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1.
J Biomed Sci ; 30(1): 87, 2023 Oct 12.
Artigo em Inglês | MEDLINE | ID: mdl-37828601

RESUMO

BACKGROUND: Human angiotensin-converting enzyme 2 (hACE2) is the receptor mediating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. hACE2 expression is low in the lungs and is upregulated after SARS-CoV-2 infection. How such a hACE2-limited pulmonary environment supports efficient virus transmission and how dynamic hACE2 expression affects SARS-CoV-2 infection are unclear. METHODS: We generated stable cell lines with different expression levels of hACE2 to evaluate how the hACE2 expression level can affect SARS-CoV-2 transmission. RESULTS: We demonstrated that the hACE2 expression level controls the mode of SARS-CoV-2 transmission. The hACE2-limited cells have an advantage for SARS-CoV-2 shedding, which leads to cell-free transmission. By contrast, enhanced hACE2 expression facilitates the SARS-CoV-2 cell-to-cell transmission. Furthermore, this cell-to-cell transmission is likely facilitated by hACE2-containing vesicles, which accommodate numerous SARS-CoV-2 virions and transport them to neighboring cells through intercellular extensions. CONCLUSIONS: This hACE2-mediated switch between cell-free and cell-to-cell transmission routes provides SARS-CoV-2 with advantages for either viral spread or evasion of humoral immunity, thereby contributing to the COVID-19 pandemic and pathogenesis.


Assuntos
COVID-19 , SARS-CoV-2 , Animais , Humanos , Camundongos , Enzima de Conversão de Angiotensina 2/genética , COVID-19/transmissão , Camundongos Transgênicos , Pandemias , Peptidil Dipeptidase A/genética , Peptidil Dipeptidase A/metabolismo , Glicoproteína da Espícula de Coronavírus/genética
2.
Viruses ; 14(10)2022 09 30.
Artigo em Inglês | MEDLINE | ID: mdl-36298716

RESUMO

The yellow crazy ant, Anoplolepis gracilipes is a widespread invasive ant that poses significant threats to local biodiversity. Yet, compared to other global invasive ant species such as the red imported fire ant (Solenopsis invicta) or the Argentine ant (Linepithema humile), little is known about the diversity of RNA viruses in the yellow crazy ant. In the current study, we generated a transcriptomic database for A. gracilipes using a high throughput sequencing approach to identify new RNA viruses and characterize their genomes. Four virus species assigned to Dicistroviridae, two to Iflaviridae, one to Polycipiviridae, and two unclassified Riboviria viruses were identified. Detailed genomic characterization was carried out on the polycipivirus and revealed that this virus comprises 11,644 nucleotides with six open reading frames. Phylogenetic analysis and pairwise amino acid identity comparison classified this virus into the genus Sopolycivirus under Polycipiviridae, which is tentatively named "Anoplolepis gracilipes virus 3 (AgrV-3)". Evolutionary analysis showed that AgrV-3 possesses a high level of genetic diversity and elevated mutation rate, combined with the common presence of multiple viral strains within single worker individuals, suggesting AgrV-3 likely evolves following the quasispecies model. A subsequent field survey placed the viral pathogen "hotspot" of A. gracilipes in the Southeast Asian region, a pattern consistent with the region being recognized as part of the ant's native range. Lastly, infection of multiple virus species seems prevalent across field colonies and may have been linked to the ant's social organization.


Assuntos
Formigas , Vírus de RNA , Humanos , Animais , Filogenia , Vírus de RNA/genética , Espécies Introduzidas , Aminoácidos/genética , Nucleotídeos
3.
Oncology ; 100(11): 602-611, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36103810

RESUMO

PURPOSE: Composite cyclin-dependent kinase (CDK) inhibition has shown potential as a treatment for hepatocellular carcinoma (HCC) in preclinical studies. We tested whether the specific inhibition of CDK9 was effective against HCC. METHODS: The effects of two specific CDK9 inhibitors, BAY1143572 and AZD4573, in HCC cell lines were examined. We tested the in vivo efficacy of CDK9 inhibition in mouse xenograft models of HuH7 human HCC cells and in an orthotopic model of BNL mouse HCC cells. Overexpression and knockdown of CDK9 were performed to confirm the efficacy of CDK9 inhibition. RESULTS: CDK9 inhibitors exhibited potent antiproliferative activities in HCC cells regardless of the levels of c-myc expression while inhibiting the downstream signals of CDK9, such as the phosphorylation of RNA polymerase II. These 2 CDK9 inhibitors induced apoptosis in HCC cells and reduced the expression of antiapoptotic proteins such as myeloid cell leukemia-1 and survivin. In the xenograft studies, mice receiving either CDK9 inhibitor exhibited significantly slower tumor growth than did the mice receiving vehicles. In the orthotopic model, the HCC growth in mice receiving a CDK9 inhibitor also tended to be slower than that in the control group. Overexpression of CDK9 in HuH7 cells reduced the efficacy of both CDK9 inhibitors. Knockdown of CDK9 expression reduced the proliferative activities of HCC cells. CONCLUSION: We demonstrated the in vitro and in vivo activity of CDK9 inhibition on multiple HCC cell lines. Our data support further clinical development of CDK9 inhibitors as a treatment for HCC.


Assuntos
Antineoplásicos , Carcinoma Hepatocelular , Neoplasias Hepáticas , Humanos , Camundongos , Animais , Carcinoma Hepatocelular/patologia , Quinase 9 Dependente de Ciclina/genética , Quinase 9 Dependente de Ciclina/metabolismo , Neoplasias Hepáticas/patologia , Linhagem Celular Tumoral , Antineoplásicos/farmacologia , Antineoplásicos/uso terapêutico , Inibidores de Proteínas Quinases/farmacologia , Inibidores de Proteínas Quinases/uso terapêutico , Apoptose/genética
4.
Viruses ; 12(11)2020 11 15.
Artigo em Inglês | MEDLINE | ID: mdl-33203145

RESUMO

Spillover of honey bee viruses have posed a significant threat to pollination services, triggering substantial effort in determining the host range of the viruses as an attempt to understand the transmission dynamics. Previous studies have reported infection of honey bee viruses in ants, raising the concern of ants serving as a reservoir host. Most of these studies, however, are restricted to a single, local ant population. We assessed the status (geographical distribution/prevalence/viral replication) and phylogenetic relationships of honey bee viruses in ants across the Asia-Pacific region, using deformed wing virus (DWV) and two widespread invasive ants, Paratrechina longicornis and Anoplolepis gracilipes, as the study system. DWV was detected in both ant species, with differential geographical distribution patterns and prevenance levels between them. These metrics, however, are consistent across the geographical range of the same ant species. Active replication was only evident in P. longicornis. We also showed that ant-associated DWV is genetically similar to that isolated from Asian populations of honey bees, suggesting that local acquisition of DWV by the invasive ants may have been common at least in some of our sampled regions. Transmission efficiency of DWV to local arthropods mediated by ant, however, may vary across ant species.


Assuntos
Formigas/classificação , Formigas/virologia , Vírus de RNA/classificação , Vírus de RNA/isolamento & purificação , Animais , Ásia , Abelhas/virologia , Especificidade de Hospedeiro , Filogenia , Filogeografia , Vírus de RNA/genética , Vírus de RNA/fisiologia , RNA Viral/genética , RNA Viral/isolamento & purificação , Replicação Viral
5.
Arch Virol ; 165(11): 2721, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-32876793

RESUMO

Authors would like to correct the error in Fig. 1 which was incorrectly updated in the original publication.

6.
Arch Virol ; 165(11): 2715-2719, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-32776255

RESUMO

We report two novel RNA viruses from yellow crazy ants, (Anoplolepis gracilipes) detected using next-generation sequencing. The complete genome sequences of the two viruses were 10,662 and 8,238 nucleotides in length, respectively, with both possessing two open reading frames with three conserved protein domains. The genome organization is characteristic of members of the genus Triatovirus in the family Dicistroviridae. The two novel viruses were tentatively named "Anoplolepis gracilipes virus 1" and "Anoplolepis gracilipes virus 2" (AgrV-1 and AgrV-2). Phylogenetic analyses based on amino acid sequences of the non-structural polyprotein (ORF1) suggest that the two viruses are triatovirus-like viruses. This is the first report on the discovery of novel triatovirus-like viruses in yellow crazy ants with a description of their genome structure (two ORFs and conserved domains of RNA helicase, RNA-dependent RNA polymerase, and capsid protein), complete sequences, and viral prevalence across the Asia-Pacific region.


Assuntos
Formigas/virologia , Dicistroviridae/classificação , Dicistroviridae/isolamento & purificação , Genoma Viral , Filogenia , Sequência de Aminoácidos , Animais , Proteínas do Capsídeo/genética , Japão , Malásia , Fases de Leitura Aberta , RNA Helicases/genética , RNA Viral/genética , RNA Polimerase Dependente de RNA/genética , Sequenciamento Completo do Genoma
7.
Insects ; 10(12)2019 Dec 04.
Artigo em Inglês | MEDLINE | ID: mdl-31817209

RESUMO

The recent discovery of multiple viruses in ants, along with the widespread infection of their hosts across geographic ranges, provides an excellent opportunity to test whether viral prevalence in the field is associated with the complexity of social interactions in the ant population. In this study, we examined whether the association exists between the field prevalence of a virus and the intercolonial aggression of its ant host, using the yellow crazy ant (Anoplolepis gracilipes) and its natural viral pathogen (TR44839 virus) as a model system. We delimitated the colony boundary and composition of A. gracilipes in a total of 12 study sites in Japan (Okinawa), Taiwan, and Malaysia (Penang), through intercolonial aggression assay. The spatial distribution and prevalence level of the virus was then mapped for each site. The virus occurred at a high prevalence in the surveyed colonies of Okinawa and Taiwan (100% infection rate across all sites), whereas virus prevalence was variable (30%-100%) or none (0%) at the sites in Penang. Coincidentally, colonies in Okinawa and Taiwan displayed a weak intercolonial boundary, as aggression between colonies is generally low or moderate. Contrastingly, sites in Penang were found to harbor a high proportion of mutually aggressive colonies, a pattern potentially indicative of complex colony composition. Our statistical analyses further confirmed the observed correlation, implying that intercolonial interactions likely contribute as one of the effective facilitators of/barriers to virus prevalence in the field population of this ant species.

8.
Cancers (Basel) ; 11(10)2019 Sep 26.
Artigo em Inglês | MEDLINE | ID: mdl-31561409

RESUMO

Alterations in cell cycle regulators are common in hepatocellular carcinoma (HCC). We tested the efficacy of composite inhibition of CDKs 1, 2, 5, and 9 through dinaciclib on HCC. In vitro, dinaciclib exhibited potent antiproliferative activities in HCC cell lines regardless of Rb or c-myc expression levels. Dinaciclib significantly downregulated the phosphorylation of Rb (target of CDKs 1 and 2), ataxia telangiectasia mutated kinase (target of CDK5), and RNA polymerase II (target of CDK9) in the HCC cells. In xenograft studies, mice receiving dinaciclib tolerated the treatment well without significant body weight changes and exhibited a significantly slower tumor growth rate than the mice receiving vehicles. RNA interference (RNAi) of CDKs 1 and 9 was more effective in inhibiting the cell proliferation of HCC cells than RNAi of CDKs 2 and 5. Overexpression of CDK9 significantly reduced the efficacy of dinaciclib in HCC cells, but overexpression of CDK1 did not. In conclusion, composite inhibition of CDKs 1, 2, 5, and 9 through dinaciclib exhibited potent in vitro and in vivo activity against HCC. CDK9 inhibition might be the crucial mechanism.

9.
Virology ; 531: 255-259, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-30953883

RESUMO

Apoptosis is considered an innate defense mechanism of insect hosts at the early stage of pathogen infection. The present study attempts to determine whether apoptosis is involved in defending the fire ant, Solenopsis invicta from a natural viral pathogen Solenopsis invicta virus 1 (SINV-1). Results of TEM examination and TUNEL assay both revealed the signature of apoptosis in the midgut epithelium of SINV-1-infected fire ant larvae. A time-course study was conducted to monitor changes in the dynamics of SINV-1 viral titers and apoptosis levels in the midgut epithelium of SINV-1-infected larvae. We found that the viral titer significantly decreases as apoptosis level increases, suggesting that the apoptotic epithelium constitutes a barrier against dissemination of SINV-1. These findings serve as the very first empirical evidence for the virus-induced apoptosis in ants and also help explain some previously observed mortality patterns and behavioral alterations associated with SINV-1 in fire ants.


Assuntos
Formigas/citologia , Formigas/virologia , Apoptose , Dicistroviridae/fisiologia , Animais , Larva/citologia , Larva/virologia
10.
Sci Rep ; 8(1): 13498, 2018 09 10.
Artigo em Inglês | MEDLINE | ID: mdl-30202033

RESUMO

Despite the presence of conserved innate immune function, many insects have evolved a variety of mechanical, chemical, and behavioral defensive responses to pathogens. Illness-induced anorexia and dietary changes are two behavioral defensive strategies found in some solitary insects, but little is known regarding the role of such behaviors in social insects, especially in ants. In the present study we examined if such reduced foraging activity exists for a social insect, the invasive fire ant Solenopsis invicta, and its viral pathogen, Solenopsis invicta virus 1 (SINV-1). Virus-free fire ant colonies were split into two colony fragments, one of which subsequently was inoculated with SINV-1. Four food resources with different macronutrient ratios were presented to both colony fragments. SINV-1-inoculated colony fragments consistently displayed reduced foraging performance (e.g., foraging intensity and recruitment efficiency), a decline in lipid intake, and a shift in dietary preference to carbohydrate-rich foods compared with virus-free fragments. These findings provide the first evidence for virus-induced behavioral responses and dietary shifts in shaping the host-pathogen interactions in fire ants. The findings also suggest a possible mechanism for how fire ant colonies respond to viral epidemics. Potential implications of these behavioral differences for current management strategies are discussed.


Assuntos
Formigas/virologia , Comportamento Animal/fisiologia , Dicistroviridae/patogenicidade , Comportamento Alimentar/fisiologia , Controle Biológico de Vetores/métodos , Animais , Formigas/fisiologia , Interações Hospedeiro-Patógeno/fisiologia , Espécies Introduzidas , Masculino , Taiwan , Viroses/fisiopatologia , Viroses/veterinária , Viroses/virologia
11.
J Biomech ; 72: 262-267, 2018 04 27.
Artigo em Inglês | MEDLINE | ID: mdl-29559240

RESUMO

Lumbar interbody fusion is currently the gold standard in treating patients with disc degeneration or segmental instability. Despite it having been used for several decades, the non-union rate remains high. A failed fusion is frequently attributed to an inadequate mechanical environment after instrumentation. Finite element (FE) models can provide insights into the mechanics of the fusion process. Previous fusion simulations using FE models showed that the geometries and material of the cage can greatly influence the fusion outcome. However, these studies used axisymmetric models which lacked realistic spinal geometries. Therefore, different modeling approaches were evaluated to understand the bone-formation process. Three FE models of the lumbar motion segment (L4-L5) were developed: 2D, Sym-3D and Nonsym-3D. The fusion process based on existing mechano-regulation algorithms using the FE simulations to evaluate the mechanical environment was then integrated into these models. In addition, the influence of different lordotic angles (5, 10 and 15°) was investigated. The volume of newly formed bone, the axial stiffness of the whole segment and bone distribution inside and surrounding the cage were evaluated. In contrast to the Nonsym-3D, the 2D and Sym-3D models predicted excessive bone formation prior to bridging (peak values with 36 and 9% higher than in equilibrium, respectively). The 3D models predicted a more uniform bone distribution compared to the 2D model. The current results demonstrate the crucial role of the realistic 3D geometry of the lumbar motion segment in predicting bone formation after lumbar spinal fusion.


Assuntos
Vértebras Lombares/fisiologia , Modelos Biológicos , Fusão Vertebral , Algoritmos , Fenômenos Biomecânicos , Análise de Elementos Finitos , Humanos , Lordose/fisiopatologia , Osteogênese
12.
Oncotarget ; 8(49): 86681-86692, 2017 Oct 17.
Artigo em Inglês | MEDLINE | ID: mdl-29156827

RESUMO

Increased angiogenic activity has been demonstrated in hepatitis C virus (HCV)-related hepatocellular carcinoma (HCC), but the mechanism was unclear. To study the role of HCV core protein, we used tube formation and Matrigel plug assays to assess the proangiogenic activity of an HCC cell line, HuH7, and 2 of its stable clones-HuH7-core-high and HuH7-core-low, with high and low HCV core protein expression, respectively. In both assays, HuH7-core-high and HuH7-core-low cells dose-dependently induced stronger angiogenesis than control cells. HuH7 cells with HCV core protein expression showed increased mRNA and protein expression of vascular endothelial growth factor (VEGF). VEGF inhibition by bevacizumab reduced the proangiogenic activity of HuH7-core-high cells. The promotor region of VEGF contains the binding site of activator protein-1 (AP-1). Compared with controls, HuH7-core-high cells had an increased AP-1 activity and nuclear localization of phospho-c-jun. AP-1 inhibition using either RNA knockdown or AP-1 inhibitors reduced the VEGF mRNA expression and the proangiogenic activity of HuH7-core-high cells. Among 131 tissue samples from HCC patients, HCV-related HCC revealed stronger VEGF expression than did hepatitis B virus-related HCC. In conclusion, increased VEGF expression through AP-1 activation is a crucial mechanism underlying the proangiogenic activity of the HCV core protein in HCC cells.

13.
Front Zool ; 14: 24, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28503187

RESUMO

BACKGROUND: Reproductive division of labor is one of the key features of social insects. Queens are adapted for reproduction while workers are adapted for foraging and colony maintenance. In many species, however, workers retain functional ovaries and can lay unfertilized male eggs or trophic eggs. Here we report for the first time on the occurrence of physogastric workers and apparent worker reproduction in the invasive yellow crazy ant Anoplolepis gracilipes (Fr. Smith). We further examined the reproductive potential and nutritional role of physogastric workers through multidisciplinary approaches including morphological characterization, laboratory manipulation, genetic analysis and behavioral observation. RESULTS: Egg production with two types of eggs, namely reproductive and trophic eggs, by physogastric workers was found. The reproductive egg was confirmed to be haploid and male-destined, suggesting that the workers produced males via arrhenotokous parthenogenesis as no spermatheca was discovered. Detailed observations suggested that larvae were mainly fed with trophic eggs. Along with consumption of trophic eggs by queens and other castes as part of their diet, the vital role of physogastric workers as "trophic specialist" is confirmed. CONCLUSION: We propose that adaptive advantages derived from worker reproduction for A. gracilipes may include 1) trophic eggs provisioned by physogastric workers likely assist colonies of A. gracilipes in overcoming unfavorable conditions such as paucity of food during critical founding stage; 2) worker-produced males are fertile and thus might offer an inclusive fitness advantage for the doomed orphaned colony.

14.
PLoS Pathog ; 11(7): e1005051, 2015 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-26197391

RESUMO

SUMOylation is associated with epigenetic regulation of chromatin structure and transcription. Epigenetic modifications of herpesviral genomes accompany the transcriptional switch of latent and lytic genes during the virus life cycle. Here, we report a genome-wide comparison of SUMO paralog modification on the KSHV genome. Using chromatin immunoprecipitation in conjunction with high-throughput sequencing, our study revealed highly distinct landscape changes of SUMO paralog genomic modifications associated with KSHV reactivation. A rapid and widespread deposition of SUMO-2/3, compared with SUMO-1, modification across the KSHV genome upon reactivation was observed. Interestingly, SUMO-2/3 enrichment was inversely correlated with H3K9me3 mark after reactivation, indicating that SUMO-2/3 may be responsible for regulating the expression of viral genes located in low heterochromatin regions during viral reactivation. RNA-sequencing analysis showed that the SUMO-2/3 enrichment pattern positively correlated with KSHV gene expression profiles. Activation of KSHV lytic genes located in regions with high SUMO-2/3 enrichment was enhanced by SUMO-2/3 knockdown. These findings suggest that SUMO-2/3 viral chromatin modification contributes to the diminution of viral gene expression during reactivation. Our previous study identified a SUMO-2/3-specific viral E3 ligase, K-bZIP, suggesting a potential role of this enzyme in regulating SUMO-2/3 enrichment and viral gene repression. Consistent with this prediction, higher K-bZIP binding on SUMO-2/3 enrichment region during reactivation was observed. Moreover, a K-bZIP SUMO E3 ligase dead mutant, K-bZIP-L75A, in the viral context, showed no SUMO-2/3 enrichment on viral chromatin and higher expression of viral genes located in SUMO-2/3 enriched regions during reactivation. Importantly, virus production significantly increased in both SUMO-2/3 knockdown and KSHV K-bZIP-L75A mutant cells. These results indicate that SUMO-2/3 modification of viral chromatin may function to counteract KSHV reactivation. As induction of herpesvirus reactivation may activate cellular antiviral regimes, our results suggest that development of viral SUMO E3 ligase specific inhibitors may be an avenue for anti-virus therapy.


Assuntos
Fatores de Transcrição de Zíper de Leucina Básica/genética , Genoma Viral , Infecções por Herpesviridae/virologia , Herpesvirus Humano 8 , Proteínas Virais/metabolismo , Linhagem Celular , Imunoprecipitação da Cromatina/métodos , Regulação Viral da Expressão Gênica , Herpesvirus Humano 8/genética , Humanos , Proteínas Modificadoras Pequenas Relacionadas à Ubiquitina/metabolismo , Ubiquitinas/metabolismo , Proteínas Virais/genética , Ativação Viral , Latência Viral/genética
15.
FEBS Lett ; 588(21): 4008-17, 2014 Nov 03.
Artigo em Inglês | MEDLINE | ID: mdl-25261251

RESUMO

A short G1 phase is a characteristic feature of the cell cycle structure of pluripotent cells, and is reestablished during Yamanaka factor-mediated pluripotent reprogramming. How cell cycle control is adjusted to meet the requirements of pluripotent cell fate commitment during reprogramming is less well understood. Elevated levels of cyclin D1 were initially found to impair pluripotency maintenance. The current work further identified Cyclin D1 to be capable of transcriptionally upregulating Pax6, which promoted reprogramming cells to commit to a neural progenitor fate rather than a pluripotent cell fate. These findings explain the importance of reestablishment of G1-phase restriction in pluripotent reprogramming.


Assuntos
Diferenciação Celular , Reprogramação Celular , Ciclina D1/metabolismo , Células-Tronco Neurais/citologia , Células-Tronco Pluripotentes/citologia , Animais , Biomarcadores/metabolismo , Ciclina D1/biossíntese , Proteínas do Olho/genética , Fibroblastos/citologia , Fase G1 , Regulação da Expressão Gênica , Proteínas de Homeodomínio/genética , Humanos , Camundongos , Proteína Homeobox Nanog , Fator de Transcrição PAX6 , Fatores de Transcrição Box Pareados/genética , Células-Tronco Pluripotentes/metabolismo , Proteínas Repressoras/genética , Transcrição Gênica
16.
BMC Genomics ; 15 Suppl 1: S1, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-24564277

RESUMO

BACKGROUND: Post-translational modification (PTM) of transcriptional factors and chromatin remodelling proteins is recognized as a major mechanism by which transcriptional regulation occurs. Chromatin immunoprecipitation (ChIP) in combination with high-throughput sequencing (ChIP-seq) is being applied as a gold standard when studying the genome-wide binding sites of transcription factor (TFs). This has greatly improved our understanding of protein-DNA interactions on a genomic-wide scale. However, current ChIP-seq peak calling tools are not sufficiently sensitive and are unable to simultaneously identify post-translational modified TFs based on ChIP-seq analysis; this is largely due to the wide-spread presence of multiple modified TFs. Using SUMO-1 modification as an example; we describe here an improved approach that allows the simultaneous identification of the particular genomic binding regions of all TFs with SUMO-1 modification. RESULTS: Traditional peak calling methods are inadequate when identifying multiple TF binding sites that involve long genomic regions and therefore we designed a ChIP-seq processing pipeline for the detection of peaks via a combinatorial fusion method. Then, we annotate the peaks with known transcription factor binding sites (TFBS) using the Transfac Matrix Database (v7.0), which predicts potential SUMOylated TFs. Next, the peak calling result was further analyzed based on the promoter proximity, TFBS annotation, a literature review, and was validated by ChIP-real-time quantitative PCR (qPCR) and ChIP-reChIP real-time qPCR. The results show clearly that SUMOylated TFs are able to be pinpointed using our pipeline. CONCLUSION: A methodology is presented that analyzes SUMO-1 ChIP-seq patterns and predicts related TFs. Our analysis uses three peak calling tools. The fusion of these different tools increases the precision of the peak calling results. TFBS annotation method is able to predict potential SUMOylated TFs. Here, we offer a new approach that enhances ChIP-seq data analysis and allows the identification of multiple SUMOylated TF binding sites simultaneously, which can then be utilized for other functional PTM binding site prediction in future.


Assuntos
Biologia Computacional/métodos , Sumoilação , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Teorema de Bayes , Sítios de Ligação , Linhagem Celular Tumoral , Montagem e Desmontagem da Cromatina , Genoma Humano , Células HeLa , Humanos , Análise de Sequência de DNA
17.
PLoS One ; 9(2): e88556, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-24551118

RESUMO

Prostate cancer (PCa) cells undergoing neuroendocrine differentiation (NED) are clinically relevant to the development of relapsed castration-resistant PCa. Increasing evidences show that autophagy involves in the development of neuroendocrine (NE) tumors, including PCa. To clarify the effect of autophagy on NED, androgen-sensitive PCa LNCaP cells were examined. Treatment of LNCaP cells with IL-6 resulted in an induction of autophagy. In the absence of androgen, IL-6 caused an even stronger activation of autophagy. Similar result was identified in NED induction. Inhibition of autophagy with chloroquine (CQ) markedly decreased NED. This observation was confirmed by beclin1 and Atg5 silencing experiments. Further supporting the role of autophagy in NED, we found that LC3 was up-regulated in PCa tissue that had relapsed after androgen-deprivation therapy when compared with their primary tumor counterpart. LC3 staining in relapsed PCa tissue showed punctate pattern similar to the staining of chromogranin A (CgA), a marker for NED cells. Moreover, autophagy inhibition induced the apoptosis of IL-6 induced NE differentiated PCa cells. Consistently, inhibition of autophagy by knockdown of beclin1 or Atg5 sensitized NE differentiated LNCaP cells to etoposide, a chemotherapy drug. To identify the mechanisms, phosphorylation of IL-6 downstream targets was analyzed. An increase in phospho-AMPK and a decrease in phospho-mTOR were found, which implies that IL-6 regulates autophagy through the AMPK/mTOR pathway. Most important to this study is the discovery of REST, a neuronal gene-specific transcriptional repressor that is involved in autophagy activation. REST was down-regulated in IL-6 treatment. Knockdown experiments suggest that REST is critical to NED and autophagy activation by IL-6. Together, our studies imply that autophagy is involved in PCa progression and plays a cytoprotective role when NED is induced in PCa cells by IL-6 treatment. These results reveal the potential of targeting autophagy as part of a combined therapeutic regime for NE tumors.


Assuntos
Autofagia/efeitos dos fármacos , Diferenciação Celular/efeitos dos fármacos , Resistencia a Medicamentos Antineoplásicos/efeitos dos fármacos , Interleucina-6/farmacologia , Células Neuroendócrinas/patologia , Neoplasias da Próstata/patologia , Transdução de Sinais/efeitos dos fármacos , Adenilato Quinase/metabolismo , Androgênios/farmacologia , Proteínas Reguladoras de Apoptose/metabolismo , Autofagia/genética , Proteína Beclina-1 , Diferenciação Celular/genética , Linhagem Celular Tumoral , Cloroquina/farmacologia , Citoproteção/efeitos dos fármacos , Citoproteção/genética , Regulação para Baixo/efeitos dos fármacos , Regulação para Baixo/genética , Regulação Neoplásica da Expressão Gênica/efeitos dos fármacos , Técnicas de Silenciamento de Genes , Humanos , Masculino , Proteínas de Membrana/metabolismo , Modelos Biológicos , Recidiva Local de Neoplasia/genética , Recidiva Local de Neoplasia/patologia , Células Neuroendócrinas/efeitos dos fármacos , Células Neuroendócrinas/metabolismo , Análise de Sequência com Séries de Oligonucleotídeos , Neoplasias da Próstata/enzimologia , Neoplasias da Próstata/genética , Proteínas Repressoras/genética , Proteínas Repressoras/metabolismo , Serina-Treonina Quinases TOR/metabolismo
18.
BMC Genomics ; 14: 824, 2013 Nov 23.
Artigo em Inglês | MEDLINE | ID: mdl-24267727

RESUMO

BACKGROUND: SUMOylation, as part of the epigenetic regulation of transcription, has been intensively studied in lower eukaryotes that contain only a single SUMO protein; however, the functions of SUMOylation during mammalian epigenetic transcriptional regulation are largely uncharacterized. Mammals express three major SUMO paralogues: SUMO-1, SUMO-2, and SUMO-3 (normally referred to as SUMO-1 and SUMO-2/3). Herpesviruses, including Kaposi's sarcoma associated herpesvirus (KSHV), seem to have evolved mechanisms that directly or indirectly modulate the SUMO machinery in order to evade host immune surveillance, thus advancing their survival. Interestingly, KSHV encodes a SUMO E3 ligase, K-bZIP, with specificity toward SUMO-2/3 and is an excellent model for investigating the global functional differences between SUMO paralogues. RESULTS: We investigated the effect of experimental herpesvirus reactivation in a KSHV infected B lymphoma cell line on genomic SUMO-1 and SUMO-2/3 binding profiles together with the potential role of chromatin SUMOylation in transcription regulation. This was carried out via high-throughput sequencing analysis. Interestingly, chromatin immunoprecipitation sequencing (ChIP-seq) experiments showed that KSHV reactivation is accompanied by a significant increase in SUMO-2/3 modification around promoter regions, but SUMO-1 enrichment was absent. Expression profiling revealed that the SUMO-2/3 targeted genes are primarily highly transcribed genes that show no expression changes during viral reactivation. Gene ontology analysis further showed that these genes are involved in cellular immune responses and cytokine signaling. High-throughput annotation of SUMO occupancy of transcription factor binding sites (TFBS) pinpointed the presence of three master regulators of immune responses, IRF-1, IRF-2, and IRF-7, as potential SUMO-2/3 targeted transcriptional factors after KSHV reactivation. CONCLUSION: Our study is the first to identify differential genome-wide SUMO modifications between SUMO paralogues during herpesvirus reactivation. Our findings indicate that SUMO-2/3 modification near protein-coding gene promoters occurs in order to maintain host immune-related gene unaltered during viral reactivation.


Assuntos
Cromatina/metabolismo , Herpesvirus Humano 8/fisiologia , Proteínas Modificadoras Pequenas Relacionadas à Ubiquitina/metabolismo , Sumoilação , Ubiquitinas/metabolismo , Ativação Viral , Linhagem Celular Tumoral , Cromatina/virologia , Imunoprecipitação da Cromatina , Epigênese Genética/imunologia , Ontologia Genética , Genes MHC da Classe II , Células HEK293 , Humanos , Fatores Reguladores de Interferon/genética , Fatores Reguladores de Interferon/metabolismo , Regiões Promotoras Genéticas , Ligação Proteica , Fatores de Transcrição/metabolismo , Transcriptoma
19.
Artigo em Inglês | MEDLINE | ID: mdl-23662114

RESUMO

Breast cancer stem cells (CSCs) are highly tumorigenic and possess the capacity to self-renew. Recent studies indicated that pluripotent gene NANOG involves in regulating self-renewal of breast CSCs, and expression of NANOG is correlated with aggressiveness of poorly differentiated breast cancer. We initially confirmed that breast cancer MCF-7 cells expressed NANOG, and overexpression of NANOG enhanced the tumorigenicity of MCF-7 cells and promoted the self-renewal expansion of CD24(-/low)CD44(+) CSC subpopulation. In contrast, knockdown of NANOG significantly affected the growth of breast CSCs. Utilizing flow cytometry, we identified five cyclohexylmethyl flavonoids that can inhibit propagation of NANOG-positive cells in both breast cancer MCF-7 and MDA-MB231 cells. Among these flavonoids, ugonins J and K were found to be able to induce apoptosis in non-CSC populations and to reduce self-renewal growth of CD24(-/low)CD44(+) CSC population. Treatment with ugonin J significantly reduced the tumorigenicity of MCF-7 cells and efficiently suppressed formation of mammospheres. This suppression was possibly due to p53 activation and NANOG reduction as either addition of p53 inhibitor or overexpression of NANOG can counteract the suppressive effect of ugonin J. We therefore conclude that cyclohexylmethyl flavonoids can possibly be utilized to suppress the propagation of breast CSCs via reduction of NANOG.

20.
Eur Spine J ; 20(11): 1850-8, 2011 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-21523456

RESUMO

The Dynesys dynamics stabilisation system was developed to maintain the mobility of motion segment of the lumbar spine in order to reduce the incidence of negative effects at the adjacent segments. However, the magnitude of cord pretension may change the stiffness of the Dynesys system and result in a diverse clinical outcome, and the effects of Dynesys cord pretension remain unclear. Displacement-controlled finite element analysis was used to evaluate the biomechanical behaviour of the lumbar spine after insertion of Dynesys with three different cord pretensions. For the implanted level, increasing the cord pretension from 100 to 300 N resulted in an increase in flexion stiffness from 19.0 to 64.5 Nm/deg, a marked increase in facet contact force (FCF) of 35% in extension and 32% in torsion, a 40% increase of the annulus stress in torsion, and an increase in the high-stress region of the pedicle screw in flexion and lateral bending. For the adjacent levels, varying the cord pretension from 100 to 300 N only had a minor influence on range of motion (ROM), FCF, and annulus stress, with changes of 6, 12, and 9%, respectively. This study found that alteration of cord pretension affects the ROM and FCF, and annulus stress within the construct but not the adjacent segment. In addition, use of a 300 N cord pretension causes a much higher stiffness at the implanted level when compared with the intact lumbar spine.


Assuntos
Vértebras Lombares/fisiologia , Modelos Anatômicos , Próteses e Implantes , Amplitude de Movimento Articular/fisiologia , Fusão Vertebral , Fenômenos Biomecânicos/fisiologia , Parafusos Ósseos , Análise de Elementos Finitos , Humanos , Vértebras Lombares/cirurgia
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