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1.
Molecules ; 26(8)2021 Apr 10.
Artigo em Inglês | MEDLINE | ID: mdl-33920081

RESUMO

The metabolite profiling of saffron (Crocus sativus L.) from several countries was measured by using ultra-performance liquid chromatography combined with high resolution mass spectrometry (UPLC-HR MS). Multivariate statistical analysis was employed to distinguish among the several samples of C. sativus L. from Greece, Italy, Morocco, Iran, India, Afghanistan and Kashmir. The results of this study showed that the phytochemical content in the samples of C. sativus L. were obviously diverse in the different countries of origin. The metabolomics approach was deemed to be the most suitable in order to evaluate the enormous array of putative metabolites among the saffron samples studied, and was able to provide a comparative phytochemical screening of these samples. Several markers have been identified that aided the differentiation of a group from its counterparts. This can be important for the selection of the appropriate saffron sample, in view of its health-promoting effect which occurs through the modulation of various biological and physiological processes.


Assuntos
Crocus/metabolismo , Metaboloma/genética , Compostos Fitoquímicos/metabolismo , Extratos Vegetais/química , Biomarcadores , Crocus/química , Crocus/classificação , Crocus/genética , Cromatografia Gasosa-Espectrometria de Massas , Grécia , Humanos , Índia , Irã (Geográfico) , Itália , Metabolômica/métodos , Marrocos , Compostos Fitoquímicos/química , Compostos Fitoquímicos/classificação , Extratos Vegetais/classificação , Extratos Vegetais/metabolismo
2.
Int J Mol Sci ; 22(6)2021 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-33804237

RESUMO

Ataxia in children is a common clinical sign of numerous neurological disorders consisting of impaired coordination of voluntary muscle movement. Its most common form, cerebellar ataxia, describes a heterogeneous array of neurologic conditions with uncountable causes broadly divided as acquired or genetic. Numerous genetic disorders are associated with chronic progressive ataxia, which complicates clinical management, particularly on the diagnostic stage. Advances in omics technologies enable improvements in clinical practice and research, so we proposed a multi-omics approach to aid in the genetic diagnosis and molecular elucidation of an undiagnosed infantile condition of chronic progressive cerebellar ataxia. Using whole-exome sequencing, RNA-seq, and untargeted metabolomics, we identified three clinically relevant mutations (rs141471029, rs191582628 and rs398124292) and an altered metabolic profile in our patient. Two POLR1C diagnostic variants already classified as pathogenic were found, and a diagnosis of hypomyelinating leukodystrophy was achieved. A mutation on the MMACHC gene, known to be associated with methylmalonic aciduria and homocystinuria cblC type, was also found. Additionally, preliminary metabolome analysis revealed alterations in our patient's amino acid, fatty acid and carbohydrate metabolism. Our findings provided a definitive genetic diagnosis reinforcing the association between POLR1C mutations and hypomyelinating leukodystrophy and highlighted the relevance of multi-omics approaches to the disease.


Assuntos
Ataxia Cerebelar/diagnóstico , RNA Polimerases Dirigidas por DNA/genética , Genoma/genética , Oxirredutases/genética , Transcriptoma/genética , Adolescente , Adulto , Ataxia Cerebelar/genética , Ataxia Cerebelar/patologia , Criança , Pré-Escolar , Feminino , Humanos , Masculino , Metaboloma/genética , Mutação/genética , Linhagem , RNA-Seq , Deficiência de Vitamina B 12/genética , Sequenciamento Completo do Exoma/métodos , Adulto Jovem
3.
Int J Mol Sci ; 22(5)2021 Mar 05.
Artigo em Inglês | MEDLINE | ID: mdl-33807564

RESUMO

Ginkgo (Ginkgo biloba L.) is a deciduous tree species with high timber, medicinal, ecological, ornamental, and scientific values, and is widely cultivated worldwide. However, for such an important tree species, the regulatory mechanisms involved in the photosynthesis of developing leaves remain largely unknown. Here, we observed variations in light response curves (LRCs) and photosynthetic parameters (photosynthetic capacity (Pnmax) and dark respiration rate (Rd)) of leaves across different developmental stages. We found the divergence in the abundance of compounds (such as 3-phospho-d-glyceroyl phosphate, sedoheptulose-1,7-bisphosphate, and malate) involved in photosynthetic carbon metabolism. Additionally, a co-expression network was constructed to reveal 242 correlations between transcription factors (TFs) and photosynthesis-related genes (p < 0.05, |r| > 0.8). We found that the genes involved in the photosynthetic light reaction pathway were regulated by multiple TFs, such as bHLH, WRKY, ARF, IDD, and TFIIIA. Our analysis allowed the identification of candidate genes that most likely regulate photosynthesis, primary carbon metabolism, and plant development and as such, provide a theoretical basis for improving the photosynthetic capacity and yield of ginkgo trees.


Assuntos
Ginkgo biloba/genética , Metaboloma/genética , Fotossíntese/genética , Transcriptoma/genética , Perfilação da Expressão Gênica/métodos , Folhas de Planta/genética , Proteínas de Plantas/genética , Fatores de Transcrição/genética
4.
Toxicol Appl Pharmacol ; 412: 115390, 2021 02 01.
Artigo em Inglês | MEDLINE | ID: mdl-33387578

RESUMO

The kidneys are metabolically active organs with importance in several physiological tasks such as the secretion of soluble wastes into the urine and synthesizing glucose and oxidizing fatty acids for energy in fasting (non-fed) conditions. Once damaged, the metabolic capability of the kidneys becomes altered. Here, we define metabolic tasks in a computational modeling framework to capture kidney function in an update to the iRno network reconstruction of rat metabolism using literature-based evidence. To demonstrate the utility of iRno for predicting kidney function, we exposed primary rat renal proximal tubule epithelial cells to four compounds with varying levels of nephrotoxicity (acetaminophen, gentamicin, 2,3,7,8-tetrachlorodibenzodioxin, and trichloroethylene) for six and twenty-four hours, and collected transcriptomics and metabolomics data to measure the metabolic effects of compound exposure. For the transcriptomics data, we observed changes in fatty acid metabolism and amino acid metabolism, as well as changes in existing markers of kidney function such as Clu (clusterin). The iRno metabolic network reconstruction was used to predict alterations in these same pathways after integrating transcriptomics data and was able to distinguish between select compound-specific effects on the proximal tubule epithelial cells. Genome-scale metabolic network reconstructions with coupled omics data can be used to predict changes in metabolism as a step towards identifying novel metabolic biomarkers of kidney function and dysfunction.


Assuntos
Metabolismo Energético/efeitos dos fármacos , Células Epiteliais/efeitos dos fármacos , Nefropatias/induzido quimicamente , Túbulos Renais Proximais/efeitos dos fármacos , Metaboloma/efeitos dos fármacos , Transcriptoma/efeitos dos fármacos , Acetaminofen/toxicidade , Animais , Células Cultivadas , Bases de Dados Genéticas , Metabolismo Energético/genética , Células Epiteliais/metabolismo , Células Epiteliais/patologia , Feminino , Perfilação da Expressão Gênica , Redes Reguladoras de Genes , Gentamicinas/toxicidade , Nefropatias/genética , Nefropatias/metabolismo , Nefropatias/patologia , Túbulos Renais Proximais/metabolismo , Túbulos Renais Proximais/patologia , Metaboloma/genética , Metabolômica , Dibenzodioxinas Policloradas/toxicidade , Ratos Sprague-Dawley , Tricloroetileno/toxicidade
5.
PLoS Comput Biol ; 17(1): e1008550, 2021 01.
Artigo em Inglês | MEDLINE | ID: mdl-33513132

RESUMO

We consider the following general family of algorithmic problems that arises in transcriptomics, metabolomics and other fields: given a weighted graph G and a subset of its nodes S, find subsets of S that show significant connectedness within G. A specific solution to this problem may be defined by devising a scoring function, the Maximum Clique problem being a classic example, where S includes all nodes in G and where the score is defined by the size of the largest subset of S fully connected within G. Major practical obstacles for the plethora of algorithms addressing this type of problem include computational efficiency and, particularly for more complex scores which take edge weights into account, the computational cost of permutation testing, a statistical procedure required to obtain a bound on the p-value for a connectedness score. To address these problems, we developed CTD, "Connect the Dots", a fast algorithm based on data compression that detects highly connected subsets within S. CTD provides information-theoretic upper bounds on p-values when S contains a small fraction of nodes in G without requiring computationally costly permutation testing. We apply the CTD algorithm to interpret multi-metabolite perturbations due to inborn errors of metabolism and multi-transcript perturbations associated with breast cancer in the context of disease-specific Gaussian Markov Random Field networks learned directly from respective molecular profiling data.


Assuntos
Algoritmos , Perfilação da Expressão Gênica/métodos , Teoria da Informação , Metabolômica/métodos , Gráficos por Computador , Humanos , Metaboloma/genética , Transcriptoma/genética
6.
Planta ; 253(1): 8, 2021 Jan 02.
Artigo em Inglês | MEDLINE | ID: mdl-33387047

RESUMO

MAIN CONCLUSION: The molecular mechanism underlying white petal color in Brassica napus was revealed by transcriptomic and metabolomic analyses. Rapeseed (Brassica napus L.) is one of the most important oilseed crops worldwide, but the mechanisms underlying flower color in this crop are known less. Here, we performed metabolomic and transcriptomic analyses of the yellow-flowered rapeseed cultivar 'Zhongshuang 11' (ZS11) and the white-flowered inbred line 'White Petal' (WP). The total carotenoid contents were 1.778-fold and 1.969-fold higher in ZS11 vs. WP petals at stages S2 and S4, respectively. Our findings suggest that white petal color in WP flowers is primarily due to decreased lutein and zeaxanthin contents. Transcriptome analysis revealed 10,116 differentially expressed genes with a fourfold or greater change in expression (P-value less than 0.001) in WP vs. ZS11 petals, including 1,209 genes that were differentially expressed at four different stages and 20 genes in the carotenoid metabolism pathway. BnNCED4b, encoding a protein involved in carotenoid degradation, was expressed at abnormally high levels in WP petals, suggesting it might play a key role in white petal formation. The results of qRT-PCR were consistent with the transcriptome data. The results of this study provide important insights into the molecular mechanisms of the carotenoid metabolic pathway in rapeseed petals, and the candidate genes identified in this study provide a resource for the creation of new B. napus germplasms with different petal colors.


Assuntos
Brassica napus , Carotenoides , Flores , Metaboloma , Pigmentação , Transcriptoma , Brassica napus/genética , Carotenoides/metabolismo , Flores/genética , Regulação da Expressão Gênica de Plantas , Metaboloma/genética , Pigmentação/genética , Transcriptoma/genética
7.
Nat Genet ; 53(1): 54-64, 2021 01.
Artigo em Inglês | MEDLINE | ID: mdl-33414548

RESUMO

In cross-platform analyses of 174 metabolites, we identify 499 associations (P < 4.9 × 10-10) characterized by pleiotropy, allelic heterogeneity, large and nonlinear effects and enrichment for nonsynonymous variation. We identify a signal at GLP2R (p.Asp470Asn) shared among higher citrulline levels, body mass index, fasting glucose-dependent insulinotropic peptide and type 2 diabetes, with ß-arrestin signaling as the underlying mechanism. Genetically higher serine levels are shown to reduce the likelihood (by 95%) and predict development of macular telangiectasia type 2, a rare degenerative retinal disease. Integration of genomic and small molecule data across platforms enables the discovery of regulators of human metabolism and translation into clinical insights.


Assuntos
Saúde , Metabolismo/genética , Diabetes Mellitus Tipo 2/genética , Oftalmopatias/genética , Frequência do Gene/genética , Loci Gênicos , Pleiotropia Genética , Genoma Humano , Receptor do Peptídeo Semelhante ao Glucagon 2/genética , Glicina/metabolismo , Humanos , Modelos Lineares , Análise da Randomização Mendeliana , Erros Inatos do Metabolismo/genética , Metaboloma/genética , Mutação de Sentido Incorreto/genética , Fenótipo , Polimorfismo de Nucleotídeo Único/genética , Telangiectasia Retiniana/genética , Tamanho da Amostra , Serina/metabolismo
8.
Int J Mol Sci ; 22(1)2021 Jan 05.
Artigo em Inglês | MEDLINE | ID: mdl-33466472

RESUMO

A viral infection that involves virus invasion, protein synthesis, and virion assembly is typically accompanied by sharp fluctuations in the intracellular levels of metabolites. Under certain conditions, dramatic metabolic shifts can result in various types of cell death. Here, we review different types of adenovirus-induced cell death associated with changes in metabolic profiles of the infected cells. As evidenced by experimental data, in most cases changes in the metabolome precede cell death rather than represent its consequence. In our previous study, the induction of autophagic cell death was observed following adenovirus-mediated lactate production, acetyl-CoA accumulation, and ATP release, while apoptosis was demonstrated to be modulated by alterations in acetate and asparagine metabolism. On the other hand, adenovirus-induced ROS production and ATP depletion were demonstrated to play a significant role in the process of necrotic cell death. Interestingly, the accumulation of ceramide compounds was found to contribute to the induction of all the three types of cell death mentioned above. Eventually, the characterization of metabolite analysis could help in uncovering the molecular mechanism of adenovirus-mediated cell death induction and contribute to the development of efficacious oncolytic adenoviral vectors.


Assuntos
Adenoviridae/genética , Adenoviridae/fisiologia , Morte Celular/genética , Morte Celular/fisiologia , Metaboloma/genética , Metaboloma/fisiologia , Apoptose/genética , Apoptose/fisiologia , Vetores Genéticos/genética , Vetores Genéticos/fisiologia , Humanos
9.
J Steroid Biochem Mol Biol ; 206: 105806, 2021 02.
Artigo em Inglês | MEDLINE | ID: mdl-33340681

RESUMO

Polycystic ovary syndrome (PCOS) is a heterogeneous disease defined by the presence of at least two of the following features: hyperandrogenism, oligoanovulation (OA), and polycystic ovarian morphology (PCOM). Hyperandrogenism is considered the cornerstone of PCOS. However, the most prevalent phenotype in Chinese women with PCOS is OA + PCOM [normo-androgenic PCOS (NA-PCOS)]. It has been reported that PCOS women have higher androgen levels in follicular fluid (FF), but whether NA-PCOS women have the same intrafollicular steroid profiles as hyperandrogenic PCOS (HA-PCOS) women has not been explored. In this study, we analyzed 17 steroids in stimulated size-matched ovarian follicles (16-18 mm) from 166 controls and 141 PCOS women [87 NA-PCOS and 54 HA-PCOS women, defined by a single serum testosterone (T) immunoassay measurement] using liquid chromatography tandem mass spectrometry, and investigated their relationship with baseline characteristics. No significant differences in intrafollicular steroid levels and product/precursor ratios between NA-PCOS and HA-PCOS women were observed, though HA-PCOS women had significantly higher serum luteinizing hormone and T levels than NA-PCOS women. NA-PCOS and HA-PCOS women had significantly higher levels of androstenedione (AD), T and free androgen index, higher enzyme activity of P450c17 (AD/17OH-progesterone), 3ßHSD2 (17OH-progesterone /17OH-pregnenolone) and P450c11 (corticosterone /11-deoxycorticosterone), lower levels of pregnenolone, 17OH-pregnenolone and 11-deoxycorticosterone, and decreased enzyme activity of P450aro (estrone/AD and estradiol/T) and 5α-reductase (dihydrotestosterone/T) in FF than controls. NA-PCOS women had significantly higher intrafollicular cortisol levels and lower 11ßHSD2 (cortisone/cortisol) activity than controls. Baseline serum T levels were slightly correlated with intrafollicular estrogens (E1: r = 0.192, p = 0.019; E2: r = 0.248, p = 0.002; E3: r = 0.248, p = 0.002) and androgens (DHEAS: r = 0.276, p = 0.001; AD: r = 0.185, p = 0.032; T: r = 0.173, p = 0.044) in controls and PCOS women respectively. Serum anti-Müllerian hormone (AMH) levels and antral follicle count (AFC) were correlated with intrafollicular cortisol (AMH: r = 0.380, p = 0.000; AFC: r = 0.177, p = 0.036) and corticosterone (AMH: r = 0.212, p = 0.048; AFC: r = 0.219, p = 0.009) levels in PCOS women. In conclusion, NA-PCOS and HA-PCOS women had statistically similar steroid metabolome profiles in FF, both of which showed a generally decreased steroidogenesis and hyperandrogenism compared to controls.


Assuntos
Hiperandrogenismo/sangue , Metaboloma/genética , Síndrome do Ovário Policístico/sangue , Esteroides/sangue , Adulto , Androgênios/sangue , Androstenodiona/sangue , Hormônio Antimülleriano , Estradiol/sangue , Estrogênios/sangue , Feminino , Líquido Folicular/metabolismo , Humanos , Hidrocortisona/sangue , Hiperandrogenismo/genética , Hiperandrogenismo/metabolismo , Hiperandrogenismo/patologia , Hormônio Luteinizante/sangue , Folículo Ovariano/metabolismo , Folículo Ovariano/patologia , Síndrome do Ovário Policístico/genética , Síndrome do Ovário Policístico/metabolismo , Síndrome do Ovário Policístico/patologia , Esteroides/metabolismo , Testosterona/sangue , Adulto Jovem
10.
Methods Mol Biol ; 2200: 413-424, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33175390

RESUMO

Although untargeted metabolomic approaches hold great promise for global identification of low molecular weight metabolites in biological samples, deep coverage and confident identification of the metabolites remains challenging due to the great diversity and number of chemical structures, especially in plants. Additionally, there is a need to employ a cell-specific research approach to many physiological and biological responses to specific environmental stimuli. Here, we report an untargeted metabolomic method using Arabidopsis thaliana guard cell samples during response to systemic signals of pathogen attack. We employed a new Acquire X MSn data acquisition technology, which uses an iterative fragmentation process to increase level-2 identification of unknown metabolites. We were able to increase the number of identified metabolites and thus the metabolome coverage in Arabidopsis guard cells. This method can be applied to studying metabolomes of other cell types and tissues.


Assuntos
Arabidopsis , Metaboloma , Metabolômica , Imunidade Vegetal , Estômatos de Plantas , Arabidopsis/genética , Arabidopsis/imunologia , Metaboloma/genética , Metaboloma/imunologia , Estômatos de Plantas/genética , Estômatos de Plantas/imunologia
11.
Methods Mol Biol ; 2225: 179-197, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33108663

RESUMO

Virotherapy, enabled by recent advances in the transdisciplinary field of biotechnology, has emerged as a powerful tool for use in anticancer treatment, gene therapy, immunotherapy, etc. Examining the effects of viruses and virus-derived immune-modulating therapeutics is of great fundamental and clinical interest. Here we describe a sample preparation protocol for metabolite extraction from virus-infected tissue, in addition to liquid chromatography-mass spectrometry conditions essential for subsequent analysis. This metabolomics approach delivers highly sensitive and specific metabolite information on various biospecimens. Such an approach may be adopted to monitor biological changes in over 30 relevant metabolic pathways in response to viral infection and also viral therapeutics.


Assuntos
Dependovirus/crescimento & desenvolvimento , Metaboloma/genética , Metabolômica/métodos , Neoplasias/metabolismo , Terapia Viral Oncolítica/métodos , Animais , Cromatografia Líquida/instrumentação , Cromatografia Líquida/métodos , Dependovirus/genética , Dependovirus/metabolismo , Humanos , Redes e Vias Metabólicas/genética , Neoplasias/genética , Neoplasias/patologia , Neoplasias/terapia , Espectrometria de Massas em Tandem/instrumentação , Espectrometria de Massas em Tandem/métodos
12.
BMC Med ; 18(1): 396, 2020 12 17.
Artigo em Inglês | MEDLINE | ID: mdl-33327948

RESUMO

BACKGROUND: Higher adiposity increases the risk of colorectal cancer (CRC), but whether this relationship varies by anatomical sub-site or by sex is unclear. Further, the metabolic alterations mediating the effects of adiposity on CRC are not fully understood. METHODS: We examined sex- and site-specific associations of adiposity with CRC risk and whether adiposity-associated metabolites explain the associations of adiposity with CRC. Genetic variants from genome-wide association studies of body mass index (BMI) and waist-to-hip ratio (WHR, unadjusted for BMI; N = 806,810), and 123 metabolites from targeted nuclear magnetic resonance metabolomics (N = 24,925), were used as instruments. Sex-combined and sex-specific Mendelian randomization (MR) was conducted for BMI and WHR with CRC risk (58,221 cases and 67,694 controls in the Genetics and Epidemiology of Colorectal Cancer Consortium, Colorectal Cancer Transdisciplinary Study, and Colon Cancer Family Registry). Sex-combined MR was conducted for BMI and WHR with metabolites, for metabolites with CRC, and for BMI and WHR with CRC adjusted for metabolite classes in multivariable models. RESULTS: In sex-specific MR analyses, higher BMI (per 4.2 kg/m2) was associated with 1.23 (95% confidence interval (CI) = 1.08, 1.38) times higher CRC odds among men (inverse-variance-weighted (IVW) model); among women, higher BMI (per 5.2 kg/m2) was associated with 1.09 (95% CI = 0.97, 1.22) times higher CRC odds. WHR (per 0.07 higher) was more strongly associated with CRC risk among women (IVW OR = 1.25, 95% CI = 1.08, 1.43) than men (IVW OR = 1.05, 95% CI = 0.81, 1.36). BMI or WHR was associated with 104/123 metabolites at false discovery rate-corrected P ≤ 0.05; several metabolites were associated with CRC, but not in directions that were consistent with the mediation of positive adiposity-CRC relations. In multivariable MR analyses, associations of BMI and WHR with CRC were not attenuated following adjustment for representative metabolite classes, e.g., the univariable IVW OR for BMI with CRC was 1.12 (95% CI = 1.00, 1.26), and this became 1.11 (95% CI = 0.99, 1.26) when adjusting for cholesterol in low-density lipoprotein particles. CONCLUSIONS: Our results suggest that higher BMI more greatly raises CRC risk among men, whereas higher WHR more greatly raises CRC risk among women. Adiposity was associated with numerous metabolic alterations, but none of these explained associations between adiposity and CRC. More detailed metabolomic measures are likely needed to clarify the mechanistic pathways.


Assuntos
Adiposidade/genética , Neoplasias Colorretais/genética , Neoplasias Colorretais/metabolismo , Metaboloma/genética , Adulto , Índice de Massa Corporal , Estudos de Casos e Controles , Neoplasias Colorretais/epidemiologia , Neoplasias Colorretais/etiologia , Europa (Continente)/epidemiologia , Feminino , Predisposição Genética para Doença , Estudo de Associação Genômica Ampla/estatística & dados numéricos , Humanos , Masculino , Análise da Randomização Mendeliana , Pessoa de Meia-Idade , Obesidade/complicações , Obesidade/epidemiologia , Obesidade/genética , Obesidade/metabolismo , Polimorfismo de Nucleotídeo Único , Fatores de Risco , Fatores Sexuais , Relação Cintura-Quadril
13.
Nat Genet ; 52(10): 1111-1121, 2020 10.
Artigo em Inglês | MEDLINE | ID: mdl-32989321

RESUMO

Wild tomato species represent a rich gene pool for numerous desirable traits lost during domestication. Here, we exploited an introgression population representing wild desert-adapted species and a domesticated cultivar to establish the genetic basis of gene expression and chemical variation accompanying the transfer of wild-species-associated fruit traits. Transcriptome and metabolome analysis of 580 lines coupled to pathogen sensitivity assays resulted in the identification of genomic loci associated with levels of hundreds of transcripts and metabolites. These associations occurred in hotspots representing coordinated perturbation of metabolic pathways and ripening-related processes. Here, we identify components of the Solanum alkaloid pathway, as well as genes and metabolites involved in pathogen defense and linking fungal resistance with changes in the fruit ripening regulatory network. Our results outline a framework for understanding metabolism and pathogen resistance during tomato fruit ripening and provide insights into key fruit quality traits.


Assuntos
Resistência à Doença/genética , Lycopersicon esculentum/genética , Metaboloma/genética , Transcriptoma/genética , Alcaloides/genética , Domesticação , Frutas/genética , Frutas/crescimento & desenvolvimento , Frutas/parasitologia , Fungos/genética , Fungos/patogenicidade , Regulação da Expressão Gênica de Plantas/genética , Lycopersicon esculentum/crescimento & desenvolvimento , Lycopersicon esculentum/microbiologia , Redes e Vias Metabólicas/genética , Fenótipo , Doenças das Plantas/genética , Doenças das Plantas/microbiologia , Solanum/genética , Solanum/microbiologia
14.
Proc Natl Acad Sci U S A ; 117(40): 24974-24985, 2020 10 06.
Artigo em Inglês | MEDLINE | ID: mdl-32958637

RESUMO

The antigen-presenting molecule MR1 (MHC class I-related protein 1) presents metabolite antigens derived from microbial vitamin B2 synthesis to activate mucosal-associated invariant T (MAIT) cells. Key aspects of this evolutionarily conserved pathway remain uncharacterized, including where MR1 acquires ligands and what accessory proteins assist ligand binding. We answer these questions by using a fluorophore-labeled stable MR1 antigen analog, a conformation-specific MR1 mAb, proteomic analysis, and a genome-wide CRISPR/Cas9 library screen. We show that the endoplasmic reticulum (ER) contains a pool of two unliganded MR1 conformers stabilized via interactions with chaperones tapasin and tapasin-related protein. This pool is the primary source of MR1 molecules for the presentation of exogenous metabolite antigens to MAIT cells. Deletion of these chaperones reduces the ER-resident MR1 pool and hampers antigen presentation and MAIT cell activation. The MR1 antigen-presentation pathway thus co-opts ER chaperones to fulfill its unique ability to present exogenous metabolite antigens captured within the ER.


Assuntos
Retículo Endoplasmático/genética , Antígenos de Histocompatibilidade Classe I/genética , Metaboloma/genética , Antígenos de Histocompatibilidade Menor/genética , Proteômica , Apresentação do Antígeno/genética , Antígenos/genética , Antígenos/imunologia , Sistemas CRISPR-Cas/genética , Humanos , Ligantes , Ativação Linfocitária/genética , Proteínas de Membrana Transportadoras/genética , Chaperonas Moleculares/genética , Chaperonas Moleculares/imunologia , Células T Invariantes Associadas à Mucosa/imunologia , Riboflavina/genética
15.
Am J Hum Genet ; 107(4): 636-653, 2020 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-32946765

RESUMO

With mounting interest in translating genome-wide association study (GWAS) hits from large meta-analyses (meta-GWAS) in diverse clinical settings, evaluating their generalizability in target populations is crucial. Here, we consider long-term survivors of childhood cancers from the St. Jude Lifetime Cohort Study, and we show the limited generalizability of 1,376 robust SNP associations reported in the general population across 12 complex anthropometric and cardiometabolic phenotypes (n = 2,231; observed-to-expected replication ratio = 0.70, p = 6.2 × 10-8). An examination of five comparable phenotypes in a second independent cohort of survivors from the Childhood Cancer Survivor Study corroborated the overall limited generalizability of meta-GWAS hits to survivors (n = 4,212; observed-to-expected replication ratio = 0.55, p = 5.6 × 10-15). Finally, in direct comparisons of survivor samples against independent equivalently powered general population samples from the UK Biobank, we consistently observed lower meta-GWAS hit replication rates and poorer polygenic risk score predictive performance in survivor samples for multiple phenotypes. As a possible explanation, we found that meta-GWAS hits were less likely to be replicated in survivors who had been exposed to cancer therapies that are associated with phenotype risk. Examination of complementary DNA methylation data in a subset of survivors revealed that treatment-related methylation patterns at genomic sites linked to meta-GWAS hits may disrupt established genetic signals in survivors.


Assuntos
Protocolos de Quimioterapia Combinada Antineoplásica/uso terapêutico , Sobreviventes de Câncer , Epigênese Genética , Regulação Neoplásica da Expressão Gênica , Genes Neoplásicos , Neoplasias Hipotalâmicas/genética , Antropometria/métodos , Criança , Estudos de Coortes , Metilação de DNA , Feminino , Estudo de Associação Genômica Ampla , Genótipo , Humanos , Neoplasias Hipotalâmicas/diagnóstico , Neoplasias Hipotalâmicas/patologia , Neoplasias Hipotalâmicas/terapia , Masculino , Metanálise como Assunto , Metaboloma/genética , Herança Multifatorial , Fenótipo , Valor Preditivo dos Testes , Medição de Risco
16.
Toxicol Lett ; 333: 290-302, 2020 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-32835833

RESUMO

Triptolide, a major active component of Triptergium wilfordii Hook. f, is used in the treatment of autoimmune disease. However, triptolide is associated with severe adverse reactions, especially hepatotoxicity, which limits its clinical application. To examine the underlying mechanism of triptolide-induced liver injury, a combination of dose- and time-dependent toxic effects, RNA-seq and metabolomics were employed. Triptolide-induced toxicity occurred in a dose- and time-dependent manners and was characterized by apoptosis and not necroptosis. Transcriptomics profiles of the dose-dependent response to triptolide suggested that PI3K/AKT, MAPK, TNFα and p53 signaling pathways were the vital steps in triptolide-induced hepatocyte apoptosis. Metabolomics further revealed that glycerophospholipid, fatty acid, leukotriene, purine and pyrimidine metabolism were the major metabolic alterations after triptolide exposure. Finally, acylcarnitines were identified as potential biomarkers for the early detection of triptolide-induced liver injury.


Assuntos
Apoptose/efeitos dos fármacos , Doença Hepática Induzida por Substâncias e Drogas , Diterpenos/toxicidade , Metaboloma/efeitos dos fármacos , Necroptose/efeitos dos fármacos , Fenantrenos/toxicidade , Transcriptoma/efeitos dos fármacos , Animais , Apoptose/genética , Doença Hepática Induzida por Substâncias e Drogas/genética , Doença Hepática Induzida por Substâncias e Drogas/metabolismo , Doença Hepática Induzida por Substâncias e Drogas/patologia , Relação Dose-Resposta a Droga , Compostos de Epóxi/toxicidade , Perfilação da Expressão Gênica , Metaboloma/genética , Metabolômica , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Knockout , Necroptose/genética
17.
Nucleic Acids Res ; 48(18): 10518-10526, 2020 10 09.
Artigo em Inglês | MEDLINE | ID: mdl-32857846

RESUMO

Riboswitches regulate genes by adopting different structures in responds to metabolite binding. The guanidine-II riboswitch is the smallest representative of the ykkC class with the mechanism of its function being centred on the idea that its two stem loops P1 and P2 form a kissing hairpin interaction upon binding of guanidinium (Gdm+). This mechanism is based on in-line probing experiments with the full-length riboswitch and crystal structures of the truncated stem loops P1 and P2. However, the crystal structures reveal only the formation of the homodimers P1 | P1 and P2 | P2 but not of the proposed heterodimer P1 | P2. Here, site-directed spin labeling (SDSL) in combination with Pulsed Electron-Electron Double Resonance (PELDOR or DEER) is used to study their structures in solution and how they change upon binding of Gdm+. It is found that both hairpins adopt different structures in solution and that binding of Gdm+ does indeed lead to the formation of the heterodimer but alongside the homodimers in a statistical 1:2:1 fashion. These results do thus support the proposed switching mechanism.


Assuntos
Guanidina/química , Metaboloma/genética , Conformação de Ácido Nucleico , Riboswitch/genética , Simulação por Computador , Cristalografia por Raios X , Dimerização , Espectroscopia de Ressonância de Spin Eletrônica , Escherichia coli/genética , Escherichia coli/ultraestrutura , Guanidina/metabolismo , Ligação de Hidrogênio , Sequências Repetidas Invertidas/genética , Ligantes , Ligação Proteica/genética , Riboswitch/efeitos dos fármacos , Marcadores de Spin
18.
PLoS Genet ; 16(7): e1008835, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32644988

RESUMO

In most organisms, dietary restriction (DR) increases lifespan. However, several studies have found that genotypes within the same species vary widely in how they respond to DR. To explore the mechanisms underlying this variation, we exposed 178 inbred Drosophila melanogaster lines to a DR or ad libitum (AL) diet, and measured a panel of 105 metabolites under both diets. Twenty four out of 105 metabolites were associated with the magnitude of the lifespan response. These included proteinogenic amino acids and metabolites involved in α-ketoglutarate (α-KG)/glutamine metabolism. We confirm the role of α-KG/glutamine synthesis pathways in the DR response through genetic manipulations. We used covariance network analysis to investigate diet-dependent interactions between metabolites, identifying the essential amino acids threonine and arginine as "hub" metabolites in the DR response. Finally, we employ a novel metabolic and genetic bipartite network analysis to reveal multiple genes that influence DR lifespan response, some of which have not previously been implicated in DR regulation. One of these is CCHa2R, a gene that encodes a neuropeptide receptor that influences satiety response and insulin signaling. Across the lines, variation in an intronic single nucleotide variant of CCHa2R correlated with variation in levels of five metabolites, all of which in turn were correlated with DR lifespan response. Inhibition of adult CCHa2R expression extended DR lifespan of flies, confirming the role of CCHa2R in lifespan response. These results provide support for the power of combined genomic and metabolomic analysis to identify key pathways underlying variation in this complex quantitative trait.


Assuntos
Envelhecimento/genética , Proteínas de Drosophila/genética , Longevidade/genética , Metaboloma/genética , Receptores Acoplados a Proteínas G/genética , Envelhecimento/metabolismo , Envelhecimento/patologia , Animais , Restrição Calórica , Dieta , Drosophila melanogaster/genética , Drosophila melanogaster/crescimento & desenvolvimento , Regulação da Expressão Gênica no Desenvolvimento/genética , Insulina/genética , Metabolômica , Mutação/genética , Transdução de Sinais/genética
19.
Nat Commun ; 11(1): 2926, 2020 06 10.
Artigo em Inglês | MEDLINE | ID: mdl-32522991

RESUMO

Metabolic changes alter the cellular milieu; can this also change intracellular protein folding? Since proteostasis can modulate mutational buffering, if change in metabolism has the ability to change protein folding, arguably, it should also alter mutational buffering. Here we find that altered cellular metabolic states in E. coli buffer distinct mutations on model proteins. Buffered-mutants have folding problems in vivo and are differently chaperoned in different metabolic states. Notably, this assistance is dependent upon the metabolites and not on the increase in canonical chaperone machineries. Being able to reconstitute the folding assistance afforded by metabolites in vitro, we propose that changes in metabolite concentrations have the potential to alter protein folding capacity. Collectively, we unravel that the metabolite pools are bona fide members of proteostasis and aid in mutational buffering. Given the plasticity in cellular metabolism, we posit that metabolic alterations may play an important role in cellular proteostasis.


Assuntos
Proteostase/fisiologia , Escherichia coli/genética , Escherichia coli/metabolismo , Metaboloma/genética , Mutação/genética , Pressão Osmótica/fisiologia , Dobramento de Proteína , Proteostase/genética
20.
BMC Plant Biol ; 20(1): 138, 2020 Apr 03.
Artigo em Inglês | MEDLINE | ID: mdl-32245415

RESUMO

BACKGROUND: Beta vulgaris L. is one of the main sugar-producing crop species and is highly adaptable to saline soil. This study explored the alterations to the carbon and nitrogen metabolism mechanisms enabling the roots of sugar beet seedlings to adapt to salinity. RESULTS: The ionome, metabolome, and transcriptome of the roots of sugar beet seedlings were evaluated after 1 day (short term) and 7 days (long term) of 300 mM Na+ treatment. Salt stress caused reactive oxygen species (ROS) damage and ion toxicity in the roots. Interestingly, under salt stress, the increase in the Na+/K+ ratio compared to the control ratio on day 7 was lower than that on day 1 in the roots. The transcriptomic results showed that a large number of differentially expressed genes (DEGs) were enriched in various metabolic pathways. A total of 1279 and 903 DEGs were identified on days 1 and 7, respectively, and were mapped mainly to 10 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Most of the genes were involved in carbon metabolism and amino acid (AA) biosynthesis. Furthermore, metabolomic analysis revealed that sucrose metabolism and the activity of the tricarboxylic acid (TCA) cycle increased in response to salt stress. After 1 day of stress, the content of sucrose decreased, whereas the content of organic acids (OAs) such as L-malic acid and 2-oxoglutaric acid increased. After 7 days of salt stress, nitrogen-containing metabolites such as AAs, betaine, melatonin, and (S)-2-aminobutyric acid increased significantly. In addition, multiomic analysis revealed that the expression of the gene encoding xanthine dehydrogenase (XDH) was upregulated and that the expression of the gene encoding allantoinase (ALN) was significantly downregulated, resulting in a large accumulation of allantoin. Correlation analysis revealed that most genes were significantly related to only allantoin and xanthosine. CONCLUSIONS: Our study demonstrated that carbon and nitrogen metabolism was altered in the roots of sugar beet plants under salt stress. Nitrogen metabolism plays a major role in the late stages of salt stress. Allantoin, which is involved in the purine metabolic pathway, may be a key regulator of sugar beet salt tolerance.


Assuntos
Alantoína/metabolismo , Beta vulgaris , Carbono/metabolismo , Nitrogênio/metabolismo , Raízes de Plantas/metabolismo , Adaptação Fisiológica , Amidoidrolases/genética , Beta vulgaris/genética , Beta vulgaris/metabolismo , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Genes de Plantas , Metaboloma/genética , Proteínas de Plantas/genética , Raízes de Plantas/genética , Purinas/metabolismo , Salinidade , Tolerância ao Sal , Estresse Fisiológico/genética , Transcriptoma/genética , Xantina Desidrogenase/genética
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