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1.
Aging Cell ; : e13073, 2019 Nov 19.
Artigo em Inglês | MEDLINE | ID: mdl-31746094

RESUMO

Aging is intimately linked to system-wide metabolic changes that can be captured in blood. Understanding biological processes of aging in humans could help maintain a healthy aging trajectory and promote longevity. We performed untargeted plasma metabolomics quantifying 770 metabolites on a cross-sectional cohort of 268 healthy individuals including 125 twin pairs covering human lifespan (from 6 months to 82 years). Unsupervised clustering of metabolic profiles revealed 6 main aging trajectories throughout life that were associated with key metabolic pathways such as progestin steroids, xanthine metabolism, and long-chain fatty acids. A random forest (RF) model was successful to predict age in adult subjects (≥16 years) using 52 metabolites (R2  = .97). Another RF model selected 54 metabolites to classify pediatric and adult participants (out-of-bag error = 8.58%). These RF models in combination with correlation network analysis were used to explore biological processes of healthy aging. The models highlighted established metabolites, like steroids, amino acids, and free fatty acids as well as novel metabolites and pathways. Finally, we show that metabolic profiles of twins become more dissimilar with age which provides insights into nongenetic age-related variability in metabolic profiles in response to environmental exposure.

2.
Nature ; 569(7758): 663-671, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-31142858

RESUMO

Type 2 diabetes mellitus (T2D) is a growing health problem, but little is known about its early disease stages, its effects on biological processes or the transition to clinical T2D. To understand the earliest stages of T2D better, we obtained samples from 106 healthy individuals and individuals with prediabetes over approximately four years and performed deep profiling of transcriptomes, metabolomes, cytokines, and proteomes, as well as changes in the microbiome. This rich longitudinal data set revealed many insights: first, healthy profiles are distinct among individuals while displaying diverse patterns of intra- and/or inter-personal variability. Second, extensive host and microbial changes occur during respiratory viral infections and immunization, and immunization triggers potentially protective responses that are distinct from responses to respiratory viral infections. Moreover, during respiratory viral infections, insulin-resistant participants respond differently than insulin-sensitive participants. Third, global co-association analyses among the thousands of profiled molecules reveal specific host-microbe interactions that differ between insulin-resistant and insulin-sensitive individuals. Last, we identified early personal molecular signatures in one individual that preceded the onset of T2D, including the inflammation markers interleukin-1 receptor agonist (IL-1RA) and high-sensitivity C-reactive protein (CRP) paired with xenobiotic-induced immune signalling. Our study reveals insights into pathways and responses that differ between glucose-dysregulated and healthy individuals during health and disease and provides an open-access data resource to enable further research into healthy, prediabetic and T2D states.


Assuntos
Biomarcadores/metabolismo , Biologia Computacional , Diabetes Mellitus Tipo 2/microbiologia , Microbioma Gastrointestinal , Interações entre Hospedeiro e Microrganismos/genética , Estado Pré-Diabético/microbiologia , Proteoma/metabolismo , Transcriptoma , Adulto , Idoso , Antibacterianos/administração & dosagem , Biomarcadores/análise , Estudos de Coortes , Conjuntos de Dados como Assunto , Diabetes Mellitus Tipo 2/genética , Diabetes Mellitus Tipo 2/metabolismo , Feminino , Glucose/metabolismo , Voluntários Saudáveis , Humanos , Inflamação/metabolismo , Vacinas contra Influenza/imunologia , Insulina/metabolismo , Resistência à Insulina , Estudos Longitudinais , Masculino , Microbiota/fisiologia , Pessoa de Meia-Idade , Estado Pré-Diabético/genética , Estado Pré-Diabético/metabolismo , Infecções Respiratórias/genética , Infecções Respiratórias/metabolismo , Infecções Respiratórias/microbiologia , Infecções Respiratórias/virologia , Estresse Fisiológico , Vacinação/estatística & dados numéricos
3.
Science ; 364(6436)2019 04 12.
Artigo em Inglês | MEDLINE | ID: mdl-30975860

RESUMO

To understand the health impact of long-duration spaceflight, one identical twin astronaut was monitored before, during, and after a 1-year mission onboard the International Space Station; his twin served as a genetically matched ground control. Longitudinal assessments identified spaceflight-specific changes, including decreased body mass, telomere elongation, genome instability, carotid artery distension and increased intima-media thickness, altered ocular structure, transcriptional and metabolic changes, DNA methylation changes in immune and oxidative stress-related pathways, gastrointestinal microbiota alterations, and some cognitive decline postflight. Although average telomere length, global gene expression, and microbiome changes returned to near preflight levels within 6 months after return to Earth, increased numbers of short telomeres were observed and expression of some genes was still disrupted. These multiomic, molecular, physiological, and behavioral datasets provide a valuable roadmap of the putative health risks for future human spaceflight.


Assuntos
Adaptação Fisiológica , Astronautas , Voo Espacial , Imunidade Adaptativa , Peso Corporal , Artérias Carótidas/diagnóstico por imagem , Espessura Intima-Media Carotídea , Dano ao DNA , Metilação de DNA , Microbioma Gastrointestinal , Instabilidade Genômica , Humanos , Masculino , Homeostase do Telômero , Fatores de Tempo , Estados Unidos , United States National Aeronautics and Space Administration
4.
NMR Biomed ; 32(5): e4075, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-30848538

RESUMO

Duchenne Muscular Dystrophy (DMD) is a fatal X-linked genetic disorder. In DMD, the absence of the dystrophin protein causes decreased sarcolemmal integrity resulting in progressive replacement of muscle with fibrofatty tissue. The effects of lacking dystrophin on muscle and systemic metabolism are still unclear. Therefore, to determine the impact of the absence of dystrophin on metabolism, we investigated the metabolic and lipid profile at two different, well-defined stages of muscle damage and stabilization in mdx mice. We measured NMR-detectable metabolite and lipid profiles in the serum and muscles of mdx mice at 6 and 24 weeks of age. Metabolites were determined in muscle in vivo using 1 H MRI/MRS, in isolated muscles using 1 H-HR-MAS NMR, and in serum using high resolution 1 H/13 C NMR. Dystrophic mice were found to have a unique lipid saturation profile compared with control mice, revealing an age-related metabolic change. In the 6-week-old mdx mice, serum lipids were increased and the degree of lipid saturation changed between 6 and 24 weeks. The serum taurine-creatine ratio increased over the life span of mdx, but not in control mice. Furthermore, the saturation index of lipids increased in the serum but decreased in the tissue over time. Finally, we demonstrated associations between MRI-T2 , a strong indicator of inflammation/edema, with tissue and serum lipid profiles. These results indicate the complex temporal changes of metabolites in the tissue and serum during repetitive bouts of muscle damage and regeneration that occur in dystrophic muscle.

5.
Bioinformatics ; 35(1): 95-103, 2019 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-30561547

RESUMO

Motivation: Multiple biological clocks govern a healthy pregnancy. These biological mechanisms produce immunologic, metabolomic, proteomic, genomic and microbiomic adaptations during the course of pregnancy. Modeling the chronology of these adaptations during full-term pregnancy provides the frameworks for future studies examining deviations implicated in pregnancy-related pathologies including preterm birth and preeclampsia. Results: We performed a multiomics analysis of 51 samples from 17 pregnant women, delivering at term. The datasets included measurements from the immunome, transcriptome, microbiome, proteome and metabolome of samples obtained simultaneously from the same patients. Multivariate predictive modeling using the Elastic Net (EN) algorithm was used to measure the ability of each dataset to predict gestational age. Using stacked generalization, these datasets were combined into a single model. This model not only significantly increased predictive power by combining all datasets, but also revealed novel interactions between different biological modalities. Future work includes expansion of the cohort to preterm-enriched populations and in vivo analysis of immune-modulating interventions based on the mechanisms identified. Availability and implementation: Datasets and scripts for reproduction of results are available through: https://nalab.stanford.edu/multiomics-pregnancy/. Supplementary information: Supplementary data are available at Bioinformatics online.


Assuntos
Metaboloma , Microbiota , Gravidez , Proteoma , Transcriptoma , Biologia Computacional , Feminino , Humanos
6.
Mol Imaging ; 16: 1536012117732439, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-29271299

RESUMO

Assessment of muscle pathology is a key outcome measure to measure the success of clinical trials studying muscular dystrophies; however, few robust minimally invasive measures exist. Indocyanine green (ICG)-enhanced near-infrared (NIR) optical imaging offers an objective, minimally invasive, and longitudinal modality that can quantify pathology within muscle by imaging uptake of ICG into the damaged muscles. Dystrophic mice lacking dystrophin (mdx) or gamma-sarcoglycan (Sgcg-/-) were compared to control mice by NIR optical imaging and magnetic resonance imaging (MRI). We determined that optical imaging could be used to differentiate control and dystrophic mice, visualize eccentric muscle induced by downhill treadmill running, and restore the membrane integrity in Sgcg-/- mice following adeno-associated virus (AAV) delivery of recombinant human SGCG (desAAV8hSGCG). We conclude that NIR optical imaging is comparable to MRI and can be used to detect muscle damage in dystrophic muscle as compared to unaffected controls, monitor worsening of muscle pathology in muscular dystrophy, and assess regression of pathology following therapeutic intervention in muscular dystrophies.


Assuntos
Imagem por Ressonância Magnética/métodos , Distrofias Musculares/diagnóstico por imagem , Imagem Óptica/métodos , Sarcoglicanas/genética , Animais , Meios de Contraste , Modelos Animais de Doenças , Distrofina/genética , Terapia Genética , Vetores Genéticos/administração & dosagem , Humanos , Camundongos , Camundongos Endogâmicos mdx , Músculo Esquelético/diagnóstico por imagem , Distrofias Musculares/genética , Distrofias Musculares/terapia , Sarcoglicanas/administração & dosagem
7.
Mol Ther Methods Clin Dev ; 7: 42-49, 2017 Dec 15.
Artigo em Inglês | MEDLINE | ID: mdl-29018835

RESUMO

The development of therapeutic clinical trials for glycogen storage disorders, including Pompe disease, has called for non-invasive and objective biomarkers. Glycogen accumulation can be measured in vivo with 13C MRS. However, clinical implementation remains challenging due to low signal-to-noise. On the other hand, the buildup of glycolytic intermediates may be detected with 31P MRS. We sought to identify new biomarkers of disease progression in muscle using 13C/31P MRS and 1H HR-MAS in a mouse model of Pompe disease (Gaa-/-). We evaluated the sensitivity of these MR biomarkers in vivo after treatment using an adeno-associated virus vector 2/9 encoding hGAA driven by the desmin promotor. 31P MRS showed significantly elevated phosphomonoesters (PMEs) in Gaa-/- compared to control at 2 (0.06 ± 0.02 versus 0.03 ± 0.01; p = 0.003), 6, 12, and 18 months of age. Correlative 1H HR-MAS measures in intact gastrocnemius muscles revealed high glucose-6-phosphate (G-6-P). After intramuscular AAV injections, glycogen, PME, and G-6-P were decreased within normal range. The changes in PME levels likely partly resulted from changes in G-6-P, one of the overlapping phosphomonoesters in the 31P MR spectra in vivo. Because 31P MRS is inherently more sensitive than 13C MRS, PME levels have greater potential as a clinical biomarker and should be considered as a complementary approach for future studies in Pompe patients.

8.
Am J Pathol ; 186(10): 2692-700, 2016 10.
Artigo em Inglês | MEDLINE | ID: mdl-27565039

RESUMO

Muscle damage is currently assessed through methods such as muscle biopsy, serum biomarkers, functional testing, and imaging procedures, each with its own inherent limitations, and a pressing need for a safe, repeatable, inexpensive, and noninvasive modality to assess the state of muscle health remains. Our aim was to develop and assess near-infrared (NIR) optical imaging as a novel noninvasive method of detecting and quantifying muscle damage. An immobilization-reambulation model was used for inducing muscle damage and recovery in the lower hindlimbs in mice. Confirmation of muscle damage was obtained using in vivo indocyanine green-enhanced NIR optical imaging, magnetic resonance imaging, and ex vivo tissue analysis. The soleus of the immobilized-reambulated hindlimb was found to have a greater amount of muscle damage compared to that in the contralateral nonimmobilized limb, confirmed by in vivo indocyanine green-enhanced NIR optical imaging (3.86-fold increase in radiant efficiency), magnetic resonance imaging (1.41-fold increase in T2), and an ex vivo spectrophotometric assay of indocyanine green uptake (1.87-fold increase in normalized absorbance). Contrast-enhanced NIR optical imaging provides a sensitive, rapid, and noninvasive screening method that can be used for imaging and quantifying muscle damage and recovery in vivo.


Assuntos
Corantes , Verde de Indocianina , Músculo Esquelético/diagnóstico por imagem , Imagem Óptica/métodos , Animais , Imagem por Ressonância Magnética , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Músculo Esquelético/lesões , Músculo Esquelético/patologia , Sensibilidade e Especificidade , Espectroscopia de Luz Próxima ao Infravermelho , Fatores de Tempo
9.
Front Plant Sci ; 6: 611, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26379677

RESUMO

Compound identification is a major bottleneck in metabolomics studies. In nuclear magnetic resonance (NMR) investigations, resonance overlap often hinders unambiguous database matching or de novo compound identification. In liquid chromatography-mass spectrometry (LC-MS), discriminating between biological signals and background artifacts and reliable determination of molecular formulae are not always straightforward. We have designed and implemented several NMR and LC-MS approaches that utilize (13)C, either enriched or at natural abundance, in metabolomics applications. For LC-MS applications, we describe a technique called isotopic ratio outlier analysis (IROA), which utilizes samples that are isotopically labeled with 5% (test) and 95% (control) (13)C. This labeling strategy leads to characteristic isotopic patterns that allow the differentiation of biological signals from artifacts and yield the exact number of carbons, significantly reducing possible molecular formulae. The relative abundance between the test and control samples for every IROA feature can be determined simply by integrating the peaks that arise from the 5 and 95% channels. For NMR applications, we describe two (13)C-based approaches. For samples at natural abundance, we have developed a workflow to obtain (13)C-(13)C and (13)C-(1)H statistical correlations using 1D (13)C and (1)H NMR spectra. For samples that can be isotopically labeled, we describe another NMR approach to obtain direct (13)C-(13)C spectroscopic correlations. These methods both provide extensive information about the carbon framework of compounds in the mixture for either database matching or de novo compound identification. We also discuss strategies in which (13)C NMR can be used to identify unknown compounds from IROA experiments. By combining technologies with the same samples, we can identify important biomarkers and corresponding metabolites of interest.

10.
Age (Dordr) ; 37(1): 9753, 2015 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-25663422

RESUMO

Declining physical function is a major health problem for older adults as it is associated with multiple comorbidities and mortality. Exercise has been shown to improve physical function, though response to exercise is variable. Conversely, drugs targeting the renin-angiotensin system (RAS) pathway, including angiotensin-converting enzyme inhibitors (ACEi) and angiotensin receptor blockers (ARBs), are also reported to improve physical function. In the past decade, significant strides have been made to understand the complexity and specificity of the RAS system as it pertains to physical function in older adults. Prior findings have also determined that interactions between antihypertensive medications and exercise may influence physical function above and beyond either factor alone. We review the latest research on RAS, exercise, and physical function for older adults. We also outline future research aims in this area, including genetic influences and clinical phenotyping, for the purpose of maintaining or improving physical function through tailored treatments.


Assuntos
Envelhecimento/fisiologia , Nível de Saúde , Sistema Renina-Angiotensina/fisiologia , Exercício/fisiologia , Tolerância ao Exercício/fisiologia , Humanos
11.
Anal Chem ; 86(18): 9242-50, 2014 Sep 16.
Artigo em Inglês | MEDLINE | ID: mdl-25140385

RESUMO

(13)C NMR has many advantages for a metabolomics study, including a large spectral dispersion, narrow singlets at natural abundance, and a direct measure of the backbone structures of metabolites. However, it has not had widespread use because of its relatively low sensitivity compounded by low natural abundance. Here we demonstrate the utility of high-quality (13)C NMR spectra obtained using a custom (13)C-optimized probe on metabolomic mixtures. A workflow was developed to use statistical correlations between replicate 1D (13)C and (1)H spectra, leading to composite spin systems that can be used to search publicly available databases for compound identification. This was developed using synthetic mixtures and then applied to two biological samples, Drosophila melanogaster extracts and mouse serum. Using the synthetic mixtures we were able to obtain useful (13)C-(13)C statistical correlations from metabolites with as little as 60 nmol of material. The lower limit of (13)C NMR detection under our experimental conditions is approximately 40 nmol, slightly lower than the requirement for statistical analysis. The (13)C and (1)H data together led to 15 matches in the database compared to just 7 using (1)H alone, and the (13)C correlated peak lists had far fewer false positives than the (1)H generated lists. In addition, the (13)C 1D data provided improved metabolite identification and separation of biologically distinct groups using multivariate statistical analysis in the D. melanogaster extracts and mouse serum.


Assuntos
Espectroscopia de Ressonância Magnética Nuclear de Carbono-13 , Drosophila melanogaster/metabolismo , Metabolômica , Soro/metabolismo , Animais , Bases de Dados Factuais , Modelos Animais de Doenças , Camundongos , Distrofia Muscular de Duchenne/metabolismo , Distrofia Muscular de Duchenne/patologia , Espectroscopia de Prótons por Ressonância Magnética , Soro/química
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