TGF-beta induced RBL2 expression in renal cancer cells by down-regulating miR-93

Using single-sample networks to identify the contrasting patterns of gene interactions and reveal the radiation dose-dependent effects in multiple tissues of spaceflight mice

Transcriptome profiles are sensitive to space stressors and serve as valuable indicators of the biological effects during spaceflight. Herein, we transformed the expression profiles into gene interaction patterns by single-sample networks (SSNs) and performed the integrated analysis on the 301 spaceflight and 290 ground control samples, which were obtained from the GeneLab platform. Specifically, an individual SSN was established for each sample. Based on the topological structures of 591 SSNs, the differentially interacted genes (DIGs) were identified between spaceflights and ground controls. The results showed that spaceflight disrupted the gene interaction patterns in mice and resulted in significant enrichment of biological processes such as protein/amino acid metabolism and nucleic acid (DNA/RNA) metabolism (P-value < 0.05). We observed that the mice exposed to radiation doses within the three intervals (4.66-7.14, 7.592-8.295, 8.49-22.099 mGy) exhibited similar gene interaction patterns. Low and medium doses resulted in changes to the circadian rhythm, while the damaging effects on genetic material became more pronounced in higher doses. The gene interaction patterns in response to space stressors varied among different tissues, with the spleen, lung, and skin being the most responsive to space radiation (P-value < 0.01). The changes observed in gene networks during spaceflight conditions might contribute to the development of various diseases, such as mental disorders, depression, and metabolic disorders, among others. Additionally, organisms activated specific gene networks in response to virus reactivation. We identified several hub genes that were associated with circadian rhythms, suggesting that spaceflight could lead to substantial circadian rhythm dysregulation.

Protective impact of nicotinamide mononucleotide (NMN) and platelet-rich fibrin (PRF) on replicative and radiation-induced senescence of human osteoblasts

The aim of this study was to investigate the cellular changes induced by spontaneous/replicative senescence and radiation in human osteoblasts (OBs), and the impact of cultivation with nicotinamide mononucleotide (NMN) and platelet-rich fibrin (PRF) on apoptosis, senescence-associated β-galactosidase staining (SA β-gal), and senescence-related gene expression using RT2 Profiler PCR array. The results showed that replicative OB aging follows a different pattern from that of radiation-induced cellular senescence. SA β-gal intensity score showed a significant elevation after spontaneous replicative aging of OB (agiT1) 7 days following the start of the experiment, compared with their initial control condition (T0) (T0 = 2.1 ± 0.47; agiT1 = 9.60 ± 1.56; p = 0.001). Concurrent treatment by NMN and PRF showed a protective effect on OBs undergoing replicative senescence, and reduced SA β-gal staining significantly (agiT1 = 9.60 ± 1.56; agiT1+PRF = 3.19 ± 0.52; agiT1+NMN = 3.38 ± 0.36; p < 0.001). These results provide evidence for the potential clinical implications of systematic NMN administration and local PRF application to prevent age-related bone disturbances in elderly patients.

MiRNA-93: a novel signature in human disorders and drug resistance

miRNA-93 is a member of the miR-106b-25 family and is encoded by a gene on chromosome 7q22.1. They play a role in the etiology of various diseases, including cancer, Parkinson's disease, hepatic injury, osteoarthritis, acute myocardial infarction, atherosclerosis, rheumatoid arthritis, and chronic kidney disease. Different studies have found that this miRNA has opposing roles in the context of cancer. Recently, miRNA-93 has been downregulated in breast cancer, gastric cancer, colorectal cancer, pancreatic cancer, bladder cancer, cervical cancer, and renal cancer. However, miRNA-93 is up-regulated in a wide variety of malignancies, such as lung, colorectal, glioma, prostate, osteosarcoma, and hepatocellular carcinoma. The aim of the current review is to provide an overview of miRNA-93's function in cancer disorder progression and non-cancer disorders, with a focus on dysregulated signaling pathways. We also give an overview of this miRNA's function as a biomarker of prognosis in cancer and emphasize how it contributes to drug resistance based on in vivo, in vitro, and human studies. Video Abstract.

Flaming the fight against cancer cells: the role of microRNA-93

There have been attempts to develop novel anti-tumor drugs in cancer therapy. Although satisfying results have been observed at a consequence of application of chemotherapeutic agents, the cancer cells are capable of making resistance into these agents. This has forced scientists into genetic manipulation as genetic alterations are responsible for generation of a high number of cancer cells. MicroRNAs (miRs) are endogenous, short non-coding RNAs that affect target genes at the post-transcriptional level. Increasing evidence reveals the potential role of miRs in regulation of biological processes including angiogenesis, metabolism, cell proliferation, cell division, and cell differentiation. Abnormal expression of miRs is associated with development of a number of pathologic events, particularly cancer. MiR-93 plays a significant role in both physiological and pathological mechanisms. At the present review, we show how this miR dually affects the proliferation and invasion of cancer cells. Besides, we elucidate the oncogenesis or oncosuppressor function of miR-93.

Biallelic loss-of-function variants in RBL2 in siblings with a neurodevelopmental disorder

The RBL2 locus has been associated with intelligence and educational attainment but not with a monogenic disorder to date. RBL2 encodes p130, a member of the retinoblastoma protein family, which is involved in mediating neuron survival and death. Previous studies on p130 knockout mice revealing embryonic death and impaired neurogenesis underscore the importance of RBL2 in brain development. Exome sequencing in two siblings with severe intellectual disability, stereotypies and dysmorphic features identified biallelic loss-of-function variants c.556C>T, p.(Arg186Ter) and a deletion of exon 13-17 in RBL2 (NM_005611.3), establishing RBL2 as a candidate gene for an autosomal recessive neurodevelopmental disorder.

TGF-β and microRNA Interplay in Genitourinary Cancers

Genitourinary cancers (GCs) include a large group of different types of tumors localizing to the kidney, bladder, prostate, testis, and penis. Despite highly divergent molecular patterns, most GCs share commonly disturbed signaling pathways that involve the activity of TGF-β (transforming growth factor beta). TGF-β is a pleiotropic cytokine that regulates key cancer-related molecular and cellular processes, including proliferation, migration, invasion, apoptosis, and chemoresistance. The understanding of the mechanisms of TGF-β actions in cancer is hindered by the "TGF-β paradox" in which early stages of cancerogenic process are suppressed by TGF-β while advanced stages are stimulated by its activity. A growing body of evidence suggests that these paradoxical TGF-β actions could result from the interplay with microRNAs: Short, non-coding RNAs that regulate gene expression by binding to target transcripts and inducing mRNA degradation or inhibition of translation. Here, we discuss the current knowledge of TGF-β signaling in GCs. Importantly, TGF-β signaling and microRNA-mediated regulation of gene expression often act in complicated feedback circuits that involve other crucial regulators of cancer progression (e.g., androgen receptor). Furthermore, recently published in vitro and in vivo studies clearly indicate that the interplay between microRNAs and the TGF-β signaling pathway offers new potential treatment options for GC patients.

Computational identification and analysis of early diagnostic biomarkers for kidney cancer

Renal cell carcinoma is one of the most common urinary system tumors in adults, it is usually asymptomatic in its early stage and the patients are often diagnosed late. MicroRNA has a higher diagnostic accuracy than traditional markers and may become a new type of early diagnostic biomarker for kidney cancer. Three computational methods and several bioinformatic methods including PPI network, overall survival analysis and enrichment analysis were used to identify the significant differentially expressed miRNAs. Thirteen miRNAs that were significantly differentially expressed in RCC patients were identified, 10 of them have been proved to be associated with kidney cancer in other studies, miR-576, miR-616 and miR-133a-2 are three newly discovered biomarkers of RCC in this study. We found that the target genes of miR-576 (CUL3 and RAC1) are involved in the regulation of multiple cancer-related biological pathways, and the target gene of miR-616 (ASB13 and FBXW2) has been reported to be associated with the development of other cancers. Our findings may have guiding significance for the early diagnosis of renal cell carcinoma.

Transformation of the Transcriptomic Profile of Mouse Periocular Mesenchyme During Formation of the Embryonic Cornea

Purpose

Defects in neural crest development are a major contributing factor in corneal dysgenesis, but little is known about the genetic landscape during corneal development. The purpose of this study was to provide a detailed transcriptome profile and evaluate changes in gene expression during mouse corneal development.

Methods

RNA sequencing was used to uncover the transcriptomic profile of periocular mesenchyme (pNC) isolated at embryonic day (E) 10.5 and corneas isolated at E14.5 and E16.5. The spatiotemporal expression of several differentially expressed genes was validated by in situ hybridization.

Results

Analysis of the whole-transcriptome profile between pNC and embryonic corneas identified 3815 unique differentially expressed genes. Pathway analysis revealed an enrichment of differentially expressed genes involved in signal transduction (retinoic acid, transforming growth factor-β, and Wnt pathways) and transcriptional regulation.

Conclusions

Our analyses, for the first time, identify a large number of differentially expressed genes during progressive stages of mouse corneal development. Our data provide a comprehensive transcriptomic profile of the developing cornea. Combined, these data serve as a valuable resource for the identification of novel regulatory networks crucial for the advancement of studies in congenital defects, stem cell therapy, bioengineering, and adult corneal diseases.

Expression Profiles of Long Noncoding RNA and mRNA in Epicardial Adipose Tissue in Patients with Heart Failure

The expression profile of long noncoding RNA (lncRNA) in human epicardial adipose tissue (EAT) has not been widely studied. In the present study, we performed RNA sequencing to analyze the expression profiles of lncRNA and mRNA in EAT in coronary artery disease (CAD) patients with and without heart failure (HF). Our results showed RNA sequencing disclosed 35673 mRNA and 11087 lncRNA corresponding to 15554 genes in EAT in total, while 30 differentially expressed lncRNAs (17 upregulated and 13 downregulated) and 278 differentially expressed mRNAs (129 upregulated and 149 downregulated) were discriminated between CAD patients with and without HF (P<0.05; fold change>2); lncRNA ENST00000610659 drew specific attention for it was the top upregulated lncRNA with highest fold change and corresponded to UNC93B1 gene, which was proved to be related to HF and encoded UNC93B1 protein regulating toll-like receptor signaling, and both of them significantly increased in HF patients in qRT-PCR validation; the top significant upregulated enriched GO terms and KEGG pathway analysis were regulation of lymphocyte activation (GO:0051249) and T cell receptor signaling pathway (hsa04660), respectively. The current findings support the fact that EAT lncRNAs are involved in the inflammatory response leading to the development of HF.

Comprehensive bioinformation analysis of the miRNA of PLCE1 knockdown in esophageal squamous cell carcinoma

Phospholipase C epsilon 1 (PLCE1) has been recognized as a novel susceptibility marker for esophageal squamous cell carcinoma (ESCC). The purpose of our study is to investigate its effect on the regulation of miRNA expression so as to translating the data into a novel strategy in control of ESCC. In this study, PLCE1 siRNA and vector-only plasmid were stably transfected into Eca109 and EC9706 cells and then subjected to miRNA array analysis, and quantitative real-time PCR was applied to validate miRNA array data. Then bioinformatic analyses, such as GO and pathway software, were conducted to obtain data on these differentially expressed miRNAs-targeted genes (DEGs) and clarify their function and pathway. The results showed that 36 miRNAs were found to be differentially expressed in PLCE1 siRNA-transfected cells compared with the control cells. In particular, 28 miRNAs were upregulated while 8 miRNAs were downregulated. Gene Ontology analysis showed that the function of the DEGs included cell cycle arrest, cell-matrix adhesion, apoptosis, etc. After this, the major pathways associated with the DEGs were regulation of actin cytoskeleton, TGF-beta signaling pathway, Notch signaling pathway and so on. Taken together, these results showed that the knockdown of PLCE1 may play a vital role in the control of ESCC. Further investigation will reveal and verify the function and pathway of the DEGs for the development of novel treatment strategy for the better control of ESCC.

miR-93-3p inhibition suppresses clear cell renal cell carcinoma proliferation, metastasis and invasion

miRNA dysregulation is associated with many human diseases, including cancer. This study explored the effects of miR-93-3p on clear cell renal cell carcinoma (ccRCC). We found that miR-93-3p is upregulated an average of 38-fold in 138 ccRCC specimens compared to matched normal kidney tissues, which correlated with poor patient outcome. miR-93-3p inhibition reduced ccRCC cell growth, invasion, and migration in vitro and in a mouse xenograft model. A search of the TargetScan, miRanda, and PicTar databases revealed that miR-93-3p is predicted to regulate pigment epithelium-derived factor (PEDF). A direct PEDF-miR-93-3p interaction was confirmed via dual-luciferase reporter assays. Like miR-93-3p inhibition, PEDF overexpression induced cell apoptosis and inhibited migration and invasion. Additionally, co-transfection with PEDF siRNA reversed the effects of miR-93-3p inhibition in ccRCC cells. Thus, miR-93-3p is a likely ccRCC oncogene that acts by regulating PEDF. These results suggest that miR-93-3p may predict ccRCC patient clinical outcome and serve as a novel anti-ccRCC therapeutic target.

microRNA-93 promotes cell proliferation via targeting of PTEN in Osteosarcoma cells

BACKGROUND

Aberrant microRNA (miRNA) expression plays an essential role in osteosarcoma (OS) pathogenesis. Recent studies have shown that dysregulation of miRNA expression is associated with increased tumorigenesis and poor prognosis in several types of cancers, including OS. The aim of this study was to investigate the relevant microRNAs involved in the development of OS.

METHODS

To explore possible oncogenic factors in OS, we used a microarray-based approach to profile changes in the expression of miRNAs and their target mRNAs in five OS cell lines and human mesenchymal stem cells (hMSCs). An miRNA, miR-93, was significantly up-regulated, whereas phosphatase and tensin homologue (PTEN) expression was significantly down-regulated in all tested OS cells, when compared with hMSCs.

RESULTS

When anti-miR-93 was transfected into OS cell lines, PTEN expression was greatly increased, suggesting that PTEN might be a target of miR-93 in ES cells. The expression of phosphorylated Akt protein, which is known to be inversely correlated with that of PTEN, was significantly down-regulated in anti-miR-93-transfected cells. Furthermore, transfection of anti-miR-93 inhibited the proliferation and cell cycle progression of ES cells. In addition, the down-regulation of miR-93 in these cells significantly suppressed tumor growth in vivo.

CONCLUSION

Ectopic expression of miR-93 decreased PTEN protein levels. Furthermore, miR-93 increased proliferation and decreased apoptosis in OS cells, whereas its silencing in these cells inhibited such carcinogenic processes. Taking these observations together, miR-93 can be seen to play a critical role in carcinogenesis through suppression of PTEN, and may serve as a therapeutic target for the treatment of OS.

MicroRNA Expression Profile of Neural Progenitor-Like Cells Derived from Rat Bone Marrow Mesenchymal Stem Cells under the Influence of IGF-1, bFGF and EGF

Insulin-like growth factor 1 (IGF-1) enhances cellular proliferation and reduces apoptosis during the early differentiation of bone marrow derived mesenchymal stem cells (BMSCs) into neural progenitor-like cells (NPCs) in the presence of epidermal growth factor (EGF) and basic fibroblast growth factor (bFGF). BMSCs were differentiated in three groups of growth factors: (A) EGF + bFGF, (B) EGF + bFGF + IGF-1, and (C) without growth factor. To unravel the molecular mechanisms of the NPCs derivation, microarray analysis using GeneChip^® miRNA arrays was performed. The profiles were compared among the groups. Annotated microRNA fingerprints (GSE60060) delineated 46 microRNAs temporally up-regulated or down-regulated compared to group C. The expressions of selected microRNAs were validated by real-time PCR. Among the 46 microRNAs, 30 were consistently expressed for minimum of two consecutive time intervals. In Group B, only miR-496 was up-regulated and 12 microRNAs, including the let-7 family, miR-1224, miR-125a-3p, miR-214, miR-22, miR-320, miR-708, and miR-93, were down-regulated. Bioinformatics analysis reveals that some of these microRNAs (miR-22, miR-214, miR-125a-3p, miR-320 and let-7 family) are associated with reduction of apoptosis. Here, we summarize the roles of key microRNAs associated with IGF-1 in the differentiation of BMSCs into NPCs. These findings may provide clues to further our understanding of the mechanisms and roles of microRNAs as key regulators of BMSC-derived NPC maintenance.