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1.
J Transl Med ; 21(1): 586, 2023 09 01.
Artigo em Inglês | MEDLINE | ID: mdl-37658364

RESUMO

BACKGROUND: As the most lethal gynecologic cancer, ovarian cancer (OV) holds the potential of being immunotherapy-responsive. However, only modest therapeutic effects have been achieved by immunotherapies such as immune checkpoint blockade. This study aims to propose a generalized stroma-immune prognostic signature (SIPS) to identify OV patients who may benefit from immunotherapy. METHODS: The 2097 OV patients included in the study were significant with high-grade serous ovarian cancer in the III/IV stage. The 470 immune-related signatures were collected and analyzed by the Cox regression and Lasso algorithm to generalize a credible SIPS. Correlations between the SIPS signature and tumor microenvironment were further analyzed. The critical immunosuppressive role of stroma indicated by the SIPS was further validated by targeting the major suppressive stroma component (CAFs, Cancer-associated fibroblasts) in vitro and in vivo. With four machine-learning methods predicting tumor immune subtypes, the stroma-immune signature was upgraded to a 23-gene signature. RESULTS: The SIPS effectively discriminated the high-risk individuals in the training and validating cohorts, where the high SIPS succeeded in predicting worse survival in several immunotherapy cohorts. The SIPS signature was positively correlated with stroma components, especially CAFs and immunosuppressive cells in the tumor microenvironment, indicating the critical suppressive stroma-immune network. The combination of CAFs' marker PDGFRB inhibitors and frontline PARP inhibitors substantially inhibited tumor growth and promoted the survival of OV-bearing mice. The stroma-immune signature was upgraded to a 23-gene signature to improve clinical utility. Several drug types that suppress stroma-immune signatures, such as EGFR inhibitors, could be candidates for potential immunotherapeutic combinations in ovarian cancer. CONCLUSIONS: The stroma-immune signature could efficiently predict the immunotherapeutic sensitivity of OV patients. Immunotherapy and auxiliary drugs targeting stroma could enhance immunotherapeutic efficacy in ovarian cancer.


Assuntos
Síndrome de DiGeorge , Neoplasias Ovarianas , Feminino , Animais , Camundongos , Humanos , Receptor beta de Fator de Crescimento Derivado de Plaquetas , Prognóstico , Neoplasias Ovarianas/tratamento farmacológico , Imunossupressores , Imunoterapia , Microambiente Tumoral
2.
Redox Biol ; 62: 102677, 2023 06.
Artigo em Inglês | MEDLINE | ID: mdl-36989572

RESUMO

Ferroptosis, an iron-dependent lipid peroxidation-driven programmed cell death, is closely related to cancer therapy. The development of druggable ferroptosis inducers and their rational application in cancer therapy are critical. Here, we identified Tubastatin A, an HDAC6 inhibitor as a novel druggable ferroptosis inducer through large-scale drug screening. Tubastatin A directly bonded to GPX4 and inhibited GPX4 enzymatic activity through biotin-linked Tubastatin A putdown and LC/MS analysis, which is independent of its inhibition of HDAC6. In addition, our results showed that radiotherapy not only activated Nrf2-mediated GPX4 transcription but also inhibited lysosome-mediated GPX4 degradation, subsequently inducing ferroptosis tolerance and radioresistance in cancer cells. Tubastatin A overcame ferroptosis resistance and radioresistance of cancer cells by inhibiting GPX4 enzymatic activity. More importantly, Tubastatin A has excellent bioavailability, as demonstrated by its ability to significantly promote radiotherapy-induced lipid peroxidation and tumour suppression in a mouse xenograft model. Our findings identify a novel druggable ferroptosis inducer, Tubastatin A, which enhances radiotherapy-mediated antitumor effects. This work provides a compelling rationale for the clinical evaluation of Tubastatin A, especially in combination with radiotherapy.


Assuntos
Ferroptose , Neoplasias , Humanos , Animais , Camundongos , Fosfolipídeo Hidroperóxido Glutationa Peroxidase/metabolismo , Apoptose , Peroxidação de Lipídeos
3.
Clin Imaging ; 82: 135-138, 2022 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-34813992

RESUMO

OBJECTIVES: To analyze the appearance of duodenal tubulovillous adenoma on multi-slice spiral CT images to facilitate early diagnosis and treatment to potentially improve prognosis. METHODS: We retrospectively analyzed clinical data and CT imaging findings of 11 cases of duodenal tubulovillous adenomas, all confirmed by pathology. The location, size, shape, CT density, relationship with surrounding structures, accompanying bile duct obstruction, and enhancement pattern of each lesion were documented. RESULTS: All 11 lesions occurred in the descending part of the duodenum. Ten cases occurred in the duodenal papilla area. Nine cases had a low-density ring sign or semicircle sign between the lesion and the adjacent normal intestinal wall on axial images. Eight cases had differing degrees of bile duct dilatation, five of which had concomitant pancreatic duct dilatation. Noncontrast images revealed uniform soft tissue density; contrast enhanced images showed moderate, mostly uniform enhancement, with the most enhancement in the venous phase. In the arterial phase, two lesions showed linear enhancing vessels. CONCLUSIONS: On multi-slice spiral CT imaging, duodenal tubulovillous adenomas have certain characteristics that could be used for clinical diagnosis and treatment. PRECIS: On multi-slice spiral CT imaging of duodenal tubulovillous adenoma, findings of nodular or cauliflower-like shape, uniform density, uniform moderate enhancement, and a peripheral low-density ring sign could improve diagnostic accuracy.


Assuntos
Adenoma , Neoplasias Duodenais , Neoplasias Duodenais/diagnóstico por imagem , Duodeno/diagnóstico por imagem , Humanos , Estudos Retrospectivos , Tomografia Computadorizada Espiral
4.
Medicine (Baltimore) ; 100(49): e28163, 2021 Dec 10.
Artigo em Inglês | MEDLINE | ID: mdl-34889286

RESUMO

OBJECTIVE: Chronic prostatitis (CP) is a common disease in the outpatient department of males and urology. Clinical studies have found that acupuncture combined with traditional Chinese medicine (TCM) has achieved good results in treating CP, but its efficacy and safety are not completely clear. This study aimed to investigate the efficacy and safety of acupuncture combined with TCM in the treatment of CP. METHODS: Randomized controlled trials of acupuncture combined with TCM in treating CP were screened by searching PubMed, Embase, Cochrane Library, CNKI, etc. The retrieval time was from the database establishment date to March 31, 2021. The Cochrane Collaborative Risk Bias Assessment tool was used to evaluate literature's methodological quality of the literature. The RevMan5.4 software was used for the meta-analysis of outcome indicators. The TSA v0.9 software was used for sequential trial analysis (TSA) of effectiveness. RESULTS: In this study, 19 related randomized controlled trial studies were included, with a total of 1831 cases. The results of the meta-analysis showed that acupuncture combined with TCM could significantly improve the clinical efficacy of CP (OR = 3.76, 95%CI: 2.82 to 5.02, P < .00001), reduce the total score of The National Institutes of Health chronic prostatitis symptom index (MD = -4.00, 95%CI: -4.67 to 3.33, P < .00001), and improve patients' urination symptoms (MD = -1.10, 95%CI: -1.23 to -0.97, P < .00001), alleviated the pain symptoms of patients (MD = -2.38, 95%CI: -2.41 to -2.35, P < .00001), improved the quality of life of patients (MD = -1.69, 95%CI: -1.97 to -1.41, P < .00001), decreased the scores of TCM symptoms of patients (MD = -2.39, 95%CI: -3.45 to -1.33, P < .00001), and did not increase the adverse reactions of patients (MD = 1.09, 95%CI: 0.57 to 2.06, P = .8). The results of publication bias showed that this study was not affected by publication bias, and the conclusion was reliable. TSA showed that acupuncture combined with TCM was effective in treating CP. CONCLUSION: Acupuncture combined with TCM is safe and effective for alleviating CP. It can be used as an effective treatment for chronic prostatitis in the clinic.Registration number: DOI 10.17605/OSF.IO/Z8FJM.


Assuntos
Terapia por Acupuntura , Medicina Tradicional Chinesa/métodos , Prostatite/terapia , Adolescente , Adulto , Idoso , Doença Crônica , Humanos , Masculino , Pessoa de Meia-Idade , Prostatite/psicologia , Qualidade de Vida , Ensaios Clínicos Controlados Aleatórios como Assunto , Resultado do Tratamento , Adulto Jovem
5.
Plant Physiol ; 187(2): 900-916, 2021 10 05.
Artigo em Inglês | MEDLINE | ID: mdl-34608957

RESUMO

Woody bamboo is environmentally friendly, abundant, and an alternative to conventional timber. Degree of lignification and lignin content and deposition affect timber properties. However, the lignification regulatory network in monocots is poorly understood. To elucidate the regulatory mechanism of lignification in moso bamboo (Phyllostachys edulis), we conducted integrated analyses using transcriptome, small RNA, and degradome sequencing followed by experimental verification. The lignification degree and lignin content increased with increased bamboo shoot height, whereas phenylalanine ammonia-lyase and Laccase activities first increased and then decreased with shoot growth. Moreover, we identified 11,504 differentially expressed genes (DEGs) in different portions of the 13th internodes of different height shoots; most DEGs associated with cell wall and lignin biosynthesis were upregulated, whereas some DEGs related to cell growth were downregulated. We identified a total of 1,502 miRNAs, of which 687 were differentially expressed. Additionally, in silico and degradome analyses indicated that 5,756 genes were targeted by 691 miRNAs. We constructed a regulatory network of lignification, including 11 miRNAs, 22 transcription factors, and 36 enzyme genes, in moso bamboo. Furthermore, PeLAC20 overexpression increased lignin content in transgenic Arabidopsis (Arabidopsis thaliana) plants. Finally, we proposed a reliable miRNA-mediated "MYB-PeLAC20" module for lignin monomer polymerization. Our findings provide definite insights into the genetic regulation of bamboo lignification. In addition to providing a platform for understanding related mechanisms in other monocots, these insights could be used to develop strategies to improve bamboo timber properties.


Assuntos
Redes Reguladoras de Genes , Lignina/fisiologia , MicroRNAs/genética , Brotos de Planta/fisiologia , Poaceae/fisiologia , RNA de Plantas/genética , Poaceae/genética , Transcriptoma
6.
Cell Mol Life Sci ; 78(23): 7379-7395, 2021 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-34698881

RESUMO

Messenger RNA (mRNA) can be transported and targeted to different subcellular compartments and locally translated. Local translation is an evolutionally conserved mechanism that in mammals, provides an important tool to exquisitely regulate the subcellular proteome in different cell types, including neurons. Local translation in axons is involved in processes such as neuronal development, function, plasticity, and diseases. Here, we summarize the current progress on axonal mRNA transport and translation. We focus on the regulatory mechanisms governing how mRNAs are transported to axons and how they are locally translated in axons. We discuss the roles of axonally synthesized proteins, which either function locally in axons, or are retrogradely trafficked back to soma to achieve neuron-wide gene regulation. We also examine local translation in neurological diseases. Finally, we give a critical perspective on the remaining questions that could be answered to uncover the fundamental rules governing local translation, and discuss how this could lead to new therapeutic targets for neurological diseases.


Assuntos
Axônios/metabolismo , Transporte Biológico/fisiologia , Biossíntese de Proteínas/genética , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Animais , Citoesqueleto/fisiologia , Regulação da Expressão Gênica/genética , Humanos , Mitocôndrias/genética , Doenças do Sistema Nervoso/genética , Doenças do Sistema Nervoso/patologia , Ratos , Transdução de Sinais , Xenopus
7.
Nat Commun ; 12(1): 5466, 2021 09 15.
Artigo em Inglês | MEDLINE | ID: mdl-34526499

RESUMO

Moso bamboo (Phyllostachys edulis) is an economically and ecologically important nontimber forestry species. Further development of this species as a sustainable bamboo resource has been hindered by a lack of population genome information. Here, we report a moso bamboo genomic variation atlas of 5.45 million single-nucleotide polymorphisms (SNPs) from whole-genome resequencing of 427 individuals covering 15 representative geographic areas. We uncover low genetic diversity, high genotype heterozygosity, and genes under balancing selection underlying moso bamboo population adaptation. We infer its demographic history with one bottleneck and its recently small population without a rebound. We define five phylogenetic groups and infer that one group probably originated by a single-origin event from East China. Finally, we conduct genome-wide association analysis of nine important property-related traits to identify candidate genes, many of which are involved in cell wall, carbohydrate metabolism, and environmental adaptation. These results provide a foundation and resources for understanding moso bamboo evolution and the genetic mechanisms of agriculturally important traits.


Assuntos
Genoma de Planta/genética , Estudo de Associação Genômica Ampla/métodos , Poaceae/genética , Transcriptoma , Adaptação Fisiológica/genética , China , Evolução Molecular , Regulação da Expressão Gênica de Plantas , Variação Genética , Genética Populacional/métodos , Genômica/métodos , Geografia , Filogenia , Proteínas de Plantas/genética , Poaceae/classificação , Poaceae/metabolismo , Polimorfismo de Nucleotídeo Único , Sequenciamento do Exoma/métodos
8.
Nanoscale ; 13(3): 1800-1806, 2021 Jan 28.
Artigo em Inglês | MEDLINE | ID: mdl-33433555

RESUMO

Stretchable electrodes are essential components for wearable electronics. However, the stretchability of the electrodes is often achieved with the sacrifice of electronic conductivity along with huge variation in resistance. In this work, stretchable metallic glass electrodes (MG-electrodes) that have both high electronic conductivity and excellent electronic stability are developed. The stretchability of the MG-electrode is significantly improved by shrinking MG films deposited on substrates with pre-strain. We demonstrate two types of MG-electrodes. One is a transparent MG-electrode for uniaxial stretching, and the other with better conductivity is for biaxial stretching. Compared with previous electrodes, the MG-electrodes exhibit a combination of high conductivity and negligible resistivity change (<5%), making them promising candidates for interconnections. Along with the excellent corrosion resistance of metallic glasses, the electrodes may be used in harsh environments.

9.
Front Chem ; 9: 802375, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34988064

RESUMO

Ceramics can achieve superlubricity under water lubrication; however, their running-in period is long and application is rather limited by wear limit. Thus, zeolite imidazole ester skeleton (ZIF), an important branch of metal organic framework materials (MOFs), is expected to improve the tribological properties of lubricants and associated additives. As such, it has broad application prospects within the field. In this paper, ZIF-8 nanoparticles of varying concentrations were prepared and linked with amino functional groups. Specimens were used in silicon nitride self-matching pairs and their tribological properties were observed. After the experiment, friction surfaces were analyzed by scanning electron microscope (SEM), energy dispersive spectrometer (EDS), and Fourier transform infrared radiation (FTIR). The experimental results have shown that ZIF-8 nanoparticles greatly reduced both friction and wear. Comprehensively considering running-in time, average COF during the whole process and smooth friction period COF, optimal performance was obtained for the ZIF-8 nanoparticle solution concentration of 1wt%. Furthermore, it was concluded that the lubrication properties of amino-modified ZIF-8 nanoparticles are significantly better compared to that of the unmodified ZIF-8. The anti-friction mechanism of ZIF-8 as a ceramic water lubrication additive was mainly through the filling and forming of nanoparticle film on the ceramic surface.

10.
Mol Cell ; 81(3): 546-557.e5, 2021 02 04.
Artigo em Inglês | MEDLINE | ID: mdl-33378643

RESUMO

Eukaryotic cells regulate 5'-triphosphorylated RNAs (ppp-RNAs) to promote cellular functions and prevent recognition by antiviral RNA sensors. For example, RNA capping enzymes possess triphosphatase domains that remove the γ phosphates of ppp-RNAs during RNA capping. Members of the closely related PIR-1 (phosphatase that interacts with RNA and ribonucleoprotein particle 1) family of RNA polyphosphatases remove both the ß and γ phosphates from ppp-RNAs. Here, we show that C. elegans PIR-1 dephosphorylates ppp-RNAs made by cellular RNA-dependent RNA polymerases (RdRPs) and is required for the maturation of 26G-RNAs, Dicer-dependent small RNAs that regulate thousands of genes during spermatogenesis and embryogenesis. PIR-1 also regulates the CSR-1 22G-RNA pathway and has critical functions in both somatic and germline development. Our findings suggest that PIR-1 modulates both Dicer-dependent and Dicer-independent Argonaute pathways and provide insight into how cells and viruses use a conserved RNA phosphatase to regulate and respond to ppp-RNA species.


Assuntos
Proteínas de Caenorhabditis elegans/metabolismo , Caenorhabditis elegans/enzimologia , Monoéster Fosfórico Hidrolases/metabolismo , Processamento Pós-Transcricional do RNA , RNA/metabolismo , Animais , Animais Geneticamente Modificados , Caenorhabditis elegans/embriologia , Caenorhabditis elegans/genética , Proteínas de Caenorhabditis elegans/genética , Regulação da Expressão Gênica no Desenvolvimento , Monoéster Fosfórico Hidrolases/genética , Fosforilação , RNA/genética , Capuzes de RNA , RNA Polimerase Dependente de RNA/genética , RNA Polimerase Dependente de RNA/metabolismo , Ribonuclease III/genética , Ribonuclease III/metabolismo , Espermatogênese , Especificidade por Substrato
11.
Aging (Albany NY) ; 12(21): 21114-21128, 2020 11 05.
Artigo em Inglês | MEDLINE | ID: mdl-33154193

RESUMO

Circular RNAs have a critical function in the pathogenesis of many diseases and can function as competing endogenous RNA or miRNA sponges to inhibit miRNA and therefore upregulate the expression of target genes. However, little is known about the role of has_circRNA_0043278 (circ_0043278) in glioblastoma multiforme (GBM) and its potential downstream miRNA targets. This work validated that circ_0043278 is highly expressed in GMB cell lines and tissues, while knockdown circ_0043278 inhibited GBM cell migration, proliferation, and invasion invitro and tumorigenesis invivo. Dual-luciferase reporter assay determined that circ_0043278 directly sponged miR-638 to upregulate the expression of HOXA9, which can activate downstream Wnt/ß-catenin signaling in GBM. Moreover, miR-638 inhibition reversed circ_0043278 silencing-induced impairment of malignant tumor behavior. These results showed that circ-0043278/miRNA-638/ Homeobox A9 (HOXA9) axis had a vital function in promoting GBM progression. Our findings may provide potential new targets for the diagnosis and therapy of GBM.


Assuntos
Neoplasias Encefálicas/metabolismo , Regulação Neoplásica da Expressão Gênica , Glioblastoma/metabolismo , MicroRNAs/metabolismo , RNA Circular/metabolismo , Linhagem Celular Tumoral , Progressão da Doença , Proteínas de Homeodomínio/metabolismo , Humanos , MicroRNAs/antagonistas & inibidores
12.
RNA ; 26(9): 1170-1183, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32444459

RESUMO

Influenza A virus (IAV) utilizes cap-snatching to obtain host capped small RNAs for priming viral mRNA synthesis, generating capped hybrid mRNAs for translation. Previous studies have been focusing on canonical cap-snatching, which occurs at the very 5' end of viral mRNAs. Here we discovered noncanonical cap-snatching, which generates capped hybrid mRNAs/noncoding RNAs mapped to the region ∼300 nucleotides (nt) upstream of each mRNA 3' end, and to the 5' region, primarily starting at the second nt, of each virion RNAs (vRNA). Like canonical cap-snatching, noncanonical cap-snatching utilizes a base-pairing between the last nt G of host capped RNAs and a nt C of template RNAs to prime RNA synthesis. However, the nt upstream of this template C is usually A/U rather than just U; prime-realignment occurs less frequently. We also demonstrate that IAV can snatch capped IAV RNAs in addition to host RNAs. Noncanonical cap-snatching likely generates novel mRNAs with start AUG encoded in viral or host RNAs. These findings expand our understanding of cap-snatching mechanisms and suggest that IAV may utilize noncanonical cap-snatching to diversify its mRNAs/ncRNAs.


Assuntos
Vírus da Influenza A/genética , Capuzes de RNA/genética , RNA Mensageiro/genética , RNA não Traduzido/genética , Células A549 , Pareamento de Bases/genética , Linhagem Celular Tumoral , Humanos , RNA Viral/genética , RNA Polimerase Dependente de RNA/genética , Transcrição Gênica/genética
13.
Plant Cell Rep ; 39(6): 751-763, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32152695

RESUMO

KEY MESSAGE: Twenty-three PeLACs have been identified in moso bamboo, overexpression of PeLAC10 increases the lignin content and confers drought and phenolic acid tolerance in transgenic Arabidopsis. Laccases (LACs) have multifunction involved in the processes of cell elongation, lignification and stress response in plants. However, the function of laccases in bamboo remain unclear. Here, a total of 23 laccase genes (PeLAC1-PeLAC23) were identified in moso bamboo (Phyllostachys edulis). The diverse gene structure and expression pattern of PeLACs suggested that their function should be spatiotemporal and complicated, which was supported by the expression profiles in different tissues of moso bamboo. Eighteen PeLACs were identified as the targets of ped-miR397. The putative ped-miR397-binding site in the coding region of PeLAC10 was further confirmed by RLM-5' RACE, indicating that PeLAC10 was regulated by ped-miR397 after transcription. With the increasing shoot height, the expression abundance of PeLAC10 was up-regulated and reached the maximum in 15 cm shoots, while that of ped-miR397 was relative lower and showed the minimum in 15 cm shoots. PeLAC10 was up-regulated obviously under both ABA (100 µmol L-1) and NaCl (400 mmol L-1) treatments, and it was down-regulated under the GA3 (100 µmol L-1) treatment. The transgenic Arabidopsis plants over-expressing PeLAC10 became slightly smaller and their petioles were shorter than those of Col-0. However, they had a stronger capacity in resistance to phenolic acids and drought besides higher lignin content in stems. These results indicated that overexpression of PeLAC10 was helpful to increase the content of lignin in transgenic Arabidopsis and improve the adaptability to phenolic acid and drought stresses.


Assuntos
Lacase/genética , Lacase/metabolismo , Lignina/biossíntese , Poaceae/genética , Poaceae/metabolismo , Estresse Fisiológico/fisiologia , Arabidopsis/genética , Sítios de Ligação , Secas , Regulação da Expressão Gênica de Plantas , Genes de Plantas/genética , Hidroxibenzoatos/farmacologia , Lignina/genética , MicroRNAs , Filogenia , Proteínas de Plantas/genética , Plantas Geneticamente Modificadas/genética , Análise de Sequência , Estresse Fisiológico/efeitos dos fármacos , Transcriptoma
14.
Cancer Lett ; 482: 126-135, 2020 07 10.
Artigo em Inglês | MEDLINE | ID: mdl-31954770

RESUMO

Glioblastoma (GBM) has limited therapeutic options. DNA repair mechanisms contribute GBM cells to escape therapies and re-establish tumor growth. Multiple studies have shown that POLD2 plays a critical role in DNA replication, DNA repair and genomic stability. We demonstrate for the first time that POLD2 is highly expressed in human glioma specimens and that expression correlates with poor patient survival. siRNA or shRNA POLD2 inhibited GBM cell proliferation, cell cycle progression, invasiveness, sensitized GBM cells to chemo/radiation-induced cell death and reversed the cytoprotective effects of EGFR signaling. Conversely, forced POLD2 expression was found to induce GBM cell proliferation, colony formation, invasiveness and chemo/radiation resistance. POLD2 expression associated with stem-like cell subsets (CD133+ and SSEA-1+ cells) and positively correlated with Sox2 expression in clinical specimens. Its expression was induced by Sox2 and inhibited by the forced differentiation of GBM neurospheres. shRNA-POLD2 modestly inhibited GBM neurosphere-derived orthotopic xenografts growth, when combined with radiation, dramatically inhibited xenograft growth in a cooperative fashion. These novel findings identify POLD2 as a new potential therapeutic target for enhancing GBM response to current standard of care therapeutics.


Assuntos
Neoplasias Encefálicas/terapia , DNA Polimerase III/genética , DNA Polimerase III/metabolismo , Glioblastoma/terapia , RNA Interferente Pequeno/administração & dosagem , Temozolomida/administração & dosagem , Regulação para Cima , Animais , Neoplasias Encefálicas/genética , Neoplasias Encefálicas/metabolismo , Linhagem Celular Tumoral , Movimento Celular/efeitos dos fármacos , Movimento Celular/efeitos da radiação , Proliferação de Células/efeitos dos fármacos , Proliferação de Células/efeitos da radiação , DNA Polimerase III/antagonistas & inibidores , Sinergismo Farmacológico , Regulação Neoplásica da Expressão Gênica/efeitos dos fármacos , Regulação Neoplásica da Expressão Gênica/efeitos da radiação , Glioblastoma/genética , Glioblastoma/metabolismo , Humanos , Camundongos , Células-Tronco Neoplásicas/efeitos dos fármacos , Células-Tronco Neoplásicas/metabolismo , Células-Tronco Neoplásicas/efeitos da radiação , RNA Interferente Pequeno/farmacologia , Radioterapia , Análise de Sobrevida , Temozolomida/uso terapêutico , Regulação para Cima/efeitos dos fármacos , Regulação para Cima/efeitos da radiação , Ensaios Antitumorais Modelo de Xenoenxerto
15.
Anal Chem ; 92(1): 1346-1354, 2020 01 07.
Artigo em Inglês | MEDLINE | ID: mdl-31815440

RESUMO

5-Methylcytosine is found in both DNA and RNA; although its functions in DNA are well established, the exact role of 5-methylcytidine (m5C) in RNA remains poorly defined. Here we identified, by employing a quantitative proteomics method, multiple candidate recognition proteins of m5C in RNA, including several YTH domain-containing family (YTHDF) proteins. We showed that YTHDF2 could bind directly to m5C in RNA, albeit at a lower affinity than that toward N6-methyladenosine (m6A) in RNA, and this binding involves Trp432, a conserved residue located in the hydrophobic pocket of YTHDF2 that is also required for m6A recognition. RNA bisulfite sequencing results revealed that, after CRISPR-Cas9-mediated knockout of the YTHDF2 gene, the majority of m5C sites in rRNA (rRNA) exhibited substantially augmented levels of methylation. Moreover, we found that YTHDF2 is involved in pre-rRNA processing in cells. Together, our data expanded the functions of the YTHDF2 protein in post-transcriptional regulations of RNA and provided novel insights into the functions of m5C in RNA biology.


Assuntos
5-Metilcitosina/química , RNA Ribossômico/química , Proteínas de Ligação a RNA/química , 5-Metilcitosina/metabolismo , Sítios de Ligação , Células Cultivadas , Células HEK293 , Células HeLa , Humanos , Metilação , Estrutura Molecular , Processamento Pós-Transcricional do RNA/genética , RNA Ribossômico/metabolismo , Proteínas de Ligação a RNA/genética , Proteínas de Ligação a RNA/metabolismo
16.
RNA ; 26(2): 218-227, 2020 02.
Artigo em Inglês | MEDLINE | ID: mdl-31754076

RESUMO

High-throughput sequencing has become a standard tool for analyzing RNA and DNA. This method usually needs a cDNA/DNA library ligated with specific 5' and 3' linkers. Unlike mRNA, small RNA often contains modifications including 5' cap or triphosphate and 2'-O-methyl, requiring additional processing steps before linker additions during cloning processes; due to low expression levels, it is difficult to clone small RNA with a small amount of total RNA. Here we present a new strategy to clone 5' modified or unmodified small RNA in an all-liquid-based reaction carried out in a single PCR tube with as little as 20 ng total RNA. The 7-h cloning process only needs ∼1 h of labor. Moreover, this method can also clone mRNA, simplifying the need to prepare two cloning systems for small RNA and mRNA; the barcoded PCR primers are also compatible with non-cDNA cloning applications, including the preparation of genomic libraries. Not only is our method more convenient for cloning modified RNA than available methods, but it is also more sensitive, versatile, and cost-effective. Moreover, the all-liquid-based reaction can be performed in an automated manner.


Assuntos
Caenorhabditis elegans/genética , Clonagem Molecular , Sequenciamento de Nucleotídeos em Larga Escala , RNA de Helmintos/genética , Animais , Primers do DNA/genética , DNA Complementar/genética , Biblioteca Gênica , Reação em Cadeia da Polimerase , RNA Mensageiro/genética , Sensibilidade e Especificidade , Análise de Sequência de RNA
17.
Gigascience ; 7(10)2018 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-30202850

RESUMO

Background: Bamboo is one of the most important nontimber forestry products worldwide. However, a chromosome-level reference genome is lacking, and an evolutionary view of alternative splicing (AS) in bamboo remains unclear despite emerging omics data and improved technologies. Results: Here, we provide a chromosome-level de novo genome assembly of moso bamboo (Phyllostachys edulis) using additional abundance sequencing data and a Hi-C scaffolding strategy. The significantly improved genome is a scaffold N50 of 79.90 Mb, approximately 243 times longer than the previous version. A total of 51,074 high-quality protein-coding loci with intact structures were identified using single-molecule real-time sequencing and manual verification. Moreover, we provide a comprehensive AS profile based on the identification of 266,711 unique AS events in 25,225 AS genes by large-scale transcriptomic sequencing of 26 representative bamboo tissues using both the Illumina and Pacific Biosciences sequencing platforms. Through comparisons with orthologous genes in related plant species, we observed that the AS genes are concentrated among more conserved genes that tend to accumulate higher transcript levels and share less tissue specificity. Furthermore, gene family expansion, abundant AS, and positive selection were identified in crucial genes involved in the lignin biosynthetic pathway of moso bamboo. Conclusions: These fundamental studies provide useful information for future in-depth analyses of comparative genome and AS features. Additionally, our results highlight a global perspective of AS during evolution and diversification in bamboo.


Assuntos
Processamento Alternativo , Cromossomos de Plantas , Regulação da Expressão Gênica de Plantas , Genoma de Planta , Poaceae/genética , Biologia Computacional/métodos , Evolução Molecular , Genômica/métodos , Sequenciamento de Nucleotídeos em Larga Escala , Lignina/biossíntese , Anotação de Sequência Molecular
19.
Physiol Plant ; 163(4): 459-471, 2018 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-29314045

RESUMO

Higher plants have an array of photoprotection mechanisms alleviating the harmful effects of light. Non-photochemical quenching (NPQ) is one of the photoprotective mechanisms, which dissipates the excess of light energy absorbed in the light-harvesting complexes (LHCs) into thermal energy. The photosystem II subunit S (PsbS), a member of the LHC family thought to be present exclusively in higher plants, is supposed to activate NPQ through interactions with antenna proteins. However, the roles of PsbS in bamboo remain unclear. Here, two genes of bamboo (Phyllostachys edulis), PePsbS1 and PePsbS2, are investigated and functionally analyzed. PePsbS1 and PePsbS2 have a similar gene structure with three introns separated by two exons, which encode 269 and 268 amino acid residues, respectively. Tissue-specific analysis showed that PePsbS1 and PePsbS2 are highly expressed in leaf blade. Besides, they are both upregulated in the leaf blade when plantlets are submitted to an increased and prolonged light intensity, suggesting that they are light-induced. Western blot analysis indicated that the accumulation level of total PePsbSs is consistent with what obtained by quantitative real-time polymerase chain reaction for PePsbS1 and PePsbS2. Transgenic Arabidopsis plants overexpressing PePsbS1 and PePsbS2 both displayed an enhanced photoprotection. Moreover, the expression of PePsbS1 and PePsbS2 could both rescue the NPQ of Arabidopsis npq4 mutant, indicating that the PsbSs are functionally conserved between monocots and dicots. These results indicated that both PePsbS1 and PePsbS2 could circumvent photoinhibition and enhance photoprotection, which are key factors for bamboo's adaptation to different light environment.


Assuntos
Complexo de Proteína do Fotossistema II/genética , Proteínas de Plantas/genética , Poaceae/genética , Arabidopsis/genética , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Clorofila/metabolismo , Regulação da Expressão Gênica de Plantas , Teste de Complementação Genética , Peróxido de Hidrogênio/metabolismo , Complexos de Proteínas Captadores de Luz/genética , Complexos de Proteínas Captadores de Luz/metabolismo , Complexo de Proteína do Fotossistema II/metabolismo , Folhas de Planta/genética , Proteínas de Plantas/metabolismo , Plantas Geneticamente Modificadas , Superóxidos/metabolismo
20.
DNA Cell Biol ; 36(9): 747-758, 2017 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-28686465

RESUMO

Zeaxanthin epoxidase (ZEP) plays important roles in plant response to various environmental stresses by involving in abscisic acid (ABA) biosynthesis and xanthophyll cycle. A full-length cDNA of PeZEP was isolated from moso bamboo (Phyllostachys edulis), which comprised of a 138-bp 5'-untranslated region (UTR), a 381-bp 3'-UTR, and a 2013-bp open reading frame (ORF) encoding a putative protein of 670 amino acids. PeZEP was mainly expressed in leaf blades and leaf sheaths, and less in roots and culms. The transcript level of PeZEP in bamboo leaf was elevated with the increasing light intensity. PeZEP was significantly upregulated in response to high light (HL: 1200 µmol·m-2·s-1) and reached to a higher level after 1 h treatment, and kept higher levels in the following hours. Besides, PeZEP was upregulated under high temperature (42°C), and downregulated under low temperature (4°C) and exogenous ABA treatment. The expression vector of PeZEP driven by CaMV 35S was constructed and transformed into Arabidopsis thaliana. The transgenic plants overexpressing PeZEP were generated and subjected to drought stress for morphological and physiological assays. Compared with Col-0, the transgenic plants demonstrated enhanced tolerance to drought stress, which appeared later wilting and higher survival rate. Moreover, higher value of Fv/Fm, higher activities of superoxide dismutase, peroxidase, and catalase, and lower concentration of malondialdehyde were also observed in transgenic plants. Transcript levels of AtP5CS and AtRD29b related to drought stress were enhanced in transgenic plants. These results indicated that PeZEP might play an important function in response to drought stress in bamboo.


Assuntos
Oxirredutases/genética , Proteínas de Plantas/genética , Poaceae/genética , Arabidopsis/genética , Clorofila/química , Clorofila/metabolismo , Secas , Fluorescência , Regulação da Expressão Gênica de Plantas , Oxirredutases/metabolismo , Filogenia , Folhas de Planta/genética , Proteínas de Plantas/metabolismo , Plantas Geneticamente Modificadas , Regiões Promotoras Genéticas , Estresse Fisiológico , Nicotiana/genética
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