Examining the biomarkers and molecular mechanisms of medulloblastoma based on bioinformatics analysis

A Prognostic Methylation-Driven Two-Gene Signature in Medulloblastoma

Medulloblastoma (MB) is one of the most common pediatric brain tumors and it is estimated that one-third of patients will not achieve long-term survival. Conventional prognostic parameters have limited and unreliable correlations with MB outcome, presenting a major challenge for patients' clinical improvement. Acknowledging this issue, our aim was to build a gene signature and evaluate its potential as a new prognostic model for patients with the disease. In this study, we used six datasets totaling 1679 samples including RNA gene expression and DNA methylation data from primary MB as well as control samples from healthy cerebellum. We identified methylation-driven genes (MDGs) in MB, genes whose expression is correlated with their methylation. We employed LASSO regression, incorporating the MDGs as a parameter to develop the prognostic model. Through this approach, we derived a two-gene signature (GS-2) of candidate prognostic biomarkers for MB (CEMIP and NCBP3). Using a risk score model, we confirmed the GS-2 impact on overall survival (OS) with Kaplan-Meier analysis. We evaluated its robustness and accuracy with receiver operating characteristic curves predicting OS at 1, 3, and 5 years in multiple independent datasets. The GS-2 showed highly significant results as an independent prognostic biomarker compared to traditional MB markers. The methylation-regulated GS-2 risk score model can effectively classify patients with MB into high and low-risk, reinforcing the importance of this epigenetic modification in the disease. Such genes stand out as promising prognostic biomarkers with potential application for MB treatment.

Hindbrain boundaries as niches of neural progenitor and stem cells regulated by the extracellular matrix proteoglycan chondroitin sulphate

The interplay between neural progenitors and stem cells (NPSCs), and their extracellular matrix (ECM) is a crucial regulatory mechanism that determines their behavior. Nonetheless, how the ECM dictates the state of NPSCs remains elusive. The hindbrain is valuable to examine this relationship, as cells in the ventricular surface of hindbrain boundaries (HBs), which arise between any two neighboring rhombomeres, express the NPSC marker Sox2, while being surrounded with the membrane-bound ECM molecule chondroitin sulphate proteoglycan (CSPG), in chick and mouse embryos. CSPG expression was used to isolate HB Sox2+ cells for RNA-sequencing, revealing their distinguished molecular properties as typical NPSCs, which express known and newly identified genes relating to stem cells, cancer, the matrisome and cell cycle. In contrast, the CSPG- non-HB cells, displayed clear neural-differentiation transcriptome. To address whether CSPG is significant for hindbrain development, its expression was manipulated in vivo and in vitro. CSPG manipulations shifted the stem versus differentiation state of HB cells, evident by their behavior and altered gene expression. These results provide further understanding of the uniqueness of hindbrain boundaries as repetitive pools of NPSCs in-between the rapidly growing rhombomeres, which rely on their microenvironment to maintain their undifferentiated state during development.

Transcriptomic profiling identifies differentially expressed genes and related pathways associated with wound healing and cuproptosis-related genes in Ganxi goats

Introduction

Wound healing is very important for the maintenance of immune barrier integrity, which has attracted wide attention in past 10 years. However, no studies on the regulation of cuproptosis in wound healing have been reported.

Methods

In this study, the skin injury model was constructed in Gnxi goats, and the function, regulatory network and hub genes of the skin before and after the injury were comprehensively analyzed by transcriptomics.

Results

The results showed that there were 1,438 differentially expressed genes (DEGs), genes up-regulated by 545 and genes down-regulated by 893, which were detected by comparing day 0 and day 5 posttraumatic skin. Based on GO-KEGG analysis, DEGs that were up-regulated tended to be enriched in lysosome, phagosome, and leukocyte transendothelial migration pathways, while down-regulated DEGs were significantly enriched in adrenergic signaling in cardiomyocytes and calcium signaling pathway. There were 166 overlapped genes (DE-CUGs) between DEGs and cuproptosis-related genes, with 72 up-regulated DE-CUGs and 94 down-regulated DE-CUGs. GOKEGG analysis showed that up-regulated DE-CUGs were significantly enriched in ferroptosis, leukocyte transendothelial migration and lysosome pathways, while down-regulated DE-CUGs were significantly enriched in Apelin signaling pathway and tyrosine metabolism pathways. By constructing and analyzing of protein-protein interaction (PPI) networks of DEGs and DE-CUGs, 10 hub DEGs (ENSCHIG00000020079, PLK1, AURKA, ASPM, CENPE, KIF20A, CCNB2, KIF2C, PRC1 and KIF4A) and 10 hub DE-CUGs (MMP2, TIMP1, MMP9, MMP14, TIMP3, MMP1, EDN1, GCAT, SARDH, and DCT) were obtained, respectively.

Discussion

This study revealed the hub genes and important wound healing pathways in Ganxi goats, and identified the correlation between wound healing and cuproptosis for the first time, and found that MMP2, TIMP1, MMP9, and EDN1 were the core genes associated. This study enriched the transcriptome data of wound healing in Ganxi goats and expanded the research direction of cuproptosis.

TOP2A correlates with poor prognosis and affects radioresistance of medulloblastoma

Radiotherapy remains the standard treatment for medulloblastoma (MB), and the radioresistance contributes to tumor recurrence and poor clinical outcomes. Nuclear DNA topoisomerase II-alpha (TOP2A) is a key catalytic enzyme that initiates DNA replication, and studies have shown that TOP2A is closely related to the therapeutic effects of radiation. In this study, we found that TOP2A was significantly upregulated in MB, and high expression of TOP2A related to poor prognosis of MB patients. Knockdown of TOP2A inhibited MB cell proliferation, migration, and invasion, whereas overexpression of TOP2A enhanced the proliferative and invasive ability of MB cells. Moreover, si-TOP2A transfection in combination with irradiation (IR) significantly reduced the tumorigenicity of MB cells, compared with those transfected with si-TOP2A alone. Cell survival curve analysis revealed that the survival fraction of MB cells was significantly reduced upon TOP2A downregulation and that si-TOP2A-transfected cells had decreased D₀, Dq, and SF₂ values, indicating that TOP2A knockdown suppresses the resistance to radiotherapy in MB cells. In addition, western blot analysis demonstrated that the activity of Wnt/β-catenin signaling pathway was inhibited after TOP2A downregulation alone or in combination with IR treatment, whereas overexpression of TOP2A exhibited the opposite effects. Gene set enrichment analysis also revealed that Wnt/β-catenin signaling pathway is enriched in TOP2A high-expression phenotypes. Collectively, these data indicate that high expression of TOP2A leads to poor prognosis of MB, and downregulation of TOP2A inhibits the malignant behaviour as well as the radioresistance of MB cells. The Wnt/β-catenin signaling pathway may be involved in the molecular mechanisms of TOP2A mediated reduced tumorigenicity and radioresistance of MB cells.

Prognostic role of NLGN2 and PTGDS in medulloblastoma based on gene expression omnibus

BACKGROUND

Medulloblastoma (MB) is the most common intracranial malignant tumour in children, but genes and pathways involved in its pathogenesis are still under investigation. This study was designed to screen and identify biomarkers of MB to provide markers for clinical diagnosis and prognosis assessment.

METHODS

The data sets of GSE109401 and GSE42656 were acquired from Gene expression omnibus (GEO). Limma package in R was adopted to identify the differentially expressed genes (DEGs), and the GSE30074 data set was adopted to analyse their prognostic role. Children with MB (n=55) diagnosed in Affiliated Ezhou Central Hospital were enrolled and assigned to the patient group, and healthy children (n=30) who received physical examination in our hospital during the same time period were assigned to the control group. The two groups were compared in serum NLGN2 and PTGDS levels, and all patients were followed up for three years to understand the associations of Neuroligin 2 (NLGN2) and Prostaglandin D2 synthase (PTGDS) with the survival of patients.

RESULTS

With Limma, 247 DEGs were screened out. The LASSO-Cox regression analysis revealed that 6 genes were associated with MB prognosis, and the established model revealed a lower survival rate in the high-risk group. According to Cox regression analysis, NLGN2 and PTGDS may be independent prognostic factors of MB. Similar to the data sets, the Real time-quantitative polymerase chain reaction (RT-qPCR) assay revealed lowly-expressed NLGN2 and PTGDS levels in MB patients, and patients with lower expression of them showed a lower 3-year survival rate.

CONCLUSION

With low expression in MB cases, NLGN2 and PTGDS have high prognostic value for MB.

Integrated Analysis of Cancer Tissue and Vitreous Humor from Retinoblastoma Eyes Reveals Unique Tumor-Specific Metabolic and Cellular Pathways in Advanced and Non-Advanced Tumors

Retinoblastoma (Rb) is a pediatric intraocular malignancy that is proposed to originate from maturing cone cell precursors in the developing retina. The molecular mechanisms underlying the biological and clinical behaviors are important to understand in order to improve the management of advanced-stage tumors. While the genetic causes of Rb are known, an integrated understanding of the gene expression and metabolic processes in tumors of human eyes is deficient. By integrating transcriptomic profiling from tumor tissues and metabolomics from tumorous eye vitreous humor samples (with healthy, age-matched pediatric retinae and vitreous samples as controls), we uncover unique functional associations between genes and metabolites. We found distinct gene expression patterns between clinically advanced and non-advanced Rb. Global metabolomic analysis of the vitreous humor of the same Rb eyes revealed distinctly altered metabolites, indicating how tumor metabolism has diverged from healthy pediatric retina. Several key enzymes that are related to cellular energy production, such as hexokinase 1, were found to be reduced in a manner corresponding to altered metabolites; notably, a reduction in pyruvate levels. Similarly, E2F2 was the most significantly elevated E2F family member in our cohort that is part of the cell cycle regulatory circuit. Ectopic expression of the wild-type RB1 gene in the Rb-null Y79 and WERI-Rb1 cells rescued hexokinase 1 expression, while E2F2 levels were repressed. In an additional set of Rb tumor samples and pediatric healthy controls, we further validated differences in the expression of HK1 and E2F2. Through an integrated omics analysis of the transcriptomics and metabolomics of Rb, we uncovered a significantly altered tumor-specific metabolic circuit that reduces its dependence on glycolytic pathways and is governed by Rb1 and HK1.

Integrated weighted gene coexpression network analysis identifies Frizzled 2 (FZD2) as a key gene in invasive malignant pleomorphic adenoma

Background

Invasive malignant pleomorphic adenoma (IMPA) is a highly malignant neoplasm of the oral salivary glands with a poor prognosis and a considerable risk of recurrence. Many disease-causing genes of IMPA have been identified in recent decades (e.g., P53, PCNA and HMGA2), but many of these genes remain to be explored. Weighted gene coexpression network analysis (WGCNA) is a newly emerged algorithm that can cluster genes and form modules based on similar gene expression patterns. This study constructed a gene coexpression network of IMPA via WGCNA and then carried out multifaceted analysis to identify novel disease-causing genes.

Methods

RNA sequencing (RNA-seq) was performed for 10 pairs of IMPA and normal tissues to acquire the gene expression profiles. Differentially expressed genes (DEGs) were screened out with the cutoff criteria of |log₂ Fold change (FC)|> 1 and adjusted p value  < 0.05. Then, WGCNA was applied to systematically identify the hidden diagnostic hub genes of IMPA.

Results

In this research, a total of 1970 DEGs were screened out in IMPA tissues, including 1056 upregulated DEGs and 914 downregulated DEGs. Functional enrichment analysis was performed for identified DEGs and revealed an enrichment of tumor-associated GO terms and KEGG pathways. We used WGCNA to identify gene module most relevant with the histological grade of IMPA. The gene FZD2 was then recognized as the hub gene of the selected module with the highest module membership (MM) value and intramodule connectivity in protein–protein interaction (PPI) network. According to immunohistochemistry (IHC) staining, the expression level of FZD2 was higher in low-grade IMPA than in high-grade IMPA.

Conclusion

FZD2 shows an expression dynamic that is negatively correlated with the clinical malignancy of IMPA and it plays a central role in the transcription network of IMPA. Thus, FZD2 serves as a promising histological indicator for the precise prediction of IMPA histological stages.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12967-021-03204-7.

Prognostic Value of miR-137 in Children with Medulloblastoma and its Regulatory Effect on Tumor Progression

Medulloblastoma is a malignant tumor with high incidence and poor prognosis in adolescents and children. MicroRNA-137 (miR-137) has been found to be abnormally expressed in cancers such as pancreatic cancer. The purpose of this study is to explore the expression of miR-137 in MB and its role in cell physiological activities to determine the significance of miR-137 in the prognosis of MB. First, the expression of miR-137 in MB tissues and cell lines was analyzed by qRT-PCR. Then the Kaplan-Meier survival curve was used to analyze the significance of miR-137 expression in the prognosis, and the Cox regression model was used to explore the correlation between miR-137 expression and clinical characteristics. The effects of miR-137 on MB cell activities were analyzed by MTT assay, Transwell assays, and flow cytometry. It can be concluded from the results that the expression of miR-137 is down-regulated in MB tissues and cells. The down-regulation of miR-137 was significantly related to the poor prognosis of MB, and significantly related to clinical indicators. Up-regulated miR-137 inhibited cell proliferation, migration, invasion, and cell cycle progression, as well as induced cell apoptosis by targeting KDM1A. This study can conclude that miR-137 may be used as a prognostic biomarker of MB.

Identification of Core Genes and Pathways in Medulloblastoma by Integrated Bioinformatics Analysis

Medulloblastoma (MB) is one of the most common intracranial malignancies in children. The present study applied integrated bioinformatics to identify potential core genes associated with the pathogenesis of MB and reveal potential molecular mechanisms. Through the integrated analysis of multiple data sets from the Gene Expression Omnibus (GEO), 414 differentially expressed genes (DEGs) were identified. Combining the protein-protein interaction (PPI) network analysis with gene set enrichment analysis (GSEA), eight core genes, including CCNA2, CCNB1, CCNB2, AURKA, CDK1, MAD2L1, BUB1B, and RRM2, as well as four core pathways, including "cell cycle", "oocyte meiosis", "p53 pathway" and "DNA replication" were selected. In independent data sets, the core genes showed superior diagnostic values and significant prognostic correlations. Moreover, in the pan-caner data of the cancer genome atlas (TCGA), the core genes were also widely abnormally expressed. In conclusion, this study identified core genes and pathways of MB through integrated analysis to deepen the understanding of the molecular mechanisms underlying the MB and provide potential targets and pathways for diagnosis and treatment of MB.

Long Noncoding RNA TP73-AS1 Modulates Medulloblastoma Progression In Vitro And In Vivo By Sponging miR-494-3p And Targeting EIF5A2

Background

Previous studies have shown that P73 antisense RNA 1T (non-protein coding), also known as TP73-AS1, is a long non-coding RNA (lncRNA) and involved in the development of medulloblastoma. However, the regulatory mechanism of lncRNA TP73-AS1 in medulloblastoma was still unclear, the present study was aimed to investigate the detailed functions and the mechanism of TP73-AS1 in regulation of medulloblastoma.

Materials and methods

The levels of TP73-AS1, miR-494-3p, and Eukaryotic initiation factor 5A2 (EIF5A2) were determined using quantitative real-time PCR (qRT-PCR), in situ hybridization (ISH), or Immunohistochemistry (IHC). The function of TP73-AS1 in proliferation, apoptosis, migration, and invasion of medulloblastoma cells was evaluated using cell counting Kit-8 (CCK-8), flow cytometry, and transwell assay, respectively. The protein levels were determined by Western blot. Bioinformatics analysis and dual-luciferase reporter assay, RNA immunoprecipitation (RIP) and pull-down assay were used to search and confirm the target gene of TP73-AS1 and miR-494-3p. The effect of TP73-AS1 knockdown in vivo was detected by animal experiment.

Results

The levels of TP73-AS1 and EIF5A2 were up-regulated, while miR-494-3p expression was down-regulated in medulloblastoma tissues and cells, ELF5A2 was a direct target of miR-494-3p, and miR-494-3p bound to TP73-AS1. The knockdown of TP73-AS1 inhibited cell proliferation, invasion, migration, and promoted apoptosis of medulloblastoma cells, while the miR-494-3p inhibitor abolished the effects of TP73-AS1 knockdown on medulloblastoma cells.

Conclusion

TP73-AS1 positively regulated EIF5A2 expression by sponging miR-494-3p. These findings suggested that TP73-AS1 served as an oncogene and promoted the progression of medulloblastoma.