Comparison of Alterations in miRNA Expression in Matched Tissue and Blood Samples during Spinal Cord Glioma Progression

Micro RNAs and Circular RNAs in Different Forms of Otitis Media

The aim of this comprehensive review was to present the current knowledge on the role of microRNAs (miRNAs) in acute, recurrent, and chronic forms of otitis media. Special attention was focused on cholesteatoma of the middle ear. MicroRNAs modulate gene expression, which, in turn, influences the development and likelihood of the recurrence of acute and aggressive chronic middle ear inflammatory processes. Moreover, this study discusses the modulating role of a specific subgroup of noncoding RNA, circular RNA (circRNA). Recognizing the precise potential pathways and the mechanisms of their function may contribute to a better understanding of the molecular bases of middle ear diseases and identifying novel methods for treating this demanding pathology. Articles published between 2009 and 2022 were used in this analysis. In this review, we provide a complete overview of the latest progress in identifying the role and mechanisms of particular miRNAs and circRNAs in acute, recurrent and chronic forms of otitis media.

The Use of Pro-Angiogenic and/or Pro-Hypoxic miRNAs as Tools to Monitor Patients with Diffuse Gliomas

IDH (isocitrate dehydrogenase) mutation, hypoxia, and neo-angiogenesis, three hallmarks of diffuse gliomas, modulate the expression of small non-coding RNAs (miRNA). In this paper, we tested whether pro-angiogenic and/or pro-hypoxic miRNAs could be used to monitor patients with glioma. The miRNAs were extracted from tumoral surgical specimens embedded in the paraffin of 97 patients with diffuse gliomas and, for 7 patients, from a blood sample too. The expression of 10 pro-angiogenic and/or pro-hypoxic miRNAs was assayed by qRT-PCR and normalized to the miRNA expression of non-tumoral brain tissues. We confirmed in vitro that IDH in hypoxia (1% O₂, 24 h) alters pro-angiogenic and/or pro-hypoxic miRNA expression in HBT-14 (U-87 MG) cells. Then, we reported that the expression of these miRNAs is (i) strongly affected in patients with glioma compared to that in a non-tumoral brain; (ii) correlated with the histology/grade of glioma according to the 2016 WHO classification; and (iii) predicts the overall and/or progression-free survival of patients with glioma in univariate but not in a multivariate analysis after adjusting for sex, age at diagnosis, and WHO classification. Finally, the expression of miRNAs was found to be the same between the plasma and glial tumor of the same patient. This study highlights a panel of seven pro-angiogenic and/or pro-hypoxic miRNAs as a potential tool for monitoring patients with glioma.

microRNA-27a-3p delivered by extracellular vesicles from glioblastoma cells induces M2 macrophage polarization via the EZH1/KDM3A/CTGF axis

Glioblastoma (GBM) cell-derived extracellular vesicles (EVs) have been demonstrated to modulate tumor microenvironment. In the present study, we attempted to discuss the role of hsa-microRNA-27a-3p (miR-27a-3p) delivered by GBM-EVs in M2 macrophage polarization. The isolated GBM-EVs were co-cultured with macrophages. After co-culture under normoxia/hypoxia, the effect of EV-derived hsa-miR-27a-3p on GBM cell biological processes was analyzed. Additionally, the target genes of hsa-miR-27a-3p were predicted. Moreover, the binding of enhancer of zeste homologue 1 (EZH1) to lysine-specific demethylase 3A (KDM3A) promoter region and the interaction between KDM3A and connective tissue growth factor (CTGF) were analyzed. GBM mouse models were established to verify the functions of EV-derived hsa-miR-27a-3p in vivo. We found increased hsa-miR-27a-3p in GBM tissues as well as GBM-EVs, which induced M2 polarization, thus promoting proliferative, migrative and invasive potentials of GBM cells. hsa-miR-27a-3p targeted EZH1 and promoted KDM3A expression to elevate the CTGF expression. GBM-EV-delivered hsa-miR-27a-3p promoted the KDM3A-upregulated CTGF by downregulating EZH1, thereby promoting M2 macrophage polarization and development of GBM in vivo. We demonstrated that EV-derived hsa-miR-27a-3p may promote M2 macrophage polarization to induce GBM.

Computing microRNA-gene interaction networks in pan-cancer using miRDriver

DNA copy number aberrated regions in cancer are known to harbor cancer driver genes and the short non-coding RNA molecules, i.e., microRNAs. In this study, we integrated the multi-omics datasets such as copy number aberration, DNA methylation, gene and microRNA expression to identify the signature microRNA-gene associations from frequently aberrated DNA regions across pan-cancer utilizing a LASSO-based regression approach. We studied 7294 patient samples associated with eighteen different cancer types from The Cancer Genome Atlas (TCGA) database and identified several cancer-specific and common microRNA-gene interactions enriched in experimentally validated microRNA-target interactions. We highlighted several oncogenic and tumor suppressor microRNAs that were cancer-specific and common in several cancer types. Our method substantially outperformed the five state-of-art methods in selecting significantly known microRNA-gene interactions in multiple cancer types. Several microRNAs and genes were found to be associated with tumor survival and progression. Selected target genes were found to be significantly enriched in cancer-related pathways, cancer hallmark and Gene Ontology (GO) terms. Furthermore, subtype-specific potential gene signatures were discovered in multiple cancer types.

Hsa_circRNA_0040462: a sensor of cells' response to CAP treatment with double-edged roles on breast cancer malignancy

Cold atmospheric plasma (CAP) represents a novel onco-therapeutic approach that has demonstrated its efficacy in many types of tumors. The efficacy of CAP is dose-dependent that determines the panel of tumors feasible for receiving CAP treatment under a certain parameter configuration. Identifying markers for easy and fast prognosis of tumors' sensitivity in response to CAP exposure is of critical value towards optimized therapeutic outcome, the lack of which has largely limited the translation of CAP into clinics. Circular RNAs represent a novel type of biomarkers for disease diagnosis that is featured by easy detection and stability. Through whole transcriptome sequencing, followed by in vitro validations, computational predictions and preliminary functional studies, we identified hsa_circRNA_0040462 as a sensor of breast cancer cells' response to CAP treatment. Yet we warrant the use of hsa_circRNA_0040462 as an onco-therapeutic target given its double-edged roles on breast cancer progression, i.e., suppressive on the growth and promotive on the migrative ability of triple negative breast cancer cells. Our study for the first time focused on markers prognostic of CAP's efficacy and tumors' sensitivity to CAP treatment under a certain parameter configuration, and reported hsa_circRNA_0040462 as a sensor of cells' response to CAP treatment. Also, the uncovered dual roles of hsa_circRNA_0040462 further advanced our knowledge on the complex yet critical regulatory functionalities of circular RNAs in cancer progression.

Unveiling the tumour-regulatory roles of miR-1275 in cancer

The rapid development of small RNA and molecular biology research in the past 20 years has enabled scientists to discover many new miRNAs that are proven to play essential roles in regulating the development of different cancer types. Among these miRNAs, miR-1275 is one of the well-studied miRNAs that has been described to act as a tumour-promoting or tumour-suppressing miRNA in various cancer types. Even though miR-1275 has been widely reported in different original research articles on its roles in modulating the progression of different cancer types, however, there is scarce an in-depth review that could constructively summarize the findings from different studies on the regulatory roles of miR-1275 in different cancer types. To fill up this literature gap, therefore, this review was aimed to provide an overview and summary of the roles of miR-1275 in modulating the development of different cancers and to unravel the mechanism of how miR-1275 regulates cancer progression. Based on the findings summarized from various sources, it was found that miR-1275 plays a vital role in regulating various cellular signaling pathways like the PI3K/AKT, ERK/JNK, MAPK, and Wnt signaling pathways, and the dysregulation of this miRNA has been shown to contribute to the development of multiple cancer types such as cancers of the liver, breast, lung, gastrointestinal tract and genitourinary tract. Therefore, miR-1275 has great potential to be employed as a biomarker to diagnose cancer and to predict the prognosis of cancer patients. In addition, by inhibiting the expression of its unique downstream targets that are involved in regulating the mentioned cellular pathways, this miRNA could also be utilized as a novel therapeutic agent to halt cancer development.

Microarray analysis and functional prediction of differentially expressed circular RNAs in acquired middle ear cholesteatoma

BACKGROUND

Middle ear cholesteatoma is characterized by hyper-proliferation of keratinocytes. Circular RNA (circRNA) plays an essential role in the pathogenesis of many proliferative diseases. However, the role of circRNA in the etiopathogenesis of middle ear cholesteatoma is rarely investigated so far. We aimed to investigate the differential expression profiling of circRNAs between acquired middle ear cholesteatoma and normal skin, and to identify potential circRNAs contributing to the etiopathogenesis of middle ear cholesteatoma. Microarray analysis and functional prediction were performed to investigate the circRNA expression profiling between middle ear cholesteatoma and normal skin. Validation of differentially expressed circRNAs was conducted by qRT-PCR. Prediction of m⁶A modification was also carried out.

RESULTS

Microarray analysis displayed that totally 93 up-regulated and 85 down-regulated circRNAs were identified in middle ear cholesteatoma. Through validation, expressions of hsa_circRNA_104327 and hsa_circRNA_404655 were significantly higher, while hsa_circRNA_000319 was significantly down-regulated in cholesteatoma. GO classification, KEGG pathway, and ceRNA network analyses suggested that these differentially expressed circRNAs might play important roles in the etiopathogenesis of middle ear cholesteatoma. Prediction of m⁶A modification exhibited that hsa_circRNA_000319 possessed 4 m⁶A sites with very high confidence, and hsa_circRNA_404655 had 3 m⁶A sites with high confidence.

CONCLUSIONS

Our study revealed that these differentially expressed circRNAs might contribute to the etiopathogenesis of middle ear cholesteatoma. Further researches should be conducted to investigate the exact mechanism of these differentially expressed circRNAs in the etiopathogenesis of middle ear cholesteatoma. Targeting on these circRNAs may provide a new strategy for middle ear cholesteatoma therapy in the future.

miR-221/222 suppression induced by activation of the cAMP/PKA/CREB1 pathway is required for cAMP-induced bidirectional differentiation of glioma cells

Factors that increase cAMP levels can induce lineage-specific differentiation of glioma cells into astrocyte-like cells. However, the differentiation pattern and underlying mechanisms remain unclear. Here, we find that cAMP/protein kinase A (PKA)/cAMP responsive element binding protein 1 (CREB1)-induced miR-221/222 suppression contributes to the neuron-like differentiation of gliomas. cAMP agonists selectively induced neuron- and astrocyte-like but not oligodendrocyte-like differentiation of C6 glioma cells. PKA inhibitors and CREB1 knockout blocked neuron-like differentiation of glioma cells. cAMP inhibited miR-221/222 in a PKA/CREB1-dependent manner. Importantly, both in vitro and in vivo assays demonstrated that transcriptional suppression of miR-221/222 is required for neuronal differentiation of glioma cells. Our findings suggest that increasing cAMP levels can induce bidirectional differentiation of glioma cells. Furthermore, the miR-221/222 cluster acts as an epigenetic brake during glioma differentiation.

Over-expression of lncRNA TMEM161B-AS1 promotes the malignant biological behavior of glioma cells and the resistance to temozolomide via up-regulating the expression of multiple ferroptosis-related genes by sponging hsa-miR-27a-3p

A growing body of evidence suggests that long-chain non-coding RNA (lncRNA) plays an important role in the malignant biological behavior and drug resistance of glioblastoma (GBM) cells. In this study, we analyzed the role and potential mechanism of lncRNA TMEM161B-AS1 in the malignant biological behavior of GBM cells and temozolomide (TMZ) resistance. Studies have found that FANCD2 and CD44 are significantly related to the occurrence of GBM, TMZ resistance and the survival of GBM patients. Knockdown of TMEM161B-AS1 down-regulated the expression of FANCD2 and CD44 by sponging hsa-miR-27a-3p, inhibited the proliferation, migration, invasion and promoted apoptosis, ferroptosis of U87 cells and U251 cells. Down-regulation of lncRNA TMEM161B-AS1 and/or over-expression of hsa-miR-27a-3p down-regulated the expression of FANCD2 and CD44, and inhibited the tumor growth in nude mice. These results demonstrated that the lncRNA TMEM161B-AS1-hsa-miR-27a-3p-FANCD2/CD44 signal axis regulated the malignant biological behavior of GBM and TMZ resistance. These findings were expected to provide promising therapeutic targets for the treatment of glioma.

Suppression of miR-106a-5p expression inhibits tumorigenesis via increasing CELF-2 expression in spinal cord glioma

Spinal cord glioma is a tumor characterized by high recurrence and mortality rates, and its treatment remains a major challenge. It has been reported that abnormal expression of microRNAs (miRNAs/miRs) is associated with tumor progression. Therefore, the current study aimed to identify novel miRNAs associated with spinal cord glioma. Herein, the expression levels of several miRNAs were determined in human spinal cord glioma and adjacent non-cancerous tissues by reverse transcription-quantitative (RT-qPCR). The results revealed that miR-106a-5p expression was markedly upregulated in spinal cord glioma tissues compared with in non-cancerous tissues. Furthermore, the biological effects of miR-106a-5p on spinal cord glioma cells were evaluated by MTT, Transwell and flow cytometric assays. In 0231SCG cells transfected with miR-106a-5p inhibitor, cell proliferation, migration and invasion were attenuated, whereas apoptosis was enhanced. A search of the TargetScan database revealed that miR-106a-5p directly targeted CUGBP Elav-like family member 2 (CELF-2). Western blot and RT-qPCR experiments further confirmed the association between miR-106a-5p and CELF-2 expression in spinal cord glioma tissues. The current results demonstrated that CELF-2 was a direct target of miR-106a-5p, and that the expression levels of CELF-2 were negatively associated with those of miR-106a-5p. In addition, overexpression of CELF-2 in spinal cord glioma cells reversed the tumor-promoting effects of miR-106a-5p both in vitro and in vivo. Overall, the aforementioned findings indicated that miR-106a-5p, which was highly expressed in spinal cord glioma tissues, may affect the proliferation, migration, invasion and apoptosis of spinal cord glioma cells via targeting CELF-2, thus indicating a potential approach to the future clinical management of spinal cord glioma.

MicroRNA regulation of prefrontal cortex development and psychiatric risk in adolescence

In this review, we examine the role of microRNAs in the development of the prefrontal cortex (PFC) in adolescence and in individual differences in vulnerability to mental illness. We describe results from clinical and preclinical research indicating that adolescence coincides with drastic changes in local microRNA expression, including microRNAs that control gene networks involved in PFC and cognitive refinement. We highlight that altered levels of microRNAs in the PFC are associated with psychopathologies of adolescent onset, notably depression and schizophrenia. We show that microRNAs can be measured non-invasively in peripheral samples and could serve as longitudinal physiological readouts of brain expression and psychiatric risk in youth.

MiR-27a-3p/miR-27b-3p Promotes Neurofibromatosis Type 1 via Targeting of NF1

The dysregulation of microRNAs (miRNAs) is a crucial molecular signature of disease development. The potential implication of miRNAs in neurofibromatosis type 1 (NF1) remains poorly investigated. The expression levels of miR-27a-3p, miR-27b-3p, and neurofibromin 1 (NF1) were detected by real-time quantitative polymerase chain reaction (RT-qPCR) analysis. The functional roles of miR-27a-3p and miR-27b-3p in NF1 were explored by CCK8 (Cell Counting Kit-8), 5-ethynyl-2'-deoxyuridine (EdU), terminal deoxynucleoitidyl transferase dUTP nick-end labeling (TUNEL), and transwell assays. Luciferase reporter, RNA pull-down, and RNA binding protein immunoprecipitation (RIP) assays were employed to study the probable target relationship between miRNA and messenger RNA (mRNA). MiR-27b-3p and miR-27a-3p were upregulated in dermal and plexiform human Schwann cells (HSC) from NF1 neurofibromas as well as cell lines of malignant peripheral nerve sheath tumors (MPNSTs). MiR-27a-3p/miR-27b-3p mimics promoted the proliferative, migratory, and invasive ability of dermal HSC and MPNST cell ST88-14, while inhibiting the apoptotic capacity. MiR-27a-3p/miR-27b-3p inhibitors elicited the opposite impacts on the above cellular behaviors in dermal HSC and ST88-14. Intriguingly, NF1 was revealed to be the target of both miR-27a-3p and miR-27b-3p, and was negatively modulated by them. MiR-27a-3p/miR-27b-3p upregulation suppressed the expression of NF1 in dermal HSC and ST88-14. Furthermore, NF1 depletion counterbalanced the functional alteration induced by miR-27a-3p/miR-27b-3p inhibition. Our study suggests that both miR-27b-3p and miR-27a-3p are involved in upstream molecular activity responsible for the depletion of NF1, representing promising targets for therapeutic application in NF1.

Unraveling Molecular Pathways Altered in MeCP2-Related Syndromes, in the Search for New Potential Avenues for Therapy

Methyl-CpG-binding protein 2 (MeCP2) is an X-linked epigenetic modulator whose dosage is critical for neural development and function. Loss-of-function mutations in MECP2 cause Rett Syndrome (RTT, OMIM #312750) while duplications in the Xq28 locus containing MECP2 and Interleukin-1 receptor-associated kinase 1 (IRAK1) cause MECP2 duplication syndrome (MDS, OMIM #300260). Both are rare neurodevelopmental disorders that share clinical symptoms, including intellectual disability, loss of speech, hand stereotypies, vasomotor deficits and seizures. The main objective of this exploratory study is to identify novel signaling pathways and potential quantitative biomarkers that could aid early diagnosis and/or the monitoring of disease progression in clinical trials. We analyzed by RT-PCR gene expression in whole blood and microRNA (miRNA) expression in plasma, in a cohort of 20 females with Rett syndrome, 2 males with MECP2 duplication syndrome and 28 healthy controls, and correlated RNA expression with disease and clinical parameters. We have identified a set of potential biomarker panels for RTT diagnostic and disease stratification of patients with microcephaly and vasomotor deficits. Our study sets the basis for larger studies leading to the identification of specific miRNA signatures for early RTT detection, stratification, disease progression and segregation from other neurodevelopmental disorders. Nevertheless, these data will require verification and validation in further studies with larger sample size including a whole range of ages.

GEO Data Sets Analysis Identifies COX-2 and Its Related Micro RNAs as Biomarkers for Non-Ischemic Heart Failure

Heart failure (HF) is a heterogeneous clinical syndrome with a variety of causes, risk factors, and pathology. Clinically, only brain natriuretic peptide (BNP) or its precursor N-terminus proBNP (NTproBNP) has been validated for HF diagnosis, but they are also affected by other conditions, such as female gender, renal disease, and acute coronary syndromes, and false low levels in the setting of obesity or flash pulmonary edema. In addition, there is no one biomarker which could encompass all heart failure phenotypes. Advances in bioinformatics have provided us with large databases that characterize the complex genetic and epigenetic changes associated with human diseases. The use of data mining strategies on public access databases to identify previously unknown disease markers is an innovative approach to identify potential biomarkers or even new therapeutic targets in complex diseases such as heart failure (HF). In this study, we analyzed the genomic and transcription data of HF peripheral blood mononuclear cell (PBMC) samples obtained from the Gene Expression Omnibus data sets using Omicsbean online database (http://www.omicsbean.cn/) and found that the prostaglandin-endoperoxide synthase 2 (PTGS2), also named as cyclooxygenase-2 (COX-2), as well as its related micro RNAs including miR-1297 and miR-4649-3p might be used as potential biomarkers for non-ischemic heart failure. Our result showed that plasma COX-2 and miR-4649-3p were significantly up-regulated, whereas the plasma miR-1297 was significantly decreased, and miR-4649-3p displayed high predictive power for non-ischemic heart failure.

Knockdown of long noncoding RNA XIST mitigates the apoptosis and inflammatory injury of microglia cells after spinal cord injury through miR-27a/Smurf1 axis

Spinal cord injury (SCI) is a devastating neuropathological condition. Long noncoding RNA X-inactive specific transcript (XIST) is an acknowledged cancer-related gene and participates in the development of SCI. However, role of XIST in SCI remains to be well revealed. Expression of XIST, miRNA-27a-3p (miR-27a) and smad ubiquitination regulatory factor 1 (Smurf1) was detected using RT-qPCR and western blotting. Cell apoptosis and inflammatory injury were assessed by sulforhodamine B (SRB) assay, flow cytometry, western blotting and enzyme-linked immunosorbent assay. The relationship among miR-27a, XIST and Smurf1 was confirmed by dual-luciferase reporter assay, RNA immunoprecipitation and RNA pull-down assay. As a result, we observed higher level of XIST and Smurf1, but lower level of miR-27a in SCI rats and lipopolysaccharide (LPS)-induced primary microglial cells. in vitro, LPS induced SCI microglia cells as described by decreased cell viability and B cell lymphoma 2 (Bcl-2) expression, and increased cell apoptosis rate, Bax and cleaved caspase 3 levels, and tumor necrosis factor α (TNF-α) and interleukin 6 (IL-6) secretions. in vivo, a T10 laminectomy caused SCI rats as evidenced by decreased Basso-Beattie-Bresnahan Locomotor Rating Scale (BBB) score and induced expression of Bax, cleaved caspase 3, TNF-α and IL-6. However, silencing of XIST could mitigate the apoptosis and inflammatory injury in LPS-induced microglia and SCI rats. Mechanically, miR-27a interacted with XIST and Smurf1 via target binding. Either miR-27a downregulation or Smurf1 overexpression partially reversed the role of XIST deletion in LPS-treated microglial cells. Collectively, knockdown of XIST could alleviate the apoptosis and inflammatory injury of SCI models in vitro and in vivo through directly modulating miR-27a/Smurf1 axis.