transcription/translation feedback loops that synchronize expression of genes. Thus, processes and factors that determine rhythmic gene expression are important to understand circadian rhythms. Among these, the poly(A) tails of RNAs play key roles in their stability, translational efficiency and degradation. In this article, we summarize current knowledge and discuss perspectives on the role and significance of poly(A) tails and associating factors in the context of the circadian clock. This article is categorized under: RNA Turnover and Surveillance > Regulation of RNA Stability RNA Processing > 3' End Processing.
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Affiliation(s)
- Rafailia A A Beta
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Nikolaos A A Balatsos
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
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Zhang JJ, Yano H, Sasaki T, Matsuo N, Yoshioka H. The pro-α1(V) collagen gene (Col5a1) is coordinately regulated by miR-29b with core promoter in cultured cells. Connect Tissue Res 2018; 59:263-273. [PMID: 28829698 DOI: 10.1080/03008207.2017.1370465] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
AIMS Col5a1 encodes the α1 chain of type V collagen, a quantitatively minor fibrillar collagen that is critical for the formation and function of the organs in the body. MicroRNAs (miRNAs) are small noncoding RNAs that posttranscriptionally regulate biological functions by binding to the 3'-untranslated region (3'UTR) of specific target mRNA. In this study, we investigated the posttranscriptional regulation of miRNAs on the Col5a1 gene expression. MATERIALS AND METHODS We cultured osteoblasts and fibroblasts of cell lines. To examine the 3'UTR activity of the Col5a1 gene, chimeric plasmids constructs containing the core promoter and 3'UTR of Col5a1 were generated and luciferase assays were performed. We also evaluated the role of miRNA using constructs that were mutated at the putative binding sites of miRNA. In addition, we evaluated the endogenous mRNA and protein, and luciferase activity of the Col5a1 gene after miRNA overexpression/knockdown or CRISPR/Cas9-induced knockout. RESULTS The luciferase assay showed a decreased activity of the 3'UTR of Col5a1 gene. However, the expression of the mutant constructs of miRNA-binding sites was restored. The overexpression of miRNA inhibited the Col5a1 gene not only with regard to the luciferase activity and endogenous mRNA but also at the protein level. In contrast, the RNAi-mediated knockdown or CRISPR/Cas9 system increased the expression of the Col5a1 gene. CONCLUSION These results provided evidence that miR-29b regulates the Col5a1 gene expression through binding to the 3'UTR, which might play an important role in the pathogenesis of disease related to bone metabolism and fibrogenic reactions.
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Affiliation(s)
- Juan Juan Zhang
- a Department of Matrix Medicine, Faculty of Medicine , Oita University , Oita , Japan
| | - Hiroyuki Yano
- b Research Promotion Institute , Oita University , Oita , Japan
| | - Takako Sasaki
- a Department of Matrix Medicine, Faculty of Medicine , Oita University , Oita , Japan
| | - Noritaka Matsuo
- a Department of Matrix Medicine, Faculty of Medicine , Oita University , Oita , Japan
| | - Hidekatsu Yoshioka
- a Department of Matrix Medicine, Faculty of Medicine , Oita University , Oita , Japan
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Lugowski A, Nicholson B, Rissland OS. Determining mRNA half-lives on a transcriptome-wide scale. Methods 2018; 137:90-98. [DOI: 10.1016/j.ymeth.2017.12.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 12/11/2017] [Accepted: 12/11/2017] [Indexed: 12/20/2022] Open
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Menon KMJ, Menon B, Gulappa T. Regulation of Luteinizing Hormone Receptor mRNA Expression in the Ovary: The Role of miR-122. VITAMINS AND HORMONES 2018; 107:67-87. [PMID: 29544643 DOI: 10.1016/bs.vh.2018.01.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The expression of luteinizing hormone receptor (LHR) in the mammalian ovary is regulated in response to changes in the secretion of follicle-stimulating hormone and luteinizing hormone by the anterior pituitary, at least in part, through posttranscriptional mechanisms. The steady-state levels of LHR mRNA are maintained by controlling its rate of degradation by an RNA-binding protein designated as LHR mRNA-binding protein (LRBP). LRBP forms a complex with LHR mRNA and targets it for degradation in the p bodies. miR-122, an 18 nucleotide noncoding RNA, regulates the expression of LRBP. Thus, the levels of miR-122 determine the cellular levels of LHR mRNA expression. This phenomenon has been examined during the induction of LHR mRNA expression that occurs during follicle maturation in response to rising levels of FSH. In this situation, miR-122 and LRBP levels decrease as LHR mRNA expression undergoes downregulation in response to preovulatory LH surge. miR-122 expression as well as LRBP levels show robust increases. The mechanism of induction of LRBP by miR-122 has also been discussed.
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Affiliation(s)
- K M J Menon
- The University of Michigan Medical School, Ann Arbor, MI, United States.
| | - Bindu Menon
- The University of Michigan Medical School, Ann Arbor, MI, United States
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Acetylation regulates the MKK4-JNK pathway in T cell receptor signaling. Immunol Lett 2018; 194:21-28. [DOI: 10.1016/j.imlet.2017.12.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Revised: 11/21/2017] [Accepted: 12/09/2017] [Indexed: 11/21/2022]
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Álvarez-Torres D, Gómez-Abellán V, Arizcun M, García-Rosado E, Béjar J, Sepulcre MP. Identification of an interferon-stimulated gene, isg15, involved in host immune defense against viral infections in gilthead seabream (Sparus aurata L.). FISH & SHELLFISH IMMUNOLOGY 2018; 73:220-227. [PMID: 29277364 DOI: 10.1016/j.fsi.2017.12.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 11/07/2017] [Accepted: 12/18/2017] [Indexed: 06/07/2023]
Abstract
Interferons (IFNs) play a key role in the innate immunity of vertebrates against viral infections by inducing hundreds of IFN-stimulated genes (ISGs), such as isg15. Isg15 is an ubiquitin-like protein, which can conjugate cellular and viral proteins in a process called ISGylation, although it can also act as a cytokine-like protein. Gilthead seabream (Sparus aurata L.) is an important asymptomatic carrier of viral haemorrhagic septicaemia virus (VHSV) and nodavirus, representing a threat to other co-cultivated susceptible species. In order to better understand virus-host interactions in this fish species, this study addresses the identification and molecular characterization of seabream isg15 (sb-isg15). In addition, the modulation of transcript levels of sb-isg15 was analysed in SAF-1 cells and seabream acidophilic granulocytes (AGs) stimulated in vitro with different pathogen-associated molecular patterns (PAMPs) or inoculated with VHSV and striped jack nervous necrosis virus (SJNNV). The full-length cDNA of sb-isg15 gene, encoding a predicted protein of 155 amino acids, was identified and seen to share the same characteristics as other fish and mammalian isg15 genes. Here we report the clear induction of sb-isg15 transcript levels in SAF-1 cells and AGs stimulated with toll-like receptor (TLR) ligands, such as polyinosinic:polycytidylic acid (poly I:C) or genomic DNA from Vibrio anguillarum (VaDNA), respectively. Furthermore, VHSV and SJNNV inoculation induced a significant degree of sb-isg15 transcription in SAF-1 cells and AGs. However, the relative levels of viral RNA transcription showed that SJNNV replication seems to be more efficient than VHSV in both in vitro systems. Interestingly, sb-isg15 transcript induction elicited by VaDNA was reduced in VHSV- and SJNNV-inoculated AGs, suggesting an interference prompted by the viruses against the type I IFN system. Taken together, these findings support the use of seabream AGs as a valuable experimental system to study virus-host interactions, in which sb-isg15 seems to play an important role.
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Affiliation(s)
- Daniel Álvarez-Torres
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain; Departamento de Genética, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
| | - Victoria Gómez-Abellán
- Departamento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia, IMIB-Arrixaca, 30100 Murcia, Spain
| | - Marta Arizcun
- Centro Oceanográfico de Murcia, Instituto Español de Oceanografía (IEO), 30860 Murcia, Spain
| | - Esther García-Rosado
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
| | - Julia Béjar
- Departamento de Genética, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
| | - María P Sepulcre
- Departamento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia, IMIB-Arrixaca, 30100 Murcia, Spain.
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Castro NP, Golubeva YG. Adaptation of Laser Microdissection Technique to Nanostring RNA Analysis in the Study of a Spontaneous Metastatic Mammary Carcinoma Mouse Model. Methods Mol Biol 2018; 1723:119-137. [PMID: 29344857 DOI: 10.1007/978-1-4939-7558-7_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The mouse model characterized by spontaneous lung metastasis from JygMC (A) cells closely resembles the human triple negative breast cancer (TNBC) subtype. The primary tumors morphologically present both epithelial and spindle-like cells, but metastases in lung parenchyma display only adenocarcinoma properties. In the study of molecular signatures, laser capture microdissection (LCM) on frozen tissue sections was used to separate the following regions of interest: the epithelial-mesenchymal transition (EMT), mesenchymal-epithelial transition (MET), carcinoma, lung metastases, normal mammary gland and normal lung parenchyma. NanoString was selected for the study of molecular signatures in LCM targets as a reliable downstream gene expression platform allowing analysis of tissue lysates without RNA extraction and amplification. This chapter provides detailed protocols for the collection of tissue, LCM sample preparation and dissection, production of lysates, extraction, and quality control of RNA for NanoString analysis, as well as the methodology of Nanostring gene expression profiling experiment.
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Affiliation(s)
- Nadia P Castro
- Tumor Growth Factor Section, Mouse Cancer Genetics Program, National Cancer Institute, Frederick, MD, USA
| | - Yelena G Golubeva
- Cancer Genomic Research Laboratory (CGR), Division of Cancer Epidemiology and Genetics, NCI, FNLCR, Leidos Biomedical Research, Inc, Gaithersburg, MD, USA.
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Laser Microdissection Workflow for Isolating Nucleic Acids from Fixed and Frozen Tissue Samples. Methods Mol Biol 2018; 1723:33-93. [PMID: 29344854 DOI: 10.1007/978-1-4939-7558-7_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Laser Capture Microdissection has earned a permanent place among modern techniques connecting histology and molecular biology. Laser Capture Microdissection has become an invaluable tool in medical research as a means for collection of specific cell populations isolated from their environment. Such genomic sample enrichment dramatically increases the sensitivity and precision of downstream molecular assays used for biomarker discovery, monitoring disease onset and progression, and in the development of personalized medicine. The diversity of research targets (cancerous and precancerous lesions in clinical and animal research, cell pellets, rodent embryos, frozen tissues, archival repository slides, etc.) and scientific objectives present a challenge in establishing standard protocols for Laser Capture Microdissection. In the present chapter, we share our experiences in design and successful execution of numerous diverse microdissection projects, and provide considerations to be taken into account in planning a microdissection study. Our workflow and protocols are standardized for a wide range of animal and human tissues and adapted to downstream analysis platforms.
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Abstract
Cellular mRNA levels are determined by the rates of mRNA synthesis and mRNA decay. Typically, mRNA degradation kinetics are measured on a population of cells that are either chemically treated or genetically engineered to inhibit transcription. However, these manipulations can affect the mRNA decay process itself by inhibiting regulatory mechanisms that govern mRNA degradation, especially if they occur on short time-scales. Recently, single molecule fluorescent in situ hybridization (smFISH) approaches have been implemented to quantify mRNA decay rates in single, unperturbed cells. Here, we provide a step-by-step protocol that allows quantification of mRNA decay in single Saccharomyces cerevisiae using smFISH. Our approach relies on fluorescent labeling of single cytoplasmic mRNAs and nascent mRNAs found at active sites of transcription, coupled with mathematical modeling to derive mRNA half-lives. Commercially available, single-stranded smFISH DNA oligonucleotides (smFISH probes) are used to fluorescently label mRNAs followed by the quantification of cellular and nascent mRNAs using freely available spot detection algorithms. Our method enables quantification of mRNA decay of any mRNA in single, unperturbed yeast cells and can be implemented to quantify mRNA turnover in a variety of cell types as well as tissues.
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Affiliation(s)
- Tatjana Trcek
- Department of Cell Biology, Skirball Institute of Biomolecular Medicine, NYU School of Medicine, New York, NY, USA.
| | - Samir Rahman
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC, Canada
| | - Daniel Zenklusen
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC, Canada
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Fang PY, Bowman JC, Gómez Ramos L, Hsiao C, Williams LD. RNA: packaged and protected by VLPs. RSC Adv 2018; 8:21399-21406. [PMID: 35539947 PMCID: PMC9080931 DOI: 10.1039/c8ra02084a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 06/04/2018] [Indexed: 01/16/2023] Open
Abstract
VLP packaging is most efficient for compact RNA, and protects RNA against assault by small diffusible damaging agents.
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Affiliation(s)
- Po-Yu Fang
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
| | - Jessica C. Bowman
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
| | - Lizzette M. Gómez Ramos
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
- School of Chemical and Biomolecular Engineering
| | - Chiaolong Hsiao
- Institute of Biochemical Sciences
- National Taiwan University
- Taipei 10617
- Republic of China
| | - Loren Dean Williams
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
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36
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Hamada J, Shoda K, Masuda K, Fujita Y, Naruto T, Kohmoto T, Miyakami Y, Watanabe M, Kudo Y, Fujiwara H, Ichikawa D, Otsuji E, Imoto I. Tumor-promoting function and prognostic significance of the RNA-binding protein T-cell intracellular antigen-1 in esophageal squamous cell carcinoma. Oncotarget 2017; 7:17111-28. [PMID: 26958940 PMCID: PMC4941375 DOI: 10.18632/oncotarget.7937] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Accepted: 02/05/2016] [Indexed: 02/06/2023] Open
Abstract
T-cell intracellular antigen-1 (TIA1) is an RNA-binding protein involved in many regulatory aspects of mRNA metabolism. Here, we report previously unknown tumor-promoting activity of TIA1, which seems to be associated with its isoform-specific molecular distribution and regulation of a set of cancer-related transcripts, in esophageal squamous cell carcinoma (ESCC). Immunohistochemical overexpression of TIA1 ectopically localized in the cytoplasm of tumor cells was an independent prognosticator for worse overall survival in a cohort of 143 ESCC patients. Knockdown of TIA1 inhibited proliferation of ESCC cells. By exogenously introducing each of two major isoforms, TIA1a and TIA1b, only TIA1a, which was localized to both the nucleus and cytoplasm, promoted anchorage-dependent and anchorage-independent ESCC cell proliferation. Ribonucleoprotein immunoprecipitation, followed by microarray analysis or massive-parallel sequencing, identified a set of TIA1-binding mRNAs, including SKP2 and CCNA2. TIA1 increased SKP2 and CCNA2 protein levels through the suppression of mRNA decay and translational induction, respectively. Our findings uncover a novel oncogenic function of TIA1 in esophageal tumorigenesis, and implicate its use as a marker for prognostic evaluation and as a therapeutic target in ESCC.
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Affiliation(s)
- Junichi Hamada
- Department of Human Genetics, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, 770-8503, Japan.,Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Katsutoshi Shoda
- Department of Human Genetics, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, 770-8503, Japan.,Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Kiyoshi Masuda
- Department of Human Genetics, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, 770-8503, Japan
| | - Yuji Fujita
- Department of Human Genetics, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, 770-8503, Japan.,Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Takuya Naruto
- Department of Human Genetics, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, 770-8503, Japan
| | - Tomohiro Kohmoto
- Department of Human Genetics, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, 770-8503, Japan.,Student Lab, Tokushima University Faculty of Medicine, Tokushima, 770-8503, Japan
| | - Yuko Miyakami
- Department of Human Genetics, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, 770-8503, Japan.,Student Lab, Tokushima University Faculty of Medicine, Tokushima, 770-8503, Japan
| | - Miki Watanabe
- Department of Human Genetics, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, 770-8503, Japan.,Student Lab, Tokushima University Faculty of Medicine, Tokushima, 770-8503, Japan
| | - Yasusei Kudo
- Department of Oral Molecular Pathology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, 770-8503, Japan
| | - Hitoshi Fujiwara
- Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Daisuke Ichikawa
- Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Eigo Otsuji
- Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Issei Imoto
- Department of Human Genetics, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, 770-8503, Japan
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Brook MS, Wilkinson DJ, Mitchell WK, Lund JL, Phillips BE, Szewczyk NJ, Kainulainen H, Lensu S, Koch LG, Britton SL, Greenhaff PL, Smith K, Atherton PJ. A novel D 2O tracer method to quantify RNA turnover as a biomarker of de novo ribosomal biogenesis, in vitro, in animal models, and in human skeletal muscle. Am J Physiol Endocrinol Metab 2017; 313:E681-E689. [PMID: 28811296 PMCID: PMC5814597 DOI: 10.1152/ajpendo.00157.2017] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 08/10/2017] [Accepted: 08/14/2017] [Indexed: 11/22/2022]
Abstract
Current methods to quantify in vivo RNA dynamics are limited. Here, we developed a novel stable isotope (D2O) methodology to quantify RNA synthesis (i.e., ribosomal biogenesis) in cells, animal models, and humans. First, proliferating C2C12 cells were incubated in D2O-enriched media and myotubes ±50 ng/ml IGF-I. Second, rat quadriceps (untrained, n = 9; 7-wk interval-"like" training, n = 13) were collected after ~3-wk D2O (70 atom %) administration, with body-water enrichment monitored via blood sampling. Finally, 10 (23 ± 1 yr) men consumed 150-ml D2O followed by 50 ml/wk and undertook 6-wk resistance exercise (6 × 8 repetitions, 75% 1-repetition maximum 3/wk) with body-water enrichment monitored by saliva sampling and muscle biopsies (for determination of RNA synthesis) at 0, 3, and 6 wk. Ribose mole percent excess (r-MPE) from purine nucleotides was analyzed via GC-MS/MS. Proliferating C2C12 cell r-MPE exhibited a rise to plateau, whereas IGF-I increased myotube RNA from 76 ± 3 to 123 ± 3 ng/μl and r-MPE by 0.39 ± 0.1% (both P < 0.01). After 3 wk, rat quadriceps r-MPE had increased to 0.25 ± 0.01% (P < 0.01) and was greater with running exercise (0.36 ± 0.02%; P < 0.01). Human muscle r-MPE increased to 0.06 ± 0.01 and 0.13 ± 0.02% at 3/6 wk, respectively, equating to synthesis rates of ~0.8%/day, increasing with resistance exercise to 1.7 ± 0.3%/day (P < 0.01) and 1.2 ± 0.1%/day (P < 0.05) at 3/6 wk, respectively. Therefore, we have developed and physiologically validated a novel technique to explore ribosomal biogenesis in a multimodal fashion.
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Affiliation(s)
- M S Brook
- Medical Research Council-Arthritis Research UK Centre for Musculoskeletal Ageing Research, Clinical, Metabolic and Molecular Physiology, University of Nottingham, Royal Derby Hospital Centre, Derby, United Kingdom
| | - D J Wilkinson
- Medical Research Council-Arthritis Research UK Centre for Musculoskeletal Ageing Research, Clinical, Metabolic and Molecular Physiology, University of Nottingham, Royal Derby Hospital Centre, Derby, United Kingdom
| | - W K Mitchell
- Medical Research Council-Arthritis Research UK Centre for Musculoskeletal Ageing Research, Clinical, Metabolic and Molecular Physiology, University of Nottingham, Royal Derby Hospital Centre, Derby, United Kingdom
| | - J L Lund
- Medical Research Council-Arthritis Research UK Centre for Musculoskeletal Ageing Research, Clinical, Metabolic and Molecular Physiology, University of Nottingham, Royal Derby Hospital Centre, Derby, United Kingdom
| | - B E Phillips
- Medical Research Council-Arthritis Research UK Centre for Musculoskeletal Ageing Research, Clinical, Metabolic and Molecular Physiology, University of Nottingham, Royal Derby Hospital Centre, Derby, United Kingdom
| | - N J Szewczyk
- Medical Research Council-Arthritis Research UK Centre for Musculoskeletal Ageing Research, Clinical, Metabolic and Molecular Physiology, University of Nottingham, Royal Derby Hospital Centre, Derby, United Kingdom
| | - H Kainulainen
- Department of Biology of Physical Activity, University of Jyväskylä, Jyväskylä, Finland; and
| | - S Lensu
- Department of Biology of Physical Activity, University of Jyväskylä, Jyväskylä, Finland; and
| | - L G Koch
- Department of Anesthesiology, University of Michigan, Ann Arbor, Michigan
| | - S L Britton
- Department of Anesthesiology, University of Michigan, Ann Arbor, Michigan
| | - P L Greenhaff
- Medical Research Council-Arthritis Research UK Centre for Musculoskeletal Ageing Research, Clinical, Metabolic and Molecular Physiology, University of Nottingham, Royal Derby Hospital Centre, Derby, United Kingdom
| | - K Smith
- Medical Research Council-Arthritis Research UK Centre for Musculoskeletal Ageing Research, Clinical, Metabolic and Molecular Physiology, University of Nottingham, Royal Derby Hospital Centre, Derby, United Kingdom
| | - P J Atherton
- Medical Research Council-Arthritis Research UK Centre for Musculoskeletal Ageing Research, Clinical, Metabolic and Molecular Physiology, University of Nottingham, Royal Derby Hospital Centre, Derby, United Kingdom;
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Pankevich EV, Astakhova AA, Chistyakov DV, Sergeeva MG. Antiinflammatory effect of rosiglitazone via modulation of mRNA stability of interleukin 10 and cyclooxygenase 2 in astrocytes. BIOCHEMISTRY (MOSCOW) 2017; 82:1276-1284. [DOI: 10.1134/s0006297917110050] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Ezegbunam W, Foronjy R. Posttranscriptional control of airway inflammation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 9. [PMID: 29071794 DOI: 10.1002/wrna.1455] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 09/07/2017] [Accepted: 09/08/2017] [Indexed: 12/18/2022]
Abstract
Acute inflammation in the lungs is a vital protective response, efficiently and swiftly eliminating inciters of tissue injury. However, in respiratory diseases characterized by chronic inflammation, such as chronic obstructive pulmonary disease and asthma, enhanced expression of inflammatory mediators leads to tissue damage and impaired lung function. Although transcription is an essential first step in the induction of proinflammatory genes, tight regulation of inflammation requires more rapid, flexible responses. Increasing evidence shows that such responses are achieved by posttranscriptional mechanisms directly affecting mRNA stability and translation initiation. RNA-binding proteins, microRNAs, and long noncoding RNAs interact with messenger RNA and each other to impact the stability and/or translation of mRNAs implicated in lung inflammation. Recent research has shown that these biological processes play a central role in the pathogenesis of several important pulmonary conditions. This review will highlight several posttranscriptional control mechanisms that influence lung inflammation and the known associations of derangements in these mechanisms with common respiratory diseases. WIREs RNA 2018, 9:e1455. doi: 10.1002/wrna.1455 This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Turnover and Surveillance > Regulation of RNA Stability.
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Affiliation(s)
- Wendy Ezegbunam
- Division of Pulmonary and Critical Care Medicine, Department of Medicine and Cell Biology, SUNY Downstate Medical Center, Brooklyn, NY, USA
| | - Robert Foronjy
- Division of Pulmonary and Critical Care Medicine, Department of Medicine and Cell Biology, SUNY Downstate Medical Center, Brooklyn, NY, USA
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Mattijssen S, Arimbasseri AG, Iben JR, Gaidamakov S, Lee J, Hafner M, Maraia RJ. LARP4 mRNA codon-tRNA match contributes to LARP4 activity for ribosomal protein mRNA poly(A) tail length protection. eLife 2017; 6:e28889. [PMID: 28895529 PMCID: PMC5626478 DOI: 10.7554/elife.28889] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 09/05/2017] [Indexed: 12/12/2022] Open
Abstract
Messenger RNA function is controlled by the 3' poly(A) tail (PAT) and poly(A)-binding protein (PABP). La-related protein-4 (LARP4) binds poly(A) and PABP. LARP4 mRNA contains a translation-dependent, coding region determinant (CRD) of instability that limits its expression. Although the CRD comprises <10% of LARP4 codons, the mRNA levels vary >20 fold with synonymous CRD substitutions that accommodate tRNA dynamics. Separately, overexpression of the most limiting tRNA increases LARP4 levels and reveals its functional activity, net lengthening of the PATs of heterologous mRNAs with concomitant stabilization, including ribosomal protein (RP) mRNAs. Genetic deletion of cellular LARP4 decreases PAT length and RPmRNA stability. This LARP4 activity requires its PABP-interaction domain and the RNA-binding module which we show is sensitive to poly(A) 3'-termini, consistent with protection from deadenylation. The results indicate that LARP4 is a posttranscriptional regulator of ribosomal protein production in mammalian cells and suggest that this activity can be controlled by tRNA levels.
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Affiliation(s)
- Sandy Mattijssen
- Eunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthBethesdaUnited States
| | | | - James R Iben
- Eunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthBethesdaUnited States
| | - Sergei Gaidamakov
- Eunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthBethesdaUnited States
| | - Joowon Lee
- Eunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthBethesdaUnited States
| | - Markus Hafner
- National Institute of Arthritis and Musculoskeletal and Skin DiseasesNational Institutes of HealthBethesdaUnited States
| | - Richard J Maraia
- Eunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthBethesdaUnited States
- Commissioned CorpsUS Public Health ServiceBethesdaUnited Staes
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Bai Z, Zhao L, Chen X, Li Q, Li J. A galectin contributes to the innate immune recognition and elimination of pathogens in the freshwater mussel Hyriopsis cumingii. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 73:36-45. [PMID: 28300581 DOI: 10.1016/j.dci.2017.03.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Revised: 03/08/2017] [Accepted: 03/09/2017] [Indexed: 06/06/2023]
Abstract
Galectins are members of the lectin superfamily. They function as pattern recognition receptors in the innate immune system of vertebrates and invertebrates. A galectin homolog from the triangle sail mussel Hyriopsis cumingii (HcGal2) was cloned and characterized. HcGal2 mRNA was expressed in all tissues examined, displaying particular enrichment in mantle tissue. Interestingly, rHcGAL2 protein was only detected in the mantle, hemocytes, and gills, suggesting that post-transcriptional regulation may occur. HcGal2 expression was induced in the mantle, liver, and hemocytes after exposure to lipopolysaccharides, Gram-negative bacteria (Aeromonas hydrophila), and Gram-positive bacteria (Staphylococcus aureus). The transcript significant upregulated was also detected after implantation in the mantle, pearl sac, liver, and hemocytes. Recombinant HcGAL2 protein (rHcGAL2) agglutinated Gram-positive and Gram-negative bacteria. In addition, rHcGAL2 promoted phagocytosis by hemocytes in vivo. Our data suggest that HcGal2 functioned as a pattern recognition receptor in against the pathogenic microbes and contributed to the "non-self" recognition and elimination in H. cumingii.
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Affiliation(s)
- Zhiyi Bai
- Key Laboratory of Genetic Resources for Freshwater Aquaculture and Fisheries, Shanghai Ocean University, Ministry of Agriculture, Shanghai 201306, PR China
| | - Liting Zhao
- Key Laboratory of Genetic Resources for Freshwater Aquaculture and Fisheries, Shanghai Ocean University, Ministry of Agriculture, Shanghai 201306, PR China
| | - Xiajun Chen
- Key Laboratory of Genetic Resources for Freshwater Aquaculture and Fisheries, Shanghai Ocean University, Ministry of Agriculture, Shanghai 201306, PR China
| | - Qingqing Li
- Key Laboratory of Genetic Resources for Freshwater Aquaculture and Fisheries, Shanghai Ocean University, Ministry of Agriculture, Shanghai 201306, PR China
| | - Jiale Li
- Key Laboratory of Genetic Resources for Freshwater Aquaculture and Fisheries, Shanghai Ocean University, Ministry of Agriculture, Shanghai 201306, PR China.
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Han F, Li Y, Lu Q, Ma L, Wang H, Jiang J, Li Z, Li Y. 3-(2-Chloropropyl amide)-4-methoxy-N-phenylbenzamide inhibits expression of HPV oncogenes in human cervical cancer cell. Virol J 2017; 14:145. [PMID: 28754129 PMCID: PMC5534069 DOI: 10.1186/s12985-017-0806-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 07/14/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Human papillomaviruses (HPVs) are the primary causative agents for cervical cancer, and HPV oncoproteins E6 and E7 are known to be the main reason for the onset and maintenance of the malignancies. Therefore, inhibition of viral E6 and E7 oncoproteins expression represents a viable strategy to cervical cancer therapies. This study is to evaluate the antiviral effect of a novel N-Phenylbenzamide derivative, 3-(2-Chloropropyl amide)-4-methoxy-N-phenylbenzamide (L17), against HPV16 in vitro and identify its associated mechanism of action in cervical cancer cells. METHODS The cytotoxic effect of L17 was assessed by MTT assay. The mRNA and protein levels of E6 and E7 oncogenes were analyzed by quantitative real-time reverse transcription PCR (qRT-PCR) and Western blot, respectively. p53 and Rb protein levels were also detected by Western blot. The effect of L17 on cell cycle was analyzed by flow cytometry. RESULTS The cytotoxic effect of L17 was greater in cervical carcinoma cells than in normal cells. L17 significantly reduced the expression of HPV16 E6 and E7 mRNA and protein, at least partly by enhancing degradation of HPV16 E6 and E7 mRNA. Moreover, reduced expression of E6 and E7 induced by L17 resulted in the up-regulation of p53 and Rb expression, which subsequently induced CaSki cells arrest at G0/G1 phase. CONCLUSIONS L17 has antiviral activity through suppressing E6 and E7 oncogene expression and could inhibit CaSki cell proliferating by inducing cells arrest at G0/G1 phase at nontoxic concentration, implying that L17 might be exploited as a candidate agent for HPV-associated cervical cancer prevention and treatment.
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Affiliation(s)
- Fang Han
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science & Peking Union Medical College, No 1, Tiantan Xili, Beijing, 100050, People's Republic of China
| | - Yanping Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science & Peking Union Medical College, No 1, Tiantan Xili, Beijing, 100050, People's Republic of China
| | - Qiaoni Lu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science & Peking Union Medical College, No 1, Tiantan Xili, Beijing, 100050, People's Republic of China
| | - Linlin Ma
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science & Peking Union Medical College, No 1, Tiantan Xili, Beijing, 100050, People's Republic of China.,Key Laboratory of Molecular Imaging of Shanghai Education Commission, Shanghai University of Medicine & Health Sciences, No 279, Zhouzhugong Road, Shanghai, 201318, People's Republic of China
| | - Huiqiang Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science & Peking Union Medical College, No 1, Tiantan Xili, Beijing, 100050, People's Republic of China
| | - Jiandong Jiang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science & Peking Union Medical College, No 1, Tiantan Xili, Beijing, 100050, People's Republic of China.,Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, No 1, Tiantan Xili, Beijing, 100050, China
| | - Zhuorong Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science & Peking Union Medical College, No 1, Tiantan Xili, Beijing, 100050, People's Republic of China.
| | - Yuhuan Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science & Peking Union Medical College, No 1, Tiantan Xili, Beijing, 100050, People's Republic of China.
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Regulation of Postoperative Ileus by Lentivirus-Mediated HuR RNA Interference via the p38/MK2 Signaling Pathway. J Gastrointest Surg 2017; 21:389-397. [PMID: 27796636 DOI: 10.1007/s11605-016-3303-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Accepted: 10/10/2016] [Indexed: 01/31/2023]
Abstract
OBJECTIVES The objective of the present study is to explore the effect of lentivirus-mediated HuR interference on the development and progression of postoperative ileus and the role of HuR in the regulation of the p38/MAPK-activated protein kinase-2 (MK2) signaling pathway during postoperative ileus. METHODS To establish a mouse model of lentiviral transduction, we first determined the optimum effective titer of lentiviral vectors for transduction of the murine small intestine via the abdominal cavity by using hematoxylin and eosin (HE) staining, immunohistochemistry, detection of GFP messenger RNA (mRNA) and protein, and Western blotting. To investigate the effect of HuR interference on gene expression during postoperative ileus, we established a mouse model of postoperative ileus and used RT-PCR to measure the expression of proinflammatory genes, ELISA to measure the expression of serum inflammatory cytokines, immunohistochemistry to evaluate inflammatory cell infiltration in the small intestine, HE staining of paraffin sections to examine the pathology of the small intestine, and Western blotting to measure HuR expression and identify its role in the regulation of the p38/MK2 inflammatory pathway. RESULTS We successfully designed a mouse model of intraperitoneal transduction of HuR-RNAi lentivirus. When HuR gene expression was suppressed in a mouse model of postoperative ileus, the infiltration of inflammatory cells, the expression of proinflammatory genes, and the levels of serum inflammatory cytokines were significantly reduced. This reduction in inflammation correlated with reduced cytoplasmic localization of HuR and reduced activation of MK2. CONCLUSIONS Within the p38/MK2 signal transduction pathway, HuR may increase the mRNA stability of various inflammatory cytokines, thereby promoting inflammation that causes postoperative ileus. Suppressing the expression of HuR in a postoperative ileus model can effectively suppress the postoperative ileus inflammatory reaction. HuR might serve as a candidate drug target for the prevention and mitigation of postoperative ileus.
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Ni Y, Zhao Y, Warren L, Higginbotham J, Wang J. cGMP Generation of Human Induced Pluripotent Stem Cells with Messenger RNA. ACTA ACUST UNITED AC 2016; 39:4A.6.1-4A.6.25. [PMID: 31816187 DOI: 10.1002/cpsc.18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Reprogramming somatic cells to generate induced pluripotent stem cells (iPSCs) has presented the biomedical community with a powerful platform to develop new models for human disease. To fully realize the promise of this technology in cell therapy and regenerative medicine, creating iPSCs under current Good Manufacture Practice (cGMP) conditions is paramount. Some reports have described efforts in this regard, resulting in iPSC lines that are cGMP compliant. The technology developed at Allele Biotechnology for footprint-free, feeder-free, and xeno-free reprogramming using only mRNA is very suitable for creating iPSC lines through an established cGMP process. This technology has resulted in a licensing agreement between Allele Biotechnology and Ocata (formerly ACT, now a wholly owned division of Astellas) for clinical applications. All reagents and vessels are certified as cGMP-produced, all equipment and software are certifiable, and all procedures are carried out in Industry ISO 7 or Class 10,000-grade cleanrooms. In this revised version of the unit, we describe the core improvements to implement steps toward cGMP-compliant generation of iPSCs. Recreating a process close to cGMP production in academic research will make these findings more applicable to translational research. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Yuhui Ni
- Allele Biotechnology and Pharmaceuticals, Inc, San Diego, California
| | - Yuanyuan Zhao
- Allele Biotechnology and Pharmaceuticals, Inc, San Diego, California
| | | | - Jennifer Higginbotham
- Allele Biotechnology and Pharmaceuticals, Inc, San Diego, California.,Scintillon Institute, San Diego, California
| | - Jiwu Wang
- Allele Biotechnology and Pharmaceuticals, Inc, San Diego, California.,Scintillon Institute, San Diego, California
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45
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Unusual Processing Generates SPA LncRNAs that Sequester Multiple RNA Binding Proteins. Mol Cell 2016; 64:534-548. [DOI: 10.1016/j.molcel.2016.10.007] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 07/22/2016] [Accepted: 10/04/2016] [Indexed: 12/13/2022]
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Moreno P, Garcia-Rosado E, Borrego JJ, Alonso MC. Genetic characterization and transcription analyses of the European sea bass (Dicentrarchus labrax) isg15 gene. FISH & SHELLFISH IMMUNOLOGY 2016; 55:642-6. [PMID: 27368533 DOI: 10.1016/j.fsi.2016.06.043] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 06/21/2016] [Accepted: 06/27/2016] [Indexed: 05/07/2023]
Abstract
Fish interferons are cytokines involved in its resistance to viral infections by inducing the transcription of several interferon-induced genes, such as isg15. The aim of the present study was the genetic characterization of the European sea bass isg15 gene, describing the regulatory motifs found in its sequence. In addition, an in vivo analysis of transcription in response to betanodavirus (RGNNV genotype) and poly I:C has been performed. The analysis of the resulting sequences showed that sea bass isg15 gene is composed of two exons and a single 276-bp intron located at the 5'-UTR region. The full length cDNA is 1143-bp, including a 102-bp 5'-UTR region, a 474-bp ORF, and a 291-bp 3'-UTR region. Several mRNA-regulatory elements, including three unusual ATTTA instability motifs in the intron, and four ATTTA motifs along with a cytoplasmic polyadenylation element in the 3'-UTR region, have been found in this sequence. The in vivo analyses revealed a similar kinetics and level of transcription in fish brain and head kidney after poly I:C inoculation; however, the induction caused by RGNNV started earlier in brain, where the upregulation of isg15 gene transcription was high. The present study contributes to further characterize the European sea bass IFN I response against RGNNV infections.
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Affiliation(s)
- Patricia Moreno
- Universidad de Málaga, Departamento de Microbiología, Facultad de Ciencias, 29071 Málaga, Spain
| | - Esther Garcia-Rosado
- Universidad de Málaga, Departamento de Microbiología, Facultad de Ciencias, 29071 Málaga, Spain
| | - Juan J Borrego
- Universidad de Málaga, Departamento de Microbiología, Facultad de Ciencias, 29071 Málaga, Spain
| | - M Carmen Alonso
- Universidad de Málaga, Departamento de Microbiología, Facultad de Ciencias, 29071 Málaga, Spain.
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Khan HA, Ibrahim KE, Khan A, Alrokayan SH, Alhomida AS, Lee YK. Comparative evaluation of immunohistochemistry and real-time PCR for measuring proinflammatory cytokines gene expression in livers of rats treated with gold nanoparticles. EXPERIMENTAL AND TOXICOLOGIC PATHOLOGY : OFFICIAL JOURNAL OF THE GESELLSCHAFT FUR TOXIKOLOGISCHE PATHOLOGIE 2016; 68:381-90. [PMID: 27287986 DOI: 10.1016/j.etp.2016.05.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 05/16/2016] [Accepted: 05/24/2016] [Indexed: 02/08/2023]
Abstract
Gold nanoparticles (GNPs) possess promising applications in targeted drug delivery and controlled release of a variety of chemical agents. However, the immunocompatibility of GNPs is poorly understood. After exposure, GNPs preferentially tend to accumulate is liver, where they induce an acute phase proinflammatory response. We therefore compared the two techniques, immunohistochemistry and real-time PCR for measuring the protein and mRNA expressions of IL-1β, IL-6 and TNF-α in liver of rats after intraperitoneal injections (5μg/animal) of 10 and 50nm diameter GNPs for 1 and 5days. The results showed that both 10nm and 50nm GNPs induced an acute phase expression of proinflammatory cytokines that receded on day 5. The proinflammatory response on day 1 was comparatively more severe with 50nm GNPs than 10nm GNPs. A comparative evaluation between immunostaining and real-time PCR showed that the latter technique is more sensitive as it could detect the cytokines mRNA expression in control samples as well. This could be partly attributed to the amplification strategy used in real-time PCR and partly to the variations in the half lives of cytokines mRNA and their resulting proteins.
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Affiliation(s)
- Haseeb A Khan
- Department of Biochemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia.
| | - Khalid E Ibrahim
- Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ayaat Khan
- Department of Zoology, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India
| | - Salman H Alrokayan
- Department of Biochemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Abdullah S Alhomida
- Department of Biochemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Yong-Kyu Lee
- Department of Chemical and Biological Engineering, Korea National University of Transportation, Chungju 380702, Republic of Korea
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Klein‐Bosgoed C, Schubert P, Devine DV. Riboflavin and ultraviolet illumination affects selected platelet mRNA transcript amounts differently. Transfusion 2016; 56:2286-95. [DOI: 10.1111/trf.13715] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 05/17/2016] [Accepted: 05/31/2016] [Indexed: 12/26/2022]
Affiliation(s)
- Christa Klein‐Bosgoed
- Department of Pathology and Laboratory Medicine and Centre for Blood ResearchUniversity of British Columbia
| | - Peter Schubert
- Department of Pathology and Laboratory Medicine and Centre for Blood ResearchUniversity of British Columbia
- Canadian Blood Services Centre for InnovationVancouver BC Canada
| | - Dana V. Devine
- Department of Pathology and Laboratory Medicine and Centre for Blood ResearchUniversity of British Columbia
- Canadian Blood Services Centre for InnovationVancouver BC Canada
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Lubiana P, Prokkola JM, Nikinmaa M, Burmester T, Kanerva M, Götting M. The effects of the painkiller diclofenac and hypoxia on gene transcription and antioxidant system in the gills of three-spined stickleback. Comp Biochem Physiol C Toxicol Pharmacol 2016; 185-186:147-154. [PMID: 27103419 DOI: 10.1016/j.cbpc.2016.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 04/08/2016] [Accepted: 04/12/2016] [Indexed: 11/22/2022]
Abstract
Aquatic organisms face multiple stressors in natural ecosystems. More and more often painkillers are detected in surface waters since their prescription has increased worldwide within the last years. Here we examined the effects of the non-steroidal anti-inflammatory drug (NSAID) diclofenac and hypoxia on three-spined sticklebacks (Gasterosteus aculeatus). We exposed sticklebacks to an environmentally relevant concentration of diclofenac (1μg/L) for 14days, to 24h of hypoxia (2.0mg O2/L), and a combination of both. Hypoxia and diclofenac both can be associated with oxidative stress in fish, but it is unclear whether they would act synergistically. Expression analysis of genes related to antioxidant response, hypoxia response, and chemical metabolism in gills showed that diclofenac alone had little effect, while the combination of hypoxia and diclofenac affected transcript levels most, indicating synergistic effects of these stressors. Of the antioxidant enzymes, only superoxide dismutase activity remained unchanged by treatments, while glutathione peroxidase (GPx) was the most affected antioxidant response on both the transcript and activity levels. Our results suggest that diclofenac may lead to suppressed catalase (CAT) activity but increased GPx activity, probably as compensatory mechanism to remove increasing H2O2 in the gills, and that this response is not affected by hypoxia. The activities of lactate dehydrogenase, CAT, and GPx also showed temporal variability during treatments, which can be attributable to tissue-specific circadian rhythms. Our study shows how responses to NSAIDs and hypoxia can interact in fish, suggesting that getting more insight into temporal variation and about the different levels of regulation of environmental responses is necessary in future studies.
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Affiliation(s)
- Pedro Lubiana
- Zoological Institute and Zoological Museum, Biocenter Grindel, University of Hamburg, D-20146 Hamburg, Germany
| | - Jenni M Prokkola
- Laboratory of Animal Physiology, Department of Biology, University of Turku, Turku FIN-20014, Finland
| | - Mikko Nikinmaa
- Laboratory of Animal Physiology, Department of Biology, University of Turku, Turku FIN-20014, Finland
| | - Thorsten Burmester
- Zoological Institute and Zoological Museum, Biocenter Grindel, University of Hamburg, D-20146 Hamburg, Germany
| | - Mirella Kanerva
- Laboratory of Animal Physiology, Department of Biology, University of Turku, Turku FIN-20014, Finland
| | - Miriam Götting
- Zoological Institute and Zoological Museum, Biocenter Grindel, University of Hamburg, D-20146 Hamburg, Germany; Laboratory of Animal Physiology, Department of Biology, University of Turku, Turku FIN-20014, Finland.
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50
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Muter J, Brighton PJ, Lucas ES, Lacey L, Shmygol A, Quenby S, Blanks AM, Brosens JJ. Progesterone-Dependent Induction of Phospholipase C-Related Catalytically Inactive Protein 1 (PRIP-1) in Decidualizing Human Endometrial Stromal Cells. Endocrinology 2016; 157:2883-93. [PMID: 27167772 PMCID: PMC4972893 DOI: 10.1210/en.2015-1914] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Decidualization denotes the transformation of endometrial stromal cells into specialized decidual cells. In pregnancy, decidual cells form a protective matrix around the implanting embryo, enabling coordinated trophoblast invasion and formation of a functional placenta. Continuous progesterone (P4) signaling renders decidual cells resistant to various environmental stressors, whereas withdrawal inevitably triggers tissue breakdown and menstruation or miscarriage. Here, we show that PLCL1, coding phospholipase C (PLC)-related catalytically inactive protein 1 (PRIP-1), is highly induced in response to P4 signaling in decidualizing human endometrial stromal cells (HESCs). Knockdown experiments in undifferentiated HESCs revealed that PRIP-1 maintains basal phosphoinositide 3-kinase/Protein kinase B activity, which in turn prevents illicit nuclear translocation of the transcription factor forkhead box protein O1 and induction of the apoptotic activator BIM. By contrast, loss of this scaffold protein did not compromise survival of decidual cells. PRIP-1 knockdown did also not interfere with the responsiveness of HESCs to deciduogenic cues, although the overall expression of differentiation markers, such as PRL, IGFBP1, and WNT4, was blunted. Finally, we show that PRIP-1 in decidual cells uncouples PLC activation from intracellular Ca(2+) release by attenuating inositol 1,4,5-trisphosphate signaling. In summary, PRIP-1 is a multifaceted P4-inducible scaffold protein that gates the activity of major signal transduction pathways in the endometrium. It prevents apoptosis of proliferating stromal cells and contributes to the relative autonomy of decidual cells by silencing PLC signaling downstream of Gq protein-coupled receptors.
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Affiliation(s)
- Joanne Muter
- Division of Biomedical Sciences (J.M., P.J.B., E.S.L., L.L., A.S., S.Q., A.M.B., J.J.B.), Warwick Medical School, University of Warwick, Coventry CV4 7AL, United Kingdom; and University Hospitals Coventry and Warwickshire National Health Service Trust (S.Q., J.J.B.), Coventry, CV2 2DX United Kingdom; and Tommy's National Miscarriage Research Centre (E.S.L., S.Q., J.J.B.), University Hospital Coventry and Warwickshire, Coventry, CV2 2DX United Kingdom
| | - Paul J Brighton
- Division of Biomedical Sciences (J.M., P.J.B., E.S.L., L.L., A.S., S.Q., A.M.B., J.J.B.), Warwick Medical School, University of Warwick, Coventry CV4 7AL, United Kingdom; and University Hospitals Coventry and Warwickshire National Health Service Trust (S.Q., J.J.B.), Coventry, CV2 2DX United Kingdom; and Tommy's National Miscarriage Research Centre (E.S.L., S.Q., J.J.B.), University Hospital Coventry and Warwickshire, Coventry, CV2 2DX United Kingdom
| | - Emma S Lucas
- Division of Biomedical Sciences (J.M., P.J.B., E.S.L., L.L., A.S., S.Q., A.M.B., J.J.B.), Warwick Medical School, University of Warwick, Coventry CV4 7AL, United Kingdom; and University Hospitals Coventry and Warwickshire National Health Service Trust (S.Q., J.J.B.), Coventry, CV2 2DX United Kingdom; and Tommy's National Miscarriage Research Centre (E.S.L., S.Q., J.J.B.), University Hospital Coventry and Warwickshire, Coventry, CV2 2DX United Kingdom
| | - Lauren Lacey
- Division of Biomedical Sciences (J.M., P.J.B., E.S.L., L.L., A.S., S.Q., A.M.B., J.J.B.), Warwick Medical School, University of Warwick, Coventry CV4 7AL, United Kingdom; and University Hospitals Coventry and Warwickshire National Health Service Trust (S.Q., J.J.B.), Coventry, CV2 2DX United Kingdom; and Tommy's National Miscarriage Research Centre (E.S.L., S.Q., J.J.B.), University Hospital Coventry and Warwickshire, Coventry, CV2 2DX United Kingdom
| | - Anatoly Shmygol
- Division of Biomedical Sciences (J.M., P.J.B., E.S.L., L.L., A.S., S.Q., A.M.B., J.J.B.), Warwick Medical School, University of Warwick, Coventry CV4 7AL, United Kingdom; and University Hospitals Coventry and Warwickshire National Health Service Trust (S.Q., J.J.B.), Coventry, CV2 2DX United Kingdom; and Tommy's National Miscarriage Research Centre (E.S.L., S.Q., J.J.B.), University Hospital Coventry and Warwickshire, Coventry, CV2 2DX United Kingdom
| | - Siobhan Quenby
- Division of Biomedical Sciences (J.M., P.J.B., E.S.L., L.L., A.S., S.Q., A.M.B., J.J.B.), Warwick Medical School, University of Warwick, Coventry CV4 7AL, United Kingdom; and University Hospitals Coventry and Warwickshire National Health Service Trust (S.Q., J.J.B.), Coventry, CV2 2DX United Kingdom; and Tommy's National Miscarriage Research Centre (E.S.L., S.Q., J.J.B.), University Hospital Coventry and Warwickshire, Coventry, CV2 2DX United Kingdom
| | - Andrew M Blanks
- Division of Biomedical Sciences (J.M., P.J.B., E.S.L., L.L., A.S., S.Q., A.M.B., J.J.B.), Warwick Medical School, University of Warwick, Coventry CV4 7AL, United Kingdom; and University Hospitals Coventry and Warwickshire National Health Service Trust (S.Q., J.J.B.), Coventry, CV2 2DX United Kingdom; and Tommy's National Miscarriage Research Centre (E.S.L., S.Q., J.J.B.), University Hospital Coventry and Warwickshire, Coventry, CV2 2DX United Kingdom
| | - Jan J Brosens
- Division of Biomedical Sciences (J.M., P.J.B., E.S.L., L.L., A.S., S.Q., A.M.B., J.J.B.), Warwick Medical School, University of Warwick, Coventry CV4 7AL, United Kingdom; and University Hospitals Coventry and Warwickshire National Health Service Trust (S.Q., J.J.B.), Coventry, CV2 2DX United Kingdom; and Tommy's National Miscarriage Research Centre (E.S.L., S.Q., J.J.B.), University Hospital Coventry and Warwickshire, Coventry, CV2 2DX United Kingdom
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