scholarly journals Comprehensive Analysis and Validation Reveal Potential MYCN Regulatory Biomarkers Associated with Prognosis of Neuroblastoma

Author(s):  
Bo Chen

Abstract Background Neuroblastoma (NB) is an embryonic malignant tumor that occurs in the sympathetic nervous system. The treatment effect of patients in the high-risk group is poor, and relapse and treatment failure can occur even with multiple combination treatments. MYCN is an independent prognostic factor for NB, and the proportion of MYCN amplification in tumor tissues of high-risk patients reaches 40-50%. Hence, exploring new MYCN targeting molecules is a meaningful way to treat high-risk NB patients. Methods The microarray datasets were obtained from Gene Expression Omnibus, and differentially expressed genes were identified. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and miRPathDB were used for function and pathway analysis. The STRING and Cytoscape were used to construct a protein-protein interaction network and modular analysis. The miRNet and NetworkAnalyst databases were used to predict and construct target gene-miRNA and target gene-TF networks. The R2 database was used for expression, correlation, and prognosis analysis. The diagnostic effect of the biomarkers was predicted by ROC analysis, and rt-PCR was used to verify the hub genes. Finally, used specific siRNA and plasmid to knockdown and overexpressed MYCN, the mRNA levels were verified. Results We identified 431 DEGs and FBXO9, HECW2, MIB2, RNF19B, RNF213, TRIM36, and ZBTB16 as novel biomarkers that affect the prognosis of the NB patients. In addition, FBXO9, RNF19B, and TRIM36 were preliminarily confirmed to be potential targeting molecules of MYCN. Conclusions Our results are expected to become novel biomarkers for the treatment of high-risk NB patients.

Proceedings ◽  
2018 ◽  
Vol 2 (25) ◽  
pp. 1538
Author(s):  
Safiye Aktas ◽  
Ayse Pinar Ercetin Ozdemir ◽  
Efe Ozgur Serinan ◽  
Zekiye Altun ◽  
Nur Olgun

Recent studies have shown that cancer cells can deceive phagocytosing macrophage cells through the CD47 protein which gives the message “don’t eat me” or “don’t kill me” to immune components. The efficacy of anti-CD47 treatment approach was shown in cancers such as, non-small cell lung cancer, non-Hodgkin lymphoma, ovarian cancer, and breast cancer. The studies on the immunobiology of neuroblastoma has increased as monoclonal antibody based immunotherapy has shown to be effective in high-risk patients such as anti disialoganglioside. Therefore, the aim of this study was to evaluate the levels of CD47 protein expression among neuroblastoma patients with different risk groups and genetic alterations. This study included paraffin-embedded tumor tissues of 66 neuroblastoma patients (28 girls, 38 boys) with an age range of 0.5 to 108 months with a mean value of 24.9 (±23.5). According to risk classifications 21 were at low risk (31, 8%), 24 were at intermediate risk (36, 4%) and 19 were at high-risk (28, 8%) groups. These samples were evaluated for MYCN amplification, 1p36 LOH, 11q23 deletion and 17q25 gain by real-time PCR. In addition, CD47 expression status (positive or negative) was detected by immunohistochemical analysis. All data was analyzed with Chi-Square and Mann-Whitney U non-parametric tests within SPSS program, version 22.0. p value lower than 0, 5 was found statistically significant. According to the results, patients at low risk did not express CD47, while patients at high-risk group were mostly expressing CD47 (p = 0.049). MYCN amplification positive patients were expressing CD47 protein (p = 0.046). Patients without 17q25 gain were found to be expressing CD47 protein (p = 0.006). In addition, CD47 expression was increasing as age was getting higher in terms of months (p = 0.018). The findings of this study suggest that positive expression pattern of CD47 may be a poor prognostic biomarker especially in high risk 17q gain negative neuroblastoma patients.


Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 5762-5762
Author(s):  
Mitsuteru Hiwatari ◽  
Kentaro Watanabe ◽  
Yasuo Kubota ◽  
Masahiro Sekiguchi ◽  
Junko Takita

Leukemic stem cells have several dysregulated pathways and the Janus kinases (JAKs) and signal transducer and activator of transcription (STAT) pathway are prominent among them. High STAT3 expression in leukemia has been associated with an increased risk for relapse and decreased overall survival. In addition, phosphorylated STAT3 can be found following prolonged activation of the anaplastic lymphoma kinase (ALK) ligand binding site, but the level of phospho-STAT3 engendered by ligand-independent activation of ALK was exponentially higher. In ALK positive tumors, ALK-STAT3 activation promotes tumor cell outgrowth and directly prevents apoptosis. The role of ALK in several types of ALK-expressing solid tumors as well as the therapeutic use of ALK inhibitors in treating these cancers also have been reviewed in a number of recent papers.However, clinical resistance to ALK inhibitors invariably occurs. Amplified ALK or mutated ALK was identified in ~14% of neuroblastomas (NB), the most common and aggressive childhood malignancy, and phase I trial of ALK inhibitor such as crizotinib showed a lack of response in patients harboring certain ALK mutations. In this study, we implemented a high throughput chemical screen in 4 NB-derived cell lines to identify compounds with the potential of inhibiting oncogenic activity of ALK in NB, using a curated library of ~450 compounds. Brefeldin A (BFA),an inhibitor of the transport of proteins from the endoplasmic reticulum (ER) to the Golgi, was identified as a suitable candidate. It was previously reported that BFA inhibited phosphorylation of ALK and its downstream molecule, STAT3. Since an increasing number of studies have found that STAT3 abnormal expression and activation are accompanied by leukemia development, which indicates the potential role of STAT3 in the pathogenesis of leukemia, we analyzed the cytotoxicity of BFA against 12 T-ALL and 6 AML cell lines. Assessment of BFA antitumor effect using an MTT assay revealed BFA to possess potent cytotoxic activity across a broad spectrum of hematopoietic malignancies, with 10 T-ALL and 5 AML being especially responsive. For example, T-ALL cell lines, as well as AML lines, were potently inhibited by BFA ( IC50 values: ICH-TALL-UK, 168.1 nM; MOLT-4, 23.2nM; Jurkat, 66.6 nM; MOLT14, 97.3 nM; ICH-TALL-SM, 54.9 nM). In an expanded panel of 20 NB cell lines, those with or without MYCN-amplification or 11q loss of heterozygousity which have been identified as two major oncogenic events in NB pathogenesis, especially in the high-risk group were the most sensitive to low nanomolar concentrations of BFA. In NB cell lines harboring F1174L or R1275Q-mutated ALK,BFAshowed cytotoxicity.BFA reduced the phosphorylation of ALK in NIH3T3 cells stably expressed F1174L ALK or TGW, cell line harboring R1275Q-mutated ALK. Of the molecules that are phosphorylated downstream of ALK that have been reported to be important for ALCL cells, the phosphorylation of STAT3, AKT and ERK was inhibited by BFA. These results suggested that BFA can be used to target STAT3 signaling pathways for leukemia treatment. Furthermore these results indicated that the effect of BFA on ALK mutated NB cell lines is accompanied by inhibition of the phosphorylation of ALK and its downstream key effector molecule STAT3.These findings provide the significance of ALK and STAT3 as they relate to NB or leukemia, explores the significance of STAT3, AKT and ERK downstream of ALK, and touches on the potential for new chemotherapeutics targeting ALK and STAT3 to improve high risk NB and leukemia patient prognosis. Disclosures No relevant conflicts of interest to declare.


2020 ◽  
Vol 48 (7) ◽  
pp. 030006052092454
Author(s):  
Fuwei Qi ◽  
Qing Li ◽  
Xiaojun Lu ◽  
Zhihua Chen

Objective There have been no recent improvements in the glioblastoma multiforme (GBM) outcome, with median survival remaining 15 months. Consequently, the need to identify novel biomarkers for GBM diagnosis and prognosis, and to develop targeted therapies is high. This study aimed to establish biomarkers for GBM pathogenesis and prognosis. Methods In total, 220 overlapping differentially expressed genes (DEGs) were obtained by integrating four microarray datasets from the Gene Expression Omnibus database (GSE4290, GSE12657, GSE15824, and GSE68848). Then a 140-node protein–protein interaction network with 343 interactions was constructed. Results The immune response and cell adhesion molecules were the most significantly enriched functions and pathways, respectively, among DEGs. The designated hub genes ITGB5 and RGS4, which have a high degree of connectivity, were closely correlated with patient prognosis, and GEPIA database mining further confirmed their differential expression in GBM versus normal tissue. We also determined the 20 most appropriate small molecules that could potentially reverse GBM gene expression, Prestwick-1080 was the most promising and had the highest negative scores. Conclusions This study identified ITGB5 and RGS4 as potential biomarkers for GBM diagnosis and prognosis. Insights into molecular mechanisms governing GBM occurrence and progression will help identify alternative biomarkers for clinical practice.


2021 ◽  
Author(s):  
Shiyuan Wen ◽  
Xin Xu ◽  
Jing Kong ◽  
Lisha Luo ◽  
Peng Yue ◽  
...  

Abstract Background Lyme disease is a zoonotic disease caused by infection with Borrelia burgdorferi (Bb), the involvement of the nervous system in Lyme disease is usually referred to as Lyme neuroborreliosis (LNB). LNB has diverse clinical manifestations, most commonly including meningitis, Bell’s palsy, and encephalitis. However, the molecular pathogenesis of neuroborreliosis is still poorly understood. Comprehensive transcriptomic analysis following Bb infection could provide new insights into the pathogenesis of LNB and may identify novel biomarkers or therapeutic targets for LNB diagnosis and treatment. Methods In the present study, we pooled transcriptomic datasets (transcriptomic rhesus data from our laboratory and the GSE85143 dataset from the Gene Expression Omnibus database) to screen common differentially expressed genes (DEGs) in the Bb infection group and the control group. Functional and enrichment analyses were conducted using the Database of Annotation Visualization and Integrated Discovery database, Protein-Protein Interaction network, and hub genes were identified using the Search Tool for the Retrieval of Interaction Genes database and the CytoHubba plugin. In addition, in vitro and ex vivo assays were performed to verify the above findings. The mRNA expression levels of these genes were verified by quantitative real-time PCR (qPCR). Results A total of 80 upregulated DEGs and 32 downregulated DEGs were identified. Among them, 11 hub genes were selected. Upregulated genes in the Gene Ontology analysis were significantly enriched in cell adhesion processes. The pathway enrichment analyses revealed that the PI3K-Akt signaling pathway was significantly enriched. The mRNA levels of ANGPT1, TLR6, SREBF1, LDLR, TNC, and ITGA2 in U251 cells and/or rhesus brain explants by exposure to Bb were validated by qPCR. Conclusion Our study suggested that TLR6, ANGPT1, LDLR, SREBF1, TNC, and ITGA were differentially highly expressed in Bb-infected astrocytes compared to normal controls, and overexpression of LDLR might be a favorable prognostic factor of LNB patients. Further study is needed to explore the value of TLR6, ANGPT1, LDLR, SREBF1, TNC, and ITGA in LNB pathogenesis.


2021 ◽  
Vol 5 (2) ◽  
Author(s):  
Arzu Yurci ◽  
Suphan Ersahin

Background: This study was designed to determine whether the risk of ovarian hyperstimulation syndrome (OHSS) contributes to the subfertility in PCOS. Endometrial HOXA-10 mRNA expression, a well-characterized gene essential to endometrial receptivity, was evaluated in PCOS patients whose embryos are planned to be frozen due to the risk of OHSSS. Methods: Twent-five women with PCOS in high risk group for OHSS and age and BMI matched 25 non-PCOS infertile patients were included the study. Five fertile women were accepted as positive control. Following egg collection each group of subject underwent total embryo freezing. After the egg collection, endometrial sampling was performed with a pipella cannula from each gruop of participant and fertile control. Expression levels of HOXA-10 mRNA were determined by RT-PCR. Gene expression results are presented as Ct (cycle threshold), ΔCt, and ΔΔCt. Reults: Average ΔCt value of HOXA-10 mRNA in PCOS, non-PCOS and fertile groups were found to 5.88, 6.77, and 7.79 respectively. Compared to endometrial HOXA-10 mRNA levels of fertile cases, the HOXA-10 mRNA levels of the patients in the PCOS group were found to be significantly lower (ΔCt 7.79 vs. ΔCt 5.88, p<0.002). Similarly, endometrial HOXA-10 mRNA levels in the non-PCOS control group were significantly lower than the HOXA-10 mRNA levels in the fertile group (ΔCt 6.77 vs. ΔCt 7.79, p<0.001). HOXA-10 mRNA levels in endometrial samples taken from patients in the PCOS group were found to be significantly lower than the HOXA-10 mRNA levels in non-PCOS control group. Conclusions: HOXA-10 mRNA levels were found to be lower in PCOS patients with high risk for OHSS compared to both fertile and infertile patients without PCOS. OHSS risk in PCOS decreases endometrial HOXA-10 mRNA expression.


2021 ◽  
Vol 2021 ◽  
pp. 1-10
Author(s):  
Rujia Wang ◽  
Qian Wang

Background. Neuroblastoma is a common solid tumor originating from the sympathetic nervous system, commonly found in children, and it is one of the leading causes of tumor-related deaths in children. In addition to pathological features, molecular-level features, such as how much gene expression is present and the mutational profile, may provide useful information for the precise treatment of neuroblastoma. Transcription factors (TFs) play an important regulatory role in all aspects of cellular life activities. But there are currently no studies on transcription factor-based biomarkers of neuroblastoma prognosis, and this study is much needed. Methods. We downloaded RNA transcriptome data and clinical data from the TARGET database to construct a prognostic model. The prognostic model was constructed by using univariate Cox analysis, LASSO, and multivariate Cox regression. We divided the patients into low-risk and high-risk groups using the median value of the risk score as the cut-off. Then, we validated the prognostic model with the dataset GSE49710. Results. We constructed a prognostic model consisting of eight genes (SATB1, ZNF564, SOX14, EN1, IKZF2, SLC2A4RG, FOXJ2, and ZNF521). Patients in the high-risk group had a lower survival rate than those in the low-risk group. The area under the 3-year ROC curve of the model reached 0.825, suggesting a good predictive efficacy. We performed target gene prediction for the eight transcription factors in the model using six online databases and found that TUT1 may be a target gene for transcription factor EN1 and is associated with immune infiltration. Conclusion. This prognostic model consisting of eight transcription factor-associated genes demonstrated reliable predictive efficacy. This prediction model may provide new potential targets for the treatment of neuroblastoma and personalized monitoring of neuroblastoma patients with high and low risk.


Author(s):  
Suresh Kumar

COVID-19 (2019-nCoV) is a pandemic disease with an estimated mortality rate of 3.4% (estimated by the WHO as of March 3, 2020). Until now there is no antiviral drug and vaccine for COVID-19. The current overwhelming situation by COVID-19 patients in hospitals is likely to increase in the next few months. About 15 percent of patients with serious disease in COVID-19 require immediate health services. Rather than waiting for new anti-viral drugs or vaccines that take a few months to years to develop and test, several researchers and public health agencies are attempting to repurpose medicines that are already approved for another similar disease and have proved to be fairly effective. This study aims to identify FDA approved drugs that can be used for drug repurposing and identify biomarkers among high- risk and asymptomatic groups. In this study gene-disease association related to COVID-19 reported mild, severe symptoms and clinical outcomes were determined. The high-risk group was studied related to SARS-CoV-2 viral entry and life cycle by using Disgenet and compared with curated COVID-19 gene data sets from the CTD database. The overlapped gene sets were enriched and the selected genes were constructed for protein-protein interaction networks. Through interactome, key genes were identified for COVID-19 and also for high risk and asymptomatic groups. The key hub genes involved in COVID-19 were VEGFA, TNF, IL-6, CXCL8, IL10, CCL2, IL1B, TLR4, ICAM1, MMP9. The identified key genes were used for drug-gene interaction for drug repurposing. The chloroquine, lenalidomide, pentoxifylline, thalidome, sorafenib, pacitaxel, rapamycin, cortisol, statins were proposed to be probable drug repurposing candidates for the treatment of COVID-19. However, these predicted drug candidates need to be validated through randomized clinical trials. Also, a key gene involved in high risk and the asymptomatic group were identified, which can be used as probable biomarkers for early identification.


Cancers ◽  
2021 ◽  
Vol 13 (17) ◽  
pp. 4360
Author(s):  
Frank Berthold ◽  
Angela Ernst ◽  
Sandra Ackermann ◽  
Christoph Bartenhagen ◽  
Holger Christiansen ◽  
...  

Background: To identify variables predicting outcome in neuroblastoma patients assigned to the high-risk group solely by the presence of MYCN oncogene amplification (MNA). Methods: Clinical characteristics, genomic information, and outcome of 190 patients solely assigned to high-risk neuroblastoma by MNA were analyzed and compared to 205 patients with stage 4 neuroblastoma aged ≥18 months with MNA (control group). Results: Event-free survival (EFS) and overall survival (OS) at 10 years were 47% (95%-CI 39–54%) and 56% (95%-CI 49–63%), respectively, which was significantly better than EFS and OS of the control group (EFS 25%, 95%-CI 18–31%, p < 0.001; OS 32% 95%-CI 25–39%, p < 0.001). The presence of RAS-/p53-pathway gene alterations was associated with impaired 10-year EFS and OS (19% vs. 55%, and 19% vs. 67%, respectively; both p < 0.001). In time-dependent multivariable analyses, alterations of RAS-/p53-pathway genes and the extent of the best primary tumor resection were the only independent prognostic variables for OS (p < 0.001 and p = 0.011, respectively). Conclusions: Neuroblastoma patients attributed to high risk solely by MYCN amplification have generally a more favorable outcome. Mutations of genes of the RAS and/or p53 pathways and incomplete resection are the main risk factors predicting poor outcome.


2020 ◽  
Author(s):  
Eunjin Lee ◽  
Ji Won Lee ◽  
Boram Lee ◽  
Kyunghee Park ◽  
Joonho Shim ◽  
...  

Abstract Background: MYCN amplification is the most important genomic feature in neuroblastoma (NB). However, limited studies have been conducted on the MYCN non-amplified NB including low- and intermediate-risk NB. Here, the genomic characteristics of MYCN non-amplified NB were studied to allow for the identification of biomarkers for molecular stratification. Methods: Fifty-eight whole exome sequencing (WES) and 48 whole transcriptome sequencing (WTS) samples of MYCN non-amplified NB were analysed. Forty-one patients harboured WES and WTS pairs . Results: In the MYCN non-amplified NB WES data, maximum recurrent mutations were found in MUC4 (26%), followed by RBMXL3 (19%), ALB (17%), and MUC16 and SEPD8 (14% each). Two gene fusions, CCDC32 - CBX3 (10%) and SAMD5 - SASH1 (6%), were recurrent in WTS analysis, and these fusions were detected mostly in non-high-risk patients with ganglioneuroblastoma histology. Analysis of risk-group-specific biomarkers showed that several genes and gene sets were differentially expressed between the risk groups, and some immune-related pathways tended to be activated in the high-risk group. Mutational signatures 6 and 18, which represent DNA mismatch repair (MMR) associated mutations, were commonly detected in 60% of the patients. In the tumour mutation burden (TMB) analysis, four patients showed high TMB (> 3 mutations/Mb), and had mutations in genes related to either MMR or homologous recombination. Excluding four outlier samples with TMB > 3 Mb, high-risk patients had significantly higher levels of TMB compared with the non-high-risk patients. Conclusions: This study provides novel insights into the genomic background of MYCN non-amplified NB. Activation of immune-related pathways in the high-risk group and the results of TMB and mutational signature analyses collectively suggest the need for further investigation to discover potential immunotherapeutic strategies for NB.


VASA ◽  
2009 ◽  
Vol 38 (3) ◽  
pp. 225-233 ◽  
Author(s):  
Aleksic ◽  
Luebke ◽  
Brunkwall

Background: In the present study the perioperative complication rate is compared between high- and low-risk patients when carotid endarterectomy (CEA) is routinely performed under local anaesthesia (LA). Patients and methods: From January 2000 through June 2008 1220 consecutive patients underwent CEA under LA. High-risk patients fulfilled at least one of the following characteristics: ASA 4 classification, “hostile neck”, recurrent ICA stenosis, contralateral ICA occlusion, age ≥ 80 years. The combined complication rate comprised any new neurological deficit (TIA or stroke), myocardial infarction or death within 30 days after CEA, which was compared between patient groups. Results: Overall 309 patients (25%) were attributed to the high-risk group, which differed significantly regarding sex distribution (more males: 70% vs. 63%, p = 0,011), neurological presentation (more asymptomatic: 72% vs. 62%, p = 0,001) and shunt necessity (33% vs. 14%, p < 0,001). In 32 patients 17 TIAs and 15 strokes were observed. In 3 patients a myocardial infarction occurred. Death occurred in one patient following a stroke and in another patient following myocardial infarction, leading to a combined complication rate of 2,9% (35/1220). In the multivariate analysis only previous neurological symptomatology (OR 2,85, 95% CI 1,38-5,91) and intraoperative shunting (OR 5,57, 95% CI 2,69-11,55) were identified as independent risk factors for an increased combined complication rate. Conclusions: With the routine use of LA, CEA was not associated with worse outcome in high-risk patients. Considering the data reported in the literature, it does not appear justified to refer high-risk patients principally to carotid angioplasty and stenting (CAS) when LA can be chosen to perform CEA.


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