Molecular Insights on Post-chemotherapy Retinoblastoma by Microarray Gene Expression Analysis

Dopachrome tautomerase is a retinoblastoma-specific gene, and its proximal promoter is preferentially active in human retinoblastoma cells

Purpose

Retinoblastoma (RB) is a malignant childhood intraocular tumor. Current treatment options for RB have undesirable side effects. A comprehensive understanding of gene expression in human RB is essential for the development of safe and effective new therapies.

Methods

We reviewed published microarray and RNA sequencing studies in which gene expression profiles were compared between human RB and normal retina tissues. We investigated the expression of genes of interest using quantitative reverse transcription PCR. We examined the activities of cloned promoter DNA fragments with luciferase assay.

Results

Dopachrome tautomerase (DCT) was among the most overexpressed genes in RB in published studies. We found that DCT was highly expressed in six of 13 samples microdissected from Thai RB tissues. Expression of DCT was absent or barely detected in retina tissues, various human ocular cells, and major organs. We also demonstrated that the -657 to +411 DCT promoter fragment efficiently directs RB cell-specific transcription of the luciferase reporter gene in cell lines.

Conclusions

The present work highlights that DCT is one of the most RB-specific genes. The regulatory elements required for this cell-specific gene expression are likely located within its proximal promoter.

UBE2T/STAT3 Signaling Promotes the Proliferation and Tumorigenesis in Retinoblastoma

Purpose

The purpose of this paper was to investigate the expression and function of Ubiquitin-conjugating enzyme 2T (UBE2T), a human E2 ubiquitin-conjugating enzyme, in human retinoblastoma.

Methods

The expression of UBE2T in normal retina and retinoblastoma was analyzed using the Gene Expression Omnibus (GEO) databases, and its expression was immunohistochemically evaluated in 29 retinoblastoma sections and 5 normal retinas. Then CCK-8, flow cytometry, RNA-sequencing analysis, and in vivo assays were performed to explore the exact role of UBE2T in retinoblastoma.

Results

We found that retinoblastoma showed higher UBE2T expression than normal retina in GEO datasets and tissues. The immunoreactive score of UBE2T ≥4 was associated with group E in IIRC, T2-T4b in pTNM staging, poorly differentiated retinoblastoma, and high-risk histopathological factors. Knockdown of UBE2T reduced the cell viability, increased the apoptosis cells and G0/G1 cells, and inhibited subcutaneous tumor growth in vivo. Mechanistic studies showed that UBE2T knockdown induced down-regulation of phosphorylation of STAT3 and its downstream genes in vitro and in vivo. Rescue assays confirmed that STAT3 signaling pathway was involved in the effect of reduced cell viability, elevated apoptosis cells, and G0/G1 cells mediated by UBE2T knockdown.

Conclusions

Our data indicate that UBE2T significantly participates in the proliferation of retinoblastoma via the STAT3 signaling pathway, suggesting the potential of UBE2T as a therapeutic target for retinoblastoma treatment.

Centromere protein E as a novel biomarker and potential therapeutic target for retinoblastoma

Retinoblastoma is the most common intraocular malignancy during childhood. Currently, there is no effective treatment for metastatic retinoblastoma. We investigated potential biomarkers of retinoblastoma by utilizing three datasets from a public database. Functional enrichment analysis, including gene ontology, Kyoto encyclopedia of genes and genomes, gene set enrichment analysis and variation analysis, suggested that differentially expressed genes in retinoblastoma were enriched in accelerated cell cycle events. Protein-protein interaction analysis constructed a network consisting of six hub genes, including benzimidazoles 1 (BUB1), cyclin dependent kinase 1 (CDK1), centromere protein E (CENPE), kinesin family member 20A (KIF20A), PDZ binding kinase (PBK), and targeting protein for xklp2 (TPX2). Drug sensitivity analysis showed that nelarabine was positively correlated with five hub genes. All six genes were expressed differently in six immune subtypes and were positively correlated with stemness indices in most human cancer types. Since CENPE is the least known hub gene in retinoblastoma, we further analyzed the potential non-coding RNAs and transcription factors that regulate CENPE and built interaction networks of competing endogenous RNA and transcription factors. Immune cell infiltration, especially by plasma and B cells, was enhanced in samples with high CENPE expression. Pan-cancer analysis illustrated that CENPE was highly expressed in a wide range of human tumors. In vitro validation revealed that CENPE was significantly upregulated at both the mRNA and protein levels in retinoblastoma cells. In conclusion, CENPE, along with other hub genes, could serve as a potential biomarker and intervention target for retinoblastoma.

TRIM59 Promotes Retinoblastoma Progression by Activating the p38-MAPK Signaling Pathway

Purpose

Retinoblastoma is a malignant tumor of the developing retina that mostly occurs in children. Our study aimed to investigate the effect of tripartite motif-containing protein 59 (TRIM59) on retinoblastoma growth and the underlying mechanisms.

Methods

We performed bioinformatic analysis of three datasets (GSE24673, GSE97508, and GSE110811) from the Gene Expression Omnibus database. Quantitative reverse-transcription PCR and immunoblotting of three retinoblastoma cell lines were conducted to verify TRIM59 as a differentially expressed gene. Specific siRNAs were used to inhibit TRIM59 expression in the HXO-Rb44 cell line. A lentiviral vector was transfected into the Y79 cell line to overexpress TRIM59. The effects of TRIM59 on retinoblastoma cell proliferation, cell cycling, and apoptosis were explored in vitro using the abovementioned cell lines. The effect of TRIM59 expression on retinoblastoma cell proliferation was evaluated in a mouse xenograft tumor model.

Results

TRIM59 expression in three retinoblastoma cell lines was remarkably elevated compared with normal control. Knocking down TRIM59 expression remarkably suppressed cell proliferation and growth and promoted cell apoptosis in HXO-Rb44 cells, whereas TRIM59 overexpression promoted tumor progression in Y79 cells. Silencing TRIM59 also markedly inhibited in vivo tumor growth in the xenograft model. Mechanistic studies revealed that TRIM59 upregulated phosphorylated p38, p-JNK1/2, p-ERK1/2, and p-c-JUN expression in retinoblastoma cells. Notably, the p38 inhibitor SB203580 attenuated the effects of TRIM59 on cell proliferation, apoptosis, and the G1/S phase transition.

Conclusions

TRIM59 plays an oncogenic role in retinoblastoma and exerts its tumor-promotive function by activating the p38-mitogen-activated protein kinase pathway.

Identification of pathogenic genes of pterygium based on the Gene Expression Omnibus database

AIM

To identify the pathogenic genes in pterygium.

METHODS

We obtained mRNA expression profiles from the Gene Expression Omnibus database (GEO) to identify differentially expressed genes (DEGs) between pterygium tissues and normal conjunctiva tissues. The Gene Ontology, Kyoto Encyclopedia of Genes and Genomes pathway analysis, protein-protein interaction (PPI) network and transcription factors (TFs)-target gene regulatory network was performed to understand the function of DEGs. The expression of selected DEGs were validated by the quantitative real-time polymerase chain reaction (qRT-PCR).

RESULTS

A total of 557 DEGs were identified between pterygium and normal individual. In PPI network, several genes were with high degrees such as FN1, KPNB1, DDB1, NF2 and BUB3. SSH1, PRSS23, LRP5L, MEOX1, RBM14, ABCA1, JOSD1, KRT6A and UPK1B were the most downstream genes regulated by TFs. qRT-PCR results showed that FN1, PRSS23, ABCA1, KRT6A, ECT2 and SPARC were significantly up-regulated in pterygium and MEOX1 and MMP3 were also up-regulated with no significance, which was consistent with the our integrated analysis.

CONCLUSION

The deregulated genes might be involved in the pathology of pterygium and could be used as treatment targets for pterygium.

miR‑34a regulates the chemosensitivity of retinoblastoma cells via modulation of MAGE‑A/p53 signaling

The present study aimed to explore the combined role of microRNA (miR)-34a, melanoma antigen-A (MAGE‑A) and p53 in altering the chemosensitivity of retinoblastoma (RB) cells. Human RB and adjacent tumor tissues, as well as human RB cell lines (HXO‑Rb44, SO‑Rb50, Y79 and WERI‑Rb-1) were used. In addition, four chemotherapeutic drugs, including carboplatin, etoposide, Adriamycin and vincristine, were used to treat the cell lines, in order to evaluate the sensitivity of RB cells. Furthermore, miR‑34a expression was detected by reverse transcription-quantitative polymerase chain reaction, and western blotting was implemented to quantify expression levels of MAGE‑A and p53. A luciferase reporter gene assay was used to validate the targeted association between miR‑34a and MAGE‑A. The results indicated that SO‑Rb50 cells exhibited the highest resistance to carboplatin, Adriamycin and vincristine (P<0.05), whereas HXO‑Rb44 cells revealed the highest inhibition rate in response to etoposide (P<0.05) out of the four cell lines. Furthermore, reduced miR‑34a expression and increased MAGE‑A expression significantly elevated the survival rate and viability of SO‑Rb50 cells following drug treatment (all P<0.05). miR‑34a was also demonstrated to directly target MAGE‑A, thereby significantly promoting the viability of RB cells and depressing apoptosis (P<0.05). p53, which was subjected to modulation by miR‑34a and MAGE‑A, also significantly reduced the proliferation rate of RB cells (P<0.05). In conclusion, the miR‑34a/MAGE‑A/p53 axis may be conducive to enhancing the efficacies of chemotherapeutic treatments for RB.

The FoxM1-ABCC4 axis mediates carboplatin resistance in human retinoblastoma Y-79 cells

Carboplatin is the most commonly used drug in the first-line treatment of human retinoblastoma (RB), but its clinical application is greatly limited due to acquired drug resistance upon the long-term treatment. Forkhead box protein M1 (FoxM1) is the transcription factor aberrantly expressed in various types of human cancers, which plays an essential role in the regulation of tumorigenesis, tumor metastasis and drug resistance. However, little is known about the role of FoxM1 in chemo-resistance of human RB. In this study, we investigated the regulatory effect of FoxM1 on carboplatin resistance in human RB Y-79 cells and carboplatin-resistant Y-79 (Y-79CR) cells, as well as the possible mechanism. Our results showed that FoxM1 was up-regulated in Y-79CR cells and silencing of FoxM1 promoted carboplatin sensitivity and accumulation, while overexpression of FoxM1 in Y-79 cells performed oppositely. Our study further revealed that FoxM1 enhanced carboplatin resistance in Y-79CR cells through directly up-regulating the transcription of ATP-binding cassette transporter C4 (ABCC4), an important drug efflux transporter. Overall, our study demonstrated the novel role of FoxM1-ABCC4 axis in human RB, which provides insights into the prevention of carboplatin resistance in human RB.

Oncogenic role of epithelial cell transforming sequence 2 in lung adenocarcinoma cells

Lung adenocarcinoma, which is the most common non-small cell lung cancer, is the leading cause of death from cancer worldwide. Epithelial cell transforming sequence 2 (ECT2) is frequently upregulated and acts as an oncogene in various human cancers. In addition, ECT2 was reported to be upregulated in early stage lung adenocarcinoma. However, the detailed role of ECT2 in mediating the malignant phenotypes of lung adenocarcinoma cells has not previously been elucidated. Reverse transcription-quantitative polymerase chain reaction and western blot analysis were used to examine ECT2 mRNA and protein expression levels, respectively. MTT, wound healing and Transwell assays were conducted to determine cell proliferation, migration and invasion abilities, respectively. In the present study, ECT2 was significantly upregulated in lung adenocarcinoma cell lines (H650, EKVX, HCC4006, HCC827, HCC2935, Hop62 and A549), as compared with a normal lung epithelial cell line (BEAS-2B). Moreover, knockdown of ECT2, induced by transfection with ECT2 siRNA, significantly inhibited the proliferation of lung adenocarcinoma A549 cells, whereas overexpression of ECT2 enhanced A549 cell proliferation. Furthermore, knockdown of ECT2 expression suppressed the migration and invasion of A549 cells, whereas overexpression of ECT2 enhanced the migration and invasion abilities of A549 cells. Notably, inhibition of ECT2 also suppressed the expression levels of N-cadherin and vimentin, whereas it enhanced the expression level of E-cadherin, indicating that ECT2 is associated with the epithelial-mesenchymal transition in A549 cells. On the contrary, overexpression of ECT2 enhanced the expression levels of N-cadherin and vimentin, whereas it reduced the expression level of E-cadherin in A549 cells. In conclusion, the results of the present study suggest that ECT2 has an oncogenic role in lung adenocarcinoma cells. Therefore, ECT2 may be a potential novel target for the treatment of lung adenocarcinoma.

Multiple Differential Networks Strategy Reveals Carboplatin and Melphalan-Induced Dynamic Module Changes in Retinoblastoma

Background

Retinoblastoma (RB) is the most common malignant tumor of the eye in childhood. The objective of this paper was to investigate carboplatin (CAR)- and melphalan (MEL)-induced dynamic module changes in RB based on multiple (M) differential networks, and to generate systems-level insights into RB progression.

Material/Methods

To achieve this goal, we constructed M-differential co-expression networks (DCNs), assigned a weight to each edge, and identified seed genes in M DCNs by ranking genes based on their topological features. Starting with seed genes, a module search was performed to explore candidate modules in CAR and MEL condition. M-DMs were detected according to significance evaluations of M-modules, which originated from refinement of candidate modules. Further, we revealed dynamic changes in M-DM activity and connectivity on the basis of significance of Module Connectivity Dynamic Score (MCDS).

Results

In the present study, M=2, a total of 21 seed genes were obtained. By assessing module search, refinement, and evaluation, we gained 18 2-DMs. Moreover, 3 significant 2-DMs (Module 1, Module 2, and Module 3) with dynamic changes across CAR and MEL condition were determined, and we denoted them as dynamic modules. Module 1 had 27 nodes of which 6 were seed genes and 56 edges. Module 2 was composed of 28 nodes and 54 edges. A total of 28 nodes interacted with 45 edges presented in Module 3.

Conclusions

We have identified 3 dynamic modules with changes induced by CAR and MEL in RB, which might give insights in revealing molecular mechanism for RB therapy.

Activation of IFN/STAT1 signalling predicts response to chemotherapy in oestrogen receptor-negative breast cancer

Background:

Oestrogen receptor-negative (ER−) breast cancer is intrinsically sensitive to chemotherapy. However, tumour response is often incomplete, and relapse occurs with high frequency. The aim of this work was to analyse the molecular characteristics of residual tumours and early response to chemotherapy in patient-derived xenografts (PDXs) of breast cancer.

Methods:

Gene and protein expression profiles were analysed in a panel of ER− breast cancer PDXs before and after chemotherapy treatment. Tumour and stromal interferon-gamma expression was measured in xenografts lysates by human and mouse cytokine arrays, respectively.

Results:

The analysis of residual tumour cells in chemo-responder PDX revealed a strong overexpression of IFN-inducible genes, induced early after AC treatment and associated with increased STAT1 phosphorylation, DNA-damage and apoptosis. No increase in IFN-inducible gene expression was observed in chemo-resistant PDXs upon chemotherapy. Overexpression of IFN-related genes was associated with human IFN-γ secretion by tumour cells.

Conclusions:

Treatment-induced activation of the IFN/STAT1 pathway in tumour cells is associated with chemotherapy response in ER− breast cancer. Further validations in prospective clinical trials will aim to evaluate the usefulness of this signature to assist therapeutic strategies in the clinical setting.

Characterization and pharmacologic targeting of EZH2, a fetal retinal protein and epigenetic regulator, in human retinoblastoma

Retinoblastoma (RB) is the most common primary intraocular cancer in children, and the third most common cancer overall in infants. No molecular-targeted therapy for this lethal tumor exists. Since the tumor suppressor RB1, whose genetic inactivation underlies RB, is upstream of the epigenetic regulator EZH2, a pharmacologic target for many solid tumors, we reasoned that EZH2 might regulate human RB tumorigenesis. Histologic and immunohistochemical analyses were performed using an EZH2 antibody in sections from 43 samples of primary, formalin-fixed, paraffin-embedded human RB tissue, cryopreserved mouse retina, and in whole cell lysates from human RB cell lines (Y79 and WERI-Rb1), primary human fetal retinal pigment epithelium (RPE) and fetal and adult retina, mouse retina and embryonic stem (ES) cells. Although enriched during fetal human retinal development, EZH2 protein was not present in the normal postnatal retina. However, EZH2 was detected in all 43 analyzed human RB specimens, indicating that EZH2 is a fetal protein expressed in postnatal human RB. EZH2 expression marked single RB cell invasion into the optic nerve, a site of invasion whose involvement may influence the decision for systemic chemotherapy. To assess the role of EZH2 in RB cell survival, human RB and primary RPE cells were treated with two EZH2 inhibitors (EZH2i), GSK126 and SAH-EZH2 (SAH). EZH2i impaired intracellular adenosine triphosphate (ATP) production, an indicator of cell viability, in a time and dose-dependent manner, but did not affect primary human fetal RPE. Thus, aberrant expression of a histone methyltransferase protein is a feature of human RB. This is the first time this mechanism has been implicated for an eye, adnexal, or orbital tumor. The specificity of EZH2i toward human RB cells, but not RPE, warrants further in vivo testing in animal models of RB, especially those EZH2i currently in clinical trials for solid tumors and lymphoma.

Small interfering RNA-induced inhibition of epithelial cell transforming sequence 2 suppresses the proliferation, migration and invasion of osteosarcoma cells

Osteosarcoma (OS) is the most common malignant tumor in bones. Although the five-year survival rate has improved to ∼60% for patients without metastasis, the prognosis remains poor for patients with metastatic OS. Epithelial cell transforming sequence 2 (ECT2) has been shown to act as an oncogene in human malignancies. More recently, ETC2 was shown to be involved in the development and progression of OS; however, the detailed role of ECT2 in the regulation of cellular biological processes in OS cells remains largely unknown. Therefore, it was investigated in the present study. It was found that the expression of ECT2 was notably increased in OS tissues when compared with that in matched normal adjacent tissues. Furthermore, it was established that the downregulation of ECT2 induced by transfection with ECT2-specific small interfering RNA effectively inhibited OS cell proliferation and induced cell apoptosis. Further investigation revealed that the inhibition of ECT2 expression suppressed OS cell migration and invasion, indicating that the overexpression of ECT2 promotes OS cell migration and invasion, while. In addition, western blotting results indicated that matrix metalloproteinases 2 and 9 may be involved in the ECT2-mediated OS cell invasion. In conclusion, the current study suggested that ECT2 acted as an oncogene in OS, and it may become a promising therapeutic target for the prevention and treatment of OS.

Integrated Analysis of Dysregulated miRNA-gene Expression in HMGA2-silenced Retinoblastoma Cells

Retinoblastoma (RB) is a primary childhood eye cancer. HMGA2 shows promise as a molecule for targeted therapy. The involvement of miRNAs in genome-level molecular dys-regulation in HMGA2-silenced RB cells is poorly understood. Through miRNA expression microarray profiling, and an integrated array analysis of the HMGA2-silenced RB cells, the dysregulated miRNAs and the miRNA-target relationships were modelled. Loop network analysis revealed a regulatory association between the transcription factor (SOX5) and the deregulated miRNAs (miR-29a, miR-9*, miR-9-3). Silencing of HMGA2 deregulated the vital oncomirs (miR-7, miR-331, miR-26a, miR-221, miR-17~92 and miR-106b∼25) in RB cells. From this list, the role of the miR-106b∼25 cluster was examined further for its expression in primary RB tumor tissues (n = 20). The regulatory targets of miR-106b∼25 cluster namely p21 (cyclin-dependent kinase inhibitor) and BIM (pro-apoptotic gene) were elevated, and apoptotic cell death was observed, in RB tumor cells treated with the specific antagomirs of the miR-106b∼25 cluster. Thus, suppression of miR-106b∼25 cluster controls RB tumor growth. Taken together, HMGA2 mediated anti-tumor effect present in RB is, in part, mediated through the miR-106b∼25 cluster.