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1.
Cell ; 187(17): 4733-4750.e26, 2024 Aug 22.
Artigo em Inglês | MEDLINE | ID: mdl-38971152

RESUMO

We identify a population of Protogenin-positive (PRTG+ve) MYChigh NESTINlow stem cells in the four-week-old human embryonic hindbrain that subsequently localizes to the ventricular zone of the rhombic lip (RLVZ). Oncogenic transformation of early Prtg+ve rhombic lip stem cells initiates group 3 medulloblastoma (Gr3-MB)-like tumors. PRTG+ve stem cells grow adjacent to a human-specific interposed vascular plexus in the RLVZ, a phenotype that is recapitulated in Gr3-MB but not in other types of medulloblastoma. Co-culture of Gr3-MB with endothelial cells promotes tumor stem cell growth, with the endothelial cells adopting an immature phenotype. Targeting the PRTGhigh compartment of Gr3-MB in vivo using either the diphtheria toxin system or chimeric antigen receptor T cells constitutes effective therapy. Human Gr3-MBs likely arise from early embryonic RLVZ PRTG+ve stem cells inhabiting a specific perivascular niche. Targeting the PRTGhigh compartment and/or the perivascular niche represents an approach to treat children with Gr3-MB.


Assuntos
Meduloblastoma , Células-Tronco Neoplásicas , Humanos , Meduloblastoma/patologia , Meduloblastoma/metabolismo , Animais , Células-Tronco Neoplásicas/metabolismo , Células-Tronco Neoplásicas/patologia , Camundongos , Rombencéfalo/metabolismo , Rombencéfalo/embriologia , Neoplasias Cerebelares/metabolismo , Neoplasias Cerebelares/patologia , Células Endoteliais/metabolismo , Nicho de Células-Tronco , Células-Tronco/metabolismo , Técnicas de Cocultura , Estruturas Embrionárias , Metencéfalo/embriologia
2.
Nucleic Acids Res ; 50(8): e44, 2022 05 06.
Artigo em Inglês | MEDLINE | ID: mdl-34967412

RESUMO

Many pathological processes are driven by RNA-protein interactions, making such interactions promising targets for molecular interventions. HIV-1 assembly is one such process, in which the viral genomic RNA interacts with the viral Gag protein and serves as a scaffold to drive Gag multimerization that ultimately leads to formation of a virus particle. Here, we develop self-assembled RNA nanostructures that can inhibit HIV-1 virus assembly, achieved through hybridization of multiple artificial small RNAs with a stem-loop structure (STL) that we identify as a prominent ligand of Gag that can inhibit virus particle production via STL-Gag interactions. The resulting STL-decorated nanostructures (double and triple stem-loop structures denoted as Dumbbell and Tribell, respectively) can elicit more pronounced viral blockade than their building blocks, with the inhibition arising as a result of nanostructures interfering with Gag multimerization. These findings could open up new avenues for RNA-based therapy.


Assuntos
HIV-1 , Nanoestruturas , HIV-1/metabolismo , RNA Viral/genética , RNA Viral/metabolismo , Vírion/metabolismo , Montagem de Vírus/fisiologia , Produtos do Gene gag do Vírus da Imunodeficiência Humana/genética , Produtos do Gene gag do Vírus da Imunodeficiência Humana/metabolismo
3.
Nucleic Acids Res ; 47(20): e131, 2019 11 18.
Artigo em Inglês | MEDLINE | ID: mdl-31504824

RESUMO

Clustered regularly interspaced short palindromic repeats (CRISPR)-based genomic imaging systems predominantly rely on fluorescent protein reporters, which lack the optical properties essential for sensitive dynamic imaging. Here, we modified the CRISPR single-guide RNA (sgRNA) to carry two distinct molecular beacons (MBs) that can undergo fluorescence resonance energy transfer (FRET) and demonstrated that the resulting system, CRISPR/dual-FRET MB, enables dynamic imaging of non-repetitive genomic loci with only three unique sgRNAs.


Assuntos
Sistemas CRISPR-Cas , Transferência Ressonante de Energia de Fluorescência/métodos , Loci Gênicos , Corantes Fluorescentes/química , Células HeLa , Humanos , RNA Guia de Cinetoplastídeos/química , RNA Guia de Cinetoplastídeos/metabolismo
4.
Proc Natl Acad Sci U S A ; 115(26): 6721-6726, 2018 06 26.
Artigo em Inglês | MEDLINE | ID: mdl-29891653

RESUMO

During HIV-1 assembly, the retroviral structural protein Gag forms an immature capsid, containing thousands of Gag molecules, at the plasma membrane (PM). Interactions between Gag nucleocapsid (NC) and viral RNA (vRNA) are thought to drive assembly, but the exact roles of these interactions have remained poorly understood. Since previous studies have shown that Gag dimer- or trimer-forming mutants (GagZiL) lacking an NC domain can form immature capsids independent of RNA binding, it is often hypothesized that vRNA drives Gag assembly by inducing Gag to form low-ordered multimers, but is dispensable for subsequent assembly. In this study, we examined the role of vRNA in HIV-1 assembly by characterizing the distribution and mobility of Gag and Gag NC mutants at the PM using photoactivated localization microscopy (PALM) and single-particle tracking PALM (spt-PALM). We showed that both Gag and GagZiL assembly involve a similar basic assembly unit, as expected. Unexpectedly, the two proteins underwent different subsequent assembly pathways, with Gag cluster density increasing asymptotically, while GagZiL cluster density increased linearly. Additionally, the directed movement of Gag, but not GagZiL, was maintained at a constant speed, suggesting that the two proteins experience different external driving forces. Assembly was abolished when Gag was rendered monomeric by NC deletion. Collectively, these results suggest that, beyond inducing Gag to form low-ordered multimer basic assembly units, vRNA is essential in scaffolding and maintaining the stability of the subsequent assembly process. This finding should advance the current understanding of HIV-1 and, potentially, other retroviruses.


Assuntos
RNA Viral/metabolismo , Imagem Individual de Molécula , Montagem de Vírus/fisiologia , Produtos do Gene gag do Vírus da Imunodeficiência Humana/metabolismo , Animais , Células COS , Chlorocebus aethiops , Difusão , HIV-1/metabolismo , Nucleocapsídeo/metabolismo , Ligação Proteica , Domínios Proteicos , Provírus/metabolismo , Proteínas Recombinantes/metabolismo
5.
BMC Med Educ ; 21(1): 39, 2021 Jan 08.
Artigo em Inglês | MEDLINE | ID: mdl-33419435

RESUMO

BACKGROUND: Medical students at The University of Manchester have the option of research intercalation on the Master of Research programme. There is a paucity of evidence for the benefits of research intercalation. However, we hypothesised that research intercalation would accelerate post-graduate career progression and aimed to objectively measure the career enhancing impact, quantify the benefits and determine the alumni perception of research intercalation. METHODS: Data was collected retrospectively by electronic questionnaire (in 2018) from those commencing research intercalation between 2005 and 2012. RESULTS: Participants (n=52) returned questionnaires (68% response), demonstrating that the cohort had completed 67 postgraduate qualifications, published 304 manuscripts (median 3 publications per person (PP); range: 0-53) and made 430 presentations (median 7 PP; range: 0-37). Alumni had been awarded 49 research grants; funding disclosed on 43% totalled £823,000. Career progression of 73% of alumni had taken the minimum number of years; 27% took longer due to time spent working abroad or to gain additional experience prior to specialty training. Fifty-five publications and 71 presentations were directly related to MRes projects. CONCLUSION: Research intercalation provides graduates with an opportunity to learn valuable transferrable skills, contribute to translational research, and objectively enhances medical career progression.


Assuntos
Medicina , Estudantes de Medicina , Escolha da Profissão , Humanos , Estudos Retrospectivos , Faculdades de Medicina , Inquéritos e Questionários
6.
Hum Mol Genet ; 27(19): 3464-3474, 2018 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-30010910

RESUMO

Osteoarthritis (OA) is a common, multifactorial and polygenic skeletal disease that, in its severest form, requires joint replacement surgery to restore mobility and to relieve chronic pain. Using tissues from the articulating joints of 260 patients with OA and a range of in vitro experiments, including CRISPR-Cas9, we have characterized an intergenic regulatory element. Here, genotype at an OA risk locus correlates with differential DNA methylation, with altered gene expression of both a transcriptional regulator (RUNX2), and a chromatin remodelling protein (SUPT3H). RUNX2 is a strong candidate for OA susceptibility, with its encoded protein being essential for skeletogenesis and healthy joint function. The OA risk locus includes single nucleotide polymorphisms (SNPs) located within and flanking the differentially methylated region (DMR). The OA association SNP, rs10948172, demonstrates particularly strong correlation with methylation, and two intergenic SNPs falling within the DMR (rs62435998 and rs62435999) demonstrate genetic and epigenetic effects on the regulatory activity of this region. We therefore posit that the OA signal mediates its effect by modulating the methylation of the regulatory element, which then impacts on gene expression, with RUNX2 being the principal target. Our study highlights the interplay between DNA methylation, OA genetic risk and the downstream regulation of genes critical to normal joint function.


Assuntos
Subunidade alfa 1 de Fator de Ligação ao Core/genética , Metilação de DNA/genética , Osteoartrite/genética , Fatores de Transcrição/genética , Adulto , Idoso , Idoso de 80 Anos ou mais , Sistemas CRISPR-Cas , Feminino , Regulação da Expressão Gênica/genética , Predisposição Genética para Doença , Genótipo , Humanos , Articulações/fisiopatologia , Masculino , Pessoa de Meia-Idade , Osteoartrite/fisiopatologia , Polimorfismo de Nucleotídeo Único , Sequências Reguladoras de Ácido Nucleico , Fatores de Risco
7.
Nucleic Acids Res ; 46(13): e80, 2018 07 27.
Artigo em Inglês | MEDLINE | ID: mdl-29718399

RESUMO

The clustered regularly interspersed short palindromic repeat (CRISPR) gene-editing system has been repurposed for live-cell genomic imaging, but existing approaches rely on fluorescent protein reporters, making sensitive and continuous imaging difficult. Here, we present a fluorophore-based live-cell genomic imaging system that consists of a nuclease-deactivated mutant of the Cas9 protein (dCas9), a molecular beacon (MB), and an engineered single-guide RNA (sgRNA) harboring a unique MB target sequence (sgRNA-MTS), termed CRISPR/MB. Specifically, dCas9 and sgRNA-MTS are first co-expressed to target a specific locus in cells, followed by delivery of MBs that can then hybridize to MTS to illuminate the target locus. We demonstrated the feasibility of this approach for quantifying genomic loci, for monitoring chromatin dynamics, and for dual-color imaging when using two orthogonal MB/MTS pairs. With flexibility in selecting different combinations of fluorophore/quencher pairs and MB/MTS sequences, our CRISPR/MB hybrid system could be a promising platform for investigating chromatin activities.


Assuntos
Sistemas CRISPR-Cas , Corantes Fluorescentes , Microscopia de Fluorescência , Sondas de Oligonucleotídeos , Proteína 9 Associada à CRISPR/genética , Proteína 9 Associada à CRISPR/metabolismo , Cromatina/metabolismo , Genômica , Células HEK293 , Células HeLa , Humanos
8.
Proc Natl Acad Sci U S A ; 114(47): E10056-E10065, 2017 11 21.
Artigo em Inglês | MEDLINE | ID: mdl-29114055

RESUMO

The packaging and budding of Gag polyprotein and viral RNA is a critical step in the HIV-1 life cycle. High-resolution structures of the Gag polyprotein have revealed that the capsid (CA) and spacer peptide 1 (SP1) domains contain important interfaces for Gag self-assembly. However, the molecular details of the multimerization process, especially in the presence of RNA and the cell membrane, have remained unclear. In this work, we investigate the mechanisms that work in concert between the polyproteins, RNA, and membrane to promote immature lattice growth. We develop a coarse-grained (CG) computational model that is derived from subnanometer resolution structural data. Our simulations recapitulate contiguous and hexameric lattice assembly driven only by weak anisotropic attractions at the helical CA-SP1 junction. Importantly, analysis from CG and single-particle tracking photoactivated localization (spt-PALM) trajectories indicates that viral RNA and the membrane are critical constituents that actively promote Gag multimerization through scaffolding, while overexpression of short competitor RNA can suppress assembly. We also find that the CA amino-terminal domain imparts intrinsic curvature to the Gag lattice. As a consequence, immature lattice growth appears to be coupled to the dynamics of spontaneous membrane deformation. Our findings elucidate a simple network of interactions that regulate the early stages of HIV-1 assembly and budding.


Assuntos
Membrana Celular/química , Produtos do Gene gag/química , HIV-1/fisiologia , RNA Viral/química , Montagem de Vírus/fisiologia , Liberação de Vírus/fisiologia , Sítios de Ligação , Membrana Celular/metabolismo , Expressão Gênica , Produtos do Gene gag/genética , Produtos do Gene gag/metabolismo , Células HEK293 , Interações Hospedeiro-Patógeno , Humanos , Cinética , Simulação de Dinâmica Molecular , Ligação Proteica , Domínios e Motivos de Interação entre Proteínas , Multimerização Proteica , Estrutura Secundária de Proteína , RNA Viral/genética , RNA Viral/metabolismo , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Termodinâmica
9.
Ophthalmology ; 126(1): 113-124, 2019 01.
Artigo em Inglês | MEDLINE | ID: mdl-30514630

RESUMO

PURPOSE: Low-concentration atropine is an emerging therapy for myopia progression, but its efficacy and optimal concentration remain uncertain. Our study aimed to evaluate the efficacy and safety of low-concentration atropine eye drops at 0.05%, 0.025%, and 0.01% compared with placebo over a 1-year period. DESIGN: Randomized, placebo-controlled, double-masked trial. PARTICIPANTS: A total of 438 children aged 4 to 12 years with myopia of at least -1.0 diopter (D) and astigmatism of -2.5 D or less. METHODS: Participants were randomly assigned in a 1:1:1:1 ratio to receive 0.05%, 0.025%, and 0.01% atropine eye drops, or placebo eye drop, respectively, once nightly to both eyes for 1 year. Cycloplegic refraction, axial length (AL), accommodation amplitude, pupil diameter, and best-corrected visual acuity were measured at baseline, 2 weeks, 4 months, 8 months, and 12 months. Visual Function Questionnaire was administered at the 1-year visit. MAIN OUTCOME MEASURES: Changes in spherical equivalent (SE) and AL were measured, and their differences among groups were compared using generalized estimating equation. RESULTS: After 1 year, the mean SE change was -0.27±0.61 D, -0.46±0.45 D, -0.59±0.61 D, and -0.81±0.53 D in the 0.05%, 0.025%, and 0.01% atropine groups, and placebo groups, respectively (P < 0.001), with a respective mean increase in AL of 0.20±0.25 mm, 0.29±0.20 mm, 0.36±0.29 mm, and 0.41±0.22 mm (P < 0.001). The accommodation amplitude was reduced by 1.98±2.82 D, 1.61±2.61 D, 0.26±3.04 D, and 0.32±2.91 D, respectively (P < 0.001). The pupil sizes under photopic and mesopic conditions were increased respectively by 1.03±1.02 mm and 0.58±0.63 mm in the 0.05% atropine group, 0.76±0.90 mm and 0.43±0.61 mm in the 0.025% atropine group, 0.49±0.80 mm and 0.23±0.46 mm in the 0.01% atropine group, and 0.13±1.07 mm and 0.02±0.55 mm in the placebo group (P < 0.001). Visual acuity and vision-related quality of life were not affected in each group. CONCLUSIONS: The 0.05%, 0.025%, and 0.01% atropine eye drops reduced myopia progression along a concentration-dependent response. All concentrations were well tolerated without an adverse effect on vision-related quality of life. Of the 3 concentrations used, 0.05% atropine was most effective in controlling SE progression and AL elongation over a period of 1 year.


Assuntos
Atropina/administração & dosagem , Antagonistas Muscarínicos/administração & dosagem , Miopia/tratamento farmacológico , Acomodação Ocular/fisiologia , Administração Oftálmica , Comprimento Axial do Olho , Criança , Pré-Escolar , Progressão da Doença , Relação Dose-Resposta a Droga , Método Duplo-Cego , Feminino , Humanos , Masculino , Miopia/diagnóstico , Miopia/fisiopatologia , Soluções Oftálmicas , Qualidade de Vida , Refração Ocular/fisiologia , Inquéritos e Questionários , Testes Visuais , Acuidade Visual/fisiologia
10.
Langmuir ; 34(37): 10993-11002, 2018 09 18.
Artigo em Inglês | MEDLINE | ID: mdl-30142976

RESUMO

Hydrophobically modified ethoxylated urethane (HEUR) thickeners are widely used as rheology modifiers for waterborne paints. Although the rheology of HEUR solutions in water is fairly well-understood, their impact on the rheology of waterborne latex/pigment suspensions (formulated paints) is more complicated. We study the shear rheology of model HEUR/latex/TiO2 suspensions in water and investigate the dependence of both oscillatory and steady shear behaviors on the strength of the HEUR hydrophobes. We observe that in both oscillatory and steady shear experiments, rheological curves could be shifted onto a single master curve, demonstrating a "time-hydrophobe superposition". We also note that the oscillatory shear behavior exhibits a power-law spectrum of relaxation times, unlike the single-Maxwellian behavior of pure HEUR solutions. On the basis of these results and earlier experimental and theoretical findings, we propose that the rheology of the HEUR-thickened latex/TiO2 suspensions is mainly determined by the transient network of HEUR-bridged latex particles, with a broad distribution of the characteristic lifetimes of the bridge. The model is found to be in good qualitative and semiquantitative agreement with the experiments for both steady shear and oscillatory shear.

11.
Proc Natl Acad Sci U S A ; 111(26): E2676-83, 2014 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-24938790

RESUMO

MicroRNAs (miRNAs) are small, 18-22 nt long, noncoding RNAs that act as potent negative gene regulators in a variety of physiological and pathological processes. To repress gene expression, miRNAs are packaged into RNA-induced silencing complexes (RISCs) that target mRNAs for degradation and/or translational repression in a sequence-specific manner. Recently, miRNAs have been shown to also interact with proteins outside RISCs, impacting cellular processes through mechanisms not involving gene silencing. Here, we define a previously unappreciated activity of miRNAs in inhibiting RNA-protein interactions that in the context of HIV-1 biology blocks HIV virus budding and reduces virus infectivity. This occurs by miRNA binding to the nucleocapsid domain of the Gag protein, the main structural component of HIV-1 virions. The resulting miRNA-Gag complexes interfere with viral-RNA-mediated Gag assembly and viral budding at the plasma membrane, with imperfectly assembled Gag complexes endocytosed and delivered to lysosomes. The blockade of virus production by miRNA is reversed by adding the miRNA's target mRNA and stimulated by depleting Argonaute-2, suggesting that when miRNAs are not mediating gene silencing, they can block HIV-1 production through disruption of Gag assembly on membranes. Overall, our findings have significant implications for understanding how cells modulate HIV-1 infection by miRNA expression and raise the possibility that miRNAs can function to disrupt RNA-mediated protein assembly processes in other cellular contexts.


Assuntos
HIV-1/fisiologia , MicroRNAs/metabolismo , Complexos Multiproteicos/metabolismo , Precursores de Proteínas/metabolismo , Montagem de Vírus/fisiologia , Liberação de Vírus/fisiologia , Proteínas Argonautas/metabolismo , Análise por Conglomerados , Primers do DNA/genética , Células HEK293 , Humanos , Microscopia de Fluorescência , RNA Interferente Pequeno/genética
12.
Langmuir ; 32(2): 428-41, 2016 Jan 19.
Artigo em Inglês | MEDLINE | ID: mdl-26735020

RESUMO

Charged particles in aqueous suspension form an electrical double layer at their surfaces, which plays a key role in suspension properties. For example, binder particles in latex paint remain suspended in the can because of repulsive forces between overlapping double layers. Existing models of the double layer assume sharp interfaces bearing fixed uniform charge, and so cannot describe aqueous binder particle surfaces, which are soft and diffuse, and bear mobile charge from ionic surfactants as well as grafted multivalent oligomers. To treat this industrially important system, we use atomistic molecular dynamics simulations to investigate a structurally realistic model of commercial binder particle surfaces, informed by extensive characterization of particle synthesis and surface properties. We determine the interfacial profiles of polymer, water, bound and free ions, from which the charge density and electrostatic potential can be calculated. We extend the traditional definitions of the inner and outer Helmholtz planes to our diffuse interfaces. Beyond the Stern layer, the simulated electrostatic potential is well described by the Poisson-Boltzmann equation. The potential at the outer Helmholtz plane compares well to the experimental zeta potential. We compare particle surfaces bearing two types of charge groups, ionic surfactant and multivalent oligomers, with and without added salt. Although the bare charge density of a surface bearing multivalent oligomers is much higher than that of a surfactant-bearing surface at realistic coverage, greater counterion condensation leads to similar zeta potentials for the two systems.

13.
World J Microbiol Biotechnol ; 30(2): 555-65, 2014 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-23996636

RESUMO

The presence of topoisomerase II inhibition activities in the intracellular extract of Streptomyces flavoviridis was investigated. One active compound inhibiting relaxation activity of topoisomerase II was determined to be a protein. This active principle was purified to homogeneity by gel filtration followed by ion exchange chromatography. The apparent molecular mass was 42 kDa as determined by SDS-PAGE. MALDI TOF peptide mass fingerprinting analysis confirmed this topoisomerase II inhibitor, as glucose-inhibited division protein A (GidA) by MOWSE score of 72. The effects of purified GidA protein on DNA relaxation and decatenation by topoisomerase II were investigated. It inhibited topoisomerase II activity and acted as a topoisomerase poison that significantly stabilized the covalent DNA-topoisomerase II reaction intermediate "cleavable complex", as observed with etoposide. Collectively, these findings indicate that GidA is a potent inhibitor of topoisomerase II enzyme, which can be exploited for rational drug design in human carcinomas.


Assuntos
Proteínas de Bactérias/isolamento & purificação , Proteínas de Bactérias/metabolismo , DNA Topoisomerases Tipo II/metabolismo , Inibidores Enzimáticos/isolamento & purificação , Inibidores Enzimáticos/metabolismo , Streptomyces/metabolismo , Proteínas de Bactérias/química , Cromatografia em Gel , Cromatografia por Troca Iônica , DNA/metabolismo , Eletroforese em Gel de Poliacrilamida , Inibidores Enzimáticos/química , Peso Molecular , Ligação Proteica , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz
14.
Sci Adv ; 10(8): eadk8297, 2024 Feb 23.
Artigo em Inglês | MEDLINE | ID: mdl-38394201

RESUMO

HIV-1 Gag proteins can multimerize upon the viral genomic RNA or multiple random cellular messenger RNAs to form a virus particle or a virus-like particle, respectively. To date, whether the two types of particles form via the same Gag multimerization process has remained unclarified. Using photoactivated localization microscopy to illuminate Gag organizations and dynamics at the nanoscale, here, we showed that genomic RNA mediates Gag multimerization in a more cluster-centric, cooperative, and spatiotemporally coordinated fashion, with the ability to drive dense Gag clustering dependent on its ability to act as a long-stranded scaffold not easily attainable by cellular messenger RNAs. These differences in Gag multimerization were further shown to affect downstream selective protein sorting into HIV membranes, indicating that the choice of RNA for packaging can modulate viral membrane compositions. These findings should advance the understanding of HIV assembly and further benefit the development of virus-like particle-based therapeutics.


Assuntos
Infecções por HIV , RNA Viral , Humanos , RNA Viral/genética , RNA Viral/metabolismo , Membrana Celular/metabolismo , Produtos do Gene gag/genética , Produtos do Gene gag/metabolismo , RNA Mensageiro/metabolismo , Infecções por HIV/metabolismo , Multimerização Proteica
15.
medRxiv ; 2024 May 06.
Artigo em Inglês | MEDLINE | ID: mdl-38766055

RESUMO

The epigenome, including the methylation of cytosine bases at CG dinucleotides, is intrinsically linked to transcriptional regulation. The tight regulation of gene expression during skeletal development is essential, with ~1/500 individuals born with skeletal abnormalities. Furthermore, increasing evidence is emerging to link age-associated complex genetic musculoskeletal diseases, including osteoarthritis (OA), to developmental factors including joint shape. Multiple studies have shown a functional role for DNA methylation in the genetic mechanisms of OA risk using articular cartilage samples taken from aged patients. Despite this, our knowledge of temporal changes to the methylome during human cartilage development has been limited. We quantified DNA methylation at ~700,000 individual CpGs across the epigenome of developing human articular cartilage in 72 samples ranging from 7-21 post-conception weeks, a time period that includes cavitation of the developing knee joint. We identified significant changes in 8% of all CpGs, and >9400 developmental differentially methylated regions (dDMRs). The largest hypermethylated dDMRs mapped to transcriptional regulators of early skeletal patterning including MEIS1 and IRX1. Conversely, the largest hypomethylated dDMRs mapped to genes encoding extracellular matrix proteins including SPON2 and TNXB and were enriched in chondrocyte enhancers. Significant correlations were identified between the expression of these genes and methylation within the hypomethylated dDMRs. We further identified 811 CpGs at which significant dimorphism was present between the male and female samples, with the majority (68%) being hypermethylated in female samples. Following imputation, we captured the genotype of these samples at >5 million variants and performed epigenome-wide methylation quantitative trait locus (mQTL) analysis. Colocalization analysis identified 26 loci at which genetic variants exhibited shared impacts upon methylation and OA genetic risk. This included loci which have been previously reported to harbour OA-mQTLs (including GDF5 and ALDH1A2), yet the majority (73%) were novel (including those mapping to CHST3, FGF1 and TEAD1). To our knowledge, this is the first extensive study of DNA methylation across human articular cartilage development. We identify considerable methylomic plasticity within the development of knee cartilage and report active epigenomic mediators of OA risk operating in prenatal joint tissues.

16.
Biotechnol Bioeng ; 110(10): 2731-41, 2013 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-23568715

RESUMO

The extracellular matrix (ECM) consists of a complex mixture of biochemical and physical stimuli that together regulate cell behavior. In this study, we engineer a model ECM consisting of fibrillar Type-1 collagen plus fibronectin that allows systematic examination of the effects of matrix composition and mechanics on cells. On this combined protein matrix, cells exhibit intermediate degrees of spreading and proliferation compared to their responses on collagen or fibronectin alone. Adhesion to the combination matrix could be blocked by peptides containing the sequence arginine-glycine-aspartic acid (RGD) and by antibodies against α1 integrin, suggesting cell-matrix engagement was mediated by a combination of integrin receptors that recognize fibronectin and collagen. Regardless of integrin engagement, cells were sensitive to the mechanical properties of the combination ECM, suggesting that cells could process biochemical and mechanical cues simultaneously and independently.


Assuntos
Proliferação de Células/efeitos dos fármacos , Forma Celular/efeitos dos fármacos , Colágeno Tipo I/farmacologia , Fibronectinas/farmacologia , Adsorção , Análise de Variância , Animais , Fenômenos Biomecânicos/fisiologia , Bovinos , Técnicas de Cultura de Células , Linhagem Celular , Colágeno Tipo I/química , Elasticidade , Matriz Extracelular/química , Matriz Extracelular/metabolismo , Fibronectinas/química , Integrina alfa1/metabolismo , Oligopeptídeos/metabolismo , Ratos
17.
J Biomol Struct Dyn ; 41(9): 4143-4153, 2023 06.
Artigo em Inglês | MEDLINE | ID: mdl-35514135

RESUMO

The interactions of ruthenium(II) complex with Glucose inhibited division protein A (GidA protein) was studied through various spectroscopic techniques with the ultimate goal of preparing adducts with good selectivity for cancer cells. In all the cases, formation of a tight metal-protein conjugate was observed. The influence of pH, reducing agents and chelators on the formation of adduct was analysed by UV- visible spectroscopy. While there was no effect on the addition of sodium ascorbate, some alterations on some selected bands were seen on the UV-visible spectra on the addition of EDTA. The adduct was stable in the pH range of 5-8. Addition of ruthenium(II) complex effectively quenched the intrinsic fluorescence of GidA and it occurred through static quenching. The effect of ruthenium(II) complex on the conformation of GidA has been examined by analyzing CD spectrum. Though, there was some conformational changes observed in the presence of ruthenium(II) complex, α- helix in the secondary structure of GidA retained its identity. Molecular docking of ruthenium(II) complex with GidA also indicated that GidA docks through hydrophobic interaction. The stable semisynthetic complex (ruthenium(II) complex with GidA) was checked for topoisomerase II inhibition. Relaxation and decatenation assay proved topoisomerase II inhibition of semisynthetic complex.Communicated by Ramaswamy H. Sarma.


Assuntos
Neoplasias , Rutênio , Humanos , Inibidores da Topoisomerase II/farmacologia , Simulação de Acoplamento Molecular , Proteína Estafilocócica A , Rutênio/farmacologia , Rutênio/química , Neoplasias/tratamento farmacológico , DNA Topoisomerases Tipo II/metabolismo
18.
Eur Geriatr Med ; 14(2): 285-293, 2023 04.
Artigo em Inglês | MEDLINE | ID: mdl-37002428

RESUMO

PURPOSE: Pre-operative scores based on patient characteristics are commonly used to predict hip fracture outcomes. Mobility, an indicator of pre-operative function, has been neglected as a potential predictor. We assessed the ability of pre-fracture mobility to predict post-operative outcomes following hip fracture. METHODS: We analysed prospectively collected data from hip fracture surgery patients at a large-volume trauma unit. Mobility was classified into four groups. Post-operative outcomes studied were mortality and residence at 30 days, medical complications within 30- or 60-days post-operatively, and prolonged length of stay (LOS, ≥ 28 days). We performed multivariate regression analyses adjusting for age and sex to assess the discriminative ability of the Nottingham Hip Fracture Score (NHFS), with and without mobility, for predicting outcomes using the area under the receiver operating characteristic curve (AUROC). RESULTS: 1919 patients were included, mean age 82.6 (SD 8.2); 1357 (70.7%) were women. Multivariate analysis demonstrated patients with worse mobility had a 1.7-5.5-fold higher 30-day mortality (p ≤ 0.001), and 1.9-3.2-fold higher likelihood of prolonged LOS (p ≤ 0.001). Worse mobility was associated with a 2.3-3.8-fold higher likelihood of living in a care home at 30-days post-operatively (p < 0.001) and a 1.3-2.0-fold higher likelihood of complications within 30 days (p ≤ 0.001). Addition of mobility improved NHFS discrimination for discharge location, AUROC NHFS 0.755 [0.733-0.777] to NHFS + mobility 0.808 [0.789-0.828], and LOS, AUROC NHFS 0.584 [0.557-0.611] to NHFS + mobility 0.616 [0.590-0.643]. CONCLUSION: Incorporating mobility assessment into risk scores may improve casemix adjustment, prognostication following hip fracture, and identify high-risk patient groups requiring enhanced post-operative care at admission.


Assuntos
Fraturas do Quadril , Humanos , Feminino , Idoso de 80 Anos ou mais , Masculino , Medição de Risco , Fraturas do Quadril/cirurgia , Fatores de Risco , Curva ROC , Hospitalização
19.
Protein Cell ; 14(6): 433-447, 2023 06 07.
Artigo em Inglês | MEDLINE | ID: mdl-37402315

RESUMO

Molecular knowledge of human gastric corpus epithelium remains incomplete. Here, by integrated analyses using single-cell RNA sequencing (scRNA-seq), spatial transcriptomics, and single-cell assay for transposase accessible chromatin sequencing (scATAC-seq) techniques, we uncovered the spatially resolved expression landscape and gene-regulatory network of human gastric corpus epithelium. Specifically, we identified a stem/progenitor cell population in the isthmus of human gastric corpus, where EGF and WNT signaling pathways were activated. Meanwhile, LGR4, but not LGR5, was responsible for the activation of WNT signaling pathway. Importantly, FABP5 and NME1 were identified and validated as crucial for both normal gastric stem/progenitor cells and gastric cancer cells. Finally, we explored the epigenetic regulation of critical genes for gastric corpus epithelium at chromatin state level, and identified several important cell-type-specific transcription factors. In summary, our work provides novel insights to systematically understand the cellular diversity and homeostasis of human gastric corpus epithelium in vivo.


Assuntos
Epigênese Genética , Mucosa Gástrica , Humanos , Mucosa Gástrica/metabolismo , Cromatina/metabolismo , Células-Tronco , Epitélio/metabolismo , Proteínas de Ligação a Ácido Graxo/metabolismo
20.
J Exp Med ; 203(4): 1117-27, 2006 Apr 17.
Artigo em Inglês | MEDLINE | ID: mdl-16606673

RESUMO

Oxidative stress is implicated in atherogenesis, yet most clinical trials with antioxidants, particularly vitamin E, have failed to protect against atherosclerotic diseases. A striking exception is probucol, which retards atherosclerosis in carotid arteries and restenosis of coronary arteries after angioplasty. Because probucol has in vitro cellular-protective effects independent of inhibiting lipid oxidation, we investigated the mode of action of probucol in vivo. We used three models of vascular disease: apolipoprotein E-deficient mice, a model of atherosclerosis; rabbit aortic balloon injury, a model of restenosis; and carotid injury in obese Zucker rats, a model of type 2 diabetes. Unexpectedly, we observed that the phenol moieties of probucol were insufficient, whereas its sulphur atoms were required for protection. Probucol and its sulphur-containing metabolite, but not a sulphur-free phenolic analogue, protected via cell-specific effects on inhibiting macrophage accumulation, stimulating reendothelialization, and inhibiting vascular smooth muscle cell proliferation. These processes were mediated via induction of heme oxygenase-1 (HO-1), an activity not shared by vitamin E. Our findings identify HO-1 as the molecular target of probucol. They indicate 2-electron rather than radical (1-electron) oxidants as important contributors to atherogenesis, and point to novel lead compounds for therapeutic intervention against atherosclerotic diseases.


Assuntos
Aterosclerose/enzimologia , Aterosclerose/prevenção & controle , Sequestradores de Radicais Livres/administração & dosagem , Heme Oxigenase-1/metabolismo , Probucol/administração & dosagem , Transdução de Sinais/fisiologia , Animais , Apolipoproteínas E/deficiência , Apolipoproteínas E/genética , Aterosclerose/genética , Reestenose Coronária/enzimologia , Reestenose Coronária/genética , Reestenose Coronária/prevenção & controle , Diabetes Mellitus Tipo 2/enzimologia , Diabetes Mellitus Tipo 2/genética , Diabetes Mellitus Tipo 2/prevenção & controle , Masculino , Camundongos , Camundongos Knockout , Coelhos , Ratos , Ratos Zucker , Transdução de Sinais/genética
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