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2.
PLoS One ; 15(7): e0235864, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32645101

RESUMO

In eukaryotic cells, KDEL receptors (KDELRs) facilitate the retrieval of endoplasmic reticulum (ER) luminal proteins from the Golgi compartment back to the ER. Apart from the well-documented retention function, recent findings reveal that the cellular KDELRs have more complex roles, e.g. in cell signalling, protein secretion, cell adhesion and tumorigenesis. Furthermore, several studies suggest that a sub-population of KDELRs is located at the cell surface, where they could form and internalize KDELR/cargo clusters after K/HDEL-ligand binding. However, so far it has been unclear whether there are species- or cell-type-specific differences in KDELR clustering. By comparing ligand-induced KDELR clustering in different mouse and human cell lines via live cell imaging, we show that macrophage cell lines from both species do not develop any clusters. Using RT-qPCR experiments and numerical analysis, we address the role of KDELR expression as well as endocytosis and exocytosis rates on the receptor clustering at the plasma membrane and discuss how the efficiency of directed transport to preferred docking sites on the membrane influences the exponent of the power-law distribution of the cluster size.


Assuntos
Receptores de Peptídeos/metabolismo , Proteínas de Transporte Vesicular/metabolismo , Animais , Linhagem Celular , Membrana Celular/metabolismo , Endocitose , Exocitose , Expressão Gênica , Humanos , Macrófagos/metabolismo , Camundongos , Transporte Proteico , RNA Mensageiro/análise , RNA Mensageiro/genética , Receptores de Peptídeos/análise , Receptores de Peptídeos/genética , Proteínas de Transporte Vesicular/análise , Proteínas de Transporte Vesicular/genética
3.
Cytogenet Genome Res ; 160(5): 255-263, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32544910

RESUMO

Fusions of the Runt-related transcription factor 1 (RUNX1) with different partner genes have been associated with various hematological disorders. Interestingly, the C-terminally truncated form of RUNX1 and RUNX1 fusion proteins are similarly considered important contributors to leukemogenesis. Here, we describe a 59-year-old male patient who was initially diagnosed with acute myeloid leukemia, inv(16)(p13;q22)/CBFB-MYH11 (FAB classification M4Eo). He achieved complete remission and negative CBFB-MYH11 status with daunorubicin/cytarabine combination chemotherapy but relapsed 3 years later. Cytogenetic analysis of relapsed leukemia cells revealed CBFB-MYH11 negativity and complex chromosomal abnormalities without inv(16)(p13;q22). RNA-seq identified the glutamate receptor, ionotropic, kinase 2 (GRIK2) gene on 6q16 as a novel fusion partner for RUNX1 in this case. Specifically, the fusion of RUNX1 to the GRIK2 antisense strand (RUNX1-GRIK2as) generated multiple missplicing transcripts. Because extremely low levels of wild-type GRIK2 were detected in leukemia cells, RUNX1-GRIK2as was thought to drive the pathogenesis associated with the RUNX1-GRIK2 fusion. The truncated RUNX1 generated from RUNX1-GRIK2as induced the expression of the granulocyte colony-stimulating factor (G-CSF) receptor on 32D myeloid leukemia cells and enhanced proliferation in response to G-CSF. In summary, the RUNX1-GRIK2as fusion emphasizes the importance of aberrantly truncated RUNX1 in leukemogenesis.


Assuntos
Subunidade alfa 2 de Fator de Ligação ao Core/genética , DNA Antissenso/genética , Fusão Gênica/genética , Fator Estimulador de Colônias de Granulócitos/farmacologia , Leucemia Mieloide Aguda/genética , Receptores de Ácido Caínico/genética , Deleção de Sequência/genética , Translocação Genética/genética , Proliferação de Células/efeitos dos fármacos , Humanos , Leucemia Mieloide Aguda/diagnóstico , Leucemia Mieloide Aguda/metabolismo , Leucemia Mieloide Aguda/patologia , Masculino , Pessoa de Meia-Idade , Reação em Cadeia da Polimerase , RNA Mensageiro/análise , RNA Mensageiro/genética , Receptores de Fator Estimulador de Colônias de Granulócitos/biossíntese , Receptores de Fator Estimulador de Colônias de Granulócitos/metabolismo
4.
Nature ; 582(7811): 240-245, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32499647

RESUMO

Meta-analyses of genome-wide association studies (GWAS) have identified more than 240 loci that are associated with type 2 diabetes (T2D)1,2; however, most of these loci have been identified in analyses of individuals with European ancestry. Here, to examine T2D risk in East Asian individuals, we carried out a meta-analysis of GWAS data from 77,418 individuals with T2D and 356,122 healthy control individuals. In the main analysis, we identified 301 distinct association signals at 183 loci, and across T2D association models with and without consideration of body mass index and sex, we identified 61 loci that are newly implicated in predisposition to T2D. Common variants associated with T2D in both East Asian and European populations exhibited strongly correlated effect sizes. Previously undescribed associations include signals in or near GDAP1, PTF1A, SIX3, ALDH2, a microRNA cluster, and genes that affect the differentiation of muscle and adipose cells3. At another locus, expression quantitative trait loci at two overlapping T2D signals affect two genes-NKX6-3 and ANK1-in different tissues4-6. Association studies in diverse populations identify additional loci and elucidate disease-associated genes, biology, and pathways.


Assuntos
Grupo com Ancestrais do Continente Asiático/genética , Diabetes Mellitus Tipo 2/genética , Predisposição Genética para Doença , Aldeído-Desidrogenase Mitocondrial/genética , Alelos , Anquirinas/genética , Índice de Massa Corporal , Estudos de Casos e Controles , Europa (Continente)/etnologia , Proteínas do Olho/genética , Extremo Oriente/etnologia , Feminino , Estudo de Associação Genômica Ampla , Proteínas de Homeodomínio/genética , Humanos , Masculino , Proteínas do Tecido Nervoso/genética , RNA Mensageiro/análise , Fatores de Transcrição/genética , Transcrição Genética
6.
Nucleic Acids Res ; 48(11): e66, 2020 06 19.
Artigo em Inglês | MEDLINE | ID: mdl-32383753

RESUMO

Multiplex single-molecule fluorescent in situ hybridization (smFISH) is a powerful method for validating RNA sequencing and emerging spatial transcriptomic data, but quantification remains a computational challenge. We present a framework for generating and analyzing smFISH data in complex tissues while overcoming autofluorescence and increasing multiplexing capacity. We developed dotdotdot (https://github.com/LieberInstitute/dotdotdot) as a corresponding software package to quantify RNA transcripts in single nuclei and perform differential expression analysis. We first demonstrate robustness of our platform in single mouse neurons by quantifying differential expression of activity-regulated genes. We then quantify spatial gene expression in human dorsolateral prefrontal cortex (DLPFC) using spectral imaging and dotdotdot to mask lipofuscin autofluorescence. We lastly apply machine learning to predict cell types and perform downstream cell type-specific expression analysis. In summary, we provide experimental workflows, imaging acquisition and analytic strategies for quantification and biological interpretation of smFISH data in complex tissues.


Assuntos
Automação , Hibridização in Situ Fluorescente/métodos , Imagem Individual de Molécula , Software , Adolescente , Adulto , Animais , Humanos , Processamento de Imagem Assistida por Computador , Lipofuscina/análise , Aprendizado de Máquina , Masculino , Camundongos , Neurônios/citologia , Neurônios/metabolismo , Especificidade de Órgãos , Córtex Pré-Frontal/citologia , Córtex Pré-Frontal/metabolismo , RNA Mensageiro/análise
7.
Braz Oral Res ; 34: e038, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32374812

RESUMO

The possible role of B-cell growth and differentiation-related cytokines on the pathogenesis of diabetes-related periodontitis has not been addressed so far. The aim of this study was to evaluate the effects of diabetes mellitus (DM) on the gene expression of proliferation-inducing ligand (APRIL) and B-lymphocyte stimulator (BLyS), two major cytokines associated to survival, differentiation and maturation of B cells in biopsies from gingival tissue with periodontitis. Gingival biopsies were obtained from subjects with periodontitis (n = 17), with periodontitis and DM (n = 19) as well as from periodontally and systemically healthy controls (n = 10). Gene expressions for APRIL, BLyS, RANKL, OPG, TRAP and DC-STAMP were evaluated using qPCR. The expressions APRIL, BLyS, RANKL, OPG, TRAP and DC-STAMP were all higher in both periodontitis groups when compared to the control group (p < 0.05). Furthermore, the expressions of BLyS, TRAP and RANKL were significantly higher in the subjects with periodontitis and DM when compared to those with periodontitis alone (p < 0.05). The mRNA levels of BLyS correlated positively with RANKL in the subjects with periodontitis and DM (p < 0.05). BLyS is overexpressed in periodontitis tissues of subjects with type 2 DM, suggesting a possible role of this cytokine on the pathogenesis DM-related periodontitis.


Assuntos
Fator Ativador de Células B/análise , Diabetes Mellitus Tipo 2/complicações , Periodontite/imunologia , Periodontite/patologia , Adulto , Idoso , Biomarcadores/análise , Biópsia , Estudos de Casos e Controles , Citocinas/análise , Citocinas/fisiologia , Diabetes Mellitus Tipo 2/imunologia , Feminino , Expressão Gênica , Gengiva/imunologia , Gengiva/patologia , Humanos , Masculino , Pessoa de Meia-Idade , Osteogênese/imunologia , RNA Mensageiro/análise , Reação em Cadeia da Polimerase em Tempo Real , Valores de Referência , Estatísticas não Paramétricas , Membro 13 da Superfamília de Ligantes de Fatores de Necrose Tumoral/análise
8.
J Appl Oral Sci ; 28: e20190699, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32401938

RESUMO

Purpose To evaluate the kinetics of apical periodontitis development in vivo , induced either by contamination of the root canals by microorganisms from the oral cavity or by inoculation of bacterial lipopolysaccharide (LPS) and the regulation of major enzymes and receptors involved in the arachidonic acid metabolism. Methodology Apical periodontitis was induced in C57BL6 mice (n=96), by root canal exposure to oral cavity (n=48 teeth) or inoculation of LPS (10 µL of a suspension of 0.1 µg/µL) from E. coli into the root canals (n= 48 teeth). Healthy teeth were used as control (n=48 teeth). After 7, 14, 21 and 28 days the animals were euthanized and tissues removed for histopathological and qRT-PCR analyses. Histological analysis data were analyzed using two-way ANOVA followed by Sidak's test, and qRT-PCR data using two-way ANOVA followed by Tukey's test (α=0.05). Results Contamination by microorganisms led to the development of apical periodontitis, characterized by the recruitment of inflammatory cells and bone tissue resorption, whereas inoculation of LPS induced inflammatory cells recruitment without bone resorption. Both stimuli induced mRNA expression for cyclooxygenase-2 and 5-lipoxygenase enzymes. Expression of prostaglandin E 2 and leukotriene B 4 cell surface receptors were more stimulated by LPS. Regarding nuclear peroxisome proliferator-activated receptors (PPAR), oral contamination induced the synthesis of mRNA for PPARδ, differently from inoculation of LPS, that induced PPARα and PPARγ expression. Conclusions Contamination of the root canals by microorganisms from oral cavity induced the development of apical periodontitis differently than by inoculation with LPS, characterized by less bone loss than the first model. Regardless of the model used, it was found a local increase in the synthesis of mRNA for the enzymes 5-lipoxygenase and cyclooxygenase-2 of the arachidonic acid metabolism, as well as in the surface and nuclear receptors for the lipid mediators prostaglandin E2 and leukotriene B4.


Assuntos
Cavidade Pulpar/microbiologia , Dinoprostona/metabolismo , Leucotrieno B4/metabolismo , Lipopolissacarídeos/metabolismo , Periodontite Periapical/microbiologia , Animais , Araquidonato 5-Lipoxigenase/análise , Araquidonato 5-Lipoxigenase/metabolismo , Reabsorção Óssea/metabolismo , Reabsorção Óssea/microbiologia , Ciclo-Oxigenase 2/análise , Ciclo-Oxigenase 2/metabolismo , Cavidade Pulpar/metabolismo , Cavidade Pulpar/patologia , Dinoprostona/análise , Expressão Gênica , Leucotrieno B4/análise , Masculino , Camundongos Endogâmicos C57BL , Periodontite Periapical/metabolismo , Periodontite Periapical/patologia , RNA Mensageiro/análise , RNA Mensageiro/metabolismo , Distribuição Aleatória , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Fatores de Tempo
10.
Nucleic Acids Res ; 48(W1): W239-W243, 2020 07 02.
Artigo em Inglês | MEDLINE | ID: mdl-32421834

RESUMO

Recent evidences suggest that the localization of mRNAs near the subcellular compartment of the translated proteins is a more robust cellular tool, which optimizes protein expression, post-transcriptionally. Retention of mRNA in the nucleus can regulate the amount of protein translated from each mRNA, thus allowing a tight temporal regulation of translation or buffering of protein levels from bursty transcription. Besides, mRNA localization performs a variety of additional roles like long-distance signaling, facilitating assembly of protein complexes and coordination of developmental processes. Here, we describe a novel machine-learning based tool, mRNALoc, to predict five sub-cellular locations of eukaryotic mRNAs using cDNA/mRNA sequences. During five fold cross-validations, the maximum overall accuracy was 65.19, 75.36, 67.10, 99.70 and 73.59% for the extracellular region, endoplasmic reticulum, cytoplasm, mitochondria, and nucleus, respectively. Assessment on independent datasets revealed the prediction accuracies of 58.10, 69.23, 64.55, 96.88 and 69.35% for extracellular region, endoplasmic reticulum, cytoplasm, mitochondria, and nucleus, respectively. The corresponding values of AUC were 0.76, 0.75, 0.70, 0.98 and 0.74 for the extracellular region, endoplasmic reticulum, cytoplasm, mitochondria, and nucleus, respectively. The mRNALoc standalone software and web-server are freely available for academic use under GNU GPL at http://proteininformatics.org/mkumar/mrnaloc.


Assuntos
RNA Mensageiro/análise , Software , Máquina de Vetores de Suporte , Núcleo Celular/química , Simulação por Computador , Citoplasma/química , Retículo Endoplasmático/química , Mitocôndrias/química , RNA Mensageiro/química , Análise de Sequência de RNA
11.
Nature ; 581(7809): 452-458, 2020 05.
Artigo em Inglês | MEDLINE | ID: mdl-32461655

RESUMO

The acceleration of DNA sequencing in samples from patients and population studies has resulted in extensive catalogues of human genetic variation, but the interpretation of rare genetic variants remains problematic. A notable example of this challenge is the existence of disruptive variants in dosage-sensitive disease genes, even in apparently healthy individuals. Here, by manual curation of putative loss-of-function (pLoF) variants in haploinsufficient disease genes in the Genome Aggregation Database (gnomAD)1, we show that one explanation for this paradox involves alternative splicing of mRNA, which allows exons of a gene to be expressed at varying levels across different cell types. Currently, no existing annotation tool systematically incorporates information about exon expression into the interpretation of variants. We develop a transcript-level annotation metric known as the 'proportion expressed across transcripts', which quantifies isoform expression for variants. We calculate this metric using 11,706 tissue samples from the Genotype Tissue Expression (GTEx) project2 and show that it can differentiate between weakly and highly evolutionarily conserved exons, a proxy for functional importance. We demonstrate that expression-based annotation selectively filters 22.8% of falsely annotated pLoF variants found in haploinsufficient disease genes in gnomAD, while removing less than 4% of high-confidence pathogenic variants in the same genes. Finally, we apply our expression filter to the analysis of de novo variants in patients with autism spectrum disorder and intellectual disability or developmental disorders to show that pLoF variants in weakly expressed regions have similar effect sizes to those of synonymous variants, whereas pLoF variants in highly expressed exons are most strongly enriched among cases. Our annotation is fast, flexible and generalizable, making it possible for any variant file to be annotated with any isoform expression dataset, and will be valuable for the genetic diagnosis of rare diseases, the analysis of rare variant burden in complex disorders, and the curation and prioritization of variants in recall-by-genotype studies.


Assuntos
Doença/genética , Haploinsuficiência/genética , Mutação com Perda de Função/genética , Anotação de Sequência Molecular , Transcrição Genética , Transcriptoma/genética , Transtorno do Espectro Autista/genética , Conjuntos de Dados como Assunto , Deficiências do Desenvolvimento/genética , Éxons/genética , Feminino , Genótipo , Humanos , Deficiência Intelectual/genética , Masculino , Anotação de Sequência Molecular/normas , Distribuição de Poisson , RNA Mensageiro/análise , RNA Mensageiro/genética , Doenças Raras/diagnóstico , Doenças Raras/genética , Reprodutibilidade dos Testes , Sequenciamento Completo do Exoma
12.
PLoS Genet ; 16(4): e1008643, 2020 04.
Artigo em Inglês | MEDLINE | ID: mdl-32294086

RESUMO

Hereditary hearing loss is challenging to diagnose because of the heterogeneity of the causative genes. Further, some genes involved in hereditary hearing loss have yet to be identified. Using whole-exome analysis of three families with congenital, severe-to-profound hearing loss, we identified a missense variant of SLC12A2 in five affected members of one family showing a dominant inheritance mode, along with de novo splice-site and missense variants of SLC12A2 in two sporadic cases, as promising candidates associated with hearing loss. Furthermore, we detected another de novo missense variant of SLC12A2 in a sporadic case. SLC12A2 encodes Na+, K+, 2Cl- cotransporter (NKCC) 1 and plays critical roles in the homeostasis of K+-enriched endolymph. Slc12a2-deficient mice have congenital, profound deafness; however, no human variant of SLC12A2 has been reported as associated with hearing loss. All identified SLC12A2 variants mapped to exon 21 or its 3'-splice site. In vitro analysis indicated that the splice-site variant generates an exon 21-skipped SLC12A2 mRNA transcript expressed at much lower levels than the exon 21-included transcript in the cochlea, suggesting a tissue-specific role for the exon 21-encoded region in the carboy-terminal domain. In vitro functional analysis demonstrated that Cl- influx was significantly decreased in all SLC12A2 variants studied. Immunohistochemistry revealed that SLC12A2 is located on the plasma membrane of several types of cells in the cochlea, including the strial marginal cells, which are critical for endolymph homeostasis. Overall, this study suggests that variants affecting exon 21 of the SLC12A2 transcript are responsible for hereditary hearing loss in humans.


Assuntos
Perda Auditiva Neurossensorial/congênito , Perda Auditiva Neurossensorial/genética , Mutação , Domínios Proteicos/genética , Membro 2 da Família 12 de Carreador de Soluto/química , Membro 2 da Família 12 de Carreador de Soluto/genética , Sequência de Aminoácidos , Animais , Sequência de Bases , Cloretos/metabolismo , Cóclea/metabolismo , Cóclea/patologia , Surdez/congênito , Surdez/genética , Éxons/genética , Feminino , Expressão Gênica , Células HEK293 , Humanos , Lactente , Macaca fascicularis , Masculino , Linhagem , Processamento de RNA , RNA Mensageiro/análise , RNA Mensageiro/genética , Membro 2 da Família 12 de Carreador de Soluto/metabolismo
13.
J Vis Exp ; (157)2020 03 04.
Artigo em Inglês | MEDLINE | ID: mdl-32202522

RESUMO

Quantifying differences in mRNA abundance is a classic approach to understand the impact of a given gene mutation on cell physiology. However, characterizing differences in the translatome (the whole of translated mRNAs) provides an additional layer of information particularly useful when trying to understand the function of RNA regulating or binding proteins. A number of methods for accomplishing this have been developed, including ribosome profiling and polysome analysis. However, both methods carry significant technical challenges and cannot be applied to specific cell populations within a tissue unless combined with additional sorting methods. In contrast, the RiboTag method is a genetic-based, efficient, and technically straightforward alternative that allows the identification of ribosome associated RNAs from specific cell populations without added sorting steps, provided an applicable cell-specific Cre driver is available. This method consists of breeding to generate the genetic models, sample collection, immunoprecipitation, and downstream RNA analyses. Here, we outline this process in adult male mouse germ cells mutant for an RNA binding protein required for male fertility. Special attention is paid to considerations for breeding with a focus on efficient colony management and the generation of correct genetic backgrounds and immunoprecipitation in order to reduce background and optimize output. Discussion of troubleshooting options, additional confirmatory experiments, and potential downstream applications is also included. The presented genetic tools and molecular protocols represent a powerful way to describe the ribosome-associated RNAs of specific cell populations in complex tissues or in systems with aberrant mRNA storage and translation with the goal of informing on the molecular drivers of mutant phenotypes.


Assuntos
Imunoprecipitação/métodos , RNA Mensageiro/análise , RNA Ribossômico/análise , Espermatozoides/metabolismo , Animais , Cruzamento , Feminino , Masculino , Camundongos , Camundongos Transgênicos , Polirribossomos/genética , RNA Ribossômico/metabolismo , Proteínas de Ligação a RNA/genética , Proteínas de Ligação a RNA/metabolismo , Proteínas Ribossômicas/genética , Proteínas Ribossômicas/metabolismo , Ribossomos/genética , Análise de Sequência de RNA/métodos
14.
Poult Sci ; 99(3): 1628-1642, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-32115035

RESUMO

The present study was carried out to investigate the changes in amino acid (AA) contents of crop milk and plasma and mRNA abundance of AA transporters and AA synthesis-related enzymes in the crop tissue of male and female pigeons during incubation and chick-rearing periods. Forty-two pairs of adult White King pigeons with 2 fertile eggs per pair were randomly divided into 7 groups by different breeding stages. The AA content of crop milk decreased from day 1 (R1) to day 25 (R25) of chick rearing (P < 0.05). In both male and female adult pigeons, the contents of Thr, Leu, Val, His, Asp, and Pro in plasma increased to maximum levels on R25. Parental sex effect and interaction between stage and sex were observed in the AA contents of pigeon plasma (P < 0.05). For AA transporters, the mRNA abundances of SNAT2, ASCT1, LAT1, and y+LAT2 in the male crops reached the highest value on day 17 of incubation (I17), and the peak mRNA levels of PAT-1, xCT, b0,+AT, and CAT1 were found on R7 (P < 0.05). In females, the abundances of ASCT1, B0AT1, asc-1, and CAT1 mRNA peaked on R1, whereas the maximum levels of LAT1, PAT-1, b0,+AT, and y+LAT2 were observed on R7. For enzymes involved in AA synthesis, the highest gene expressions of glutamate dehydrogenase 1, acetolactate synthase in both parent pigeons, and L-threonine 3-dehydrogenase in female pigeon crops were attained on I17. The expressions of ornithine-δ-aminotransferase, glutamic-oxal(o)acetic transaminase 1, glutamic-oxal(o)acetic transaminase 2, asparagine synthetase, serine hydroxymethyltransferase 2, and glutamic-pyruvic transaminase 2 in both sexes and argininosuccinate lyase and L-threonine 3-dehydrogenase in males were the highest on R1. In conclusion, AA used for pigeon crop milk formation may originate from plasma and intracellular synthesis. The genes involved in AA transport and synthesis varied significantly with sexual effects, indicating that other factors should be considered in future explorations of the mechanism of protein formation in crop milk.


Assuntos
Aminoácidos/análise , Columbidae/fisiologia , Papo das Aves/fisiologia , Sistemas de Transporte de Aminoácidos/genética , Sistemas de Transporte de Aminoácidos/metabolismo , Aminoácidos/biossíntese , Animais , Proteínas Aviárias/deficiência , Proteínas Aviárias/genética , Proteínas Aviárias/metabolismo , Columbidae/sangue , Columbidae/genética , Feminino , Expressão Gênica , Masculino , Comportamento Materno , Comportamento Paterno , RNA Mensageiro/análise
15.
Anticancer Res ; 40(3): 1513-1517, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-32132051

RESUMO

BACKGROUND/AIM: Cervical cancer is the most common cancer among women in Ethiopia. The objective was to evaluate the participation rate of a free of charge vaginal self-sample (Aptima multitest swab, Hologic) for the detection of human papillomavirus (HPV) in an Ethiopian cohort. PATIENTS AND METHODS: Specimens were collected from women employed by Ethiopian Airlines in Addis Abeba (N=5950). Samples were analysed for the presence of high-risk (HR) HPV mRNA by the Aptima HPV assay (Hologic) and HPV positive women were referred for cytology. Identification of HPV types among HPV positive samples was performed by Modified general primer-PCR and Luminex assay. RESULTS: Participation rate was 3.1% and the prevalence of HPV mRNA was 20.6% (37/180). CONCLUSION: Primary HPV mRNA screening with vaginal self-sampling may be an acceptable approach in Ethiopia. One out of five women harbor HPV in their vaginal self-sample in agreement with other similar studies from the region.


Assuntos
Papillomaviridae/genética , RNA Mensageiro/análise , RNA Viral/análise , Vagina/virologia , Adolescente , Adulto , Detecção Precoce de Câncer/métodos , Detecção Precoce de Câncer/estatística & dados numéricos , Etiópia/epidemiologia , Feminino , Humanos , Pessoa de Meia-Idade , Papillomaviridae/isolamento & purificação , Infecções por Papillomavirus/epidemiologia , Infecções por Papillomavirus/patologia , Infecções por Papillomavirus/virologia , Prevalência , Neoplasias do Colo do Útero/patologia , Neoplasias do Colo do Útero/virologia , Vagina/patologia , Esfregaço Vaginal , Adulto Jovem
16.
BMC Med Genet ; 21(1): 46, 2020 03 02.
Artigo em Inglês | MEDLINE | ID: mdl-32122327

RESUMO

BACKGROUND: Osteoarthritis (OA) is the most common form of arthritis and a leading cause of disability. This study attempted to investigate the key mRNAs and miRNAs related to OA. PATIENTS AND METHODS: From April 17th, 2018 to May 17th, 2018, five patients with OA and three normal controls were enrolled in this present study. To identify the differentially expressed mRNAs (DEmRNAs) and miRNAs (DEmiRNAs) between patients with OA and normal controls, RNA-sequencing was performed. Then, DEmiRNA-target DEmRNAs analysis and functional annotation of DEmiRNA-target DEmRNAs were performed. To validate the RNA-sequencing results, quantitative real time-PCR (RT-PCR) and western blot analysis were performed as well. RESULTS: A total of 1068 DEmRNAs, 21 DEmiRNAs and 395 DEmiRNA-DEmRNA pairs were identified in synovial tissues of patients with OA. The functional annotation of DEmiRNA-target DEmRNAs revealed that Pathways in cancer and PI3K-Akt signaling pathway were significantly enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. QRT-PCR and western blot results revealed that except for TLR7, the expression level of the others was consistent with the RNA-sequencing results, generally. CONCLUSION: The findings of this present study may provide new clues for the roles of DEmRNAs and DEmiRNAs in the pathogenesis of OA.


Assuntos
MicroRNAs/genética , Osteoartrite/genética , RNA Mensageiro/genética , Membrana Sinovial/metabolismo , Estudos de Casos e Controles , Progressão da Doença , Perfilação da Expressão Gênica/métodos , Regulação da Expressão Gênica , Humanos , MicroRNAs/análise , Osteoartrite/metabolismo , Osteoartrite/patologia , RNA Mensageiro/análise , Análise de Sequência de RNA/métodos , Membrana Sinovial/química , Membrana Sinovial/patologia , Sequenciamento Completo do Exoma
17.
Nature ; 579(7799): 409-414, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-32188942

RESUMO

Plants are essential for life and are extremely diverse organisms with unique molecular capabilities1. Here we present a quantitative atlas of the transcriptomes, proteomes and phosphoproteomes of 30 tissues of the model plant Arabidopsis thaliana. Our analysis provides initial answers to how many genes exist as proteins (more than 18,000), where they are expressed, in which approximate quantities (a dynamic range of more than six orders of magnitude) and to what extent they are phosphorylated (over 43,000 sites). We present examples of how the data may be used, such as to discover proteins that are translated from short open-reading frames, to uncover sequence motifs that are involved in the regulation of protein production, and to identify tissue-specific protein complexes or phosphorylation-mediated signalling events. Interactive access to this resource for the plant community is provided by the ProteomicsDB and ATHENA databases, which include powerful bioinformatics tools to explore and characterize Arabidopsis proteins, their modifications and interactions.


Assuntos
Proteínas de Arabidopsis/análise , Proteínas de Arabidopsis/química , Arabidopsis/química , Espectrometria de Massas , Proteoma/análise , Proteoma/química , Proteômica , Motivos de Aminoácidos , Arabidopsis/anatomia & histologia , Arabidopsis/genética , Arabidopsis/metabolismo , Proteínas de Arabidopsis/biossíntese , Proteínas de Arabidopsis/genética , Bases de Dados de Proteínas , Conjuntos de Dados como Assunto , Regulação da Expressão Gênica de Plantas , Anotação de Sequência Molecular , Fases de Leitura Aberta , Especificidade de Órgãos , Fosfoproteínas/análise , Fosfoproteínas/química , Fosfoproteínas/genética , Fosforilação , Proteoma/biossíntese , Proteoma/genética , RNA Mensageiro/análise , RNA Mensageiro/biossíntese , RNA Mensageiro/genética , Transcriptoma
18.
Nature ; 581(7808): 303-309, 2020 05.
Artigo em Inglês | MEDLINE | ID: mdl-32214235

RESUMO

Single-cell analysis is a valuable tool for dissecting cellular heterogeneity in complex systems1. However, a comprehensive single-cell atlas has not been achieved for humans. Here we use single-cell mRNA sequencing to determine the cell-type composition of all major human organs and construct a scheme for the human cell landscape (HCL). We have uncovered a single-cell hierarchy for many tissues that have not been well characterized. We established a 'single-cell HCL analysis' pipeline that helps to define human cell identity. Finally, we performed a single-cell comparative analysis of landscapes from human and mouse to identify conserved genetic networks. We found that stem and progenitor cells exhibit strong transcriptomic stochasticity, whereas differentiated cells are more distinct. Our results provide a useful resource for the study of human biology.


Assuntos
Células/citologia , Células/metabolismo , Análise de Célula Única/métodos , Adulto , Animais , Grupo com Ancestrais do Continente Asiático , Diferenciação Celular , Linhagem Celular , Separação Celular , China , Bases de Dados Factuais , Corpos Embrioides/citologia , Corpos Embrioides/metabolismo , Grupos Étnicos , Feto/citologia , Células-Tronco Hematopoéticas/citologia , Células-Tronco Hematopoéticas/metabolismo , Humanos , Imunidade , Células-Tronco Pluripotentes Induzidas/citologia , Células-Tronco Pluripotentes Induzidas/metabolismo , Ilhotas Pancreáticas/citologia , Ilhotas Pancreáticas/metabolismo , Camundongos , Especificidade de Órgãos , RNA Mensageiro/análise , RNA Mensageiro/genética , Análise de Sequência de RNA , Análise de Célula Única/instrumentação , Processos Estocásticos
19.
Chembiochem ; 21(15): 2214-2218, 2020 08 03.
Artigo em Inglês | MEDLINE | ID: mdl-32187837

RESUMO

The reliable detection of transcription events through the quantification of the corresponding mRNA is of paramount importance for the diagnostics of infections and diseases. The quantification and localization analysis of the transcripts of a particular gene allows disease states to be characterized more directly compared to an analysis on the transcriptome wide level. This is particularly needed for the early detection of virus infections as now required for emergent viral diseases, e. g. Covid-19. In situ mRNA analysis, however, is a formidable challenge and currently performed with sets of single-fluorophore-containing oligonucleotide probes that hybridize to the mRNA in question. Often a large number of probe strands (>30) are required to get a reliable signal. The more oligonucleotide probes are used, however, the higher the potential off-target binding effects that create background noise. Here, we used click chemistry and alkyne-modified DNA oligonucleotides to prepare multiple-fluorophore-containing probes. We found that these multiple-dye probes allow reliable detection and direct visualization of mRNA with only a very small number (5-10) of probe strands. The new method enabled the in situ detection of viral transcripts as early as 4 hours after infection.


Assuntos
Química Click/métodos , Diagnóstico Precoce , Hibridização in Situ Fluorescente/métodos , Sondas de Oligonucleotídeos/química , RNA Mensageiro/análise , RNA Viral/análise , Alquinos/química , Betacoronavirus/genética , Infecções por Coronavirus/diagnóstico , Humanos , Oligodesoxirribonucleotídeos/química , Pandemias , Pneumonia Viral/diagnóstico
20.
Transplantation ; 104(9): 1853-1861, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32150044

RESUMO

BACKGROUND: MicroRNAs (miRNAs) are short noncoding RNAs which each cause repression of many target genes. Previous work has demonstrated that therapeutic blockade of single miRNAs is possible. miR-24-3p and miR-145-5p are reported to have a detrimental role in ischemia-reperfusion injury. As the action of miRNAs is inhibitory, we hypothesized that dual blockade of both miRNAs could synergistically upregulate shared target genes. METHODS: Quantification of miRNA expression in donated kidneys was performed using polymerase chain reaction (PCR) panels. Ischemia-reperfusion injury was modeled in vitro by placing human umbilical vein endothelial cells into a hypoxic incubator (1% O2) for 24 hours, with reoxygenation for 6 hours. RNA expression was quantified with reverse transcription quantitative polymerase chain reaction and protein expression assessed with Western blot. Antisense oligonucleotides were used to inhibit miRNAs. RESULTS: miR-24-3p and miR-145-5p were highly expressed in human kidneys following extended cold ischemia. In vitro, hypoxia caused significant upregulation of miR-24-3p (P ≤ 0.001) and miR-145-5p (P ≤ 0.001) and significant downregulation in messenger RNA of shared targets superoxide dismutase 2 (P ≤ 0.001) and heme oxygenase 1 (P ≤ 0.001). These changes were mirrored at the protein level. Dual inhibition of both miR-24-3p and miR-145-5p caused significant upregulation of superoxide dismutase 2 and heme oxygenase 1 protein following hypoxia-reoxygenation; fold change of 3.17 (P ≤ 0.05) and 6.97 (P ≤ 0.05) respectively. Dual inhibition resulted in reduced cellular reactive oxygen species production compared with negative control (P ≤ 0.05) and single blockade of miR-24-3p (P ≤ 0.01) or miR-145-5p (P ≤ 0.05). CONCLUSIONS: Dual blockade of 2 miRNAs can act synergistically to increase the expression of shared gene targets. Dual blockade of miR-24-3p and miR-145-5p represents a novel therapeutic option worthy of further research.


Assuntos
Heme Oxigenase-1/genética , Rim/metabolismo , MicroRNAs/antagonistas & inibidores , Traumatismo por Reperfusão/terapia , Superóxido Dismutase/genética , Células Endoteliais da Veia Umbilical Humana , Humanos , MicroRNAs/análise , RNA Mensageiro/análise , Espécies Reativas de Oxigênio/metabolismo , Traumatismo por Reperfusão/etiologia
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