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1.
PLoS Biol ; 21(9): e3002317, 2023 09.
Artigo em Inglês | MEDLINE | ID: mdl-37747887

RESUMO

Translational control is critical for cell fate transitions during development, lineage specification, and tumorigenesis. Here, we show that the transcription factor double homeobox protein 4 (DUX4), and its previously characterized transcriptional program, broadly regulates translation to change the cellular proteome. DUX4 is a key regulator of zygotic genome activation in human embryos, whereas misexpression of DUX4 causes facioscapulohumeral muscular dystrophy (FSHD) and is associated with MHC-I suppression and immune evasion in cancer. We report that translation initiation and elongation factors are disrupted downstream of DUX4 expression in human myoblasts. Genome-wide translation profiling identified mRNAs susceptible to DUX4-induced translation inhibition, including those encoding antigen presentation factors and muscle lineage proteins, while DUX4-induced mRNAs were robustly translated. Endogenous expression of DUX4 in human FSHD myotubes and cancer cell lines also correlated with reduced protein synthesis and MHC-I presentation. Our findings reveal that DUX4 orchestrates cell state conversion by suppressing the cellular proteome while maintaining translation of DUX4-induced mRNAs to promote an early developmental program.


Assuntos
Proteínas de Homeodomínio , Distrofia Muscular Facioescapuloumeral , Fatores de Transcrição , Humanos , Proteínas de Homeodomínio/genética , Proteínas de Homeodomínio/metabolismo , Músculo Esquelético/metabolismo , Distrofia Muscular Facioescapuloumeral/genética , Distrofia Muscular Facioescapuloumeral/metabolismo , Proteoma/metabolismo , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo
2.
Nucleic Acids Res ; 52(6): e34, 2024 Apr 12.
Artigo em Inglês | MEDLINE | ID: mdl-38375914

RESUMO

Nonsense-mediated mRNA decay (NMD) is a network of pathways that degrades transcripts that undergo premature translation termination. In mammals, NMD can be divided into the exon junction complex (EJC)-enhanced and EJC-independent branches. Fluorescence- and luminescence-based reporters have long been effective tools to investigate NMD, yet existing reporters largely focus on the EJC-enhanced pathway. Here, we present a system of reporters for comparative studies of EJC-independent and EJC-enhanced NMD. This system also enables the study of NMD-associated outcomes such as premature termination codon (PTC) readthrough and truncated protein degradation. These reporters are compatible with fluorescence or luminescence-based readouts via transient transfection or stable integration. Using this reporter system, we show that EJC-enhanced NMD RNA levels are reduced by 2- or 9-fold and protein levels are reduced by 7- or 12-fold compared to EJC-independent NMD, depending on the reporter gene used. Additionally, the extent of readthrough induced by G418 and an NMD inhibitor (SMG1i), alone and in combination, varies across NMD substrates. When combined, G418 and SMG1i increase readthrough product levels in an additive manner for EJC-independent reporters, while EJC-enhanced reporters show a synergistic effect. We present these reporters as a valuable toolkit to deepen our understanding of NMD and its associated mechanisms.


Assuntos
Éxons , Genes Reporter , Técnicas Genéticas , Degradação do RNAm Mediada por Códon sem Sentido , Éxons/genética , Degradação do RNAm Mediada por Códon sem Sentido/genética , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Humanos , Células HEK293 , Genes Reporter/genética
3.
Wound Repair Regen ; 2024 Apr 26.
Artigo em Inglês | MEDLINE | ID: mdl-38666460

RESUMO

Wound dressing changes are essential procedures for wound management. However, ~50% of patients experience severe pain during these procedures despite the availability of analgesic medications, indicating a need for novel therapeutics that address underlying causes of pain. Along with other clinical factors, wound pathogens and inflammatory immune responses have previously been implicated in wound pain. To test whether these factors could contribute to severe pain during wound dressing changes, we conducted an exploratory, cross-sectional analysis of patient-reported pain, inflammatory immune responses, and wound microbiome composition in 445 wounds at the time of a study dressing change. We profiled the bacterial composition of 406 wounds using 16S ribosomal RNA amplicon sequencing and quantified gene expression of 13 inflammatory markers in wound fluid using quantitative real-time polymerase chain reaction (qPCR). Neither inflammatory gene expression nor clinically observed inflammation were associated with severe pain, but Corynebacterium and Streptococcus were of lower relative abundance in wounds of patients reporting severe pain than those reporting little or no pain. Wound microbiome composition differed by wound location, and correlated with six of the inflammatory markers, including complement receptor C5AR1, pro-inflammatory cytokine interleukin (IL)1ß, chemokine IL-8, matrix metalloproteinase MMP2, and the antimicrobial peptide encoding cathelicidin antimicrobial peptide. Interestingly, we found a relationship between the wound microbiome and vacuum-assisted wound closure (VAC). These findings identify preliminary, associative relationships between wound microbiota and host factors which motivate future investigation into the directional relationships between wound care pain, wound closure technologies, and the wound microbiome.

4.
Br J Cancer ; 128(9): 1723-1732, 2023 05.
Artigo em Inglês | MEDLINE | ID: mdl-36807337

RESUMO

BACKGROUND: A non-invasive endometrial cancer detection tool that can accurately triage symptomatic women for definitive testing would improve patient care. Urine is an attractive biofluid for cancer detection due to its simplicity and ease of collection. The aim of this study was to identify urine-based proteomic signatures that can discriminate endometrial cancer patients from symptomatic controls. METHODS: This was a prospective case-control study of symptomatic post-menopausal women (50 cancers, 54 controls). Voided self-collected urine samples were processed for mass spectrometry and run using sequential window acquisition of all theoretical mass spectra (SWATH-MS). Machine learning techniques were used to identify important discriminatory proteins, which were subsequently combined in multi-marker panels using logistic regression. RESULTS: The top discriminatory proteins individually showed moderate accuracy (AUC > 0.70) for endometrial cancer detection. However, algorithms combining the most discriminatory proteins performed well with AUCs > 0.90. The best performing diagnostic model was a 10-marker panel combining SPRR1B, CRNN, CALML3, TXN, FABP5, C1RL, MMP9, ECM1, S100A7 and CFI and predicted endometrial cancer with an AUC of 0.92 (0.96-0.97). Urine-based protein signatures showed good accuracy for the detection of early-stage cancers (AUC 0.92 (0.86-0.9)). CONCLUSION: A patient-friendly, urine-based test could offer a non-invasive endometrial cancer detection tool in symptomatic women. Validation in a larger independent cohort is warranted.


Assuntos
Biomarcadores Tumorais , Neoplasias do Endométrio , Humanos , Feminino , Estudos de Casos e Controles , Proteômica/métodos , Biomarcadores , Espectrometria de Massas/métodos , Neoplasias do Endométrio/diagnóstico , Proteínas de Ligação a Ácido Graxo , Proteínas da Matriz Extracelular
5.
EMBO J ; 38(21): e100847, 2019 10 04.
Artigo em Inglês | MEDLINE | ID: mdl-31433507

RESUMO

Phosphorylation is a key regulator of protein function under (patho)physiological conditions, and defining site-specific phosphorylation is essential to understand basic and disease biology. In vertebrates, the investigative focus has primarily been on serine, threonine and tyrosine phosphorylation, but mounting evidence suggests that phosphorylation of other "non-canonical" amino acids also regulates critical aspects of cell biology. However, standard methods of phosphoprotein characterisation are largely unsuitable for the analysis of non-canonical phosphorylation due to their relative instability under acidic conditions and/or elevated temperature. Consequently, the complete landscape of phosphorylation remains unexplored. Here, we report an unbiased phosphopeptide enrichment strategy based on strong anion exchange (SAX) chromatography (UPAX), which permits identification of histidine (His), arginine (Arg), lysine (Lys), aspartate (Asp), glutamate (Glu) and cysteine (Cys) phosphorylation sites on human proteins by mass spectrometry-based phosphoproteomics. Remarkably, under basal conditions, and having accounted for false site localisation probabilities, the number of unique non-canonical phosphosites is approximately one-third of the number of observed canonical phosphosites. Our resource reveals the previously unappreciated diversity of protein phosphorylation in human cells, and opens up avenues for high-throughput exploration of non-canonical phosphorylation in all organisms.


Assuntos
Ânions/química , Cromatografia por Troca Iônica/métodos , Fosfopeptídeos/análise , Fosfoproteínas/análise , Proteoma/análise , Biologia Computacional , Células HeLa , Humanos , Espectrometria de Massas , Fosforilação
6.
Biochem J ; 479(19): 2063-2086, 2022 10 14.
Artigo em Inglês | MEDLINE | ID: mdl-36240066

RESUMO

Previously, we discovered that deletion of c-Rel in the Eµ-Myc mouse model of lymphoma results in earlier onset of disease, a finding that contrasted with the expected function of this NF-κB subunit in B-cell malignancies. Here we report that Eµ-Myc/cRel-/- cells have an unexpected and major defect in the CHK1 pathway. Total and phospho proteomic analysis revealed that Eµ-Myc/cRel-/- lymphomas highly resemble wild-type (WT) Eµ-Myc lymphomas treated with an acute dose of the CHK1 inhibitor (CHK1i) CCT244747. Further analysis demonstrated that this is a consequence of Eµ-Myc/cRel-/- lymphomas having lost expression of CHK1 protein itself, an effect that also results in resistance to CCT244747 treatment in vivo. Similar down-regulation of CHK1 protein levels was also seen in CHK1i resistant U2OS osteosarcoma and Huh7 hepatocellular carcinoma cells. Further investigation revealed that the deubiquitinase USP1 regulates CHK1 proteolytic degradation and that its down-regulation in our model systems is responsible, at least in part, for these effects. We demonstrate that treating WT Eµ-Myc lymphoma cells with the USP1 inhibitor ML323 was highly effective at reducing tumour burden in vivo. Targeting USP1 activity may thus be an alternative therapeutic strategy in MYC-driven tumours.


Assuntos
Linfoma , Proteínas Proto-Oncogênicas c-myc , Aminopiridinas , Animais , Enzimas Desubiquitinantes , Linfoma/metabolismo , Linfoma/patologia , Camundongos , NF-kappa B/metabolismo , Inibidores de Proteínas Quinases/farmacologia , Proteômica , Proteínas Proto-Oncogênicas c-myc/genética , Proteínas Proto-Oncogênicas c-myc/metabolismo , Pirimidinas
7.
Biochem J ; 479(19): 2131-2151, 2022 10 14.
Artigo em Inglês | MEDLINE | ID: mdl-36240067

RESUMO

The development of resistance and the activation of bypass pathway signalling represents a major problem for the clinical application of protein kinase inhibitors. While investigating the effect of either a c-Rel deletion or RelAT505A phosphosite knockin on the Eµ-Myc mouse model of B-cell lymphoma, we discovered that both NF-κB subunit mutations resulted in CHK1 inhibitor resistance, arising from either loss or alteration of CHK1 activity, respectively. However, since Eµ-Myc lymphomas depend on CHK1 activity to cope with high levels of DNA replication stress and consequent genomic instability, it was not clear how these mutant NF-κB subunit lymphomas were able to survive. To understand these survival mechanisms and to identify potential compensatory bypass signalling pathways in these lymphomas, we applied a multi-omics strategy. With c-Rel-/- Eµ-Myc lymphomas we observed high levels of Phosphatidyl-inositol 3-kinase (PI3K) and AKT pathway activation. Moreover, treatment with the PI3K inhibitor Pictilisib (GDC-0941) selectively inhibited the growth of reimplanted c-Rel-/- and RelAT505A, but not wild type (WT) Eµ-Myc lymphomas. We also observed up-regulation of a RHO/RAC pathway gene expression signature in both Eµ-Myc NF-κB subunit mutation models. Further investigation demonstrated activation of the RHO/RAC effector p21-activated kinase (PAK) 2. Here, the PAK inhibitor, PF-3758309 successfully overcame resistance of RelAT505A but not WT lymphomas. These findings demonstrate that up-regulation of multiple bypass pathways occurs in CHK1 inhibitor resistant Eµ-Myc lymphomas. Consequently, drugs targeting these pathways could potentially be used as either second line or combinatorial therapies to aid the successful clinical application of CHK1 inhibitors.


Assuntos
Linfoma , Fosfatidilinositol 3-Quinases , Animais , Inositol , Linfoma/tratamento farmacológico , Linfoma/genética , Linfoma/metabolismo , Camundongos , Camundongos Transgênicos , NF-kappa B/metabolismo , Fosfatidilinositol 3-Quinase/genética , Fosfatidilinositol 3-Quinases/genética , Fosfatidilinositol 3-Quinases/metabolismo , Inibidores de Proteínas Quinases , Proteínas Proto-Oncogênicas c-akt/metabolismo , Proteínas Proto-Oncogênicas c-myc/genética , Proteínas Proto-Oncogênicas c-myc/metabolismo , Regulação para Cima , Quinases Ativadas por p21/genética
8.
Eur J Appl Physiol ; 123(5): 1051-1066, 2023 May.
Artigo em Inglês | MEDLINE | ID: mdl-36637510

RESUMO

PURPOSE: Aging females are at risk of declining vascular and cognitive function. Exercise can augment both factors independently; however, the influence of exercise on their interdependence is less clearly understood. Ultrasound speckle tracking is a sensitive novel measure of arterial aging but has not previously been used in middle-aged females. We aimed to elucidate the potential interactions between vascular and cognitive variables in active aging females. METHODS: Twelve active (56 ± 5 years; [Formula: see text]: 34.5 ± 6.1 ml.kg.min-1) and 13 inactive (57 ± 4 years; 22.8 ± 2.6 ml.kg.min-1) healthy middle-aged females were included. Ultrasound speckle tracking assessed short-axis common carotid artery (CCA) compliance via peak circumferential strain (PCS) and strain rate (PSR) at rest, during, and after 3-min isometric handgrip exercise. Flow-mediated dilation (FMD) of the brachial artery was assessed using ultrasound. Cognitive function was measured using Verbal Fluency, Trail Making, Stroop, and Digit Span tests. RESULTS: PCS (P = 0.003) and PSR (P = 0.004), were higher in the active cohort. FMD was similar between groups (P > 0.05). Minimal differences in cognitive function existed between groups, although the inactive group performed better in one test of animal Verbal Fluency (P < 0.01). No associations were observed between PCS, PSR, or FMD with cognitive function (all P > 0.05). CONCLUSION: This is the first study to assess PCS and PSR in middle-aged females and demonstrates that active middle-aged females exhibit a superior carotid artery profile compared to their inactive counterparts. However, PCS and PSR of the carotid artery may not be linked with cognitive function in middle-aged females.


Assuntos
Artérias Carótidas , Força da Mão , Feminino , Animais , Artérias Carótidas/diagnóstico por imagem , Artéria Carótida Primitiva/diagnóstico por imagem , Exercício Físico , Ultrassonografia , Endotélio Vascular , Artéria Braquial , Vasodilatação
9.
Hum Mol Genet ; 29(6): 1030-1043, 2020 04 15.
Artigo em Inglês | MEDLINE | ID: mdl-32083293

RESUMO

Advances in understanding the pathophysiology of facioscapulohumeral dystrophy (FSHD) have led to the discovery of candidate therapeutics, and it is important to identify markers of disease activity to inform clinical trial design. For drugs that inhibit DUX4 expression, measuring DUX4 or DUX4-target gene expression might be an interim measure of drug activity; however, only a subset of FHSD muscle biopsies shows evidence of DUX4 expression. Our prior study showed that MRI T2-STIR-positive muscles had a higher probability of showing DUX4 expression than muscles with normal MRI characteristics. In the current study, we performed a 1-year follow-up assessment of the same muscle with repeat MRI and muscle biopsy. There was little change in MRI characteristics over the 1-year period and, similar to the initial evaluation, MRI T2-STIR-postive muscles had a higher expression of DUX4-regulated genes, as well as genes associated with inflammation, extracellular matrix and cell cycle. Compared to the initial evaluation, overall the level of expression in these gene categories remained stable over the 1-year period; however, there was some variability for each individual muscle biopsied. The pooled data from both the initial and 1-year follow-up evaluations identified several FSHD subgroups based on gene expression, as well as a set of genes-composed of DUX4-target genes, inflammatory and immune genes and cell cycle control genes-that distinguished all of the FSHD samples from the controls. These candidate markers of disease activity need to be replicated in independent datasets and, if validated, may provide useful measures of disease progression and response to therapy.


Assuntos
Biomarcadores/análise , Regulação da Expressão Gênica , Proteínas de Homeodomínio/genética , Músculo Esquelético/patologia , Distrofia Muscular Facioescapuloumeral/genética , Distrofia Muscular Facioescapuloumeral/patologia , RNA-Seq/métodos , Adulto , Idoso , Estudos de Casos e Controles , Feminino , Humanos , Estudos Longitudinais , Masculino , Pessoa de Meia-Idade , Músculo Esquelético/metabolismo , Adulto Jovem
10.
Biochem J ; 478(3): 533-551, 2021 02 12.
Artigo em Inglês | MEDLINE | ID: mdl-33438746

RESUMO

Different types of DNA damage can initiate phosphorylation-mediated signalling cascades that result in stimulus specific pro- or anti-apoptotic cellular responses. Amongst its many roles, the NF-κB transcription factor RelA is central to these DNA damage response pathways. However, we still lack understanding of the co-ordinated signalling mechanisms that permit different DNA damaging agents to induce distinct cellular outcomes through RelA. Here, we use label-free quantitative phosphoproteomics to examine the temporal effects of exposure of U2OS cells to either etoposide (ETO) or hydroxyurea (HU) by monitoring the phosphorylation status of RelA and its protein binding partners. Although few stimulus-specific differences were identified in the constituents of phosphorylated RelA interactome after exposure to these DNA damaging agents, we observed subtle, but significant, changes in their phosphorylation states, as a function of both type and duration of treatment. The DNA double strand break (DSB)-inducing ETO invoked more rapid, sustained responses than HU, with regulated targets primarily involved in transcription, cell division and canonical DSB repair. Kinase substrate prediction of ETO-regulated phosphosites suggest abrogation of CDK and ERK1 signalling, in addition to the known induction of ATM/ATR. In contrast, HU-induced replicative stress mediated temporally dynamic regulation, with phosphorylated RelA binding partners having roles in rRNA/mRNA processing and translational initiation, many of which contained a 14-3-3ε binding motif, and were putative substrates of the dual specificity kinase CLK1. Our data thus point to differential regulation of key cellular processes and the involvement of distinct signalling pathways in modulating DNA damage-specific functions of RelA.


Assuntos
Dano ao DNA , Processamento de Proteína Pós-Traducional , Fator de Transcrição RelA/fisiologia , Motivos de Aminoácidos , Sequência de Aminoácidos , Apoptose/efeitos dos fármacos , Apoptose/fisiologia , Neoplasias Ósseas/patologia , Linhagem Celular Tumoral , Cromatografia Líquida , Sequência Consenso , Quebras de DNA de Cadeia Dupla , Replicação do DNA , DNA de Neoplasias/efeitos dos fármacos , DNA de Neoplasias/metabolismo , Etoposídeo/farmacologia , Humanos , Hidroxiureia/farmacologia , Osteossarcoma/patologia , Fosforilação , Mapas de Interação de Proteínas , Proteínas Quinases/metabolismo , Proteômica/métodos , Espectrometria de Massas em Tandem , Fatores de Tempo
11.
Adv Physiol Educ ; 46(3): 498-506, 2022 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-35796466

RESUMO

There is extensive and increasing use of ultrasound in medical care and scientific research, so it is important that the technique, indication, and interpretation of ultrasound investigations are included in medical and biological education. Applications of ultrasound in medical care and education employ not only noninvasive imaging of structure but also the evaluation of organ function. Vascular ultrasound is one such application that has been hitherto relatively neglected in physiology education. The techniques of vascular ultrasound and the physiological regulation of human limb blood flow are reviewed to inform students and curriculum designers. Emphasis is placed on the value of converting velocity measurement by ultrasound to volumetric flow and on the mechanisms involved in rapidly changing flows with interventions. Live collection of real data by ultrasound can show macrovascular and microvascular features of vascular physiology. Macrovascular features include imaging and flow velocity profiles. Microvascular perfusion studies show conductance changes with interventions such as exercise and ischemia. Vascular ultrasound offers exciting opportunities for undergraduate research projects using human subjects. The literature is interesting and, though complex, offers excellent educational experience, with scope for the development of critical thinking and meaningful original research.NEW & NOTEWORTHY Ultrasound imaging has emergent prominence in clinical investigation and education. Vascular ultrasound also evaluates function. Simple methods are described that enable the application of basic ultrasound principles to the measurement of velocity and, importantly, to calculate absolute volumetric blood flow. These methods should be useful in undergraduate and graduate education, with application in clinical practice and research.


Assuntos
Artéria Braquial , Velocidade do Fluxo Sanguíneo/fisiologia , Artéria Braquial/diagnóstico por imagem , Artéria Braquial/fisiologia , Humanos , Ultrassonografia
12.
Adv Physiol Educ ; 46(1): 162-178, 2022 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-34990300

RESUMO

Recommendations for enhancing scientific literacy, inclusivity, and the ecosystem for innovation call for transitioning from teacher-centered to learner-centered science classrooms, particularly at the introductory undergraduate level. Yet little is documented about the challenges that undergraduates perceive in such classrooms and the students' ways of navigating them. Via mixed methods, we studied undergraduates' lived experience in one form of learner-centered teaching, hybrid project-/problem-based learning (PBL), in introductory organismal biology at a baccalaureate institution. Prominent in qualitative analyses of student interviews and written reflections were undergraduates' initial expectation of and longing for an emphasis on facts and transmission of them. The prominence diminished from semester's middle to end, as students came to value developing ideas, solving problems collaboratively, and engaging in deep ways of learning. Collaboration and personal resources such as belief in self emerged as supports for these shifts. Quantitative analyses corroborated that PBL students transformed as learners, moving toward informed views on the nature of science, advancing in multivariable causal reasoning, and more frequently adopting deep approaches for learning than students in lecture-based sections. The qualitative and quantitative findings portray the PBL classroom as an intercultural experience in which culture shock yields over time to acceptance in a way supported by students' internal resources and peer collaboration. The findings have value to those seeking to implement PBL and other complex-learning approaches in a manner responsive to the lived experience of the learner.


Assuntos
Ecossistema , Aprendizagem Baseada em Problemas , Biologia , Humanos , Aprendizagem , Estudantes
13.
Int J Mol Sci ; 23(20)2022 Oct 11.
Artigo em Inglês | MEDLINE | ID: mdl-36292938

RESUMO

Treatments for COVID-19 infections have improved dramatically since the beginning of the pandemic, and glucocorticoids have been a key tool in improving mortality rates. The UK's National Institute for Health and Care Excellence guidance is for treatment to be targeted only at those requiring oxygen supplementation, however, and the interactions between glucocorticoids and COVID-19 are not completely understood. In this work, a multi-omic analysis of 98 inpatient-recruited participants was performed by quantitative metabolomics (using targeted liquid chromatography-mass spectrometry) and data-independent acquisition proteomics. Both 'omics datasets were analysed for statistically significant features and pathways differentiating participants whose treatment regimens did or did not include glucocorticoids. Metabolomic differences in glucocorticoid-treated patients included the modulation of cortisol and bile acid concentrations in serum, but no alleviation of serum dyslipidemia or increased amino acid concentrations (including tyrosine and arginine) in the glucocorticoid-treated cohort relative to the untreated cohort. Proteomic pathway analysis indicated neutrophil and platelet degranulation as influenced by glucocorticoid treatment. These results are in keeping with the key role of platelet-associated pathways and neutrophils in COVID-19 pathogenesis and provide opportunity for further understanding of glucocorticoid action. The findings also, however, highlight that glucocorticoids are not fully effective across the wide range of 'omics dysregulation caused by COVID-19 infections.


Assuntos
Tratamento Farmacológico da COVID-19 , Glucocorticoides , Humanos , Glucocorticoides/farmacologia , Glucocorticoides/uso terapêutico , Proteômica/métodos , Hidrocortisona , Metabolômica/métodos , Aminoácidos/metabolismo , Tirosina , Arginina , Ácidos e Sais Biliares
14.
Behav Brain Sci ; 45: e158, 2022 09 13.
Artigo em Inglês | MEDLINE | ID: mdl-36098429

RESUMO

Cultural effects can influence the results of causal genetic analyses, such as Mendelian randomisation, but the potential influences of culture on genotype-phenotype associations are not currently well understood. Different genetic variants could be associated with different phenotypes in different populations, or culture could confound or influence the direction of the association between genotypes and phenotypes in different populations.


Assuntos
Análise da Randomização Mendeliana , Análise da Randomização Mendeliana/métodos
15.
Hum Mol Genet ; 28(23): 3997-4011, 2019 12 01.
Artigo em Inglês | MEDLINE | ID: mdl-31630170

RESUMO

The DUX4 transcription factor is normally expressed in the cleavage-stage embryo and regulates genes involved in embryonic genome activation. Misexpression of DUX4 in skeletal muscle, however, is toxic and causes facioscapulohumeral muscular dystrophy (FSHD). We recently showed DUX4-induced toxicity is due, in part, to the activation of the double-stranded RNA (dsRNA) response pathway and the accumulation of intranuclear dsRNA foci. Here, we determined the composition of DUX4-induced dsRNAs. We found that a subset of DUX4-induced dsRNAs originate from inverted Alu repeats embedded within the introns of DUX4-induced transcripts and from DUX4-induced dsRNA-forming intergenic transcripts enriched for endogenous retroviruses, Alu and LINE-1 elements. However, these repeat classes were also represented in dsRNAs from cells not expressing DUX4. In contrast, pericentric human satellite II (HSATII) repeats formed a class of dsRNA specific to the DUX4 expressing cells. Further investigation revealed that DUX4 can initiate the bidirectional transcription of normally heterochromatin-silenced HSATII repeats. DUX4-induced HSATII RNAs co-localized with DUX4-induced nuclear dsRNA foci and with intranuclear aggregation of EIF4A3 and ADAR1. Finally, gapmer-mediated knockdown of HSATII transcripts depleted DUX4-induced intranuclear ribonucleoprotein aggregates and decreased DUX4-induced cell death, suggesting that HSATII-formed dsRNAs contribute to DUX4 toxicity.


Assuntos
DNA Satélite/genética , Proteínas de Homeodomínio/metabolismo , Distrofia Muscular Facioescapuloumeral/genética , Adenosina Desaminase/genética , Adenosina Desaminase/metabolismo , Linhagem Celular , DNA Satélite/metabolismo , Regulação da Expressão Gênica , Proteínas de Homeodomínio/genética , Humanos , Íntrons , Modelos Biológicos , Músculo Esquelético/metabolismo , Distrofia Muscular Facioescapuloumeral/metabolismo , Mioblastos/metabolismo , RNA de Cadeia Dupla/metabolismo , Proteínas de Ligação a RNA/metabolismo , Fatores de Transcrição/genética
16.
Hum Mol Genet ; 28(3): 476-486, 2019 02 01.
Artigo em Inglês | MEDLINE | ID: mdl-30312408

RESUMO

Facioscapulohumeral muscular dystrophy (FSHD) is a common, dominantly inherited disease caused by the epigenetic de-repression of the DUX4 gene, a transcription factor normally repressed in skeletal muscle. As targeted therapies are now possible in FSHD, a better understanding of the relationship between DUX4 activity, muscle pathology and muscle magnetic resonance imaging (MRI) changes is crucial both to understand disease mechanisms and for the design of future clinical trials. Here, we performed MRIs of the lower extremities in 36 individuals with FSHD, followed by needle muscle biopsies in safely accessible muscles. We examined the correlation between MRI characteristics, muscle pathology and expression of DUX4 target genes. Results show that the presence of elevated MRI short tau inversion recovery signal has substantial predictive value in identifying muscles with active disease as determined by histopathology and DUX4 target gene expression. In addition, DUX4 target gene expression was detected only in FSHD-affected muscles and not in control muscles. These results support the use of MRI to identify FSHD muscles most likely to have active disease and higher levels of DUX4 target gene expression and might be useful in early phase therapeutic trials to demonstrate target engagement in therapies aiming to suppress DUX4 expression.


Assuntos
Proteínas de Homeodomínio/genética , Músculo Esquelético/patologia , Distrofia Muscular Facioescapuloumeral/diagnóstico por imagem , Adulto , Idoso , Biópsia , Feminino , Expressão Gênica , Proteínas de Homeodomínio/biossíntese , Humanos , Imageamento por Ressonância Magnética/métodos , Masculino , Pessoa de Meia-Idade , Músculo Esquelético/metabolismo , Distrofia Muscular Facioescapuloumeral/genética , Distrofia Muscular Facioescapuloumeral/metabolismo , Distrofia Muscular Facioescapuloumeral/patologia , Fatores de Transcrição/genética
17.
Biochem J ; 477(13): 2451-2475, 2020 07 17.
Artigo em Inglês | MEDLINE | ID: mdl-32501498

RESUMO

Polo-like kinase 4 (PLK4) is the master regulator of centriole duplication in metazoan organisms. Catalytic activity and protein turnover of PLK4 are tightly coupled in human cells, since changes in PLK4 concentration and catalysis have profound effects on centriole duplication and supernumerary centrosomes, which are associated with aneuploidy and cancer. Recently, PLK4 has been targeted with a variety of small molecule kinase inhibitors exemplified by centrinone, which rapidly induces inhibitory effects on PLK4 and leads to on-target centrosome depletion. Despite this, relatively few PLK4 substrates have been identified unequivocally in human cells, and PLK4 signalling outside centriolar networks remains poorly characterised. We report an unbiased mass spectrometry (MS)-based quantitative analysis of cellular protein phosphorylation in stable PLK4-expressing U2OS human cells exposed to centrinone. PLK4 phosphorylation was itself sensitive to brief exposure to the compound, resulting in PLK4 stabilisation. Analysing asynchronous cell populations, we report hundreds of centrinone-regulated cellular phosphoproteins, including centrosomal and cell cycle proteins and a variety of likely 'non-canonical' substrates. Surprisingly, sequence interrogation of ∼300 significantly down-regulated phosphoproteins reveals an extensive network of centrinone-sensitive [Ser/Thr]Pro phosphorylation sequence motifs, which based on our analysis might be either direct or indirect targets of PLK4. In addition, we confirm that NMYC and PTPN12 are PLK4 substrates, both in vitro and in human cells. Our findings suggest that PLK4 catalytic output directly controls the phosphorylation of a diverse set of cellular proteins, including Pro-directed targets that are likely to be important in PLK4-mediated cell signalling.


Assuntos
Proteínas Serina-Treonina Quinases/metabolismo , Pirimidinas/farmacologia , Sulfonas/farmacologia , Linhagem Celular Tumoral , Citometria de Fluxo , Fluorometria , Humanos , Imunoprecipitação , Leupeptinas/farmacologia , Microscopia de Fluorescência , Fosforilação/efeitos dos fármacos , Proteínas Serina-Treonina Quinases/antagonistas & inibidores , Espectrometria de Massas em Tandem
18.
J Nurs Scholarsh ; 53(3): 333-342, 2021 05.
Artigo em Inglês | MEDLINE | ID: mdl-33786985

RESUMO

PURPOSE: To explore how big data can be used to identify the contribution or influence of six specific workload variables: patient count, medication count, task count call lights, patient sepsis score, and hours worked on the occurrence of a near miss (NM) by individual nurses. DESIGN: A correlational and cross-section research design was used to collect over 82,000 useable data points of historical workload data from the three unique systems on a medical-surgical unit in a midsized hospital in the southeast United States over a 60-day period. Data were collected prior to the start of the Covid-19 pandemic in the United States. METHODS: Combined data were analyzed using JMP Pro version 12. Mean responses from two groups were compared using a t-test and those from more than two groups using analysis of variance. Logistic regression was used to determine the significance of impact each workload variable had on individual nurses' ability to administer medications successfully as measured by occurrence of NMs. FINDINGS: The mean outcome of each of the six workload factors measured differed significantly (p < .0001) among nurses. The mean outcome for all workload factors except the hours worked was found to be significantly higher (p < .0001) for those who committed an NM compared to those who did not. At least one workload variable was observed to be significantly associated (p < .05) with the occurrence or nonoccurrence of NMs in 82.6% of the nurses in the study. CONCLUSIONS: For the majority of the nurses in our study, the occurrence of an NM was significantly impacted by at least one workload variable. Because the specific variables that impact performance are different for each individual nurse, decreasing only one variable, such as patient load, will not adequately address the risk for NMs. Other variables not studied here, such as education and experience, might be associated with the occurrence of NMs. CLINICAL RELEVANCE: In the majority of nurses, different workload variables increase their risk for an NM, suggesting that interventions addressing medication errors should be implemented based on the individual's risk profile.


Assuntos
Big Data , Near Miss/estatística & dados numéricos , Recursos Humanos de Enfermagem Hospitalar , Carga de Trabalho/estatística & dados numéricos , Humanos , Fatores de Risco , Sudeste dos Estados Unidos
19.
J Nurs Adm ; 51(9): 461-467, 2021 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-34411062

RESUMO

OBJECTIVE: Nurse (RN) and nursing assistant (NA) relational quality was examined along with associations between relational quality and evaluations of teamwork and communication. BACKGROUND: RN and NA teams constitute the primary nursing care delivery method, and the quality of their relationship affects system capacity for improving patient outcomes; adverse events are linked to communication and teamwork breakdowns. METHODS: RN (N = 889) and NA (263) relational quality was examined using a cross-sectional secondary analysis from system assessment with the Agency for Healthcare Research and Quality Hospital Survey on Patient Safety Culture. RESULTS: RN and NA perceived relational quality indicated significant differences in teamwork and safety grade ratings, with both groups reporting perceived teamwork as high when patient safety grade was low. CONCLUSIONS: This study supports the benefits of improving the RN-NA teamwork-communication relationship. An enhanced RN-NA relational quality can be used by nurse leaders to optimize patient care delivery outcomes.


Assuntos
Comportamento Cooperativo , Assistentes de Enfermagem , Recursos Humanos de Enfermagem Hospitalar , Equipe de Assistência ao Paciente , Comunicação , Humanos
20.
Genes Dev ; 27(24): 2648-62, 2013 Dec 15.
Artigo em Inglês | MEDLINE | ID: mdl-24285714

RESUMO

Cancer cells frequently depend on chromatin regulatory activities to maintain a malignant phenotype. Here, we show that leukemia cells require the mammalian SWI/SNF chromatin remodeling complex for their survival and aberrant self-renewal potential. While Brg1, an ATPase subunit of SWI/SNF, is known to suppress tumor formation in several cell types, we found that leukemia cells instead rely on Brg1 to support their oncogenic transcriptional program, which includes Myc as one of its key targets. To account for this context-specific function, we identify a cluster of lineage-specific enhancers located 1.7 Mb downstream from Myc that are occupied by SWI/SNF as well as the BET protein Brd4. Brg1 is required at these distal elements to maintain transcription factor occupancy and for long-range chromatin looping interactions with the Myc promoter. Notably, these distal Myc enhancers coincide with a region that is focally amplified in ∼3% of acute myeloid leukemias. Together, these findings define a leukemia maintenance function for SWI/SNF that is linked to enhancer-mediated gene regulation, providing general insights into how cancer cells exploit transcriptional coactivators to maintain oncogenic gene expression programs.


Assuntos
Proteínas de Ligação a DNA/metabolismo , Elementos Facilitadores Genéticos/fisiologia , Regulação Neoplásica da Expressão Gênica , Leucemia Mieloide Aguda/fisiopatologia , Proteínas Proto-Oncogênicas c-myc/genética , Fatores de Transcrição/metabolismo , Linhagem Celular Tumoral , Proliferação de Células , DNA Helicases/genética , DNA Helicases/metabolismo , Proteínas de Ligação a DNA/genética , Elementos Facilitadores Genéticos/genética , Técnicas de Silenciamento de Genes , Humanos , Proteínas Nucleares/genética , Proteínas Nucleares/metabolismo , Regiões Promotoras Genéticas/genética , Ligação Proteica , Proteínas Proto-Oncogênicas c-myc/metabolismo , Fatores de Transcrição/genética
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