Epigenomics in cancer management

The identification of all epigenetic modifications implicated in gene expression is the next step for a better understanding of human biology in both normal and pathological states. This field is referred to as epigenomics, and it is defined as epigenetic changes (ie, DNA methylation, histone modifications and regulation by noncoding RNAs such as microRNAs) on a genomic scale rather than a single gene. Epigenetics modulate the structure of the chromatin, thereby affecting the transcription of genes in the genome. Different studies have already identified changes in epigenetic modifications in a few genes in specific pathways in cancers. Based on these epigenetic changes, drugs against different types of tumors were developed, which mainly target epimutations in the genome. Examples include DNA methylation inhibitors, histone modification inhibitors, and small molecules that target chromatin-remodeling proteins. However, these drugs are not specific, and side effects are a major problem; therefore, new DNA sequencing technologies combined with epigenomic tools have the potential to identify novel biomarkers and better molecular targets to treat cancers. The purpose of this review is to discuss current and emerging epigenomic tools and to address how these new technologies may impact the future of cancer management

Identification of Differentially Expressed MicroRNAs in Osteosarcoma

A limited number of reports have investigated the role of microRNAs in osteosarcoma. In this study, we performed miRNA expression profiling of osteosarcoma cell lines, tumor samples, and normal human osteoblasts. Twenty-two differentially expressed microRNAs were identified using high throughput real-time PCR analysis, and 4 (miR-135b, miR-150, miR-542-5p, and miR-652) were confirmed and validated in a different group of tumors. Both miR-135b and miR-150 have been previously shown to be important in cancer. We hypothesize that dysregulation of differentially expressed microRNAs may contribute to tumorigenesis. They might also represent molecular biomarkers or targets for drug development in osteosarcoma

Global Demethylation of Rat Chondrosarcoma Cells after Treatment with 5-Aza-2′-Deoxycytidine Results in Increased Tumorigenicity

Abnormal patterns of DNA methylation are observed in several types of human cancer. While localized DNA methylation of CpG islands has been associated with gene silencing, the effect that genome-wide loss of methylation has on tumorigenesis is not completely known. To examine its effect on tumorigenesis, we induced DNA demethylation in a rat model of human chondrosarcoma using 5-aza-2-deoxycytidine. Rat specific pyrosequencing assays were utilized to assess the methylation levels in both LINEs and satellite DNA sequences following 5-aza-2-deoxycytidine treatment. Loss of DNA methylation was accompanied by an increase in invasiveness of the rat chondrosarcoma cells, in vitro, as well as by an increase in tumor growth in vivo. Subsequent microarray analysis provided insight into the gene expression changes that result from 5-aza-2-deoxycytidine induced DNA demethylation. In particular, two genes that may function in tumorigenesis, sox-2 and midkine, were expressed at low levels in control cells but upon 5-aza-2-deoxycytidine treatment these genes became overexpressed. Promoter region DNA analysis revealed that these genes were methylated in control cells but became demethylated following 5-aza-2-deoxycytidine treatment. Following withdrawal of 5-aza-2-deoxycytidine, the rat chondrosarcoma cells reestablished global DNA methylation levels that were comparable to that of control cells. Concurrently, invasiveness of the rat chondrosarcoma cells, in vitro, decreased to a level indistinguishable to that of control cells. Taken together these experiments demonstrate that global DNA hypomethylation induced by 5-aza-2-deoxycytidine may promote specific aspects of tumorigenesis in rat chondrosarcoma cells

Human rhinovirus infection causes different DNA methylation changes in nasal epithelial cells from healthy and asthmatic subjects

BACKGROUND: Mechanisms underlying the development of virus-induced asthma exacerbations remain unclear. To investigate if epigenetic mechanisms could be involved in virus-induced asthma exacerbations, we undertook DNA methylation profiling in asthmatic and healthy nasal epithelial cells (NECs) during Human Rhinovirus (HRV) infection in vitro. METHODS: Global and loci-specific methylation profiles were determined via Alu element and Infinium Human Methylation 450 K microarray, respectively. Principal components analysis identified the genomic loci influenced the most by disease-status and infection. Real-time PCR and pyrosequencing were used to confirm gene expression and DNA methylation, respectively. RESULTS: HRV infection significantly increased global DNA methylation in cells from asthmatic subjects only (43.6% to 44.1%, p = 0.04). Microarray analysis revealed 389 differentially methylated loci either based on disease status, or caused by virus infection. There were disease-associated DNA methylation patterns that were not affected by HRV infection as well as HRV-induced DNA methylation changes that were unique to each group. A common methylation locus stood out in response to HRV infection in both groups, where the small nucleolar RNA, H/ACA box 12 (SNORA12) is located. Further analysis indicated that a relationship existed between SNORA12 DNA methylation and gene expression in response to HRV infection. CONCLUSIONS: We describe for the first time that Human rhinovirus infection causes DNA methylation changes in airway epithelial cells that differ between asthmatic and healthy subjects. These epigenetic differences may possibly explain the mechanism by which respiratory viruses cause asthma exacerbations

Identification of MicroRNAs as Potential Prognostic Markers in Ependymoma

INTRODUCTION: We have examined expression of microRNAs (miRNAs) in ependymomas to identify molecular markers of value for clinical management. miRNAs are non-coding RNAs that can block mRNA translation and affect mRNA stability. Changes in the expression of miRNAs have been correlated with many human cancers. MATERIALS AND METHODS: We have utilized TaqMan Low Density Arrays to evaluate the expression of 365 miRNAs in ependymomas and normal brain tissue. We first demonstrated the similarity of expression profiles of paired frozen tissue (FT) and paraffin-embedded specimens (FFPE). We compared the miRNA expression profiles of 34 FFPE ependymoma samples with 8 microdissected normal brain tissue specimens enriched for ependymal cells. miRNA expression profiles were then correlated with tumor location, histology and other clinicopathological features. RESULTS: We have identified miRNAs that are over-expressed in ependymomas, such as miR-135a and miR-17-5p, and down-regulated, such as miR-383 and miR-485-5p. We have also uncovered associations between expression of specific miRNAs which portend a worse prognosis. For example, we have identified a cluster of miRNAs on human chromosome 14q32 that is associated with time to relapse. We also found that miR-203 is an independent marker for relapse compared to the parameters that are currently used. Additionally, we have identified three miRNAs (let-7d, miR-596 and miR-367) that strongly correlate to overall survival. CONCLUSION: We have identified miRNAs that are differentially expressed in ependymomas compared with normal ependymal tissue. We have also uncovered significant associations of miRNAs with clinical behavior. This is the first report of clinically relevant miRNAs in ependymomas

The lectin-specific activity of Toxoplasma gondii microneme proteins 1 and 4 binds Toll-like receptor 2 and 4 N-glycans to regulate innate immune priming.

Infection of host cells by Toxoplasma gondii is an active process, which is regulated by secretion of microneme (MICs) and rhoptry proteins (ROPs and RONs) from specialized organelles in the apical pole of the parasite. MIC1, MIC4 and MIC6 assemble into an adhesin complex secreted on the parasite surface that functions to promote infection competency. MIC1 and MIC4 are known to bind terminal sialic acid residues and galactose residues, respectively and to induce IL-12 production from splenocytes. Here we show that rMIC1- and rMIC4-stimulated dendritic cells and macrophages produce proinflammatory cytokines, and they do so by engaging TLR2 and TLR4. This process depends on sugar recognition, since point mutations in the carbohydrate-recognition domains (CRD) of rMIC1 and rMIC4 inhibit innate immune cells activation. HEK cells transfected with TLR2 glycomutants were selectively unresponsive to MICs. Following in vitro infection, parasites lacking MIC1 or MIC4, as well as expressing MIC proteins with point mutations in their CRD, failed to induce wild-type (WT) levels of IL-12 secretion by innate immune cells. However, only MIC1 was shown to impact systemic levels of IL-12 and IFN-γ in vivo. Together, our data show that MIC1 and MIC4 interact physically with TLR2 and TLR4 N-glycans to trigger IL-12 responses, and MIC1 is playing a significant role in vivo by altering T. gondii infection competency and murine pathogenesis

Combinations of Metarhizium anisopliae with chemical insecticides and their effectiveness in Mahanarva fimbriolata (Hemiptera: Cercopidae) control on sugarcane

Some insecticides can be used jointly with entomopathogenic fungi, and therefore the combi- nation of chemical and biological control measures can be a safe and effective method to con- trol insect pests. The aim of this study was to evaluate the costs and efficacy of combinations of Metarhizium anisopliae (Metschnikoff) Sorokin (Hypocreales: Clavicipitaceae) with thiameth- oxam and imidacloprid on spittlebug (Mahanarva fimbriolata (Stål); Hemiptera: Cercopidae) control on sugarcane. The experiment was conducted as a randomized block design (RBD) with 10 treatments and 4 replications. The treatments included a control (untreated), thia- −1 −1 12 −1 methoxam (250 g ha ), imidacloprid (700 g ha ), M. anisopliae (M. a.) (3 × 10 conidia ha ), A1 (3 × 10 12 M. a. conidia ha −1 + 65 g ha −1 of thiamethoxam), A2 (3 × 10 12 M. a. conidia ha −1 + 125 g ha −1 of thiamethoxam), A3 (3 × 10 12 M. a. conidia ha −1 + 187.5 g ha −1 of thiamethoxam), A4 (3 × 10 12 M. a. conidia ha −1 + 175 g ha −1 of imidacloprid), A5 (3 × 10 12 M. a. conidia ha −1 + 350 g ha −1 of imidacloprid), and A6 (3 × 10 12 M. a. conidia ha −1 + 525g ha −1 of imidacloprid). The reductions in the numbers of M. fimbriolata nymphs per treatment compared to the control were similar at 15 DAT (days after treatment) in all treatments except combination A5 (M. anisopliae and thiamethoxam). At 30 DAT, the numbers of nymphs were significantly reduced in all treatments except A3, and their effectiveness ranged from 14.28% to 92.85%. At 45 DAT the numbers of M. fimbriolata nymphs per treatment were significantly reduced in the following treatments: imidacloprid alone at 700g ha -1 , A1, A2, A3, A4 and A6; and the combinations A1 and A2 caused the lowest M. fimbriolata nymph infestations and effectiveness rates of 77.41 and 87.09 %, respectively. At 75 DAT the 2 best control efficacies occurred in treatments A1 (3 × 10 12 M. a. conidia ha -1 of + 65g ha -1 of thiamethoxam) (82.1%) and A5 (78.6%) (3 × 10 12 M. a. conidia ha −1 + 350 g ha −1 of imidacloprid). At 90 DAT the number of nymphs in the control had increased 2.8 fold over the number at 75 DAT. Very good control efficacies at 90 DAT occurred in all treatments with the combination of the fungus with an insecticide. At 105 DAT the numbers of nymphs had surged in all treatments, and no treatment provided effective control. The treatments with the highest earnings per hectare were A1 (3 × 10 12 M. a. conidia ha -1 + 65 g thiamethoxam) and M. anisopliae alone at the recommended dose of 3 × 10 12 M. a. conidia ha -1 . Our findings demonstrate the effectiveness of using either thiamethoxam or imidacloprid in combination with M. anisopliae to control M. fimbriolata nymphs on sugarcane, but greater net earnings per hectare occurred with the lowest rate of the thiamethoxam combination than with any of the imidacloprid combinations.Algunos insecticidas se puede utilizar con hongos entomopatógenos y por lo tanto, la aso- ciación de los controles químico y biológico puede ser una estrategia segura y eficaz para el control de insectos-plaga. El objetivo de este estudio fue evaluar los costos y eficacia de combinaciones de Metarhizium anisopliae (Metschnikoff) Sorokin (Hypocreales: Clavi- cipitaceae) con insecticidas thiamethoxam e imidacloprid para el control de la chicharrita (Mahanarva fimbriolata (Stål); Hemiptera: Cercopidae) en caña de azúcar . El experimento fue conducido en un delineamiento en bloques casualizados (DBC), con 10 tratamientos y 4 repeticiones. Los tratamientos que incluidos el control (sin tratamiento), thiamethoxam (250 g ha −1 ), imidacloprido (700 g ha −1 ), M. anisopliae (M.a.) (3×10 12 conidios ha −1 ), A1 (3×10 12 conidios ha −1 de M. a. + 65 g ha −1 de thiamethoxam), A2 (3×10 12 conidios ha −1 de M. a. + 125g ha −1 de thiamethoxam), A3 (3×10 12 conidios ha −1 de M. a. + 187.5 g ha −1 de thiamethoxam), A4 (3×10 12 conidios ha −1 de M.a + 175 g ha −1 de imidacloprido), A5 (3×10 12 conidios ha −1 de M. a. + 350 g ha −1 de imidacloprido) y A6 (3×10 12 conidios ha −1 de M. a. + 525g ha −1 de imidacloprido). Las reducciones en el número de ninfas M. fimbriolata por tratamiento en comparación con el control fueron similares a los 15 DAT (días pos tratamiento) en todos los tratamientos excepto A5 combinación (M. anisopliae y thiamethoxam). A los 30 DAT, el número de ninfas se redujeron significativamente en todos los tratamientos, excepto A3, y su eficacia varió de 14,28% para 92,85%. A los 45 DAT, los números de ninfas M. fimbriolata por tratamiento se redujeron significativamente en los siguientes tratamientos: imidacloprido solo en 700 g ha -1 , A1, A2, A3, A4 y A6; y las combinaciones de A1 y A2 causaron la más bajo infestaciones de ninfas M. fimbriolata y sus tasas de eficacia fueron de 77,41 y 87,09%, respectivamente. A los 75 DAT, los 2 mejores eficacias de control se produjeron en tratamientos A1 (3×10 12 conidios ha −1 de M. a. + 65 g ha −1 de thiamethoxam) y A5 (78.6%) (3×10 12 conidios ha −1 de M. a.+ 350 g ha −1 de imidacloprido). A los 90 DAT, el número de ninfas en el control había aumentado 2,8 veces más el número a 75 DAT. Muy buenas eficacias de control en 90 DAT, se produjo en todos los tratamientos con la combinación del hongo con un insecticida. A los 105 DAT, el número de ninfas habían aumentado en todos los tratamientos, y ningún tratamiento había proporcionado un control efectivo. Los tratamientos con los mayores rendimientos hectárea fueron A1 (3×10 12 conidios ha −1 de M. a.+ 65 g de thiamethoxam) y M. anisopliae solo a la dosis recomendada de 3×10 12 conidios ha −1 de M. a. Nuestros resultados demuestran la eficacia de thiamethoxam y imidacloprido en combinación con M. anisopliae para el control de ninfas M. fimbriolata en caña de azúcar, pero mayores beneficio neto por hectárea se produjeron con la tasa más baja de la combinación de thiamethoxam que con cualquiera de las combinaciones de imidacloprid

SARS-CoV-2 uses CD4 to infect T helper lymphocytes

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the agent of a major global outbreak of respiratory tract disease known as Coronavirus Disease 2019 (COVID-19). SARS-CoV-2 infects mainly lungs and may cause several immune-related complications, such as lymphocytopenia and cytokine storm, which are associated with the severity of the disease and predict mortality. The mechanism by which SARS-CoV-2 infection may result in immune system dysfunction is still not fully understood. Here, we show that SARS-CoV-2 infects human CD4+ T helper cells, but not CD8+ T cells, and is present in blood and bronchoalveolar lavage T helper cells of severe COVID-19 patients. We demonstrated that SARS-CoV-2 spike glycoprotein (S) directly binds to the CD4 molecule, which in turn mediates the entry of SARS-CoV-2 in T helper cells. This leads to impaired CD4 T cell function and may cause cell death. SARS-CoV-2-infected T helper cells express higher levels of IL-10, which is associated with viral persistence and disease severity. Thus, CD4-mediated SARS-CoV-2 infection of T helper cells may contribute to a poor immune response in COVID-19 patients.</p

SARS-CoV-2 uses CD4 to infect T helper lymphocytes

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the agent of a major global outbreak of respiratory tract disease known as Coronavirus Disease 2019 (COVID-19). SARS-CoV-2 infects mainly lungs and may cause several immune-related complications, such as lymphocytopenia and cytokine storm, which are associated with the severity of the disease and predict mortality. The mechanism by which SARS-CoV-2 infection may result in immune system dysfunction is still not fully understood. Here, we show that SARS-CoV-2 infects human CD4+ T helper cells, but not CD8+ T cells, and is present in blood and bronchoalveolar lavage T helper cells of severe COVID-19 patients. We demonstrated that SARS-CoV-2 spike glycoprotein (S) directly binds to the CD4 molecule, which in turn mediates the entry of SARS-CoV-2 in T helper cells. This leads to impaired CD4 T cell function and may cause cell death. SARS-CoV-2-infected T helper cells express higher levels of IL-10, which is associated with viral persistence and disease severity. Thus, CD4-mediated SARS-CoV-2 infection of T helper cells may contribute to a poor immune response in COVID-19 patients.</p