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Eftekhari Z, Zohrabi H, Oghalaie A, Ebrahimi T, Shariati FS, Behdani M, Kazemi-Lomedasht F. Advancements and challenges in mRNA and ribonucleoprotein-based therapies: From delivery systems to clinical applications. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102313. [PMID: 39281702 PMCID: PMC11402252 DOI: 10.1016/j.omtn.2024.102313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/18/2024]
Abstract
The use of mRNA and ribonucleoproteins (RNPs) as therapeutic agents is a promising strategy for treating diseases such as cancer and infectious diseases. This review provides recent advancements and challenges in mRNA- and RNP-based therapies, focusing on delivery systems such as lipid nanoparticles (LNPs), which ensure efficient delivery to target cells. Strategies such as microfluidic devices are employed to prepare LNPs loaded with mRNA and RNPs, demonstrating effective genome editing and protein expression in vitro and in vivo. These applications extend to cancer treatment and infectious disease management, with promising results in genome editing for cancer therapy using LNPs encapsulating Cas9 mRNA and single-guide RNA. In addition, tissue-specific targeting strategies offer potential for improved therapeutic outcomes and reduced off-target effects. Despite progress, challenges such as optimizing delivery efficiency and targeting remain. Future research should enhance delivery efficiency, explore tissue-specific targeting, investigate combination therapies, and advance clinical translation. In conclusion, mRNA- and RNP-based therapies offer a promising avenue for treating various diseases and have the potential to revolutionize medicine, providing new hope for patients worldwide.
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Affiliation(s)
- Zohre Eftekhari
- Venom and Biotherapeutics Molecules Laboratory, Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Horieh Zohrabi
- Venom and Biotherapeutics Molecules Laboratory, Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Akbar Oghalaie
- Venom and Biotherapeutics Molecules Laboratory, Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Tahereh Ebrahimi
- Department of Nanobiotechnology, New Technologies Research Group, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Fatemeh Sadat Shariati
- Department of Influenza and other Respiratory Viruses, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Mahdi Behdani
- Venom and Biotherapeutics Molecules Laboratory, Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Fatemeh Kazemi-Lomedasht
- Venom and Biotherapeutics Molecules Laboratory, Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
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Moreno RY, Panina SB, Irani S, Hardtke HA, Stephenson R, Floyd BM, Marcotte EM, Zhang Q, Zhang YJ. Thr 4 phosphorylation on RNA Pol II occurs at early transcription regulating 3'-end processing. SCIENCE ADVANCES 2024; 10:eadq0350. [PMID: 39241064 PMCID: PMC11378909 DOI: 10.1126/sciadv.adq0350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 08/01/2024] [Indexed: 09/08/2024]
Abstract
RNA polymerase II relies on a repetitive sequence domain (YSPTSPS) within its largest subunit to orchestrate transcription. While phosphorylation on serine-2/serine-5 of the carboxyl-terminal heptad repeats is well established, threonine-4's role remains enigmatic. Paradoxically, threonine-4 phosphorylation was only detected after transcription end sites despite functionally implicated in pausing, elongation, termination, and messenger RNA processing. Our investigation revealed that threonine-4 phosphorylation detection was obstructed by flanking serine-5 phosphorylation at the onset of transcription, which can be removed selectively. Subsequent proteomic analyses identified many proteins recruited to transcription via threonine-4 phosphorylation, which previously were attributed to serine-2. Loss of threonine-4 phosphorylation greatly reduces serine-2 phosphorylation, revealing a cross-talk between the two marks. Last, the function analysis of the threonine-4 phosphorylation highlighted its role in alternative 3'-end processing within pro-proliferative genes. Our findings unveil the true genomic location of this evolutionarily conserved phosphorylation mark and prompt a reassessment of functional assignments of the carboxyl-terminal domain.
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Affiliation(s)
| | - Svetlana B. Panina
- Department of Molecular Biosciences, University of Texas, Austin, TX, USA
| | - Seema Irani
- Department of Molecular Biosciences, University of Texas, Austin, TX, USA
| | - Haley A. Hardtke
- Department of Molecular Biosciences, University of Texas, Austin, TX, USA
| | - Renee Stephenson
- Department of Molecular Biosciences, University of Texas, Austin, TX, USA
| | - Brendan M. Floyd
- Department of Molecular Biosciences, University of Texas, Austin, TX, USA
| | - Edward M. Marcotte
- Department of Molecular Biosciences, University of Texas, Austin, TX, USA
| | - Qian Zhang
- Department of Molecular Biosciences, University of Texas, Austin, TX, USA
| | - Y. Jessie Zhang
- Department of Molecular Biosciences, University of Texas, Austin, TX, USA
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Rajan AAN, Hutchins EJ. Post-transcriptional regulation as a conserved driver of neural crest and cancer-cell migration. Curr Opin Cell Biol 2024; 89:102400. [PMID: 39032482 PMCID: PMC11346372 DOI: 10.1016/j.ceb.2024.102400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 06/26/2024] [Accepted: 06/26/2024] [Indexed: 07/23/2024]
Abstract
Cells have evolved mechanisms to migrate for diverse biological functions. A process frequently deployed during metazoan cell migration is the epithelial-mesenchymal transition (EMT). During EMT, adherent epithelial cells undergo coordinated cellular transitions to mesenchymalize and reduce their intercellular attachments. This is achieved via tightly regulated changes in gene expression, which modulates cell-cell and cell-matrix adhesion to allow movement. The acquisition of motility and invasive properties following EMT allows some mesenchymal cells to migrate through complex environments to form tissues during embryogenesis; however, these processes may also be leveraged by cancer cells, which often co-opt these endogenous programs to metastasize. Post-transcriptional regulation is now emerging as a major conserved mechanism by which cells modulate EMT and migration, which we discuss here in the context of vertebrate development and cancer.
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Affiliation(s)
- Arvind Arul Nambi Rajan
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Erica J Hutchins
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA.
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Cochran K, Yin M, Mantripragada A, Schreiber J, Marinov GK, Kundaje A. Dissecting the cis-regulatory syntax of transcription initiation with deep learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.596138. [PMID: 38853896 PMCID: PMC11160661 DOI: 10.1101/2024.05.28.596138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Despite extensive characterization of mammalian Pol II transcription, the DNA sequence determinants of transcription initiation at a third of human promoters and most enhancers remain poorly understood. Hence, we trained and interpreted a neural network called ProCapNet that accurately models base-resolution initiation profiles from PRO-cap experiments using local DNA sequence. ProCapNet learns sequence motifs with distinct effects on initiation rates and TSS positioning and uncovers context-specific cryptic initiator elements intertwined within other TF motifs. ProCapNet annotates predictive motifs in nearly all actively transcribed regulatory elements across multiple cell-lines, revealing a shared cis-regulatory logic across promoters and enhancers mediated by a highly epistatic sequence syntax of cooperative and competitive motif interactions. ProCapNet models of RAMPAGE profiles measuring steady-state RNA abundance at TSSs distill initiation signals on par with models trained directly on PRO-cap profiles. ProCapNet learns a largely cell-type-agnostic cis-regulatory code of initiation complementing sequence drivers of cell-type-specific chromatin state critical for accurate prediction of cell-type-specific transcription initiation.
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Affiliation(s)
- Kelly Cochran
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | | | | | - Jacob Schreiber
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Anshul Kundaje
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
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Smith AB, Ganguly DR, Moore M, Bowerman AF, Janapala Y, Shirokikh NE, Pogson BJ, Crisp PA. Dynamics of mRNA fate during light stress and recovery: from transcription to stability and translation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:818-839. [PMID: 37947266 PMCID: PMC10952913 DOI: 10.1111/tpj.16531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 09/20/2023] [Accepted: 10/23/2023] [Indexed: 11/12/2023]
Abstract
Transcript stability is an important determinant of its abundance and, consequently, translational output. Transcript destabilisation can be rapid and is well suited for modulating the cellular response. However, it is unclear the extent to which RNA stability is altered under changing environmental conditions in plants. We previously hypothesised that recovery-induced transcript destabilisation facilitated a phenomenon of rapid recovery gene downregulation (RRGD) in Arabidopsis thaliana (Arabidopsis) following light stress, based on mathematical calculations to account for ongoing transcription. Here, we test this hypothesis and investigate processes regulating transcript abundance and fate by quantifying changes in transcription, stability and translation before, during and after light stress. We adapt syringe infiltration to apply a transcriptional inhibitor to soil-grown plants in combination with stress treatments. Compared with measurements in juvenile plants and cell culture, we find reduced stability across a range of transcripts encoding proteins involved in RNA binding and processing. We also observe light-induced destabilisation of transcripts, followed by their stabilisation during recovery. We propose that this destabilisation facilitates RRGD, possibly in combination with transcriptional shut-off that was confirmed for HSP101, ROF1 and GOLS1. We also show that translation remains highly dynamic over the course of light stress and recovery, with a bias towards transcript-specific increases in ribosome association, independent of changes in total transcript abundance, after 30 min of light stress. Taken together, we provide evidence for the combinatorial regulation of transcription and stability that occurs to coordinate translation during light stress and recovery in Arabidopsis.
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Affiliation(s)
- Aaron B. Smith
- Research School of BiologyThe Australian National UniversityCanberraAustralian Capital Territory2601Australia
| | - Diep R. Ganguly
- CSIRO Synthetic Biology Future Science PlatformCanberraAustralian Capital Territory2601Australia
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Marten Moore
- Research School of BiologyThe Australian National UniversityCanberraAustralian Capital Territory2601Australia
| | - Andrew F. Bowerman
- Research School of BiologyThe Australian National UniversityCanberraAustralian Capital Territory2601Australia
| | - Yoshika Janapala
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery InstituteMonash UniversityClaytonVictoria3800Australia
| | - Nikolay E. Shirokikh
- The John Curtin School of Medical Research, The Shine‐Dalgarno Centre for RNA InnovationThe Australian National UniversityCanberraAustralian Capital Territory2601Australia
| | - Barry J. Pogson
- Research School of BiologyThe Australian National UniversityCanberraAustralian Capital Territory2601Australia
| | - Peter A. Crisp
- School of Agriculture and Food SciencesThe University of QueenslandBrisbaneQueensland4072Australia
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6
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Guzman-Espinoza M, Kim M, Ow C, Hutchins EJ. "Beyond transcription: How post-transcriptional mechanisms drive neural crest EMT". Genesis 2024; 62:e23553. [PMID: 37735882 PMCID: PMC10954587 DOI: 10.1002/dvg.23553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 09/02/2023] [Accepted: 09/13/2023] [Indexed: 09/23/2023]
Abstract
The neural crest is a stem cell population that originates from the ectoderm during the initial steps of nervous system development. Neural crest cells delaminate from the neuroepithelium by undergoing a spatiotemporally regulated epithelial-mesenchymal transition (EMT) that proceeds in a coordinated wave head-to-tail to exit from the neural tube. While much is known about the transcriptional programs and membrane changes that promote EMT, there are additional levels of gene expression control that neural crest cells exert at the level of RNA to control EMT and migration. Yet, the role of post-transcriptional regulation, and how it drives and contributes to neural crest EMT, is not well understood. In this mini-review, we explore recent advances in our understanding of the role of post-transcriptional regulation during neural crest EMT.
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Affiliation(s)
- Mariann Guzman-Espinoza
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Minyoung Kim
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
- Oral and Craniofacial Sciences Graduate Program, School of Dentistry, University of California San Francisco, San Francisco, CA, USA
| | - Cindy Ow
- Developmental and Stem Cell Biology Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Erica J. Hutchins
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
- Oral and Craniofacial Sciences Graduate Program, School of Dentistry, University of California San Francisco, San Francisco, CA, USA
- Developmental and Stem Cell Biology Graduate Program, University of California San Francisco, San Francisco, CA, USA
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Hirch T, Brander N, Schenk F, Pöllmann SJ, Reichenbach J, Schubert R, Modlich U. Expression of a large coding sequence: Gene therapy vectors for Ataxia Telangiectasia. Sci Rep 2023; 13:19386. [PMID: 37938627 PMCID: PMC10632516 DOI: 10.1038/s41598-023-46332-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/31/2023] [Indexed: 11/09/2023] Open
Abstract
Ataxia telangiectasia is a monogenetic disorder caused by mutations in the ATM gene. Its encoded protein kinase ATM plays a fundamental role in DNA repair of double strand breaks (DSBs). Impaired function of this kinase leads to a multisystemic disorder including immunodeficiency, progressive cerebellar degeneration, radiation sensitivity, dilated blood vessels, premature aging and a predisposition to cancer. Since allogenic hematopoietic stem cell (HSC) transplantation improved disease outcome, gene therapy based on autologous HSCs is an alternative promising concept. However, due to the large cDNA of ATM (9.2 kb), efficient packaging of retroviral particles and sufficient transduction of HSCs remains challenging.We generated lentiviral, gammaretroviral and foamy viral vectors with a GFP.F2A.Atm fusion or a GFP transgene and systematically compared transduction efficiencies. Vector titers dropped with increasing transgene size, but despite their described limited packaging capacity, we were able to produce lentiviral and gammaretroviral particles. The reduction in titers could not be explained by impaired packaging of the viral genomes, but the main differences occurred after transduction. Finally, after transduction of Atm-deficient (ATM-KO) murine fibroblasts with the lentiviral vector expressing Atm, we could show the expression of ATM protein which phosphorylated its downstream substrates (pKap1 and p-p53).
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Affiliation(s)
- Tanja Hirch
- Division of Veterinary Medicine, RG Gene Modification in Stem Cells, Paul-Ehrlich-Institute, Langen, Germany
| | - Nadine Brander
- Division of Veterinary Medicine, RG Gene Modification in Stem Cells, Paul-Ehrlich-Institute, Langen, Germany
| | - Franziska Schenk
- Division of Veterinary Medicine, RG Gene Modification in Stem Cells, Paul-Ehrlich-Institute, Langen, Germany
| | - Simon J Pöllmann
- Division of Veterinary Medicine, RG Gene Modification in Stem Cells, Paul-Ehrlich-Institute, Langen, Germany
- Department of Gene and Cell Therapy, Institute for Regenerative Medicine - IREM, University of Zurich, Schlieren, Switzerland
| | - Janine Reichenbach
- Department of Gene and Cell Therapy, Institute for Regenerative Medicine - IREM, University of Zurich, Schlieren, Switzerland
- Deptartment of Somatic Gene Therapy, University Children's Hospital Zurich, Zurich, Switzerland
- Competence Center for Applied Biotechnology and Molecular Medicine (CABMM), University of Zurich, Zurich, Switzerland
| | - Ralf Schubert
- Department for Children and Adolescents, University Hospital Frankfurt, Goethe University, Frankfurt, Germany
| | - Ute Modlich
- Division of Veterinary Medicine, RG Gene Modification in Stem Cells, Paul-Ehrlich-Institute, Langen, Germany.
- Department of Gene and Cell Therapy, Institute for Regenerative Medicine - IREM, University of Zurich, Schlieren, Switzerland.
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8
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Kim YR, Hong SH. Associations of leptin receptors and miRNA polymorphisms with susceptibility to hypertension. Biomed Rep 2023; 19:79. [PMID: 37829260 PMCID: PMC10565717 DOI: 10.3892/br.2023.1661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 08/02/2023] [Indexed: 10/14/2023] Open
Abstract
Leptin receptors (LEPR) are located in the central nervous system and other tissues including adipocytes and endothelial cells, where they play a key role in mediating the effects of leptin. MicroRNA (miR/miRNA)-27a and miR-155 have been shown to play an important role in the regulation of LEPR expression and are differentially expressed in various diseases. Therefore, the present study analyzed potential associations of LEPR deletion/insertion (Del/Ins), miR-27aA>G (rs895819) and miR-155T>A (rs767649) polymorphisms with a predisposition to hypertension (HTN). Genotyping was performed by a PCR-restriction fragment length polymorphism assay. Frequencies of LEPR Del/Ins and miRNA gene polymorphisms in patients diagnosed with HTN (n=232) and randomly selected healthy controls (n=247) were assessed. The present study found that Del/Ins and Ins/Ins genotypes and the Ins allele of the LEPR Del/Ins polymorphism were associated with a decreased risk of HTN compared with controls, whereas the miR-27aA>G rs895819 polymorphism was associated with an increased risk of HTN. Combined genotype and allele analyses for LEPR Del/Ins and two miRNA polymorphisms revealed an association with an increased risk or a decreased risk of HTN. Furthermore, stratification analysis revealed that HTN risk factors were associated with waist circumference (WC) and high-density lipoprotein cholesterol (HDL-C) values in LEPR Del/Ins polymorphism. They were also associated with body mass index, WC, triglyceride and HDL-C values in miR-27aA>G polymorphism. The present study revealed a combined effect of LEPR Del/Ins and miR-27aA>G polymorphisms on the risk of HTN in Koreans, suggesting that these gene polymorphisms could be potential markers for predicting HTN risk.
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Affiliation(s)
- Young Ree Kim
- Department of Laboratory Medicine, School of Medicine, Jeju National University Hospital, Jeju 63241, Republic of Korea
| | - Seung-Ho Hong
- Department of Science Education, Teachers College, Jeju National University, Jeju 63294, Republic of Korea
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Jamous YF, Alhomoud DA. The Safety and Effectiveness of mRNA Vaccines Against SARS-CoV-2. Cureus 2023; 15:e45602. [PMID: 37868494 PMCID: PMC10588549 DOI: 10.7759/cureus.45602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2023] [Indexed: 10/24/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in numerous deaths worldwide, along with devastating economic disruptions, and has posed unprecedented challenges to healthcare systems around the world. In the wake of COVID-19's emergence in 2019, a variety of vaccine technologies were formulated and developed, including those that drew from the technology employed in messenger RNA (mRNA) vaccines, designed to curb the disease's transmission and manage the pandemic. mRNA vaccine has several advantages over traditional ones, and hence its development has received considerable attention recently. Researchers believe the mRNA vaccine technology will emerge as the leading technology because it is potent, inexpensive, rapidly developed, and safe. This article provides an overview of mRNA vaccines with a special focus on the efficacy and safety of the Moderna and Pfizer-BioNTech mRNA vaccines against the different variants of COVID-19 and compare them with the Oxford-AstraZeneca (viral vector) and Sinopharm (inactivated virus) vaccines. The clinical data reviewed in this article demonstrate that the currently authorized Moderna and Pfizer-BioNTech mRNA vaccines are highly safe and potent against different variants of COVID-19, especially in comparison with Oxford-AstraZeneca (viral vector) and Sinopharm (inactivated virus) vaccines.
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Affiliation(s)
- Yahya F Jamous
- National Center of Vaccine and Bioprocessing, King Abdulaziz City for Science and Technology, Riyadh, SAU
| | - Dalal A Alhomoud
- National Center of Vaccine and Bioprocessing, King Abdulaziz City for Science and Technology, Riyadh, SAU
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Yihunie W, Nibret G, Aschale Y. Recent Advances in Messenger Ribonucleic Acid (mRNA) Vaccines and Their Delivery Systems: A Review. Clin Pharmacol 2023; 15:77-98. [PMID: 37554660 PMCID: PMC10405914 DOI: 10.2147/cpaa.s418314] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 07/28/2023] [Indexed: 08/10/2023] Open
Abstract
Messenger ribonucleic acid (mRNA) was found as the intermediary that transfers genetic information from DNA to ribosomes for protein synthesis in 1961. The emergency use authorization of the two covid-19 mRNA vaccines, BNT162b2 and mRNA-1273, is a significant achievement in the history of vaccine development. Because they are generated in a cell-free environment using the in vitro transcription (IVT) process, mRNA vaccines are risk-free. Moreover, chemical modifications to the mRNA molecule, such as cap structures and changed nucleosides, have proved critical in overcoming immunogenicity concerns, achieving sustained stability, and achieving effective, accurate protein production in vivo. Several vaccine delivery strategies (including protamine, lipid nanoparticles (LNPs), polymers, nanoemulsions, and cell-based administration) were also optimized to load and transport RNA into the cytosol. LNPs, which are composed of a cationic or a pH-dependent ionizable lipid layer, a polyethylene glycol (PEG) component, phospholipids, and cholesterol, are the most advanced systems for delivering mRNA vaccines. Moreover, modifications of the four components that make up the LNPs showed to increase vaccine effectiveness and reduce side effects. Furthermore, the introduction of biodegradable lipids improved LNP biocompatibility. Furthermore, mRNA-based therapies are expected to be effective treatments for a variety of refractory conditions, including infectious diseases, metabolic genetic diseases, cancer, cardiovascular and cerebrovascular diseases. Therefore, the present review aims to provide the scientific community with up-to-date information on mRNA vaccines and their delivery systems.
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Affiliation(s)
- Wubetu Yihunie
- Department of Pharmacy, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Getinet Nibret
- Department of Pharmacy, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Yibeltal Aschale
- Department of Medical Laboratory Science, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
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Kong L, Zhou Y, Yuan J, Lv T, Yang J, Shi Y, Yang J. Mitochondrial miR-23b-5p is a new biomarker of warm ischaemic injury in donor livers and a candidate for graft evaluation: experimental studies. Int J Surg 2023; 109:1880-1892. [PMID: 37184476 PMCID: PMC10389456 DOI: 10.1097/js9.0000000000000263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 01/31/2023] [Indexed: 05/16/2023]
Abstract
BACKGROUND AND AIMS Warm ischaemic injury (WII) stems from incorrect energy metabolism and is the main cause of graft dysfunction. Mitochondria, as the centre of cellular metabolic activities, may be the key in identifying accurate indicators for evaluating the quality of grafts. Our research focuses on the screening, clinical application, and mechanism of the optimal WII mitochondrion biomarker. APPROACH AND RESULTS Using a 100% hepatic warm ischaemia mouse model, without reperfusion, transmission electron microscopy demonstrated evident morphological changes of hepatic mitochondria at 15 min of ischaemia. However, all 13 mt-mRNAs could not display continuously upregulated consistency at 0-15-30-60 min during WII. High-throughput analysis of miRNA expression in both purified mitochondria and liver tissues suggested miR-23b-5p was a potential mitochondrial microRNA (mitomiR) biomarker with high sensitivity and 0-15-30-60 min change consistency. Fluorescence in-situ hybridization and reverse transcription quantitative polymerase chain reaction (RT-qPCR) further confirmed the results. Through overexpression and inhibition, the functionality of this mitomiR during WII was identified as a protective regulator in vitro and then verified in Dicer1 fl/fl Alb Cre mice by downregulation of other miRNAs and supplementation of mature mitomiR-23b-5p. Dual-luciferase reporter assay and the Seahorse XF analyzer determined that mitomiR-23b-5p reduced mitochondrial respiratory function by silencing mt-RNR2 (16S). Clinically, mitomiR-23b-5p was positively correlated with serum alanine aminotransferase levels 3 days after the operation ( P =0.032), and the C-statistic for 90-day graft survival rate was 0.698. CONCLUSIONS MitomiR-23b-5p plays a protective regulatory role and implements a special mitochondrial regulation mechanism not yet reported in WII. These clinical results further support the experimental result that the expression of MitomiR-23b-5p is closely related to the prognosis of clinical liver transplantation patients. This is a promising new biomarker for WII evaluation of donor livers.
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Affiliation(s)
- Lingxiang Kong
- Department of Liver transplantation Laboratory
- Department of Liver transplantation Center, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China
| | | | - Jingsheng Yuan
- Department of Liver transplantation Center, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China
| | - Tao Lv
- Department of Liver transplantation Center, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China
| | - Jian Yang
- Department of Liver transplantation Center, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China
| | - Yujun Shi
- Department of Liver transplantation Laboratory
| | - Jiayin Yang
- Department of Liver transplantation Laboratory
- Department of Liver transplantation Center, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China
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12
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Prawer YDJ, Gleeson J, De Paoli-Iseppi R, Clark MB. Pervasive effects of RNA degradation on Nanopore direct RNA sequencing. NAR Genom Bioinform 2023; 5:lqad060. [PMID: 37305170 PMCID: PMC10251640 DOI: 10.1093/nargab/lqad060] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 04/18/2023] [Accepted: 06/07/2023] [Indexed: 06/13/2023] Open
Abstract
Oxford Nanopore direct RNA sequencing (DRS) is capable of sequencing complete RNA molecules and accurately measuring gene and isoform expression. However, as DRS is designed to profile intact RNA, expression quantification may be more heavily dependent upon RNA integrity than alternative RNA sequencing methodologies. It is currently unclear how RNA degradation impacts DRS or whether it can be corrected for. To assess the impact of RNA integrity on DRS, we performed a degradation time series using SH-SY5Y neuroblastoma cells. Our results demonstrate that degradation is a significant and pervasive factor that can bias DRS measurements, including a reduction in library complexity resulting in an overrepresentation of short genes and isoforms. Degradation also biases differential expression analyses; however, we find that explicit correction can almost fully recover meaningful biological signal. In addition, DRS provided less biased profiling of partially degraded samples than Nanopore PCR-cDNA sequencing. Overall, we find that samples with RNA integrity number (RIN) > 9.5 can be treated as undegraded and samples with RIN > 7 can be utilized for DRS with appropriate correction. These results establish the suitability of DRS for a wide range of samples, including partially degraded in vivo clinical and post-mortem samples, while limiting the confounding effect of degradation on expression quantification.
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Affiliation(s)
- Yair D J Prawer
- Centre for Stem Cell Systems, Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Josie Gleeson
- Centre for Stem Cell Systems, Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ricardo De Paoli-Iseppi
- Centre for Stem Cell Systems, Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Michael B Clark
- To whom correspondence should be addressed. Tel: +61 3 9035 3669;
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13
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Guha A, Husain MA, Si Y, Nabors LB, Filippova N, Promer G, Smith R, King PH. RNA regulation of inflammatory responses in glia and its potential as a therapeutic target in central nervous system disorders. Glia 2023; 71:485-508. [PMID: 36380708 DOI: 10.1002/glia.24288] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/29/2022] [Accepted: 10/14/2022] [Indexed: 11/17/2022]
Abstract
A major hallmark of neuroinflammation is the activation of microglia and astrocytes with the induction of inflammatory mediators such as IL-1β, TNF-α, iNOS, and IL-6. Neuroinflammation contributes to disease progression in a plethora of neurological disorders ranging from acute CNS trauma to chronic neurodegenerative disease. Posttranscriptional pathways of mRNA stability and translational efficiency are major drivers for the expression of these inflammatory mediators. A common element in this level of regulation centers around the adenine- and uridine-rich element (ARE) which is present in the 3' untranslated region (UTR) of the mRNAs encoding these inflammatory mediators. (ARE)-binding proteins (AUBPs) such as Human antigen R (HuR), Tristetraprolin (TTP) and KH- type splicing regulatory protein (KSRP) are key nodes for directing these posttranscriptional pathways and either promote (HuR) or suppress (TTP and KSRP) glial production of inflammatory mediators. This review will discuss basic concepts of ARE-mediated RNA regulation and its impact on glial-driven neuroinflammatory diseases. We will discuss strategies to target this novel level of gene regulation for therapeutic effect and review exciting preliminary studies that underscore its potential for treating neurological disorders.
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Affiliation(s)
- Abhishek Guha
- Department Neurology, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Mohammed Amir Husain
- Department Neurology, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Ying Si
- Department Neurology, The University of Alabama at Birmingham, Birmingham, Alabama, USA
- Department Cell, Developmental, and Integrative Biology, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - L Burt Nabors
- Department Neurology, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Natalia Filippova
- Department Neurology, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Grace Promer
- Department Neurology, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Reed Smith
- Department Neurology, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Peter H King
- Department Neurology, The University of Alabama at Birmingham, Birmingham, Alabama, USA
- Department Cell, Developmental, and Integrative Biology, The University of Alabama at Birmingham, Birmingham, Alabama, USA
- Birmingham Department of Veterans Health Care System, Birmingham, Alabama, USA
- Center for Neurodegeneration and Experimental Therapeutics, The University of Alabama at Birmingham, Birmingham, USA
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14
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Wenzlow N, Mills D, Byrd J, Warren M, Long MT. Review of the current and potential use of biological and molecular methods for the estimation of the postmortem interval in animals and humans. J Vet Diagn Invest 2023; 35:97-108. [PMID: 36744749 PMCID: PMC9999395 DOI: 10.1177/10406387231153930] [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: 02/07/2023] Open
Abstract
We provide here an overview of the state of applied techniques in the estimation of the early period of the postmortem interval (PMI). The biological methods included consist of body cooling, CSF potassium, body cooling combined with CSF potassium, and tissue autolysis. For each method, we present its application in human and veterinary medicine and provide current methodology, strengths, and weaknesses, as well as target areas for improvement. We examine current and future molecular methods as they pertain to DNA and primarily to messenger RNA degradation for the estimation of the PMI, as well as the use of RNA in aging wounds, aging blood stains, and the identification of body fluids. Various types of RNA have different lengths, structures, and functions in cells. These differences in RNAs determine various intrinsic properties, such as their half-lives in cells, and, hence, their decay rate as well as their unique use for specific forensic tests. Future applications and refinements of RNA-based techniques provide opportunities for the use of molecular methods in the estimation of PMI and other general forensic applications.
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Affiliation(s)
- Nanny Wenzlow
- Louisiana Animal Disease Diagnostic Laboratory, Louisiana State University, Baton Rouge, LA, USA
| | - DeEtta Mills
- Department of Biological Sciences and International Forensic Research Institute, Florida International University, Miami, FL, USA
| | - Jason Byrd
- Maples Center for Forensic Medicine, University of Florida, Gainesville, FL, USA
| | - Mike Warren
- Maples Center for Forensic Medicine, University of Florida, Gainesville, FL, USA
| | - Maureen T. Long
- Department of Comparative, Diagnostic, and Population Medicine, University of Florida, Gainesville, FL, USA
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15
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Aljabali AAA, Bashatwah RM, Obeid MA, Mishra V, Mishra Y, Serrano-Aroca Á, Lundstrom K, Tambuwala MM. Current state of, prospects for, and obstacles to mRNA vaccine development. Drug Discov Today 2023; 28:103458. [PMID: 36427779 DOI: 10.1016/j.drudis.2022.103458] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/15/2022] [Accepted: 11/17/2022] [Indexed: 11/25/2022]
Abstract
Given their superior efficacy, rapid engineering, low-cost manufacturing, and safe delivery prospects, mRNA vaccines offer an intriguing alternative to conventional vaccination technologies. Several mRNA vaccine platforms targeting infectious diseases and various types of cancer have exhibited beneficial results both in vivo and in vitro. Issues related to mRNA stability and immunogenicity have been addressed. Current mRNA vaccines can generate robust immune responses, without being constrained by the major histocompatibility complex (MHC) haplotype of the recipient. Given that mRNA vaccinations are the only transient genetic information carriers, they are also safe. In this review, we provide an update and overview on mRNA vaccines, including their current state, and the problems that have prevented them from being used in more general therapeutic ways.
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Affiliation(s)
- Alaa A A Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Yarmouk University, Irbid 21163, Jordan.
| | - Rasha M Bashatwah
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Yarmouk University, Irbid 21163, Jordan
| | - Mohammad A Obeid
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Yarmouk University, Irbid 21163, Jordan.
| | - Vijay Mishra
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara 144411, Punjab, India
| | - Yachana Mishra
- Department of Zoology, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, Punjab, India
| | - Ángel Serrano-Aroca
- Biomaterials & Bioengineering Lab, Centro de Investigación Traslacional San Alberto Magno, Universidad Católica de Valencia, San Vicente Mártir, Valencia 46001, Spain
| | | | - Murtaza M Tambuwala
- Lincoln Medical School, University of Lincoln, Brayford Pool Campus, Lincoln LN6 7TS, UK.
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16
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mRNA-From COVID-19 Treatment to Cancer Immunotherapy. Biomedicines 2023; 11:biomedicines11020308. [PMID: 36830845 PMCID: PMC9953480 DOI: 10.3390/biomedicines11020308] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/05/2023] [Accepted: 01/09/2023] [Indexed: 01/24/2023] Open
Abstract
This review provides an overview covering mRNA from its use in the COVID-19 pandemic to cancer immunotherapy, starting from the selection of appropriate antigens, tumor-associated and tumor-specific antigens, neoantigens, the basics of optimizing the mRNA molecule in terms of stability, efficacy, and tolerability, choosing the best formulation and the optimal route of administration, to summarizing current clinical trials of mRNA vaccines in tumor therapy.
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17
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Sedighikamal H, Karimi Mostofi R, Sattarzadeh A, Shahbazi M, Aghazadeh H. Comparative study of commercial media to improve GMP manufacturing of recombinant human interferon β-1a by CHO cells in perfusion bioreactor. Cytotechnology 2022; 74:669-680. [PMID: 36389287 PMCID: PMC9652187 DOI: 10.1007/s10616-022-00554-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 10/03/2022] [Indexed: 11/25/2022] Open
Abstract
Chinese hamster ovary cells are the main cellular factories for production of a wide range of recombinant proteins in biopharmaceutical industry. Recombinant human Interferon beta-1a (rh-IFN β-1a), as a cytokine is broadly used to treat multiple sclerosis. In this work, the cell line producing rh-IFN β-1a was studied to improve cell density along with the specific expression. For this reason different cell culture experiments were done using different commercial serum-free media to find the appropriate media providing higher cell density. It was shown DMEMF12, DMEM:ProCHO5, and CHO-S-SFM II led to higher cell density and shorter doubling time. Next, using these media, fed-batch, and perfusion culture with temperature shift were implemented to investigate the best condition for industrial-scale manufacturing of rh-IFN β-1a in terms of higher cell density and product expression yield. The results demonstrated that CHO-S-SFM II media and a thermally biphasic condition provide enhanced expression of rh-IFN β-1a in perfusion bioreactor.
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Affiliation(s)
- Hossein Sedighikamal
- API Production Plant, Actoverco Biotech Company, Alborz, Iran
- Division of Industrial Biotechnology, Department of Chemical Engineering, Sharif University of Technology, Tehran, Iran
| | - Reza Karimi Mostofi
- API Production Plant, Actoverco Biotech Company, Alborz, Iran
- Department of Pharmaceutics, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
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18
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Agarwal V, Kelley DR. The genetic and biochemical determinants of mRNA degradation rates in mammals. Genome Biol 2022; 23:245. [PMID: 36419176 PMCID: PMC9684954 DOI: 10.1186/s13059-022-02811-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 11/02/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Degradation rate is a fundamental aspect of mRNA metabolism, and the factors governing it remain poorly characterized. Understanding the genetic and biochemical determinants of mRNA half-life would enable more precise identification of variants that perturb gene expression through post-transcriptional gene regulatory mechanisms. RESULTS We establish a compendium of 39 human and 27 mouse transcriptome-wide mRNA decay rate datasets. A meta-analysis of these data identified a prevalence of technical noise and measurement bias, induced partially by the underlying experimental strategy. Correcting for these biases allowed us to derive more precise, consensus measurements of half-life which exhibit enhanced consistency between species. We trained substantially improved statistical models based upon genetic and biochemical features to better predict half-life and characterize the factors molding it. Our state-of-the-art model, Saluki, is a hybrid convolutional and recurrent deep neural network which relies only upon an mRNA sequence annotated with coding frame and splice sites to predict half-life (r=0.77). The key novel principle learned by Saluki is that the spatial positioning of splice sites, codons, and RNA-binding motifs within an mRNA is strongly associated with mRNA half-life. Saluki predicts the impact of RNA sequences and genetic mutations therein on mRNA stability, in agreement with functional measurements derived from massively parallel reporter assays. CONCLUSIONS Our work produces a more robust ground truth for transcriptome-wide mRNA half-lives in mammalian cells. Using these revised measurements, we trained Saluki, a model that is over 50% more accurate in predicting half-life from sequence than existing models. Saluki succinctly captures many of the known determinants of mRNA half-life and can be rapidly deployed to predict the functional consequences of arbitrary mutations in the transcriptome.
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Affiliation(s)
- Vikram Agarwal
- Calico Life Sciences LLC, South San Francisco, CA, 94080, USA.
- Present Address: mRNA Center of Excellence, Sanofi Pasteur Inc., Waltham, MA, 02451, USA.
| | - David R Kelley
- Calico Life Sciences LLC, South San Francisco, CA, 94080, USA.
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19
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The RNA-Binding Protein ELAVL1 Regulates Hepatitis B Virus Replication and Growth of Hepatocellular Carcinoma Cells. Int J Mol Sci 2022; 23:ijms23147878. [PMID: 35887229 PMCID: PMC9316910 DOI: 10.3390/ijms23147878] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/11/2022] [Accepted: 07/14/2022] [Indexed: 12/19/2022] Open
Abstract
Previous RNA immunoprecipitation followed by proteomic approaches successfully demonstrated that Embryonic Lethal, Abnormal Vision, Drosophila-Like 1 (ELAVL1) interacts with hepatitis B virus (HBV)-derived RNAs. Although ELAVL family proteins stabilize AU-rich element (ARE)-containing mRNAs, their role in HBV transcription remains unclear. This study conducted loss-of-function assays of ELAVL1 for inducible HBV-replicating HepAD38 cells and HBx-overexpressed HepG2 cells. In addition, clinicopathological analyses in primary hepatocellular carcinoma (HCC) surgical samples were also conducted. Lentivirus-mediated short hairpin RNA knockdown of ELAVL1 resulted in a decrease in both viral RNA transcription and production of viral proteins, including HBs and HBx, probably due to RNA stabilization by ELAVL1. Cell growth of HepAD38 cells was more significantly impaired in ELAVL1-knockdown than those in the control group, with or without HBV replication, indicating that ELAVL1 is involved in proliferation by factors other than HBV-derived RNAs. Immunohistochemical analyses of 77 paired HCC surgical specimens demonstrated that diffuse ELAVL1 expression was detected more frequently in HCC tissues (61.0%) than in non-tumor tissues (27.3%). In addition, the abundant expression of ELAVL1 tended to affect postoperative recurrence in HBV-related HCC patients. In conclusion, ELAVL1 contributes not only to HBV replication but also to HCC cell growth. It may be a potent therapeutic target for HBV-related HCC treatment.
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20
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Diez M, Medina-Muñoz SG, Castellano LA, da Silva Pescador G, Wu Q, Bazzini AA. iCodon customizes gene expression based on the codon composition. Sci Rep 2022; 12:12126. [PMID: 35840631 PMCID: PMC9287306 DOI: 10.1038/s41598-022-15526-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 06/24/2022] [Indexed: 11/09/2022] Open
Abstract
Messenger RNA (mRNA) stability substantially impacts steady-state gene expression levels in a cell. mRNA stability is strongly affected by codon composition in a translation-dependent manner across species, through a mechanism termed codon optimality. We have developed iCodon (www.iCodon.org), an algorithm for customizing mRNA expression through the introduction of synonymous codon substitutions into the coding sequence. iCodon is optimized for four vertebrate transcriptomes: mouse, human, frog, and fish. Users can predict the mRNA stability of any coding sequence based on its codon composition and subsequently generate more stable (optimized) or unstable (deoptimized) variants encoding for the same protein. Further, we show that codon optimality predictions correlate with both mRNA stability using a massive reporter library and expression levels using fluorescent reporters and analysis of endogenous gene expression in zebrafish embryos and/or human cells. Therefore, iCodon will benefit basic biological research, as well as a wide range of applications for biotechnology and biomedicine.
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Affiliation(s)
- Michay Diez
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO, 64110, USA
| | - Santiago Gerardo Medina-Muñoz
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO, 64110, USA.,National Laboratory of Genomics for Biodiversity (LANGEBIO), Unit of Advanced Genomics, 36824, Irapuato, Mexico
| | | | | | - Qiushuang Wu
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO, 64110, USA
| | - Ariel Alejandro Bazzini
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO, 64110, USA. .,Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS, 66160, USA.
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21
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Kloczewiak M, Banks JM, Jin L, Brader ML. A Biopharmaceutical Perspective on Higher-Order Structure and Thermal Stability of mRNA Vaccines. Mol Pharm 2022; 19:2022-2031. [PMID: 35715255 PMCID: PMC9257798 DOI: 10.1021/acs.molpharmaceut.2c00092] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 05/13/2022] [Accepted: 05/16/2022] [Indexed: 12/27/2022]
Abstract
Preservation of the integrity of macromolecular higher-order structure is a tenet central to achieving biologic drug and vaccine product stability toward manufacturing, distribution, storage, handling, and administration. Given that mRNA lipid nanoparticles (mRNA-LNPs) are held together by an intricate ensemble of weak forces, there are some intriguing parallels to biologic drugs, at least at first glance. However, mRNA vaccines are not without unique formulation and stabilization challenges derived from the instability of unmodified mRNA and its limited history as a drug or vaccine. Since certain learning gained from biologic drug development may be applicable for the improvement of mRNA vaccines, we present a perspective on parallels and contrasts between the emerging role of higher-order structure pertaining to mRNA-LNPs compared to pharmaceutical proteins. In a recent publication, the location of mRNA encapsulated within lipid nanoparticles was identified, revealing new insights into the LNP structure, nanoheterogeneity, and microenvironment of the encapsulated mRNA molecules [Brader et al. Biophys. J. 2021, 120, 2766]. We extend those findings by considering the effect of encapsulation on mRNA thermal unfolding with the observation that encapsulation in LNPs increases mRNA unfolding temperatures.
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Affiliation(s)
- Marek Kloczewiak
- Moderna, Inc., 200 Technology Square, Cambridge, Massachusetts 02139, United States
| | - Jessica M. Banks
- Moderna, Inc., 200 Technology Square, Cambridge, Massachusetts 02139, United States
| | - Lin Jin
- Moderna, Inc., 200 Technology Square, Cambridge, Massachusetts 02139, United States
| | - Mark L. Brader
- Moderna, Inc., 200 Technology Square, Cambridge, Massachusetts 02139, United States
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22
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Rahman MU, Bilal M, Shah JA, Kaushik A, Teissedre PL, Kujawska M. CRISPR-Cas9-Based Technology and Its Relevance to Gene Editing in Parkinson's Disease. Pharmaceutics 2022; 14:1252. [PMID: 35745824 PMCID: PMC9229276 DOI: 10.3390/pharmaceutics14061252] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 12/12/2022] Open
Abstract
Parkinson's disease (PD) and other chronic and debilitating neurodegenerative diseases (NDs) impose a substantial medical, emotional, and financial burden on individuals and society. The origin of PD is unknown due to a complex combination of hereditary and environmental risk factors. However, over the last several decades, a significant amount of available data from clinical and experimental studies has implicated neuroinflammation, oxidative stress, dysregulated protein degradation, and mitochondrial dysfunction as the primary causes of PD neurodegeneration. The new gene-editing techniques hold great promise for research and therapy of NDs, such as PD, for which there are currently no effective disease-modifying treatments. As a result, gene therapy may offer new treatment options, transforming our ability to treat this disease. We present a detailed overview of novel gene-editing delivery vehicles, which is essential for their successful implementation in both cutting-edge research and prospective therapeutics. Moreover, we review the most recent advancements in CRISPR-based applications and gene therapies for a better understanding of treating PD. We explore the benefits and drawbacks of using them for a range of gene-editing applications in the brain, emphasizing some fascinating possibilities.
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Affiliation(s)
- Mujeeb ur Rahman
- Department of Toxicology, Faculty of Pharmacy, Poznan University of Medical Sciences, Dojazd 30, 60-631 Poznan, Poland;
| | - Muhammad Bilal
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China;
| | - Junaid Ali Shah
- College of Life Sciences, Jilin University, Changchun 130012, China;
- Fergana Medical Institute of Public Health Uzbekistan, Fergana 150110, Uzbekistan
| | - Ajeet Kaushik
- NanoBioTech Laboratory, Health System Engineering, Department of Environmental Engineering, Florida Polytechnic University, Lakeland, FL 33805, USA;
- School of Engineering, University of Petroleum and Energy Studies (UPES), Dehradun 248007, Uttarakhand, India
| | - Pierre-Louis Teissedre
- Institut des Sciences de la Vigne et du Vin, Université de Bordeaux, EA 4577, Œnologie, 210 Chemin de Leysotte, F-33140 Villenave d’Ornon, France;
- Institut des Sciences de la Vigne et du Vin, INRA, USC 1366 INRA, IPB, 210 Chemin de Leysotte, F-33140 Villenave d’Ornon, France
| | - Małgorzata Kujawska
- Department of Toxicology, Faculty of Pharmacy, Poznan University of Medical Sciences, Dojazd 30, 60-631 Poznan, Poland;
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23
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Meng Y, Xu X, Niu D, Xu Y, Qiu Y, Zhu Z, Zhang H, Yin D. Organophosphate flame retardants induce oxidative stress and Chop/Caspase 3-related apoptosis via Sod1/p53/Map3k6/Fkbp5 in NCI-1975 cells. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 819:153160. [PMID: 35051466 DOI: 10.1016/j.scitotenv.2022.153160] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 01/11/2022] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Organophosphate flame retardants (OPFRs) have been ubiquitously detected in dust and air which could cause damage to human health through inhalation. Currently the understanding of their adverse effects and potential mechanisms on the lung are still limited. In this study, human non-small cell lung cancer cell line NCI-H1975 was used to investigate the cytotoxicity, oxidative stress, cellular apoptosis of 9 typical OPFRs with concentrations varied from 0 to 200 μM, and their toxic mechanism associated with molecular structure was compared. After 72 h, tris(1,3-dichloro-2-propyl) phosphate (TDCIPP) displayed the highest cytotoxicity, followed by 2-ethylhexyl diphenyl phosphate (EHDPP), tris(2-butoxyethyl) phosphate (TBOEP) and tris(2-chloroisopropyl) phosphate (TCIPP), while tris(2-chloroethyl) phosphate (TCEP) and tris(2-ethylhexyl) phosphate (TEHP) exhibited the least suppression on cell viability. These results indicated that the variation of cytotoxicity on OPFRs could only be partially explained by their ester linkage. Moreover, the overexpression of intracellular reactive oxygen species (ROS), free Ca2+ and cellular apoptosis suggested that exposure to OPFRs can lead to apoptosis related to oxidative stress. Six genes associated with oxidative stress and apoptosis were upregulated dramatically compared with the control, demonstrating OPFRs induced Chop/Caspase 3-related apoptosis by activating Sod1/p53/Map3k6/Fkbp5 expression in NCI-H1975 cells. This is the first study to investigate cytotoxicity and related mechanism on commonly-used OPFRs in NCI-H1975 cells.
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Affiliation(s)
- Yuan Meng
- Key Laboratory of Yangtze River Water Environment, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, 1239 Siping Road, Shanghai 200092, China
| | - Xiaojuan Xu
- Department of Pathology and Pathophysiology, Tongji University School of Medicine, Shanghai 200092, China
| | - Dong Niu
- Key Laboratory of Yangtze River Water Environment, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, 1239 Siping Road, Shanghai 200092, China
| | - Yangjie Xu
- Key Laboratory of Yangtze River Water Environment, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, 1239 Siping Road, Shanghai 200092, China
| | - Yanling Qiu
- Key Laboratory of Yangtze River Water Environment, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, 1239 Siping Road, Shanghai 200092, China.
| | - Zhiliang Zhu
- Key Laboratory of Yangtze River Water Environment, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, 1239 Siping Road, Shanghai 200092, China
| | - Hua Zhang
- Key Laboratory of Yangtze River Water Environment, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, 1239 Siping Road, Shanghai 200092, China
| | - Daqiang Yin
- Key Laboratory of Yangtze River Water Environment, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, 1239 Siping Road, Shanghai 200092, China
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24
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Kwak Y, Kwak H. Genome-Wide Identification of Polyadenylation Dynamics with TED-Seq. Methods Mol Biol 2022; 2404:281-298. [PMID: 34694615 DOI: 10.1007/978-1-0716-1851-6_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Polyadenylation and deadenylation of mRNA are major RNA modifications associated with nucleus-to-cytoplasm translocation, mRNA stability, translation efficiency, and mRNA decay pathways. Our current knowledge of polyadenylation and deadenylation has been expanded due to recent advances in transcriptome-wide poly(A) tail length assays. Whereas these methods measure poly(A) length by quantifying the adenine (A) base stretch at the 3' end of mRNA, we developed a more cost-efficient technique that does not rely on A-base counting, called tail-end-displacement sequencing (TED-seq). Through sequencing highly size-selected 3' RNA fragments including the poly(A) tail pieces, TED-seq provides accurate measure of transcriptome-wide poly(A)-tail lengths in high resolution, economically suitable for larger scale analysis under various biologically transitional contexts.
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Affiliation(s)
- Yeonui Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
- Graduate Field of Genetics, Genomics, and Developmental Biology, Cornell University, Ithaca, NY, USA
| | - Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
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25
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Mohamed HMA, Takahashi A, Nishijima S, Adachi S, Murai I, Okamura H, Yamamoto T. CNOT1 regulates circadian behaviour through Per2 mRNA decay in a deadenylation-dependent manner. RNA Biol 2021; 19:703-718. [PMID: 35510877 PMCID: PMC9090297 DOI: 10.1080/15476286.2022.2071026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/15/2022] [Accepted: 04/20/2022] [Indexed: 11/18/2022] Open
Abstract
Circadian clocks are an endogenous internal timekeeping mechanism that drives the rhythmic expression of genes, controlling the 24 h oscillatory pattern in behaviour and physiology. It has been recently shown that post-transcriptional mechanisms are essential for controlling rhythmic gene expression. Controlling the stability of mRNA through poly(A) tail length modulation is one such mechanism. In this study, we show that Cnot1, encoding the scaffold protein of the CCR4-NOT deadenylase complex, is highly expressed in the suprachiasmatic nucleus, the master timekeeper. CNOT1 deficiency in mice results in circadian period lengthening and alterations in the mRNA and protein expression patterns of various clock genes, mainly Per2. Per2 mRNA exhibited a longer poly(A) tail and increased mRNA stability in Cnot1+/- mice. CNOT1 is recruited to Per2 mRNA through BRF1 (ZFP36L1), which itself oscillates in antiphase with Per2 mRNA. Upon Brf1 knockdown, Per2 mRNA is stabilized leading to increased PER2 expression levels. This suggests that CNOT1 plays a role in tuning and regulating the mammalian circadian clock.
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Affiliation(s)
| | - Akinori Takahashi
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Saori Nishijima
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Shungo Adachi
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Iori Murai
- Laboratory of Molecular Brain Science, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Hitoshi Okamura
- Laboratory of Molecular Brain Science, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
- Department of Neuroscience, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tadashi Yamamoto
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
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26
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Milota T, Strizova Z, Smetanova J, Sediva A. An immunologist's perspective on anti-COVID-19 vaccines. Curr Opin Allergy Clin Immunol 2021; 21:545-552. [PMID: 34545040 DOI: 10.1097/aci.0000000000000788] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
PURPOSE OF REVIEW Antisevere acute respiratory syndrome-corona virus 2 (SARS-CoV-2) vaccines may provide prompt, effective, and safe solution for the COVID-19 pandemic. Several vaccine candidates have been evaluated in randomized clinical trials (RCTs). Furthermore, data from observational studies mimicking real-life practice and studies on specific groups, such as pregnant women or immunocompromised patients who were excluded from RCTs, are currently available. The main aim of the review is to summarize and provide an immunologist's view on mechanism of action, efficacy and safety, and future challenges in vaccination against SARS-CoV-2. RECENT FINDINGS mRNA and recombinant viral vector-based vaccines have been approved for conditional use in Europe and the USA. They show robust humoral and cellular responses, high with efficacy in prevention of COVID-19 infection (66.9 95%) and favorable safety profile in RCTs. High efficacy of 80-92% was observed in real-life practice. A pilot study also confirmed good safety profile of the mRNA vaccines in pregnant women. Unlike in those with secondary immunodeficiencies where postvaccination responses did not occur, encouraging results were obtained in patients with inborn errors of immunity. SUMMARY Although both RCTs and observational studies suggest good efficacy and safety profiles of the vaccines, their long-term efficacy and safety are still being discussed. Despite the promising results, clinical evidence for specific groups such as children, pregnant and breastfeeding women, and immunocompromised patients, and for novel virus variants are lacking. VIDEO ABSTRACT http://links.lww.com/COAI/A21.
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Affiliation(s)
- Tomas Milota
- Department of Immunology, Second Faculty of Medicine, Charles University
- Department of Pediatric and Adult Rheumatology, Motol University Hospital, Prague, Czech Republic
| | - Zuzana Strizova
- Department of Immunology, Second Faculty of Medicine, Charles University
| | - Jitka Smetanova
- Department of Immunology, Second Faculty of Medicine, Charles University
| | - Anna Sediva
- Department of Immunology, Second Faculty of Medicine, Charles University
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27
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Integrity and Stability of PTC Bearing CFTR mRNA and Relevance to Future Modulator Therapies in Cystic Fibrosis. Genes (Basel) 2021; 12:genes12111810. [PMID: 34828417 PMCID: PMC8621375 DOI: 10.3390/genes12111810] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 12/26/2022] Open
Abstract
Major advances have recently been made in the development and application of CFTR (cystic fibrosis transmembrane conductance regulator) mutation class-specific modulator therapies, but to date, there are no approved modulators for Class I mutations, i.e., those introducing a premature termination codon (PTC) into the CFTR mRNA. Such mutations induce nonsense-mediated decay (NMD), a cellular quality control mechanism that reduces the quantity of PTC bearing mRNAs, presumably to avoid translation of potentially deleterious truncated CFTR proteins. The NMD-mediated reduction of PTC-CFTR mRNA molecules reduces the efficacy of one of the most promising approaches to treatment of such mutations, namely, PTC readthrough therapy, using molecules that induce the incorporation of near-cognate amino acids at the PTC codon, thereby enabling translation of a full-length protein. In this study, we measure the effect of three different PTC mutations on the abundance, integrity, and stability of respective CFTR mRNAs, using CFTR specific RT-qPCR-based assays. Altogether, our data suggest that optimized rescue of PTC mutations has to take into account (1) the different steady-state levels of the CFTR mRNA associated with each specific PTC mutation; (2) differences in abundance between the 3' and 5' regions of CFTR mRNA, even following PTC readthrough or NMD inhibition; and (3) variable effects on CFTR mRNA stability for each specific PTC mutation.
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28
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Gameiro PA, Encheva V, Dos Santos MS, MacRae JI, Ule J. Metabolic turnover and dynamics of modified ribonucleosides by 13C labeling. J Biol Chem 2021; 297:101294. [PMID: 34634303 PMCID: PMC8567201 DOI: 10.1016/j.jbc.2021.101294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 01/27/2023] Open
Abstract
Tandem mass spectrometry (MS/MS) is an accurate tool to assess modified ribonucleosides and their dynamics in mammalian cells. However, MS/MS quantification of lowly abundant modifications in non-ribosomal RNAs is unreliable, and the dynamic features of various modifications are poorly understood. Here, we developed a 13C labeling approach, called 13C-dynamods, to quantify the turnover of base modifications in newly transcribed RNA. This turnover-based approach helped to resolve mRNA from ncRNA modifications in purified RNA or free ribonucleoside samples and showed the distinct kinetics of the N6-methyladenosine (m6A) versus 7-methylguanosine (m7G) modification in polyA+-purified RNA. We uncovered that N6,N6-dimethyladenosine (m62A) exhibits distinct turnover in small RNAs and free ribonucleosides when compared to known m62A-modified large rRNAs. Finally, combined measurements of turnover and abundance of these modifications informed on the transcriptional versus posttranscriptional sensitivity of modified ncRNAs and mRNAs, respectively, to stress conditions. Thus, 13C-dynamods enables studies of the origin of modified RNAs at steady-state and subsequent dynamics under nonstationary conditions. These results open new directions to probe the presence and biological regulation of modifications in particular RNAs.
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Affiliation(s)
- Paulo A Gameiro
- RNA Networks Laboratory, Francis Crick Institute, London, UK; Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK.
| | - Vesela Encheva
- Mass Spectrometry Science Technology Platform, Francis Crick Institute, London, UK
| | | | - James I MacRae
- Mass Spectrometry Science Technology Platform, Francis Crick Institute, London, UK
| | - Jernej Ule
- RNA Networks Laboratory, Francis Crick Institute, London, UK; Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
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Sa-nguanmoo N, Namdee K, Khongkow M, Ruktanonchai U, Zhao Y, Liang XJ. Review: Development of SARS-CoV-2 immuno-enhanced COVID-19 vaccines with nano-platform. NANO RESEARCH 2021; 15:2196-2225. [PMID: 34659650 PMCID: PMC8501370 DOI: 10.1007/s12274-021-3832-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 08/19/2021] [Accepted: 08/19/2021] [Indexed: 05/04/2023]
Abstract
Vaccination is the most effective way to prevent coronavirus disease 2019 (COVID-19). Vaccine development approaches consist of viral vector vaccines, DNA vaccine, RNA vaccine, live attenuated virus, and recombinant proteins, which elicit a specific immune response. The use of nanoparticles displaying antigen is one of the alternative approaches to conventional vaccines. This is due to the fact that nano-based vaccines are stable, able to target, form images, and offer an opportunity to enhance the immune responses. The diameters of ultrafine nanoparticles are in the range of 1-100 nm. The application of nanotechnology on vaccine design provides precise fabrication of nanomaterials with desirable properties and ability to eliminate undesirable features. To be successful, nanomaterials must be uptaken into the cell, especially into the target and able to modulate cellular functions at the subcellular levels. The advantages of nano-based vaccines are the ability to protect a cargo such as RNA, DNA, protein, or synthesis substance and have enhanced stability in a broad range of pH, ambient temperatures, and humidity for long-term storage. Moreover, nano-based vaccines can be engineered to overcome biological barriers such as nonspecific distribution in order to elicit functions in antigen presenting cells. In this review, we will summarize on the developing COVID-19 vaccine strategies and how the nanotechnology can enhance antigen presentation and strong immunogenicity using advanced technology in nanocarrier to deliver antigens. The discussion about their safe, effective, and affordable vaccines to immunize against COVID-19 will be highlighted.
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Affiliation(s)
- Nawamin Sa-nguanmoo
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of China, Beijing, 100190 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Katawut Namdee
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency, Pathum Thani, 12120 Thailand
| | - Mattaka Khongkow
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency, Pathum Thani, 12120 Thailand
| | - Uracha Ruktanonchai
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency, Pathum Thani, 12120 Thailand
| | - YongXiang Zhao
- National Center for International Research of Biotargeting Theranostics, Guangxi Key Laboratory of Biotargeting Theranostics, Collaborative Innovation Center for Targeting Tumour Theranostics and Therapy, Guangxi Medical University, Nanning, 530021 China
| | - Xing-Jie Liang
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of China, Beijing, 100190 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
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30
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Lee JW, Choi SR, Heo JH. Simultaneous Stabilization and Functionalization of Gold Nanoparticles via Biomolecule Conjugation: Progress and Perspectives. ACS APPLIED MATERIALS & INTERFACES 2021; 13:42311-42328. [PMID: 34464527 DOI: 10.1021/acsami.1c10436] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Gold nanoparticles (AuNPs) are used in various biological applications because of their small surface area-to-volume ratios, ease of synthesis and modification, low toxicity, and unique optical properties. These properties can vary significantly with changes in AuNP size, shape, composition, and arrangement. Thus, the stabilization of AuNPs is crucial to preserve the properties required for biological applications. In recent years, various polymer-based physical and chemical methods have been extensively used for AuNP stabilization. However, a new stabilization approach using biomolecules has recently attracted considerable attention. Biomolecules such as DNA, RNA, peptides, and proteins are representative of the biomoieties that can functionalize AuNPs. According to several studies, biomolecules can stabilize AuNPs in biological media; in addition, AuNP-conjugated biomolecules can retain certain biological functions. Furthermore, the presence of biomolecules on AuNPs significantly enhances their biocompatibility. This review provides a representative overview of AuNP functionalization using various biomolecules. The strategies and mechanisms of AuNP functionalization using biomolecules are comprehensively discussed in the context of various biological fields.
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Affiliation(s)
- Jin Woong Lee
- School of Advanced Materials Science and Engineering, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
| | - Seok-Ryul Choi
- School of Advanced Materials Science and Engineering, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
| | - Jun Hyuk Heo
- School of Advanced Materials Science and Engineering, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
- Advanced Materials Technology Research Center, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
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31
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Tang D, Zhang Z, Zboril E, Wetzel MD, Xu X, Zhang W, Chen L, Liu Z. Pontin Functions as A Transcriptional Co-activator for Retinoic Acid-induced HOX Gene Expression. J Mol Biol 2021; 433:166928. [PMID: 33713676 PMCID: PMC8184613 DOI: 10.1016/j.jmb.2021.166928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/18/2021] [Accepted: 03/04/2021] [Indexed: 12/12/2022]
Abstract
Pontin is a AAA+ ATPase protein that has functions in various biological contexts including gene transcription regulation, chromatin remodeling, DNA damage sensing and repair, as well as assembly of protein and ribonucleoprotein complexes. Pontin is known to regulate the transcription of several important signaling pathways, including Wnt signaling. However, its role in early embryonic signaling regulation remains unclear. Retinoic acid (RA) signaling plays a central role in vertebrate development. Using an in vivo biotin tagging technology, we mapped the genome-wide binding pattern of Pontin before and after RA-induced differentiation in the pluripotent embryo carcinoma cell line NTERA-2. Biotin ChIP-seq revealed significant changes in genome-wide Pontin binding sites upon RA stimulation. We also identified a substantial amount of overlapping binding peaks between Pontin and RARα, especially on all of the HOX gene loci (A-D clusters). Pontin knockdown experiments showed that its chromatin binding at the HOX gene clusters is required for RA-induced HOX gene expression. Furthermore, we performed Global Run-On sequencing (GRO-seq) to map de novo transcripts genome-wide and found that Pontin knockdown significantly diminished nascent HOX gene transcripts, indicating that Pontin regulates HOX gene expression at the transcriptional level. Finally, proteomic analysis demonstrated that Pontin associates with chromatin organization/remodeling complexes and various other functional complexes. Altogether, we have demonstrated that Pontin is a critical transcriptional co-activator for RA-induced HOX gene activation.
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Affiliation(s)
- Dan Tang
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; Department of General Practice, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
| | - Zhao Zhang
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Emily Zboril
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Michael D Wetzel
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Xinping Xu
- Jiangxi Institute of Respiratory Disease, The Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
| | - Wei Zhang
- Jiangxi Institute of Respiratory Disease, The Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
| | - Lizhen Chen
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; Barshop Institute for Longevity and Aging Studies, Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Zhijie Liu
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA.
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32
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Chakraborty C, Sharma AR, Bhattacharya M, Lee SS. From COVID-19 to Cancer mRNA Vaccines: Moving From Bench to Clinic in the Vaccine Landscape. Front Immunol 2021; 12:679344. [PMID: 34305909 PMCID: PMC8293291 DOI: 10.3389/fimmu.2021.679344] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 06/18/2021] [Indexed: 12/12/2022] Open
Abstract
Recently, mRNA vaccines have become a significant type of therapeutic and have created new fields in the biopharmaceutical industry. mRNA vaccines are promising next-generation vaccines that have introduced a new age in vaccinology. The recent approval of two COVID-19 mRNA vaccines (mRNA-1273 and BNT162b2) has accelerated mRNA vaccine technology and boosted the pharmaceutical and biotechnology industry. These mRNA vaccines will help to tackle COVID-19 pandemic through immunization, offering considerable hope for future mRNA vaccines. Human trials with data both from mRNA cancer vaccines and mRNA infectious disease vaccines have provided encouraging results, inspiring the pharmaceutical and biotechnology industries to focus on this area of research. In this article, we discuss current mRNA vaccines broadly in two parts. In the first part, mRNA vaccines in general and COVID-19 mRNA vaccines are discussed. We presented the mRNA vaccine structure in general, the different delivery systems, the immune response, and the recent clinical trials for mRNA vaccines (both for cancer mRNA vaccines and different infectious diseases mRNA vaccines). In the second part, different COVID-19 mRNA vaccines are explained. Finally, we illustrated a snapshot of the different leading mRNA vaccine developers, challenges, and future prospects of mRNA vaccines.
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Affiliation(s)
- Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, India
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, Gangwon-do, South Korea
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, Gangwon-do, South Korea
| | | | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, Gangwon-do, South Korea
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33
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Patel YD, Brown AJ, Zhu J, Rosignoli G, Gibson SJ, Hatton D, James DC. Control of Multigene Expression Stoichiometry in Mammalian Cells Using Synthetic Promoters. ACS Synth Biol 2021; 10:1155-1165. [PMID: 33939428 PMCID: PMC8296667 DOI: 10.1021/acssynbio.0c00643] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Indexed: 01/22/2023]
Abstract
To successfully engineer mammalian cells for a desired purpose, multiple recombinant genes are required to be coexpressed at a specific and optimal ratio. In this study, we hypothesized that synthetic promoters varying in transcriptional activity could be used to create single multigene expression vectors coexpressing recombinant genes at a predictable relative stoichiometry. A library of 27 multigene constructs was created comprising three discrete fluorescent reporter gene transcriptional units in fixed series, each under the control of either a relatively low, medium, or high transcriptional strength synthetic promoter in every possible combination. Expression of each reporter gene was determined by absolute quantitation qRT-PCR in CHO cells. The synthetic promoters did generally function as designed within a multigene vector context; however, significant divergences from predicted promoter-mediated transcriptional activity were observed. First, expression of all three genes within a multigene vector was repressed at varying levels relative to coexpression of identical reporter genes on separate single gene vectors at equivalent gene copies. Second, gene positional effects were evident across all constructs where expression of the reporter genes in positions 2 and 3 was generally reduced relative to position 1. Finally, after accounting for general repression, synthetic promoter transcriptional activity within a local multigene vector format deviated from that expected. Taken together, our data reveal that mammalian synthetic promoters can be employed in vectors to mediate expression of multiple genes at predictable relative stoichiometries. However, empirical validation of functional performance is a necessary prerequisite, as vector and promoter design features can significantly impact performance.
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Affiliation(s)
- Yash D. Patel
- Department
of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, U.K.
| | - Adam J. Brown
- Department
of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, U.K.
| | - Jie Zhu
- Cell
Culture and Fermentation Sciences, BioPharmaceuticals Development,
R&D, AstraZeneca, Gaithersburg, Maryland 20878, United States
| | - Guglielmo Rosignoli
- Dynamic
Omics, Antibody Discovery & Protein Engineering, R&D, AstraZeneca, Cambridge, CB21 6GH, U.K.
| | - Suzanne J. Gibson
- Cell
Culture and Fermentation Sciences, BioPharmaceuticals Development,
R&D, AstraZeneca, Cambridge, CB21 6GH, U.K.
| | - Diane Hatton
- Cell
Culture and Fermentation Sciences, BioPharmaceuticals Development,
R&D, AstraZeneca, Cambridge, CB21 6GH, U.K.
| | - David C. James
- Department
of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, U.K.
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34
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Hintze M, Katsanos D, Shahrezaei V, Barkoulas M. Phenotypic Robustness of Epidermal Stem Cell Number in C. elegans Is Modulated by the Activity of the Conserved N-acetyltransferase nath-10/NAT10. Front Cell Dev Biol 2021; 9:640856. [PMID: 34084768 PMCID: PMC8168469 DOI: 10.3389/fcell.2021.640856] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 04/19/2021] [Indexed: 12/14/2022] Open
Abstract
Individual cells and organisms experience perturbations from internal and external sources, yet manage to buffer these to produce consistent phenotypes, a property known as robustness. While phenotypic robustness has often been examined in unicellular organisms, it has not been sufficiently studied in multicellular animals. Here, we investigate phenotypic robustness in Caenorhabditis elegans seam cells. Seam cells are stem cell-like epithelial cells along the lateral edges of the animal, which go through asymmetric and symmetric divisions contributing cells to the hypodermis and neurons, while replenishing the stem cell reservoir. The terminal number of seam cells is almost invariant in the wild-type population, allowing the investigation of how developmental precision is achieved. We report here that a loss-of-function mutation in the highly conserved N-acetyltransferase nath-10/NAT10 increases seam cell number variance in the isogenic population. RNA-seq analysis revealed increased levels of mRNA transcript variability in nath-10 mutant populations, which may have an impact on the phenotypic variability observed. Furthermore, we found disruption of Wnt signaling upon perturbing nath-10 function, as evidenced by changes in POP-1/TCF nuclear distribution and ectopic activation of its GATA transcription factor target egl-18. These results highlight that NATH-10/NAT-10 can influence phenotypic variability partly through modulation of the Wnt signaling pathway.
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Affiliation(s)
- Mark Hintze
- Department of Life Sciences, Imperial College, London, United Kingdom
| | - Dimitris Katsanos
- Department of Life Sciences, Imperial College, London, United Kingdom
| | - Vahid Shahrezaei
- Department of Mathematics, Imperial College, London, United Kingdom
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35
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Fang J, Guo T, Xie Z, Chun Y, Zhao J, Peng L, Zafar SA, Yuan S, Xiao L, Li X. The URL1-ROC5-TPL2 transcriptional repressor complex represses the ACL1 gene to modulate leaf rolling in rice. PLANT PHYSIOLOGY 2021; 185:1722-1744. [PMID: 33793928 PMCID: PMC8133684 DOI: 10.1093/plphys/kiaa121] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 12/13/2020] [Indexed: 05/31/2023]
Abstract
Moderate leaf rolling is beneficial for leaf erectness and compact plant architecture. However, our understanding regarding the molecular mechanisms of leaf rolling is still limited. Here, we characterized a semi-dominant rice (Oryza sativa L.) mutant upward rolled leaf 1 (Url1) showing adaxially rolled leaves due to a decrease in the number and size of bulliform cells. Map-based cloning revealed that URL1 encodes the homeodomain-leucine zipper (HD-Zip) IV family member RICE OUTERMOST CELL-SPECIFIC 8 (ROC8). A single-base substitution in one of the two conserved complementary motifs unique to the 3'-untranslated region of this family enhanced URL1 mRNA stability and abundance in the Url1 mutant. URL1 (UPWARD ROLLED LEAF1) contains an ethylene-responsive element binding factor-associated amphiphilic repression motif and functions as a transcriptional repressor via interaction with the TOPLESS co-repressor OsTPL2. Rather than homodimerizing, URL1 heterodimerizes with another HD-ZIP IV member ROC5. URL1 could bind directly to the promoter and suppress the expression of abaxially curled leaf 1 (ACL1), a positive regulator of bulliform cell development. Knockout of OsTPL2 or ROC5 or overexpression of ACL1 in the Url1 mutant partially suppressed the leaf-rolling phenotype. Our results reveal a regulatory network whereby a transcriptional repression complex composed of URL1, ROC5, and the transcriptional corepressor TPL2 suppresses the expression of the ACL1 gene, thus modulating bulliform cell development and leaf rolling in rice.
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Affiliation(s)
- Jingjing Fang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Tingting Guo
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Hunan Provincial Key Laboratory of Phytohormones, Hunan Provincial Key Laboratory for Crop Germplasm Innovation and Utilization, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, China
| | - Zhiwei Xie
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yan Chun
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jinfeng Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lixiang Peng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Syed Adeel Zafar
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shoujiang Yuan
- Shandong Rice Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Langtao Xiao
- Hunan Provincial Key Laboratory of Phytohormones, Hunan Provincial Key Laboratory for Crop Germplasm Innovation and Utilization, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Xueyong Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Borah P, Deb PK, Al-Shar’i NA, Dahabiyeh LA, Venugopala KN, Singh V, Shinu P, Hussain S, Deka S, Chandrasekaran B, Jaradat DMM. Perspectives on RNA Vaccine Candidates for COVID-19. Front Mol Biosci 2021; 8:635245. [PMID: 33869282 PMCID: PMC8044912 DOI: 10.3389/fmolb.2021.635245] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/13/2021] [Indexed: 01/08/2023] Open
Abstract
With the current outbreak caused by SARS-CoV-2, vaccination is acclaimed as a public health care priority. Rapid genetic sequencing of SARS-CoV-2 has triggered the scientific community to search for effective vaccines. Collaborative approaches from research institutes and biotech companies have acknowledged the use of viral proteins as potential vaccine candidates against COVID-19. Nucleic acid (DNA or RNA) vaccines are considered the next generation vaccines as they can be rapidly designed to encode any desirable viral sequence including the highly conserved antigen sequences. RNA vaccines being less prone to host genome integration (cons of DNA vaccines) and anti-vector immunity (a compromising factor of viral vectors) offer great potential as front-runners for universal COVID-19 vaccine. The proof of concept for RNA-based vaccines has already been proven in humans, and the prospects for commercialization are very encouraging as well. With the emergence of COVID-19, mRNA-1273, an mRNA vaccine developed by Moderna, Inc. was the first to enter human trials, with the first volunteer receiving the dose within 10 weeks after SARS-CoV-2 genetic sequencing. The recent interest in mRNA vaccines has been fueled by the state of the art technologies that enhance mRNA stability and improve vaccine delivery. Interestingly, as per the "Draft landscape of COVID-19 candidate vaccines" published by the World Health Organization (WHO) on December 29, 2020, seven potential RNA based COVID-19 vaccines are in different stages of clinical trials; of them, two candidates already received emergency use authorization, and another 22 potential candidates are undergoing pre-clinical investigations. This review will shed light on the rationality of RNA as a platform for vaccine development against COVID-19, highlighting the possible pros and cons, lessons learned from the past, and the future prospects.
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Affiliation(s)
- Pobitra Borah
- School of Pharmacy, Graphic Era Hill University, Dehradun, India
- Pratiksha Institute of Pharmaceutical Sciences, Assam, India
| | - Pran Kishore Deb
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Philadelphia University, Amman, Jordan
| | - Nizar A. Al-Shar’i
- Department of Medicinal Chemistry and Pharmacognosy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid, Jordan
| | - Lina A. Dahabiyeh
- Department of Pharmaceutical Sciences, School of Pharmacy, The University of Jordan, Amman, Jordan
| | - Katharigatta N. Venugopala
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Saudi Arabia
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban, South Africa
| | - Vinayak Singh
- Drug Discovery and Development Centre (H3D), University of Cape Town, Rondebosch, South Africa
- South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, South Africa
| | - Pottathil Shinu
- Department of Biomedical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Snawar Hussain
- Department of Biomedical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Satyendra Deka
- Pratiksha Institute of Pharmaceutical Sciences, Assam, India
| | - Balakumar Chandrasekaran
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Philadelphia University, Amman, Jordan
| | - Da’san M. M. Jaradat
- Department of Chemistry, Faculty of Science, Al-Balqa Applied University, Al-Salt, Jordan
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Zhou Y, Yamamoto Y, Takeshita F, Yamamoto T, Xiao Z, Ochiya T. Delivery of miR-424-5p via Extracellular Vesicles Promotes the Apoptosis of MDA-MB-231 TNBC Cells in the Tumor Microenvironment. Int J Mol Sci 2021; 22:ijms22020844. [PMID: 33467725 PMCID: PMC7831022 DOI: 10.3390/ijms22020844] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/13/2021] [Accepted: 01/13/2021] [Indexed: 12/22/2022] Open
Abstract
Programmed cell death ligand-1 (PD-L1) overexpressed on cancer cells has emerged as a key inhibitor that maintains the immunosuppressive microenvironment through its interaction with the PD-1 receptor in cancer. Here, we demonstrated that miR-424-5p delivery via extracellular vesicles (EVs) derived from adipose tissue-mesenchymal stromal cells (AT-MSCs) partly promotes proinflammation and enhances antitumor cytotoxicity in vitro and in vivo. Triple negative breast cancer (TNBC) exhibits increased expression of PD-L1, and PD-L1 is positively correlated with the overall survival of patients with TNBC. PD-L1 shows relatively higher expression in MDA-MB-231 (MM231) cells and can be downregulated by miR-424-5p. Furthermore, miR-424-5p transported by EVs can increase the secretion of proinflammatory cytokines, decrease the secretion of anti-inflammatory cytokines and promote the apoptosis of tumor cells. The intratumoral administration of miR-424-5p-EVs significantly slowed tumor growth. In conclusion, these results demonstrate that EVs may serve as a delivery system for novel immunotherapies for TNBC through the miR-424-5p/PD-L1 pathway.
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Affiliation(s)
- Yueyuan Zhou
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China;
- Division of Molecular and Cellular Medicine, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (Y.Y.); (T.Y.)
| | - Yusuke Yamamoto
- Division of Molecular and Cellular Medicine, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (Y.Y.); (T.Y.)
| | - Fumitaka Takeshita
- Department of Functional Analysis, FIOC, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan;
| | - Tomofumi Yamamoto
- Division of Molecular and Cellular Medicine, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (Y.Y.); (T.Y.)
| | - Zhongdang Xiao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China;
- Correspondence: (Z.X.); (T.O.); Tel.: +86-025-83790820 (Z.X.); +81-3-3342-6111 (ext. 6168) (T.O.)
| | - Takahiro Ochiya
- Division of Molecular and Cellular Medicine, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (Y.Y.); (T.Y.)
- Department of Molecular and Cellular Medicine, Institute of Medical Science, Tokyo Medical University, 6-1-1 Shinjuku, Shinjuku-ku, Tokyo 160-8402, Japan
- Correspondence: (Z.X.); (T.O.); Tel.: +86-025-83790820 (Z.X.); +81-3-3342-6111 (ext. 6168) (T.O.)
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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: 63] [Impact Index Per Article: 21.0] [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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Medina-Muñoz SG, Kushawah G, Castellano LA, Diez M, DeVore ML, Salazar MJB, Bazzini AA. Crosstalk between codon optimality and cis-regulatory elements dictates mRNA stability. Genome Biol 2021; 22:14. [PMID: 33402205 PMCID: PMC7783504 DOI: 10.1186/s13059-020-02251-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 12/17/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The regulation of messenger RNA (mRNA) stability has a profound impact on gene expression dynamics during embryogenesis. For example, in animals, maternally deposited mRNAs are degraded after fertilization to enable new developmental trajectories. Regulatory sequences in 3' untranslated regions (3'UTRs) have long been considered the central determinants of mRNA stability. However, recent work indicates that the coding sequence also possesses regulatory information. Specifically, translation in cis impacts mRNA stability in a codon-dependent manner. However, the strength of this mechanism during embryogenesis, as well as its relationship with other known regulatory elements, such as microRNA, remains unclear. RESULTS Here, we show that codon composition is a major predictor of mRNA stability in the early embryo. We show that this mechanism works in combination with other cis-regulatory elements to dictate mRNA stability in zebrafish and Xenopus embryos as well as in mouse and human cells. Furthermore, we show that microRNA targeting efficacy can be affected by substantial enrichment of optimal (stabilizing) or non-optimal (destabilizing) codons. Lastly, we find that one microRNA, miR-430, antagonizes the stabilizing effect of optimal codons during early embryogenesis in zebrafish. CONCLUSIONS By integrating the contributions of different regulatory mechanisms, our work provides a framework for understanding how combinatorial control of mRNA stability shapes the gene expression landscape.
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Affiliation(s)
- Santiago Gerardo Medina-Muñoz
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO, 64110, USA
- Present Address: National Laboratory of Genomics for Biodiversity (LANGEBIO), Unit of Advanced Genomics, 36824, Irapuato, Mexico
| | - Gopal Kushawah
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO, 64110, USA
| | | | - Michay Diez
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO, 64110, USA
| | - Michelle Lynn DeVore
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO, 64110, USA
| | - María José Blanco Salazar
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO, 64110, USA
- Present Address: Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510, México City, Mexico
| | - Ariel Alejandro Bazzini
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO, 64110, USA.
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS, 66160, USA.
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ELAV Proteins Bind and Stabilize C/EBP mRNA in the Induction of Long-Term Memory in Aplysia. J Neurosci 2020; 41:947-959. [PMID: 33298536 DOI: 10.1523/jneurosci.2284-20.2020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/22/2020] [Accepted: 11/23/2020] [Indexed: 12/27/2022] Open
Abstract
Long-term memory (LTM) formation is a critical survival process by which an animal retains information about prior experiences to guide future behavior. In the experimentally advantageous marine mollusk Aplysia, LTM for sensitization can be induced by the presentation of two aversive shocks to the animal's tail. Each of these training trials recruits distinct growth factor signaling systems that promote LTM formation. Specifically, whereas intact TrkB signaling during Trial 1 promotes an initial and transient increase of the immediate early gene apc/ebp mRNA, a prolonged increase in apc/ebp gene expression required for LTM formation requires the addition of TGFβ signaling during Trial 2. Here we explored the molecular mechanisms by which Trial 2 achieves the essential prolonged gene expression of apc/ebp We find that this prolonged gene expression is not dependent on de novo transcription, but that apc/ebp mRNA synthesized by Trial 1 is post-transcriptionally stabilized by interacting with the RNA-binding protein ApELAV. This interaction is promoted by p38 MAPK activation initiated by TGFβ. We further demonstrate that blocking the interaction of ApELAV with its target mRNA during Trial 2 blocks both the prolonged increase in apc/ebp gene expression and the behavioral induction of LTM. Collectively, our findings elucidate both when and how ELAV proteins are recruited for the stabilization of mRNA in LTM formation. Stabilization of a transiently expressed immediate early gene mRNA by a repeated training trial may therefore serve as a "filter" for learning, permitting only specific events to cause lasting transcriptional changes and behavioral LTM.SIGNIFICANCE STATEMENT: In the present paper, we significantly extend the general field of molecular processing in long-term memory (LTM) by describing a novel form of pretranslational processing required for LTM, which relies on the stabilization of a newly synthesized mRNA by a class of RNA binding proteins (ELAVs). There are now compelling data showing that important processing can occur after transcription of a gene, but before translation of the message into protein. Although the potential importance of ELAV proteins in LTM formation has previously been reported, the specific actions of ELAV proteins during LTM formation remained to be understood. Our new findings thus complement and extend this literature by demonstrating when and how this post-transcriptional gene regulation is mediated in the induction of LTM.
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Block TM, Young JAT, Javanbakht H, Sofia MJ, Zhou T. Host RNA quality control as a hepatitis B antiviral target. Antiviral Res 2020; 186:104972. [PMID: 33242518 DOI: 10.1016/j.antiviral.2020.104972] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/30/2020] [Accepted: 11/03/2020] [Indexed: 12/12/2022]
Abstract
Inhibition of the host RNA polyadenylating polymerases, PAPD5 and PAPD7 (PAPD5/7), with dihydroquinolizinone, a small orally available, molecule, results in a rapid and selective degradation of hepatitis B virus (HBV) RNA, and hence reduction in the amounts of viral gene products. DHQ, is a first in class investigational agent and could represent an entirely new category of HBV antivirals. PAPD5 and PAPD7 are non-canonical, cell specified, polyadenylating polymerases, also called terminal nucleotidyl transferases 4B and 4A (TENT4B/A), respectively. They are involved in the degradation of poor-quality cell transcripts, mostly non-coding RNAs and in the maturation of a sub-set of transcripts. They also appear to play a role in shielding some mRNA from degradation. The results of studies with DHQ, along with other recent findings, provide evidence that repression of the PAPD5/7 arm of the cell "RNA quality control" pathway, causes a profound (multi-fold) reduction rather than increase, in the amount of HBV pre-genomic, pre-core and HBsAg mRNA levels in tissue culture and animal models, as well. In this review we will briefly discuss the need for new HBV therapeutics and provide background about HBV transcription. We also discuss cellular degradation of host transcripts, as it relates to a new family of anti-HBV drugs that interfere with these processes. Finally, since HBV mRNA maturation appears to be selectively sensitive to PAPD5/7 inhibition in hepatocytes, we discuss the possibility of targeting host RNA "quality control" as an antiviral strategy.
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Affiliation(s)
| | - John A T Young
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, F.Hoffmann-La Roche Ltd, Basel, Switzerland.
| | - Hassan Javanbakht
- SQZ Biotechnologies, 200 Arsenal Yards Blvd, Suite 210, Watertown, MA, 02472, USA.
| | - Michael J Sofia
- Arbutus Biopharma, Inc, 701 Veterans Circle, Warminster, PA, 18974, USA.
| | - Tianlun Zhou
- Baruch S. Blumberg Institute, Doylestown, PA, 18902, USA.
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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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Molecular assays to detect the presence and viability of Phytophthora ramorum and Grosmannia clavigera. PLoS One 2020; 15:e0221742. [PMID: 32023247 PMCID: PMC7001964 DOI: 10.1371/journal.pone.0221742] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 11/28/2019] [Indexed: 12/18/2022] Open
Abstract
Wood and wood products can harbor microorganisms that can raise phytosanitary concerns in countries importing or exporting these products. To evaluate the efficacy of wood treatment on the survival of microorganisms of phytosanitary concern the method of choice is to grow microbes in petri dishes for subsequent identification. However, some plant pathogens are difficult or impossible to grow in axenic cultures. A molecular methodology capable of detecting living fungi and fungus-like organisms in situ can provide a solution. RNA represents the transcription of genes and can become rapidly unstable after cell death, providing a proxy measure of viability. We designed and used RNA-based molecular diagnostic assays targeting genes essential to vital processes and assessed their presence in wood colonized by fungi and oomycetes through reverse transcription and real-time polymerase chain reaction (PCR). A stability analysis was conducted by comparing the ratio of mRNA to gDNA over time following heat treatment of mycelial cultures of the Oomycete Phytophthora ramorum and the fungus Grosmannia clavigera. The real-time PCR results indicated that the DNA remained stable over a period of 10 days post treatment in heat-treated samples, whereas mRNA could not be detected after 24 hours for P. ramorum or 96 hours for G. clavigera. Therefore, this method provides a reliable way to evaluate the viability of these pathogens and offers a potential way to assess the effectiveness of existing and emerging wood treatments. This can have important phytosanitary impacts on assessing both timber and non-timber forest products of commercial value in international wood trade.
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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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45
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Vopálenský V, Sýkora M, Mašek T, Pospíšek M. Messenger RNAs of Yeast Virus-Like Elements Contain Non-templated 5' Poly(A) Leaders, and Their Expression Is Independent of eIF4E and Pab1. Front Microbiol 2019; 10:2366. [PMID: 31736885 PMCID: PMC6831550 DOI: 10.3389/fmicb.2019.02366] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 09/30/2019] [Indexed: 02/01/2023] Open
Abstract
We employed virus-like elements (VLEs) pGKL1,2 from Kluyveromyces lactis as a model to investigate the previously neglected transcriptome of the broader group of yeast cytoplasmic linear dsDNA VLEs. We performed 5′ and 3′ RACE analyses of all pGKL1,2 mRNAs and found them not 3′ polyadenylated and containing frequently uncapped 5′ poly(A) leaders that are not complementary to VLE genomic DNA. The degree of 5′ capping and/or 5′ mRNA polyadenylation is specific to each gene and is controlled by the corresponding promoter region. The expression of pGKL1,2 transcripts is independent of eIF4E and Pab1 and is enhanced in lsm1Δ and pab1Δ strains. We suggest a model of primitive pGKL1,2 gene expression regulation in which the degree of 5′ mRNA capping and 5′ non-template polyadenylation, together with the presence of negative regulators such as Pab1 and Lsm1, play important roles. Our data also support a hypothesis of a close relationship between yeast linear VLEs and poxviruses.
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Affiliation(s)
- Václav Vopálenský
- Laboratory of RNA Biochemistry, Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czechia
| | - Michal Sýkora
- Laboratory of RNA Biochemistry, Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czechia
| | - Tomáš Mašek
- Laboratory of RNA Biochemistry, Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czechia
| | - Martin Pospíšek
- Laboratory of RNA Biochemistry, Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czechia
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Kingston ER, Bartel DP. Global analyses of the dynamics of mammalian microRNA metabolism. Genome Res 2019; 29:1777-1790. [PMID: 31519739 PMCID: PMC6836734 DOI: 10.1101/gr.251421.119] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 08/29/2019] [Indexed: 12/30/2022]
Abstract
Rates of production and degradation together specify microRNA (miRNA) abundance and dynamics. Here, we used approach-to-steady-state metabolic labeling to assess these rates for 176 miRNAs in contact-inhibited mouse embryonic fibroblasts (MEFs), 182 miRNAs in dividing MEFs, and 127 miRNAs in mouse embryonic stem cells (mESCs). MicroRNA duplexes, each comprising a mature miRNA and its passenger strand, are produced at rates as fast as 110 ± 50 copies/cell/min, which exceeds rates reported for any mRNAs. These duplexes are rapidly loaded into Argonaute, with <30 min typically required for duplex loading and silencing-complex maturation. Within Argonaute, guide strands have stabilities that vary by 100-fold. Half-lives also vary globally between cell lines, with median values ranging from 11 to 34 h in mESCs and contact-inhibited MEFs, respectively. Moreover, relative half-lives for individual miRNAs vary between cell types, implying the influence of cell-specific factors in dictating turnover rate. The apparent influence of miRNA regions most important for targeting, together with the effect of one target on miR-7 accumulation, suggest that targets fulfill this role. Analysis of the tailing and trimming of miRNA 3' termini showed that the flux was typically greatest through the isoform tailed with a single uridine, although changes in this flux did not correspond to changes in stability, which suggested that the processes of tailing and trimming might be independent from that of decay. Together, these results establish a framework for describing the dynamics and regulation of miRNAs throughout their life cycle.
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Affiliation(s)
- Elena R Kingston
- Howard Hughes Medical Institute and Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - David P Bartel
- Howard Hughes Medical Institute and Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Abstract
Similar to many other biological molecules, RNA is vulnerable to chemical insults from endogenous and exogenous sources. Noxious agents such as reactive oxygen species or alkylating chemicals have the potential to profoundly affect the chemical properties and hence the function of RNA molecules in the cell. Given the central role of RNA in many fundamental biological processes, including translation and splicing, changes to its chemical composition can have a detrimental impact on cellular fitness, with some evidence suggesting that RNA damage has roles in diseases such as neurodegenerative disorders. We are only just beginning to learn about how cells cope with RNA damage, with recent studies revealing the existence of quality-control processes that are capable of recognizing and degrading or repairing damaged RNA. Here, we begin by reviewing the most abundant types of chemical damage to RNA, including oxidation and alkylation. Focusing on mRNA damage, we then discuss how alterations to this species of RNA affect its function and how cells respond to these challenges to maintain proteostasis. Finally, we briefly discuss how chemical damage to noncoding RNAs such as rRNA, tRNA, small nuclear RNA, and small nucleolar RNA is likely to affect their function.
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Affiliation(s)
- Liewei L. Yan
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
| | - Hani S. Zaher
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130, To whom correspondence should be addressed:
Dept. of Biology, Washington University in St. Louis, Campus Box 1137, One Brookings Dr., St. Louis, MO 63130. Tel.:
314-935-7662; Fax:
314-935-4432; E-mail:
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48
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Li YX, Guo X, Gulappa T, Menon B, Menon KMJ. SREBP Plays a Regulatory Role in LH/hCG Receptor mRNA Expression in Human Granulosa-Lutein Cells. J Clin Endocrinol Metab 2019; 104:4783-4792. [PMID: 31150065 PMCID: PMC6736214 DOI: 10.1210/jc.2019-00913] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 05/24/2019] [Indexed: 01/29/2023]
Abstract
CONTEXT LH receptor (LHR) expression has been shown to be regulated posttranscriptionally by LHR mRNA binding protein (LRBP) in rodent and human ovaries. LRBP was characterized as mevalonate kinase. The gene that encodes mevalonate kinase is a member of a family of genes that encode enzymes involved in lipid synthesis and are regulated by the transcription factor sterol regulatory element binding proteins (SREBPs). OBJECTIVE The current study examined the regulation of LHR mRNA expression in human granulosa-lutein cells in response to alterations in cholesterol metabolism. DESIGN Using atorvastatin, an inhibitor of 3-hydroxy-3-methyl-glutaryl-coenzyme A reductase to inhibit cholesterol biosynthesis, we examined its effect on LHR mRNA expression. The effect of atorvastatin on SREBP and mRNA expression as well as LHR mRNA binding protein expression was examined. Finally, the effect of atorvastatin on human chorionic gonadotropin (hCG)-stimulated progesterone production and the expression of key steroidogenic enzymes was also examined. RESULTS Statin treatment reduced LHR mRNA expression by increasing the levels of SREBP1a and SREBP2, leading to an increase in LRBP. RNA gel shift assay showed that increased binding of LHR mRNA to LRBP occurred in response to atorvastatin, leading to LHR mRNA degradation. The granulosa-lutein cells pretreated with atorvastatin also showed decreased responsiveness to hCG by decreasing the mRNA and protein expression of steroidogenic enzymes. Atorvastatin also attenuated LH/hCG-induced progesterone production. CONCLUSION These results imply that LHR mRNA expression by the human granulosa-lutein cells is regulated by cholesterol, through a mechanism involving SREBP and SREBP cleavage activating protein serving as the cholesterol sensor.
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Affiliation(s)
- Yin-Xia Li
- Departments of Obstetrics and Gynecology and Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan
| | - Xingzi Guo
- Departments of Obstetrics and Gynecology and Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan
| | - Thippeswamy Gulappa
- Departments of Obstetrics and Gynecology and Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan
| | - Bindu Menon
- Departments of Obstetrics and Gynecology and Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan
| | - K M J Menon
- Departments of Obstetrics and Gynecology and Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan
- Correspondence and Reprint Requests: K. M. J. Menon, PhD, Departments of Obstetrics/Gynecology and Biological Chemistry, University of Michigan Medical School, 6428 Medical Sciences Building I, 1301 Catherine Street, Ann Arbor, Michigan 48109. E-mail:
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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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