Identification of Global DNA Methylation Signatures in Glioblastoma-Derived Cancer Stem Cells

Exploring Combined Effects of DNA Methylation and Copy Number on Gene Expression With a Two-Stage Approach

DNA methylation and copy number may be associated with each other to some extent, in positive or negative ways. Whether differential methylation and copy number variation have combined effects on gene expression is largely unknown. We use a multivariate linear model to formulate the relationship among the three genomic measurements, gene expression, copy number, and methylation levels. We propose a method that combines a distance covariance measure and the group LASSO to analyze multiple types of genomic data collectively for the purpose of insightfully revealing how gene expression is potentially affected by both copy number variation and differential methylation levels in cellular process. Our approach is of two stages, the first is a variable screening process in which a variable selection method is utilized by employing the concept of joint distance covariance (JdCov) of random vectors, and the second is to implement a penalized regression approach, a group LASSO, on the screened data of much lower dimension. The two-stage approach is tested in extensive simulation studies and shown to be effective. The approach is then applied to the TCGA Melanoma data, which consists of gene expression, methylation and copy number measurements of more than 300 patients and relationship of some genes with methylation and copy number measurements were revealed for the involved subjects.

A novel BRAF::PTPRN2 fusion in meningioma: a case report

Gene fusion events have been linked to oncogenesis in many cancers. However, gene fusions in meningioma are understudied compared to somatic mutations, chromosomal gains/losses, and epigenetic changes. Fusions involving B-raf proto-oncogene, serine/threonine kinase (BRAF) are subtypes of oncogenic BRAF genetic abnormalities that have been reported in certain cases of brain tumors, such as pilocytic astrocytomas. However, BRAF fusions have not been recognized in meningioma. We present the case of an adult female presenting with episodic partial seizures characterized by déjà vu, confusion, and cognitive changes. Brain imaging revealed a cavernous sinus and sphenoid wing mass and she underwent resection. Histopathology revealed a World Health Organization (WHO) grade 1 meningioma. Genetic profiling with next generation sequencing and microarray analysis revealed an in-frame BRAF::PTPRN2 fusion affecting the BRAF kinase domain as well as chromothripsis of chromosome 7q resulting in multiple segmental gains and losses including amplifications of cyclin dependent kinase 6 (CDK6), tyrosine protein-kinase Met (MET), and smoothened (SMO). Elevated pERK staining in tumor cells provided evidence of activated mitogen-activated protein kinase (MAPK) signaling. This report raises the possibility that gene fusion events may be involved in meningioma pathogenesis and warrant further investigation.

Preclinical Efficacy of LP-184, a Tumor Site Activated Synthetic Lethal Therapeutic, in Glioblastoma

PURPOSE

Glioblastoma (GBM) is the most common brain malignancy with median survival <2 years. Standard-of-care temozolomide has marginal efficacy in approximately 70% of patients due to MGMT expression. LP-184 is an acylfulvene-derived prodrug activated by the oxidoreductase PTGR1 that alkylates at N3-adenine, not reported to be repaired by MGMT. This article examines LP-184 efficacy against preclinical GBM models and identifies molecular predictors of LP-184 efficacy in clinical GBM.

EXPERIMENTAL DESIGN

LP-184 effects on GBM cell viability and DNA damage were determined using cell lines, primary PDX-derived cells and patient-derived neurospheres. GBM cell sensitivities to LP-184 relative to temozolomide and MGMT expression were examined. Pharmacokinetics and CNS bioavailability were evaluated in mice with GBM xenografts. LP-184 effects on GBM xenograft growth and animal survival were determined. Machine learning, bioinformatic tools, and clinical databases identified molecular predictors of GBM cells and tumors to LP-184 responsiveness.

RESULTS

LP-184 inhibited viability of multiple GBM cell isolates including temozolomide-resistant and MGMT-expressing cells at IC50 = approximately 22-310 nmol/L. Pharmacokinetics showed favorable AUCbrain/plasma and AUCtumor/plasma ratios of 0.11 (brain Cmax = 839 nmol/L) and 0.2 (tumor Cmax = 2,530 nmol/L), respectively. LP-184 induced regression of GBM xenografts and prolonged survival of mice bearing orthotopic xenografts. Bioinformatic analyses identified PTGR1 elevation in clinical GBM subtypes and associated LP-184 sensitivity with EGFR signaling, low nucleotide excision repair (NER), and low ERCC3 expression. Spironolactone, which induces ERCC3 degradation, decreased LP-184 IC50 3 to 6 fold and enhanced GBM xenograft antitumor responses.

CONCLUSIONS

These results establish LP-184 as a promising chemotherapeutic for GBM with enhanced efficacy in intrinsic or spironolactone-induced TC-NER-deficient tumors.

Hypermethylation of HIC2 is a potential prognostic biomarker and tumor suppressor of glioma based on bioinformatics analysis and experiments

INTRODUCTION

Glioma is the most common primary tumor in the central nervous system, and prognostic biomarkers are still lacking. HIC ZBTB transcriptional repressor 2 (HIC2) is a hypermethylated gene that plays an important functional role in cardiac development. However, the actual role of HIC2 in glioma progression remains unclear. This study aimed to investigate the function of HIC2 and whether it could be a prognostic biomarker in glioma.

METHODS

The DNA methylation and mRNA expression profiles of HIC2 were downloaded from public databases. The prognostic prediction ability and mechanism research of HIC2 were evaluated.

RESULTS

We found that HIC2 was hypermethylated and expressed at low levels in glioma samples. Hypermethylation and low expression of HIC2 predicted poor prognosis. Multivariate Cox regression analysis suggested that HIC2 was an independent prognostic factor for gliomas. Co-IP assays demonstrated that HIC2 interacts with RNF44, and dual-luciferase reporter assays and ChIP assays revealed that HIC2 transcriptionally inhibits PTPRN2 expression.

CONCLUSIONS

Our findings suggest that HIC2 represents a tumor suppressor gene and prognostic biomarker for glioma progression and that overexpression of HIC2 inhibits the proliferation of glioma in vitro and in vivo by interacting with RNF44 and PTPRN2.

Advances in 3D culture systems for therapeutic discovery and development in brain cancer

This review focuses on recent advances in 3D culture systems that promise more accurate therapeutic models of the glioblastoma multiforme (GBM) tumor microenvironment (TME), such as the unique anatomical, cellular, and molecular features evident in human GBM. The key components of a GBM TME are outlined, including microbiomes, vasculature, extracellular matrix (ECM), infiltrating parenchymal and peripheral immune cells and molecules, and chemical gradients. 3D culture systems are evaluated against 2D culture systems and in vivo animal models. The main 3D culture techniques available are compared, with an emphasis on identifying key gaps in knowledge for the development of suitable platforms to accurately model the intricate components of the GBM TME.

Molecular Pathways and Genomic Landscape of Glioblastoma Stem Cells: Opportunities for Targeted Therapy

Glioblastoma (GBM) is an aggressive tumor of the central nervous system categorized by the World Health Organization as a Grade 4 astrocytoma. Despite treatment with surgical resection, adjuvant chemotherapy, and radiation therapy, outcomes remain poor, with a median survival of only 14-16 months. Although tumor regression is often observed initially after treatment, long-term recurrence or progression invariably occurs. Tumor growth, invasion, and recurrence is mediated by a unique population of glioblastoma stem cells (GSCs). Their high mutation rate and dysregulated transcriptional landscape augment their resistance to conventional chemotherapy and radiation therapy, explaining the poor outcomes observed in patients. Consequently, GSCs have emerged as targets of interest in new treatment paradigms. Here, we review the unique properties of GSCs, including their interactions with the hypoxic microenvironment that drives their proliferation. We discuss vital signaling pathways in GSCs that mediate stemness, self-renewal, proliferation, and invasion, including the Notch, epidermal growth factor receptor, phosphatidylinositol 3-kinase/Akt, sonic hedgehog, transforming growth factor beta, Wnt, signal transducer and activator of transcription 3, and inhibitors of differentiation pathways. We also review epigenomic changes in GSCs that influence their transcriptional state, including DNA methylation, histone methylation and acetylation, and miRNA expression. The constituent molecular components of the signaling pathways and epigenomic regulators represent potential sites for targeted therapy, and representative examples of inhibitory molecules and pharmaceuticals are discussed. Continued investigation into the molecular pathways of GSCs and candidate therapeutics is needed to discover new effective treatments for GBM and improve survival.

Effect of aberrant DNA methylation on cancer stem cell properties

DNA methylation, as an epigenetic mechanism, occurs by adding a methyl group of cytosines in position 5 by DNA methyltransferases and has essential roles in cellular function, especially in the transcriptional regulation of embryonic and adult stem cells. Hypomethylation and hypermethylation cause either the expression or inhibition of genes, and there is a tight balance between regulating the activation or repression of genes in normal cellular activity. Abnormal methylation is well-known hallmark of cancer development and progression and can switch normal stem cells into cancer stem cells. Cancer Stem Cells (CSCs) are minor populations of tumor cells that exhibit unique properties such as self-regeneration, resistance to chemotherapy, and high ability of metastasis. The purpose of this paper is to show how aberrant DNA methylation accumulation affects self-renewal, differentiation, multidrug-resistant, and metastasis processes in cancer stem cells.

Epigenetic modifications from arsenic exposure: A comprehensive review

Arsenic is a notorious element with the potential to harm exposed individuals in ways that include cancerous and non-cancerous health complications. Millions of people across the globe (especially in South and Southeast Asian countries including China, Vietnam, India and Bangladesh) are currently being unknowingly exposed to precarious levels of arsenic. Among the diverse effects associated with such arsenic levels of exposure is the propensity to alter the epigenome. Although a large volume of literature exists on arsenic-induced genotoxicity, cytotoxicity, and inter-individual susceptibility due to active research on these subject areas from the last millennial, it is only recently that attention has turned on the ramifications and mechanisms of arsenic-induced epigenetic changes. The present review summarizes the possible mechanisms involved in arsenic induced epigenetic alterations. It focuses on the mechanisms underlying epigenome reprogramming from arsenic exposure that result in improper cell signaling and dysfunction of various epigenetic components. The mechanistic information articulated from the review is used to propose a number of novel therapeutic strategies with a potential for ameliorating the burden of worldwide arsenic poisoning.

Sweet Taste Preference: Relationships with Other Tastes, Liking for Sugary Foods and Exploratory Genome-Wide Association Analysis in Subjects with Metabolic Syndrome

Taste perception and its association with nutrition and related diseases (type 2 diabetes, obesity, metabolic syndrome, cardiovascular, etc.) are emerging fields of biomedicine. There is currently great interest in investigating the environmental and genetic factors that influence sweet taste and sugary food preferences for personalized nutrition. Our aims were: (1) to carry out an integrated analysis of the influence of sweet taste preference (both in isolation and in the context of other tastes) on the preference for sugary foods and its modulation by type 2 diabetes status; (2) as well as to explore new genetic factors associated with sweet taste preference. We studied 425 elderly white European subjects with metabolic syndrome and analyzed taste preference, taste perception, sugary-foods liking, biochemical and genetic markers. We found that type 2 diabetic subjects (38%) have a small, but statistically higher preference for sweet taste (p = 0.021) than non-diabetic subjects. No statistically significant differences (p > 0.05) in preferences for the other tastes (bitter, salty, sour or umami) were detected. For taste perception, type 2 diabetic subjects have a slightly lower perception of all tastes (p = 0.026 for the combined “total taste score”), bitter taste being statistically lower (p = 0.023). We also carried out a principal component analysis (PCA), to identify latent variables related to preferences for the five tastes. We identified two factors with eigenvalues >1. Factor 2 was the one with the highest correlation with sweet taste preference. Sweet taste preference was strongly associated with a liking for sugary foods. In the exploratory SNP-based genome-wide association study (GWAS), we identified some SNPs associated with sweet taste preference, both at the suggestive and at the genome-wide level, especially a lead SNP in the PTPRN2 (Protein Tyrosine Phosphatase Receptor Type N2) gene, whose minor allele was associated with a lower sweet taste preference. The PTPRN2 gene was also a top-ranked gene obtained in the gene-based exploratory GWAS analysis. In conclusion, sweet taste preference was strongly associated with sugary food liking in this population. Our exploratory GWAS identified an interesting candidate gene related with sweet taste preference, but more studies in other populations are required for personalized nutrition.

FOXO3 regulates a common genomic program in aging and glioblastoma stem cells

Background

Glioblastoma (GBM) is an aggressive, age-associated malignant glioma that contains populations of cancer stem cells. These glioma stem cells (GSCs) evade therapeutic interventions and repopulate tumors due to their existence in a slowly cycling quiescent state. Although aging is well known to increase cancer initiation, the extent to which the mechanisms supporting GSC tumorigenicity are related to physiological aging remains unknown.

Aims

Here, we investigate the transcriptional mechanisms by which Forkhead Box O3 (FOXO3), a transcriptional regulator that promotes healthy aging, affects GSC function and the extent to which FOXO3 transcriptional networks are dysregulated in aging and GBM.

Methods and results

We performed transcriptome analysis of clinical GBM tumors and observed that high FOXO3 activity is associated with gene expression signatures of stem cell quiescence, reduced oxidative metabolism, and improved patient outcomes. Consistent with these findings, we show that elevated FOXO3 activity significantly reduces the proliferation of GBM-derived GSCs. Using RNA-seq, we find that functional ablation of FOXO3 in GSCs rewires the transcriptional circuitry associated with metabolism, epigenetic stability, quiescence, and differentiation. Since FOXO3 has been implicated in healthy aging, we then investigated the extent to which it regulates common transcriptional programs in aging neural stem cells (NSCs) and GSCs. We uncover a shared transcriptional program and, most strikingly, find that FOXO3-regulated pathways are associated with altered mitochondrial functions in both aging and GBM.

Conclusions

This work identifies a FOXO-associated transcriptional program that correlates between GSCs and aging NSCs and is enriched for metabolic and stemness pathways connected with GBM and aging.

Functional Characterization of Brain Tumor-Initiating Cells and Establishment of GBM Preclinical Models that Incorporate Heterogeneity, Therapy, and Sex Differences

Glioblastoma (GBM) is the most common primary brain cancer in adults where tumor cell heterogeneity and sex differences influence clinical outcomes. Here, we functionally characterize three male and three female patient-derived GBM cell lines, identify protumorigenic BTICs, and create novel male and female preclinical models of GBM. Cell lines were evaluated on the following features: proliferation, stemness, migration, tumorigenesis, clinical characteristics, and sensitivity to radiation, TMZ, rhTNFSF10 (rhTRAIL), and rhBMP4 All cell lines were classified as GBM according to epigenetic subtyping, were heterogenous and functionally distinct from one another, and re-capitulated features of the original patient tumor. In establishing male and female preclinical models, it was found that two male-derived GBM cell lines (QNS108 and QNS120) and one female-derived GBM cell line (QNS315) grew at a faster rate in female mice brains. One male-derived GBM cell line (QNS108) decreased survival in female mice in comparison with male mice. However, no survival differences were observed for mice injected with a female-derived cell line (QNS315). In summary, a panel of six GBM patient-derived cell lines were functionally characterized, and it was shown that BTIC lines can be used to construct sex-specific models with differential phenotypes for additional studies.

Development of a Machine Learning Classifier for Brain Tumors Diagnosis Based on DNA Methylation Profile

Background: More than 150 types of brain tumors have been documented. Accurate diagnosis is important for making appropriate therapeutic decisions in treating the diseases. The goal of this study is to develop a DNA methylation profile-based classifier to accurately identify various kinds of brain tumors.

Methods: Thirteen datasets of DNA methylation profiles were downloaded from the Gene Expression Omnibus (GEO) database, of which GSE90496 and GSE109379 were used as the training set and the validation set, respectively, and the remaining 11 sets were used as the independent test set. The random forest algorithm was used to select the CpG sites based on the importance of the features and a multilayer perceptron (MLP) model was trained to classify the samples. Deconvolution with the debCAM package was used to explore the cellular composition difference among tumors.

Results: From training datasets with 2,801 samples, 396,568 CpG sites were retained after preprocessing, of which 767 were selected as the modeling features. A three-layer MLP model was developed, which consists of 1,320 nodes in the hidden layer, to predict the histological types of brain tumors. The prediction accuracy is 99.2, 87.0, and 96.58%, respectively, on the training, validation and test sets. The results of deconvolution analysis showed that the cell proportions of different tumor subtypes were different, and it is approximately enough to distinguish different tumor entities.

Conclusion: We developed a classifier that is robust for the classification of central nervous system tumors, and tried to analyze the reasons for the classification performance.

In Vitro Glioblastoma Models: A Journey into the Third Dimension

Simple Summary

In this review, the thorny issue of glioblastoma models is addressed, with a focus on 3D in vitro models. In the first part of the manuscript, glioblastoma features and classification are recapitulated, in order to highlight the major critical aspects that should be taken into account when choosing a glioblastoma 3D model. In the second part of the review, the 3D models described in the literature are critically discussed, considering the advantages, disadvantages, and feasibility for each experimental model, in the light of the potential issues that researchers want to address.

Abstract

Glioblastoma multiforme (GBM) is the most lethal primary brain tumor in adults, with an average survival time of about one year from initial diagnosis. In the attempt to overcome the complexity and drawbacks associated with in vivo GBM models, together with the need of developing systems dedicated to screen new potential drugs, considerable efforts have been devoted to the implementation of reliable and affordable in vitro GBM models. Recent findings on GBM molecular features, revealing a high heterogeneity between GBM cells and also between other non-tumor cells belonging to the tumoral niche, have stressed the limitations of the classical 2D cell culture systems. Recently, several novel and innovative 3D cell cultures models for GBM have been proposed and implemented. In this review, we first describe the different populations and their functional role of GBM and niche non-tumor cells that could be used in 3D models. An overview of the current available 3D in vitro systems for modeling GBM, together with their major weaknesses and strengths, is presented. Lastly, we discuss the impact of groundbreaking technologies, such as bioprinting and multi-omics single cell analysis, on the future implementation of 3D in vitro GBM models.

The evolution of the cancer stem cell state in glioblastoma: emerging insights into the next generation of functional interactions

Cellular heterogeneity is a hallmark of advanced cancers and has been ascribed in part to a population of self-renewing, therapeutically resistant cancer stem cells (CSCs). Glioblastoma (GBM), the most common primary malignant brain tumor, has served as a platform for the study of CSCs. In addition to illustrating the complexities of CSC biology, these investigations have led to a deeper understanding of GBM pathogenesis, revealed novel therapeutic targets, and driven innovation towards the development of next-generation therapies. While there continues to be an expansion in our knowledge of how CSCs contribute to GBM progression, opportunities have emerged to revisit this conceptual framework. In this review, we will summarize the current state of CSCs in GBM using key concepts of evolution as a paradigm (variation, inheritance, selection, and time) to describe how the CSC state is subject to alterations of cell intrinsic and extrinsic interactions that shape their evolutionarily trajectory. We identify emerging areas for future consideration, including appreciating CSCs as a cell state that is subject to plasticity, as opposed to a discrete population. These future considerations will not only have an impact on our understanding of this ever-expanding field but will also provide an opportunity to inform future therapies to effectively treat this complex and devastating disease.

miRNA-mediated loss of m6A increases nascent translation in glioblastoma

Within the glioblastoma cellular niche, glioma stem cells (GSCs) can give rise to differentiated glioma cells (DGCs) and, when necessary, DGCs can reciprocally give rise to GSCs to maintain the cellular equilibrium necessary for optimal tumor growth. Here, using ribosome profiling, transcriptome and m6A RNA sequencing, we show that GSCs from patients with different subtypes of glioblastoma share a set of transcripts, which exhibit a pattern of m6A loss and increased protein translation during differentiation. The target sequences of a group of miRNAs overlap the canonical RRACH m6A motifs of these transcripts, many of which confer a survival advantage in glioblastoma. Ectopic expression of the RRACH-binding miR-145 induces loss of m6A, formation of FTO/AGO1/ILF3/miR-145 complexes on a clinically relevant tumor suppressor gene (CLIP3) and significant increase in its nascent translation. Inhibition of miR-145 maintains RRACH m6A levels of CLIP3 and inhibits its nascent translation. This study highlights a critical role of miRNAs in assembling complexes for m6A demethylation and induction of protein translation during GSC state transition.

Epigenetic dynamics in cancer stem cell dormancy

Cancer remains one of the most challenging diseases despite significant advances of early diagnosis and therapeutic treatments. Cancerous tumors are composed of various cell types including cancer stem cells capable of self-renewal, proliferation, differentiation, and invasion of distal tumor sites. Most notably, these cells can enter a dormant cellular state that is resistant to conventional therapies. Thereby, cancer stem cells have the intrinsic potential for tumor initiation, tumor growth, metastasis, and tumor relapse after therapy. Both genetic and epigenetic alterations are attributed to the formation of multiple tumor types. This review is focused on how epigenetic dynamics involving DNA methylation and DNA oxidations are implicated in breast cancer and glioblastoma multiforme. The emergence and progression of these cancer types rely on cancer stem cells with the capacity to enter quiescence also known as a dormant cellular state, which dictates the distinct tumorigenic aggressiveness between breast cancer and glioblastomas.

Effect of alkylglycerone phosphate synthase on the expression levels of lncRNAs in glioma cells and its functional prediction

Alkylglycerone phosphate synthase (AGPS) is a key enzyme for ether ester synthesis and acts as an oncogene in malignant tumors. The present study aimed to investigate the effect of AGPS silencing on the expression levels of long non-coding RNAs (lncRNAs) and the co-expression with mRNAs in glioma U251 cells using microarray analysis. Furthermore, the underlying biological functions of crucial lncRNAs identified were investigated. It was discovered that in vitro U251 cell proliferation was suppressed following the genetic silencing of AGPS. Differentially expressed lncRNAs and mRNAs in U251 cells were sequenced following AGPS silencing. The results from the Gene Ontology analysis identified that the co-expressed mRNAs were mainly involved in biological processes, such as 'cellular response to hypoxia', 'extracellular matrix organization' and 'PERK-mediated unfolded protein response'. In addition, Kyoto Encyclopedia of Genes and Genomes signaling pathway enrichment analysis revealed that the co-expressed mRNAs were the most enriched in the 'AGE/RAGE signaling pathway in diabetic conditions'. Additionally, the PI3K/Akt and epidermal growth factor receptor signaling pathways serve important roles in tumor processes, for example carcinogenesis and angiogenesis. Furthermore, it was identified that the lncRNA AK093732 served a vital role in the regulatory network and the core pathway in this network regulated by this lncRNA was discovered to be the 'Cytokine-cytokine receptor interaction'. In conclusion, the findings of the present study suggested that AGPS may affect cell proliferation and the degree of malignancy. In addition, the identified lncRNAs and their co-expressed mRNAs screened using microarrays may have significant biological effects in the occurrence, development and metastasis of glioma, and thus may be novel markers of glioma.

Glioblastoma stem cells and Wnt signaling pathway: molecular mechanisms and therapeutic targets

Glioblastoma is the most common form of primary brain tumor. Glioblastoma stem cells play an important role in tumor formation by activation of several signaling pathways. Wnt signaling pathway is one such important pathway which helps cellular differentiation to promote tumor formation in the brain. Glioblastoma remains to be a highly destructive type of tumor despite availability of treatment strategies like surgery, chemotherapy, and radiation. Advances in the field of cancer biology have revolutionized therapy by allowing targeting of tumor-specific molecular deregulation. In this review, we discuss about the significance of glioblastoma stem cells in cancer progression through Wnt signaling pathway and highlight the clinical targets being potentially considered for therapy in glioblastoma.

LINC00294 negatively modulates cell proliferation in glioma through a neurofilament medium-mediated pathway via interacting with miR-1278

BACKGROUND

Accumulating long noncoding RNAs (lncRNAs) have been recognized to participate in glioma development. Nevertheless, knowledge of the role of linc00294 in glioma remains incomplete.

METHODS

Bioinformatics analysis predicted the differential expression of LINC00294 and neurofilament medium (NEFM) in tumors and normal tissues, as well as the binding between LINC00294 and miR-1278, miR-1278 and NEFM. Luciferase and RNA immunoprecipitation assays were used for the verification of interactions. The potential role of LINC00294 in glioma development was investigated using functional assays, singly and in parallel with its interplay with miR-1278 and NEFM. Cell counting kit-8 and EdU assays were applied to measure cellular proliferation, whereas the terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) method was employed to detect apoptosis.

RESULTS

A new lncRNA, LINC00294, was highly expressed in normal brain tissues. However, it was markedly down-regulated in GBM tissues and glioma cell lines. Overexpression of LINC00294 abates glioma cell proliferation but induces apoptosis. Meanwhile, tumor suppressor NEFM was revealed to be distinctly diminished in cancerous conditions and enhanced in glioma cells by LINC00294 up-regulation. Interactions of miR-1278 with LINC00294 or NEFM occur, and the expression of NEFM is up-regulated by LINC00294 through their competition with respect to binding to miR-1278. Finally, the rescue assays further confirmed that LINC00294 inhibits glioma cell proliferation by absorbing miR-1278 to enhance NEFM.

CONCLUSIONS

Collectively, our observations demonstrate the tumor-suppressive function of LINC00294 in glioma development by sponging miR-1278 and promoting NEFM, suggesting a potential use in therapy for glioma.

Quantum scale organic semiconductors for SERS detection of DNA methylation and gene expression

Cancer stem cells (CSC) can be identified by modifications in their genomic DNA. Here, we report a concept of precisely shrinking an organic semiconductor surface-enhanced Raman scattering (SERS) probe to quantum size, for investigating the epigenetic profile of CSC. The probe is used for tag-free genomic DNA detection, an approach towards the advancement of single-molecule DNA detection. The sensor detected structural, molecular and gene expression aberrations of genomic DNA in femtomolar concentration simultaneously in a single test. In addition to pointing out the divergences in genomic DNA of cancerous and non-cancerous cells, the quantum scale organic semiconductor was able to trace the expression of two genes which are frequently used as CSC markers. The quantum scale organic semiconductor holds the potential to be a new tool for label-free, ultra-sensitive multiplexed genomic analysis.

Loss of SPINT2 expression frequently occurs in glioma, leading to increased growth and invasion via MMP2

PURPOSE

High-grade gliomas (HGG) remain one of the most aggressive tumors, which is primarily due to its diffuse infiltrative nature. Serine proteases and metalloproteases are known to play key roles in cellular migration and invasion mechanisms. SPINT2, also known as HAI-2, is an important serine protease inhibitor that can affect MET signaling. SPINT2 has been found to be frequently downregulated in various tumors, whereby hypermethylation of its promoter appears to serve as a common mechanism. Here, we assessed the clinical relevance of SPINT2 expression and promoter hypermethylation in pediatric and adult HGG and explored its functional role.

METHODS

A series of 371 adult and 77 pediatric primary HGG samples was assessed for SPINT2 protein expression (immunohistochemistry) and promoter methylation (methylation-specific PCR) patterns. After SPINT2 knockdown and knock-in in adult and pediatric HGG cell lines, a variety of in vitro assays was carried out to determine the role of SPINT2 in glioma cell viability and invasion, as well as their mechanistic associations with metalloprotease activities.

RESULTS

We found that SPINT2 protein expression was frequently absent in adult (85.3%) and pediatric (100%) HGG samples. The SPINT2 gene promoter was found to be hypermethylated in approximately half of both adult and pediatric gliomas. Through functional assays we revealed a suppressor activity of SPINT2 in glioma cell proliferation and viability, as well as in their migration and invasion. These functions appear to be mediated in part by MMP2 expression and activity.

CONCLUSIONS

We conclude that dysregulation of SPINT2 is a common event in both pediatric and adult HGG, in which SPINT2 may act as a tumor suppressor.

Patient-Derived Glioma Models: From Patients to Dish to Animals

Glioblastoma (GBM) is the most common and malignant primary brain tumor in adults associated with a poor survival. Current standard of care consists of surgical resection followed by radiation and chemotherapy. GBMs are highly heterogeneous, having a complex interaction among different cells within the tumor as well as the tumor microenvironment. One of the main challenges in the neuro-oncology field in general, and GBM in particular, is to find an optimum culture condition that maintains the molecular genotype and phenotype as well as heterogeneity of the original tumor in vitro and in vivo. Established cell lines were shown to be a poor model of the disease, failing to recapitulate the phenotype and harboring non-parental genotypic mutations. Given the growing understanding of GBM biology, the discovery of glioma cancer stem-like cells (GSCs), and their role in tumor formation and therapeutic resistance, scientists are turning more towards patient-derived cells and xenografts as a more representative model. In this review, we will discuss the current state of patient-derived GSCs and their xenografts; and provide an overview of different established models to study GBM biology and to identify novel therapeutics in the pre-clinical phase.

Next-Generation Sequencing Profiles of the Methylome and Transcriptome in Peripheral Blood Mononuclear Cells of Rheumatoid Arthritis

Using next-generation sequencing to decipher methylome and transcriptome and underlying molecular mechanisms contributing to rheumatoid arthritis (RA) for improving future therapies, we performed methyl-seq and RNA-seq on peripheral blood mononuclear cells (PBMCs) from RA subjects and normal donors. Principal component analysis and hierarchical clustering revealed distinct methylation signatures in RA with methylation aberrations noted across chromosomes. Methylation alterations varied with CpG features and genic characteristics. Typically, CpG islands and CpG shores were hypermethylated and displayed the greatest methylation variance. Promoters were hypermethylated and enhancers/gene bodies were hypomethylated, with methylation variance associated with expression variance. RA genetically associated genes preferentially displayed differential methylation and differential expression or interacted with differentially methylated and differentially expressed genes. These differentially methylated and differentially expressed genes were enriched with several signaling pathways and disease categories. 10 genes (CD86, RAB20, XAF1, FOLR3, LTBR, KCNH8, DOK7, PDGFA, PITPNM2, CELSR1) with concomitantly differential methylation in enhancers/promoters/gene bodies and differential expression in B cells were validated. This integrated analysis of methylome and transcriptome identified novel epigenetic signatures associated with RA and highlighted the interaction between genetics and epigenetics in RA. These findings help our understanding of the pathogenesis of RA and advance epigenetic studies in regards to the disease.

Quantitative proteomic analysis of cerebrospinal fluid from patients with diffuse large B-cell lymphoma with central nervous system involvement: A novel approach to diagnosis

The outcome of patients with diffuse large B-cell lymphoma (DLBCL) with central nervous system (CNS) recurrence is poor. However, there is currently no consensus regarding diagnostic techniques. The aim of the present study was to investigate the cerebrospinal fluid (CSF) protein profile of DLBCL and identify a potential novel method for the early diagnosis of patients with DLBCL at high risk for subsequent CNS involvement. The CSF proteomic profiling of patients with DLBCL and a control group were compared using label-free liquid chromatography-tandem mass spectrometry. Gene Ontology and pathway analyses were conducted using the Database for Annotation, Visualization and Integrated Discovery. The protein interactions were analyzed using the Search Tool for the Retrieval of Interacting Genes/Proteins database. In the present study, a total of 53 differentially expressed proteins with >1 log₂ fold change (false discovery rate <0.01, P<0.05) were identified and quantified. These proteins appeared to be involved in platelet degranulation, innate immune response and cell adhesion. Two hub gene network modules were obtained by protein-protein interaction network analysis. Of these proteins, secreted protein acidic and rich in cysteine (SPARC) and proenkephalin (PENK) were significantly decreased in the CSF of patients with DLBCL, which appeared to be correlated with CNS involvement. The findings of the present study indicate that decreased expression levels of SPARC and PENK in the CSF may serve as early-phase biomarkers to evaluate the risk of CNS involvement in patients with DLBCL, enabling clinicians to offer prophylactic therapy at the time of diagnosis.

Identifying DNA methylation biomarkers for non-endoscopic detection of Barrett's esophagus

We report a biomarker-based non-endoscopic method for detecting Barrett's esophagus (BE) based on detecting methylated DNAs retrieved via a swallowable balloon-based esophageal sampling device. BE is the precursor of, and a major recognized risk factor for, developing esophageal adenocarcinoma. Endoscopy, the current standard for BE detection, is not cost-effective for population screening. We performed genome-wide screening to ascertain regions targeted for recurrent aberrant cytosine methylation in BE, identifying high-frequency methylation within the CCNA1 locus. We tested CCNA1 DNA methylation as a BE biomarker in cytology brushings of the distal esophagus from 173 individuals with or without BE. CCNA1 DNA methylation demonstrated an area under the curve of 0.95 for discriminating BE-related metaplasia and neoplasia cases versus normal individuals, performing identically to methylation of VIM DNA, an established BE biomarker. When combined, the resulting two biomarker panel was 95% sensitive and 91% specific. These results were replicated in an independent validation cohort of 149 individuals who were assayed using the same cutoff values for test positivity established in the training population. To progress toward non-endoscopic esophageal screening, we engineered a well-tolerated, swallowable, encapsulated balloon device able to selectively sample the distal esophagus within 5 min. In balloon samples from 86 individuals, tests of CCNA1 plus VIM DNA methylation detected BE metaplasia with 90.3% sensitivity and 91.7% specificity. Combining the balloon sampling device with molecular assays of CCNA1 plus VIM DNA methylation enables an efficient, well-tolerated, sensitive, and specific method of screening at-risk populations for BE.

SPINT2 is hypermethylated in both IDH1 mutated and wild-type glioblastomas, and exerts tumor suppression via reduction of c-Met activation

PURPOSE

Both IDH1-mutated and wild-type gliomas abundantly display aberrant CpG island hypermethylation. However, the potential role of hypermethylation in promoting gliomas, especially the most aggressive form, glioblastoma (GBM), remains poorly understood.

METHODS

We analyzed RRBS-generated methylation profiles for 11 IDH1^WT gliomas (including 7 GBMs), 24 IDH1^MUT gliomas (including 6 GBMs), and 5 normal brain samples and employed TCGA GBM methylation profiles as a validation set. Upon classification of differentially methylated CpG islands by IDH1 status, we used integrated analysis of methylation and gene expression to identify SPINT2 as a top cancer related gene. To explore functional consequences of SPINT2 methylation in GBM, we validated SPINT2 methylation status using targeted bisulfite sequencing in a large cohort of GBM samples. We assessed DNA methylation-mediated SPINT2 gene regulation using 5-aza-2'-deoxycytidine treatment, DNMT1 knockdown and luciferase reporter assays. We conducted functional analyses of SPINT2 in GBM cell lines in vitro and in vivo.

RESULTS

We identified SPINT2 as a candidate tumor-suppressor gene within a group of CpG islands (designated G_T-CMG) that are hypermethylated in both IDH1^MUT and IDH1^WT gliomas but not in normal brain. We established that SPINT2 downregulation results from promoter hypermethylation, and that restoration of SPINT2 expression reduces c-Met activation and tumorigenic properties of GBM cells.

CONCLUSIONS

We defined a previously under-recognized group of coordinately methylated CpG islands common to both IDH1^WT and IDH1^MUT gliomas (G_T-CMG). Within G_T-CMG, we identified SPINT2 as a top cancer-related candidate and demonstrated that SPINT2 suppressed GBM via down-regulation of c-Met activation.

MBD4 guards against methylation damage and germ line deficiency predisposes to clonal hematopoiesis and early-onset AML

The tendency of 5-methylcytosine (5mC) to undergo spontaneous deamination has had a major role in shaping the human genome, and this methylation damage remains the primary source of somatic mutations that accumulate with age. How 5mC deamination contributes to cancer risk in different tissues remains unclear. Genomic profiling of 3 early-onset acute myeloid leukemias (AMLs) identified germ line loss of MBD4 as an initiator of 5mC-dependent hypermutation. MBD4-deficient AMLs display a 33-fold higher mutation burden than AML generally, with >95% being C>T in the context of a CG dinucleotide. This distinctive signature was also observed in sporadic cancers that acquired biallelic mutations in MBD4 and in Mbd4 knockout mice. Sequential sampling of germ line cases demonstrated repeated expansion of blood cell progenitors with pathogenic mutations in DNMT3A, a key driver gene for both clonal hematopoiesis and AML. Our findings reveal genetic and epigenetic factors that shape the mutagenic influence of 5mC. Within blood cells, this links methylation damage to the driver landscape of clonal hematopoiesis and reveals a conserved path to leukemia. Germ line MBD4 deficiency enhances cancer susceptibility and predisposes to AML.

Malignant Transformation and Spine Metastasis of an Intracranial Grade I Meningioma: In Situ Immunofluorescence Analysis of Cancer Stem Cells Case Report and Literature Review

BACKGROUND

Malignant meningiomas are rare neoplasms of the central nervous system that occur de novo or rarely as a result of transformation. They have a higher rate of recurrence and metastasis accompanied by a significantly shorter survivorship compared with benign variants. Meningioma cancer stem cells (CSCs) have been previously shown to be associated with resistance and aggressiveness. However, the role they play in meningioma progression is still being investigated.

CASE DESCRIPTION

We report a 29-year-old man who underwent a resection of a grade I meningioma in 2011. The patient had multiple local recurrences of the tumor that showed an aggressive change in behavior and transformation to grade III meningioma, and developed extracranial metastasis to the cervical spine. He underwent multiple operations and received radiotherapy. Analysis of the tissues indicated the presence of CSC markers before metastasis, and showed increased expressions of associated markers in the metastasized tissue. In addition, similar to the patient's profile, the pharmacological testing of a primary cell line retrieved from the metastasized tissues showed a high level of drug tolerance and a diminished ability to initiate apoptosis.

CONCLUSIONS

Malignant progression of grade I meningioma can occur, and its eventuality may be anticipated by detecting CSCs. We performed a comprehensive literature review of relevant cases and discussed the clinical, diagnostic, and management characteristics of the reported cases.

Aberrant methylation and silencing of the SPINT2 gene in high-grade gliomas

Hepatocyte growth factor activator inhibitor type 2 (HAI‐2), encoded by the SPINT2 gene, is a membrane‐anchored protein that inhibits proteases involved in the activation of hepatocyte growth factor (HGF), a ligand of MET receptor. Epigenetic silencing of the SPINT2 gene has been reported in a human glioblastoma cell line (U87) and glioblastoma‐derived cancer stem cells. However, the incidence of SPINT2 methylation in tumor tissues obtained from glioma patients is unknown. In this study, we analyzed the methylation status of the SPINT2 gene of eight human glioblastoma cell lines and surgically resected glioma tissues of different grades (II, III, and IV) by bisulfite sequence analysis and methylation‐specific PCR. Most glioblastoma lines (7/8) showed methylation of the SPINT2 gene with a significantly reduced level of SPINT2mRNA compared to cultured astrocytes and normal brain tissues. However, all glioblastoma lines expressed mRNA for HGF activator (HGFAC), a target protease of HAI‐2/SPINT2. Forced expression of SPINT2 reduced MET phosphorylation of U87 glioblastoma cells both in vitro and in intracranial xenografts in nude mice. Methylation‐specific PCR analysis of the resected glioma tissues indicated notable methylation of the SPINT2 gene in 33.3% (2/6), 71.4% (10/14), and 74.3% (26/35) of grade II, III, and IV gliomas, respectively. Analysis of RNA sequencing data in a public database indicated an increased HGFAC/SPINT2 expression ratio in high‐grade compared to low‐grade gliomas (P = .01). In summary, aberrant methylation of the SPINT2 gene is frequently observed in high‐grade gliomas and might confer MET signaling in the glioma cells.

Epigenome-wide association study in hepatocellular carcinoma: Identification of stochastic epigenetic mutations through an innovative statistical approach

Hepatocellular carcinoma (HCC) results from accumulation of both genetic and epigenetic alterations. We investigated the genome-wide DNA methylation profile in 69 pairs of HCC and adjacent non-cancerous liver tissues using the Infinium HumanMethylation 450K BeadChip array. An innovative analytical approach has been adopted to identify Stochastic Epigenetic Mutations (SEMs) in HCC.HCC and peritumoral tissues showed a different epigenetic profile, mainly characterized by loss of DNA methylation in HCC. Total number of SEMs was significantly higher in HCC tumor (median: 77,370) than in peritumoral (median: 5,656) tissues and correlated with tumor grade. A significant positive association emerged between SEMs measured in peritumoral tissue and hepatitis B and/or C virus infection status. A restricted number of SEMs resulted to be shared by more than 90% of HCC tumor samples and never present in peritumoral tissue. This analysis allowed the identification of four epigenetically regulated candidate genes (AJAP1, ADARB2, PTPRN2, SDK1), potentially involved in the pathogenesis of HCC.In conclusion, HCC showed a methylation profile completely deregulated and very far from adjacent non-cancerous liver tissues. The SEM analysis provided valuable clues for further investigations in understanding the process of tumorigenesis in HCC.

Distinctive epigenomes characterize glioma stem cells and their response to differentiation cues

BACKGROUND

Glioma stem cells (GSCs) are a subpopulation of stem-like cells that contribute to glioblastoma (GBM) aggressiveness, recurrence, and resistance to radiation and chemotherapy. Therapeutically targeting the GSC population may improve patient survival, but unique vulnerabilities need to be identified.

RESULTS

We isolate GSCs from well-characterized GBM patient-derived xenografts (PDX), characterize their stemness properties using immunofluorescence staining, profile their epigenome including 5mC, 5hmC, 5fC/5caC, and two enhancer marks, and define their transcriptome. Fetal brain-derived neural stem/progenitor cells are used as a comparison to define potential unique and common molecular features between these different brain-derived cells with stem properties. Our integrative study reveals that abnormal expression of ten-eleven-translocation (TET) family members correlates with global levels of 5mC and 5fC/5caC and may be responsible for the distinct levels of these marks between glioma and neural stem cells. Heterogenous transcriptome and epigenome signatures among GSCs converge on several genes and pathways, including DNA damage response and cell proliferation, which are highly correlated with TET expression. Distinct enhancer landscapes are also strongly associated with differential gene regulation between glioma and neural stem cells; they exhibit unique co-localization patterns with DNA epigenetic mark switching events. Upon differentiation, glioma and neural stem cells exhibit distinct responses with regard to TET expression and DNA mark changes in the genome and GSCs fail to properly remodel their epigenome.

CONCLUSIONS

Our integrative epigenomic and transcriptomic characterization reveals fundamentally distinct yet potentially targetable biologic features of GSCs that result from their distinct epigenomic landscapes.

Serine peptidase inhibitor Kunitz type 2 (SPINT2) in cancer development and progression

Understanding the molecular basis and mechanisms involved in neoplastic transformation and progression is important for the development of novel selective target therapeutic strategies. Hepatocyte growth factor (HGF)/c-MET signaling plays an important role in cell proliferation, survival, migration and motility of cancer cells. Serine peptidase inhibitor Kunitz type 2 (SPINT2) binds to and inactivates the HGF activator (HGFA), behaving as an HGFA inhibitor (HAI) and impairing the conversion of pro-HGF into bioactive HGF. The scope of the present review is to recapitulate and review the evidence of SPINT2 participation in cancer development and progression, exploring the clinical, biological and functional descriptions of the involvement of this protein in diverse neoplasias. Most studies are in agreement as to the belief that, in a large range of human cancers, the SPINT2 gene promoter is frequently methylated, resulting in the epigenetic silence of this gene. Functional assays indicate that SPINT2 reactivation ameliorates the malignant phenotype, specifically reducing cell viability, migration and invasion in diverse cancer cell lines. In sum, the SPINT2 gene is epigenetically silenced or downregulated in human cancers, altering the balance of HGF activation/inhibition ratio, which contributes to cancer development and progression.

Temporal stability of MGMT promoter methylation in glioblastoma patients undergoing STUPP protocol

Epigenetic silencing of O-6-methylguanine-DNA methyltransferase (MGMT) promoter via methylation in a glioblastoma (GBM), has been correlated with a more favourable response to alkylating chemotherapeutic agents such as temozolomide. The use of global methylation surrogates such as Long Interspersed Nucleotide Element 1 (LINE1) may also be valuable in order to fully understand these highly heterogeneous tumours. In this study, we analysed both original and recurrent GBMs in 22 patients (i.e. 44 tumours), for both MGMT and LINE1 methylation status. In the 22 patients: 14 (63.6%) displayed MGMT methylation stability in the recurrent GBM versus 8 (36.4%), with instability of methylation status. No significant differences in overall and progression free survival was evident between these two groups. LINE1 methylation status remained stable for 12 (54.5%) of recurrent GBM patients versus 9 (41%) of the patients with instability in LINE1 methylation status (p = 0.02), resulting in an increase in overall survival of the stable LINE1 group (p = 0.04). The results obtained demonstrated major epigenetic instability of GBMs treated with temozolomide as part of the STUPP protocol. GBMs appear to undergo selective evolution post-treatment, and have the ability to recur with a newly reprogrammed epigenetic status. Selective targeting of the altered epigenomes in recurrent GBMs may facilitate the future development of both prognostic biomarkers and enhanced therapeutic strategies.

Targeting transferrin receptor delivery of temozolomide for a potential glioma stem cell-mediated therapy

Glioma stem cells, which are sub-populations of tumor cells, are responsible for resistant responses to radiotherapy and chemotherapy after surgery. Targeting resistant glioma stem cell sub-populations might present a novel means to prevent tumor recurrence. Due to the high expression of transferrin receptors at the surface of brain capillary endothelial and tumor cells, especially glioma stem cells, targeting the transferrin receptor system provides an avenue for the entry of drug molecules into the brain. Nanoparticles that target glioma stem cell sub-populations, conjugate transferrin and encapsulate temozolomide, were developed as a potential therapeutic strategy to evaluate their effectiveness at damaging tumor cells. Nanoparticles were highly effective at penetrating the blood-brain barrier and delivering a high therapeutic dose of temozolomide. This effective means of delivery provoked enhanced cytotoxicity against glioma cells, and especially against glioma stem cells. The targeting transferrin receptor nanoparticles display an inherent capacity for a highly therapeutic approach in targeting glioma stem cells and non-stem cells tumors. In addition, transferrin nanoparticles encapsulating temozolomide have the potential of a promising anti-tumor strategy against glioma of the O6-methylguanine-DNA-methyltransferase gene promoter methylation.

The interplay between the lysine demethylase KDM1A and DNA methyltransferases in cancer cells is cell cycle dependent

DNA methylation and histone modifications are key epigenetic regulators of gene expression, and tight connections are known between the two. DNA methyltransferases are upregulated in several tumors and aberrant DNA methylation profiles are a cancer hallmark. On the other hand, histone demethylases are upregulated in cancer cells. Previous work on ES cells has shown that the lysine demethylase KDM1A binds to DNMT1, thereby affecting DNA methylation. In cancer cells, the occurrence of this interaction has not been explored. Here we demonstrate in several tumor cell lines an interaction between KDM1A and both DNMT1 and DNMT3B. Intriguingly and in contrast to what is observed in ES cells, KDM1A depletion in cancer cells was found not to trigger any reduction in the DNMT1 or DNMT3B protein level or any change in DNA methylation. In the S-phase, furthermore, KDM1A and DNMT1 were found, to co-localize within the heterochromatin. Using P-LISA, we revealed substantially increased binding of KDM1A to DNMT1 during the S-phase. Together, our findings propose a mechanistic link between KDM1A and DNA methyltransferases in cancer cells and suggest that the KDM1A/DNMT1 interaction may play a role during replication. Our work also strengthens the idea that DNMTs can exert functions unrelated to act on DNA methylation.

Adhering towards tumorigenicity: altered adhesion mechanisms in glioblastoma cancer stem cells

Glioblastoma (GBM) is the most aggressive malignant primary brain tumor in adults with a high recurrence and mortality rate. GBM tumors contain a high degree of cellular heterogeneity, with cells exhibiting stem-like properties (cancer stem cells; CSCs) that are highly efficient at tumor initiation and are resistant to conventional therapies. CSCs interact with their tumor microenvironment by a large group of diverse cell adhesion molecules (CAMs) that participate in intercellular, intracellular and cell-extracellular matrix interactions. Despite the initial description of CAMs as tumor suppressors, recent work has highlighted specific CAMs that are essential for CSC maintenance and tumor progression. This review will highlight recent findings that provide support for a context-specific role of CAMs in CSC function and GBM progression.

Comprehensive protein tyrosine phosphatase mRNA profiling identifies new regulators in the progression of glioma

The infiltrative behavior of diffuse gliomas severely reduces therapeutic potential of surgical resection and radiotherapy, and urges for the identification of new drug-targets affecting glioma growth and migration. To address the potential role of protein tyrosine phosphatases (PTPs), we performed mRNA expression profiling for 91 of the 109 known human PTP genes on a series of clinical diffuse glioma samples of different grades and compared our findings with in silico knowledge from REMBRANDT and TCGA databases. Overall PTP family expression levels appeared independent of characteristic genetic aberrations associated with lower grade or high grade gliomas. Notably, seven PTP genes (DUSP26, MTMR4, PTEN, PTPRM, PTPRN2, PTPRT and PTPRZ1) were differentially expressed between grade II-III gliomas and (grade IV) glioblastomas. For DUSP26, PTEN, PTPRM and PTPRT, lower expression levels correlated with poor prognosis, and overexpression of DUSP26 or PTPRT in E98 glioblastoma cells reduced tumorigenicity. Our study represents the first in-depth analysis of PTP family expression in diffuse glioma subtypes and warrants further investigations into PTP-dependent signaling events as new entry points for improved therapy.

Caspase-related apoptosis genes in gliomas by RNA-seq and bioinformatics analysis

Gliomas are the most common malignant tumors of the brain. The aim of this study is to identify caspase-dependent apoptotic genes and uncover their potential regulatory mechanism in glioma progression. Human glioma cell line U251 was used. Three experiment groups were set as control group, H₂O₂ group (treated with H₂O₂) and caspase inhibitor group (treated with caspase inhibitor). For samples in each group, RNA-sequencing was performed on Illumina platform and differentially expressed genes (DEGs) between any two of the three groups were selected using NOISeq package. By overlapping analysis, the caspase inhibitor-related DEGs were further screened out, followed by enrichment analyses. Drugs associating with these genes were selected by WebGestalt. Protein-protein interaction (PPI) network analysis was conducted based on SRINIG database. A set of 105 caspase inhibitor-related DEGs were identified, which were significantly enriched in cellular components related functions (for example, TUBB2A, RPSA and RPL5); and metabolism related pathways (for example, PSMC3, KHSRP, RPL5 and RPSA). In addition, KHSRP and TUBB2A were significantly associated with several drugs such as cefotaxime, cefacetrile and netilmicin. Besides, PSMC3 and RPL5 were identified as crucial nodes in the PPI network. Several crucial genes in gliomas cells such as TUBB2A, RPSA, RPL5, PSMC3 and KHSRP were identified, which might play significant roles in apoptosis in a caspase-dependent manner. These genes might also involve in the regulation of metabolism related functions and pathways. KHSRP and TUBB2A might be novel targets of three drugs, cefotaxime, cefacetrile and netilmicin.

Clinical significance of expression of receptor-type tyrosine-protein phosphatase N2 and proliferation cell nuclear antigen in hepatocellular carcinoma

AIM: To explore the correlation of receptor-type tyrosine-protein phosphatase N2 (PTPRN2) and proliferation cell nuclear antigen (Ki-67) expression with clinical parameters in hepatocellular carcinoma (HCC).

METHODS: We collected 186 HCC specimens from patients treated at the First Affiliated Hospital of Zhengzhou University, 180 tumor adjacent normal liver tissues, and 138 non-neoplastic distant tissues. The expression of PTPRN2 and Ki-67 proteins was examined by immunohistochemistry in the above tissues.

RESULTS: The positive expression rates of PTPRN2 and Ki-67 were 55.9% and 49.5%, respectively. The positive expression of PTPRN2 was correlated with serum AFP level, tumor size, TNM stage, and histopathological differentiation (P < 0.05). The expression of Ki-67 was correlated with lymph node metastasis, TNM stage, and histopathological differentiation (P < 0.05). There was no significant correlation between PTPRN2 and Ki-67 expression (r = -0.161, P > 0.05).

CONCLUSION: The high expression of PTPRN2 and Ki-67 is closely associated with HCC development, but there is no significant correlation between them.

Epigenetic and Immune Regulation of Colorectal Cancer Stem Cells

Colorectal cancer stem cells (CSCs) were initially considered to be a subset of undifferentiated tumor cells with well-defined phenotypic and molecular markers. However, emerging evidence indicates instead that colorectal CSCs are heterogeneous subsets of tumor cells that are continuously reshaped by the dynamic interactions between genetic, epigenetic, and immune factors in the tumor microenvironment. Thus, the colorectal CSC phenotypes and responsiveness to therapy may not only be a tumor cell-intrinsic feature, but also depend on tumor-extrinsic microenvironmental factors. Furthermore, emerging evidence also implicates colorectal CSCs in potential immune evasion. Therefore, understanding how colorectal CSC-intrinsic mechanisms cooperate with the extrinsic microenvironmental factors to dynamically shape colorectal CSC resistance to chemotherapy and immunotherapy holds great promise for development of targeted CSC therapies of advanced human CRC.