Integrated miRNA-mRNA analysis revealing the potential roles of miRNAs in chordomas

MicroRNA‑1224 inhibits cell proliferation by downregulating CBX3 expression in chordoma

MicroRNAs (miRNAs/miRs) have abnormal expression in numerous tumors and are closely related to tumor development and resistance to radiotherapy and chemotherapy. However, there are few studies assessing the role and mechanism of miRNA in chordoma. The sequencing data of three pairs of chordoma and notochord tissues from the GSE56183 dataset were analyzed in the present study. Cell proliferation was assessed in vitro using Cell Counting Kit-8. Bioinformatics analysis and the dual luciferase reporter assay were used to evaluate the regulatory relationship between miR-1224 and chromobox 3 (CBX3) in chordoma. The results demonstrated that miR-1224 had a significantly lower expression level in chordoma tissues and cell lines. Overexpression of miR-1224 inhibited proliferation in the chordoma cells, while the knockdown of miR-1224 promoted proliferation of the chordoma cells. Bioinformatics analysis and the dual luciferase reporter assay confirmed that CBX3 was a direct target gene of miR-1224 and that miR-1224 induced the proliferation of chordoma cells through the inhibition of CBX3. In summary, miR-1224 reduced the proliferation of chordoma cells through inhibition of CBX3, which provides a theoretical basis for selecting a novel therapeutic target for chordoma.

Dysregulation of noncoding RNA in chordoma; implications in identifying potential targets for novel therapeutic approaches

Chordoma is a rare form of bone cancer develops in the spinal cord and skull. Instead of conventional (radio/chemotherapies) and targeted therapies, the disease is associated with high rate of recurrence and poor patient survival. Thus, for better disease management, the molecular pathogenesis of chordoma should be studied in detail to identify dysregulated biomolecules that can be targeted by novel therapeutics. Recent research showed frequent dysregulation of long noncoding RNA (lncRNA), microRNA (miRNA), and circular RNA (circRNA) in association with aggressive tumor phenotypes like cell proliferation, migration, invasion, and metastasis in a variety of cancers, including chordoma. Apart from diagnostic and prognostic importance, noncoding RNAs may serve as promising targets for novel therapeutics in cancer. In this review, we summarized a list of miRNAs, lncRNAs, and circRNA found to be dysregulated in chordoma from available data published in relevant databases (PubMed), as such an approach seems to be rare to date. The dysregulated noncoding RNAs were also associated with adverse tumor phenotypes to assess the impact on disease pathogenesis and, associated downstream molecular pathways were focused. Synthetic compounds and natural products that were reported to target the noncoding RNAs in other malignancies were also listed from published literature and proposed as potential therapeutic agents in chordoma. This review will provide information for further research on chordoma focusing on detailed characterization of dysregulated lncRNAs, miRNAs, and circRNA to understand the disease pathogenesis and, exploration of suitable natural and synthetic products targeting dysregulated non-coding RNAs to develop effective therapeutic measures.

Pilot Study of High-Dose Pemetrexed in Patients with Progressive Chordoma

PURPOSE

Chordomas are ultrarare tumors of the axial spine and skull-base without approved systemic therapy. Most chordomas have negative expression of thymidylate synthase (TS), suggesting a potential for responding to the antifolate agent pemetrexed, which inhibits TS and other enzymes involved in nucleotide biosynthesis. We evaluated the therapeutic activity and safety of high-dose pemetrexed in progressive chordoma.

PATIENTS AND METHODS

Adult patients with previously treated, progressive chordoma participated in an open-label, single-institution, single-arm, pilot clinical trial of intravenous pemetrexed 900 mg/m2 every 3 weeks and supportive medications of folic acid, vitamin B12, and dexamethasone. The primary endpoint was objective response rate according to RECIST v1.1. Secondary endpoints included adverse events, progression-free survival (PFS), tumor molecular profiles, and alterations in tissue and blood-based biomarkers.

RESULTS

Fifteen patients were enrolled and the median number of doses administered was 15 (range, 4-31). One patient discontinued treatment due to psychosocial issues after four cycles and one contracted COVID-19 after 13 cycles. Of the 14 response-evaluable patients, 2 (14%) achieved a partial response and 10 (71%) demonstrated stable disease. Median PFS was 10.5 months (95% confidence interval: 9 months-undetermined) and 6-month PFS was 67%. Adverse events were expected and relatively mild, with one grade 3 creatinine increased, and one each of grade 3 and 4 lymphopenia. No grade 5 adverse events, unexpected toxicities, or dose-limiting toxicities were observed. Several patients reported clinical improvement in disease-related symptoms.

CONCLUSIONS

High-dose pemetrexed appears tolerable and shows objective antitumor activity in patients with chordoma. Phase II studies of high-dose pemetrexed are warranted.

miR‑149‑3p suppresses the proliferation and metastasis of glioma cells by targeting the CBX2/Wnt/β‑catenin pathway

The present study aimed to investigate the role of miR-149-3p/chromobox 2 (CBX2)/Wnt/β-catenin pathway in the proliferation and metastasis of glioma cells. The expression and clinical significance of miR-149-3p and CBX2 were analyzed using data from public databases. Cell Counting Kit-8 and colony formation assays were performed to measure cell proliferation. Transwell assays were used to assess cell invasion. The results showed that miR-149-3p was downregulated and CBX2 was upregulated in glioma, and that the downregulated expression of miR-149-3p promoted the proliferation and invasion of glioma cells. In addition, downregulated expression of CBX2 suppressed the proliferation and invasion of glioma cells. Dual-luciferase assay indicated that CBX2 is a target gene of miR149-3p. The possible molecular mechanism of CBX2 was probed by western blotting, which showed that it may further affect the Wnt/β-catenin pathway. These present findings demonstrated that miR-149-3p may function as a tumor suppressor miRNA by directly regulating CBX2 and serve important roles in the malignancy of glioma.

EMP3 as a key downstream target of miR-663a regulation interferes with MAPK/ERK signaling pathway to inhibit gallbladder cancer progression

Gallbladder carcinoma (GBC) is the most common malignancy of the biliary tract, and its molecular pathogenesis remains unclear. Here we explore the functional roles of epithelial membrane protein 3 (EMP3) in GBC progression, which is aberrantly expressed in various types of cancers. The results showed that the expression level of EMP3 was reduced in human GBC tissues compared with non-malignant tissues. Further, the low expression of EMP3 was associated with the poor prognosis of GBC patients by Kaplan-Meier analysis. The ectopic expression of EMP3 inhibited GBC cell proliferation, migration and invasion in vitro and in vivo. Conversely, the depletion of EMP3 promoted GBC cell growth and metastasis. In addition, we found that EMP3 was a target gene of miR-663a, and the downregulation of EMP3 in GBC was attributed to the overexpression of miR-663a. MiR-663a was also shown to be a tumor-promoting factor mediating GBC development. In this study, we demonstrate that downregulation of EMP3 activates MAPK/ERK signaling, which regulates GBC progression. These data reveal the mechanism by which EMP3 inhibits the progression of GBC, suggesting that the miR-663a/EMP3/MAPK/ERK axis may be a new therapeutic target for GBC treatment.

Systematic identification of molecular mechanisms for aryl hydrocarbon receptor mediated neuroblastoma cell migration

Tumor cell migration is affected by the aryl hydrocarbon receptor (AhR). However, the systematic molecular mechanisms underlying AhR-mediated migration of human neuroblastoma cells are not fully understood. To address this issue, we performed an integrative analysis of mRNA and microRNA (miR) expression profiles in human neuroblastoma SK-N-SH cells treated with 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), a potent agonist of AhR. The cell migration was increased in a time- and concentration- dependent manner, and was blocked by AhR antagonist (CH223191). A total of 4,377 genes were differentially expressed after 24-hour-treatment with 10-10 M TCDD, of which the upregulated genes were significantly enriched in cell migration-related biological pathways. Thirty-four upregulated genes, of which 25 were targeted by 78 differentially expressed miRs, in the axon guidance pathway were experimentally confirmed, and the putative dioxin-responsive elements were present in the promoter regions of most genes (79 %) and miRs (82 %) in this pathway. Furthermore, two promigratory genes (CFL2 and NRP1) induced by TCDD was reversed by blockade of AhR. In conclusion, AhR-mediated mRNA-miR networks in the axon guidance pathway may represent a potential molecular mechanism of dioxin-induced directional migration of human neuroblastoma cells.

miR-1908: a microRNA with diverse functions in cancers and non-malignant conditions

MicroRNAs (miRNAs) are small-sized transcripts with about 22 nucleotide length. They have been shown to influence almost every aspect of cellular functions through regulation of expression of target genes. miR-1908 is a miRNA with diverse roles in human disorders. This miRNA is encoded by MIR1908 gene on chr11:61,815,161-61,815,240, minus strand. Expression assays have confirmed dysregulation of miR-1908 in cancer-derived cell lines in addition to biological samples obtained from patients affected with cancer. In most assessed cell lines, miR-1908 has an oncogenic role. However, this miRNA has been shown to act as a tumor suppressor in chordoma, lung cancer and ovarian cancer. In addition, several lines of evidence have shown involvement of this miRNA in the pathoetiology of bipolar disorder, myocardial infarction, obesity, renal fibrosis, rheumatoid arthritis and scar formation. In the current review, we elucidate the results of diverse studies which evaluated participation of miR-1908 in these conditions.

miR-1908 Dysregulation in Human Cancers

MiR-1908 is a miRNA located in the intron of the fatty acid desaturase 1 (FADS1) gene. The expression level of miR-1908 is abnormal in many diseases such as cancer. miR-1908 can inhibit the expression of at least 27 target genes by binding to the 3’ untranslated region (3’ UTR) of target genes. miR-1908 is involved in the biological processes of cell proliferation, cell differentiation, cell apoptosis, cancer cell invasion, and metastasis. The expression of miR-1908 is regulated by 11 factors, including lncRNA HOTTIP, adipokines (TNF-α, leptin, and resistin), NF-κB, free fatty acid (FFA), cholesterol, stearoyl-CoA desaturase (SCD1), immune-related transcription factors (STAT1, RB1, and IRF1). The expression of miR-1908 is also affected by the anticancer drug OSW-1, growth hormone (GH), and the anticonvulsant drug sodium valproate. In addition, the aberrant expression of miR-1908 is also related to the prognosis of a variety of cancers, including non-small cell lung cancer (NSCLC), ovarian cancer (OC), breast cancer, cervical cancer, glioma, high-grade serous ovarian carcinoma (HGSOC), osteosarcoma, etc. This article summarizes the abnormal expression pattern of miR-1908 in various diseases and its molecular regulation mechanisms. Our work will provide potential hints and direction for future miR-1908-related research.

Dysregulated Epigenetics of Chordoma: Prognostic Markers and Therapeutic Targets

Chordoma is a rare, slow-growing sarcoma that is locally aggressive, and typically resistant to conventional chemo- and radiotherapies. Despite its low incidence, chordoma remains a clinical challenge because therapeutic options for chordoma are limited, and little is known about the molecular mechanisms involved in resistance to therapies. Furthermore, there are currently no established predictive or prognostic biomarkers to follow disease progression or treatment. Whole-genome sequencing of chordoma tissues has demonstrated a low-frequency mutation rate compared to other cancers. This has generated interest in the role of epigenetic events in chordoma pathogenesis. In this review, we discuss the current understanding of the epigenetic drivers of chordoma and their potential applications in prognosis and the development of new therapies.

miRcorrNet: machine learning-based integration of miRNA and mRNA expression profiles, combined with feature grouping and ranking

A better understanding of disease development and progression mechanisms at the molecular level is critical both for the diagnosis of a disease and for the development of therapeutic approaches. The advancements in high throughput technologies allowed to generate mRNA and microRNA (miRNA) expression profiles; and the integrative analysis of these profiles allowed to uncover the functional effects of RNA expression in complex diseases, such as cancer. Several researches attempt to integrate miRNA and mRNA expression profiles using statistical methods such as Pearson correlation, and then combine it with enrichment analysis. In this study, we developed a novel tool called miRcorrNet, which performs machine learning-based integration to analyze miRNA and mRNA gene expression profiles. miRcorrNet groups mRNAs based on their correlation to miRNA expression levels and hence it generates groups of target genes associated with each miRNA. Then, these groups are subject to a rank function for classification. We have evaluated our tool using miRNA and mRNA expression profiling data downloaded from The Cancer Genome Atlas (TCGA), and performed comparative evaluation with existing tools. In our experiments we show that miRcorrNet performs as good as other tools in terms of accuracy (reaching more than 95% AUC value). Additionally, miRcorrNet includes ranking steps to separate two classes, namely case and control, which is not available in other tools. We have also evaluated the performance of miRcorrNet using a completely independent dataset. Moreover, we conducted a comprehensive literature search to explore the biological functions of the identified miRNAs. We have validated our significantly identified miRNA groups against known databases, which yielded about 90% accuracy. Our results suggest that miRcorrNet is able to accurately prioritize pan-cancer regulating high-confidence miRNAs. miRcorrNet tool and all other supplementary files are available at https://github.com/malikyousef/miRcorrNet.

TGFB3 downregulation causing chordomagenesis and its tumor suppression role maintained by Smad7

Chordoma is a rare bone tumor arising from notochordal remnants, but the underlying mechanism remains elusive. By integrated mRNA and microRNA analyses, we found significant downregulation of TGFB3 along with upregulation of its inhibitor, miR-29 family in chordoma comparing with notochord. Somatic copy number gains of miR-29 loci in chordoma highlighted a mechanism of inactivation of TGFB3 signaling in tumor formation. In zebrafish, knockout and knockdown homologous tgfb3 resulted in a chordoma-like neoplasm. On the other hand, Smad7 negative feedback regulation of transforming growth factor-β (TGF-β) signaling is retentive in chordoma cell UM-Chor1 despite its disruption in most cancer cells (e.g. A549). Therefore, contrary to other cancers, exogenous TGF-β activated Smad7 by downregulating miR-182 and inhibited cell migration and invasion in UM-Chor1. Meanwhile, TGF-β decreased chordoma characteristic protein Brachyury. Altogether, downregulation of TGFB3 causes chordomagenesis, showing a feasible target for therapies. The retention of Smad7 negative regulation may maintain the suppressor role of TGF-β in chordoma.

Model for the prediction of mechanical asphyxia as the cause of death based on four biological indexes in human cardiac tissue

Determination of mechanical asphyxia as the cause of death has always been difficult for forensic pathologists, particularly when signs of asphyxia are not obvious on the body. Currently, depending on only physical examination of corpses, pathologists must be cautious when making cause-of-death appraisals. In a previous study, four biomarkers-dual-specificity phosphatase 1 (DUSP1), potassium voltage-gated channel subfamily J member 2 (KCNJ2), miR-122, and miR-3185-were screened in human cardiac tissue from cadavers that died from mechanical asphyxia compared with those that died from craniocerebral injury, hemorrhagic shock, or other causes. Expression of the markers correlated with death from mechanical asphyxia regardless of age, environmental temperature, and postmortem interval. However, a single biological index is not an accurate basis for the identification of the cause of death. In this study, receiver operating characteristic curves of the ΔCq values of the four indexes were generated. The diagnostic accuracy of the indexes was judged according to their area under the curve (DUSP1: 0.773, KCNJ2: 0.775, miR-122: 0.667, and miR-3185: 0.801). Finally, a nomogram was generated, and single blind experiment was conducted to verify the cause of death of mechanical asphyxia.

Identification of the miRNA-3185/CYP4A11 axis in cardiac tissue as a biomarker for mechanical asphyxia

Death by mechanical asphyxia is one of the most difficult conclusions to make in forensic science, especially in corpses displaying slight or no trauma to the surface of the body. Therefore, death by mechanical asphyxia is difficult to prove in medico-legal practice. MicroRNAs (miRNAs) are a class of small, non-coding RNAs involved in the regulation of numerous physiological and pathological cellular processes. In the present study, we demonstrate that significantly increased expression of miR-3185 in cardiac tissues was detected among cases of mechanical asphyxia compared to case of craniocerebral injury, hemorrhagic shock, sudden cardiac death and poisoning. We observed no correlation between the expression of miR-3185 and postmortem interval, age or temperature. Further work indicated that CYP4A11 is a putative target gene of miR-3185 and expressed at a relatively low level in cardiac tissue specimens from cases of mechanical asphyxia compared with specimens from cases of craniocerebral injury, hemorrhagic shock, sudden cardiac death and poisoning. Our results suggest that the miRNA-3185/CYP4A11 axis is associated with mechanical asphyxia-induced death and may provide new insight into asphyxial death investigations.

Upregulation Of miR-149-3p Suppresses Spinal Chordoma Malignancy By Targeting Smad3

Purpose

Dysregulation of miRNAs plays an important role in the malignancy of different tumors including chordoma. Expression of miR-149-3p was earlier reported to be downregulated in chordoma tissue. However, its biological role remains to be unrevealed in chordoma, especially in spinal chordoma.

Methods

Expression of miR-149-3p and Smad3 was detected by RT-qPCR and Western blot. Chordoma malignancy was evaluated by cell proliferation, migration, invasion, and apoptosis using MTT assay, transwell assay, flow cytometry analyzing apoptosis rate, and Western blot-determined expression of Bcl-2, Bax, and cleaved caspase 3, respectively. The target binding between miR-149-3p and Smad3 was predicted by TargetScan Human website and confirmed by luciferase reporter assay and RNA immunoprecipitation. Xenograft tumors were generated, and expression of miR-149-3p and Smad3 was investigated in vivo.

Results

miR-149-3p was downregulated in spinal chordoma tissues and cells, and its overexpression promoted chordoma cell apoptosis and inhibited proliferation, migration, and invasion in U-CH1 and MUG-Chor1 cells. Unexpectedly, Smad3 was a downstream target of miR-149-3p and negatively correlated with miR-149-3p expression in chordoma tissues. Besides, Smad3 was upregulated in chordoma tissues and its silencing had a similar effect as miR-149-3p overexpression in U-CH1 and MUG-Chor1 cells. Moreover, Smad3 upregulation could partially reverse the tumor-suppressive effect of miR-149-3p in chordoma cells. In vivo, the tumorigenesis of U-CH1 and MUG-Chor1 cells was impaired by upregulated miR-149-3p through decreasing Smad3 expression.

Conclusion

miR-149-3p could serve as a tumor suppressor in spinal chordoma through targeting and downregulating Smad3.

High Expression of TGF-β1 Predicting Tumor Progression in Skull Base Chordomas

OBJECTIVE

To investigate the expression characteristics and prognostic value of transforming growth factor β1 (TGF-β1) in primary skull base chordomas (SBCs).

METHODS

The mRNA expression levels of TGF-β1 were measured in 57 frozen samples from patients with primary SBCs. Clinical data collection, follow-up, correlations, and survival analyses were performed.

RESULTS

In the series of 57 patients (29 men and 28 women) with primary SBCs, the mean value of TGF-β1 mRNA was 1.713 with a median of 0.904. Twenty-four SBCs were soft type and 33 were hard type. The Mann-Whitney U test revealed that the expression level of TGF-β1 mRNA in hard type SBCs was significantly higher than the expression level found in the soft type (P = 0.03). The independent-samples median test suggested that the expression level of TGF-β1 mRNA in female patients' SBCs was significantly higher than that in male patients' SBCs (P = 0.01). Expression differences of TGF-β1 were not seen among different pathological subtypes, tumor blood supply, or degree of resection. The Spearman rank correlation coefficient clarified that TGF-β1 mRNA levels were not correlated with tumor diameter, preoperative Karnofsky Performance Status (KPS), postoperative KPS, follow-up KPS, age, or intraoperative blood loss. The multivariate Cox analysis revealed that pathological subtype (P = 0.008), expression level of TGF-β1 mRNA (P = 0.01), and tumor texture (P = 0.03) were all independent prognostic factors for tumor progression.

CONCLUSIONS

SBCs in female patients and SBCs with hard texture were prone to have high TGF-β1 mRNA expression. High expression of TGF-β1, hard tumor texture, and conventional subtype were all independent risk factors for tumor progression.

Oncogenic miR-663a is associated with cellular function and poor prognosis in renal cell carcinoma

BACKGROUND

MicroRNA(miRNA) plays a key regulatory role in various stages of tumorigenesis, including cell growth, cell cycle control, apoptosis avoidance, tissue invasion, and metastasis. Several microRNAs are involved in the development of renal cell carcinoma (RCC) and the malignant transformation process. However, the effects of miR-663a on RCC have rarely been reported.

METHODS

In the present study, the expression of miR-663a was examined in RCC using matched normal kidney tissues and four cell lines (786-O, Caki-1, ACHN and HK-2). MicroRNA mimics were transiently transfected into RCC cells and the effects of over expression on proliferation, migration, invasion, and apoptosis was observed. In addition, the relationship between miR-663a expression in 42 formalin-fixed paraffin-embedded (FFPE) clear cell renal carcinoma (ccRCC) samples and clinical pathological variables and overall survival was investigated. We evaluated the prognostic value of miR-663a expression in ccRCC by experimental results.

RESULTS

The results showed that the expression of miR-663a was up-regulated in RCC cells and tissues and miR-663a was associated with proliferation, migration, invasion, and apoptosis of RCC. Cox proportional hazard regression analysis showed that a high expression of miR-663a patients had a significantly shorter overall survival in univariate and multivariate analysis. Kaplan-Meier survival curves showed that a high expression of miR-663a patients had a significantly shorter overall survival.

CONCLUSIONS

These results indicate that miR-663a can be used as an independent marker for the poor prognosis of ccRCC, and may also play an important role as a tumor oncogene in the occurrence and development of RCC.

RETRACTED: EMP3, which is regulated by miR-663a, suppresses gallbladder cancer progression via interference with the MAPK/ERK pathway

This article has been retracted: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy). This article has been retracted at the request of the Editor. Following the publication of the above article, the Editor was notified that images were duplicated in the migration and invasion experiments in Figures 3A, 6C, 7D and 8D: https://pubpeer.com/publications/76E82FD26E33503D7CCAC01C324AFA. The Editor has taken the decision to retract the paper as it is no longer acceptable in its current form

Regulation and functions of MicroRNA-149 in human cancers

MicroRNAs are small non-coding RNAs that play critical roles in the regulatory mechanisms involving cell differentiation, proliferation, apoptosis and tumorigenesis. Recent research efforts have been conducted to apply these discoveries into clinical functions, including the early diagnosis and therapeutic outcome of patients with cancer. Previous studies have shown that microRNA-149 (miR-149) is dysregulated in various human cancers and exerts its effects on tumorigenesis and tumour progression. In this review, we summarized the potential roles of miR-149 dysregulation and its target genes during tumorigenesis and clinical treatment of human cancers.

MiR-663a Stimulates Proliferation and Suppresses Early Apoptosis of Human Spermatogonial Stem Cells by Targeting NFIX and Regulating Cell Cycle

Human spermatogonial stem cells (SSCs) could have significant applications in reproductive medicine and regenerative medicine because of their great plasticity. The fate determinations of human SSCs are mediated by epigenetic factors. However, nothing is known about the regulation of non-coding RNA on human SSCs. Here we have explored for the first time the expression, function, and target of miR-663a in human SSCs. MiR-663a was upregulated in human spermatogonia compared with pachytene spermatocytes, as indicated by microRNA microarray and real-time PCR. CCK-8 and 5-Ethynyl-2′-deoxyuridine (EDU) assays revealed that miR-663a stimulated cell proliferation and DNA synthesis of human SSCs. Annexin V and propidium iodide (PI) staining and flow cytometry demonstrated that miR-663a inhibited early and late apoptosis of human SSCs. Furthermore, NFIX was predicted and verified as a direct target of miR-663a. NFIX silencing led to an enhancement of cell proliferation and DNA synthesis and a reduction of the early apoptosis of human SSCs. NFIX silencing neutralized the influence of miR-663a inhibitor on the proliferation and apoptosis of human SSCs. Finally, both miR-663a mimics and NFIX silencing upregulated the levels of cell cycle regulators, including Cyclin A2, Cyclin B1, and Cyclin E1, whereas miR-663a inhibitor had an adverse effect. Knockdown of Cyclin A2, Cyclin B1, and Cyclin E1 led to the decrease in the proliferation of human SSCs. Collectively, miR-663a has been identified as the first microRNA that promotes the proliferation and DNA synthesis and suppresses the early apoptosis of human SSCs by targeting NFIX via cell cycle regulators Cyclin A2, Cyclin B1, and Cyclin E1. This study thus provides novel insights into the molecular mechanisms underlying human spermatogenesis, and it could offer novel targets for treating male infertility and other human diseases.

miR-16-5p inhibits chordoma cell proliferation, invasion and metastasis by targeting Smad3

Aberrantly expressed miRNAs play a crucial role in the development of multiple cancer types, including chordoma. However, the detailed molecular mechanisms are unclear and need to be elucidated. In this study, miRNAs were screened by miRNA array analysis and then confirmed by real-time PCR analysis. We found that miR-16-5p was significantly downregulated in chordoma, and overexpression of miR-16-5p suppressed chordoma cell proliferation, invasion and migration in vitro and in vivo and correlated with the upregulated expression of E-cadherin and downregulated expression of N-cadherin and vimentin. Furthermore, Smad3 was identified as a target of miR-16-5p, and Smad3 was highly expressed in chordoma tissues. Further research showed that knockdown of Smad3 had an effect similar to that of overexpression of miR-16-5p in chordoma cells. Our findings demonstrate that miR-16-5p plays a tumor suppressor role in chordoma progression by targeting Smad3, which could provide a promising prognostic and therapeutic strategy for chordoma treatment.

A historical recount of chordoma

Chordoma, a rare bone tumor that occurs along the spine, has led scientists on a fascinating journey of discoveries. In this historical vignette, the authors track these discoveries in diagnosis and treatment, noting events and clinicians that played pivotal roles in our current understanding of chordoma. The study of chordoma begins in 1846 when Rudolf Virchow first observed its occurrence on a dorsum sellae; he coined the term “chordomata” 11 years later. The chordoma’s origin was greatly disputed by members of the scientific community. Eventually, Müller’s notochord hypothesis was accepted 36 years after its proposal. Chordomas were considered benign and slow growing until the early 1900s, when reported autopsy cases drew attention to their possible malignant nature. Between 1864 and 1919, the first-ever symptomatic descriptions of various forms of chordoma were reported, with the subsequent characterization of chordoma histology and the establishment of classification criteria shortly thereafter. The authors discuss the critical historical steps in diagnosis and treatment, as well as pioneering operations and treatment modalities, noting the physicians and cases responsible for advancing our understanding of chordoma.

RBiomirGS: an all-in-one miRNA gene set analysis solution featuring target mRNA mapping and expression profile integration

Background

With the continuous discovery of microRNA's (miRNA) association with a wide range of biological and cellular processes, expression profile-based functional characterization of such post-transcriptional regulation is crucial for revealing its significance behind particular phenotypes. Profound advancement in bioinformatics has been made to enable in depth investigation of miRNA's role in regulating cellular and molecular events, resulting in a huge quantity of software packages covering different aspects of miRNA functional analysis. Therefore, an all-in-one software solution is in demand for a comprehensive yet highly efficient workflow. Here we present RBiomirGS, an R package for a miRNA gene set (GS) analysis.

Methods

The package utilizes multiple databases for target mRNA mapping, estimates miRNA effect on the target mRNAs through miRNA expression profile and conducts a logistic regression-based GS enrichment. Additionally, human ortholog Entrez ID conversion functionality is included for target mRNAs.

Results

By incorporating all the core steps into one package, RBiomirGS eliminates the need for switching between different software packages. The modular structure of RBiomirGS enables various access points to the analysis, with which users can choose the most relevant functionalities for their workflow.

Conclusions

With RBiomirGS, users are able to assess the functional significance of the miRNA expression profile under the corresponding experimental condition by minimal input and intervention. Accordingly, RBiomirGS encompasses an all-in-one solution for miRNA GS analysis. RBiomirGS is available on GitHub (http://github.com/jzhangc/RBiomirGS). More information including instruction and examples can be found on website (http://kenstoreylab.com/?page_id=2865).

Chordoma of the Head and Neck: A Review

Chordoma is a rare malignant bone tumor that can arise anywhere along the central neural axis and many involve head and neck sites, most commonly the skull base. The relative rarity of these tumors, combined with the complex anatomy of the head and neck, pose diagnostic challenges to pathologists. This article describes the pertinent clinical, pathologic, and molecular features of chordomas and describes how these features can be used to aid in formulating a differential diagnosis. Emphasis is placed on key diagnostic pitfalls and the importance of incorporating immunohistochemical information into the diagnosis.

MicroRNA profiling and bioinformatics analyses reveal the potential roles of microRNAs in chordoma

Chordoma is a rare aggressive bone tumor arising from remnants of the notochord, and patients with chordoma have a poor prognosis. However, the unique expression profiles of microRNAs (miRNAs/miRs) and their downstream signaling pathways in chordoma remain incompletely characterized. The aim of the present study was to delineate the global miRNA expression profile and associated signaling networks in chordoma. miRNA profiling was performed on chordoma and fetal notochord tissues. Differentially expressed miRNAs in chordoma were analyzed using microarrays with hierarchical clustering analysis. The target genes of the differentially expressed miRNAs were predicted, and Gene Ontology (GO) and pathway analyses were performed for the intersecting genes. A total of 42 miRNAs were significantly dysregulated in chordoma compared with that in fetal nucleus pulposus tissues. The expression of hsa-miR-21-3p, hsa-miR-150-5p, hsa-miR-1290 and hsa-miR-623 were validated using the reverse transcription-quantitative polymerase chain reaction. On the basis of the intersection predicted by three databases (Targetscan, microRNA.org and PITA), 10,292 potential miRNA targets were identified. Bioinformatic analyses suggested that these dysregulated miRNAs and their predicted targets were functions of signaling pathways in cancer, the mitogen-activated protein kinase signaling pathway, regulation of actin cytoskeleton, focal adhesion and endocytosis. In particular, human (hsa-)miR-185-5p was identified as a crucial miRNA in chordoma development via the Wnt signaling pathway. The results of the present study provide a comprehensive expression and functional profile of differentially expressed miRNAs associated with chordoma. This profile may serve as a potential tool for biomarker and therapeutic target identification in patients with chordoma.

Low expression of microRNA-1908 predicts a poor prognosis for patients with ovarian cancer

MicroRNAs (miRs) serve important roles in cancer genesis and progression. The expression of miR-1908 has been reported in a number of types of cancer; however, the clinical significance of miR-1908 in human ovarian cancer (OC) remains unclear. A total of 491 patients with OC from The Cancer Genome Atlas project cohort were selected and divided into two groups according to the median expression level of miR-1908. Univariate and multivariate analyses, using the Kaplan-Meier method and Cox regression, were performed to identify the characteristics that predict OC prognosis. Bioinformatics tools were used to identify potential targets of miR-1908. It was identified that the low expression of miR-1908 is associated with a poor prognosis for OC (P<0.05). The potential target genes of miR-1908 included podocan-like 1, JunB AP-1 transcription factor subunit, homeobox B8, SET binding factor 1 and sirtuin 2; high expression of these five genes additionally predicted a poor prognosis. These results suggest that miR-1908 may be a suitable target for the development of novel approaches in OC diagnosis and therapy in the future.

Expression of far upstream element-binding protein 1 correlates with c-Myc expression in sacral chordomas and is associated with tumor progression and poor prognosis

The far upstream element (FUSE)-binding protein 1 (FUBP1), a well-known transcriptional regulator of the proto-oncogene c-Myc, has been demonstrated by previous work to be aberrantly expressed in a variety of tumors and plays a critical role in tumor progression; however, its expression and function in relatively rare and aggressive chordomas remains unclear. In this retrospective study, we reviewed clinicopathologic characteristics of 40 patients diagnosed with sacral chordoma, and analyzed 40 tumor and 20 distant normal tissues obtained from patients during the primary surgical tumor excision. Using immunohistochemistry, we observed an up-regulation in the expression of FUBP1 and c-Myc in sacral chordomas compared with the normal tissues (P = 0.001 for both). Additionally, positive correlations of FUBP1 expression with c-Myc (γ = 0.651, P < 0.001) and the cell proliferation index Ki-67 expression (γ = 0.447, P = 0.004) were indicated using Spearman's rank correlation coefficient. Increased expression of FUBP1 was significantly associated with tumor invasion into the surrounding muscles (P = 0.002). Kaplan-Meier curves demonstrated the association between FUBP1 levels and the patients' local recurrence-free survival (LRFS) (P < 0.001) but not with the overall survival (OS) (P = 0.070). The independent prognostic significance of FUBP1 levels for the LRFS was indicated by multivariate analysis (HR = 4.272; 95% CI, 1.133-16.112; P = 0.032). Our findings demonstrate an association between FUBP1 levels and chordoma progression and prognosis, suggesting that FUBP1 can be used as a biomarker and a potential therapeutic target.

Genetic aberrations and molecular biology of skull base chordoma and chondrosarcoma

Chordomas and chondrosarcomas are two major malignant bone neoplasms located at the skull base. These tumors are rarely metastatic, but can be locally invasive and resistant to conventional chemotherapies and radiotherapies. Accordingly, therapeutic approaches for the treatment of these tumors can be difficult. Additionally, their location at the skull base makes them problematic. Although accurate diagnosis of these tumors is important because of their distinct prognoses, distinguishing between these tumor types is difficult due to overlapping radiological and histopathological findings. However, recent accumulation of molecular and genetic studies, including extracranial location analysis, has provided us clues for accurate diagnosis. In this report, we review the genetic aberrations and molecular biology of these two tumor types. Among the abundant genetic features of these tumors, brachyury immunohistochemistry and direct sequencing of IDH1/2 are simple and useful techniques that can be used to distinguish between these tumors. Although it is still unclear why these tumors, which have such distinct genetic backgrounds, show similar histopathological findings, comparison of their genetic backgrounds could provide essential information.

miR-1908 Overexpression Inhibits Proliferation, Changing Akt Activity and p53 Expression in Hypoxic NSCLC Cells

The ribosomal protein (RP)-p53 pathway has been shown to play a key role in apoptosis and senescence of cancer cells. miR-1908 is a newly found miRNA that was reported to have prognostic potential in melanoma. However, its role and mechanism in the progression of non-small cell lung cancer (NSCLC) are largely unknown. In this study, we found that expression of miR-1908 was significantly downregulated in human NSCLC cell lines, including SK-MES-1, A549, and NCI-H460. Then the role of miR-1908 in NSCLC cell proliferation was explored. The miR-1908 mimic was transfected into NSCLC cell lines, and their proliferation was detected. MTT and Cell Titer-Blue H analyses showed that the cell proliferation was notably reduced by the miR-1908 mimic transfection. Moreover, we found the RP-p53 pathway was activated by miR-1908 mimic. Moreover, the miR-1908 inhibitor transfection had a completely opposite effect on the NSCLC cell proliferation than that of miR-1908 mimic. To explore the underlying mechanism of that, TargetScan bioinformatics server and 3'-UTR luciferase reporter assay were applied to identify the targets of miR-1908. Our results showed that AKT1 substrate 1 (AKT1S1), a newly proven suppressor of the RP-p53 pathway, was a target of miR-1908, suggesting a probable mechanism for miR-191 suppressing NSCLC cell proliferation. Our findings provide a novel molecular target for the regulation of NSCLC cell proliferation.

Long-term exposure of MCF-7 breast cancer cells to ethanol stimulates oncogenic features

Alcohol consumption is a risk factor for breast cancer. Little is known regarding the mechanism, although it is assumed that acetaldehyde or estrogen mediated pathways play a role. We previously showed that long-term exposure to 2.5 mM ethanol (blood alcohol ~0.012%) of MCF-12A, a human normal epithelial breast cell line, induced epithelial mesenchymal transition (EMT) and oncogenic transformation. In this study, we investigated in the human breast cancer cell line MCF-7, whether a similar exposure to ethanol at concentrations ranging up to peak blood levels in heavy drinkers would increase malignant progression. Short-term (1-week) incubation to ethanol at as low as 1-5 mM (corresponding to blood alcohol concentration of ~0.0048-0.024%) upregulated the stem cell related proteins Oct4 and Nanog, but they were reduced after exposure at 25 mM. Long-term (4-week) exposure to 25 mM ethanol upregulated the Oct4 and Nanog proteins, as well as the malignancy marker Ceacam6. DNA microarray analysis in cells exposed for 1 week showed upregulated expression of metallothionein genes, particularly MT1X. Long-term exposure upregulated expression of some malignancy related genes (STEAP4, SERPINA3, SAMD9, GDF15, KRT15, ITGB6, TP63, and PGR, as well as the CEACAM, interferon related, and HLA gene families). Some of these findings were validated by RT-PCR. A similar treatment also modulated numerous microRNAs (miRs) including one regulator of Oct4 as well as miRs involved in oncogenesis and/or malignancy, with only a few estrogen-induced miRs. Long-term 25 mM ethanol also induced a 5.6-fold upregulation of anchorage-independent growth, an indicator of malignant-like features. Exposure to acetaldehyde resulted in little or no effect comparable to that of ethanol. The previously shown alcohol induction of oncogenic transformation of normal breast cells is now complemented by the current results suggesting alcohol's potential involvement in malignant progression of breast cancer.

miR-219-5p inhibits proliferation and clonogenicity in chordoma cells and is associated with tumor recurrence

Chordoma is a rare malignant bone tumor that is usually localized to the skull base, vertebral column and sacrum. The transcription factor brachyury, which is encoded by the T gene, has a critical role in the development and progression of chordoma, although the mechanisms underlying brachyury regulation remain unclear. The aim of the current study was to identify and characterize microRNAs (miRs) that regulate brachyury expression in chordoma. MicroRNAs that target brachyury were predicted using miRanda and TargetScan. Using reverse transcription-quantitative polymerase chain reaction, miR-219-5p was shown to be significantly downregulated in chordoma tissues and the U-CH2 chordoma cell lines. A dual-luciferase reporter assay was used to validate the inhibitory effect of miR-219-5p on brachyury mRNA expression. The expression level of brachyury was downregulated in U-CH2 cells following transfection with miR-219-5p mimics and upregulated following transfection with the miR-219-5p inhibitor. The effects of miR-219-5p on the proliferation and clonogenicity of chordoma cells were assessed using cell counting kit-8, EdU and clone formation assays. These in vitro results indicated that miR-219-5p may have an important role in regulating the cell proliferation and clonogenicity of human chordoma cells, potentially by targeting brachyury. Furthermore, the associations between the expression levels of miR-219-5p and various clinicopathological factors were analyzed, and miR-219-5p expression was shown to correlate with tumor extent and recurrence. These results suggested that miR-219-5p functions as a tumor suppressor in chordoma and, therefore, that miR-219-50 may be a potential target for therapeutic intervention.

MicroRNA Profiling of the Effect of the Heptapeptide Angiotensin-(1-7) in A549 Lung Tumor Cells Reveals a Role for miRNA149-3p in Cellular Migration Processes

Lung cancer is one of the most frequent types of cancer in humans and a leading cause of death worldwide. The high mortality rates are correlated with late diagnosis, which leads to high rates of metastasis found in patients. Thus, despite all the improvement in therapeutic approaches, the development of new drugs that control cancer cell migration and metastasis are required. The heptapeptide angiotensin-(1-7) [ang-(1-7)] has demonstrated the ability to control the growth rates of human lung cancer cells in vitro and in vivo, and the elucidation of central elements that control the fine-tuning of cancer cells migration in the presence of the ang-(1-7), will support the development of new therapeutic approaches. Ang-(1-7) is a peptide hormone of the renin-angiotensin system (RAS) and this study investigates the modulatory effect of the heptapeptide on the expression pattern of microRNAs (miRNAs) in lung tumor cells, to elucidate mechanistic concerns about the effect of the peptide in the control of tumor migratory processes. Our primary aim was to compare the miRNA profiling between treated and untreated-heptapeptide cells to characterize the relevant molecule that modulates cellular migration rates. The analyses selected twenty one miRNAs, which are differentially expressed between the groups; however, statistical analyses indicated miRNA-149-3p as a relevant molecule. Once functional analyses were performed, we demonstrated that miRNA-149-3p plays a role in the cellular migration processes. This information could be useful for future investigations on drug development.

MiR-1908 promotes scar formation post-burn wound healing by suppressing Ski-mediated inflammation and fibroblast proliferation

The cell biological basis for scar formation is mainly via excessive fibroblast proliferation accompanied by hypernomic Col I accumulation and inflammation. The role of miR-1908 in scar formation has not been investigated. In this study, we found that miR-1908 expression was inversely associated with the scar suppressor Ski in normal, burn-wounded, healing and scar dermal tissues in humans. Bioinformatics and luciferase reporter gene assays confirmed that miR-1908 targeted the 3'UTR region of Ski mRNA and suppressed Ski expression. Next, human scar epidermal fibroblasts were isolated and the miR-1908 oligonucleotide mimic and inhibitor were respectively transfected into the cells. Western blot analysis proved that Ski expression was sharply reduced by the miR-1908 mimic. MTT and Cell Counting Kit-8 analyses showed that miR-1908 mimic transfection promoted cell proliferation. Simultaneously, data on real-time qPCR analysis indicated that expression of the fibrotic master gene TGF-β1, Ski-suppressing gene Meox2, Col I and proinflammatory markers IL-1α and TNF-α, were all significantly upregulated. In contrast, the miR-1908 inhibitor had a completely opposite effect on cell proliferation and gene expression. The mimic and inhibitor were locally injected into rats with abdominal burn-wounded scars during a 180-day, post-healing experiment. The miR-1908 mimic injection significantly reduced Ski expression, as well as the area, volume and fibrosis of scars in vivo. And, in contrast, the miR-1908 inhibitor injection had an opposite effect to that of the miR-1908 mimic injection. In conclusion, miR-1908 had a positive role in scar formation by suppressing Ski-mediated inflammation and fibroblast proliferation in vitro and in vivo.

The potential function of microRNA in chordomas

Little is known about the molecular biology of chordomas, which are rare, chemoresistant tumors with no well-established treatment. miRNAs regulate gene networks and pathways. We aimed to evaluate the effects of dysregulated miRNA in chordomas would help reveal the underlying mechanisms of chordoma initiation and progression. In this study, miR-31, anti-miR-140-3p, anti-miR148a, and miR-222 were transiently transfected to chordoma cell lines and an MTS assay, apoptosis assay, and cell-cycle analysis were conducted to evaluate the effects. The mRNA level of predicted and confirmed targets of each miRNA, as well as the EMT and MET markers of U-CH1 and MUG-Chor1, were assessed with real-time polymerase chain reaction. Transient transfection of miRNA mimics was achieved, as each mimic increased or decreased the level of its corresponding miRNA. miR-31 decreased cell viability in MUG-Chor1 and U-CH2 after 72h, which is consistent with previous findings for U-CH1. Both miR-31 and anti-miR-148a induced apoptosis in all three cell lines. Although each miRNA had a similar pattern, miR-31 had the most effective S-phase arrest in all three cell lines. RDX, MET, DNMT1, DNMT3B, TRPS1, BIRC5, and KIT were found to be targeted by the selected miRNAs. The level of miR-222 in chordoma cell lines U-CH1 and MUG-Chor1 correlated positively with EMT markers and negatively with MET markers. This study uncovered the potential of miR-31, miR-140-3p, miR-148a, and miR-222-3p to be key molecules in the cell viability, cell cycle, and apoptosis in chordomas, as well as initiation, differentiation, and progression.

Chordoma: The Quest for Better Treatment Options

Chordoma is an extremely rare cancer, with an incidence of about one case per million persons per year in the USA and Europe (about 300 and 450 cases per year, respectively). The estimated median overall survival of patients with chordoma is approximately 6–7 years, yielding a rough estimate of chordoma prevalence at about 2000 in the USA and 3000 in Europe. Primary tumor develops along the axial spine between the clivus and sacrum and develops from the residual embryonic notochord. Brachyury (T), a transcription factor required for normal embryonic development, is expressed in the notochord and overexpressed in almost all cases of chordoma. The primary treatment for chordoma is surgical excision with wide local margins, when possible. Radiotherapy also plays a significant role in the adjuvant setting and when surgery is not possible. Unfortunately, in the advanced and/or metastatic setting, where the role of surgery and/or radiation is less clear, treatment options are very limited. To date, there have been no randomized, controlled trials in chordoma that have resulted in defined agents of clinical benefit for systemic treatment. This review briefly describes the natural history and initial treatment of chordoma and focuses on treatment options for advanced disease and potential avenues of research that may lead to improved treatment options in the future.

MicroRNA-155 expression is independently predictive of outcome in chordoma

Background

Chordoma pathogenesis remains poorly understood. In this study, we aimed to evaluate the relationships between microRNA-155 (miR-155) expression and the clinicopathological features of chordoma patients, and to evaluate the functional role of miR-155 in chordoma.

Methods

The miRNA expression profiles were analyzed using miRNA microarray assays. Regulatory activity of miR-155 was assessed using bioinformatic tools. miR-155 expression levels were validated by reverse transcription-polymerase chain reaction. The relationships between miR-155 expression and the clinicopathological features of chordoma patients were analyzed. Proliferative, migratory and invasive activities were assessed by MTT, wound healing, and Matrigel invasion assays, respectively.

Results

The miRNA microarray assay revealed miR-155 to be highly expressed and biologically active in chordoma. miR-155 expression in chordoma tissues was significantly elevated, and this expression correlated significantly with disease stage (p = 0.036) and the presence of metastasis (p = 0.035). miR-155 expression also correlated significantly with poor outcomes for chordoma patients (hazard ratio, 5.32; p = 0.045). Inhibition of miR-155 expression suppressed proliferation, and the migratory and invasive activities of chordoma cells.

Conclusions

We have shown miR-155 expression to independently affect prognosis in chordoma. These results collectively indicate that miR-155 expression may serve not only as a prognostic marker, but also as a potential therapeutic target in chordoma.

Chordoma: an update on the pathophysiology and molecular mechanisms

Chordoma is a rare low-grade primary malignant skeletal tumor, which is presumed to derive from notochord remnants. The pathogenesis of chordoma has not been fully elucidated. However, recent advances in the molecular biology studies have identified brachyury underlying the initiation and progression of chordoma cells. More efforts have been made on accumulating evidence of the notochordal origin of chordoma, discovering signaling pathways and identifying crucial targets in chordomagenesis. In this review, we summarize the most recent research findings and focus on the pathophysiology and molecular mechanisms of chordoma.

The molecular aspects of chordoma

Chordomas are one of the rarest bone tumors, and they originate from remnants of embryonic notochord along the spine, more frequently at the skull base and sacrum. Although they are relatively slow growing and low grade, chordomas are highly recurrent, aggressive, locally invasive, and prone to metastasize to the lungs, bone, and the liver. Chordomas highly and generally show a dual epithelial-mesenchymal differentiation. These tumors resist chemotherapy and radiotherapy; therefore, radical surgery and high-dose radiation are the most used treatments, although there is no standard way to treat the disease. The molecular biology process behind the initiation and progression of a chordoma needs to be revealed for a better understanding of the disease and to develop more effective therapies. Efforts to discover the mysteries of these molecular aspects have delineated several molecular and genetic alterations in this tumor. Here, we review and describe the emerging insights into the molecular landscape of chordomas.

Acute hypoxia induces upregulation of microRNA-210 expression in glioblastoma spheroids

AIM

Tumor hypoxia and presence of tumor stem cells are related to therapeutic resistance and tumorigenicity in glioblastomas. The aim of the present study was therefore to identify microRNAs deregulated in acute hypoxia and to identify possible associated changes in stem cell markers.

MATERIALS & METHODS

Glioblastoma spheroid cultures were grown in either 2 or 21% oxygen. Subsequently, miRNA profiling was performed and expression of ten stem cell markers was examined.

RESULTS

MiRNA-210 was significantly upregulated in hypoxia in patient-derived spheroids. The stem cell markers displayed a complex regulatory pattern.

CONCLUSION

MiRNA-210 appears to be upregulated in hypoxia in immature glioblastoma cells. This miRNA may represent a therapeutic target although it is not clear from the results whether this miRNA may be related to specific cancer stem cell functions.

MicroRNA-1908 is upregulated in human osteosarcoma and regulates cell proliferation and migration by repressing PTEN expression

Osteosarcoma is a high-grade malignant bone neoplasm. Although the introduction of chemotherapy has reduced its mortality, >50% of patients develop chemoresistance and have an extremely poor prognosis due to pulmonary metastasis. Several molecular pathways contributing to osteosarcoma development and progression have recently been identified. Various studies have addressed the genes involved in the metastasis of osteosarcoma. However, the highly complex molecular mechanisms of metastasis remain to be elucidated. Recent studies have emphasized causative links between aberrant microRNA expression patterns and osteosarcoma progression. miR-1908 is dysregulated in certain human types of cancer. The expression pattern, clinical significance and biological role of miR-1908 in osteosarcoma, however, remain largely undefined. In the present study, we showed that miR-1908 was markedly upregulated in osteosarcoma cells and tissues compared with normal bone tissues using RT-qPCR. miR-1908 upregulation in osteosarcoma tissues was significantly associated with cell proliferation, invasion, advanced TNM stage and tumor growth. Both gain- and loss-of-function studies showed that miR-1908 markedly increased the ability of osteosarcoma cells to proliferate and to invade through Matrigel in vitro. Analyses using mouse xenograft model revealed that xenografts of miR-1908 stable-expressing osteosarcoma cells exhibited a significant increase in tumor volume and weight, compared with the control group. Subsequent investigations revealed that miR-1908 directly inhibited the expression of phosphatase and tensin homolog deleted on chromosome ten (PTEN). Using a luciferase reporter carrying the 3'-untranslated region (3'-UTR) of PTEN, we identified PTEN as a direct target of miR-1908. Collectively, the results showed that, miR-1908 promotes proliferation and invasion of osteosarcoma cells by repressing PTEN expression.

Analysis of the differential expression of circulating microRNAs during the progression of hepatic fibrosis in patients with chronic hepatitis B virus infection

Considering the limitations of liver biopsy, reliable non‑invasive serum biomarkers of liver fibrosis are required for early diagnosis. The present study analyzed the expression profile of circulating micro (mi)RNAs during the development and progression of hepatic fibrosis in patients with chronic hepatitis B virus (HBV) infection, aiming to identify novel earlier diagnostic biomarkers. Fresh plasma samples were collected from 50 patients diagnosed with chronic HBV infection and hepatic fibrosis. These patients were classified into five groups (S0, S1, S2, S3 and S4; n=10 per group) based on Scheuer's staging criteria. The differential expression of the circulating miRNAs was determined by performing miRNA microarray hybridization. Finally, the target genes of the miRNAs were predicted and classified using gene ontology analysis. A total of 140 miRNAs were detected in the S1‑S4 patient groups, and their expression levels were >2‑fold higher compared with those in the S0 group. The numbers of miRNAs differentially expressed in the S1‑S4 patient groups were 48, 97, 84 and 56, respectively, with 12 miRNAs differentially expressed at all stages, 10 of which were upregulated and two of which were downregulated. The target genes of the miRNAs identified were found to be involved in 100 signal transduction pathways, the majority of which affected hepatic fibrosis via the TGF‑/Smad, Wnt, MAPK, Jak/STAT and VEGF pathways. The differential expression levels of miRNAs were closely associated with the staging of hepatic fibrosis. The results of the present study provide evidence to facilitate the development and application of non‑invasive biomarkers for earlier diagnosis of hepatic fibrosis.

MicroRNA Let-7i negatively regulates cardiac inflammation and fibrosis

Angiotensin II stimulates fibroblast proliferation and substantially alters gene expression patterns leading to cardiac remodeling, but the mechanisms for such differences are unknown. MicroRNAs are a novel mechanism for gene expression regulation. Herein, we tested the miRNA and mRNA expression patterns in mouse heart using microarray assay and investigated their role in angiotensin II-induced cardiac remodeling. We found that let-7i was dynamically downregulated in angiotensin II-infused heart at day 3 and 7 and had the most targets that were mainly associated with cardiac inflammation and fibrosis. Overexpression or knockdown of let-7i in cultured cardiac fibroblasts demonstrated that let-7i played an inhibitory effect on the expression of its targets interleukin-6 and collagens. Furthermore, delivery of let-7i to mouse significantly inhibited angiotensin II-induced cardiac inflammation and fibrosis in a dose-dependent manner. Conversely, knockdown of let-7i aggravated this effect. Together, our results clearly demonstrate that let-7i acts as a novel negative regulator of angiotensin II-induced cardiac inflammation and fibrosis by suppressing the expression of interleukin-6 and multiple collagens in the heart and may represent a new potential therapeutic target for treating hypertensive cardiac fibrosis.

miRNA Regulation Network Analysis in Qianliening Capsule Treatment of Benign Prostatic Hyperplasia

Objective. The objective of this study was to evaluate the molecular mechanism by which Qianliening capsule (QC) treats benign prostatic hyperplasia (BPH). Methods. Benign prostatic hyperplasia epithelial cell line BPH-1 was treated with 0, 1.25, 2.5, and 5 mg/mL QC for 48 h, respectively. Evaluation of cell viability and observation of morphologic changes of BPH-1 cell gene expression and miRNA expression profiles were analyzed. Real-time quantitative PCR was used to confirm changes in miRNA and gene expression. GO and KEGG pathway-based approaches were used to investigate biological functions and signaling pathways affected by differentially expressed mRNAs. Results. QC inhibited BPH-1 cell proliferation. Differential expression of 19 upregulated and 2 downregulated miRNAs was observed in QC-treated BPH-1 cells compared to untreated control cells. 107 upregulated and 71 downregulated genes were identified between the two groups. Significantly enriched signaling pathways based on deregulated mRNAs were mainly involved in regulation of cell proliferation, apoptosis, and so on. Additionally, miRNA-mRNA network analysis integrated these miRNAs and genes by outlining interactions of miRNA and related genes. Conclusion. The study was the first report of differentially expressed miRNA and mRNA in QC-treated BPH-1 cells.

Pathway analysis from lists of microRNAs: common pitfalls and alternative strategy

MicroRNAs (miRNAs) are involved in the regulation of gene expression at a post-transcriptional level. As such, monitoring miRNA expression has been increasingly used to assess their role in regulatory mechanisms of biological processes. In large scale studies, once miRNAs of interest have been identified, the target genes they regulate are often inferred using algorithms or databases. A pathway analysis is then often performed in order to generate hypotheses about the relevant biological functions controlled by the miRNA signature. Here we show that the method widely used in scientific literature to identify these pathways is biased and leads to inaccurate results. In addition to describing the bias and its origin we present an alternative strategy to identify potential biological functions specifically impacted by a miRNA signature. More generally, our study exemplifies the crucial need of relevant negative controls when developing, and using, bioinformatics methods.

Aberrant expression of microRNAs in serum may identify individuals with pancreatic cancer

Pancreatic cancer (PC) has the poorest survival rate among all types of human cancer due to the lack of sensitive and non-invasive diagnostic screen methods for PC screening. Our aim was to identify novel serum microRNA (miRNA) biomarkers for the early detection of PC. We used microarray to screen differential expression of miRNAs in two pooled serum samples (6 PC patients and 6 healthy controls). A panel of miRNAs (22 over-expression and 23 decreased) were deregulated in serum of PC patients in comparison to controls. The expressions of 8 selected miRNAs were further evaluated in sera from 49 PC patients and 27 controls using quantitative reverse transcription-polymerase chain reaction. The levels of serum miR-492 and miR-663a were significantly decreased in PC patients compared with controls (P < 0.05). ROC curve analysis showed that serum miR-492 and miR-663a yield an AUC of 0.787 with 75.5% sensitivity and 70.0% specificity and 0.870 with 85.7% sensitivity and 80.0% specificity, respectively, for discriminating between PC patients and healthy controls. In addition, the level of miR-663a was significantly and inversely associated with TNM stage (P = 0.027). These results suggested that serum miR-492 and miR-663a could have strong potential as novel non-invasive biomarkers for the early detection of PC.

The biological effects of hsa-miR-1908 in human adipocytes

MicroRNAs (miRNAs) are small non-coding RNAs involved in the regulation of gene expression. MiR-1908 is a recently identified miRNA that is highly expressed in human adipocytes. However, it is not known what role of miR-1908 is involved in the regulation of human adipocytes. In this study, we demonstrate that the level of miR-1908 increases during the adipogenesis of human multipotent adipose-derived stem (hMADS) cells and human preadipocytes-visceral. Overexpression of miR-1908 in hMADS cells inhibited adipogenic differentiation and increased cell proliferation, suggesting that miR-1908 is involved in the regulation of adipocyte cell differentiation and metabolism, and, thus, may have an effect on human obesity.

Identification of dysregulated miRNAs and their regulatory signature in glioma patients using the partial least squares method

Using microarray data, the present study identified differentially expressed microRNAs (miRNAs) and evaluated their regulatory characteristics in high-grade glioma patients, with the aim to further the understanding into the underlying etiology of the condition. Previously, studies have generally implemented regression or variance analysis, which ignores various background biological factors. However, in the present study, analysis was performed with microarray data collected from the Gene Expression Omnibus database using a partial least squares-based method, which is more sensitive in handling microarray data. Among the six identified differentially expressed miRNAs, hsa-miR-21 and hsa-miR-612 have been previously reported to be associated with glioma. In addition, the remaining miRNAs, hsa-miR-4680, hsa-miR-1908, hsa-miR-4656 and hsa-miR-4467, may also contribute to glioma progression since they are all associated with the tumorigenesis of other types of cancer. Moreover, the expression levels of hsa-miR-1908, hsa-miR-4656 and hsa-miR-4680 have been identified to significantly correlate with the survival rate. Enrichment analysis of the dysregulated target genes revealed that the selected miRNAs primarily affect biological processes in the nervous system and the protein phosphorylation process. Therefore, the results may offer a new understanding into the pathogenesis of high-grade glioma.