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1.
Immunity ; 56(7): 1533-1547.e7, 2023 07 11.
Artigo em Inglês | MEDLINE | ID: mdl-37354904

RESUMO

The crosstalk between the immune and neuroendocrine systems is critical for intestinal homeostasis and gut-brain communications. However, it remains unclear how immune cells participate in gut sensation of hormones and neurotransmitters release in response to environmental cues, such as self-lipids and microbial lipids. We show here that lipid-mediated engagement of invariant natural killer T (iNKT) cells with enterochromaffin (EC) cells, a subset of intestinal epithelial cells, promoted peripheral serotonin (5-HT) release via a CD1d-dependent manner, regulating gut motility and hemostasis. We also demonstrated that inhibitory sphingolipids from symbiotic microbe Bacteroides fragilis represses 5-HT release. Mechanistically, CD1d ligation on EC cells transduced a signal and restrained potassium conductance through activation of protein tyrosine kinase Pyk2, leading to calcium influx and 5-HT secretion. Together, our data reveal that by engaging with iNKT cells, gut chemosensory cells selectively perceive lipid antigens via CD1d to control 5-HT release, modulating intestinal and systemic homeostasis.


Assuntos
Células T Matadoras Naturais , Serotonina , Serotonina/metabolismo , Lipídeos , Antígenos CD1d/metabolismo
2.
PLoS Biol ; 20(11): e3001812, 2022 11.
Artigo em Inglês | MEDLINE | ID: mdl-36318572

RESUMO

Sleep is an essential process that consolidates memories by modulating synapses through poorly understood mechanisms. Here, we report that GABAergic synapses in hippocampal CA1 pyramidal neurons undergo daily rhythmic alterations. Specifically, wake inhibits phasic inhibition, whereas it promotes tonic inhibition compared to sleep. We further utilize a model of chemically induced inhibitory long-term potentiation (iLTP) to examine inhibitory plasticity. Intriguingly, while CA1 pyramidal neurons in both wake and sleep mice undergo iLTP, wake mice have a much higher magnitude. We also employ optogenetics and observe that inhibitory inputs from parvalbumin-, but not somatostatin-, expressing interneurons contribute to dynamic iLTP during sleep and wake. Finally, we demonstrate that synaptic insertion of α5-GABAA receptors underlies the wake-specific enhancement of iLTP at parvalbumin-synapses, which is independent of time of the day. These data reveal a previously unappreciated daily oscillation of inhibitory LTP in hippocampal neurons and uncover a dynamic contribution of inhibitory synapses in memory mechanisms across sleep and wake.


Assuntos
Hipocampo , Parvalbuminas , Animais , Camundongos , Hipocampo/fisiologia , Interneurônios/metabolismo , Plasticidade Neuronal/fisiologia , Parvalbuminas/metabolismo , Sono , Vigília
3.
J Neurosci ; 43(44): 7264-7275, 2023 11 01.
Artigo em Inglês | MEDLINE | ID: mdl-37699715

RESUMO

Neuroligins (NLGNs) are postsynaptic cell adhesion molecules that are involved in synapse assembly and function. The NLGN gene family consists of 5 genes (NLGN1-3, 4X, and 4Y). NLGN3 forms heterodimers with other NLGNs and is expressed at both excitatory and inhibitory synapses, although the distinct role at different synapses is not fully understood. Cyclin-dependent kinase 5 (Cdk5) is a proline-directed serine/threonine kinase that targets various neuronal substrates to impact neuronal migration, neurite outgrowth, synaptic transmission, and plasticity. Both NLGNs and their presynaptic binding partners neurexins are highly associated with neurodevelopmental disorders. The NLGN3 gene is on the X chromosome and variants in NLGN3 have been linked to the pathophysiology in neurodevelopmental disorders. To better understand the endogenous modulation of NLGN3, we generated an HA-tagged knock-in mouse. We found that Cdk5 associates with NLGN3 in vivo and phosphorylates NLGN3 on serine 725 (S725) in the knock-in mouse of either sex. The phosphorylation affects the NLGN3 association with Kalirin-7, a postsynaptic guanine nucleotide exchange factors for Rho GTPase family proteins. We further observed that the phosphorylation modulates NLGN3 surface expression and NLGN3-mediated synaptic currents in cultured rat neurons. Thus, we characterized NLGN3 as a novel Cdk5 substrate and revealed the functional consequences of NLGN3 S725 phosphorylation in neurons. Our study provides a novel molecular mechanism underlying Cdk5-mediated regulation of postsynaptic cell adhesion molecules.SIGNIFICANCE STATEMENT NLGN3 is involved in synapse assembly and function at both excitatory and inhibitory synapses and has been associated with the pathophysiology of neurodevelopmental disorders. Cdk5 has brain-specific activity and is involved in neuronal transmission, synapse function, and plasticity. Here, we characterize NLGN3 as a Cdk5 substrate for the first time and show that Cdk5-mediated phosphorylation regulates NLGN3 function. We demonstrate that NLGN3 S725 is a Cdk5 phosphorylation site, and reveal that the site is important for NLGN3 association with Kalirin-7, NLGN3 surface expression, and NLGN3-mediated synaptic transmission.


Assuntos
Quinase 5 Dependente de Ciclina , Sinapses , Animais , Camundongos , Ratos , Moléculas de Adesão Celular/metabolismo , Quinase 5 Dependente de Ciclina/genética , Quinase 5 Dependente de Ciclina/metabolismo , Fosforilação/fisiologia , Fatores de Troca de Nucleotídeo Guanina Rho/metabolismo , Serina/metabolismo , Sinapses/metabolismo , Transmissão Sináptica
4.
BMC Plant Biol ; 21(1): 521, 2021 Nov 09.
Artigo em Inglês | MEDLINE | ID: mdl-34753426

RESUMO

BACKGROUND: Shoot branching is one of the important agronomic traits affecting yields and quality of tea plant (Camellia sinensis). Cytokinins (CTKs) play critical roles in regulating shoot branching. However, whether and how differently alternative splicing (AS) variant of CTKs-related genes can influence shoot branching of tea plant is still not fully elucidated. RESULTS: In this study, five AS variants of CTK biosynthetic gene adenylate isopentenyltransferase (CsA-IPT5) with different 3' untranslated region (3' UTR) and 5' UTR from tea plant were cloned and investigated for their regulatory effects. Transient expression assays showed that there were significant negative correlations between CsA-IPT5 protein expression, mRNA expression of CsA-IPT5 AS variants and the number of ATTTA motifs, respectively. Shoot branching processes induced by exogenous 6-BA or pruning were studied, where CsA-IPT5 was demonstrated to regulate protein synthesis of CsA-IPT5, as well as the biosynthesis of trans-zeatin (tZ)- and isopentenyladenine (iP)-CTKs, through transcriptionally changing ratios of its five AS variants in these processes. Furthermore, the 3' UTR AS variant 2 (3AS2) might act as the predominant AS transcript. CONCLUSIONS: Together, our results indicate that 3AS2 of the CsA-IPT5 gene is potential in regulating shoot branching of tea plant and provides a gene resource for improving the plant-type of woody plants.


Assuntos
Alquil e Aril Transferases/fisiologia , Camellia sinensis/enzimologia , Camellia sinensis/crescimento & desenvolvimento , Regiões 3' não Traduzidas , Alquil e Aril Transferases/genética , Camellia sinensis/genética , Clonagem Molecular , DNA de Plantas , Motivos de Nucleotídeos , Desenvolvimento Vegetal/genética , Brotos de Planta/genética , Brotos de Planta/crescimento & desenvolvimento , Análise de Sequência de DNA
5.
Molecules ; 24(2)2019 Jan 21.
Artigo em Inglês | MEDLINE | ID: mdl-30669582

RESUMO

The phytohormone salicylic acid (SA) is a secondary metabolite that regulates plant growth, development and responses to stress. However, the role of SA in the biosynthesis of flavonoids (a large class of secondary metabolites) in tea (Camellia sinensis L.) remains largely unknown. Here, we show that exogenous methyl salicylate (MeSA, the methyl ester of SA) increased flavonoid concentration in tea leaves in a dose-dependent manner. While a moderate concentration of MeSA (1 mM) resulted in the highest increase in flavonoid concentration, a high concentration of MeSA (5 mM) decreased flavonoid concentration in tea leaves. A time-course of flavonoid concentration following 1 mM MeSA application showed that flavonoid concentration peaked at 2 days after treatment and then gradually declined, reaching a concentration lower than that of control after 6 days. Consistent with the time course of flavonoid concentration, MeSA enhanced the activity of phenylalanine ammonia-lyase (PAL, a key enzyme for the biosynthesis of flavonoids) as early as 12 h after the treatment, which peaked after 1 day and then gradually declined upto 6 days. qRT-PCR analysis of the genes involved in flavonoid biosynthesis revealed that exogenous MeSA upregulated the expression of genes such as CsPAL, CsC4H, Cs4CL, CsCHS, CsCHI, CsF3H, CsDFR, CsANS and CsUFGT in tea leaves. These results suggest a role for MeSA in modulating the flavonoid biosynthesis in green tea leaves, which might have potential implications in manipulating the tea quality and stress tolerance in tea plants.


Assuntos
Flavonoides/biossíntese , Redes e Vias Metabólicas , Folhas de Planta/metabolismo , Propanóis/metabolismo , Salicilatos/metabolismo , Chá/metabolismo , Regulação da Expressão Gênica de Plantas , Redes e Vias Metabólicas/efeitos dos fármacos , Folhas de Planta/genética , Salicilatos/farmacologia , Chá/genética , Transcrição Gênica
6.
Molecules ; 23(1)2018 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-29342935

RESUMO

The unprecedented early spring frost that appears as a cold stress adversely affects growth and productivity in tea (Camellia sinensis L.); therefore, it is indispensable to develop approaches to improve the cold tolerance of tea. Here, we investigated the effect of pretreatment with exogenous melatonin on the net photosynthetic rate, the maximum photochemical efficiency of PSII, chlorophyll content, lipid peroxidation, reactive oxygen species (ROS) accumulation, antioxidant potential, and redox homeostasis in leaves of tea plants following cold stress. Our results revealed that cold treatment induced oxidative stress by increasing ROS accumulation, which in turn affected the photosynthetic process in tea leaves. However, treatment with melatonin mitigated cold-induced reductions in photosynthetic capacity by reducing oxidative stress through enhanced antioxidant potential and redox homeostasis. This study provides strong evidence that melatonin could alleviate cold-induced adverse effects in tea plants.


Assuntos
Antioxidantes/farmacologia , Camellia sinensis/fisiologia , Resposta ao Choque Frio/efeitos dos fármacos , Homeostase/efeitos dos fármacos , Melatonina/farmacologia , Estresse Oxidativo/efeitos dos fármacos , Clorofila/metabolismo , Regulação Enzimológica da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Fotossíntese/efeitos dos fármacos , Folhas de Planta/metabolismo , Espécies Reativas de Oxigênio , Chá
7.
Phytopathology ; 106(11): 1270-1277, 2016 11.
Artigo em Inglês | MEDLINE | ID: mdl-27392179

RESUMO

Caffeine, the major purine alkaloid in tea has long been known for its role in plant defense. However, its effect on Colletotrichum gloeosporioides that causes brown blight disease in tea is largely unknown especially under elevated CO2. Here we show that elevated CO2 reduced endogenous caffeine content in tea leaves, but sharply increased susceptibility of tea to C. gloeosporioides. The expression of C. gloeosporioides actin gene was gradually increased during the postinoculation period. In contrast, foliar application of caffeine decreased the C. gloeosporioides-induced necrotic lesions and the expression of C. gloeosporioides actin. Analysis of endogenous jasmonic acid (JA) content revealed that exogenous caffeine could induce JA content under both CO2 conditions in absence of fungal infection; however, in presence of fungal infection, caffeine increased JA content only under elevated CO2. Furthermore, exogenous caffeine enhanced lipoxygenase (LOX) activity and its biosynthetic gene expression under both CO2 conditions, indicating that increased JA biosynthesis via LOX pathway by caffeine might strengthen plant defense only under elevated CO2, while caffeine-induced defense under ambient CO2 might be associated with JA-independent LOX pathway in tea. These results provide novel insights into caffeine-induced plant defense mechanisms that might help to develop an eco-friendly approach for disease control.


Assuntos
Cafeína/farmacologia , Camellia sinensis/efeitos dos fármacos , Colletotrichum/patogenicidade , Ciclopentanos/metabolismo , Lipoxigenases/efeitos dos fármacos , Oxilipinas/metabolismo , Doenças das Plantas/imunologia , Reguladores de Crescimento de Plantas/metabolismo , Cafeína/metabolismo , Camellia sinensis/imunologia , Camellia sinensis/microbiologia , Dióxido de Carbono/farmacologia , Resistência à Doença , Regulação da Expressão Gênica de Plantas , Lipoxigenases/genética , Lipoxigenases/metabolismo , Doenças das Plantas/microbiologia , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Plântula/efeitos dos fármacos , Plântula/imunologia , Plântula/microbiologia
8.
MedComm (2020) ; 5(4): e541, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38585234

RESUMO

Exosomes are indispensable for intercellular communications. Tumor microenvironment (TME) is the living environment of tumor cells, which is composed of various components, including immune cells. Based on TME, immunotherapy has been recently developed for eradicating cancer cells by reactivating antitumor effect of immune cells. The communications between tumor cells and TME are crucial for tumor development, metastasis, and drug resistance. Exosomes play an important role in mediating these communications and regulating the reprogramming of TME, which affects the sensitivity of immunotherapy. Therefore, it is imperative to investigate the role of exosomes in TME reprogramming and the impact of exosomes on immunotherapy. Here, we review the communication role of exosomes in regulating TME remodeling and the efficacy of immunotherapy, as well as summarize the underlying mechanisms. Furthermore, we also introduce the potential application of the artificially modified exosomes as the delivery systems of antitumor drugs. Further efforts in this field will provide new insights on the roles of exosomes in intercellular communications of TME and cancer progression, thus helping us to uncover effective strategies for cancer treatment.

9.
Science ; 384(6698): 920-928, 2024 May 24.
Artigo em Inglês | MEDLINE | ID: mdl-38781377

RESUMO

Excitatory and inhibitory synapses do not overlap even when formed on one submicron-sized dendritic protrusion. How excitatory and inhibitory postsynaptic cytomatrices or densities (e/iPSDs) are segregated is not understood. Broadly, why membraneless organelles are naturally segregated in cellular subcompartments is unclear. Using biochemical reconstitutions in vitro and in cells, we demonstrate that ePSDs and iPSDs spontaneously segregate into distinct condensed molecular assemblies through phase separation. Tagging iPSD scaffold gephyrin with a PSD-95 intrabody (dissociation constant ~4 nM) leads to mistargeting of gephyrin to ePSD condensates. Unexpectedly, formation of iPSD condensates forces the intrabody-tagged gephyrin out of ePSD condensates. Thus, instead of diffusion-governed spontaneous mixing, demixing is a default process for biomolecules in condensates. Phase separation can generate biomolecular compartmentalization specificities that cannot occur in dilute solutions.


Assuntos
Condensados Biomoleculares , Separação de Fases , Densidade Pós-Sináptica , Humanos , Condensados Biomoleculares/química , Condensados Biomoleculares/metabolismo , Proteína 4 Homóloga a Disks-Large/metabolismo , Proteínas de Membrana/metabolismo , Proteínas de Membrana/química , Densidade Pós-Sináptica/metabolismo , Células HeLa
10.
Plants (Basel) ; 13(2)2024 Jan 11.
Artigo em Inglês | MEDLINE | ID: mdl-38256755

RESUMO

Shading is an effective agronomic technique to protect tea plants from intense sunlight. However, there are currently very few studies on more effective shading methods to improve the quality of summer tea. In this study, 'Longjing43' plants were grown under four different shading treatments for 14 days, with no shading as the control. Among the four shading treatments, double-layer-net shadings had the most positive impact on the tea quality, resulting in higher levels of amino acids but lower levels of tea polyphenols. Additionally, double-layer-net shadings provided more suitable microenvironments for tea plants. The tea leaves in T4 (double nets 50 cm above the plant canopy) contained 16.13 mg∙g-1 of umami and sweet amino acids, which was significantly higher than in other treatments. T4 had the lowest air temperature and the most suitable and stable soil water content. Interestingly, the ratio of red light to far-red light in T4 was only 1.65, much lower than other treatments, which warrants further study. In conclusion, the microenvironment induced by shading can greatly affect the tea quality, and double-layer-net shading is better for improving the quality of summer tea.

11.
Front Mol Neurosci ; 17: 1222935, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38495551

RESUMO

This study reports on biallelic homozygous and monoallelic de novo variants in SLITRK3 in three unrelated families presenting with epileptic encephalopathy associated with a broad neurological involvement characterized by microcephaly, intellectual disability, seizures, and global developmental delay. SLITRK3 encodes for a transmembrane protein that is involved in controlling neurite outgrowth and inhibitory synapse development and that has an important role in brain function and neurological diseases. Using primary cultures of hippocampal neurons carrying patients' SLITRK3 variants and in combination with electrophysiology, we demonstrate that recessive variants are loss-of-function alleles. Immunostaining experiments in HEK-293 cells showed that human variants C566R and E606X change SLITRK3 protein expression patterns on the cell surface, resulting in highly accumulating defective proteins in the Golgi apparatus. By analyzing the development and phenotype of SLITRK3 KO (SLITRK3-/-) mice, the study shows evidence of enhanced susceptibility to pentylenetetrazole-induced seizure with the appearance of spontaneous epileptiform EEG as well as developmental deficits such as higher motor activities and reduced parvalbumin interneurons. Taken together, the results exhibit impaired development of the peripheral and central nervous system and support a conserved role of this transmembrane protein in neurological function. The study delineates an emerging spectrum of human core synaptopathies caused by variants in genes that encode SLITRK proteins and essential regulatory components of the synaptic machinery. The hallmark of these disorders is impaired postsynaptic neurotransmission at nerve terminals; an impaired neurotransmission resulting in a wide array of (often overlapping) clinical features, including neurodevelopmental impairment, weakness, seizures, and abnormal movements. The genetic synaptopathy caused by SLITRK3 mutations highlights the key roles of this gene in human brain development and function.

12.
PeerJ ; 11: e14384, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36684675

RESUMO

The method of anticancer bioactive peptide (ACBP) functionalized selenium particle (Se), which has enhanced anticancer activity, inhibited the growth of gastric cancer (GC) cells, and increased the ability of apoptosis in vitro, has been reported in previous studies. We used tandem mass spectrometry (TMT) labeling to construct a complete atlas of the acetylation-modified proteome in GC MKN-45 cells treated with ACBP-Se. The proteomics data database was searched and analyzed by bioinformatics: Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), functional enrichment, and protein-protein interaction network. Finally, we conducted a quantitative PRM analysis of the selected target-modified peptides. We identified 4,958 acetylation sites from 1,926 proteins in this research. Among these, 4,467 acetylation sites corresponding to 1,777 proteins were quantified. Based on the above data and standards, we found that in the ACBP-Se group vs. the control group, 297 sites were upregulated, and 665 sites were downregulated. We systematically assessed the proteins containing quantitative information sites, including protein annotation, functional classification, and functional enrichment, cluster analysis supported by functional enrichment, domain structures, and protein interaction networks. Finally, we evaluated differentially expressed lysine acetylation sites. We revealed that SHMT2 K200 and PGK1 K97 were the most critical acetylated non-histone proteins, which may have an essential role in ACBP-Se treatment. Here, we identified and quantified the lysine acetylation proteins in GC cells treated with ACBP-Se. The characterization of acetylation indicates that acetylated proteins might be pivotal in the biological process, molecular binding, and metabolic pathways of ACBP-Se treatment progress. Our findings provide a broad understanding of acetylation ACBP-Se treatment of GC, suggesting a potential application for molecular targeted therapy.


Assuntos
Antineoplásicos , Selênio , Neoplasias Gástricas , Humanos , Acetilação , Antineoplásicos/farmacologia , Antineoplásicos/uso terapêutico , Lisina/farmacologia , Peptídeos/farmacologia , Proteoma/metabolismo , Selênio/farmacologia , Selênio/uso terapêutico , Neoplasias Gástricas/tratamento farmacológico
13.
Nat Protoc ; 18(11): 3194-3228, 2023 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-37794072

RESUMO

Fusing apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like cytidine deaminase with catalytically impaired Cas proteins (e.g., nCas9 or dCas9) provides a novel gene-editing technology, base editing, that grants targeted base substitutions with high efficiency. However, genome-wide and transcriptome-wide off-target mutations are observed in base editing, which raises safety concerns regarding therapeutic applications. Previously, we developed a new base editing system, the transformer base editor (tBE), to induce efficient editing with no observable genome-wide or transcriptome-wide off-target mutations both in mammalian cells and in mice. Here we describe a detailed protocol for the design and application of the tBE. Steps for designing single-guide RNA (sgRNA) and helper sgRNA pairs, making constructs, determining the genome-wide and transcriptome-wide off-target mutations, producing the tBE-containing adeno-associated viruses, delivering adeno-associated viruses into mice and examining the in vivo editing effects are included in this protocol. High-precision base editing by the tBE can be completed within 2-3 weeks (in mammalian cells) or within 6-8 weeks (in mice), with sgRNA-helper sgRNA pairs. The whole process can be collaboratively accomplished by researchers using standard techniques from molecular biology, bioinformatics and mouse husbandry.


Assuntos
Sistemas CRISPR-Cas , RNA Guia de Sistemas CRISPR-Cas , Camundongos , Animais , Edição de Genes/métodos , Proteína 9 Associada à CRISPR/metabolismo , Mutação , Mamíferos/genética
14.
bioRxiv ; 2023 Jan 13.
Artigo em Inglês | MEDLINE | ID: mdl-36711526

RESUMO

Background: Quantitative Trait Locus (QTL) analysis and Genome-Wide Association Studies (GWAS) have the power to identify variants that capture significant levels of phenotypic variance in complex traits. However, effort and time are required to select the best methods and optimize parameters and pre-processing steps. Although machine learning approaches have been shown to greatly assist in optimization and data processing, applying them to QTL analysis and GWAS is challenging due to the complexity of large, heterogenous datasets. Here, we describe proof-of-concept for an automated machine learning approach, AutoQTL, with the ability to automate many complex decisions related to analysis of complex traits and generate diverse solutions to describe relationships that exist in genetic data. Results: Using a dataset of 18 putative QTL from a large-scale GWAS of body mass index in the laboratory rat, Rattus norvegicus , AutoQTL captures the phenotypic variance explained under a standard additive model while also providing evidence of non-additive effects including deviations from additivity and 2-way epistatic interactions from simulated data via multiple optimal solutions. Additionally, feature importance metrics provide different insights into the inheritance models and predictive power of multiple GWAS-derived putative QTL. Conclusions: This proof-of-concept illustrates that automated machine learning techniques can be applied to genetic data and has the potential to detect both additive and non-additive effects via various optimal solutions and feature importance metrics. In the future, we aim to expand AutoQTL to accommodate omics-level datasets with intelligent feature selection strategies.

15.
BioData Min ; 16(1): 14, 2023 Apr 10.
Artigo em Inglês | MEDLINE | ID: mdl-37038201

RESUMO

BACKGROUND: Quantitative Trait Locus (QTL) analysis and Genome-Wide Association Studies (GWAS) have the power to identify variants that capture significant levels of phenotypic variance in complex traits. However, effort and time are required to select the best methods and optimize parameters and pre-processing steps. Although machine learning approaches have been shown to greatly assist in optimization and data processing, applying them to QTL analysis and GWAS is challenging due to the complexity of large, heterogenous datasets. Here, we describe proof-of-concept for an automated machine learning approach, AutoQTL, with the ability to automate many complicated decisions related to analysis of complex traits and generate solutions to describe relationships that exist in genetic data. RESULTS: Using a publicly available dataset of 18 putative QTL from a large-scale GWAS of body mass index in the laboratory rat, Rattus norvegicus, AutoQTL captures the phenotypic variance explained under a standard additive model. AutoQTL also detects evidence of non-additive effects including deviations from additivity and 2-way epistatic interactions in simulated data via multiple optimal solutions. Additionally, feature importance metrics provide different insights into the inheritance models and predictive power of multiple GWAS-derived putative QTL. CONCLUSIONS: This proof-of-concept illustrates that automated machine learning techniques can complement standard approaches and have the potential to detect both additive and non-additive effects via various optimal solutions and feature importance metrics. In the future, we aim to expand AutoQTL to accommodate omics-level datasets with intelligent feature selection and feature engineering strategies.

16.
Cell Stem Cell ; 30(12): 1624-1639.e8, 2023 12 07.
Artigo em Inglês | MEDLINE | ID: mdl-37989316

RESUMO

Reactivating silenced γ-globin expression through the disruption of repressive regulatory domains offers a therapeutic strategy for treating ß-hemoglobinopathies. Here, we used transformer base editor (tBE), a recently developed cytosine base editor with no detectable off-target mutations, to disrupt transcription-factor-binding motifs in hematopoietic stem cells. By performing functional screening of six motifs with tBE, we found that directly disrupting the BCL11A-binding motif in HBG1/2 promoters triggered the highest γ-globin expression. Via a side-by-side comparison with other clinical and preclinical strategies using Cas9 nuclease or conventional BEs (ABE8e and hA3A-BE3), we found that tBE-mediated disruption of the BCL11A-binding motif at the HBG1/2 promoters triggered the highest fetal hemoglobin in healthy and ß-thalassemia patient hematopoietic stem/progenitor cells while exhibiting no detectable DNA or RNA off-target mutations. Durable therapeutic editing by tBE persisted in repopulating hematopoietic stem cells, demonstrating that tBE-mediated editing in HBG1/2 promoters is a safe and effective strategy for treating ß-hemoglobinopathies.


Assuntos
Edição de Genes , Hemoglobinopatias , Humanos , Hemoglobina Fetal/genética , Hemoglobina Fetal/metabolismo , gama-Globinas/genética , gama-Globinas/metabolismo , Sistemas CRISPR-Cas , Mutação/genética , Hemoglobinopatias/genética , Hemoglobinopatias/metabolismo , Células-Tronco Hematopoéticas/metabolismo , Fatores de Transcrição/metabolismo
17.
Cell Rep ; 42(8): 112873, 2023 08 29.
Artigo em Inglês | MEDLINE | ID: mdl-37527041

RESUMO

A vexing observation in genome-wide association studies (GWASs) is that parallel analyses in different species may not identify orthologous genes. Here, we demonstrate that cross-species translation of GWASs can be greatly improved by an analysis of co-localization within molecular networks. Using body mass index (BMI) as an example, we show that the genes associated with BMI in humans lack significant agreement with those identified in rats. However, the networks interconnecting these genes show substantial overlap, highlighting common mechanisms including synaptic signaling, epigenetic modification, and hormonal regulation. Genetic perturbations within these networks cause abnormal BMI phenotypes in mice, too, supporting their broad conservation across mammals. Other mechanisms appear species specific, including carbohydrate biosynthesis (humans) and glycerolipid metabolism (rodents). Finally, network co-localization also identifies cross-species convergence for height/body length. This study advances a general paradigm for determining whether and how phenotypes measured in model species recapitulate human biology.


Assuntos
Índice de Massa Corporal , Redes Reguladoras de Genes , Estudo de Associação Genômica Ampla , Humanos , Animais , Ratos , Tamanho Corporal , Camundongos , Especificidade da Espécie
18.
Genetics ; 224(2)2023 05 26.
Artigo em Inglês | MEDLINE | ID: mdl-36974931

RESUMO

Power analyses are often used to determine the number of animals required for a genome-wide association study (GWAS). These analyses are typically intended to estimate the sample size needed for at least 1 locus to exceed a genome-wide significance threshold. A related question that is less commonly considered is the number of significant loci that will be discovered with a given sample size. We used simulations based on a real data set that consisted of 3,173 male and female adult N/NIH heterogeneous stock rats to explore the relationship between sample size and the number of significant loci discovered. Our simulations examined the number of loci identified in subsamples of the full data set. The subsampling analysis was conducted for 4 traits with low (0.15 ± 0.03), medium (0.31 ± 0.03 and 0.36 ± 0.03), and high (0.46 ± 0.03) SNP-based heritabilities. For each trait, we subsampled the data 100 times at different sample sizes (500, 1,000, 1,500, 2,000, and 2,500). We observed an exponential increase in the number of significant loci with larger sample sizes. Our results are consistent with similar observations in human GWAS and imply that future rodent GWAS should use sample sizes that are significantly larger than those needed to obtain a single significant result.


Assuntos
Estudo de Associação Genômica Ampla , Locos de Características Quantitativas , Masculino , Feminino , Humanos , Animais , Ratos , Estudo de Associação Genômica Ampla/métodos , Tamanho da Amostra , Polimorfismo de Nucleotídeo Único , Fenótipo
19.
Addict Biol ; 17(4): 758-69, 2012 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-22507692

RESUMO

Oxytocin (OT), a neurohypophyseal neuropeptide, affects adaptive processes of the central nervous system. In the present study, we investigated the effects of OT on extracellular levels of glutamate (Glu) and γ-aminobutyric acid (GABA) induced by methamphetamine (MAP) in the medial prefrontal cortex (mPFC) and dorsal hippocampus (DHC) of freely moving mice, using in vivo microdialysis coupled to high-performance liquid chromatography and fluorescence detection. The results showed that OT had no effect on basal Glu levels, but attenuated MAP-induced Glu increase in the mPFC and decrease in the DHC. OT increased the basal levels of extracellular GABA in mPFC and DHC of mice, and inhibited the MAP-induced GABA decrease in DHC. Western blot results indicated that OT significantly inhibited the increased glutamatergic receptor (NR1 subunit) levels in the PFC after acute MAP administration, whereas OT further enhanced the elevated levels of glutamatergic transporter (GLT1) induced by MAP in the hippocampus of mice. Atosiban, a selective inhibitor of OT receptor, antagonized the effects of OT. The results provided the first neurochemical evidence that OT, which exerted its action via its receptor, decreased Glu release induced by MAP, and attenuated the changes in glutamatergic neurotransmission partially via regulation of NR1 and GLT1 expression. OT-induced extracellular GABA increase also suggests that OT acts potentially as an inhibitory neuromodulator in mPFC and DHC of mice.


Assuntos
Encéfalo/metabolismo , Fármacos do Sistema Nervoso Central/farmacologia , Ácido Glutâmico/metabolismo , Metanfetamina/farmacologia , Ocitocina/farmacologia , Ácido gama-Aminobutírico/metabolismo , Animais , Hipocampo/metabolismo , Antagonistas de Hormônios/farmacologia , Camundongos , Atividade Motora/efeitos dos fármacos , Córtex Pré-Frontal/metabolismo , Receptores de Ocitocina/antagonistas & inibidores , Vasotocina/análogos & derivados , Vasotocina/farmacologia
20.
Neuropsychopharmacology ; 47(12): 2160-2170, 2022 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-35534528

RESUMO

GABA-A receptors (GABAARs) are crucial for development and function of the brain. Altered GABAergic transmission is hypothesized to be involved in neurodevelopmental disorders. Recently, we identified Shisa7 as a GABAAR auxiliary subunit that modulates GABAAR trafficking and GABAergic transmission. However, the underlying molecular mechanisms remain elusive. Here we generated a knock-in (KI) mouse line that is phospho-deficient at a phosphorylation site in Shisa7 (S405) and combined with electrophysiology, imaging and behavioral assays to illustrate the role of this site in GABAergic transmission and plasticity as well as behaviors. We found that expression of phospho-deficient mutants diminished α2-GABAAR trafficking in heterologous cells. Additionally, α1/α2/α5-GABAAR surface expression and GABAergic inhibition were decreased in hippocampal neurons in KI mice. Moreover, chemically induced inhibitory long-term potentiation was abolished in KI mice. Lastly, KI mice exhibited hyperactivity, increased grooming and impaired sleep homeostasis. Collectively, our study reveals a phosphorylation site critical for Shisa7-dependent GABAARs trafficking which contributes to behavioral endophenotypes displayed in neurodevelopmental disorders.


Assuntos
Hipocampo , Receptores de GABA-A , Animais , Hipocampo/metabolismo , Camundongos , Neurônios/metabolismo , Fosforilação , Receptores de GABA-A/metabolismo , Ácido gama-Aminobutírico/metabolismo
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