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1.
BMC Bioinformatics ; 21(Suppl 14): 369, 2020 Sep 30.
Artigo em Inglês | MEDLINE | ID: mdl-32998686

RESUMO

BACKGROUND: Chromosome conformation capture-based methods, especially Hi-C, enable scientists to detect genome-wide chromatin interactions and study the spatial organization of chromatin, which plays important roles in gene expression regulation, DNA replication and repair etc. Thus, developing computational methods to unravel patterns behind the data becomes critical. Existing computational methods focus on intrachromosomal interactions and ignore interchromosomal interactions partly because there is no prior knowledge for interchromosomal interactions and the frequency of interchromosomal interactions is much lower while the search space is much larger. With the development of single-cell technologies, the advent of single-cell Hi-C makes interrogating the spatial structure of chromatin at single-cell resolution possible. It also brings a new type of frequency information, the number of single cells with chromatin interactions between two disjoint chromosome regions. RESULTS: Considering the lack of computational methods on interchromosomal interactions and the unsurprisingly frequent intrachromosomal interactions along the diagonal of a chromatin contact map, we propose a computational method dedicated to analyzing interchromosomal interactions of single-cell Hi-C with this new frequency information. To the best of our knowledge, our proposed tool is the first to identify regions with statistically frequent interchromosomal interactions at single-cell resolution. We demonstrate that the tool utilizing networks and binomial statistical tests can identify interesting structural regions through visualization, comparison and enrichment analysis and it also supports different configurations to provide users with flexibility. CONCLUSIONS: It will be a useful tool for analyzing single-cell Hi-C interchromosomal interactions.


Assuntos
Cromossomos/metabolismo , Análise de Célula Única/métodos , Animais , Cromatina/metabolismo , Fase G1 , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Camundongos , Células-Tronco Embrionárias Murinas/citologia , Células-Tronco Embrionárias Murinas/metabolismo , Oócitos/citologia , Oócitos/metabolismo , Fase S , Zigoto/citologia , Zigoto/metabolismo
2.
Urol Clin North Am ; 47(4): 475-485, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-33008498

RESUMO

Cancer is a highly complex and heterogeneous disease and immunotherapy has shown promise as a therapeutic approach. The increased resolution afforded by single-cell analysis offers the hope of finding and characterizing previously underappreciated populations of cells that could prove useful in understanding cancer progression and treatment. Urologic and prostate cancers are inherently heterogeneous diseases, and the potential for single-cell analysis to help understand and develop immunotherapeutic approaches to treat these diseases is very exciting. In this review, we view cancer immunotherapy through a single-cell lens and discuss the state-of-the-art technologies that enable advances in this field.


Assuntos
Imunoterapia/métodos , Terapia de Alvo Molecular/métodos , Neoplasias da Próstata/genética , Neoplasias da Próstata/terapia , Microambiente Tumoral/efeitos dos fármacos , Feminino , Previsões , Humanos , Masculino , Terapia de Alvo Molecular/tendências , Prognóstico , Neoplasias da Próstata/patologia , Medição de Risco , Análise de Sequência de DNA , Análise de Sequência de RNA , Análise de Célula Única , Resultado do Tratamento , Microambiente Tumoral/genética , Neoplasias Urológicas/genética , Neoplasias Urológicas/patologia , Neoplasias Urológicas/terapia
3.
Nat Commun ; 11(1): 5077, 2020 10 08.
Artigo em Inglês | MEDLINE | ID: mdl-33033240

RESUMO

Although substantial progress has been made in cancer biology and treatment, clinical outcomes of bladder carcinoma (BC) patients are still not satisfactory. The tumor microenvironment (TME) is a potential target. Here, by single-cell RNA sequencing on 8 BC tumor samples and 3 para tumor samples, we identify 19 different cell types in the BC microenvironment, indicating high intra-tumoral heterogeneity. We find that tumor cells down regulated MHC-II molecules, suggesting that the downregulated immunogenicity of cancer cells may contribute to the formation of an immunosuppressive microenvironment. We also find that monocytes undergo M2 polarization in the tumor region and differentiate. Furthermore, the LAMP3 + DC subgroup may be able to recruit regulatory T cells, potentially taking part in the formation of an immunosuppressive TME. Through correlation analysis using public datasets containing over 3000 BC samples, we identify a role for inflammatory cancer-associated fibroblasts (iCAFs) in tumor progression, which is significantly related to poor prognosis. Additionally, we characterize a regulatory network depending on iCAFs. These results could help elucidate the protumor mechanisms of iCAFs. Our results provide deep insight into cancer immunology and provide an essential resource for drug discovery in the future.


Assuntos
Fibroblastos/patologia , Inflamação/patologia , Análise de Sequência de RNA , Análise de Célula Única , Bexiga Urinária/patologia , Área Sob a Curva , Fibroblastos Associados a Câncer/metabolismo , Fibroblastos Associados a Câncer/patologia , Linhagem Celular Tumoral , Polaridade Celular , Proliferação de Células , Citocinas/metabolismo , Variações do Número de Cópias de DNA/genética , Células Dendríticas/metabolismo , Redes Reguladoras de Genes , Humanos , Ligantes , Glicoproteínas de Membrana Associadas ao Lisossomo/metabolismo , Monócitos/patologia , Células Mieloides/patologia , Proteínas de Neoplasias/metabolismo , Linfócitos T Reguladores/imunologia , Microambiente Tumoral , Bexiga Urinária/imunologia
4.
Nat Commun ; 11(1): 4854, 2020 09 25.
Artigo em Inglês | MEDLINE | ID: mdl-32978383

RESUMO

Chronic imaging of neuronal networks in vitro has provided fundamental insights into mechanisms underlying neuronal function. Current labeling and optical imaging methods, however, cannot be used for continuous and long-term recordings of the dynamics and evolution of neuronal networks, as fluorescent indicators can cause phototoxicity. Here, we introduce a versatile platform for label-free, comprehensive and detailed electrophysiological live-cell imaging of various neurogenic cells and tissues over extended time scales. We report on a dual-mode high-density microelectrode array, which can simultaneously record in (i) full-frame mode with 19,584 recording sites and (ii) high-signal-to-noise mode with 246 channels. We set out to demonstrate the capabilities of this platform with recordings from primary and iPSC-derived neuronal cultures and tissue preparations over several weeks, providing detailed morpho-electrical phenotypic parameters at subcellular, cellular and network level. Moreover, we develop reliable analysis tools, which drastically increase the throughput to infer axonal morphology and conduction speed.


Assuntos
Rede Nervosa/fisiologia , Neurônios/fisiologia , Imagem Óptica/métodos , Análise de Célula Única/métodos , Animais , Axônios , Encéfalo , Células Cultivadas , Células-Tronco Pluripotentes Induzidas , Camundongos , Microeletrodos , Modelos Animais , Rede Nervosa/diagnóstico por imagem , Imagem Óptica/instrumentação , Ratos , Ratos Wistar , Gravação em Vídeo
5.
Nat Commun ; 11(1): 4458, 2020 09 07.
Artigo em Inglês | MEDLINE | ID: mdl-32895383

RESUMO

In rodent models of type 2 diabetes (T2D), sustained remission of hyperglycemia can be induced by a single intracerebroventricular (icv) injection of fibroblast growth factor 1 (FGF1), and the mediobasal hypothalamus (MBH) was recently implicated as the brain area responsible for this effect. To better understand the cellular response to FGF1 in the MBH, we sequenced >79,000 single-cell transcriptomes from the hypothalamus of diabetic Lepob/ob mice obtained on Days 1 and 5 after icv injection of either FGF1 or vehicle. A wide range of transcriptional responses to FGF1 was observed across diverse hypothalamic cell types, with glial cell types responding much more robustly than neurons at both time points. Tanycytes and ependymal cells were the most FGF1-responsive cell type at Day 1, but astrocytes and oligodendrocyte lineage cells subsequently became more responsive. Based on histochemical and ultrastructural evidence of enhanced cell-cell interactions between astrocytes and Agrp neurons (key components of the melanocortin system), we performed a series of studies showing that intact melanocortin signaling is required for the sustained antidiabetic action of FGF1. These data collectively suggest that hypothalamic glial cells are leading targets for the effects of FGF1 and that sustained diabetes remission is dependent on intact melanocortin signaling.


Assuntos
Diabetes Mellitus Experimental/dietoterapia , Diabetes Mellitus Tipo 2/tratamento farmacológico , Fator 1 de Crescimento de Fibroblastos/administração & dosagem , Hipoglicemiantes/administração & dosagem , Hipotálamo/efeitos dos fármacos , Proteínas Recombinantes/administração & dosagem , Proteína Relacionada com Agouti/metabolismo , Animais , Astrócitos/efeitos dos fármacos , Astrócitos/metabolismo , Glicemia/análise , Comunicação Celular , Núcleo Celular/efeitos dos fármacos , Núcleo Celular/metabolismo , Diabetes Mellitus Experimental/sangue , Diabetes Mellitus Experimental/etiologia , Diabetes Mellitus Experimental/patologia , Diabetes Mellitus Tipo 2/sangue , Diabetes Mellitus Tipo 2/etiologia , Diabetes Mellitus Tipo 2/patologia , Dieta Hiperlipídica/efeitos adversos , Sacarose na Dieta/administração & dosagem , Sacarose na Dieta/efeitos adversos , Humanos , Hipotálamo/citologia , Hipotálamo/patologia , Injeções Intraventriculares , Leptina/genética , Masculino , Melanocortinas/metabolismo , Hormônios Estimuladores de Melanócitos/administração & dosagem , Camundongos , Camundongos Knockout , Neurônios/efeitos dos fármacos , Neurônios/metabolismo , Oligodendroglia/efeitos dos fármacos , Oligodendroglia/metabolismo , RNA-Seq , Receptor Tipo 4 de Melanocortina/genética , Receptores de Melanocortina/antagonistas & inibidores , Receptores de Melanocortina/metabolismo , Indução de Remissão/métodos , Transdução de Sinais/efeitos dos fármacos , Análise de Célula Única , Técnicas Estereotáxicas , Transcriptoma/efeitos dos fármacos
6.
Nat Commun ; 11(1): 4483, 2020 09 08.
Artigo em Inglês | MEDLINE | ID: mdl-32900993

RESUMO

The Drosophila lymph gland, the larval hematopoietic organ comprised of prohemocytes and mature hemocytes, has been a valuable model for understanding mechanisms underlying hematopoiesis and immunity. Three types of mature hemocytes have been characterized in the lymph gland: plasmatocytes, lamellocytes, and crystal cells, which are analogous to vertebrate myeloid cells, yet molecular underpinnings of the lymph gland hemocytes have been less investigated. Here, we use single-cell RNA sequencing to comprehensively analyze heterogeneity of developing hemocytes in the lymph gland, and discover previously undescribed hemocyte types including adipohemocytes, stem-like prohemocytes, and intermediate prohemocytes. Additionally, we identify the developmental trajectory of hemocytes during normal development as well as the emergence of the lamellocyte lineage following active cellular immunity caused by wasp infestation. Finally, we establish similarities and differences between embryonically derived- and larval lymph gland hemocytes. Altogether, our study provides detailed insights into the hemocyte development and cellular immune responses at single-cell resolution.


Assuntos
Drosophila melanogaster/citologia , Drosophila melanogaster/genética , Hemócitos/citologia , Hemócitos/metabolismo , Transcriptoma , Animais , Animais Geneticamente Modificados , Diferenciação Celular/genética , Linhagem da Célula/genética , Drosophila melanogaster/metabolismo , Ectoparasitoses/genética , Ectoparasitoses/metabolismo , Ectoparasitoses/patologia , Perfilação da Expressão Gênica , Hematopoese/genética , Interações Hospedeiro-Parasita/genética , Interações Hospedeiro-Parasita/fisiologia , Tecido Linfoide/citologia , Tecido Linfoide/metabolismo , Tecido Linfoide/parasitologia , RNA-Seq , Análise de Célula Única , Vespas/patogenicidade
7.
Nat Commun ; 11(1): 4477, 2020 09 08.
Artigo em Inglês | MEDLINE | ID: mdl-32901019

RESUMO

Individual cells detach from cohesive ensembles during development and can inappropriately separate in disease. Although much is known about how cells separate from epithelia, it remains unclear how cells disperse from clusters lacking apical-basal polarity, a hallmark of advanced epithelial cancers. Here, using live imaging of the developmental migration program of Drosophila primordial germ cells (PGCs), we show that cluster dispersal is accomplished by stabilizing and orienting migratory forces. PGCs utilize a G protein coupled receptor (GPCR), Tre1, to guide front-back migratory polarity radially from the cluster toward the endoderm. Posteriorly positioned myosin-dependent contractile forces pull on cell-cell contacts until cells release. Tre1 mutant cells migrate randomly with transient enrichment of the force machinery but fail to separate, indicating a temporal contractile force threshold for detachment. E-cadherin is retained on the cell surface during cell separation and augmenting cell-cell adhesion does not impede detachment. Notably, coordinated migration improves cluster dispersal efficiency by stabilizing cell-cell interfaces and facilitating symmetric pulling. We demonstrate that guidance of inherent migratory forces is sufficient to disperse cell clusters under physiological settings and present a paradigm for how such events could occur across development and disease.


Assuntos
Drosophila melanogaster/embriologia , Células Germinativas Embrionárias/fisiologia , Animais , Animais Geneticamente Modificados , Fenômenos Biomecânicos , Padronização Corporal/fisiologia , Caderinas/metabolismo , Adesão Celular/fisiologia , Movimento Celular/fisiologia , Proteínas de Drosophila/metabolismo , Drosophila melanogaster/citologia , Drosophila melanogaster/fisiologia , Células Germinativas Embrionárias/citologia , Microscopia de Fluorescência por Excitação Multifotônica , Miosina Tipo II/metabolismo , Transdução de Sinais , Análise de Célula Única , Proteínas rho de Ligação ao GTP/metabolismo
8.
Nat Commun ; 11(1): 4549, 2020 09 11.
Artigo em Inglês | MEDLINE | ID: mdl-32917889

RESUMO

Arterial macrophages have different developmental origins, but the association of macrophage ontogeny with their phenotypes and functions in adulthood is still unclear. Here, we combine macrophage fate-mapping analysis with single-cell RNA sequencing to establish their cellular identity during homeostasis, and in response to angiotensin-II (AngII)-induced arterial inflammation. Yolk sac erythro-myeloid progenitors (EMP) contribute substantially to adventitial macrophages and give rise to a defined cluster of resident immune cells with homeostatic functions that is stable in adult mice, but declines in numbers during ageing and is not replenished by bone marrow (BM)-derived macrophages. In response to AngII inflammation, increase in adventitial macrophages is driven by recruitment of BM monocytes, while EMP-derived macrophages proliferate locally and provide a distinct transcriptional response that is linked to tissue regeneration. Our findings thus contribute to the understanding of macrophage heterogeneity, and associate macrophage ontogeny with distinct functions in health and disease.


Assuntos
Artérias/citologia , Arterite/imunologia , Diferenciação Celular/fisiologia , Homeostase/fisiologia , Macrófagos/fisiologia , Envelhecimento/fisiologia , Angiotensina II/administração & dosagem , Angiotensina II/imunologia , Animais , Artérias/fisiologia , Medula Óssea/fisiologia , Transplante de Medula Óssea , Linhagem da Célula , Modelos Animais de Doenças , Feminino , Células-Tronco Hematopoéticas/fisiologia , Humanos , Masculino , Camundongos , Camundongos Transgênicos , RNA-Seq , Regeneração/fisiologia , Análise de Célula Única , Quimeras de Transplante
9.
Nat Commun ; 11(1): 4516, 2020 09 09.
Artigo em Inglês | MEDLINE | ID: mdl-32908137

RESUMO

Acinar metaplasia is an initial step in a series of events that can lead to pancreatic cancer. Here we perform single-cell RNA-sequencing of mouse pancreas during the progression from preinvasive stages to tumor formation. Using a reporter gene, we identify metaplastic cells that originated from acinar cells and express two transcription factors, Onecut2 and Foxq1. Further analyses of metaplastic acinar cell heterogeneity define six acinar metaplastic cell types and states, including stomach-specific cell types. Localization of metaplastic cell types and mixture of different metaplastic cell types in the same pre-malignant lesion is shown. Finally, single-cell transcriptome analyses of tumor-associated stromal, immune, endothelial and fibroblast cells identify signals that may support tumor development, as well as the recruitment and education of immune cells. Our findings are consistent with the early, premalignant formation of an immunosuppressive environment mediated by interactions between acinar metaplastic cells and other cells in the microenvironment.


Assuntos
Células Acinares/patologia , Carcinoma Ductal Pancreático/genética , Regulação Neoplásica da Expressão Gênica , Pâncreas/patologia , Neoplasias Pancreáticas/genética , Lesões Pré-Cancerosas/genética , Animais , Animais Geneticamente Modificados , Biópsia , Carcinoma Ductal Pancreático/mortalidade , Carcinoma Ductal Pancreático/patologia , Carcinoma Ductal Pancreático/cirurgia , Diferenciação Celular , Modelos Animais de Doenças , Feminino , Fatores de Transcrição Forkhead/genética , Fatores de Transcrição Forkhead/metabolismo , Heterogeneidade Genética , Proteínas de Homeodomínio/genética , Proteínas de Homeodomínio/metabolismo , Humanos , Estimativa de Kaplan-Meier , Masculino , Metaplasia/genética , Camundongos , Mutação , Pâncreas/citologia , Pâncreas/cirurgia , Pancreatectomia , Neoplasias Pancreáticas/mortalidade , Neoplasias Pancreáticas/patologia , Neoplasias Pancreáticas/cirurgia , Lesões Pré-Cancerosas/patologia , Proteínas Proto-Oncogênicas p21(ras)/genética , RNA-Seq , Análise de Célula Única , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Microambiente Tumoral/genética
10.
Nat Commun ; 11(1): 4498, 2020 09 09.
Artigo em Inglês | MEDLINE | ID: mdl-32908142

RESUMO

The androgen receptor (AR) is the master regulator of prostate cancer (PCa) development, and inhibition of AR signalling is the most effective PCa treatment. AR is expressed in PCa cells and also in the PCa-associated stroma, including infiltrating macrophages. Macrophages have a decisive function in PCa initiation and progression, but the role of AR in macrophages remains largely unexplored. Here, we show that AR signalling in the macrophage-like THP-1 cell line supports PCa cell line migration and invasion in culture via increased Triggering Receptor Expressed on Myeloid cells-1 (TREM-1) signalling and expression of its downstream cytokines. Moreover, AR signalling in THP-1 and monocyte-derived macrophages upregulates IL-10 and markers of tissue residency. In conclusion, our data suggest that AR signalling in macrophages may support PCa invasiveness, and blocking this process may constitute one mechanism of anti-androgen therapy.


Assuntos
Macrófagos/metabolismo , Neoplasias da Próstata/patologia , Receptores Androgênicos/metabolismo , Receptor Gatilho 1 Expresso em Células Mieloides/metabolismo , Idoso , Antagonistas de Androgênios/farmacologia , Antagonistas de Androgênios/uso terapêutico , Anilidas/farmacologia , Anilidas/uso terapêutico , Biópsia , Buffy Coat/citologia , Estudos de Casos e Controles , Linhagem Celular Tumoral , Movimento Celular/efeitos dos fármacos , Movimento Celular/imunologia , Quimioterapia Adjuvante , Técnicas de Cocultura , Intervalo Livre de Doença , Humanos , Macrófagos/imunologia , Masculino , Pessoa de Meia-Idade , Terapia Neoadjuvante , Invasividade Neoplásica/imunologia , Invasividade Neoplásica/prevenção & controle , Nitrilos/farmacologia , Nitrilos/uso terapêutico , Intervalo Livre de Progressão , Próstata/patologia , Próstata/cirurgia , Prostatectomia , Neoplasias da Próstata/imunologia , Neoplasias da Próstata/mortalidade , Neoplasias da Próstata/terapia , Procedimentos Cirúrgicos Robóticos , Transdução de Sinais/imunologia , Análise de Célula Única , Células THP-1 , Compostos de Tosil/farmacologia , Compostos de Tosil/uso terapêutico
11.
BMC Bioinformatics ; 21(Suppl 13): 392, 2020 Sep 17.
Artigo em Inglês | MEDLINE | ID: mdl-32938367

RESUMO

BACKGROUND: In recent years, the rapid development of single-cell RNA-sequencing (scRNA-seq) techniques enables the quantitative characterization of cell types at a single-cell resolution. With the explosive growth of the number of cells profiled in individual scRNA-seq experiments, there is a demand for novel computational methods for classifying newly-generated scRNA-seq data onto annotated labels. Although several methods have recently been proposed for the cell-type classification of single-cell transcriptomic data, such limitations as inadequate accuracy, inferior robustness, and low stability greatly limit their wide applications. RESULTS: We propose a novel ensemble approach, named EnClaSC, for accurate and robust cell-type classification of single-cell transcriptomic data. Through comprehensive validation experiments, we demonstrate that EnClaSC can not only be applied to the self-projection within a specific dataset and the cell-type classification across different datasets, but also scale up well to various data dimensionality and different data sparsity. We further illustrate the ability of EnClaSC to effectively make cross-species classification, which may shed light on the studies in correlation of different species. EnClaSC is freely available at https://github.com/xy-chen16/EnClaSC . CONCLUSIONS: EnClaSC enables highly accurate and robust cell-type classification of single-cell transcriptomic data via an ensemble learning method. We expect to see wide applications of our method to not only transcriptome studies, but also the classification of more general data.


Assuntos
Análise de Célula Única/métodos , Transcriptoma/genética , Humanos , Projetos de Pesquisa
12.
Nat Commun ; 11(1): 4375, 2020 09 01.
Artigo em Inglês | MEDLINE | ID: mdl-32873797

RESUMO

In the testis, interstitial macrophages are thought to be derived from the yolk sac during fetal development, and later replaced by bone marrow-derived macrophages. By contrast, the peritubular macrophages have been reported to emerge first in the postnatal testis and solely represent descendants of bone marrow-derived monocytes. Here, we define new monocyte and macrophage types in the fetal and postnatal testis using high-dimensional single-cell analyses. Our results show that interstitial macrophages have a dominant contribution from fetal liver-derived precursors, while peritubular macrophages are generated already at birth from embryonic precursors. We find that bone marrow-derived monocytes do not substantially contribute to the replenishment of the testicular macrophage pool even after systemic macrophage depletion. The presence of macrophages prenatally, but not postnatally, is necessary for normal spermatogenesis. Our multifaceted data thus challenge the current paradigms in testicular macrophage biology by delineating their differentiation, homeostasis and functions.


Assuntos
Macrófagos/fisiologia , Testículo/crescimento & desenvolvimento , Animais , Animais Recém-Nascidos , Diferenciação Celular , Embrião de Mamíferos , Feminino , Masculino , Camundongos , Camundongos Knockout , Monócitos/fisiologia , Análise de Célula Única , Espermatogênese/fisiologia
13.
Nat Commun ; 11(1): 4301, 2020 09 02.
Artigo em Inglês | MEDLINE | ID: mdl-32879317

RESUMO

Copy-number aberrations (CNAs) and whole-genome duplications (WGDs) are frequent somatic mutations in cancer but their quantification from DNA sequencing of bulk tumor samples is challenging. Standard methods for CNA inference analyze tumor samples individually; however, DNA sequencing of multiple samples from a cancer patient has recently become more common. We introduce HATCHet (Holistic Allele-specific Tumor Copy-number Heterogeneity), an algorithm that infers allele- and clone-specific CNAs and WGDs jointly across multiple tumor samples from the same patient. We show that HATCHet outperforms current state-of-the-art methods on multi-sample DNA sequencing data that we simulate using MASCoTE (Multiple Allele-specific Simulation of Copy-number Tumor Evolution). Applying HATCHet to 84 tumor samples from 14 prostate and pancreas cancer patients, we identify subclonal CNAs and WGDs that are more plausible than previously published analyses and more consistent with somatic single-nucleotide variants (SNVs) and small indels in the same samples.


Assuntos
Neoplasias da Mama/genética , Variações do Número de Cópias de DNA , Duplicação Gênica , Neoplasias Pancreáticas/genética , Neoplasias da Próstata/genética , Neoplasias da Mama/patologia , Conjuntos de Dados como Assunto , Feminino , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Mutação INDEL , Masculino , Taxa de Mutação , Metástase Neoplásica/genética , Neoplasias Pancreáticas/patologia , Polimorfismo de Nucleotídeo Único , Neoplasias da Próstata/patologia , Análise de Célula Única , Sequenciamento Completo do Exoma
14.
Medicine (Baltimore) ; 99(33): e21707, 2020 Aug 14.
Artigo em Inglês | MEDLINE | ID: mdl-32872047

RESUMO

Osteoarthritis (OA) is a chronic degenerative joint disease with its onset closely related to the growth of synovial fibroblasts (SFs), yet the genes involved in are few reported. In our study, we aimed to identify the OA-associated key gene and pathways via the single-cell RNA sequencing (scRNA-seq) analysis on SFs.scRNA-seq data of SFs from OA sufferers were accessed from GEO database, then the genes involved in were subjected to principal component analysis (PCA) and T-Stochastic Neighbor Embedding (TSNE) Analysis. GO and KEGG enrichment analyses were performed to find the most enriched functions and pathways associated with marker genes and a PPI network was constructed to identify the key gene associated with OA occurrence.Findings revealed that marker genes in three cell types identified by TSNE were mainly activated in pathways firmly related to fibroblasts growth, such as extracellular matrix, immune and cell adhesion molecule binding-associated functions and pathways. Moreover, fibronectin1 (FN1) was validated as the key gene that was tightly related to the growth of SFs, as well as had the potential to play a key role in OA occurrence.Our study explored the key gene and pathways associated with OA occurrence, which were of great value in further investigation of OA diagnosis as well as pathogenesis.


Assuntos
Fibroblastos/metabolismo , Fibronectinas/genética , Osteoartrite/genética , Humanos , Osteoartrite/metabolismo , Mapas de Interação de Proteínas , Análise de Sequência de RNA , Análise de Célula Única , Membrana Sinovial/citologia
15.
Nat Commun ; 11(1): 4360, 2020 08 31.
Artigo em Inglês | MEDLINE | ID: mdl-32868762

RESUMO

The hypothalamus is a central regulator of many innate behaviors essential for survival, but the molecular mechanisms controlling hypothalamic patterning and cell fate specification are poorly understood. To identify genes that control hypothalamic development, we have used single-cell RNA sequencing (scRNA-Seq) to profile mouse hypothalamic gene expression across 12 developmental time points between embryonic day 10 and postnatal day 45. This identified genes that delineated clear developmental trajectories for all major hypothalamic cell types, and readily distinguished major regional subdivisions of the developing hypothalamus. By using our developmental dataset, we were able to rapidly annotate previously unidentified clusters from existing scRNA-Seq datasets collected during development and to identify the developmental origins of major neuronal populations of the ventromedial hypothalamus. We further show that our approach can rapidly and comprehensively characterize mutants that have altered hypothalamic patterning, identifying Nkx2.1 as a negative regulator of prethalamic identity. These data serve as a resource for further studies of hypothalamic development, physiology, and dysfunction.


Assuntos
Diferenciação Celular , Hipotálamo , Neurônios/metabolismo , Fator Nuclear 1 de Tireoide/metabolismo , Animais , Sequência de Bases , Padronização Corporal , Regulação da Expressão Gênica no Desenvolvimento , Hipotálamo/citologia , Hipotálamo/embriologia , Hipotálamo/crescimento & desenvolvimento , Hipotálamo/metabolismo , Camundongos , Mutação , Análise de Célula Única , Fator Nuclear 1 de Tireoide/genética
16.
PLoS Comput Biol ; 16(9): e1008195, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32898151

RESUMO

We present VALERIE (Visualising alternative splicing events from single-cell ribonucleic acid-sequencing experiments), an R package for visualising alternative splicing events at single-cell resolution. To explore any given specified genomic region, corresponding to an alternative splicing event, VALERIE generates an ensemble of informative plots to visualise cell-to-cell heterogeneity of alternative splicing profiles across single cells and performs statistical tests to compare percent spliced-in (PSI) values across the user-defined groups of cells. Among the features available, VALERIE displays PSI values, in lieu of read coverage, which is more suitable for representing alternative splicing profiles for a large number of samples typically generated by single-cell RNA-sequencing experiments. VALERIE is available on the Comprehensive R Archive Network (CRAN): https://cran.r-project.org/web/packages/VALERIE/index.html.


Assuntos
Processamento Alternativo/genética , Análise de Sequência de RNA/métodos , Análise de Célula Única/métodos , Software , Animais , Células Cultivadas , Biologia Computacional , Camundongos
17.
PLoS Comput Biol ; 16(9): e1008205, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32903255

RESUMO

Single-cell RNA sequencing (scRNA-seq) can map cell types, states and transitions during dynamic biological processes such as tissue development and regeneration. Many trajectory inference methods have been developed to order cells by their progression through a dynamic process. However, when time series data is available, most of these methods do not consider the available time information when ordering cells and are instead designed to work only on a single scRNA-seq data snapshot. We present Tempora, a novel cell trajectory inference method that orders cells using time information from time-series scRNA-seq data. In performance comparison tests, Tempora inferred known developmental lineages from three diverse tissue development time series data sets, beating state of the art methods in accuracy and speed. Tempora works at the level of cell clusters (types) and uses biological pathway information to help identify cell type relationships. This approach increases gene expression signal from single cells, processing speed, and interpretability of the inferred trajectory. Our results demonstrate the utility of a combination of time and pathway information to supervise trajectory inference for scRNA-seq based analysis.


Assuntos
Biologia Computacional/métodos , Perfilação da Expressão Gênica/métodos , Análise de Sequência de RNA/métodos , Análise de Célula Única/métodos , Software , Algoritmos , Animais , Células Cultivadas , Humanos , Camundongos , Mioblastos/metabolismo , RNA/genética , RNA/metabolismo , Reprodutibilidade dos Testes
18.
PLoS Comput Biol ; 16(9): e1008182, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32931516

RESUMO

Recent advances in experimental biology allow creation of datasets where several genome-wide data types (called omics) are measured per sample. Integrative analysis of multi-omic datasets in general, and clustering of samples in such datasets specifically, can improve our understanding of biological processes and discover different disease subtypes. In this work we present MONET (Multi Omic clustering by Non-Exhaustive Types), which presents a unique approach to multi-omic clustering. MONET discovers modules of similar samples, such that each module is allowed to have a clustering structure for only a subset of the omics. This approach differs from most existent multi-omic clustering algorithms, which assume a common structure across all omics, and from several recent algorithms that model distinct cluster structures. We tested MONET extensively on simulated data, on an image dataset, and on ten multi-omic cancer datasets from TCGA. Our analysis shows that MONET compares favorably with other multi-omic clustering methods. We demonstrate MONET's biological and clinical relevance by analyzing its results for Ovarian Serous Cystadenocarcinoma. We also show that MONET is robust to missing data, can cluster genes in multi-omic dataset, and reveal modules of cell types in single-cell multi-omic data. Our work shows that MONET is a valuable tool that can provide complementary results to those provided by existent algorithms for multi-omic analysis.


Assuntos
Algoritmos , Genômica/métodos , Análise por Conglomerados , Bases de Dados Genéticas , Humanos , Neoplasias/genética , Neoplasias/metabolismo , Análise de Célula Única
19.
PLoS Comput Biol ; 16(9): e1008173, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32946435

RESUMO

Single-cell Hi-C (scHi-C) interrogates genome-wide chromatin interaction in individual cells, allowing us to gain insights into 3D genome organization. However, the extremely sparse nature of scHi-C data poses a significant barrier to analysis, limiting our ability to tease out hidden biological information. In this work, we approach this problem by applying topic modeling to scHi-C data. Topic modeling is well-suited for discovering latent topics in a collection of discrete data. For our analysis, we generate nine different single-cell combinatorial indexed Hi-C (sci-Hi-C) libraries from five human cell lines (GM12878, H1Esc, HFF, IMR90, and HAP1), consisting over 19,000 cells. We demonstrate that topic modeling is able to successfully capture cell type differences from sci-Hi-C data in the form of "chromatin topics." We further show enrichment of particular compartment structures associated with locus pairs in these topics.


Assuntos
Cromatina , Biologia Computacional/métodos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Análise de Célula Única/métodos , Linhagem Celular , Cromatina/química , Cromatina/genética , Análise por Conglomerados , Biblioteca Gênica , Humanos , Processamento de Linguagem Natural
20.
Front Immunol ; 11: 2145, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32983174

RESUMO

SARS-CoV-2 infection has recently been declared a pandemic. Some patients showing severe symptoms exhibit drastic inflammation and airway damage. In this study, we re-analyzed published scRNA-seq data of COVID-19 patient bronchoalveolar lavage fluid to further classify and compare immunological features according to the patient's disease severity. Patients with severe symptoms showed DNA damage and apoptotic features of epithelial cells. Our results suggested that epithelial damage was associated with neutrophil infiltration. Myeloid cells of severe patients showed higher expression of proinflammatory cytokines and chemokines such as CXCL8. As a result, neutrophils were abundant in lungs of patients from the severe group. Furthermore, recruited neutrophils highly expressed genes related to neutrophil extracellular traps. Neutrophil-mediated inflammation was regulated by glucocorticoid receptor expression and activity. Based on these results, we suggest that severe COVID-19 symptoms may be determined by differential expression of glucocorticoid receptors and neutrophils.


Assuntos
Betacoronavirus/imunologia , Infecções por Coronavirus/imunologia , Interleucina-8/genética , Neutrófilos/imunologia , Pneumonia Viral/imunologia , Receptores de Glucocorticoides/genética , Índice de Gravidade de Doença , Transcriptoma , Adulto , Idoso , Líquido da Lavagem Broncoalveolar/imunologia , Infecções por Coronavirus/virologia , Células Epiteliais/patologia , Armadilhas Extracelulares/imunologia , Feminino , Perfilação da Expressão Gênica/métodos , Humanos , Inflamação/imunologia , Interleucina-8/metabolismo , Masculino , Pessoa de Meia-Idade , Células Mieloides/imunologia , Infiltração de Neutrófilos/imunologia , Pandemias , Pneumonia Viral/virologia , RNA-Seq , Receptores de Glucocorticoides/metabolismo , Análise de Célula Única/métodos
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