Predictive and Prognostic Roles of Abnormal Expression of Tissue miR-125b, miR-221, and miR-222 in Glioma

Non-Coding RNA as a Biomarker in Lung Cancer

INTRODUCTION

Lung cancer remains one of the most prevalent and deadly cancers globally, with high mortality rates largely due to late-stage diagnosis, aggressive progression, and frequent recurrence. Despite advancements in diagnostic techniques and therapeutic interventions, the overall prognosis for lung cancer patients continues to be dismal.

METHOD

Emerging research has identified non-coding RNAs (ncRNAs), including microRNAs, long non-coding RNAs, and circular RNAs, as critical regulators of gene expression, significantly influencing cancer biology. These ncRNAs play pivotal roles in various aspects of lung cancer pathogenesis, including tumor initiation, progression, metastasis, and resistance to therapy.

RESULTS

We provide a comprehensive analysis of the current understanding of ncRNAs in lung cancer, emphasizing their potential as biomarkers for early diagnosis, prognostication, and the prediction of the therapeutic response. We explore the biological functions of ncRNAs, their involvement in key oncogenic pathways, and the molecular mechanisms by which they modulate gene expression and cellular processes in lung cancer. Furthermore, this review highlights recent advances in ncRNA-based diagnostic tools and therapeutic strategies, such as miRNA mimics and inhibitors, lncRNA-targeted therapies, and circRNA-modulating approaches, offering promising avenues for personalized medicine.

CONCLUSION

Finally, we discuss the challenges and future directions in ncRNA research, including the need for large-scale validation studies and the development of efficient delivery systems for ncRNA-based therapies. This review underscores the potential of ncRNAs to revolutionize lung cancer management by providing novel diagnostic and therapeutic options that could improve patient outcomes.

Comparison of Oncogenes, Tumor Suppressors, and MicroRNAs Between Schizophrenia and Glioma: The Balance of Power

The risk of cancer in schizophrenia has been controversial. Confounders of the issue are cigarette smoking in schizophrenia, and antiproliferative effects of antipsychotic medications. The author has previously suggested comparison of a specific cancer like glioma to schizophrenia might help determine a more accurate relationship between cancer and schizophrenia. To accomplish this goal, the author performed three comparisons of data; the first a comparison of conventional tumor suppressors and oncogenes between schizophrenia and cancer including glioma. This comparison determined schizophrenia has both tumor-suppressive and tumor-promoting characteristics. A second, larger comparison between brain-expressed microRNAs in schizophrenia with their expression in glioma was then performed. This identified a core carcinogenic group of miRNAs in schizophrenia offset by a larger group of tumor-suppressive miRNAs. This proposed "balance of power" between oncogenes and tumor suppressors could cause neuroinflammation. This was assessed by a third comparison between schizophrenia, glioma and inflammation in asbestos-related lung cancer and mesothelioma (ALRCM). This revealed that schizophrenia shares more oncogenic similarity to ALRCM than glioma.

Recent advances in label-free optical, electrochemical, and electronic biosensors for glioma biomarkers

Gliomas are the most commonly occurring primary brain tumor with poor prognosis and high mortality rate. Currently, the diagnostic and monitoring options for glioma mainly revolve around imaging techniques, which often provide limited information and require supervisory expertise. Liquid biopsy is a great alternative or complementary monitoring protocol that can be implemented along with other standard diagnosis protocols. However, standard detection schemes for sampling and monitoring biomarkers in different biological fluids lack the necessary sensitivity and ability for real-time analysis. Lately, biosensor-based diagnostic and monitoring technology has attracted significant attention due to several advantageous features, including high sensitivity and specificity, high-throughput analysis, minimally invasive, and multiplexing ability. In this review article, we have focused our attention on glioma and presented a literature survey summarizing the diagnostic, prognostic, and predictive biomarkers associated with glioma. Further, we discussed different biosensory approaches reported to date for the detection of specific glioma biomarkers. Current biosensors demonstrate high sensitivity and specificity, which can be used for point-of-care devices or liquid biopsies. However, for real clinical applications, these biosensors lack high-throughput and multiplexed analysis, which can be achieved via integration with microfluidic systems. We shared our perspective on the current state-of-the-art different biosensor-based diagnostic and monitoring technologies reported and the future research scopes. To the best of our knowledge, this is the first review focusing on biosensors for glioma detection, and it is anticipated that the review will offer a new pathway for the development of such biosensors and related diagnostic platforms.

Fibronectin Modulates the Expression of miRNAs in Prostate Cancer Cell Lines

Prostate cancer (PCa) is a significant cause of cancer-related deaths among men and companion animals, such as dogs. However, despite its high mortality and incidence rates, the molecular mechanisms underlying this disease remain to be fully elucidated. Among the many factors involved in prostate carcinogenesis, the extracellular matrix (ECM) plays a crucial role. This ECM in the prostate is composed mainly of collagen fibers, reticular fibers, elastic fibers, proteoglycans and glycoproteins, such as fibronectin. Fibronectin is a glycoprotein whose dysregulation has been implicated in the development of multiple types of cancer, and it has been associated with cell migration, invasion, and metastasis. Furthermore, our research group has previously shown that fibronectin induces transcriptional changes by modulating the expression of protein coding genes in LNCaP cells. However, potential changes at the post-transcriptional level are still not well understood. This study investigated the impact of exposure to fibronectin on the expression of a key class of regulatory RNAs, the microRNAs (miRNAs), in prostate cancer cell lines LNCaP and PC-3. Five mammalian miRNAs (miR-21, miR-29b, miR-125b, miR-221, and miR-222) were differentially expressed after fibronectin exposure in prostate cell lines. The expression profile of hundreds of mRNAs predicted to be targeted by these miRNAs was analyzed using publicly available RNA-Sequencing data (GSE64025, GSE68645, GSE29155). Also, protein-protein interaction networks and enrichment analysis were performed to gain insights into miRNA biological functions. Altogether, these functional analyzes revealed that fibronectin exposure impacts the expression of miRNAs potentially involved in PCa causing changes in critical signaling pathways such as PI3K-AKT, and response to cell division, death, proliferation, and migration. The relationship here demonstrated between fibronectin exposure and altered miRNA expression improves the comprehension of PCa in both men and other animals, such as dogs, which naturally develop prostate cancer.

Prognostic Potential of MicroRNAs in Glioma Patients: A Meta-Analysis

Introduction MicroRNAs are a noncoding RNA involved in affecting several transcription and translation pathways. Their use has been discussed as potential predictors of several tumors. Their use as potential biomarker in glioma patients is still controversial. The purpose of this meta-analysis is to explore the possible role of such microRNAs in glioma patients.

Methods After an extensive literature search done on PubMed and Embase, 20 studies were chosen for our analyses with the 9 discussing 11 tumor promoting microRNAs and 11 studies discussing 11 tumor suppressing microRNAs. The data needed was extracted from these studies including the hazard ratio that was used as the effect size for the purpose of our analysis. The needed analysis was performed using Stata and Excel.

Results The pooled hazard ratio for our analysis with patients having a lower microRNA expression for tumor promoting microRNAs came to be 2.63 (p < 0.001), while the hazard ratio for patients with higher expression of tumor promoting microRNA was 2.47 (p < 0.001) with both results being statistically significant. However, as significant heterogeneity was observed a random effect model for analysis was used. Subgroup analysis was further performed using grade, cutoff value (mean or median), sample type (Serum or Blood), and Karnofsky performance score, all of them showing a high hazard ratio.

Conclusion Our results showed that both tumor inhibitory and promoting microRNA can be used as prognostic tool in glioma patients with a poorer prognosis associated with a lower expression in tumor suppressive and higher expression in tumor promoting microRNA, respectively. However, to support this, future studies on a much larger scale would be needed.

Prognostic Value of microRNA-221/2 and 17-92 Families in Primary Glioblastoma Patients Treated with Postoperative Radiotherapy

MicroRNAs (miRs) are non-coding master regulators of transcriptome that could act as tumor suppressors (TSs) or oncogenes (oncomiRs). We aimed to systematically investigate the relevance of miRs as prognostic biomarkers in primary glioblastoma multiforme (GBM) treated with postoperative radio(chemo)therapy (PORT). For hypothesis generation, tumor miR expression by Agilent 8x15K human microRNA microarrays and survival data from 482 GBM patients of The Cancer Genome Atlas (TCGA cohort) were analyzed using Cox-PH models. Expression of candidate miRs with prognostic relevance (miR-221/222; miR-17-5p, miR-18a, miR-19b) was validated by qRT-PCR using Taqman technology on an independent validation cohort of GBM patients (n = 109) treated at Heidelberg University Hospital (HD cohort). In TCGA, 50 miRs showed significant association with survival. Among the top ranked prognostic miRs were members of the two miR families miR-221/222 and miR-17-92. Loss of miR-221/222 was correlated with improved prognosis in both cohorts (TCGA, HD) and was an independent prognostic marker in a multivariate analysis considering demographic characteristics (age, sex, Karnofsky performance index (KPI)), molecular markers (O-6-methylguanine-DNA methyltransferase (MGMT) methylation, IDH mutation status) and PORT as co-variables. The prognostic value of miR-17-92 family members was ambiguous and in part contradictory by direct comparison of the two cohorts, thus warranting further validation in larger prospective trials.

High expression of microRNA 221 is a poor predictor for glioma

BACKGROUND

MicroRNA 221 has been found to be a good marker for several cancers. Some studies also focused on the relationship between microRNA 221 and glioma. However, the results are controversial. We aimed to systematically evaluate the prognostic role of microRNA 221 in glioma through performing a meta-analysis.

METHODS

The articles which were included in our study were searched on the Web of Science, EMBASE, PubMed, Cochrane Library and China National Knowledge Infrastructure. The basic characteristics and relevant data were extracted. Hazard ratios (HRs) with 95% confidence intervals (CIs) were pooled to evaluate the prognostic role of microRNA 221 in glioma.

RESULTS

Eight studies with 1069 patients were included. We systematically evaluated the role of microRNA 221 for overall survival (OS) and disease free survival (DFS) in glioma patients (HR for OS = 1.66, 95% CI, 1.34-2.04; HR for DFS = 1.14, 95% CI, 1.02-1.26). Subgroup analyses were performed according to the nation of the studies, the origin of the samples, the stage of the tumors, the cut-off value, and the method for detecting the microRNA 221. No significant publication bias was found (P = .133).

CONCLUSION

In conclusion, high expression of microRNA 221 was related to poor prognosis of glioma. These findings may assist future exploration on microRNA 221 and help predict the prognosis of glioma. However, due to the significant heterogeneity of these studies, more studies are warranted.

Prognostic Role of MicroRNA 222 in Patients with Glioma: A Meta-analysis

Background

Several studies have focused on the prognostic role of microRNA 222 in glioma. But different conclusions were drawn by these studies. We aimed to systematically evaluate the role of microRNA 222 in glioma by conducting a meta-analysis.

Methods

A systematic literature search until January 2020 was conducted in Web of Science, EMBASE, Cochrane Library, PubMed, and China National Knowledge Infrastructure. The general characteristics and relevant data of nine articles were extracted. Hazard ratios (HRs) with 95% confidence intervals (CIs) were applied to evaluate the prognostic role of microRNA 222 in glioma. The primary outcomes were overall survival (OS) and disease-free survival (DFS).

Results

Nine articles (11 data sets) with 1564 patients were included. We systematically evaluated the role of microRNA 222 for OS and DFS in glioma patients (HR for OS = 1.72; 95% CI, 1.31-2.26; p = 0.001; HR for DFS = 1.02; 95% CI, 0.86-1.22; p = 0.032). Subgroup analyses were performed according to the sources of patients, the types of the samples, the stages of the tumors, the methods for detecting the microRNA 222, and the sample size. No significant publication bias was found.

Conclusion

In conclusion, our study provided evidence that a high expression of microRNA 222 was related to worse overall survival in glioma patients. However, given the limited study number, more high-quality studies are warranted in the future.

Therapeutically Significant MicroRNAs in Primary and Metastatic Brain Malignancies

Simple Summary

The overall survival of brain cancer patients remains grim, with conventional therapies such as chemotherapy and radiotherapy only providing marginal benefits to patient survival. Cancers are complex, with multiple pathways being dysregulated simultaneously. Non-coding RNAs such as microRNA (miRNAs) are gaining importance due to their potential in regulating a variety of targets implicated in the pathology of cancers. This could be leveraged for the development of targeted and personalized therapies for cancers. Since miRNAs can upregulate and/or downregulate proteins, this review aims to understand the role of these miRNAs in primary and metastatic brain cancers. Here, we discuss the regulatory mechanisms of ten miRNAs that are highly dysregulated in glioblastoma and metastatic brain tumors. This will enable researchers to develop miRNA-based targeted cancer therapies and identify potential prognostic biomarkers.

Abstract

Brain cancer is one among the rare cancers with high mortality rate that affects both children and adults. The most aggressive form of primary brain tumor is glioblastoma. Secondary brain tumors most commonly metastasize from primary cancers of lung, breast, or melanoma. The five-year survival of primary and secondary brain tumors is 34% and 2.4%, respectively. Owing to poor prognosis, tumor heterogeneity, increased tumor relapse, and resistance to therapies, brain cancers have high mortality and poor survival rates compared to other cancers. Early diagnosis, effective targeted treatments, and improved prognosis have the potential to increase the survival rate of patients with primary and secondary brain malignancies. MicroRNAs (miRNAs) are short noncoding RNAs of approximately 18–22 nucleotides that play a significant role in the regulation of multiple genes. With growing interest in the development of miRNA-based therapeutics, it is crucial to understand the differential role of these miRNAs in the given cancer scenario. This review focuses on the differential expression of ten miRNAs (miR-145, miR-31, miR-451, miR-19a, miR-143, miR-125b, miR-328, miR-210, miR-146a, and miR-126) in glioblastoma and brain metastasis. These miRNAs are highly dysregulated in both primary and metastatic brain tumors, which necessitates a better understanding of their role in these cancers. In the context of the tumor microenvironment and the expression of different genes, these miRNAs possess both oncogenic and/or tumor-suppressive roles within the same cancer.

Noninvasive quantification of SIRT1 expression-activity and pharmacologic inhibition in a rat model of intracerebral glioma using 2-[18F]BzAHA PET/CT/MRI

Background

Several studies demonstrated that glioblastoma multiforme progression and recurrence is linked to epigenetic regulatory mechanisms. Sirtuin 1 (SIRT1) plays an important role in glioma progression, invasion, and treatment response and is a potential therapeutic target. The aim of this study is to test the feasibility of 2-[¹⁸F]BzAHA for quantitative imaging of SIRT1 expression–activity and monitoring pharmacologic inhibition in a rat model of intracerebral glioma.

Methods

Sprague Dawley rats bearing 9L (N = 12) intracerebral gliomas were injected with 2-[¹⁸F]BzAHA (300–500 µCi/animal i.v.) and dynamic positron-emission tomography (PET) imaging was performed for 60 min. Then, SIRT1 expression in 9L tumors (N = 6) was studied by immunofluorescence microscopy (IF). Two days later, rats with 9L gliomas were treated either with SIRT1 specific inhibitor EX-527 (5 mg/kg, i.p.; N = 3) or with histone deacetylases class IIa specific inhibitor MC1568 (30 mg/kg, i.p.; N = 3) and 30 min later were injected i.v. with 2-[¹⁸F]BzAHA. PET-computerized tomography-magnetic resonance (PET/CT/MR) images acquired after EX-527 and MC1568 treatments were co-registered with baseline images.

Results

Standard uptake values (SUVs) of 2-[¹⁸F]BzAHA in 9L tumors measured at 20 min post-radiotracer administration were 1.11 ± 0.058 and had a tumor-to-brainstem SUV ratio of 2.73 ± 0.141. IF of 9L gliomas revealed heterogeneous upregulation of SIRT1, especially in hypoxic and peri-necrotic regions. Significant reduction in 2-[¹⁸F]BzAHA SUV and distribution volume in 9L tumors was observed after administration of EX-527, but not MC1568.

Conclusions

PET/CT/MRI with 2-[¹⁸F]BzAHA can facilitate studies to elucidate the roles of SIRT1 in gliomagenesis and progression, as well as to optimize therapeutic doses of novel SIRT1 inhibitors.

A review of the relationship between long noncoding RNA and post-stroke injury repair

Stroke is a cerebrovascular circulation disorder with sudden onset, which causes disorder of ion balance, inflammation, and acidosis, and that in turn induces ischemia-reperfusion injury, influencing the prognosis of stroke patients. Long noncoding RNAs (lncRNAs) are regulatory sequences involved at the transcriptional, post-transcriptional, and epigenetic levels, have high specific expression in the central nervous system, and effectively regulate the development of the central nervous system and progression of diseases. Stroke induces changes in the expression of many lncRNAs. Therefore, lncRNAs play an important role in the complex pathological process of stroke. Exploring lncRNA could facilitate a comprehensive understanding of the pathological mechanism of stroke and the post-injury molecular regulatory network. However, there are few reports on the role of lncRNA in the pathological development of stroke. In the present review, we discuss the association of lncRNA with post-stroke injury repair.

Prognostic Role of miR-221 and miR-222 Expression in Cancer Patients: A Systematic Review and Meta-Analysis

Background: A wealth of evidence has shown that microRNAs (miRNAs) can modulate specific genes, increasing our knowledge on the fine-tuning regulation of protein expression. miR-221 and miR-222 have been frequently identified as deregulated across different cancer types; however, their prognostic significance in cancer remains controversial. In view of these considerations, we performed an updated systematic review and meta-analysis of published data investigating the effects of miR-221/222 on overall survival (OS) and other secondary outcomes among cancer patients. A systematic search of PubMed, Web of Knowledge, and Cochrane Library databases was performed. Hazard ratios (HRs) and 95% confidence intervals (95% CIs) were used to assess the strength of association. Results: Fifty studies, analyzing 6086 patients, were included in the systematic review. Twenty-five studies for miR-221 and 17 studies for miR-222 which assessed OS were included in the meta-analysis. High expression of miR-221 and miR-222 significantly predicted poor OS (HR: 1.48, 95% CI: 1.14–1.93, p = 0.003 and HR: 1.90, 95% CI: 1.43–2.54, p < 0.001, respectively). Subgroup analysis revealed that the finding on miR-221 was not as robust as the one on miR-222. Furthermore, high miR-222 expression was also associated with worse progression-free survival and disease-free survival pooled with recurrence-free survival. Conclusions: The meta-analysis demonstrated that high expression of miR-222 is associated with poor prognosis in cancer patients, whereas the significance of miR-221 remains unclear. More work is required to fully elucidate the role of miR-221 and miR-222 in cancer prognosis, particularly in view of the limitations of existing results, including the significant heterogeneity and limited number of studies for some cancers.

The proliferation of cervical cancer is promoted by miRNA-125b through the regulation of the HMGA1

Background

It has been reported that miRNA-125b is associated with carcinogenesis and development of several different kinds of cancers. Nevertheless, there is no clarity regarding the significance and mechanism of action of miR-125b in clinical practice for cervical cancer (CC).

Materials and methods

In the current investigation, the expression of miR-125b in cervical clinical specimens and CC cell lines was analyzed via real-time quantitative PCR, and the relationship of miR-125b with the chromatin-associated protein high mobility group A (HMGA1) expression and clinicopathological parameters of CC patients was explored.

Results

The results indicated that miR-125b expression was remarkably upregulated in CC cell lines as well as in the tissues of humans. miR-125b overexpression was significantly related to a decrease in HMGA1 expression, progression-free survival, overall survival, and prognosis as well. Besides, knockdown of miR-125b inhibited proliferation and colony formation in SW756 and C4-1 cells, where the 3'-UTR of HMGA1 mRNA was directly targeted. Moreover, PI3K/Akt pathway was regulated by miR-125b through suppression of HMGA1.

Conclusion

These findings illustrated that a new regulatory role of HMGA1 is involved in the progression of CC. Our data demonstrated that miR-125b could play a critical role in the carcinogenesis and progression of CC, revealing that miR-125b might serve as a potential new target for treating CC.

Prognostic Significance of MicroRNAs in Glioma: A Systematic Review and Meta-Analysis

PURPOSE

Different microRNAs (miRs) have been demonstrated to relate with the outcome of glioma patients, while the conclusions are inconsistent. We perform a meta-analysis to clarify the relationship between different miRs and prognosis of glioma.

METHODS

Related studies were retrieved from PubMed, Embase, and Cochrane Library. Pooled hazard ratios (HRs) of different miRs expression for survival and 95% confidence intervals (CIs) were calculated using random-effects model.

RESULTS

A total of 15 miRs with 4708 glioma patients were ultimately included. Increased expression of miR-15b (HR, 1.584; 95% CI, 1.199-2.092), 21 (HR, 1.591; 95% CI, 1.278-1.981), 148a (HR, 1.122; 95% CI, 1.023-1.231), 196 (HR, 1.877; 95% CI, 1.033-3.411), 210 (HR, 1.251; 95% CI, 1.010-1.550), and 221 (HR, 1.269; 95% CI, 1.054-1.527) or decreased expression of miR-106a (HR, 0.809; 95% CI, 0.655-0.998) and 124 (HR, 0.833; 95% CI, 0.729-0.952) was correlated with poor outcome of glioma patients.

CONCLUSIONS

miR-15b, 21, 148a, 196, 210, 221, 106a, and 124 are valuable biomarkers for the prognosis of glioma which might be used in clinical settings.

Regulatory network reconstruction of five essential microRNAs for survival analysis in breast cancer by integrating miRNA and mRNA expression datasets

Although many of the genetic loci associated with breast cancer risk have been reported, there is a lack of systematic analysis of regulatory networks composed of different miRNAs and mRNAs on survival analysis in breast cancer. To reconstruct the microRNAs-genes regulatory network in breast cancer, we employed the expression data from The Cancer Genome Atlas (TCGA) related to five essential miRNAs including miR-21, miR-22, miR-210, miR-221, and miR-222, and their associated functional genomics data from the GEO database. Then, we performed an integration analysis to identify the essential target factors and interactions for the next survival analysis in breast cancer. Based on the results of our integrated analysis, we have identified significant common regulatory signatures including differentially expressed genes, enriched pathways, and transcriptional regulation such as interferon regulatory factors (IRFs) and signal transducer and activator of transcription 1 (STAT1). Finally, a reconstructed regulatory network of five miRNAs and 34 target factors was established and then applied to survival analysis in breast cancer. When we used expression data for individual miRNAs, only miR-21 and miR-22 were significantly associated with a survival change. However, we identified 45 significant miRNA-gene pairs that predict overall survival in breast cancer out of 170 one-on-one interactions in our reconstructed network covering all of five miRNAs, and several essential factors such as PSMB9, HLA-C, RARRES3, UBE2L6, and NMI. In our study, we reconstructed regulatory network of five essential microRNAs for survival analysis in breast cancer by integrating miRNA and mRNA expression datasets. These results may provide new insights into regulatory network-based precision medicine for breast cancer.

MicroRNAs as potential biomarkers for the diagnosis of glioma: A systematic review and meta-analysis

Glioma is the most common central nervous system tumor and associated with poor prognosis. Identifying effective diagnostic biomarkers for glioma is particularly important in order to guide optimizing treatment. MicroRNAs (miRNAs) have drawn much attention because of their diagnostic value in diverse cancers, including glioma. We summarized studies to identify the potential diagnostic values of miRNAs in glioma patients. We included articles reporting miRNAs for differentiation of glioma patients from controls. We calculated sensitivities, specificities, and area under the curves (AUC) of individual miRNA and miRNA panels. We found that overall sensitivity, specificity, and AUC of miRNAs in diagnosis of glioma were 85% (95% confidence interval [CI]: 0.81-0.89), 90% (95% CI 0.85-0.93), and 93% (95% CI 0.91-0.95), respectively. Meta-regression analysis showed that the detection of miRNAs expression in cerebrospinal fluid (CSF) and brain tissue largely improved the diagnostic accuracy. Likewise, panels of multiple miRNAs could enhance the pooled sensitivity. Moreover, AUC of miR-21 was 0.88, with 86% sensitivity and 94% specificity. This study demonstrated that miRNAs could function as potential diagnosis markers in glioma. Detection of miRNAs in CSF and brain tissue displays high accuracy in the diagnosis of glioma.

Upregulation of miR-125b, miR-181d, and miR-221 Predicts Poor Prognosis in MGMT Promoter-Unmethylated Glioblastoma Patients

OBJECTIVES

To evaluate the prognostic values of microRNAs (miRNAs) in glioblastoma, and to see if there is an association between miRNAs and MGMT promoter methylation status.

METHODS

We collected paraffin blocks from resection specimens from 114 glioblastoma patients who had received temozolomide treatment and radiotherapy. Real-time quantitative PCR was performed to determine the expression levels of five miRNAs.

RESULTS

Upregulation of miR 125b-5p, miR 181d-3p, miR 221-3p, miR-222-3p, and miR 224-5p was observed in 13.2%, 5.3%, 12.3%, 32.5%, and 78.9% of the cases, respectively. The expression level of miRNAs was not significantly different in tumors with MGMT promoter methylation vs tumors without such methylation. Upregulation of miR 125b-5p, miR 181d-3p, or miR 221-3p was significantly associated with shorter survival in MGMT-unmethylated glioblastoma patients.

CONCLUSIONS

miR 125b-5p, miR 181d-3p, and miR 221-3p are useful in predicting poor prognosis in patients with MGMT-unmethylated glioblastomas.

Biomarker significance of plasma and tumor miR-21, miR-221, and miR-106a in osteosarcoma

Osteosarcoma is the most common malignant bone tumor in children and young adults. Despite the use of surgery and multi-agent chemotherapy, osteosarcoma patients who have a poor response to chemotherapy or develop relapses have a dismal outcome. Identification of biomarkers for active disease may help to monitor tumor burden, detect early relapses, and predict prognosis in these patients. In this study, we examined whether circulating miRNAs can be used as biomarkers in osteosarcoma patients. We performed genome-wide miRNA profiling on a discovery cohort of osteosarcoma and control plasma samples. A total of 56 miRNAs were upregulated and 164 miRNAs were downregulated in osteosarcoma samples when compared to control plasma samples. miR-21, miR-221 and miR-106a were selected for further validation based on their known biological importance. We showed that all three circulating miRNAs were expressed significantly higher in osteosarcoma samples than normal samples in an independent cohort obtained from the Children's Oncology Group. Furthermore, we demonstrated that miR-21 was expressed significantly higher in osteosarcoma tumors compared with normal bone controls. More importantly, lower expressions of miR-21 and miR-221, but not miR-106a, significantly correlated with a poor outcome. In conclusion, our results indicate that miR-21, miR-221 and miR-106a were elevated in the circulation of osteosarcoma patients, whereas tumor expressions of miR-21 and miR-221 are prognostically significant. Further investigation of these miRNAs may lead to a better prognostic method and potential miRNA therapeutics for osteosarcoma.

Identifying Novel Glioma-Associated Noncoding RNAs by Their Expression Profiles

Long noncoding RNAs (lncRNAs) and microRNAs (miRNAs) play a significant role in cancer development as regulators of protein-coding genes. Their dysregulation was in some extent already associated with glioma, the most aggressive primary brain tumours in adults. The correct diagnosis and treatment selection due to high tumour heterogeneity might be difficult and inadequate, resulting in poor prognosis. Studies of expression patterns of noncoding RNAs (ncRNAs) could provide useful insight in glioma molecular development. We used the qPCR approach to screen and investigate the expression of lncRNAs that were previously deregulated in other cancer types. The study showed altered expression levels for numerous lncRNAs across histologically different glioma samples. Validation of few lncRNAs showed association of expression levels with histological subtype and/or malignancy grade. We also observed deregulated and subtype-distinctive expression for four lncRNA-associated miRNAs. Expression of few lncRNAs and miRNA was also associated with patients' survival, showing potential prognostic value. Several ncRNAs, some already related to glioma and some, to the best of our knowledge, investigated for the first time, might be of greater importance in glioma molecular development and progression. Finding the subtype-specific lncRNA and/or miRNA expression patterns may contribute additional information for a more objective classification.

Differential expression of miR16 in glioblastoma and glioblastoma stem cells: their correlation with proliferation, differentiation, metastasis and prognosis

The function of miR16 in multiforme glioblastoma multiforme (GBM) and its stem cells (GSCs) remains elusive. To this end, we investigated the patterns of miR16 expression in these cells and their correlation with malignant behaviors and clinical outcomes. The levels of miR16 and its targeted genes in tumor tissue of GBM and GBM SGH44, U87, U251 cells as well as their stem cell counterparts were measured by qRT–PCR or western blot or immunohistochemistry. Luciferase reporter assay was used to confirm the binding of miR16 to 3′-UTR of its target genes. The effects of miR16 on malignant behaviors were investigated, including tumor cell viability, soft-agar colony formation, GSCs Matrigel colony forming and migration and invasion as well as nude mice xenograft model. Differentially expression patterns of miR16 in glioblastoma cells and GSCs cells were found in this study. Changes of miR16 targeted genes, Bcl2 (B cell lymphoma 2), CDK6 (Cyclin-dependent kinase 6), CCND1 (cyclin D1), CCNE1 (cyclin E1) and SOX5 were confirmed in glioblastoma cell lines and tissue specimens. In vitro and in vivo studies showed that tumor cell proliferation was inhibited by miR16 mimic, but enhanced by miR16 inhibitor. The expression level of miR16 positively correlates with GSCs differentiation, but negatively with the abilities of migration, motility, invasion and colony formation in glioblastoma cells. The inhibitory effects of miR16 on its target genes were also found in nude mice xenograft model. Our findings revealed that the miR16 functions as a tumor suppressor in GSCs and its association with prognosis in GBM.

Sex and age differences in the expression of liver microRNAs during the life span of F344 rats

Background

Physiological factors such as age and sex have been shown to be risk factors for adverse effects in the liver, including liver diseases and drug-induced liver injury. Previously, we have reported age- and sex-related significant differences in hepatic basal gene expression in rats during the life span that may be related to susceptibility to such adverse effects. However, the underlying mechanisms of the gene expression changes were not fully understood. In recent years, increasing evidence for epigenetic mechanisms of gene regulation has fueled interest in the role of microRNAs (miRNAs) in toxicogenomics and biomarker discovery. We therefore proposed that significant age and sex differences exist in baseline liver miRNA expression, and that comprehensive profiling of miRNAs will provide insights into the epigenetic regulation of gene expression in rat liver.

Methods

To address this, liver tissues from male and female F344 rats were examined at 2, 5, 6, 8, 15, 21, 52, 78, and 104 weeks of age for the expression of 677 unique miRNAs. Following data processing, predictive pathway analysis was performed on selected miRNAs that exhibited prominent age and/or sex differences in expression.

Results

Of the 314 miRNAs found to be expressed, 214 were differentially expressed; 65 and 212 miRNAs showed significant (false discovery rate (FDR) <5% and ≥1.5-fold change) sex- and age-related differences in expression, respectively. Thirty-eight miRNAs showed 2-week-specific expression, of which 31 miRNAs were found to be encoded within the Dlk1-Dio3 cluster located on chromosome 6. This cluster has been associated with tissue proliferation and differentiation, and liver energy homeostasis in postnatal development. Predictive pathway analysis linked sex-biased miRNA expression with sexually dimorphic molecular functions and toxicological functions that may reflect sex differences in hepatic physiology and disease. The expression of miRNAs (miR-18a, miR-99a, and miR-203, miR-451) was also found to associate with specific sexually dimorphic hepatic histopathology. The expression of miRNAs involved in regulating cell death, cell proliferation, and cell cycle was found to change as the rats matured from adult to old age.

Conclusions

Overall, significant age- and sex-related differences in liver miRNA expression were identified and linked to histopathological findings and predicted functional pathways that may underlie susceptibilities to liver toxicity and disease.

Electronic supplementary material

The online version of this article (doi:10.1186/s13293-017-0127-9) contains supplementary material, which is available to authorized users.

A five-miRNA signature with prognostic and predictive value for MGMT promoter-methylated glioblastoma patients

Although O(6)-methylguanine DNA methyltransferase (MGMT) promoter methylation status is an important marker for glioblastoma multiforme (GBM), there is considerable variability in the clinical outcome of patients with similar methylation profiles. The present study aimed to refine the prognostic and predictive value of MGMT promoter status in GBM by identifying a micro (mi)RNA risk signature. Data from The Cancer Genome Atlas was used for this study, with MGMT promoter-methylated samples randomly divided into training and internal validation sets. Data from The Chinese Glioma Genome Atlas was used for independent validation. A five miRNA-based risk signature was established for MGMT promoter-methylated GBM to distinguish cases as high- or low-risk with distinct prognoses, which was confirmed using internal and external validation sets. Importantly, the prognostic value of the signature was significant in different cohorts stratified by clinicopathologic factors and alkylating chemotherapy, and a multivariate Cox analysis found it to be an independent prognostic marker along with age and chemotherapy. Based on these three factors, we developed a quantitative model with greater accuracy for predicting the 1-year survival of patients with MGMT promoter-methylated GBM. These results indicate that the five-miRNA signature is an independent risk predictor for GBM with MGMT promoter methylation and can be used to identify patients at high risk of unfavorable outcome and resistant to alkylating chemotherapy, underscoring its potential for personalized GBM management.

DNA methylation in adult diffuse gliomas

Adult diffuse gliomas account for the majority of primary malignant brain tumours, and are in most cases lethal. Current therapies are often only marginally effective, and improved options will almost certainly benefit from further insight into the various processes contributing to gliomagenesis and pathology. While molecular characterization of these tumours classifies them on the basis of genetic alterations and chromosomal abnormalities, DNA methylation patterns are increasingly understood to play a role in glioma pathogenesis. Indeed, a subset of gliomas associated with improved survival is characterized by the glioma CpG island methylator phenotype (G-CIMP), which can be induced by the expression of mutant isocitrate dehydrogenase (IDH1/2). Aberrant methylation of particular genes or regulatory elements, within the context of G-CIMP-positive and/or negative tumours, has also been shown to be associated with differential survival. In this review, we provide an overview of the current knowledge regarding the role of DNA methylation in adult diffuse gliomas. In particular, we discuss IDH mutations and G-CIMP, MGMT promoter methylation, DNA methylation-mediated microRNA regulation and aberrant methylation of specific genes or groups of genes.

Normalization of gene expression measurement of tissue samples obtained by transurethral resection of bladder tumors

Background

Sample processing is a crucial step for all types of genomic studies. A major challenge for researchers is to understand and predict how RNA quality affects the identification of transcriptional differences (by introducing either false-positive or false-negative errors). Nanotechnologies help improve the quality and quantity control for gene expression studies.

Patients and methods

The study was performed on 14 tumor and matched normal pairs of tissue from patients with bladder urothelial carcinomas. We assessed the RNA quantity by using the NanoDrop spectrophotometer and the quality by nano-microfluidic capillary electrophoresis technology provided by Agilent 2100 Bioanalyzer. We evaluated the amplification status of three housekeeping genes and one small nuclear RNA gene using the ViiA 7 platform, with specific primers.

Results

Every step of the sample handling protocol, which begins with sample harvest and ends with the data analysis, is of utmost importance due to the fact that it is time consuming, labor intensive, and highly expensive. High temperature of the surgical procedure does not affect the small nucleic acid sequences in comparison with the mRNA.

Conclusion

Gene expression is clearly affected by the RNA quality, but less affected in the case of small nuclear RNAs. We proved that the high-temperature, highly invasive transurethral resection of bladder tumor procedure damages the tissue and affects the integrity of the RNA from biological specimens.

Suppression of miR-221 inhibits glioma cells proliferation and invasion via targeting SEMA3B

Background

Gliomas are the most common primary tumors in the central nervous system. Due to complicated signaling pathways involved in glioma progression, effective targets for treatment and biomarkers for prognosis prediction are still scant.

Results

In this study we revealed that a new microRNA (miR), the miR-221, was highly expressed in the glioma cells, and suppression of miR-221 resulted in decreased cellular proliferation, migration, and invasion in glioma cells. Mechanistic experiments validated that miR-221 participates in regulating glioma cells proliferation and invasion via suppression of a direct target gene, the Semaphorin 3B (SEMA3B). The rescue experiment with miR-221 and SEMA3B both knockdown results in significant reversion of miR-221 induced phenotypes.

Conclusion

Taken together, our findings highlight an unappreciated role for miR-221 and SEMA3B in glioma.