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1.
BMC Genomics ; 23(1): 512, 2022 Jul 14.
Artigo em Inglês | MEDLINE | ID: mdl-35836120

RESUMO

BACKGROUND: Chinese chestnut is an economically important tree species whose yield and quality are seriously affected by red spider attack. Tannins is one of the most important class secondary metabolites in plants, and is closely associated with plant defense mechanisms against insect and herbivory. In our previous studies, it was revealed that several low-tannin foxtail millet varieties growing under the Chinese chestnut trees could attract red spiders to feed on their leaves and protect the chestnut trees from the infestation of red spiders, meanwhile, the growth and yield of foxtail millet plants themselves were not greatly affected. RESULTS: To identify genes related to leaf tannin content and selection of foxtail millet germplasm resources with low tannin content for interplanting with Chinese chestnut and preventing the red spider attack, the leaves of 4 varieties with different levels of tannin content were harvested for comparative transcriptome analysis. In total, 335 differentially expressed genes (DEGs) were identified. For acquisition of gene functions and biological pathways they involved in, gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analyses were performed, and several DEGs were found to possibly participate in the tannins biosynthesis pathway and transport processes of precursors. In addition, according to the PlantTFDB database, some transcription factors were predicted among the DEGs, suggesting their role in regulation of tannins biosynthesis pathway. CONCLUSION: Our results provide valuable gene resources for understanding the biosynthesis and regulation mechanisms of tannins in foxtail millet, and pave the way for speeding up the breeding of low-tannin varieties through marker-assisted selection, which could be utilized for interplanting with Chinese chestnut trees to confer protection against red spider attack.


Assuntos
Setaria (Planta)/química , Taninos/análise , Transcriptoma/fisiologia , Animais , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Melhoramento Vegetal , Folhas de Planta/química , Folhas de Planta/genética , Folhas de Planta/metabolismo , Folhas de Planta/parasitologia , Setaria (Planta)/genética , Setaria (Planta)/metabolismo , Setaria (Planta)/parasitologia , Aranhas/patogenicidade , Taninos/genética , Transcriptoma/genética
2.
Development ; 149(5)2022 03 01.
Artigo em Inglês | MEDLINE | ID: mdl-35253855

RESUMO

During mammalian brain development, how different astrocytes are specified from progenitor cells is not well understood. In particular, whether astrocyte progenitor cells (APCs) start as a relatively homogenous population or whether there is early heterogeneity remains unclear. Here, we have dissected subpopulations of embryonic mouse forebrain progenitors using single-cell transcriptome analyses. Our sequencing data revealed two molecularly distinct APC subgroups at the start of gliogenesis from both dorsal and ventral forebrains. The two APC subgroups were marked, respectively, by specific expression of Sparc and Sparcl1, which are known to function in mature astrocytes with opposing activities for regulating synapse formation. Expression analyses showed that SPARC and SPARCL1 mark APC subgroups that display distinct temporal and spatial patterns, correlating with major waves of astrogliogenesis during development. Our results uncover an early molecular divergence of APCs in the mammalian brain and provide a useful transcriptome resource for the study of glial cell specification.


Assuntos
Astrócitos/fisiologia , Mamíferos/fisiologia , Neurogênese/fisiologia , Neuroglia/fisiologia , Células-Tronco/fisiologia , Animais , Astrócitos/metabolismo , Diferenciação Celular/fisiologia , Linhagem da Célula/fisiologia , Proliferação de Células/fisiologia , Mamíferos/metabolismo , Camundongos , Células-Tronco Neurais/metabolismo , Células-Tronco Neurais/fisiologia , Neuroglia/metabolismo , Osteonectina/metabolismo , Prosencéfalo/metabolismo , Prosencéfalo/fisiologia , Análise de Célula Única/métodos , Células-Tronco/metabolismo , Transcriptoma/fisiologia
3.
Sci Rep ; 12(1): 2667, 2022 02 17.
Artigo em Inglês | MEDLINE | ID: mdl-35177672

RESUMO

Anther development is precisely regulated by a complex gene network, which is of great significance to plant breeding. However, the molecular mechanism of anther development in Chinese cabbage is unclear. Here, we identified microRNAs (miRNAs), mRNAs, long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) related to anther development in Chinese cabbage (Brassica campestris L. ssp. pekinensis) to construct competitive endogenous RNA (ceRNA) regulatory networks and provide valuable knowledge on anther development. Using whole-transcriptome sequencing, 9055, 585, 1344, and 165 differentially expressed mRNAs (DEmRNAs), miRNAs (DEmiRNAs), lncRNAs (DElncRNAs), and circRNAs (DEcircRNAs) were identified, respectively, in the anthers of Chinese cabbage compared with those in samples of the vegetative mass of four true leaves. An anther-related ceRNA regulatory network was constructed using miRNA targeting relationships, and 450 pairs of ceRNA relationships, including 97 DEmiRNA-DEmRNA, 281 DEmiRNA-DElncRNA, and 23 DEmiRNA-DEcircRNA interactions, were obtained. We identified important genes and their interactions with lncRNAs, circRNAs, and miRNAs involved in microsporogenesis, tapetum and callose layer development, pollen wall formation, and anther dehiscence. We analyzed the promoter activity of six predominant anther expression genes, which were expressed specifically in the anthers of Arabidopsis thaliana, indicating that they may play an important role in anther development of Chinese cabbage. This study lays the foundation for further research on the molecular mechanisms of anther growth and development in Chinese cabbage.


Assuntos
Brassica , Regulação da Expressão Gênica de Plantas , RNA de Plantas , Transcriptoma/fisiologia , Brassica/genética , Brassica/metabolismo , Estudo de Associação Genômica Ampla , RNA de Plantas/biossíntese , RNA de Plantas/genética
4.
Dev Cell ; 57(4): 543-560.e9, 2022 02 28.
Artigo em Inglês | MEDLINE | ID: mdl-35134336

RESUMO

In all multicellular organisms, transcriptional networks orchestrate organ development. The Arabidopsis root, with its simple structure and indeterminate growth, is an ideal model for investigating the spatiotemporal transcriptional signatures underlying developmental trajectories. To map gene expression dynamics across root cell types and developmental time, we built a comprehensive, organ-scale atlas at single-cell resolution. In addition to estimating developmental progressions in pseudotime, we employed the mathematical concept of optimal transport to infer developmental trajectories and identify their underlying regulators. To demonstrate the utility of the atlas to interpret new datasets, we profiled mutants for two key transcriptional regulators at single-cell resolution, shortroot and scarecrow. We report transcriptomic and in vivo evidence for tissue trans-differentiation underlying a mixed cell identity phenotype in scarecrow. Our results support the atlas as a rich community resource for unraveling the transcriptional programs that specify and maintain cell identity to regulate spatiotemporal organ development.


Assuntos
Proteínas de Arabidopsis/metabolismo , Arabidopsis/metabolismo , Regulação da Expressão Gênica de Plantas/genética , Redes Reguladoras de Genes/genética , Raízes de Plantas/genética , Arabidopsis/genética , Proteínas de Arabidopsis/genética , Regulação da Expressão Gênica de Plantas/fisiologia , Redes Reguladoras de Genes/fisiologia , Mutação/genética , Raízes de Plantas/metabolismo , Análise de Célula Única/métodos , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Transcriptoma/fisiologia
5.
Cell Rep ; 38(6): 110333, 2022 02 08.
Artigo em Inglês | MEDLINE | ID: mdl-35139376

RESUMO

Cellular gene expression changes throughout a dynamic biological process, such as differentiation. Pseudotimes estimate cells' progress along a dynamic process based on their individual gene expression states. Ordering the expression data by pseudotime provides information about the underlying regulator-gene interactions. Because the pseudotime distribution is not uniform, many standard mathematical methods are inapplicable for analyzing the ordered gene expression states. Here we present single-cell inference of networks using Granger ensembles (SINGE), an algorithm for gene regulatory network inference from ordered single-cell gene expression data. SINGE uses kernel-based Granger causality regression to smooth irregular pseudotimes and missing expression values. It aggregates predictions from an ensemble of regression analyses to compile a ranked list of candidate interactions between transcriptional regulators and target genes. In two mouse embryonic stem cell differentiation datasets, SINGE outperforms other contemporary algorithms. However, a more detailed examination reveals caveats about poor performance for individual regulators and uninformative pseudotimes.


Assuntos
Diferenciação Celular/fisiologia , Perfilação da Expressão Gênica , Redes Reguladoras de Genes/fisiologia , Transcriptoma/fisiologia , Algoritmos , Animais , Biologia Computacional/métodos , Perfilação da Expressão Gênica/métodos , Camundongos , Software
6.
BMC Plant Biol ; 22(1): 8, 2022 Jan 03.
Artigo em Inglês | MEDLINE | ID: mdl-34979910

RESUMO

BACKGROUND: High soil salinity often adversely affects plant physiology and agricultural productivity of almost all crops worldwide, such as the crude drug known as wolfberry. However, the mechanism of this action in wolfberry is not fully understood yet. RESULTS: Here in this study, we studied different mechanisms potentially in Chinese wolfberry (Lycium chinese, LC) and black wolfberry (L. ruthenicum, LR) under salinity stress, by analyzing their transcriptome, metabolome, and hormone changes. The hormone detection analysis revealed that the ABA content was significantly lower in LR than LC under normal condition, and increased sharply under salinity stress in LR but not in LC. The transcriptome analysis showed that the salinity-responsive genes in wolfberry were mainly enriched in MAPK signaling, amino sugar and nucleotide sugar metabolism, carbon metabolism, and plant hormone signal transduction pathways in LC, while mainly related to carbon metabolism and protein processing in endoplasmic reticulum in LR. Metabolome results indicated that LR harbored higher flavone and flavonoid contents than LC under normal condition. However, the flavone and flavonoid contents were hardly changed in LR, but increased substantially in LC when exposed to salinity stress. CONCLUSIONS: Our results adds ABA and flavone to mechanism understanding of salinity tolerance in wolfberry. In addition, flavone plays a positive role in resistance to salinity stress in wolfberry.


Assuntos
Lycium/fisiologia , Metaboloma/fisiologia , Estresse Salino/genética , Transcriptoma/fisiologia , Lycium/genética , Especificidade da Espécie
7.
Elife ; 112022 01 13.
Artigo em Inglês | MEDLINE | ID: mdl-35025731

RESUMO

Maternal obesity during pregnancy has immediate and long-term detrimental effects on the offspring heart. In this study, we characterized the cardiac and circulatory lipid profiles in late gestation E18.5 fetuses of diet-induced obese pregnant mice and established the changes in lipid abundance and fetal cardiac transcriptomics. We used untargeted and targeted lipidomics and transcriptomics to define changes in the serum and cardiac lipid composition and fatty acid metabolism in male and female fetuses. From these analyses we observed: (1) maternal obesity affects the maternal and fetal serum lipidome distinctly; (2) female fetal heart lipidomes are more sensitive to maternal obesity than males; (3) changes in lipid supply might contribute to early expression of lipolytic genes in mouse hearts exposed to maternal obesity. These results highlight the existence of sexually dimorphic responses of the fetal heart to the same in utero obesogenic environment and identify lipids species that might mediate programming of cardiovascular health.


Assuntos
Feto/metabolismo , Metabolismo dos Lipídeos/fisiologia , Miocárdio/metabolismo , Obesidade Materna/fisiopatologia , Animais , Feminino , Lipidômica , Masculino , Camundongos , Miocárdio/química , Gravidez , Transcriptoma/fisiologia
8.
PLoS One ; 17(1): e0261723, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35025912

RESUMO

Skeletal muscle atrophy is a physiological response to disuse, aging, and disease. We compared changes in muscle mass and the transcriptome profile after short-term immobilization in a divergent model of high and low responders to endurance training to identify biological processes associated with the early atrophy response. Female rats selectively bred for high response to endurance training (HRT) and low response to endurance training (LRT; n = 6/group; generation 19) underwent 3 day hindlimb cast immobilization to compare atrophy of plantaris and soleus muscles with line-matched controls (n = 6/group). RNA sequencing was utilized to identify Gene Ontology Biological Processes with differential gene set enrichment. Aerobic training performed prior to the intervention showed HRT improved running distance (+60.6 ± 29.6%), while LRT were unchanged (-0.3 ± 13.3%). Soleus atrophy was greater in LRT vs. HRT (-9.0 ±8.8 vs. 6.2 ±8.2%; P<0.05) and there was a similar trend in plantaris (-16.4 ±5.6% vs. -8.5 ±7.4%; P = 0.064). A total of 140 and 118 biological processes were differentially enriched in plantaris and soleus muscles, respectively. Soleus muscle exhibited divergent LRT and HRT responses in processes including autophagy and immune response. In plantaris, processes associated with protein ubiquitination, as well as the atrogenes (Trim63 and Fbxo32), were more positively enriched in LRT. Overall, LRT demonstrate exacerbated atrophy compared to HRT, associated with differential gene enrichments of biological processes. This indicates that genetic factors that result in divergent adaptations to endurance exercise, may also regulate biological processes associated with short-term muscle unloading.


Assuntos
Treino Aeróbico/métodos , Elevação dos Membros Posteriores/métodos , Músculo Esquelético/metabolismo , Atrofia Muscular/metabolismo , Transcriptoma/fisiologia , Adaptação Fisiológica , Animais , Terapia por Exercício , Feminino , Biblioteca Genômica , Humanos , Masculino , Condicionamento Físico Animal , Ratos , Análise de Sequência de RNA
9.
Parasit Vectors ; 15(1): 22, 2022 Jan 10.
Artigo em Inglês | MEDLINE | ID: mdl-35012632

RESUMO

BACKGROUND: Long non-coding RNAs (lncRNAs) are important regulators of various biological and pathological processes, in particular the inflammatory response by modulating the transcriptional control of inflammatory genes. However, the role of lncRNAs in regulating the immune and inflammatory responses during infection with the protozoan parasite Toxoplasma gondii remains largely unknown. METHODS: We performed a longitudinal RNA sequencing analysis of human foreskin fibroblast (HFF) cells infected by T. gondii to identify differentially expressed long non-coding RNAs (lncRNAs) and messenger RNAs (mRNAs), and dysregulated pathways over the course of T. gondii lytic cycle. The transcriptome data were validated by qRT-PCR. RESULTS: RNA sequencing revealed significant transcriptional changes in the infected HFFs. A total of 697, 1234, 1499, 873, 1466, 561, 676 and 716 differentially expressed lncRNAs (DElncRNAs), and 636, 1266, 1843, 2303, 3022, 1757, 3088 and 2531 differentially expressed mRNAs (DEmRNAs) were identified at 1.5, 3, 6, 9, 12, 24, 36 and 48 h post-infection, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of DElncRNAs and DEmRNAs revealed that T. gondii infection altered the expression of genes involved in the regulation of host immune response (e.g., cytokine-cytokine receptor interaction), receptor signaling (e.g., NOD-like receptor signaling pathway), disease (e.g., Alzheimer's disease), and metabolism (e.g., fatty acid degradation). CONCLUSIONS: These results provide novel information for further research on the role of lncRNAs in immune regulation of T. gondii infection.


Assuntos
RNA Longo não Codificante/genética , RNA Mensageiro/genética , RNA de Protozoário/genética , Toxoplasma/genética , Transcriptoma/fisiologia , Células Cultivadas , Prepúcio do Pênis/citologia , Regulação da Expressão Gênica , Humanos , Masculino , RNA Longo não Codificante/química , RNA Longo não Codificante/isolamento & purificação , RNA Mensageiro/química , RNA Mensageiro/isolamento & purificação , RNA de Protozoário/química , RNA de Protozoário/isolamento & purificação , Reação em Cadeia da Polimerase em Tempo Real , Análise de Sequência de RNA , Toxoplasma/imunologia , Toxoplasma/metabolismo
10.
Dev Cell ; 57(4): 526-542.e7, 2022 02 28.
Artigo em Inglês | MEDLINE | ID: mdl-35063083

RESUMO

Shoot regeneration is mediated by the sequential action of two phytohormones, auxin and cytokinin. However, the chromatin regulatory landscapes underlying this dynamic response have not yet been studied. In this study, we jointly profiled chromatin accessibility, histone modifications, and transcriptomes to demonstrate that a high auxin/cytokinin ratio environment primes Arabidopsis shoot regeneration by increasing the accessibility of the gene loci associated with pluripotency and shoot fate determination. Cytokinin signaling not only triggers the commitment of the shoot progenitor at later stages but also allows chromatin to maintain shoot identity genes at the priming stage. Our analysis of transcriptional regulatory dynamics further identifies a catalog of regeneration cis-elements dedicated to cell fate transitions and uncovers important roles of BES1, MYC, IDD, and PIF transcription factors in shoot regeneration. Our results, thus, provide a comprehensive resource for studying cell reprogramming in plants and provide potential targets for improving future shoot regeneration efficiency.


Assuntos
Cromatina/metabolismo , Citocininas/metabolismo , Ácidos Indolacéticos/metabolismo , Regeneração/fisiologia , Arabidopsis/metabolismo , Proteínas de Arabidopsis/metabolismo , Diferenciação Celular/fisiologia , Regulação da Expressão Gênica de Plantas/genética , Regulação da Expressão Gênica de Plantas/fisiologia , Brotos de Planta/metabolismo , Fatores de Transcrição/metabolismo , Transcriptoma/fisiologia
11.
Arch Biochem Biophys ; 715: 109085, 2022 01 15.
Artigo em Inglês | MEDLINE | ID: mdl-34800440

RESUMO

The identification of biomolecules associated with papillary thyroid cancer (PTC) has upmost importance for the elucidation of the disease mechanism and the development of effective diagnostic and treatment strategies. Despite particular findings in this regard, a holistic analysis encompassing molecular data from different biological levels has been lacking. In the present study, a meta-analysis of four transcriptome datasets was performed to identify gene expression signatures in PTC, and reporter molecules were determined by mapping gene expression data onto three major cellular networks, i.e., transcriptional regulatory, protein-protein interaction, and metabolic networks. We identified 282 common genes that were differentially expressed in all PTC datasets. In addition, six proteins (FYN, JUN, LYN, PML, SIN3A, and RARA), two Erb-B2 receptors (ERBB2 and ERBB4), two cyclin-dependent receptors (CDK1 and CDK2), and three histone deacetylase receptors (HDAC1, HDAC2, and HDAC3) came into prominence as proteomic signatures in addition to several metabolites including lactaldehyde and proline at the metabolome level. Significant associations with calcium and MAPK signaling pathways and transcriptional and post-transcriptional activities of 12 TFs and 110 miRNAs were also observed at the regulatory level. Among them, six miRNAs (miR-30b-3p, miR-15b-5p, let-7a-5p, miR-130b-3p, miR-424-5p, and miR-193b-3p) were associated with PTC for the first time in the literature, and the expression levels of miR-30b-3p, miR-15b-5p, and let-7a-5p were found to be predictive of disease prognosis. Drug repositioning and molecular docking simulations revealed that 5 drugs (prochlorperazine, meclizine, rottlerin, cephaeline, and tretinoin) may be useful in the treatment of PTC. Consequently, we report here biomolecule candidates that may be considered as prognostic biomarkers or potential therapeutic targets for further experimental and clinical trials for PTC.


Assuntos
Biomarcadores Tumorais/genética , MicroRNAs/genética , Câncer Papilífero da Tireoide/genética , Neoplasias da Glândula Tireoide/genética , Antineoplásicos/metabolismo , Reposicionamento de Medicamentos , Expressão Gênica/fisiologia , Perfilação da Expressão Gênica , Humanos , Simulação de Acoplamento Molecular , Ligação Proteica , Proteômica , Transcriptoma/fisiologia
12.
Biochem Pharmacol ; 196: 114735, 2022 02.
Artigo em Inglês | MEDLINE | ID: mdl-34411566

RESUMO

Uncontrolled overgrowth of cells, such as in cancer, is an unavoidable risk in life that affects nearly every second individual in industrialized countries. However, in part this risk can be controlled through lifestyle adjustments, such as the avoidance of smoking, unhealthy diet, obesity, physical inactivity and other cancer risk factors. A low vitaminD status is a risk in particular for cancers of colon, prostate, breast and leukocytes. VitaminD3 is produced non-enzymatically, when the cholesterol precursor 7-dehydrocholesterol is exposed to UV-B from sunlight, i.e., all cholesterol synthesizing species, including humans, can make vitaminD3. VitaminD endocrinology started some 550million years ago, when the metabolite 1α,25-dihydroxyvitaminD3 and the transcription factor vitaminD receptor teamed up for regulating the expression of hundreds of target genes in a multitude of different tissues and cell types. Initially, these genes were focused on the control of energy homeostasis, which later also involved energy-demanding innate and adaptive immunity. Rapidly growing cells of the immune system as well as those of malignant tumors rely on comparable genes and pathways, some of which are modulated by vitaminD. Accordingly, vitaminD has anti-cancer effects both directly via controling the differentiation, proliferation and apoptosis of neoplastic cells as well as indirectly through regulating immune cells that belong to the microenvironment of malignant tumors. This review discusses effects of vitaminD on the epigenome and transcriptome of stromal and tumor cells, inter-individual variations in vitaminD responsiveness and their relation to the prevention and possible therapy of cancer.


Assuntos
Neoplasias/genética , Neoplasias/metabolismo , Transcriptoma/fisiologia , Microambiente Tumoral/fisiologia , Vitamina D/genética , Vitamina D/metabolismo , Animais , Diferenciação Celular/efeitos dos fármacos , Diferenciação Celular/fisiologia , Humanos , /uso terapêutico , Neoplasias/tratamento farmacológico , Receptores de Calcitriol/genética , Receptores de Calcitriol/metabolismo , Fatores de Risco , Transcriptoma/efeitos dos fármacos , Microambiente Tumoral/efeitos dos fármacos , Vitamina D/administração & dosagem
13.
Mol Cell Biol ; 42(1): e0048321, 2022 01 20.
Artigo em Inglês | MEDLINE | ID: mdl-34748401

RESUMO

From initiation through progression, cancer cells are subjected to a magnitude of endogenous and exogenous stresses, which aid in their neoplastic transformation. Exposure to these classes of stress induces imbalance in cellular homeostasis and, in response, cancer cells employ informative adaptive mechanisms to rebalance biochemical processes that facilitate survival and maintain their existence. Different kinds of stress stimuli trigger epigenetic alterations in cancer cells, which leads to changes in their transcriptome and metabolome, ultimately resulting in suppression of growth inhibition or induction of apoptosis. Whether cancer cells show a protective response to stress or succumb to cell death depends on the type of stress and duration of exposure. A thorough understanding of epigenetic and molecular architecture of cancer cell stress response pathways can unveil a plethora of information required to develop novel anticancer therapeutics. The present view highlights current knowledge about alterations in epigenome and transcriptome of cancer cells as a consequence of exposure to different physicochemical stressful stimuli such as reactive oxygen species (ROS), hypoxia, radiation, hyperthermia, genotoxic agents, and nutrient deprivation. Currently, an anticancer treatment scenario involving the imposition of stress to target cancer cells is gaining traction to augment or even replace conventional therapeutic regimens. Therefore, a comprehensive understanding of stress response pathways is crucial for devising and implementing novel therapeutic strategies.


Assuntos
Metaboloma/fisiologia , Neoplasias/etiologia , Espécies Reativas de Oxigênio/metabolismo , Transcriptoma/fisiologia , Transformação Celular Neoplásica/genética , Transformação Celular Neoplásica/metabolismo , Epigenômica/métodos , Humanos , Hipóxia/metabolismo , Estresse Oxidativo/fisiologia
14.
Biol Reprod ; 106(1): 185-199, 2022 01 13.
Artigo em Inglês | MEDLINE | ID: mdl-34686873

RESUMO

The complex physiologic process of parturition includes the onset of labor, which requires the orchestrated stimulation of a common pathway involving uterine contractility, cervical ripening, and chorioamniotic membrane activation. However, the labor-specific processes taking place in these tissues have limited use as predictive biomarkers unless they can be probed in non-invasive samples, such as the peripheral blood. Herein, we utilized a transcriptomic dataset to assess labor-specific changes in the peripheral blood of women who delivered at term. We identified a set of genes that were differentially expressed with labor and enriched for immunological processes, and these gene expression changes were strongly correlated with results from prior studies, providing in silico validation of our findings. We then identified significant correlations between labor-specific transcriptomic changes in the maternal circulation and those detected in the chorioamniotic membranes, myometrium, and cervix of women at term, demonstrating that tissue-specific labor signatures are partly mirrored in the peripheral blood. Finally, we demonstrated a significant overlap between the peripheral blood transcriptomic changes in term parturition and those observed in asymptomatic women, prior to the diagnosis of preterm prelabor rupture of the membranes, who ultimately delivered preterm. Collectively, we provide evidence that the normal process of labor at term is characterized by a unique immunological expression signature, which may serve as a useful tool for assessing labor status and for potentially identifying women at risk for preterm birth.


Assuntos
Parto/sangue , Nascimento Prematuro/sangue , Transcriptoma/fisiologia , Adulto , Colo do Útero/química , Membranas Extraembrionárias/química , Feminino , Ruptura Prematura de Membranas Fetais/sangue , Humanos , Inflamação/sangue , Inflamação/imunologia , Trabalho de Parto/sangue , Trabalho de Parto/imunologia , Miométrio/química , Gravidez
15.
Exp Neurol ; 347: 113913, 2022 01.
Artigo em Inglês | MEDLINE | ID: mdl-34752785

RESUMO

INTRODUCTION: Neural stem cell (NSC) transplantation offers great potential for treating ischemic stroke. Clinically, ischemia followed by reperfusion results in robust cerebrovascular injury that upregulates proinflammatory factors, disrupts neurovascular units, and causes brain cell death. NSCs possess multiple actions that can be exploited for reducing the severity of neurovascular injury. Our previous studies in young adult mice showed that human NSC transplantation during the subacute stage diminishes stroke pathophysiology and improves behavioral outcome. METHODS: We employed a well-established and commonly used stroke model, middle cerebral artery occlusion with subsequent reperfusion (MCAO/R). Here, we assessed the outcomes of hNSC transplantation 48 h post-MCAO (24 h post-transplant) in aged mouse brains in response to stroke because aging is a crucial risk factor for cerebral ischemia. Next, we tested whether administration of the integrin α5ß1 inhibitor, ATN-161, prior to hNSC transplantation further affects stoke outcome as compared with NSCs alone. RNA sequencing (RNA-seq) was used to assess the impact of hNSC transplantation on differentially expressed genes (DEGs) on a transcriptome-wide level. RESULTS: Here, we report that hNSC-engrafted brains with or without ATN-161 showed significantly reduced infarct size, and attenuated the induction of proinflammatory factors and matrix metalloproteases. RNA-seq analysis revealed DEGs and molecular pathways by which hNSCs induce a beneficial post-stroke outcome in aged stroke brains. 811 genes were differentially expressed (651 downregulated and 160 upregulated) in hNSC-engrafted stroke brains. Functional pathway analysis identified enriched and depleted pathways in hNSC-engrafted aged mouse stroke brains. Depletion of pathways following hNSC-engraftment included signaling involving neuroinflammation, acute phase response, leukocyte extravasation, and phagosome formation. On the other hand, enrichment of pathways in hNSC-engrafted brains was associated with PPAR signaling, LXR/RXR activation, and inhibition of matrix metalloproteases. Hierarchical cluster analysis of DEGs in hNSC-engrafted brains indicate decreased expression of genes encoding TNF receptors, proinflammatory factors, apoptosis factors, adhesion and leukocyte extravasation, and Toll-like receptors. CONCLUSIONS: Our study is the first to show global transcripts differentially expressed following hNSC transplantation in the subacute phase of stroke in aged mice. The outcome of our transcriptome study would be useful to develop new therapies ameliorating early-stage stroke injury.


Assuntos
Envelhecimento/genética , Células-Tronco Neurais/fisiologia , Transplante de Células-Tronco/métodos , Acidente Vascular Cerebral/genética , Acidente Vascular Cerebral/terapia , Transcriptoma/fisiologia , Envelhecimento/efeitos dos fármacos , Envelhecimento/metabolismo , Animais , Células Cultivadas , Infarto Cerebral/genética , Infarto Cerebral/metabolismo , Infarto Cerebral/terapia , Feto , Regulação da Expressão Gênica , Humanos , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Células-Tronco Neurais/efeitos dos fármacos , Células-Tronco Neurais/transplante , Oligopeptídeos/administração & dosagem , Acidente Vascular Cerebral/metabolismo , Transcriptoma/efeitos dos fármacos
16.
ACS Appl Mater Interfaces ; 14(1): 201-213, 2022 Jan 12.
Artigo em Inglês | MEDLINE | ID: mdl-34929079

RESUMO

Bioengineering functional hepatic tissue constructs that physiologically replicate the human native liver tissue in vitro is sought for clinical research and drug discovery. However, the intricate architecture and specific biofunctionality possessed by the native liver tissue remain challenging to mimic in vitro. In the present study, a versatile strategy to fabricate lobular-like silk protein scaffolds with radially aligned lamellar sheets, interconnected channels, and a converging central cavity was designed and implemented. A proof-of-concept study to bioengineer biomimetic hepatic lobules was conducted through coculturing human hepatocytes and primary endothelial cells on these lobular-like scaffolds. Relatively long-term viability of hepatocyte/endothelial cells was found along with cell alignment and organization in vitro. The hepatocytes showed special epithelial polarity and bile duct formation, similar to the liver plate, while the aligned endothelial cells generated endothelial networks, similar to natural hepatic sinuses. This endowed the three-dimensional (3D) tissue constructs with the capability to recapitulate hepatic-like parenchymal-mesenchymal growth patterns in vitro. More importantly, the cocultured hepatocytes outperformed monocultures or monolayer cultures, displaying significantly enhanced hepatocyte functions, including functional gene expression, albumin (ALB) secretion, urea synthesis, and metabolic activity. Thus, this functional unit with a biomimetic phenotype provides a novel technology for bioengineering biomimetic hepatic lobules in vitro, with potential utility as a building block for bioartificial liver (BAL) engineering or as a robust tool for drug metabolism investigation.


Assuntos
Fibroínas/química , Fígado/metabolismo , Tecidos Suporte/química , Albuminas/metabolismo , Biomimética/métodos , Linhagem Celular Tumoral , Técnicas de Cocultura , Células Endoteliais da Veia Umbilical Humana , Humanos , Porosidade , Estudo de Prova de Conceito , Engenharia Tecidual/métodos , Transcriptoma/fisiologia , Ureia/metabolismo
17.
Endocrinology ; 163(3)2022 03 01.
Artigo em Inglês | MEDLINE | ID: mdl-34918063

RESUMO

Successful lactation and the risk for developing breast cancer depend on growth and differentiation of the mammary gland (MG) epithelium that is regulated by ovarian steroids (17ß-estradiol [E] and progesterone [P]) and pituitary-derived prolactin (PRL). Given that the MG of pigs share histomorphogenic features present in the normal human breast, we sought to define the transcriptional responses within the MG of pigs following exposure to all combinations of these hormones. Hormone-ablated female pigs were administered combinations of E, medroxyprogesterone 17-acetate (source of P), and either haloperidol (to induce PRL) or 2-bromo-α-ergocryptine. We subsequently monitored phenotypic changes in the MG including mitosis, receptors for E and P (ESR1 and PGR), level of phosphorylated STAT5 (pSTAT5), and the frequency of terminal ductal lobular unit (TDLU) subtypes; these changes were then associated with all transcriptomic changes. Estrogen altered the expression of approximately 20% of all genes that were mostly associated with mitosis, whereas PRL stimulated elements of fatty acid metabolism and an inflammatory response. Several outcomes, including increased pSTAT5, highlighted the ability of E to enhance PRL action. Regression of transcriptomic changes against several MG phenotypes revealed 1669 genes correlated with proliferation, among which 29 were E inducible. Additional gene expression signatures were associated with TDLU formation and the frequency of ESR1 or PGR. These data provide a link between the hormone-regulated genome and phenome of the MG in a species having a complex histoarchitecture like that in the human breast, and highlight an underexplored synergy between the actions of E and PRL during MG development.


Assuntos
Estrogênios/fisiologia , Glândulas Mamárias Animais/crescimento & desenvolvimento , Progesterona/fisiologia , Prolactina/fisiologia , Porco Miniatura/fisiologia , Transcriptoma/fisiologia , Animais , Bromocriptina/administração & dosagem , Sinergismo Farmacológico , Estradiol/administração & dosagem , Receptor alfa de Estrogênio/análise , Receptor alfa de Estrogênio/genética , Estrogênios/deficiência , Feminino , Haloperidol/administração & dosagem , Glândulas Mamárias Animais/química , Glândulas Mamárias Animais/efeitos dos fármacos , Acetato de Medroxiprogesterona/administração & dosagem , Modelos Animais , Morfogênese/efeitos dos fármacos , Morfogênese/genética , Ovariectomia , Progesterona/deficiência , Prolactina/deficiência , Receptores de Progesterona/análise , Receptores de Progesterona/genética , Suínos , Transcriptoma/efeitos dos fármacos
18.
Artigo em Inglês | MEDLINE | ID: mdl-34759019

RESUMO

BACKGROUND AND OBJECTIVES: Compared with stroke controls, patients with varicella zoster virus (VZV) vasculopathy have increased amyloid in CSF, along with increased amylin (islet amyloid polypeptide [IAPP]) and anti-VZV antibodies. Thus, we examined the gene expression profiles of VZV-infected primary human brain vascular adventitial fibroblasts (HBVAFs), one of the initial arterial cells infected in VZV vasculopathy, to determine whether they are a potential source of amyloid that can disrupt vasculature and potentiate inflammation. METHODS: Mock- and VZV-infected quiescent HBVAFs were harvested at 3 days postinfection. Targeted RNA sequencing of the whole-human transcriptome (BioSpyder Technologies, TempO-Seq) was conducted followed by gene set enrichment and pathway analysis. Selected pathways unique to VZV-infected cells were confirmed by enzyme-linked immunoassays, migration assays, and immunofluorescence analysis (IFA) that included antibodies against amylin and amyloid-beta, as well as amyloid staining by Thioflavin-T. RESULTS: Compared with mock, VZV-infected HBVAFs had significantly enriched gene expression pathways involved in vascular remodeling and vascular diseases; confirmatory studies showed secretion of matrix metalloproteinase-3 and -10, as well increased migration of infected cells and uninfected cells when exposed to conditioned media from VZV-infected cells. In addition, significantly enriched pathways involved in amyloid-associated diseases (diabetes mellitus, amyloidosis, and Alzheimer disease), tauopathy, and progressive neurologic disorder were identified; predicted upstream regulators included amyloid precursor protein, apolipoprotein E, microtubule-associated protein tau, presenilin 1, and IAPP. Confirmatory IFA showed that VZV-infected HBVAFs contained amyloidogenic peptides (amyloid-beta and amylin) and intracellular amyloid. DISCUSSION: Gene expression profiles and pathway enrichment analysis of VZV-infected HBVAFs, as well as phenotypic studies, reveal features of pathologic vascular remodeling (e.g., increased cell migration and changes in the extracellular matrix) that can contribute to cerebrovascular disease. Furthermore, the discovery of amyloid-associated transcriptional pathways and intracellular amyloid deposition in HBVAFs raise the possibility that VZV vasculopathy is an amyloid disease. Amyloid deposition may contribute to cell death and loss of vascular wall integrity, as well as potentiate chronic inflammation in VZV vasculopathy, with disease severity and recurrence determined by the host's ability to clear virus infection and amyloid deposition and by the coexistence of other amyloid-associated diseases (i.e., Alzheimer disease and diabetes mellitus).


Assuntos
Túnica Adventícia , Peptídeos beta-Amiloides/metabolismo , Transtornos Cerebrovasculares , Fibroblastos , Infecção pelo Vírus da Varicela-Zoster , Remodelação Vascular , Túnica Adventícia/citologia , Túnica Adventícia/metabolismo , Túnica Adventícia/patologia , Túnica Adventícia/virologia , Células Cultivadas , Transtornos Cerebrovasculares/metabolismo , Transtornos Cerebrovasculares/patologia , Transtornos Cerebrovasculares/virologia , Fibroblastos/citologia , Fibroblastos/metabolismo , Fibroblastos/patologia , Fibroblastos/virologia , Humanos , Análise de Sequência de RNA , Transcriptoma/fisiologia , Infecção pelo Vírus da Varicela-Zoster/metabolismo , Infecção pelo Vírus da Varicela-Zoster/patologia , Infecção pelo Vírus da Varicela-Zoster/virologia , Remodelação Vascular/fisiologia
19.
Front Endocrinol (Lausanne) ; 12: 774997, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34867824

RESUMO

Objective: Supraphysiological hormone exposure, in vitro culture and embryo transfer throughout the in vitro fertilization-embryo transfer (IVF-ET) procedures may affect placental development. The present study aimed to identify differences in genomic expression profiles between IVF-ET and naturally conceived placentals and to use this as a basis for understanding the underlying effects of IVF-ET on placental function. Methods: Full-term human placental tissues were subjected to next-generation sequencing to determine differentially expressed miRNAs (DEmiRs) and genes (DEGs) between uncomplicated IVF-ET assisted and naturally conceived pregnancies. Gene ontology (GO) enrichment analysis and transcription factor enrichment analysis were used for DEmiRs. MiRNA-mRNA interaction and protein-protein interaction (PPI) networks were constructed. In addition, hub genes were obtained by using the STRING database and Cytoscape. DEGs were analyzed using GO and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Differentially expressed miRNAs were validated through qRT-PCR. Results: Compared against natural pregnancies, 12 DEmiRs and 258 DEGs were identified in IVF-ET placental tissues. In a validation cohort, it was confirmed that hsa-miR-204-5p, hsa-miR-1269a, and hsa-miR-941 were downregulation, while hsa-miR-4286, hsa-miR-31-5p and hsa-miR-125b-5p were upregulation in IVF-ET placentas. Functional analysis suggested that these differentially expressed genes were significantly enriched in angiogenesis, pregnancy, PI3K-Akt and Ras signaling pathways. The miRNA-mRNA regulatory network revealed the contribution of 10 miRNAs and 109 mRNAs while EGFR was the most highly connected gene among ten hub genes in the PPI network. Conclusion: Even in uncomplicated IVF-ET pregnancies, differences exist in the placental transcriptome relative to natural pregnancies. Many of the differentially expressed genes in IVF-ET are involved in essential placental functions, and moreover, they provide a ready resource of molecular markers to assess the association between placental function and safety in IVF-ET offspring.


Assuntos
Transferência Embrionária , Fertilização In Vitro , MicroRNAs/genética , Placenta/metabolismo , RNA Mensageiro/genética , Adulto , Células Cultivadas , Implantação do Embrião/genética , Feminino , Perfilação da Expressão Gênica , Redes Reguladoras de Genes , Humanos , Recém-Nascido , Infertilidade/genética , Infertilidade/metabolismo , Infertilidade/terapia , Masculino , MicroRNAs/metabolismo , Placentação/genética , Gravidez , Mapas de Interação de Proteínas/genética , RNA Mensageiro/metabolismo , Transcriptoma/fisiologia , Adulto Jovem
20.
Cell Rep ; 37(6): 109920, 2021 11 09.
Artigo em Inglês | MEDLINE | ID: mdl-34731648

RESUMO

It is urgent to develop disease models to dissect mechanisms regulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Here, we derive airway organoids from human pluripotent stem cells (hPSC-AOs). The hPSC-AOs, particularly ciliated-like cells, are permissive to SARS-CoV-2 infection. Using this platform, we perform a high content screen and identify GW6471, which blocks SARS-CoV-2 infection. GW6471 can also block infection of the B.1.351 SARS-CoV-2 variant. RNA sequencing (RNA-seq) analysis suggests that GW6471 blocks SARS-CoV-2 infection at least in part by inhibiting hypoxia inducible factor 1 subunit alpha (HIF1α), which is further validated by chemical inhibitor and genetic perturbation targeting HIF1α. Metabolic profiling identifies decreased rates of glycolysis upon GW6471 treatment, consistent with transcriptome profiling. Finally, xanthohumol, 5-(tetradecyloxy)-2-furoic acid, and ND-646, three compounds that suppress fatty acid biosynthesis, also block SARS-CoV-2 infection. Together, a high content screen coupled with transcriptome and metabolic profiling reveals a key role of the HIF1α-glycolysis axis in mediating SARS-CoV-2 infection of human airway epithelium.


Assuntos
COVID-19/metabolismo , Glicólise/fisiologia , Subunidade alfa do Fator 1 Induzível por Hipóxia/metabolismo , Pulmão/metabolismo , Organoides/metabolismo , Animais , Linhagem Celular , Chlorocebus aethiops , Células Epiteliais/metabolismo , Células HEK293 , Humanos , Células-Tronco Pluripotentes/metabolismo , SARS-CoV-2/patogenicidade , Transcriptoma/fisiologia , Células Vero
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