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1.
Cell ; 184(7): 1858-1864.e10, 2021 04 01.
Artigo em Inglês | MEDLINE | ID: mdl-33631096

RESUMO

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly spread within the human population. Although SARS-CoV-2 is a novel coronavirus, most humans had been previously exposed to other antigenically distinct common seasonal human coronaviruses (hCoVs) before the coronavirus disease 2019 (COVID-19) pandemic. Here, we quantified levels of SARS-CoV-2-reactive antibodies and hCoV-reactive antibodies in serum samples collected from 431 humans before the COVID-19 pandemic. We then quantified pre-pandemic antibody levels in serum from a separate cohort of 251 individuals who became PCR-confirmed infected with SARS-CoV-2. Finally, we longitudinally measured hCoV and SARS-CoV-2 antibodies in the serum of hospitalized COVID-19 patients. Our studies indicate that most individuals possessed hCoV-reactive antibodies before the COVID-19 pandemic. We determined that ∼20% of these individuals possessed non-neutralizing antibodies that cross-reacted with SARS-CoV-2 spike and nucleocapsid proteins. These antibodies were not associated with protection against SARS-CoV-2 infections or hospitalizations, but they were boosted upon SARS-CoV-2 infection.


Assuntos
Alphacoronavirus/imunologia , Anticorpos Antivirais , Betacoronavirus/imunologia , COVID-19/imunologia , Adolescente , Adulto , Animais , Anticorpos Antivirais/sangue , Anticorpos Antivirais/imunologia , Teste Sorológico para COVID-19 , Criança , Pré-Escolar , Chlorocebus aethiops , Proteção Cruzada , Reações Cruzadas , Suscetibilidade a Doenças , Células HEK293 , Humanos , Lactente , Recém-Nascido , Células Vero
2.
Cell ; 176(6): 1282-1294.e20, 2019 03 07.
Artigo em Inglês | MEDLINE | ID: mdl-30849372

RESUMO

Multiple signatures of somatic mutations have been identified in cancer genomes. Exome sequences of 1,001 human cancer cell lines and 577 xenografts revealed most common mutational signatures, indicating past activity of the underlying processes, usually in appropriate cancer types. To investigate ongoing patterns of mutational-signature generation, cell lines were cultured for extended periods and subsequently DNA sequenced. Signatures of discontinued exposures, including tobacco smoke and ultraviolet light, were not generated in vitro. Signatures of normal and defective DNA repair and replication continued to be generated at roughly stable mutation rates. Signatures of APOBEC cytidine deaminase DNA-editing exhibited substantial fluctuations in mutation rate over time with episodic bursts of mutations. The initiating factors for the bursts are unclear, although retrotransposon mobilization may contribute. The examined cell lines constitute a resource of live experimental models of mutational processes, which potentially retain patterns of activity and regulation operative in primary human cancers.


Assuntos
Desaminases APOBEC/genética , Neoplasias/genética , Desaminases APOBEC/metabolismo , Linhagem Celular , Linhagem Celular Tumoral , DNA/metabolismo , Análise Mutacional de DNA/métodos , Bases de Dados Genéticas , Exoma , Genoma Humano/genética , Xenoenxertos , Humanos , Mutagênese , Mutação/genética , Taxa de Mutação , Retroelementos , Sequenciamento do Exoma/métodos
3.
Nature ; 604(7906): 517-524, 2022 04.
Artigo em Inglês | MEDLINE | ID: mdl-35418684

RESUMO

The rates and patterns of somatic mutation in normal tissues are largely unknown outside of humans1-7. Comparative analyses can shed light on the diversity of mutagenesis across species, and on long-standing hypotheses about the evolution of somatic mutation rates and their role in cancer and ageing. Here we performed whole-genome sequencing of 208 intestinal crypts from 56 individuals to study the landscape of somatic mutation across 16 mammalian species. We found that somatic mutagenesis was dominated by seemingly endogenous mutational processes in all species, including 5-methylcytosine deamination and oxidative damage. With some differences, mutational signatures in other species resembled those described in humans8, although the relative contribution of each signature varied across species. Notably, the somatic mutation rate per year varied greatly across species and exhibited a strong inverse relationship with species lifespan, with no other life-history trait studied showing a comparable association. Despite widely different life histories among the species we examined-including variation of around 30-fold in lifespan and around 40,000-fold in body mass-the somatic mutation burden at the end of lifespan varied only by a factor of around 3. These data unveil common mutational processes across mammals, and suggest that somatic mutation rates are evolutionarily constrained and may be a contributing factor in ageing.


Assuntos
Longevidade , Taxa de Mutação , Animais , Humanos , Longevidade/genética , Mamíferos/genética , Mutagênese/genética , Mutação
4.
Proc Natl Acad Sci U S A ; 121(22): e2306229121, 2024 May 28.
Artigo em Inglês | MEDLINE | ID: mdl-38722826

RESUMO

The Amazon River Basin's extraordinary social-ecological system is sustained by various water phases, fluxes, and stores that are interconnected across the tropical Andes mountains, Amazon lowlands, and Atlantic Ocean. This "Andes-Amazon-Atlantic" (AAA) pathway is a complex hydroclimatic system linked by the regional water cycle through atmospheric circulation and continental hydrology. Here, we aim to articulate the AAA hydroclimate pathway as a foundational system for research, management, conservation, and governance of aquatic systems of the Amazon Basin. We identify and describe the AAA pathway as an interdependent, multidirectional, and multiscale hydroclimate system. We then present an assessment of recent (1981 to 2020) changes in the AAA pathway, primarily reflecting an acceleration in the rates of hydrologic fluxes (i.e., water cycle intensification). We discuss how the changing AAA pathway orchestrates and impacts social-ecological systems. We conclude with four recommendations for the sustainability of the AAA pathway in ongoing research, management, conservation, and governance.

5.
Nature ; 578(7794): 266-272, 2020 02.
Artigo em Inglês | MEDLINE | ID: mdl-31996850

RESUMO

Tobacco smoking causes lung cancer1-3, a process that is driven by more than 60 carcinogens in cigarette smoke that directly damage and mutate DNA4,5. The profound effects of tobacco on the genome of lung cancer cells are well-documented6-10, but equivalent data for normal bronchial cells are lacking. Here we sequenced whole genomes of 632 colonies derived from single bronchial epithelial cells across 16 subjects. Tobacco smoking was the major influence on mutational burden, typically adding from 1,000 to 10,000 mutations per cell; massively increasing the variance both within and between subjects; and generating several distinct mutational signatures of substitutions and of insertions and deletions. A population of cells in individuals with a history of smoking had mutational burdens that were equivalent to those expected for people who had never smoked: these cells had less damage from tobacco-specific mutational processes, were fourfold more frequent in ex-smokers than current smokers and had considerably longer telomeres than their more-mutated counterparts. Driver mutations increased in frequency with age, affecting 4-14% of cells in middle-aged subjects who had never smoked. In current smokers, at least 25% of cells carried driver mutations and 0-6% of cells had two or even three drivers. Thus, tobacco smoking increases mutational burden, cell-to-cell heterogeneity and driver mutations, but quitting promotes replenishment of the bronchial epithelium from mitotically quiescent cells that have avoided tobacco mutagenesis.


Assuntos
Brônquios/metabolismo , Mutagênese , Mutação/genética , Mucosa Respiratória/metabolismo , Fumar Tabaco/genética , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Brônquios/citologia , Brônquios/patologia , Criança , Células Clonais/citologia , Células Clonais/metabolismo , Análise Mutacional de DNA , Feminino , Humanos , Neoplasias Pulmonares/etiologia , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/patologia , Masculino , Pessoa de Meia-Idade , Mucosa Respiratória/citologia , Mucosa Respiratória/patologia , Fumantes , Telômero/genética , Telômero/metabolismo , Fumar Tabaco/efeitos adversos , Fumar Tabaco/patologia , Adulto Jovem
6.
J Virol ; 98(3): e0162723, 2024 Mar 19.
Artigo em Inglês | MEDLINE | ID: mdl-38305150

RESUMO

Ebola virus disease (EVD) caused by Ebola virus (EBOV) is a severe, often fatal, hemorrhagic disease. A critical component of the public health response to curb EVD epidemics is the use of a replication-competent, recombinant vesicular stomatitis virus (rVSV)-vectored Ebola vaccine, rVSVΔG-ZEBOV-GP (ERVEBO). In this Gem, we will discuss the past and ongoing development of rVSVΔG-ZEBOV-GP, highlighting the importance of basic science and the strength of public-private partnerships to translate fundamental virology into a licensed VSV-vectored Ebola vaccine.


Assuntos
Vacinas contra Ebola , Ebolavirus , Vetores Genéticos , Doença pelo Vírus Ebola , Vesiculovirus , Humanos , Vacinas contra Ebola/genética , Vacinas contra Ebola/imunologia , Ebolavirus/genética , Ebolavirus/imunologia , Vetores Genéticos/genética , Doença pelo Vírus Ebola/imunologia , Doença pelo Vírus Ebola/prevenção & controle , Vesiculovirus/genética , Parcerias Público-Privadas
7.
PLoS Pathog ; 19(2): e1011168, 2023 02.
Artigo em Inglês | MEDLINE | ID: mdl-36812267

RESUMO

Angiotensin-converting enzyme 2 (ACE2), part of the renin-angiotensin system (RAS), serves as an entry point for SARS-CoV-2, leading to viral proliferation in permissive cell types. Using mouse lines in which the Ace2 locus has been humanized by syntenic replacement, we show that regulation of basal and interferon induced ACE2 expression, relative expression levels of different ACE2 transcripts, and sexual dimorphism in ACE2 expression are unique to each species, differ between tissues, and are determined by both intragenic and upstream promoter elements. Our results indicate that the higher levels of expression of ACE2 observed in the lungs of mice relative to humans may reflect the fact that the mouse promoter drives expression of ACE2 in populous airway club cells while the human promoter drives expression in alveolar type 2 (AT2) cells. In contrast to transgenic mice in which human ACE2 is expressed in ciliated cells under the control of the human FOXJ1 promoter, mice expressing ACE2 in club cells under the control of the endogenous Ace2 promoter show a robust immune response after infection with SARS-CoV-2, leading to rapid clearance of the virus. This supports a model in which differential expression of ACE2 determines which cell types in the lung are infected, and this in turn modulates the host response and outcome of COVID-19.


Assuntos
Enzima de Conversão de Angiotensina 2 , COVID-19 , Receptores Virais , Animais , Humanos , Camundongos , Enzima de Conversão de Angiotensina 2/genética , COVID-19/genética , Camundongos Transgênicos , Receptores Virais/genética , SARS-CoV-2 , Tropismo Viral
8.
J Am Chem Soc ; 146(40): 27622-27643, 2024 Oct 09.
Artigo em Inglês | MEDLINE | ID: mdl-39348182

RESUMO

Lysine acylations are ubiquitous and structurally diverse post-translational modifications that vastly expand the functional heterogeneity of the human proteome. Hence, the targeted acylation of lysine residues has emerged as a strategic approach to exert biomimetic control over the protein function. However, existing strategies for targeted lysine acylation in cells often rely on genetic intervention, recruitment of endogenous acylation machinery, or nonspecific acylating agents and lack methods to quantify the magnitude of specific acylations on a global level. In this study, we develop activity-based acylome profiling (ABAP), a chemoproteomic strategy that exploits elaborate N-(cyanomethyl)-N-(phenylsulfonyl)amides and lysine-centric probes for site-specific introduction and proteome-wide mapping of posttranslational lysine acylations in human cells. Harnessing this framework, we quantify various artificial acylations and rediscover numerous endogenous lysine acylations. We validate site-specific acetylation of target lysines and establish a structure-activity relationship for N-(cyanomethyl)-N-(phenylsulfonyl)amides in proteins from diverse structural and functional classes. We identify paralog-selective chemical probes that acetylate conserved lysines within interferon-stimulated antiviral RNA-binding proteins, generating de novo proteoforms with obstructed RNA interactions. We further demonstrate that targeted acetylation of a key enzyme in retinoid metabolism engenders a proteoform with a conformational change in the protein structure, leading to a gain-of-function phenotype and reduced drug potency. These findings underscore the versatility of our strategy in biomimetic control over protein function through targeted delivery and global profiling of endogenous and artificial lysine acylations, potentially advancing therapeutic modalities and our understanding of biological processes orchestrated by these post-translational modifications.


Assuntos
Amidas , Lisina , Processamento de Proteína Pós-Traducional , Acilação , Lisina/química , Lisina/metabolismo , Humanos , Amidas/química , Amidas/metabolismo , Proteoma/metabolismo , Proteoma/química , Relação Estrutura-Atividade
9.
J Am Chem Soc ; 146(4): 2524-2548, 2024 01 31.
Artigo em Inglês | MEDLINE | ID: mdl-38230968

RESUMO

Natural products perennially serve as prolific sources of drug leads and chemical probes, fueling the development of numerous therapeutics. Despite their scarcity, natural products that modulate protein function through covalent interactions with lysine residues hold immense potential to unlock new therapeutic interventions and advance our understanding of the biological processes governed by these modifications. Phloroglucinol meroterpenoids constitute one of the most expansive classes of natural products, displaying a plethora of biological activities. However, their mechanism of action and cellular targets have, until now, remained elusive. In this study, we detail the concise biomimetic synthesis, computational mechanistic insights, physicochemical attributes, kinetic parameters, molecular mechanism of action, and functional cellular targets of several phloroglucinol meroterpenoids. We harness synthetic clickable analogues of natural products to probe their disparate proteome-wide reactivity and subcellular localization through in-gel fluorescence scanning and cell imaging. By implementing sample multiplexing and a redesigned lysine-targeting probe, we streamline a quantitative activity-based protein profiling, enabling the direct mapping of global reactivity and ligandability of proteinaceous lysines in human cells. Leveraging this framework, we identify numerous lysine-meroterpenoid interactions in breast cancer cells at tractable protein sites across diverse structural and functional classes, including those historically deemed undruggable. We validate that phloroglucinol meroterpenoids perturb biochemical functions through stereoselective and site-specific modification of lysines in proteins vital for breast cancer metabolism, including lipid signaling, mitochondrial respiration, and glycolysis. These findings underscore the broad potential of phloroglucinol meroterpenoids for targeting functional lysines in the human proteome.


Assuntos
Produtos Biológicos , Neoplasias da Mama , Humanos , Feminino , Proteoma/química , Lisina/química , Proteômica/métodos , Floroglucinol/farmacologia , Biomimética , Produtos Biológicos/farmacologia
10.
Breast Cancer Res Treat ; 205(2): 359-370, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38424364

RESUMO

PURPOSE: For breast cancer survivors (BCS) living with breast cancer-related lymphedema (BCRL), what outcome domains (OD) should be measured to assess the burden of the disease and efficacy of interventions? A Core Outcome Set (COS) that promotes standardized measurement of outcomes within the constraints of time influenced by work environments is essential for patients and the multidisciplinary professionals that manage and research BCRL. METHODS: Using Delphi methodology, a multidisciplinary group of BCRL experts (physical and occupational therapists, physicians, researchers, physical therapist assistants, nurses, and massage therapist) completed two waves of online surveys. BCRL expert respondents that completed the first survey (n = 78) had an average of 26.5 years in practice, whereas, respondents who completed the second survey (n = 33) had an average of 24.9 years. ODs were included in the COS when consensus thresholds, ranging from 70% to 80%, were met. RESULTS: A total of 12 ODs made up the COS. Reaching a minimum consensus of 70%; volume, tissue consistency, pain, patient-reported upper quadrant function, patient-reported health-related quality of life, and upper extremity activity and motor control were recommended at different phases of the BCRL continuum in a time-constrained environment. Joint function, flexibility, strength, sensation, mobility and balance, and fatigue met an 80% consensus to be added when time and resources were not constrained. CONCLUSION: The COS developed in this study thoroughly captures the burden of BCRL. Using this COS may reduce selective reporting, inconsistency in clinical use, and variability of reporting across interdisciplinary healthcare fields, which manage or research BCRL.


Assuntos
Linfedema Relacionado a Câncer de Mama , Sobreviventes de Câncer , Técnica Delphi , Qualidade de Vida , Humanos , Feminino , Linfedema Relacionado a Câncer de Mama/terapia , Linfedema Relacionado a Câncer de Mama/etiologia , Neoplasias da Mama/complicações , Inquéritos e Questionários , Medidas de Resultados Relatados pelo Paciente , Avaliação de Resultados em Cuidados de Saúde/métodos , Pessoa de Meia-Idade
11.
Breast Cancer Res Treat ; 205(3): 439-449, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38517603

RESUMO

PURPOSE: For breast cancer survivors (BCS) living with breast cancer-related lymphedema (BCRL), what outcome measures (OMs) are recommended to be used to measure standardized outcome domains to fully assess the burden of the disease and efficacy of interventions? An integral component of a standardized core outcome set (COS) are the OMs used to measure the COS. METHODS: A supplemental online survey was linked to a Delphi study investigating a COS for BCRL. OMs were limited to a maximum of 10 options for each outcome domain (OD). There were 14 ODs corresponding to the International Classification of Functioning, Disability, and Health (ICF) framework and respondents rated the OMs with a Likert level of recommendation. The feasibility of the listed OMs was also investigated for most outpatient, inpatient, and research settings. RESULTS: This study identified 27 standardized OMs with a few ODs having 2-3 highly recommended OMs for proper measurement. A few of the recommended OMs have limitations with reliability due to being semi-quantitative measures requiring the interpretation of the rater. CONCLUSION: Narrowing the choices of OMs to 27 highly recommended by BCRL experts may reduce selective reporting, inconsistency in clinical use, and variability of reporting across interdisciplinary healthcare fields which manage or research BCRL. There is a need for valid, reliable, and feasible OMs that measure tissue consistency. Measures of upper extremity activity and motor control need further research in the BCS with BCRL population.


Assuntos
Linfedema Relacionado a Câncer de Mama , Sobreviventes de Câncer , Técnica Delphi , Avaliação de Resultados em Cuidados de Saúde , Humanos , Feminino , Linfedema Relacionado a Câncer de Mama/terapia , Linfedema Relacionado a Câncer de Mama/diagnóstico , Linfedema Relacionado a Câncer de Mama/etiologia , Avaliação de Resultados em Cuidados de Saúde/métodos , Neoplasias da Mama/complicações , Inquéritos e Questionários , Qualidade de Vida , Pessoa de Meia-Idade , Reprodutibilidade dos Testes
12.
Crit Care Med ; 52(6): 930-941, 2024 06 01.
Artigo em Inglês | MEDLINE | ID: mdl-38391282

RESUMO

OBJECTIVES: To evaluate the impact of intubation timing, guided by severity criteria, on mortality in critically ill COVID-19 patients, amidst existing uncertainties regarding optimal intubation practices. DESIGN: Prospective, multicenter, observational study conducted from February 1, 2020, to November 1, 2022. SETTING: Ten academic institutions in the United States and Europe. PATIENTS: Adults (≥ 18 yr old) confirmed with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and hospitalized specifically for COVID-19, requiring intubation postadmission. Exclusion criteria included patients hospitalized for non-COVID-19 reasons despite a positive SARS-CoV-2 test. INTERVENTIONS: Early invasive mechanical ventilation (EIMV) was defined as intubation in patients with less severe organ dysfunction (Sequential Organ Failure Assessment [SOFA] < 7 or Pa o2 /F io2 ratio > 250), whereas late invasive mechanical ventilation (LIMV) was defined as intubation in patients with SOFA greater than or equal to 7 and Pa o2 /F io2 ratio less than or equal to 250. MEASUREMENTS AND MAIN RESULTS: The primary outcome was mortality within 30 days of hospital admission. Among 4464 patients, 854 (19.1%) required mechanical ventilation (mean age 60 yr, 61.7% male, 19.3% Black). Of those, 621 (72.7%) were categorized in the EIMV group and 233 (27.3%) in the LIMV group. Death within 30 days after admission occurred in 278 patients (42.2%) in the EIMV and 88 patients (46.6%) in the LIMV group ( p = 0.28). An inverse probability-of-treatment weighting analysis revealed a statistically significant association with mortality, with patients in the EIMV group being 32% less likely to die either within 30 days of admission (adjusted hazard ratio [HR] 0.68; 95% CI, 0.52-0.90; p = 0.008) or within 30 days after intubation irrespective of its timing from admission (adjusted HR 0.70; 95% CI, 0.51-0.90; p = 0.006). CONCLUSIONS: In severe COVID-19 cases, an early intubation strategy, guided by specific severity criteria, is associated with a reduced risk of death. These findings underscore the importance of timely intervention based on objective severity assessments.


Assuntos
COVID-19 , Intubação Intratraqueal , Respiração Artificial , Índice de Gravidade de Doença , Humanos , COVID-19/mortalidade , COVID-19/terapia , Masculino , Feminino , Pessoa de Meia-Idade , Estudos Prospectivos , Intubação Intratraqueal/estatística & dados numéricos , Idoso , Respiração Artificial/estatística & dados numéricos , Europa (Continente)/epidemiologia , Escores de Disfunção Orgânica , Mortalidade Hospitalar , Estados Unidos/epidemiologia , SARS-CoV-2 , Estado Terminal/mortalidade
13.
J Med Virol ; 96(1): e29389, 2024 01.
Artigo em Inglês | MEDLINE | ID: mdl-38235904

RESUMO

Severe coronavirus disease 2019 (COVID-19) is a hyperinflammatory syndrome. The biomarkers of inflammation best suited to triage patients with COVID-19 are unknown. We conducted a prospective multicenter observational study of adult patients hospitalized specifically for COVID-19 from February 1, 2020 to October 19, 2022. Biomarkers measured included soluble urokinase plasminogen activator receptor (suPAR), C-reactive protein, interleukin-6, procalcitonin, ferritin, and D-dimer. In-hospital outcomes examined include death and the need for mechanical ventilation. Patients admitted in the United States (US, n = 1962) were used to compute area under the curves (AUCs) and identify biomarker cutoffs. The combined European cohorts (n = 1137) were used to validate the biomarker cutoffs. In the US cohort, 356 patients met the composite outcome of death (n = 197) or need for mechanical ventilation (n = 290). SuPAR was the most important predictor of the composite outcome and had the highest AUC (0.712) followed by CRP (0.642), ferritin (0.619), IL-6 (0.614), D-dimer (0.606), and lastly procalcitonin (0.596). Inclusion of other biomarkers did not improve discrimination. A suPAR cutoff of 4.0 ng/mL demonstrated a sensitivity of 95.4% (95% CI: 92.4%-98.0%) and negative predictive value (NPV) of 92.5% (95% CI: 87.5%-96.9%) for the composite outcome. Patients with suPAR < 4.0 ng/mL comprised 10.6% of the cohort and had a 0.8% probability of the composite outcome. Applying this cutoff to the validation cohort yielded a sensitivity of 93.8% (90.4%-96.7%) and NPV of 95.5% (93.1%-97.8%) for the composite outcome. Among commonly measured biomarkers, suPAR offered stronger discriminatory ability and may be useful in triaging low-risk patients with COVID-19.


Assuntos
COVID-19 , Receptores de Ativador de Plasminogênio Tipo Uroquinase , Adulto , Humanos , Estudos Prospectivos , Pró-Calcitonina , COVID-19/diagnóstico , Biomarcadores , Inflamação/diagnóstico , Ferritinas , Prognóstico
14.
Br J Dermatol ; 2024 Oct 11.
Artigo em Inglês | MEDLINE | ID: mdl-39392932

RESUMO

BACKGROUND: Cutaneous leiomyosarcoma (cLMS) is a rare soft tissue neoplasm, showing smooth muscle differentiation, that arises from the mesenchymal cells of the dermis. To-date, genetic investigation of these tumours has involved studies with small sample sizes and limited analyses that identified recurrent somatic mutations in RB1 and TP53, copy number gain of MYCOD and IGF1R, and copy number loss of PTEN. OBJECTIVES: To better understand the molecular pathogenesis of cLMS, we comprehensively explored the mutational landscape of these rare tumours to identify candidate driver events. METHODS: In this retrospective, multi-institutional study, we performed whole-exome sequencing and RNA sequencing on 38 cases of cLMS. RESULTS: TP53 and RB1 were identified as significantly mutated, thus, represent validated driver genes of cLMS. COSMIC mutational signatures SBS7a/b and DBS1 were recurrent, thus, ultraviolet light exposure may be an aetiological factor driving cLMS. Analysis of significantly recurrent somatic copy number alterations, which represent candidate driver events, found focal (<10Mb) deletions encompassing TP53 and KDM6B, and amplifications encompassing ZMYM2, MYOCD, MAP2K4 and NCOR1. A larger (24 Mb) recurrent deletion encompassing CYLD was also identified as significant. Significantly recurrent broad copy number alterations, involving at least half of a chromosome arm, included deletions of 6p/q, 10p/q, 11q, 12q, 13q and 16p/q, and amplification of 15q. Notably PTEN is located on 10q, RB1 on 13q and IGFR1 on 15q. Fusion gene analysis identified recurrent CRTC1/3::MAML2 fusions, as well as many novel fusions in individual samples. CONCLUSIONS: Our analysis of the largest number of cLMS cases to-date highlights the importance of large cohort sizes and the exploration beyond small targeted gene panels when performing molecular analyses, as it allowed a comprehensive exploration of the mutational landscape of these tumours and identification of novel candidate driver events. It also uniquely afforded the opportunity to compare the molecular phenotype of cLMS with LMS of other tissue types, such as uterine and soft tissue LMS. Given that molecular profiling has resulted in the development of novel targeted treatment approaches for uterine and soft tissue LMS, our study now allows the same opportunities to become available for patients with cLMS.

15.
PLoS Biol ; 19(9): e3001398, 2021 09.
Artigo em Inglês | MEDLINE | ID: mdl-34555021

RESUMO

Hypothesis generation in observational, biomedical data science often starts with computing an association or identifying the statistical relationship between a dependent and an independent variable. However, the outcome of this process depends fundamentally on modeling strategy, with differing strategies generating what can be called "vibration of effects" (VoE). VoE is defined by variation in associations that often lead to contradictory results. Here, we present a computational tool capable of modeling VoE in biomedical data by fitting millions of different models and comparing their output. We execute a VoE analysis on a series of widely reported associations (e.g., carrot intake associated with eyesight) with an extended additional focus on lifestyle exposures (e.g., physical activity) and components of the Framingham Risk Score for cardiovascular health (e.g., blood pressure). We leveraged our tool for potential confounder identification, investigating what adjusting variables are responsible for conflicting models. We propose modeling VoE as a critical step in navigating discovery in observational data, discerning robust associations, and cataloging adjusting variables that impact model output.


Assuntos
Ciência de Dados/métodos , Modelos Estatísticos , Estudos Observacionais como Assunto/estatística & dados numéricos , Métodos Epidemiológicos , Humanos
16.
Acta Psychiatr Scand ; 149(6): 445-457, 2024 06.
Artigo em Inglês | MEDLINE | ID: mdl-38566334

RESUMO

INTRODUCTION: Problem gambling (PBG) is more common in people with mental health disorders, including substance use, bipolar, and personality disorders, than in the general population. Although individuals with psychotic disorders might be expected to be more vulnerable to PBG, fewer studies have focused on this comorbidity. The aim of this review was to estimate the prevalence of PBG in people with psychotic disorders. METHODS: Medline (Ovid), EMBASE, PsycINFO (Ovid), CINAHL, CENTRAL, Web of science, and ProQuest were searched on November 1, 2023, without language restrictions. Observational and experimental studies including individuals with psychotic disorders and reporting the prevalence of PBG were included. Risk of bias was assessed using the Joanna Briggs Institute critical appraisal for systematic reviews of prevalence data. The pooled prevalence of PBG was calculated using a fixed effects generalized linear mixed model and presented through forest plots. RESULTS: Of 1271 records screened, 12 studies (n = 3443) were included. The overall prevalence of PBG was 8.7% (95% CI = 7.8%-9.7%, I2 = 69%). A lower prevalence was found in studies with a low risk of bias (5.6%; 95% CI = 4.4%-7.0%) compared with studies with a moderate risk of bias (10.4%; 95% CI = 9.2%-11.7%). Different methods used to assess PBG also contributed to the heterogeneity found. CONCLUSION: This meta-analysis found substantial heterogeneity, partly due to the risk of bias of the included studies and a lack of uniformity in PBG assessment. Although more research is needed to identify those at increased risk for PBG, its relatively high prevalence warrants routine screening for gambling in clinical practice.


Assuntos
Comorbidade , Jogo de Azar , Transtornos Psicóticos , Humanos , Jogo de Azar/epidemiologia , Transtornos Psicóticos/epidemiologia , Prevalência
17.
Nature ; 556(7702): 457-462, 2018 04.
Artigo em Inglês | MEDLINE | ID: mdl-29643510

RESUMO

Every cancer originates from a single cell. During expansion of the neoplastic cell population, individual cells acquire genetic and phenotypic differences from each other. Here, to investigate the nature and extent of intra-tumour diversification, we characterized organoids derived from multiple single cells from three colorectal cancers as well as from adjacent normal intestinal crypts. Colorectal cancer cells showed extensive mutational diversification and carried several times more somatic mutations than normal colorectal cells. Most mutations were acquired during the final dominant clonal expansion of the cancer and resulted from mutational processes that are absent from normal colorectal cells. Intra-tumour diversification of DNA methylation and transcriptome states also occurred; these alterations were cell-autonomous, stable, and followed the phylogenetic tree of each cancer. There were marked differences in responses to anticancer drugs between even closely related cells of the same tumour. The results indicate that colorectal cancer cells experience substantial increases in somatic mutation rate compared to normal colorectal cells, and that genetic diversification of each cancer is accompanied by pervasive, stable and inherited differences in the biological states of individual cancer cells.


Assuntos
Antineoplásicos/farmacologia , Células Clonais/efeitos dos fármacos , Neoplasias Colorretais/genética , Neoplasias Colorretais/patologia , Evolução Molecular , Mutação , Análise de Célula Única , Proliferação de Células , Células Clonais/metabolismo , Células Clonais/patologia , Neoplasias Colorretais/tratamento farmacológico , Neoplasias Colorretais/metabolismo , Metilação de DNA , Análise Mutacional de DNA , Regulação Neoplásica da Expressão Gênica , Humanos , Mucosa Intestinal/metabolismo , Intestinos/citologia , Intestinos/efeitos dos fármacos , Intestinos/patologia , Taxa de Mutação , Organoides/citologia , Organoides/efeitos dos fármacos , Organoides/metabolismo , Organoides/patologia , Transcriptoma
18.
Nature ; 561(7724): 473-478, 2018 09.
Artigo em Inglês | MEDLINE | ID: mdl-30185910

RESUMO

Haematopoietic stem cells drive blood production, but their population size and lifetime dynamics have not been quantified directly in humans. Here we identified 129,582 spontaneous, genome-wide somatic mutations in 140 single-cell-derived haematopoietic stem and progenitor colonies from a healthy 59-year-old man and applied population-genetics approaches to reconstruct clonal dynamics. Cell divisions from early embryogenesis were evident in the phylogenetic tree; all blood cells were derived from a common ancestor that preceded gastrulation. The size of the stem cell population grew steadily in early life, reaching a stable plateau by adolescence. We estimate the numbers of haematopoietic stem cells that are actively making white blood cells at any one time to be in the range of 50,000-200,000. We observed adult haematopoietic stem cell clones that generate multilineage outputs, including granulocytes and B lymphocytes. Harnessing naturally occurring mutations to report the clonal architecture of an organ enables the high-resolution reconstruction of somatic cell dynamics in humans.


Assuntos
Células Sanguíneas/citologia , Células Sanguíneas/metabolismo , Linhagem da Célula/genética , Análise Mutacional de DNA , Mutação , Células-Tronco Adultas/citologia , Teorema de Bayes , Contagem de Células , Divisão Celular , Células Clonais/citologia , Células Clonais/metabolismo , Desenvolvimento Embrionário/genética , Genoma Humano/genética , Granulócitos/citologia , Granulócitos/metabolismo , Hematopoese/genética , Células-Tronco Hematopoéticas/citologia , Células-Tronco Hematopoéticas/metabolismo , Humanos , Linfócitos/citologia , Linfócitos/metabolismo , Masculino , Pessoa de Meia-Idade , Fatores de Tempo
19.
Med Educ ; 2024 Aug 06.
Artigo em Inglês | MEDLINE | ID: mdl-39105273

RESUMO

BACKGROUND: The Spectrum of Involvement describes six levels of active patient involvement in healthcare education. Only at the highest levels are patients described as 'equal partners'. Although this framework was never intended to be hierarchical, healthcare educators continue to strive towards aspirations for involving patients as 'equal partners' in education. However, we do not know what these partnerships mean for all stakeholders and how they can be achieved in practice. This study explores key stakeholders' understandings and experiences of patient partnerships in healthcare education. METHODS: A qualitative case study design was adopted, underpinned by a social constructivist philosophical stance. Semi-structured interviews were conducted with patients (n = 10) and educators (n = 10) from across a Medical School and a Healthcare School. Five focus groups were held with penultimate year students (n = 20) from across the two Schools. Data were analysed using reflexive thematic analysis. RESULTS: Three themes were generated: (i) equal partnerships are neither feasible nor desirable; (ii) partnership is about being and feeling valued; and (iii) valuing patients as partners. Patients did not always desire the highest levels of involvement, as 'equal partners' in education. All stakeholders agreed that partnership need not be synonymous with equality. Instead, they contended that true partnerships were about valuing patients for their contributions at any level of involvement. Remuneration, student feedback, training and providing institutional access were viewed as important methods of valuing patients as partners. CONCLUSION: Patients, educators and students questioned the notion that patient partnerships are only achievable at the highest levels of involvement. Critical application of the Spectrum of Involvement in future research and education is encouraged. This study addresses a gap in the literature, providing tangible approaches to valuing patients as partners that are endorsed by all stakeholders. We propose a model for achieving valued patient partnerships in educational practice.

20.
Ethn Health ; : 1-16, 2024 Sep 18.
Artigo em Inglês | MEDLINE | ID: mdl-39292977

RESUMO

BACKGROUND: Advance care planning empowers people by allowing them some control over certain healthcare decisions in the event they are unable. Yet, advance care planning rates in the American Indian and Alaska Native populations are low. Thus, we culturally tailored the Make Your Wishes About You (MY WAY), an intervention to improve advance care planning access and completion for American Indian peoples. METHODS: In partnership with an American Indian Tribe, the project took a community-based participatory orientation and relied on a Community Advisory Board and a Professional Advisory Board. The culturally tailoring was a 15-step process. These steps allowed us to ensure that the tailoring reflects community-specific norms and preferences, greater reliance on visual images and local idioms of expression, more appropriate attention to family roles, and inclusion of spiritual elements. RESULTS: A four-phase cultural tailoring framework emerged with each phase centering around listening, learning, and analyzing with tailoring occurring between each phase. A culturally tailored MY WAY was created, which was delivered in a manner that reflected Tribal citizenss' preferences. Materials included Tribal language, local idioms of expression, attention to family roles, and appropriate inclusion of spiritual elements. The materials were rated high on a content validity index by the advisory board members. CONCLUSION: There is a growing interest in tailoring existing evidence-based programs with relatively little in the literature offering guidance. By sharing our efforts and experiences in culturally tailoring an advance care planning program for an American Indian Tribe, we hope that it will serve useful for future efforts in ensuring that evidence-based programming reaches those in greatest need. While this project was rooted in the core Indigenous values of community, ceremony or spirituality, language, and place it also lends itself to broader translation across different populations.

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