Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 5.285
Filtrar
1.
PLoS Genet ; 18(1): e1009666, 2022 01.
Artigo em Inglês | MEDLINE | ID: mdl-35061661

RESUMO

Dynamic and temporally specific gene regulatory changes may underlie unexplained genetic associations with complex disease. During a dynamic process such as cellular differentiation, the overall cell type composition of a tissue (or an in vitro culture) and the gene regulatory profile of each cell can both experience significant changes over time. To identify these dynamic effects in high resolution, we collected single-cell RNA-sequencing data over a differentiation time course from induced pluripotent stem cells to cardiomyocytes, sampled at 7 unique time points in 19 human cell lines. We employed a flexible approach to map dynamic eQTLs whose effects vary significantly over the course of bifurcating differentiation trajectories, including many whose effects are specific to one of these two lineages. Our study design allowed us to distinguish true dynamic eQTLs affecting a specific cell lineage from expression changes driven by potentially non-genetic differences between cell lines such as cell composition. Additionally, we used the cell type profiles learned from single-cell data to deconvolve and re-analyze data from matched bulk RNA-seq samples. Using this approach, we were able to identify a large number of novel dynamic eQTLs in single cell data while also attributing dynamic effects in bulk to a particular lineage. Overall, we found that using single cell data to uncover dynamic eQTLs can provide new insight into the gene regulatory changes that occur among heterogeneous cell types during cardiomyocyte differentiation.


Assuntos
Perfilação da Expressão Gênica/métodos , Células-Tronco Pluripotentes Induzidas/citologia , Miócitos Cardíacos/citologia , Análise de Célula Única/métodos , Técnicas de Cultura de Células , Diferenciação Celular , Linhagem Celular , Linhagem da Célula , Regulação da Expressão Gênica , Humanos , Células-Tronco Pluripotentes Induzidas/química , Miócitos Cardíacos/química , RNA-Seq
2.
Nat Commun ; 13(1): 3224, 2022 Jun 09.
Artigo em Inglês | MEDLINE | ID: mdl-35680885

RESUMO

The growing availability of single-cell data, especially transcriptomics, has sparked an increased interest in the inference of cell-cell communication. Many computational tools were developed for this purpose. Each of them consists of a resource of intercellular interactions prior knowledge and a method to predict potential cell-cell communication events. Yet the impact of the choice of resource and method on the resulting predictions is largely unknown. To shed light on this, we systematically compare 16 cell-cell communication inference resources and 7 methods, plus the consensus between the methods' predictions. Among the resources, we find few unique interactions, a varying degree of overlap, and an uneven coverage of specific pathways and tissue-enriched proteins. We then examine all possible combinations of methods and resources and show that both strongly influence the predicted intercellular interactions. Finally, we assess the agreement of cell-cell communication methods with spatial colocalisation, cytokine activities, and receptor protein abundance and find that predictions are generally coherent with those data modalities. To facilitate the use of the methods and resources described in this work, we provide LIANA, a LIgand-receptor ANalysis frAmework as an open-source interface to all the resources and methods.


Assuntos
Comunicação Celular , Transcriptoma , Comunicação Celular/genética , Ligantes , RNA-Seq , Transdução de Sinais , Análise de Célula Única/métodos , Transcriptoma/genética
3.
Int J Mol Sci ; 23(11)2022 May 25.
Artigo em Inglês | MEDLINE | ID: mdl-35682592

RESUMO

(1) Background: Systemic infection is associated with increased neuroinflammation and accelerated cognitive decline in AD patients. Activated neutrophils produce neutrophil-derived microvesicles (NMV), which are internalised by human brain microvascular endothelial cells and increase their permeability in vitro, suggesting that NMV play a role in blood-brain barrier (BBB) integrity during infection. The current study investigated whether microRNA content of NMV from AD patients is significantly different compared to healthy controls and could impact cerebrovascular integrity. (2) Methods: Neutrophils isolated from peripheral blood samples of five AD and five healthy control donors without systemic infection were stimulated to produce NMV. MicroRNAs isolated from NMV were analysed by RNA-Seq, and online bioinformatic tools were used to identify significantly differentially expressed microRNAs in the NMV. Target and pathway analyses were performed to predict the impact of the candidate microRNAs on vascular integrity. (3) Results: There was no significant difference in either the number of neutrophils (p = 0.309) or the number of NMV (p = 0.3434) isolated from AD donors compared to control. However, 158 microRNAs were significantly dysregulated in AD NMV compared to controls, some of which were associated with BBB dysfunction, including miR-210, miR-20b-5p and miR-126-5p. Pathway analysis revealed numerous significantly affected pathways involved in regulating vascular integrity, including the TGFß and PDGFB pathways, as well as Hippo, IL-2 and DNA damage signalling. (4) Conclusions: NMV from AD patients contain miRNAs that may alter the integrity of the BBB and represent a novel neutrophil-mediated mechanism for BBB dysfunction in AD and the accelerated cognitive decline seen as a result of a systemic infection.


Assuntos
Doença de Alzheimer , MicroRNAs , Doença de Alzheimer/metabolismo , Barreira Hematoencefálica/metabolismo , Células Endoteliais/metabolismo , Humanos , MicroRNAs/metabolismo , Neutrófilos/metabolismo , RNA-Seq
4.
Int J Mol Sci ; 23(11)2022 May 25.
Artigo em Inglês | MEDLINE | ID: mdl-35682649

RESUMO

In this work, we examined the differentiation of oligodendrocytic MO3.13 cells and changes in their gene expression after treatment with phorbol 12-myristate 13-acetate, PMA, or with RNA polymerase I (Pol I) inhibitor, CX-5461. We found that MO3.13 cells changed their morphology when treated with both agents. Interestingly, CX-5461, but not PMA, induced noticeable changes in the integrity of the nucleoli. Then, we analyzed the p53 transcriptional activity in MO3.13 cells and found that it was increased in both cell populations, but particularly in cells treated with PMA. Interestingly, this high p53 transcriptional activity in PMA-treated cells coincided with a lower level of an unmodified (non-phosphorylated) form of this protein. Since morphological changes in MO3.13 cells after PMA and CX-5461 treatment were evident, suggesting that cells were induced to differentiate, we performed RNA-seq analysis of PMA-treated cells, to reveal the direction of alterations in gene expression. The analysis showed that the largest group of upregulated genes consisted of those involved in myogenesis and K-RAS signaling, rather than those associated with oligodendrocyte lineage progression.


Assuntos
Perfilação da Expressão Gênica , Proteína Supressora de Tumor p53 , Humanos , Desenvolvimento Muscular/genética , RNA-Seq , Acetato de Tetradecanoilforbol/farmacologia , Regulação para Cima
5.
Nat Commun ; 13(1): 3242, 2022 Jun 10.
Artigo em Inglês | MEDLINE | ID: mdl-35688820

RESUMO

Previous studies have demonstrated the highly specific expression of circular RNAs (circRNAs) in different tissues and organisms, but the cellular architecture of circRNA has never been fully characterized. Here, we present a collection of 171 full-length single-cell RNA-seq datasets to explore the cellular landscape of circRNAs in human and mouse tissues. Through large-scale integrative analysis, we identify a total of 139,643 human and 214,747 mouse circRNAs in these scRNA-seq libraries. We validate the detected circRNAs with the integration of 11 bulk RNA-seq based resources, where 216,602 high-confidence circRNAs are uniquely detected in the single-cell cohort. We reveal the cell-type-specific expression pattern of circRNAs in brain samples, developing embryos, and breast tumors. We identify the uniquely expressed circRNAs in different cell types and validate their performance in tumor-infiltrating immune cell composition deconvolution. This study expands our knowledge of circRNA expression to the single-cell level and provides a useful resource for exploring circRNAs at this unprecedented resolution.


Assuntos
RNA Circular , RNA , Animais , Humanos , Camundongos , RNA/genética , RNA/metabolismo , RNA Circular/genética , RNA-Seq , Sequenciamento Completo do Exoma
6.
J Mol Biol ; 434(11): 167560, 2022 Jun 15.
Artigo em Inglês | MEDLINE | ID: mdl-35662457

RESUMO

The advent of single-cell sequencing is providing unprecedented opportunities to disentangle tissue complexity and investigate cell identities and functions. However, the analysis of single cell data is a challenging, multi-step process that requires both advanced computational skills and biological sensibility. When dealing with single cell RNA-seq (scRNA-seq) data, the presence of technical artifacts, noise, and biological biases imposes to first identify, and eventually remove, unreliable signals from low-quality cells and unwanted sources of variation that might affect the efficacy of subsequent downstream modules. Pre-processing and quality control (QC) of scRNA-seq data is a laborious process consisting in the manual combination of different computational strategies to quantify QC-metrics and define optimal sets of pre-processing parameters. Here we present popsicleR, a R package to interactively guide skilled and unskilled command line-users in the pre-processing and QC analysis of scRNA-seq data. The package integrates, into several main wrapper functions, methods derived from widely used pipelines for the estimation of quality-control metrics, filtering of low-quality cells, data normalization, removal of technical and biological biases, and for cell clustering and annotation. popsicleR starts from either the output files of the Cell Ranger pipeline from 10X Genomics or from a feature-barcode matrix of raw counts generated from any scRNA-seq technology. Open-source code, installation instructions, and a case study tutorial are freely available at https://github.com/bicciatolab/popsicleR.


Assuntos
RNA-Seq , Análise de Célula Única , Software , Perfilação da Expressão Gênica/métodos , Controle de Qualidade , RNA-Seq/métodos , Análise de Célula Única/métodos
7.
Sci Data ; 9(1): 343, 2022 Jun 16.
Artigo em Inglês | MEDLINE | ID: mdl-35710652

RESUMO

Researchers studying cystic fibrosis (CF) pathogens have produced numerous RNA-seq datasets which are available in the gene expression omnibus (GEO). Although these studies are publicly available, substantial computational expertise and manual effort are required to compare similar studies, visualize gene expression patterns within studies, and use published data to generate new experimental hypotheses. Furthermore, it is difficult to filter available studies by domain-relevant attributes such as strain, treatment, or media, or for a researcher to assess how a specific gene responds to various experimental conditions across studies. To reduce these barriers to data re-analysis, we have developed an R Shiny application called CF-Seq, which works with a compendium of 128 studies and 1,322 individual samples from 13 clinically relevant CF pathogens. The application allows users to filter studies by experimental factors and to view complex differential gene expression analyses at the click of a button. Here we present a series of use cases that demonstrate the application is a useful and efficient tool for new hypothesis generation. (CF-Seq: http://scangeo.dartmouth.edu/CFSeq/ ).


Assuntos
Fibrose Cística , Análise de Sequência de RNA , Fibrose Cística/genética , Análise de Dados , Humanos , RNA-Seq , Software
8.
Sci Rep ; 12(1): 10158, 2022 Jun 16.
Artigo em Inglês | MEDLINE | ID: mdl-35710789

RESUMO

Autism Spectrum Disorders (ASD) have a strong, yet heterogeneous, genetic component. Among the various methods that are being developed to help reveal the underlying molecular aetiology of the disease one approach that is gaining popularity is the combination of gene expression and clinical genetic data, often using the SFARI-gene database, which comprises lists of curated genes considered to have causative roles in ASD when mutated in patients. We build a gene co-expression network to study the relationship between ASD-specific transcriptomic data and SFARI genes and then analyse it at different levels of granularity. No significant evidence is found of association between SFARI genes and differential gene expression patterns when comparing ASD samples to a control group, nor statistical enrichment of SFARI genes in gene co-expression network modules that have a strong correlation with ASD diagnosis. However, classification models that incorporate topological information from the whole ASD-specific gene co-expression network can predict novel SFARI candidate genes that share features of existing SFARI genes and have support for roles in ASD in the literature. A statistically significant association is also found between the absolute level of gene expression and SFARI's genes and Scores, which can confound the analysis if uncorrected. We propose a novel approach to correct for this that is general enough to be applied to other problems affected by continuous sources of bias. It was found that only co-expression network analyses that integrate information from the whole network are able to reveal signatures linked to ASD diagnosis and novel candidate genes for the study of ASD, which individual gene or module analyses fail to do. It was also found that the influence of SFARI genes permeates not only other ASD scoring systems, but also lists of genes believed to be involved in other neurodevelopmental disorders.


Assuntos
Transtorno do Espectro Autista , Transtorno do Espectro Autista/genética , Transtorno do Espectro Autista/metabolismo , Redes Reguladoras de Genes , Humanos , RNA-Seq , Transcriptoma
9.
Gene ; 834: 146660, 2022 Aug 05.
Artigo em Inglês | MEDLINE | ID: mdl-35680029

RESUMO

The evolution mechanism of sheep tail fat has not yet been clear, many researches focus on this issue, yet there still many gaps to be filled in the targets and non-coding RNA regulation. In our study, the differential expression mRNAs and miRNAs were detected by RNA-seq and constructed a mRNA-miRNA network related to the lipid deposition in tail of fat-tailed sheep and F2 of Argali with domestic sheep (thin-tailed). Then 6 kinds of tissues from thin-tailed and control group were extracted for function validation of candidate genes and its regulator miRNAs. 125 differentially expressed miRNAs were identified by RNA-seq, and enrichment analysis of their target genes revealed 10 significantly enriched pathways related to lipid metabolism. In these pathways, 126 DE-miRNA target genes were also differentially expression in the same tissues in our previous transcriptomic data. In PPI network, 6 hubgenes (SCD, ACACA, GPD2, ELOVL6, ELOVL5, GPAM) were extracted using the cytoHubba application, and they may be target genes for 3 candidate DE-miRNAs (miR-320d, miR-151b, miR-6715). The validation results of RT-qPCR show: the expression trend of miR-320d is opposite to the target gene SCD, and that of miR-151b and the target gene ACACA are also opposite in 6 tissues, implying that they may have direct targeting relationships. Moreover, the expression of miR-320d in F2 tail fat was significantly higher than that in fat-tailed sheep (P < 0.05), and the expression of SCD in F2 tail fat was extremely significantly lower than that in fat-tailed sheep (P < 0.01). The expression of miR-151b in F2 tail fat and subcutaneous fat was significantly higher than that in fat-tailed sheep (P < 0.05), and the expression of ACACA in F2 subcutaneous fat was significantly lower than that in fat-tailed sheep. miR-320d may directly and negatively regulate tail fat deposition by targeting SCD, while miR-151b may indirectly and negatively regulate tail fat deposition by targeting ACACA.


Assuntos
MicroRNAs , Animais , Metabolismo dos Lipídeos/genética , MicroRNAs/genética , RNA Mensageiro/genética , RNA-Seq , Ovinos/genética , Transcriptoma/genética
10.
Sci Rep ; 12(1): 9851, 2022 Jun 14.
Artigo em Inglês | MEDLINE | ID: mdl-35701599

RESUMO

Single nuclei RNA sequencing (snRNA-seq) has evolved as a powerful tool to study complex human diseases. Single cell resolution enables the study of novel cell types, biological processes, cell trajectories, and cell-cell signaling pathways. snRNA-seq largely relies on the dissociation of intact nuclei from human tissues. However, the study of complex tissues using small core biopsies presents many technical challenges. Here, an optimized protocol for single nuclei isolation is presented for frozen and RNAlater preserved human kidney biopsies. The described protocol is fast, low cost, and time effective due to the elimination of cell sorting and ultra-centrifugation. Samples can be processed in 90 min or less. This method is effective for obtaining normal nuclei morphology without signs of structural damage. Using snRNA-seq, 16 distinct kidney cell clusters were recovered from normal and peri-transplant acute kidney injury allograft samples, including immune cell clusters. Quality control measurements demonstrated that these optimizations eliminated cellular debris and allowed for a high yield of high-quality nuclei and RNA for library preparation and sequencing. Cellular disassociation did not induce cellular stress responses, which recapitulated transcriptional patterns associated with standardized methods of nuclei isolation. Future applications of this protocol will allow for thorough investigations of small biobank biopsies, identifying cell-specific injury pathways and driving the discovery of novel diagnostics and therapeutic targets.


Assuntos
Perfilação da Expressão Gênica , RNA Nuclear Pequeno , Biópsia , Perfilação da Expressão Gênica/métodos , Humanos , RNA Nuclear Pequeno/genética , RNA-Seq , Análise de Sequência de RNA/métodos , Análise de Célula Única/métodos
11.
Cell Rep ; 39(10): 110916, 2022 Jun 07.
Artigo em Inglês | MEDLINE | ID: mdl-35675780

RESUMO

We analyze transposable elements (TEs) in glioblastoma (GBM) patients using a proteogenomic pipeline that combines single-cell transcriptomics, bulk RNA sequencing (RNA-seq) samples from tumors and healthy-tissue cohorts, and immunopeptidomic samples. We thus identify 370 human leukocyte antigen (HLA)-I-bound peptides encoded by TEs differentially expressed in GBM. Some of the peptides are encoded by repeat sequences from intact open reading frames (ORFs) present in up to several hundred TEs from recent long interspersed nuclear element (LINE)-1, long terminal repeat (LTR), and SVA subfamilies. Other HLA-I-bound peptides are encoded by single copies of TEs from old subfamilies that are expressed recurrently in GBM tumors and not expressed, or very infrequently and at low levels, in healthy tissues (including brain). These peptide-coding, GBM-specific, highly recurrent TEs represent potential tumor-specific targets for cancer immunotherapies.


Assuntos
Glioblastoma , Antígenos de Histocompatibilidade Classe I , Proteogenômica , Elementos de DNA Transponíveis , Glioblastoma/genética , Antígenos de Histocompatibilidade Classe I/genética , Humanos , Peptídeos/genética , RNA-Seq
12.
Sci Rep ; 12(1): 9996, 2022 Jun 15.
Artigo em Inglês | MEDLINE | ID: mdl-35705694

RESUMO

Reference cell atlases powered by single cell and spatial transcriptomics technologies are becoming available to study healthy and diseased tissue at single cell resolution. One important use of these data resources is to compare cell types from new dataset with cell types in the reference atlases to evaluate their phenotypic similarities and differences, for example, for identifying novel cell types under disease conditions. For this purpose, rigorously-validated computational algorithms are needed to perform these cell type matching tasks that can compare datasets from different experiment platforms and sample types. Here, we present significant enhancements to FR-Match (v2.0)-a multivariate nonparametric statistical testing approach for matching cell types in query datasets to reference atlases. FR-Match v2.0 includes a normalization procedure to facilitate cross-platform cluster-level comparisons (e.g., plate-based SMART-seq and droplet-based 10X Chromium single cell and single nucleus RNA-seq and spatial transcriptomics) and extends the pipeline to also allow cell-level matching. In the use cases evaluated, FR-Match showed robust and accurate performance for identifying common and novel cell types across tissue regions, for discovering sub-optimally clustered cell types, and for cross-platform and cross-sample cell type matching.


Assuntos
Algoritmos , Perfilação da Expressão Gênica , Perfilação da Expressão Gênica/métodos , RNA , RNA-Seq , Análise de Sequência de RNA/métodos , Análise de Célula Única/métodos
13.
STAR Protoc ; 3(2): 101432, 2022 Jun 17.
Artigo em Inglês | MEDLINE | ID: mdl-35677606

RESUMO

We describe a consensus approach for network construction based on fully conserved gene-gene interactions from randomly downsampled data subsets for an unbiased differential analysis of gene co-expression networks. The pipeline allows users to identify network nodes lost, conserved, and acquired in cancer as well as interpret the functional significance of these network changes. For proof of concept, the protocol is used to leverage RNA-seq data of tumor samples from TCGA and healthy tissue samples from the GTEx database. For complete details on the use and execution of this protocol, please refer to Arshad and McDonald (2021).


Assuntos
Biologia Computacional , Perfilação da Expressão Gênica , Biologia Computacional/métodos , Perfilação da Expressão Gênica/métodos , Redes Reguladoras de Genes/genética , RNA-Seq , Análise de Sequência de RNA/métodos
14.
PLoS One ; 17(5): e0265989, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35613128

RESUMO

Hetian sheep is a breed of sheep unique to the Hetian area of Xinjiang whose wool is used for producing blankets. Individual differences and hair follicle density are the key factors affecting wool production. Therefore, this study aimed to assess the Hetian sheep having different wool densities to statistically analyze the wool traits and hair follicle parameters. Furthermore, the transcriptome sequencing analysis was performed on the skins with different wool densities. The results showed that wool quantity and total hair follicle density of the high wool density sheep was significantly higher than low wool density sheep. The sheepskin with high wool density was found to grow more and finer wool than sheepskin with low wool density. A total of 1,452 differentially expressed genes were screened from the two sets of samples, including 754 upregulated and 698 downregulated genes. The differentially expressed genes were involved in the TGF-ß/BMP and MAPK signaling pathways related to hair growth. Eleven differentially expressed genes belonging to the KAPs and KIFs might affect the fineness of the wool. The key genes, like the TNF, MAP2K2, INHBA, FST, PTPN11, MAP3K7, KIT, and BMPR1A, were found to probably affect the growth and density of the wool. The qPCR verified eight genes related to the MAPK pathway whose gene expression trends were consistent with the transcriptome sequencing results. This study furnishes valuable resources for enhancing the quality and production of wool in the Hetian sheep.


Assuntos
Perfilação da Expressão Gênica , Ovinos , Transdução de Sinais , , Animais , Folículo Piloso/metabolismo , RNA-Seq , Ovinos/genética , Transdução de Sinais/genética
15.
Sci Rep ; 12(1): 7170, 2022 05 03.
Artigo em Inglês | MEDLINE | ID: mdl-35505053

RESUMO

Due to the overall high costs, technical replicates are usually omitted in RNA-seq experiments, but several methods exist to generate them artificially. Bootstrapping reads from FASTQ-files has recently been used in the context of other NGS analyses and can be used to generate artificial technical replicates. Bootstrapping samples from the columns of the expression matrix has already been used for DNA microarray data and generates a new artificial replicate of the whole experiment. Mixing data of individual samples has been used for data augmentation in machine learning. The aim of this comparison is to evaluate which of these strategies are best suited to study the reproducibility of differential expression and gene-set enrichment analysis in an RNA-seq experiment. To study the approaches under controlled conditions, we performed a new RNA-seq experiment on gene expression changes upon virus infection compared to untreated control samples. In order to compare the approaches for artificial replicates, each of the samples was sequenced twice, i.e. as true technical replicates, and differential expression analysis and GO term enrichment analysis was conducted separately for the two resulting data sets. Although we observed a high correlation between the results from the two replicates, there are still many genes and GO terms that would be selected from one replicate but not from the other. Cluster analyses showed that artificial replicates generated by bootstrapping reads produce it p values and fold changes that are close to those obtained from the true data sets. Results generated from artificial replicates with the approaches of column bootstrap or mixing observations were less similar to the results from the true replicates. Furthermore, the overlap of results among replicates generated by column bootstrap or mixing observations was much stronger than among the true replicates. Artificial technical replicates generated by bootstrapping sequencing reads from FASTQ-files are better suited to study the reproducibility of results from differential expression and GO term enrichment analysis in RNA-seq experiments than column bootstrap or mixing observations. However, FASTQ-bootstrapping is computationally more expensive than the other two approaches. The FASTQ-bootstrapping may be applicable to other applications of high-throughput sequencing.


Assuntos
Perfilação da Expressão Gênica , Sequenciamento de Nucleotídeos em Larga Escala , Perfilação da Expressão Gênica/métodos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , RNA-Seq , Reprodutibilidade dos Testes , Análise de Sequência de RNA/métodos
16.
Science ; 376(6597): eabo0510, 2022 06 03.
Artigo em Inglês | MEDLINE | ID: mdl-35549310

RESUMO

Single-cell genomics studies have decoded the immune cell composition of several human prenatal organs but were limited in describing the developing immune system as a distributed network across tissues. We profiled nine prenatal tissues combining single-cell RNA sequencing, antigen-receptor sequencing, and spatial transcriptomics to reconstruct the developing human immune system. This revealed the late acquisition of immune-effector functions by myeloid and lymphoid cell subsets and the maturation of monocytes and T cells before peripheral tissue seeding. Moreover, we uncovered system-wide blood and immune cell development beyond primary hematopoietic organs, characterized human prenatal B1 cells, and shed light on the origin of unconventional T cells. Our atlas provides both valuable data resources and biological insights that will facilitate cell engineering, regenerative medicine, and disease understanding.


Assuntos
Sistema Imunitário , Linfócitos , Monócitos , Genômica , Humanos , Sistema Imunitário/embriologia , Linfócitos/metabolismo , Monócitos/metabolismo , Especificidade de Órgãos , RNA-Seq , Análise de Célula Única
17.
Viruses ; 14(5)2022 Apr 21.
Artigo em Inglês | MEDLINE | ID: mdl-35632602

RESUMO

Infectious hematopoietic necrosis virus (IHNV) is a pathogen that causes high rates of mortality in salmonid fishes. Therefore, an RNA-seq-based transcriptome analysis was performed in the head kidney of rainbow trout infected with a highly virulent IHNV strain to understand the pathogenesis of and defense strategies for IHNV infection in rainbow trout. The results showed that the numbers of DEGs were 618, 2626, and 774 (control vs. IHNV) on days 1, 3, and 5, respectively. Furthermore, the enrichment analysis of gene ontology (GO) annotations to classify DEGs showed that GO terms considerably associated with DEGs were gluconeogenesis, inflammatory response, and cell adhesion in the Biological Process (BP) category, apical plasma membrane, extracellular matrix (ECM) in the Cellular Component category, and transporter activity, integrin binding, and protein homodimerization activity in the Molecular Function category, on days 1, 3, and 5, respectively. Notably, GO terms in the BP category, including the negative regulation of type I interferon production and positive regulation of interleukin-1ß secretion, were commonly identified at all time points. In the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, complement and coagulation cascades were commonly identified at all time points. Importantly, the widely recognized GO terms and KEGG pathways extensively linked to DEGs were related to energy metabolism on day 1, the immune response on day 3, and cell proliferation on day 5. Furthermore, protein-protein interaction networks and centrality analysis showed that the metabolism and signaling transduction pathways were majorly upregulated. Conclusively, the virulent IHNV infection drives pathogenesis by activating the metabolic energy pathway for energy use for viral replication, facilitating necrosis through autophagy, and causing a shutoff response of the host immune system through the downregulation of type I IFN at the initial stage of infection.


Assuntos
Doenças dos Peixes , Vírus da Necrose Hematopoética Infecciosa , Oncorhynchus mykiss , Infecções por Rhabdoviridae , Animais , Perfilação da Expressão Gênica , Rim Cefálico , Vírus da Necrose Hematopoética Infecciosa/genética , RNA-Seq
18.
Gene ; 831: 146563, 2022 Jul 15.
Artigo em Inglês | MEDLINE | ID: mdl-35577040

RESUMO

Ultraviolet rays are a potential threat to nature. It can accelerate skin aging by causing skin damage, cell infiltration, and inflammation. The present study investigated UV-irradiated mouse skin through single-cell sequencing. We observed that UV-irradiated mouse skin mainly induced inflammation of fibroblasts and demonstrated differential gene expression. Cell prediction revealed the significance of macrophages in tissue repair. Furthermore, cell culture studies substantiated vitamin D-induced inhibitory effect on skin inflammation. These findings thus indicate some references for skin photo-protection.


Assuntos
Envelhecimento da Pele , Animais , Fibroblastos/metabolismo , Inflamação/genética , Inflamação/metabolismo , Camundongos , RNA-Seq , Pele/metabolismo , Envelhecimento da Pele/genética , Raios Ultravioleta/efeitos adversos , Vitamina D/metabolismo , Vitamina D/farmacologia , Vitaminas/farmacologia
19.
Proc Natl Acad Sci U S A ; 119(22): e2116797119, 2022 May 31.
Artigo em Inglês | MEDLINE | ID: mdl-35613054

RESUMO

SignificanceMemory formation relies on a plethora of functions, including epigenetic modifications. Over recent years, multiple studies have indicated the potential of HDAC inhibitors (HDACis) as cognitive enhancers, but their mode of action is not fully understood. Here, we tested whether HDACi treatment improves memory formation via "cognitive epigenetic priming," stipulating that HDACis-without inherent target specificity-specifically enhance naturally occurring plasticity processes. We found that combining HDACis with fear learning, but not either treatment alone, enhances synaptic plasticity as well as memory-promoting transcriptional signaling in the hippocampus, a brain area recruited by fear learning, but not in unrelated areas. These results lend experimental support to the theory of cognitive epigenetic priming.


Assuntos
Benzamidas , Giro Denteado , Inibidores de Histona Desacetilases , Memória de Longo Prazo , Fenilenodiaminas , Animais , Benzamidas/farmacologia , Comunicação Celular/efeitos dos fármacos , Giro Denteado/citologia , Giro Denteado/efeitos dos fármacos , Giro Denteado/fisiologia , Inibidores de Histona Desacetilases/farmacologia , Memória de Longo Prazo/efeitos dos fármacos , Camundongos , Plasticidade Neuronal , Neurônios/efeitos dos fármacos , Neurônios/metabolismo , Fenilenodiaminas/farmacologia , RNA-Seq , Análise de Célula Única
20.
J Anim Sci ; 100(5)2022 May 01.
Artigo em Inglês | MEDLINE | ID: mdl-35552417

RESUMO

Low birth weight (LBW) is associated with metabolic disorders in early life. While dietary l-tryptophan (Trp) can ameliorate postprandial plasma triglycerides (TG) disposal in LBW piglets, the genetic and biological basis underlying Trp-caused alterations in lipid metabolism is poorly understood. In this study, we collected 24 liver samples from 1-mo-old LBW and normal birth weight (NBW) piglets supplemented with different concentrations of dietary Trp (NBW with 0% Trp, N0; LBW with 0% Trp, L0; LBW with 0.4% Trp, L4; LBW with 0.8% Trp, L8; N = 6 in each group.) and conducted systematic, transcriptome-wide analysis using RNA sequencing (RNA-seq). We identified 39 differentially expressed genes (DEG) between N0 and L0, and genes within "increased dose effect" clusters based on dose-series expression profile analysis, enriched in fatty acid response of gene ontology (GO) biological process (BP). We then identified RNA-binding proteins including SRSF1, DAZAP1, PUM2, PCBP3, IGF2BP2, and IGF2BP3 significantly (P < 0.05) enriched in alternative splicing events (ASE) in comparison with L0 as control. There were significant positive and negative relationships between candidate genes from co-expression networks (including PID1, ANKRD44, RUSC1, and CYP2J34) and postprandial plasma TG concentration. Further, we determined whether these candidate hub genes were also significantly associated with metabolic and cardiovascular traits in humans via human phenome-wide association study (Phe-WAS), and analysis of mammalian orthologs suggests a functional conservation between human and pig. Our work demonstrates that transcriptomic changes during dietary Trp supplementation in LBW piglets. We detected candidate genes and related BP that may play roles on lipid metabolism restoration. These findings will help to better understand the amino acid support in LBW metabolic complications.


Low birth weight (LBW) has been associated with higher rate of mortality and morbidity and the development of metabolic complications, leaving burdens on livestock production and human health care. The feasibility of LBW metabolic restoration via postnatal nutrition compensation has been verified and the role of one of essential amino acids, l-tryptophan (Trp), on rescuing lipid metabolism in LBW was determined, while the underlying molecular mechanism and key gene regulation is little known. Our study was conducted to identify the unique molecular mechanisms between LBW and normal birth weight (NBW), and to identify the metabolic restoration related genes and biological processes after dietary Trp supplementation in LBW piglet model. We found that differentially expressed genes (DEG) between LBW and NBW were related to fatty acid response based on gene ontology enrichment analysis, and LBW piglets supplemented with Trp showed lower postprandial plasma triglycerides (TG) level as NBW, with similar expression feature of lipid metabolism related genes.


Assuntos
Suplementos Nutricionais , Triptofano , Animais , Peso ao Nascer , Humanos , Mamíferos/metabolismo , Proteínas de Ligação a RNA , RNA-Seq/veterinária , Análise de Sequência de RNA/veterinária , Fatores de Processamento de Serina-Arginina , Suínos , Triglicerídeos , Triptofano/metabolismo , Triptofano/farmacologia
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA
...