More epigenetic hits than meets the eye: microRNAs and genes associated with the tumorigenesis of retinoblastoma

Comprehensive investigation of long non-coding RNA HOTAIR polymorphisms and cancer risk: a current meta-analysis encompassing 96,458 participants

Cancer ranks as the second leading cause of mortality worldwide, prompting extensive investigations into factors contributing to its development. Among these factors, genetic variations, known as genotypic polymorphisms, have been identified as significant influencers in the susceptibility to various types of cancer. Recent research has focused on exploring the connection between polymorphisms in the Long Non-coding RNA HOTAIR and cancer risk. However, the results from these studies have been inconsistent, leading to ambiguity and controversy. To address this uncertainty, we conducted a systematic analysis by gathering relevant studies from PubMed, EMBASE, and Google Scholar. Specifically, we focused on three well-studied polymorphisms within the HOTAIR lncRNA (HOTAIR rs920778 C > T, HOTAIR rs1899663 G > T, HOTAIR rs4759314 A > G) and their association with cancer risk. Our meta-analysis included data from 48 case-control studies involving 42,321 cases and 54,137 controls. The results of our updated meta-analysis revealed a significant correlation between HOTAIR rs1899663 G > T and HOTAIR rs4759314 A > G polymorphisms and overall cancer risk, particularly in the homozygous and recessive genetic models. Subgroup analysis further revealed that these associations were notably pronounced in the Asian population but not observed in the Iranian population. Furthermore, our findings underscore the potential of HOTAIR polymorphisms as diagnostic markers for overall cancer risk, particularly in gynecological cancers, precisely, HOTAIR rs1899663 G > T polymorphism in breast cancer. In conclusion, our systematic analysis provides compelling evidence that Long Non-coding RNA HOTAIR polymorphisms are linked to cancer risk, particularly in certain populations and cancer types, suggesting their potential clinical relevance as diagnostic indicators.

Molecular Biological Research on the Pathogenic Mechanism of Retinoblastoma

Retinoblastoma (RB) is the most common intraocular malignant tumor in children, primarily attributed to the bi-allelic loss of the RB1 gene in the developing retina. Despite significant progress in understanding the basic pathogenesis of RB, comprehensively unravelling the intricate network of genetics and epigenetics underlying RB tumorigenesis remains a major challenge. Conventional clinical treatment options are limited, and despite the continuous identification of genetic loci associated with cancer pathogenesis, the development of targeted therapies lags behind. This review focuses on the reported genomic and epigenomic alterations in retinoblastoma, summarizing potential therapeutic targets for RB and providing insights for research into targeted therapies.

miRNAs as potential game-changers in retinoblastoma: Future clinical and medicinal uses

Retinoblastoma (RB) is a rare tumor in children, but it is the most common primitive intraocular malignancy in childhood age, especially those below three years old. The RB gene (RB1) undergoes mutations in individuals with RB. Although mortality rates remain high in developing countries, the survival rate for this type of cancer is greater than 95-98% in industrialized countries. However, it is lethal if left untreated, so early diagnosis is essential. As a non-coding RNA, miRNA significantly impacts RB development and treatment resistance because it can control various cellular functions. In this review, we illustrate the recent advances in the role of miRNAs in RB. That includes the clinical importance of miRNAs in RB diagnosis, prognosis, and treatment. Moreover, the regulatory mechanisms of miRNAs in RB and therapeutic interventions are discussed.

Second hit impels oncogenesis of retinoblastoma in patient-induced pluripotent stem cell-derived retinal organoids: direct evidence for Knudson's theory

Retinoblastoma (Rb) is a type of malignant tumor due to abnormal retinogenesis with biallelic mutations of the RB1 gene. Its pathogenesis has been proposed as a "two-mutation hypothesis" by Knudson since 1971; however, there remain some debates on disease onset sufficiency of the biallelic RB1 mutations. To obtain straightforward evidence for this hypothesis, we investigated whether two-hit mutations of the RB1 gene drive tumorigenesis in patient-induced pluripotent stem cell (hiPSC)-derived human retinal organoids (hROs) and whether single allelic mutation hiPSC-derived hROs exhibit molecular and cellular defects. We generated hiPSCs with a heterozygous germline mutation (RB1^{m1/ wt} ) from a Rb patient. A second-allele RB1 gene mutation was knocked in to produce compound heterozygous mutations (RB1^m1/m2 ) in the hiPSCs. These two hiPSC lines were independently developed into hROs through a stepwise differentiation. The hiPSC-RB1^m1/m2 derived organoids demonstrated tumorigenesis in dishes, consistent with Rb profiles in spatiotemporal transcriptomes, in which developmentally photoreceptor fate-determining markers, CRX and OTX2, were highly expressed in hiPSC-RB1^m1/m2 derived hROs. Additionally, ARR3⁺ maturing cone precursors were co-labeled with proliferative markers Ki67 or PCNA, in agreement with the consensus that human Rb is originated from maturing cone precursors. Finally, we demonstrated that retinal cells of hROs with monoallelic RB1 mutation were abnormal in molecular aspects due to its haploinsufficiency. In conclusion, this study provides straightforward supporting evidence in a way of reverse genetics for "two-hit hypothesis" in the Rb tumorigenesis and opens new avenues for development of early intervention and treatment of Rb.

Identification of Epigenetically Modified Hub Genes and Altered Pathways Associated With Retinoblastoma

Retinoblastoma (Rb) is the most common childhood malignancy initiated by biallelic mutation in RB1 gene and driven by various epigenetic events including DNA methylation and microRNA dysregulation. Hence, understanding the key genes that are critically modulated by epigenetic modifications in RB1 -/- cells is very important to identify prominent biomarkers and therapeutic targets of Rb. In this study, we for the first time have integrated various Rb microarray NCBI-GEO datasets including DNA Methylation (GSE57362), miRNA (GSE7072) and mRNA (GSE110811) to comprehensively investigate the epigenetic consequences of RB loss in retinoblastoma tumors and identify genes with the potential to serve as early diagnostic markers and therapeutic targets for Rb. Interestingly, the GEO2R and co-expression network analysis have identified three genes namely E2F3, ESR1, and UNC5D that are significantly deregulated by modified DNA methylation, mRNA and microRNA expression in Rb tumors. Due to their recognition in all epigenetic, transcriptomic, and miRNA datasets, we have termed these genes as "common genes". The results of our integrative bioinformatics analysis were validated in vitro by studying the gene and protein expression of these common genes in Y79, WERI-Rb-1, Rb cell lines and non-tumorigenic retinal pigment epithelial cell line (hTERT-RPE). The expression of E2F3 and UNC5D were up-regulated and that of ESR1 was down-regulated in Rb tumor cells when compared to that in non-tumorigenic hTERT-RPE cells. More importantly, UNC5D, a potent tumor suppressor gene in most cancers is significantly up-regulated in Y79 and Weri Rb1 cells, which, in turn, questions its anti-cancer properties. Together, our study shows that E2F3, ESR1, and UNC5D may be crucially involved in Rb tumorigenesis and possess the potential to act as early diagnostic biomarkers and therapeutic targets of Rb.

Update on the Treatment of Retinoblastoma

Retinoblastoma (Rb) is the most common pediatric ocular malignancy and accounts for 2% of all childhood cancers. Rb is initiated by a mutation of the RB1 tumor suppressor gene and occurs in 2 forms: 1) unilateral and unifocal, characterized by a single tumor in 1 eye, and 2) bilateral or unilateral, multifocal Rb with multiple tumor foci in 1 or both eyes. Rb is a disease of young children and if left untreated can result in visual morbidity as well as systemic mortality. Fortunately, because of the greater availability of genetic testing and earlier diagnosis, novel targeted therapies, and multimodal treatment approaches, disease-free survival rates and visual prognoses have improved dramatically. Current efforts to expand the accessibility of the newest Rb treatments aim to improve Rb outcomes worldwide. In this article, we will review the clinical presentation, diagnosis, and management of Rb, with a focus on the newest treatment approaches.

Genetics of congenital solid tumors

When we discuss the genetics of tumors, we cannot fail to remember that in the second decade of the twentieth century, more precisely in 1914, Theodore Boveri defined for the first time the chromosomal bases of cancer. In the last 30 years, progresses in genetics have only confirmed Boveri's remarkable predictions made more than 80 years ago. Before the cloning of the retinoblastoma 1 (RB1) gene, the existence of a genetic component in most, if not all, solid childhood tumors were well known. The existence of familial tumor aggregations has been found much more frequently than researchers expected to find at random. Sometimes, the demonstration of this family predisposition was very difficult, because the survival of children diagnosed as having a certain tumor, up to an age at which reproduction and procreation is possible, was very rare. In recent years, advances in the diagnosis and treatment of these diseases have made it possible for these children to survive until the age when they were able to start their own families, including the ability to procreate. Four distinct groups of so-called cancer genes have been identified: oncogenes, which promote tumor cell proliferation; tumor suppressor genes, which inhibit this growth/proliferation; anti-mutational genes, with a role in deoxyribonucleic acid (DNA) stability; and micro-ribonucleic acid (miRNA) genes, with a role in the posttranscriptional process.

Long Non-coding RNA FEZF1-AS1 Promotes Growth and Reduces Apoptosis Through Regulation of miR-363-3p/PAX6 Axis in Retinoblastoma

Retinoblastoma is the most common malignancy in children's eyes with high incidence. Long non-coding RNAs (lncRNAs) play important roles in the progression of retinoblastoma. LncRNA FEZF1 antisense RNA 1 (FEZF1-AS1) has been found to stimulate retinoblastoma. However, the mechanism of FEZF1-AS1 underlying progression of retinoblastoma is still unclear. In current study, FEZF1-AS1 was up-regulated in retinoblastoma tissues and cells. FEZF1-AS1 overexpression enhanced retinoblastoma cell viability, promoted cell cycle, and inhibited apoptosis. Conversely, FEZF1-AS1 knockdown reduced cell viability, cycle, and elevated apoptosis. The interaction between FEZF1-AS1 and microRNA-363-3p (miR-363-3p) was confirmed. FEZF1-AS1 down-regulated miR-363-3p and up-regulated PAX6. PAX6 was a target gene of miR-363-3p. EZF1-AS1 promoted retinoblastoma cell viability and suppressed apoptosis via PAX6. Further, we demonstrated that FEZF1-AS1 contribute to tumor formation in vivo. In conclusion, FEZF1-AS1 elevated growth and inhibited apoptosis by regulating miR-363-3p/PAX6 in retinoblastoma, which provide a new target for retinoblastoma treatment.

CircRNA Is a Rising Star in Researches of Ocular Diseases

A newly rediscovered subclass of noncoding RNAs, circular RNAs (circRNAs), is produced by a back-splicing mechanism with a covalently closed loop structure. They not only serve as the sponge for microRNAs (miRNAs) and proteins but also regulate gene expression and epigenetic modification, translate into peptides, and generate pseudogenes. Dysregulation of circRNA expression has opened a new chapter in the etiology of various human disorders, including cancer and cardiovascular, neurodegenerative, and ocular diseases. Recent studies recognized the vital roles that circRNAs played in the pathogenesis of various eye diseases, highlighting circRNAs as promising biomarkers for diagnosis and assessment of progression and prognosis. Interventions targeting circRNAs provide insights for developing novel treatments for these ocular diseases. This review summarizes our current perception of the properties, biogenesis, and functions of circRNAs and the development of circRNA researches related to ophthalmologic diseases, including diabetic retinopathy, age-related macular degeneration, retinopathy of prematurity, glaucoma, corneal neovascularization, cataract, pterygium, proliferative vitreoretinopathy, retinoblastoma, and ocular melanoma.

Biomarkers in retinoblastoma

Retinoblastoma (RB) is the most common intraocular malignancy of childhood caused by inactivation of the Rb genes. The prognosis of RB is better with an earlier diagnosis. Many diagnostic approaches and appropriate clinical treatments have been developed to improve clinical outcomes. However, limitations exist when utilizing current methods. Recently, many studies have identified identify new RB biomarkers which can be used in diagnosis, as prognostic indicators and may contribute to understanding the pathogenesis of RB and help determine specific treatment strategies. This review focuses on recent advances in the discovery of RB biomarkers and discusses their clinical utility and challenges from areas such as epigenetics, proteomics and radiogenomics.

Epigenetic response profiles into environmental epigenotoxicant screening and health risk assessment: A critical review

The epigenome may be an important interface between exposure to environmental contaminants and adverse outcome on human health. Many environmental pollutants deregulate gene expression and promote diseases by modulating the epigenome. Adverse epigenetic responses have been widely used for risk assessment of chemical substances. Various pollutants, including trace elements and persistent organic pollutants, have been detected frequently in the environment. Epigenetic toxicity of environmental matrices including water, air, soil, and food cannot be ignored. This review provides a comprehensive overview of epigenetic effects of pollutants and environmental matrices. We start with an overview of the mechanisms of epigenetic regulation and the effects of several types of environmental pollutants (trace elements, persistent organic pollutants, endocrine disrupting chemicals, and volatile organic pollutants) on epigenetic modulation. We then discuss the epigenetic responses to environmental water, air, and soil based on in vivo and in vitro assays. Finally, we discuss recommendations to promote the incorporation of epigenotoxicity into contamination screening and health risk assessment.

Association of rs11801299 and rs1380576 polymorphisms at MDM4 with risk, clinicopathological features and prognosis in patients with retinoblastoma

BACKGROUND

rs11801299 and rs1380576, two novel polymorphisms in MDM4 gene, have been investigated in several different cancer types. However, the role of these two polymorphisms in retinoblastoma (RB) remains unclear.

METHODS

A total of 126 patients with primary RB and 148 age-/gender-matched controls were included in this retrospective study. The frequency of rs11801299 and rs1380576 were determined between RB patients and controls. The association of these two polymorphisms with clinicopathological characteristics, prognosis were further evaluated.

RESULTS

AA genotype at rs11801299 was significantly associated with an increased risk of developing RB (OR = 2.06, 95%CI 1.09-3.90). The possibility of developing RB was also significantly increased in individuals with A allele at rs11801299 (OR = 1.49, 95%CI 1.06-2.08). RB patients carrying AA genotype and A allele at rs11801299 were more likely to have tumor invasion and poor differentiation. As for rs1380576, a significantly lower risk of developing RB was observed in patients with G allele (CG + GG) compared with wild-type CC genotype (OR = 0.59, 95%CI 0.36-3.95). RB patients with GG genotype or G allele had a lower risk of developing highly aggressive cancer. Kaplan-Meier curves and log-rank results revealed that RB patients carrying AA genotype or A allele (AA + GA) at rs11801299 had significantly poorer prognosis. Multivariate COX analysis showed that the rs11801299 G allele was associated with decreased survival but was not an independent prognostic factor.

CONCLUSION

rs11801299 was significantly associated with RB risk, pathological differentiation, tumor aggressiveness and poor prognosis.

Expression profiles and prognostic value of miRNAs in retinoblastoma

Current cure rates for retinoblastoma (RB) are very high in developed countries. Nonetheless, in less privileged places worldwide, delayed diagnosis and refusal to adhere to treatment still endure an obstacle to improve overall patient survival. Thus, the access to consistent biomarkers for diagnosis at an earlier stage may facilitate treatment and improve outcomes. Over recent years, much attention has been focused on miRNAs, key post-transcriptional regulators that when altered, largely contribute to carcinogenesis and tumor progression. Many of the ~ 2500 microRNAs described in humans have shown differential expression profiles in tumors. In this review, we summarize current data about the roles of miRNAs in RB along with their value as diagnostic/prognostic factors using electronic databases such as PubMed. We reviewed the importance of miRNA in RB biology and discussed their implications in clinic intervention. Several miRNAs have pointed out reliable diagnostic and prognostic molecular biomarkers. The emergence of targeted therapies has significantly improved cancer treatment. In the near future, the modulation of miRNAs will represent a good treatment strategy.

Downregulation of microRNA‑182 inhibits cell viability, invasion and angiogenesis in retinoblastoma through inhibition of the PI3K/AKT pathway and CADM2 upregulation

Retinoblastoma (RB) is a well‑vascularized tumor dependent on angiogenesis. The present study aimed to explore whether microRNA (miR)‑182 regulates cell viability, invasion and angiogenesis in RB via the phosphatidylinositol‑3‑OH kinase (PI3K)/protein kinase B (AKT) signaling pathway and by targeting cell adhesion molecule 2 (CADM2). The expression levels of miR‑182 and CADM2 were initially detected in RB tissues from patients with RB who underwent ophthalmectomy, and normal retinal tissues collected from other trauma patients who underwent eye enucleation. To determine whether CADM2 was targeted by miR‑182, a dual luciferase reporter assay was conducted. Subsequently, Y79 and WERI‑Rb‑1 RB cells were transfected with a miR‑182 mimic or miR‑182 inhibitor, or small interfering RNA against CADM2, in order to investigate the effects of miR‑182 on viability and invasion, which were detected using MTT and Transwell assays, respectively. In addition, to determine whether the regulatory mechanism underlying the effects of miR‑182 was associated with the PI3K/AKT signaling pathway, the expression levels of associated genes were detected by reverse transcription‑quantitative polymerase chain reaction and western blot analysis. A xenograft tumor model in nude mice was also established, in order to evaluate the effects of miR‑182 on tumor growth and angiogenesis. The results indicated that miR‑182 expression was increased and CADM2 expression was reduced in RB tissues; CADM2 was confirmed to be targeted and negatively regulated by miR‑182. When the expression of miR‑182 was downregulated, cell viability, invasion, tumor volume and angiogenesis were significantly decreased. Furthermore, the expression levels of PI3K/AKT signaling pathway‑associated genes were increased in response to miR‑182 overexpression or CADM2 silencing. Taken together, these results suggested that inhibition of miR‑182 may suppress cell viability, invasion and angiogenesis in RB through inactivation of the PI3K/AKT pathway and CADM2 upregulation. This mechanism may reveal a novel potential therapeutic target.

MicroRNAs in retinoblastoma: Potential diagnostic and therapeutic biomarkers

Retinoblastoma (Rb) is known as one of important childhood malignancies which due to inactivation of the RB gene (tumor suppressor gene in various patients). The early detection of Rb could provide better treatment for Rb patients. Imaging techniques (e.g., MRI and CT) are known as one of effective diagnosis approaches for detection of patients with Rb. It has been shown that utilization of imaging techniques is associated with some limitations. Hence, identification of new diagnosis approaches might provide a better treatment for Rb patients. Identification of new biomarkers could contribute to better understanding of pathogenesis events involved in Rb and provide new insights into design better treatment approaches for these patients. Among the various biomarkers, microRNAs (miRNAs) have emerged as attractive tools for Rb detection. miRNAs are one classes of small non-coding RNAs which could anticipate in a variety of biological process via targeting sequence of cellular and molecular pathways. Deregulations of these molecules are associated with cancerous condition. Multiple lines of evidence indicated that deregulation of various miRNAs involved in various stages of Rb. Here, we summarized a variety of tissue-specific and circulating miRNAs involved in Rb pathogenesis which could be used as diagnostic, prognostic, and therapeutic biomarkers in Rb patients.

Observation of significant biomarkers in osteosarcoma via integrating module- identification method with attract

OBJECTIVE

Osteosarcoma (OS) is the most frequent type of bone malignancy, and this disease has a poor prognosis. We aimed to identify the significant genes related with OS by integrating module-identification method and attract approach.

METHODS

OS-related microarray data E-GEOD-36001 were obtained from ArrayExpress database, and then protein-protein interaction (PPI) networks of normal and OS were re-weighted by means of spearman correlation coefficient (SCC). Next, maximal cliques were detected from the re-weighted PPI networks using clusteringbased on maximal cliques approach. Afterwards, highly overlapped cliques were merged according to the interconnectivity, following by candidate modules and seed modules identification. Attract proposed by Mar et al. who have suggested that this approach can extract and annotate the gene-sets which can distinguish between disease and control samples, and obtained differences of these gene-sets among the expression profile of samples were defined as attractors. Thus, we applied attract method to extract differential modules from the seed modules, and these obtained differential modules were defined as attractors. The genes in attractors were determined as attractor genes.

RESULTS

After eliminating the maximal cliques with nodes less than 4, there were 1,884 and 528 maximal cliques in normal and OS PPI networks, which were used to conduct module analysis. A total of 60 and 19 candidate modules were obtained in control and OS PPI networks, respectively. By comparing with normal group, 2 seed module pairs with similar gene composition were found. Significantly, based on attract method, we found that these 2 modules were differential. These 2 modules had the same gene size with 4 genes. Of note, genes CCNB1 and KIF11 simultaneously appeared in these two attractors.

CONCLUSIONS

We successfully identified two attractors via integrating module-identification method and attract approach, and attractor genes, for example, CCNB1 and KIF11 might play pathophysiological roles in OS development and progression.

Identification of hub genes and pathways associated with hepatocellular carcinoma based on network strategy

The objective of this study was to identify hub genes and pathways associated with hepatocellular carcinoma (HCC) by centrality analysis of a co-expression network. A co-expression network based on differentially expressed (DE) genes of HCC was constructed using the Differentially Co-expressed Genes and Links (DCGL) package. Centrality analyses, for centrality of degree, clustering coefficient, closeness, stress and betweenness for the co-expression network were performed to identify hub genes, and the hub genes were combined together to overcome inconsistent results. Enrichment analyses were conducted using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases. Finally, validation of hub genes was conducted utilizing reverse transcription-polymerase chain reaction (RT-PCR) analysis. In total, 260 DE genes between normal controls and HCC patients were obtained and a co-expression network with 154 nodes and 326 edges was constructed. From this, 13 hub genes were identified according to degree, clustering coefficient, closeness, stress and betweenness centrality analysis. It was found that reelin (RELN), potassium voltage-gated channel subfamily J member 10 (KCNJ10) and neural cell adhesion molecule 1 (NCAM1) were common hub genes across the five centralities, and the results of RT-PCR analysis for RELN, KCNJ10 and NCAM1 were consistent with the centrality analyses. Pathway enrichment analysis of DE genes showed that cell cycle, metabolism of xenobiotics by cytochrome P450 and p53 signaling pathway were the most significant pathways. This study may contribute to understanding the molecular pathogenesis of HCC and provide potential biomarkers for its early detection and effective therapies.

A Functional Polymorphism (rs937283) in the MDM2 Promoter Region is Associated with Poor Prognosis of Retinoblastoma in Chinese Han Population

The effect of single nucleotide polymorphisms (SNPs) at MDM2 has been investigated in several cancer types. Three MDM2 SNPs(rs937283, rs2270744 and rs769412) have previously been suggested to be positively correlated with cancer. In this study, we aimed to explore the association of rs937283, rs2270744 and rs769412 polymorphisms with retinoblastoma (RB) risk, clinicopathological characteristics, and prognosis. Compared with wild-type genotype AA at rs937283, individuals carrying AG and GG genotype had a significantly increased risk for developing RB (OR = 1.86, 95% CI 1.13–3.08; OR = 2.48, 95% CI 1.10–5.62, respectively). RB patients with allele G at rs937283 were more susceptible to invasion and high tumor aggression (OR = 2.42, 95% CI 1.43–4.11; OR = 2.15, 95% CI 1.27–3.64, respectively). Kaplan-Meier curves and log-rank results revealed that RB patients harboring genotype GG and G allele at rs937283 had worse survival (P < 0.02 and P < 0.01, respectively). In addition, the A to G substitution at rs937283 significantly enhanced the transcription activity of the MDM2 gene in vitro. In vivo, we found that MDM2 mRNA and protein were overexpressed in individuals who carried the G allele at rs937283. This study suggested that the MDM2 rs937283 polymorphism is a novel functional SNP both in vitro and in vivo as well as a biomarker for poor prognosis in RB.

Epigenetics of dementia: understanding the disease as a transformation rather than a state

Alzheimer's disease and other idiopathic dementias are associated with epigenetic transformations. These transformations connect the environment and genes to pathogenesis, and have led to the investigation of epigenetic-based therapeutic targes for the treatment of these diseases. Epigenetic changes occur over time in response to environmental effects. The epigenome-based latent early-life associated regulation (LEARn) hypothetical model indicates that accumulated environmental hits produce latent epigenetic changes. These hits can alter biochemical pathways until a pathological threshold is reached, which appears clinically as the onset of dementia. The hypotheses posed by LEARn are testable via longitudinal epigenome-wide, envirome-wide, and exposome-wide association studies (LEWAS) of the genome, epigenome, and environment. We posit that the LEWAS design could lead to effective prevention and treatments by identifying potential therapeutic strategies. Epigenetic evidence suggests that dementia is not a suddenly occurring and sharply delineated state, but rather a gradual change in crucial cellular pathways, that transforms an otherwise healthy state, as a result of neurodegeneration, to a dysfunctional state. Evidence from epigenetics could lead to ways to detect, prevent, and reverse such processes before clinical dementia.

Orchestrating epigenetic roles targeting ocular tumors

Epigenetics is currently one of the most promising areas of study in the field of biomedical research. Scientists have dedicated their efforts to studying epigenetic mechanisms in cancer for centuries. Additionally, the field has expanded from simply studying DNA methylation to other areas, such as histone modification, non-coding RNA, histone variation, nucleosome location, and chromosome remodeling. In ocular tumors, a large amount of epigenetic exploration has expanded from single genes to the genome-wide level. Most importantly, because epigenetic changes are reversible, several epigenetic drugs have been developed for the treatment of cancer. Herein, we review the current understanding of epigenetic mechanisms in ocular tumors, including but not limited to retinoblastoma and uveal melanoma. Furthermore, the development of new pharmacological strategies is summarized.

Pathogenic Network Analysis Predicts Candidate Genes for Cervical Cancer

Purpose. The objective of our study was to predicate candidate genes in cervical cancer (CC) using a network-based strategy and to understand the pathogenic process of CC. Methods. A pathogenic network of CC was extracted based on known pathogenic genes (seed genes) and differentially expressed genes (DEGs) between CC and normal controls. Subsequently, cluster analysis was performed to identify the subnetworks in the pathogenic network using ClusterONE. Each gene in the pathogenic network was assigned a weight value, and then candidate genes were obtained based on the weight distribution. Eventually, pathway enrichment analysis for candidate genes was performed. Results. In this work, a total of 330 DEGs were identified between CC and normal controls. From the pathogenic network, 2 intensely connected clusters were extracted, and a total of 52 candidate genes were detected under the weight values greater than 0.10. Among these candidate genes, VIM had the highest weight value. Moreover, candidate genes MMP1, CDC45, and CAT were, respectively, enriched in pathway in cancer, cell cycle, and methane metabolism. Conclusion. Candidate pathogenic genes including MMP1, CDC45, CAT, and VIM might be involved in the pathogenesis of CC. We believe that our results can provide theoretical guidelines for future clinical application.

miRNA signature identification of retinoblastoma and the correlations between differentially expressed miRNAs during retinoblastoma progression

PURPOSE

Retinoblastoma (RB) is a common pediatric cancer. The study aimed to uncover the mechanisms of RB progression and identify novel therapeutic biomarkers.

METHODS

The miRNA expression profile GSE7072, which includes three RB samples and three healthy retina samples, was used. After data normalization using the preprocessCore package, differentially expressed miRNAs (DE-miRs) were selected by the limma package. The targets of the DE-miRs were predicted based on two databases, followed by construction of the miRNA-target network. Pathway enrichment analysis was conducted for the targets of the DE-miRNAs using DAVID. The CTD database was used to predict RB-related genes, followed by clustering analysis using the pvclust package. The correlation network of DE-miRs was established. MiRNA expression was validated in another data set, GSE41321.

RESULTS

In total, 24 DE-miRs were identified whose targets were correlated with the cell cycle pathway. Among them, hsa-miR-373, hsa-miR-125b, and hsa-miR-181a were highlighted in the miRNA-target regulatory network; 14 DE-miRs, including hsa-miR-373, hsa-miR-125b, hsa-miR-18a, hsa-miR-25, hsa-miR-20a, and hsa-let-7 (a, b, c), were shown to distinguish RB from healthy tissue. In addition, hsa-miR-25, hsa-miR-18a, and hsa-miR-20a shared the common target BCL2L11; hsa-let-7b and hsa-miR-125b targeted the genes CDC25A, CDK6, and LIN28A. Expression of three miRNAs in GSE41321 was consistent with that in GSE7072.

CONCLUSIONS

Several critical miRNAs were identified in RB progression. Hsa-miR-373 might regulate RB invasion and metastasis, hsa-miR-181a might involve in the CDKN1B-mediated cell cycle pathway, and hsa-miR-125b and hsa-let-7b might serve as tumor suppressors by coregulating CDK6, CDC25A, and LIN28A. The miRNAs hsa-miR-25, hsa-miR-18a, and hsa-miR-20a might exert their function by coregulating BCL2L1.

Association of p53 rs1042522, MDM2 rs2279744, and p21 rs1801270 polymorphisms with retinoblastoma risk and invasion in a Chinese population

Single nucleotide polymorphisms (SNPs) of p53 rs1042522, MDM2 rs2279744 and p21 rs1801270, all in the p53 pathway, which plays a crucial role in DNA damage and genomic instability, were reported to be associated with cancer risk and pathologic characteristics. This case-control study was designed to analyse the association between these SNPs and retinoblastoma (RB) in a Chinese Han population. These SNPs in 168 RB patients and 185 adult controls were genotyped using genomic DNA from venous blood. No significant difference was observed in allele or genotypic frequencies of these SNPs between Chinese RB patients and controls (all P > 0.05). However, the rs1042522 GC genotype showed a protective effect against RB invasion, as demonstrated by event-free survival (HR = 0.53, P = 0.007 for GC versus GG/CC). This effect was significant for patients with a lag time >1 month and no pre-enucleation treatment (P = 0.007 and P = 0.010, respectively), indicating an interaction between p53 rs1042522 and clinical characteristics, including lag time and pre-enucleation treatment status. Thus, the rs1042522 SNP may be associated with RB invasion in the Han Chinese population; however, further large and functional studies are needed to assess the validity of this association.

Down-Regulation of miR-146a Expression Induces Allergic Conjunctivitis in Mice by Increasing TSLP Level

Background

Pollen is the most common aeroallergen to cause conjunctivitis. In this study, we established a short ragweed (SRW)-induced mouse model of allergic conjunctivitis (AC) and aimed to explore the potential role of miR-146a and its downstream molecules in the development of ocular allergic inflammation.

Material/Methods

The mouse model of challenge pollen was used for in vivo study. The culture model of primary human limbal epithelium (HLE) exposed to lipopolysaccharide (LPS) was performed for in vitro research. The numbers of eosinophils and total inflammatory cells were examined using Giemsa staining. The expression of mRNA and miR-146a was determined by quantitative RT-PCR, and protein production was evaluated by Western blotting.

Results

In vivo of mice, pollen challenge induced conjunctiva inflammatory response indicated by increased number of eosinophils and total inflammatory cells. Interestingly, pollen significantly attenuated miR-146a expression while it enhanced expression of thymic stromal lymphopoietin (TSLP) and its downstream molecules, including TSLP receptor (TSLPR)/ OX40 ligand (OX40L)/CD11C. In vitro of HCE, downregulation effect of miR-146a expression induced by LPS was reversed by Bay treatment, an inhibitor for nuclear factor kappa B (NF-κB), and LPS-induced cell inflammation is mediated by miR-146a-TSLP/TSLPR/OX40L/CD11C signaling pathway. This was further demonstrated by overexpression of miR-146a in mouse abrogated pollen-triggered conjunctiva inflammatory reaction as well as pollen-induced activity of TSLP/TSLPR/OX40L/CD11C signaling.

Conclusions

Down-regulation of miR-146a expression induces allergic conjunctivitis in mice by increasing TSLP level.

Genetics and epigenetics of human retinoblastoma

Retinoblastoma is a pediatric tumor of the developing retina from which the genetic basis for cancer development was first described. Inactivation of both copies of the RB1 gene is the predominant initiating genetic lesion in retinoblastoma and is rate limiting for tumorigenesis. Recent whole-genome sequencing of retinoblastoma uncovered a tumor that had no coding-region mutations or focal chromosomal lesions other than in the RB1 gene, shifting the paradigm in the field. The retinoblastoma genome can be very stable; therefore, epigenetic deregulation of tumor-promoting pathways is required for tumorigenesis. This review highlights the genetic and epigenetic changes in retinoblastoma that have been reported, with special emphasis on recent whole-genome sequencing and epigenetic analyses that have identified novel candidate genes as potential therapeutic targets.

Suppressor of Zeste 12 homolog RNA interference inhibits retinoblastoma cell invasion

Suppressor of Zeste 12 homolog (SUZ12) is known to regulate tumor phenotype through altering gene expression, with an important regulatory role in tumor genesis and development. SUZ12 has been widely investigated; however, no studies regarding the role of the SUZ12 gene in retinoblastoma (RB) have been conducted. In this study, SUZ12 small interfering (si)RNA was transfected into SO-RB50 human RB cells. The influence of SUZ siRNA on RB cell invasion was detected using a soft agar colony forming assay and a Transwell cabin model. The effect of the SUZ12 siRNA on the expression levels of the associated proteins, vascular endothelial growth factor (VEGF), matrix metalloproteinase (MMP)-9 and MMP-2, was detected by western blotting. The number of cell clones was found to be reduced by the siRNA in a dose-dependent manner, and the number of cells that had permeated through the filter membrane was reduced following transfection with the siRNA. SUZ12 inhibition resulted in a marked reduction in VEGF, MMP-2 and MMP-9 expression levels (0.26±0.04, 0.16±0.02 and 0.12±0.02, respectively) compared with the levels in the non-transfected group (0.80±0.10, 0.94±0.16 and 1.15±0.18, respectively) (P<0.01). In conclusion, SUZ12 siRNA inhibited cell invasion and the expression of VEGF, MMP-2 and MMP-9 in SO-RB50 retinoblastoma cells.

MiR-101, downregulated in retinoblastoma, functions as a tumor suppressor in human retinoblastoma cells by targeting EZH2

Accumulating evidence indicates that microRNAs are involved in multiple processes in cancer development and progression, and several miRNAs have emerged as candidate components of oncogene or tumor-suppressor networks in retinoblastoma. miR-101 has been identified as a tumor suppressor in several types of human cancer. However, the specific function of miR-101 in retinoblastoma remains unclear. In the present study, we found that the expression of miR-101 in retinoblastoma tissues was much lower than that in the normal controls. In addition, downregulation of miR-101 more frequently occurred in retinoblastoma specimens with adverse clinicopathological and histopathological features. In addition, miR-101 inhibited cell viability and progression in retinoblastoma cells by promoting cell apoptosis and arresting the cell cycle. Finally, we found that miR-101 directly inhibited EZH2 expression by targeting its 3'-UTR, and EZH2 was upregulated and inversely correlated with miR-101 expression in the retinoblastoma tissues. Thus, for the first time, we provide convincing evidence that downregulation of miR-101 is associated with tumor aggressiveness in retinoblastoma and inhibits cell growth and proliferation of retinoblastoma cells by targeting EZH2. In conclusion, all the evidence supports the tumor-suppressor role of miR-101 in human retinoblastoma.

MicroRNA-183 suppresses retinoblastoma cell growth, invasion and migration by targeting LRP6

Our study demonstrates the downregulation of microRNA-183 (miR-183) in retinoblastoma (RB) tissues and RB cell lines compared with normal retinal tissues. The ectopic expression of miR-183 in the RB cell lines Y79, SO-RB50 and WERI-RB1 suppresses cell viability, migration and invasion. Furthermore, the Wnt co-receptor low-density lipoprotein receptor-related protein 6 (LRP6) was identified as a new target of miR-183, and restoration of the expression of LRP6 rescues the effects induced by miR-183 in RB cells. These results indicate that miR-183 targets and downregulates LRP6 in the growth, migration and invasion of RB cells.

Characterizing the Retinoblastoma 1 locus: putative elements for Rb1 regulation by in silico analysis

Limited understanding of the Rb1 locus hinders genetic and epigenetic analyses of Retinoblastoma, a childhood cancer of the nervous systems. In this study, we used in silico tools to investigate and review putative genetic and epigenetic elements of the Rb1 gene. We report transcription start sites, CpG islands, and regulatory moieties that are likely to influence transcriptional states of this gene. These might contribute genetic and epigenetic information modulating tissue-specific transcripts and expression levels of Rb1. The elements we identified include tandem repeats that reside within or next to CpG islands near Rb1's transcriptional start site, and that are likely to be polymorphic among individuals. Our analyses highlight the complexity of this gene and suggest opportunities and limitations for future studies of retinoblastoma, genetic counseling, and the accurate identification of patients at greater risk of developing the malignancy.

Down-regulation of PTEN expression modulated by dysregulated miR-21 contributes to the progression of esophageal cancer

BACKGROUND AND AIM

miR-21, a putative tumor oncomiR, is a frequently overexpressed miRNA in a variety of tumors. Because it targets tumor-suppressor genes it has been linked to tumor progression. In this study we investigated the role of miR-21 in esophageal squamous cell carcinoma (ESCC), and its possible mechanism.

METHODS

Expression of miR-21 was detected by stem-loop RT-PCR in tissue from 76 invasive ESCC at stage I-IV and in their corresponding para-cancerous histological normal tissues (PCHNT). Thirty endoscopic esophageal mucosal biopsy specimens from non-tumor patients were used as controls. Expression of PTEN in 76 paired ESCC and PCHNT was investigated by real-time RT-PCR and an immunohistochemical method, respectively. Paired tumor and PCHNT specimens of 20 ESCC cases were randomly selected for western blot analysis. The effect of miR-21 on PTEN expression was assessed in the ESCC cell line with an miR-21 inhibitor to reduce miR-21 expression. Furthermore, the roles of miR-21 in cell biology were analyzed by use of miR-21 inhibitor-transfected cells.

RESULTS

Stem-loop RT-PCR revealed miR-21 was significantly overexpressed in ESCC tissues and cell lines. Overexpression of miR-21 correlated with tumor status, lymph node metastasis, and clinical stage. We demonstrated that knockdown of miR-21 significantly increased expression of PTEN protein. Consequent PTEN expression reduced cell proliferation, invasion, and migration.

CONCLUSIONS

Our findings suggest that miR-21 could be a potential oncomiR, probably by regulation of PTEN, and a novel prognostic factor for ESCC patients.

Diffuse anterior retinoblastoma: A review

Diffuse anterior retinoblastoma is a rare variant of diffuse infiltrating retinoblastoma which occurs in up to 1-2% of cases of retinoblastoma. In diffuse anterior retinoblastoma there is a small focus of tumor in the peripheral retina from which free tumor cells enter the aqueous humor and implant on the ciliary body, iris, lens and trabecular meshwork. Patients most commonly present with pseudouveitis, pseudohypopyon and increased intraocular pressure. The differential diagnosis is broad and all of the reported cases relied upon aspirates from the aqueous humor in order to make the diagnosis prior to proceeding with treatment. Treatment involves enucleation and, depending upon the extent of the tumor, may require systemic chemotherapy or external beam radiation. This review summarizes the 7 previously reported cases of diffuse anterior retinoblastoma, discusses pathologic features, and addresses the challenges of early diagnosis and future directions.

MiR-181b targets Six2 and inhibits the proliferation of metanephric mesenchymal cells in vitro

MicroRNAs (miRNAs) are small non-coding RNAs that down-regulate gene expression by binding to target mRNA for cleavage or translational repression, and play important regulatory roles in renal development. Despite increasing genes have been predicted to be miRNA targets by bioinformatic analysis during kidney development, few of them have been verified by experiment. The objective of our study is to identify the miRNAs targeting Six2, a critical transcription factor that maintains the mesenchymal progenitor pool via self-renewal (proliferation) during renal development. We initially analyzed the 3'UTR of Six2 and found 37 binding sites targeted by 50 putative miRNAs in the 3'UTR of Six2. Among the 50 miRNAs, miR-181b is the miRNAs predicted by the three used websites. In our study, the results of luciferase reporter assay, realtime-PCR and Western blot demonstrated that miR-181b directly targeted on the 3'UTR of Six2 and down-regulate the expression of Six2 at mRNA and protein levels. Furthermore, EdU proliferation assay along with the Six2 rescue strategy showed that miR-181b suppresses the proliferation of metanephric mesenchymal by targeting Six2 in part. In our research, we concluded that by targeting the transcription factor gene Six2, miR-181b inhibits the proliferation of metanephric mesenchymal cells in vitro and might play an important role in the formation of nephrons.

Polymorphisms of CDKN1A gene and risk of retinoblastoma

Retinoblastoma (RB) is a malignant neoplasia that occurs mostly in children under 5 years. Recently, CDKN1A gene has been shown to be up-regulated in a context of loss of function of pRb. This gene encodes the p21 protein, which is the bona fide effector of p53. We hypothesized whether two putatively functional single nucleotide polymorphisms (SNPs) of CDKN1A (rs1801270 C>A and rs1059234 C>T) may influence the risk and/or survival of RB patients. We genotyped both SNPs in 141 RB patients and 120 unrelated healthy individuals. Statistical analyses consisted of chi-square (χ(2)), odds ratio (OR) and survival curves by Kaplan-Meier method. We found that patients who carry the genotype CA for rs1801270 and CT for rs1059234 were associated to an increased risk of RB [OR = 2.5, 95% confidence interval (CI) = 1.38-4.53], whereas patients with CC for both polymorphisms were associated to a lower risk of developing RB (OR = 0.43, 95% CI = 0.25-0.74). On the other hand, Kaplan-Meier curves did not show statistically significant differences in survival among the studied polymorphisms. We conclude that the minor alleles of rs1801270 and rs1059234 polymorphisms may act as risk factors for the development of RB in our sample.

SUMMARY

The minor alleles of polymorphisms rs1801270 C>A and rs1059234 C>T in CDKN1A (p21) gene may act as risk factors for the development of RB; however, they do not seem to influence overall survival.

The genomic landscape of retinoblastoma: a review

Retinoblastoma is a paediatric ocular tumour that continues to reveal much about the genetic basis of cancer development. Study of genomic aberrations in retinoblastoma tumours has exposed important mechanisms of cancer development and identified oncogenes and tumour suppressors that offer potential points of therapeutic intervention. The recent development of next-generation genomic technologies has allowed further refinement of the genomic landscape of retinoblastoma at high resolution. In a relatively short period of time, a wealth of genetic and epigenetic data has emerged on a small number of tumour samples. These data highlight the inherent molecular complexity of this cancer despite the fact that most retinoblastomas are initiated by the inactivation of a single tumour suppressor gene. This review outlines the current understanding of the genomic, genetic and epigenetic changes in retinoblastoma, highlighting recent genome-wide analyses that have identified exciting candidate genes worthy of further validation as potential prognostic and therapeutic targets.