Integrative meta-analysis identifies microRNA-regulated networks in infantile hemangioma

Construction of miRNA-mRNA Regulatory Network to Identify Potential Biomarkers in Infantile Hemangioma by Integrated Bioinformatics Analysis

Infantile hemangioma (IH) is the most common vascular tumor among infants and children. However, the understanding of pathogenesis about IH has not been fully elucidated, and the potential diagnostic maker remains further explored. In this study, we aimed to find miRNAs as potential biomarkers of IH through bioinformatic analysis. The microarray datasets GSE69136, GSE100682 were downloaded from the GEO database. The co-expressed differential miRNAs were identified by analyzing these two datasets. The downstream common target genes were predicted by the ENCORI, Mirgene, miRWalk, and Targetscan databases. GO annotation and KEGG pathway enrichment analysis for target genes were performed. The STRING database and Cytoscape software were used to construct the protein-protein interaction network and screen hub genes. Then potential diagnostic markers for IH were further screened and identified by using Receiver operating characteristic curve analysis. A total of thirteen co-expressed up-regulated miRNAs were screened out in the above two datasets, and 778 down-regulated target genes were then predicted. GO annotation and KEGG pathway enrichment analysis indicated that the common target genes strongly correlated with IH. Through the DEM-hub gene network construction, six miRNAs associated with the hub genes were identified. Finally, has-miR-522-3p, has-miR-512-3p, has-miR-520a-5p with high diagnostic values were screened out by receiver operating characteristic analysis. In the study, the potential miRNA-mRNA regulatory network was firstly constructed in IH. And, the three miRNAs might be used as potential biomarkers for IH, which also provided novel strategies for the therapeutic intervention of IH.

Comprehensive Analysis of the Transcriptome-Wide m6A Methylome in Pterygium by MeRIP Sequencing

Aim

Pterygium is a common ocular surface disease, which is affected by a variety of factors. Invasion of the cornea can cause severe vision loss. N6-methyladenosine (m6A) is a common post-transcriptional modification of eukaryotic mRNA, which can regulate mRNA splicing, stability, nuclear transport, and translation. To our best knowledge, there is no current research on the mechanism of m6A in pterygium.

Methods

We obtained 24 pterygium tissues and 24 conjunctival tissues from each of 24 pterygium patients recruited from Shanghai Yangpu Hospital, and the level of m6A modification was detected using an m6A RNA Methylation Quantification Kit. Expression and location of METTL3, a key m6A methyltransferase, were identified by immunostaining. Then we used m6A-modified RNA immunoprecipitation sequencing (MeRIP-seq), RNA sequencing (RNA-seq), and bioinformatics analyses to compare the differential expression of m6A methylation in pterygium and normal conjunctival tissue.

Results

We identified 2,949 dysregulated m6A peaks in pterygium tissue, of which 2,145 were significantly upregulated and 804 were significantly downregulated. The altered m6A peak of genes were found to play a key role in the Hippo signaling pathway and endocytosis. Joint analyses of MeRIP-seq and RNA-seq data identified 72 hypermethylated m6A peaks and 15 hypomethylated m6A peaks in mRNA. After analyzing the differentially methylated m6A peaks and synchronously differentially expressed genes, we searched the Gene Expression Omnibus database and identified five genes related to the development of pterygium (DSP, MXRA5, ARHGAP35, TMEM43, and OLFML2A).

Conclusion

Our research shows that m6A modification plays an important role in the development of pterygium and can be used as a potential new target for the treatment of pterygium in the future.

MiR-206 promotes extracellular matrix accumulation and relieves infantile hemangioma through targeted inhibition of DNMT3A

MiR-206 is abnormally expressed in infant hemangioma endothelial cells (HemECs), but the mechanism is not clear. We explored the intervention of miR-206 in HemECs in relation to extracellular matrix (ECM) metabolism. We selected 48 cases of infantile hemangioma (IH) from volunteer organizations. After the isolated and extracted HemECs were interfered with overexpressed or silenced miR-206, the effects of miR-206 on the proliferation, migration and invasion of HemECs were examined through basic cell function experiments. The expression differences of miR-206, DNA Methyltransferase 3A (DNMT3A) and ECM-related genes were analyzed as needed by qRT-PCR or Western blot. TargetScan and dual-luciferase experiments were applied to predict and confirm the binding relationship between miR-206 and DNMT3A. The correlation between miR-206 and DNMT3A was analyzed in IH tissues by Pearson correlation coefficient, and further confirmed in HemECs by conducting rescue experiments. A nude mouse model of xenograft tumor was constructed to verify the results of in vitro experiments. MiR-206, which was downregulated in proliferative hemangioma, suppressed the malignant development of HemECs by regulating ECM-related genes. As the target gene of miR-206, DNMT3A was high-expressed in IH tissues and was negatively correlated with miR-206. Overexpressed DNMT3A counteracted the inhibitory effect of miR-206 mimic on HemECs and its regulatory effect on ECM. The results of in vivo experiments were consistent with those from cell experiments. Thus, miR-206 could promote ECM accumulation through targeted inhibition of DNMT3A, further inhibiting the malignant development of HemECs and relieving IH.

Circular RNA expression profiles in the plasma of patients with infantile hemangioma determined using microarray analysis

Circular RNAs (circRNAs) are noncoding RNAs that have important roles in tumor progression. Previous studies have examined the circRNAs involved in infantile hemangioma (IH) tumors. The present study compared the circRNA levels in plasma samples from patients with IH and control individuals. The circRNA expression profiles were determined using microarray in three pairs of plasma samples from patients with proliferative IH and healthy control subjects. Expression of the identified differentially expressed circRNAs was verified using reverse transcription-quantitative PCR (RT-qPCR) and a bioinformatics analysis was performed to predict the microRNAs targeted by the validated circRNAs. From the circRNA expression profiles in the plasma of patients with IHs, 128 differentially expressed circRNAs were identified, of which 72 were upregulated and 56 were downregulated. The downregulated expression of three circRNAs [Homo sapiens (hsa)_circRNA_101566, hsa_circRNA_103546 and hsa_circRNA_103573] was verified using RT-qPCR. Gene Ontology term and Kyoto Encyclopedia of Genes and Genomes pathway analyses indicated that all identified networks participated in angiogenesis and tumor formation and progression. It was determined that hsa_circRNA_101566, which is able to regulate the mTOR signaling pathway, may be an important regulatory molecule in IH development and that targeting of hsa_miR_520c is able to indirectly regulate the vascular endothelial growth factor signaling pathway. Further studies are required to clarify these effects and the underlying mechanisms.

Propranolol suppresses infantile hemangioma cell proliferation and promotes apoptosis by upregulating miR-125b expression

Propranolol could repress infantile hemangioma cell growth and induce apoptosis. miR-125b could inhibit cell proliferation in some tumors. However, whether propranolol exerts its proliferation inhibition and apoptosis-promoting effect by regulating the expression of miR-125b needs to be further investigated. In tumor tissue and endothelial cells isolated from infantile hemangioma patients, we found that the expression levels of miR-125b were significantly decreased. In-vitro analysis revealed that propranolol increased the expression of miR-125b in hemangioma cells in a dose-dependent and time-dependent manner. Interestingly, it was observed that regression of miR-125b expression by its inhibitor could abrogate the effect of propranolol on hemangioma cell growth and apoptosis. In addition, our data further identified TFAP4 as a direct target of miR-125b. Collectively, our data provided evidence that propranolol may repress infantile hemangioma cell growth and promote apoptosis through upregulating the miR-125b expression, which exerted its suppression of tumor development by targeting TFAP4.

Efficacy of propranolol and pingyangmycin, respectively, combined with pulsed dye laser on children with hemangioma

Clinical efficacy of propranolol and pingyangmycin, respectively, combined with pulsed dye laser in the treatment of children with hemangioma was analyzed, to provide a new therapeutic idea for their clinical treatment. A total of 120 children with hemangioma were selected into the study. Children treated with propranolol combined with pulsed dye laser were in group A, those treated with pingyangmycin combined with pulsed dye laser were in group B, and 60 healthy children were selected as control group (group C). Blood samples of children were taken before and after treatment for miR-4295 detection. The expression of miR-4295 was observed after treatment, and the total clinical remission rate and adverse reactions after treatment were compared between the two groups. The tumor volume of the two groups was significantly reduced after treatment, with statistically significant difference (P<0.05); miR-4295 expression was reduced in the two groups (P<0.05); adverse reactions in propranolol group were less than pingyangmycin group during treatment (P<0.05). Propranolol and pingyangmycin, respectively, combined with pulsed dye laser had ideal efficacy on hemangioma in children. Moreover, miR-4295 was highly expressed in children with hemangioma, and the expression level reduced after two methods of treatment. However, adverse reactions in propranolol group were less and its safety was higher.

MicroRNAs for the pediatric otolaryngologist

The scope of pediatric otolaryngology is broad and encompasses a wide variety of diseases in which the fundamental phenotype-causing abnormality exists at the level of gene regulation and expression. Development of novel molecular biology instruments to diagnose disease, monitor treatment response, and prevent recurrence will facilitate the delivery of appropriate surgical and adjuvant medical treatments with lower morbidity. MicroRNAs (miRNAs) have emerged as a relatively new class of molecules that directly modulate gene expression and are abnormally expressed in a multitude of disease processes including those within the scope of pediatric otolaryngology. Functionally, miRNAs control multiple cellular functions including angiogenesis, cell proliferation, cell survival, genome stability, and inflammation. These short, non-protein coding RNA molecules are present and stable in tissue, blood, saliva, and urine, making them ideal disease biomarkers. The simple structure of miRNAs and their ability to directly modulate the expression of specific genes lends exciting therapeutic potential to miRNA-based therapies. Here we review the current literature of miRNAs as it relates to diseases within the scope of pediatric otolaryngology, and discuss their potential as diagnostic biomarkers and therapeutic targets.

LncRNA SNHG16 drives proliferation, migration, and invasion of hemangioma endothelial cell through modulation of miR-520d-3p/STAT3 axis

It has been verified that long noncoding RNAs (lncRNAs) have great effects on various biological behaviors of human diseases. Although more and more lncRNAs have been studied in human cancers, countless lncRNAs still need to be excavated. This study aims to investigate the impacts of lncRNA SNHG16 on proliferation and metastasis of human hemangioma endothelial cell (HemECs). qRT-PCR analysis was carried out to explore the expression pattern of SNHG16, miR-520d-3p, and STAT3. The effect of SNHG16 on cell proliferation was detected by MTT and colony formation assay. Flow cytometry analysis was performed to test the apoptosis of HemECs cells. Migration and invasion of HemECs cells were determined and examined by transwell assays. Tube formation assay helped to observe the influence of SNHG16 expression on the vasoformation of HemECs cells. The correlations among SNHG16, miR-520d-3p, and STAT3 were certified by bioinformatics analysis, pull-down assay, and dual-luciferase reporter assay. Finally, rescue assays were conducted to demonstrate the effects of SNHG16-miR-520d-3p-STAT3 axis on biological behaviors of HemECs cell. SNHG16 was strongly expressed in proliferating phase hemangioma tissues and HemECs cells. Silenced SNHG16 negatively affected proliferation, migration, and invasion of HemECs cell. LncRNA SNHG16 acted as a ceRNA to upregulate STAT3 through binding with miR-520d-3p in HemECs cell. LncRNA SNHG16 acted as a ceRNA to drive proliferation, vasoformation, migration, and invasion of HemECs cells through modulating miR-520d-3p/STAT3 axis.

Expression profile of circular RNAs in infantile hemangioma detected by RNA-Seq

BACKGROUND

Circular RNAs (circRNAs) have emerged as a novel class of widespread non-coding RNAs, and they play crucial roles in various biological processes. However, the characterization and function of circRNAs in infantile hemangioma (IH) remain elusive.

METHODS

In this study, we used RNA-Seq and circRNA prediction to study and characterize the circRNAs in IH tissue and a matched normal skin control. Specific circRNAs were verified using real-time polymerase chain reaction.

RESULTS AND CONCLUSION

We found that of the 9811 identified circRNAs, 249 candidates were differentially expressed, including 124 upregulated and 125 downregulated circRNAs in the IH group compared with the matched normal skin control group. A set of differentially expressed circRNAs (in particular, hsa_circRNA001885 and hsa_circRNA006612 expression) were confirmed using qRT-PCR. Gene ontology and pathway analysis revealed that compared to matched normal skin tissues, many processes that were over-represented in IH group were related to the binding, protein binding, gap junction, and focal adhesion. Specific circRNAs were associated with several micro-RNAs (miRNAs) predicted using miRanda. Altogether, our findings highlight the potential importance of circRNAs in the biology of IH and its response to treatment.

Competitive endogenous RNA networks: integrated analysis of non-coding RNA and mRNA expression profiles in infantile hemangioma

Infantile hemangioma (IH) is the most common vascular tumour in infants. The pathogenesis of IH is complex and poorly understood. Therefore, achieving a deeper understanding of IH pathogenesis is of great importance. Here, we used the Ribo-Zero RNA-Seq and HiSeq methods to examine the global expression profiles of protein-coding transcripts and non-coding RNAs, including miRNAs and lncRNAs, in IH and matched normal skin controls. Bioinformatics assessments including gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) pathway analyses were performed. Of the 16370 identified coding transcripts, only 144 were differentially expressed (fold change ≥ 2, P ≤ 0.05), including 84 up-regulated and 60 down-regulated transcripts in the IH samples compared with the matched normal skin controls. Gene ontology analysis of these differentially expressed transcripts revealed 60 genes involved in immune system processes, 62 genes involved in extracellular region regulation, and 35 genes involved in carbohydrate derivative binding. In addition, 256 lncRNAs and 142 miRNAs were found to be differentially expressed. Of these, 177 lncRNAs and 42 miRNAs were up-regulated in IH, whereas 79 lncRNAs and 100 miRNAs were down-regulated. By analysing the Ribo-Zero RNA-Seq data in combination with the matched miRNA profiles, we identified 1256 sponge modulators that participate in 87 miRNA-mediated, 70 lncRNA-mediated and 58 mRNA-mediated interactions. In conclusion, our study uncovered a competitive endogenous RNA (ceRNA) network that could further the understanding of the mechanisms underlying IH development and supply new targets for investigation.

Infantile hemangioma: factors causing recurrence after propranolol treatment

BackgroundPropranolol is the first-choice treatment for severe infantile hemangioma (IH). However, 10- 30% of lesions relapse after propranolol treatment. The mechanisms underlying IH recurrence after propranolol treatment have not been completely elucidated.MethodsThis study combined an examination of hemodynamic changes with research regarding hemangioma stem cells (hscs) with differentially expressed microRNAs (miRNAs) to identify the factors affecting IH recurrence after propranolol treatment. Hemodynamic changes were monitored in 21 recurrent cases using high-frequency color Doppler ultrasound, and hscs were treated with different concentrations of propranolol. The levels of differentially expressed miRNAs and the activity of related pathways were then compared between 18 recurrent and 20 non-recurrent IH cases.ResultsDuring treatment, lesion depth and vessel density decreased, and the lesion resistance index increased. Obvious lesions and vessel signals were observed in recurrent cases compared with non-recurrent cases. Propranolol effectively inhibited hscs proliferation. Twenty-two differentially expressed miRNAs were found in the recurrent group compared with the non-recurrent group.ConclusionRecurrence may be attributed to a combination of events. Serum biomarkers and drug treatments for IH recurrence must be studied further.

miR-199a-5p inhibits proliferation and induces apoptosis in hemangioma cells through targeting HIF1A

MicroRNAs (miRNAs) exhibit a crucial role in the regulation of angiogenesis and tumor progression, of which miR-199a-5p (miR-199a) has been reported to function as a tumor suppressor in multiple malignancies. However, the precise mechanisms underlying miR-199a in hemangiomas (HAs) remain elusive. In this study, we found that miR-199a had low expression level, while proliferating cell nuclear antigen (PCNA) had high expression level in proliferating-phase HAs compared with the involuting-phase HAs and normal tissues. Spearman correlation analysis revealed the negative correlation of miR-199a with PCNA expression in proliferating-phase HAs. In vitro experiments showed that restoration of miR-199a suppressed cell proliferation capability and induced cell apoptosis in HA-derived endothelial cells (HDEC) and CRL-2586 EOMA cells, followed with decreased PCNA expression and increased cleaved caspase-3 expression, but miR-199a inhibitor reversed these effects. Furthermore, HIF1A was identified as a target of miR-199a and had negative correlation with miR-199a expression in proliferating-phase HAs. Overexpression of HIF1A attenuated the anti-proliferation effect of miR-199a mimic in HAs cells. Taken together, our findings demonstrate that miR-199a may inhibit proliferation and induce apoptosis in HAs cells via targeting HIF1A and provide a potential therapeutic target for HAs.

Mechanisms of Action of MicroRNAs in Infantile Hemangioma Tissue and Vascular Endothelial Cells in Different Periods

Background

The aim of this study was to investigate the developmental mechanisms of infantile hemangioma (IH) from the microRNA level.

Material/Methods

A total of 63 biological specimens of IH were obtained from the First Affiliated Hospital of Jinzhou Medical University and we assessed related miRNAs. Magnetic bead sorting, endocytosis test, canalization assay, and immunofluorescence detection were performed. The IH-derived cells were transfected with related factors and then we assessed the apoptosis and invasion.

Results

The contents of MiR-455, miR-206, and miR-29a in the proliferative period group (PP) were lower than in the complete regression period group (CR) (P<0.05), and the content of miR-29a in the regression period group (RP) was lower than in the group CR (P<0.05). The post-sorting proliferation capacity was faster than in human umbilical vein endothelial cells, and IH-derived vascular endothelial cells (VECs) exhibited faster canalization ability. The cells transfected with miR-29a exhibited obvious apoptosis 48 h later, the cells transfected with miR-206 exhibited significantly reduced proliferation capacity as well as apoptosis 48 h later, and the invasion capacity was decreased 24 h after transfection.

Conclusions

miR-29a, miR-206, and miR-455 are differently expressed in different periods of IH, and may participate in regulating multiple functions during the progression of IH.