miR-128-3p serves as an oncogenic microRNA in osteosarcoma cells by downregulating ZC3H12D

Identification of lncRNA PCAT19 as potential novel biomarker for colorectal cancer

Long non-coding RNAs have been implicated in biological processes, and are dysregulated in types of cancer. Studies have shown that PCAT19 and CKMT2-AS1 lncRNAs promote tumor growth, invasion, and metastasis by regulating signaling pathways and modulating the gene expression. This study investigated the expression levels of lncRNAs PCAT19 and CKMT2-AS1 in colorectal tumors and normal tissues. First, Using GEPIA2 database, we compared the expression level of target lncRNAs between primary colon adenocarcinoma tumor and normal tissues. Then, the expression levels of lncRNAs PCAT19 and CKMT2-AS1 were detected in 35 colorectal tumors and paired adjacent tissues using qRT-PCR. A receiver operating characteristic (ROC) curve was used to evaluate the value of these lncRNAs as biomarkers. Statistical analysis based on GEPIA2 showed that both lncRNAs PCAT19 and CKMT2-AS1 were significantly decreased in colon adenocarcinoma compared to the normal group (P < 0.001). Experimental analysis showed that the expression level of lncRNA PCAT19 was decreased in colorectal tumors (p < 0.0001) compared to normal tissues. While the expression level of lncRNA CKMT2-AS1 did not change in tumor tissues, it decreased in non-metastatic tumors compared to normal tissues (p = 0.04). The significantly downregulation of lncRNA PCAT19 expression in both metastatic and non-metastatic colorectal tumors compared to normal tissue suggests that PCAT19 may play a role in the carcinogenesis and progression of colorectal cancer and may provide potential therapeutic targets for colorectal cancer. Based on the results of ROC curve analysis, lncRNA PCAT19 may also serves as a novel potential good biomarker in diagnosis colorectal cancer (AUC = 0.94, p < 0.0001) but no significant was found for lncRNA CKMT2-AS1 (p > 0.05).

miR-128-3p increases the radiosensitivity in nasopharyngeal carcinoma via regulating vascular endothelial growth factor C

PURPOSE

This study aims to investigate the role of miR-128-3p in the radiosensitivity of nasopharyngeal carcinoma (NPC) and its underlying mechanism.

METHODS

6-10B cells were transfected with miR-128-3p mimic, pcDNA-VEGFC, and the corresponding negative control. C666-1 cells were transfected with miR-128-3p inhibitor, sh-VEGFC, and the corresponding negative control. RT-qPCR was used to determine the miR-128-3p and VEGFC mRNA expression level. Dual-luciferase assay was used to investigate the relationship between miR-128-3p and VEGFC. The protein levels of VEGFC, H2AX, γ-H2AX, p-P50, p-P65, p-IκB, and the apoptosis markers Bcl-2, caspase3, caspase9, and Bax were detected by Western blot. The proliferation activity was detected by CCK-8, and cell DNA damage was assessed by comet assay. The apoptosis rate was detected by flow cytometry. The growth of NPC in vivo was observed in mice through xenotransplantation. TUNEL staining was used to detect cell apoptosis in tumor tissues.

RESULTS

miR-128-3p was targeted and was negatively regulated with VEGFC. Overexpression of miR-128-3p or knockdown VEGFC significantly inhibited the proliferation of 6-10B and C666-1 cells, induced DNA damage and apoptosis and promoted the radiosensitivity of cells. Knocking down miR-128-3p or up-regulated VEGFC promoted the proliferation of C666-1 and 6-10B cells, reduced cell DNA damage and apoptosis, and enhanced cell resistance to radiotherapy. Overexpression of miR-128-3p reversed the effect of VEGFC on 6-10B cells and inhibited P50/P65/IKB signal pathway. In vivo, experiments in mice confirmed that miR-128-3p significantly inhibited NPC proliferation and promoted DNA damage and apoptosis by targeting VEGFC.

CONCLUSION

The miR-128-3p pathway is a novel therapy target to overcome radiation resistance in NPC.

Transcriptional repression of lncRNA and miRNA subsets mediated by LRF during erythropoiesis

Non-coding RNA (ncRNA) species, mainly long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) have been currently imputed for lesser or greater involvement in human erythropoiesis. These RNA subsets operate within a complex circuit with other epigenetic components and transcription factors (TF) affecting chromatin remodeling during cell differentiation. Lymphoma/leukemia-related (LRF) TF exerts higher occupancy on DNA CpG rich sites and is implicated in several differentiation cell pathways and erythropoiesis among them and also directs the epigenetic regulation of hemoglobin transversion from fetal (HbF) to adult (HbA) form by intervening in the γ-globin gene repression. We intended to investigate LRF activity in the evolving landscape of cells' commitment to the erythroid lineage and specifically during HbF to HbA transversion, to qualify this TF as potential repressor of lncRNAs and miRNAs. Transgenic human erythroleukemia cells, overexpressing LRF and further induced to erythropoiesis, were subjected to expression analysis in high LRF occupancy genetic loci-producing lncRNAs. LRF abundance in genetic loci transcribing for studied lncRNAs was determined by ChIP-Seq data analysis. qPCRs were performed to examine lncRNA expression status. Differentially expressed miRNA pre- and post-erythropoiesis induction were assessed by next-generation sequencing (NGS), and their promoter regions were charted. Expression levels of lncRNAs were correlated with DNA methylation status of flanked CpG islands, and contingent co-regulation of hosted miRNAs was considered. LRF-binding sites were overrepresented in LRF overexpressing cell clones during erythropoiesis induction and exerted a significant suppressive effect towards lncRNAs and miRNA collections. Based on present data interpretation, LRF's multiplied binding capacity across genome is suggested to be transient and associated with higher levels of DNA methylation. KEY MESSAGES: During erythropoiesis, LRF displays extensive occupancy across genetic loci. LRF significantly represses subsets of lncRNAs and miRNAs during erythropoiesis. Promoter region CpG islands' methylation levels affect lncRNA expression. MiRNAs embedded within lncRNA loci show differential regulation of expression.

miRNAs as potential game-changers in bone diseases: Future medicinal and clinical uses

MicroRNAs (miRNAs), short, highly conserved non-coding RNA, influence gene expression by sequential mechanisms such as mRNA breakdown or translational repression. Many biological processes depend on these regulating substances, thus changes in their expression have an impact on the maintenance of cellular homeostasis and result in the emergence of a variety of diseases. Relevant studies have shown in recent years that miRNAs are involved in many stages of bone development and growth. Additionally, abnormal production of miRNA in bone tissues has been closely associated with the development of numerous bone disorders, such as osteonecrosis, bone cancer, and bone metastases. Many pathological processes, including bone loss, metastasis, the proliferation of osteosarcoma cells, and differentiation of osteoblasts and osteoclasts, are under the control of miRNAs. By bringing together the most up-to-date information on the clinical relevance of miRNAs in such diseases, this study hopes to further the study of the biological features of miRNAs in bone disorders and explore their potential as a therapeutic target.

The promising roles of exosomal microRNAs in osteosarcoma: A new insight into the clinical therapy

Osteosarcoma is the most common malignant bone sarcoma in children. Chemotherapy drugs resistance significantly hinders the overall survival of patients. Due to high biocompatibility and immunocompatibility, exosomes have been explored extensively. Multiple parent cells can actively secrete numerous exosomes, and the membrane structure of exosomes can protect miRNAs from degradation. Based on these characteristics, exosomal miRNAs play an important role in the occurrence, development, drug resistance. Therefore, in-depth exploration of exosome biogenesis and role of exosomal miRNAs will provide new strategies and targets for understanding the pathogenesis of osteosarcoma and overcoming chemotherapy drug resistance. Moreover, advancing evidences have showed that engineering modification could attribute stronger targeting to exosomes to deliver cargos to recipient cells more effectively. In this review, we focus on the mechanisms of exosomal miRNAs on the occurrence and development of osteosarcoma and the potential to function as tumor biomarkers for diagnosis and prognosis prediction. In addition, we also summarize recent advances in the clinical application values of engineering exosomes to provide novel ideas and directions for overcoming the chemotherapy resistance in osteosarcoma.

MiR-128-3p as blood based liquid biopsy biomarker in childhood acute lymphoblastic leukemia

BACKGROUND

Minimal residual disease (MRD) is one of the most valuable independent prognostic factors in acute lymphoblastic leukemia (ALL). Bone marrow (BM) aspiration, however, is an invasive process. Previous studies have shown that microRNAs (miR) and extracellular vesicle (EV)-related miRs show different expression profiles at the presence of malignant cells compared to healthy controls. In our previous project, we have reported that two miRs previously described to be overexpressed in blasts were significantly decreased over the first week of the therapy of patients with ALL in the platelet free plasma fraction (PFP) of peripheral blood samples (PB). The aim of the current study was to assess the relation between day 15 flow cytometry (FC) MRD and expression of miR-128-3p and miR-222-3p miRs in exosome-enriched fraction (EEF) of PFP to evaluate whether their expression in EEF correlates with day 15 FC MRD more precisely.

METHODS

PB was collected from 13 patients diagnosed with pediatric pre-B ALL at 4 time points. Expression of miR-128-3p and miR-222-3p was measured by qPCR in PFP and EEF.

RESULTS

Positive correlation was found between changes of miR-128-3p expression in EEF or PFP by day 8 of chemotherapy and day 15 FC MRD (r_EEF = 0.99, p_EEF = 1.13E-9 and r_PFP = 0.99, p_PFP = 4.75E-9, respectively). Furthermore, the decrease of miR-128-3p in EEF by day 15 of treatment also showed a positive correlation with day 15 FC MRD (r_EEF = 0.96; p_EEF = 4.89E-5).

CONCLUSION

Our results show that circulating miRs are potential biomarkers of ALL MRD, asmiR-128-3p level both in PFP and EEF predicts day 15 FC MRD. In addition, the assessment of the EEF gave a more promising result.

Long noncoding RNA KCNQ1OT1 inhibits osteoclast differentiation by regulating the miR-128-3p/NFAT5 axis

Noncoding RNAs play an important role in regulating osteoclast differentiation. We investigated whether and how potassium voltage-gated channel subfamily Q member 1 overlapping transcript 1 (KCNQ1OT1), a long noncoding RNA, regulates osteoclast differentiation. We found that the expression of KCNQ1OT1 was downregulated in osteoporotic bone tissue. Then transfection of KCNQ1OT1 overexpression vectors or small interfering RNAs showed that the proliferation, migration, and osteoclast differentiation of RAW 264.7 cells were inhibited by KCNQ1OT1 upregulation, while they were promoted by KCNQ1OT1 knockdown. Interestingly, we found and confirmed that miR-128-3p was a target of KCNQ1OT1 using online databases, dual luciferase reporter assays and quantitative real-time polymerase chain reaction, and that it inhibited the expression of miR-128-3p. Moreover, we confirmed that miR-128-3p directly targeted nuclear factor of activated T cell 5 (NFAT5), a protein that combines with osteoprotegerin and thus regulates osteoclastogenesis with the presence of the receptor activator of nuclear factor κB ligand. Furthermore, we demonstrated that both the knockdown of KCNQ1OT1 and the overexpression of miR-128-3p attenuate the expression of NFAT5, while upregulating the osteoclastogenesis markers c-Fos, NFATc1, and Ctsk. The results from overexpression of KCNQ1OT1 and the inhibition of miR-128-3p were contrary to the above. Finally, we found that the inhibition of osteoclast differentiation by KCNQ1OT1 overexpression could be rescued using a miR-128-3p mimic, while the enhancement of migration and osteoclast differentiation by si-NFAT5 could be reversed with a miR-128-3p inhibitor. These results suggested that KCNQ1OT1 regulates the osteoclast differentiation via the miR-128-3p/NFAT5 axis.

Long noncoding RNA BBOX1-AS1 promotes the progression of gastric cancer by regulating the miR-361-3p/Mucin 13 signaling axis

Gastric cancer (GC) places a heavy burden on global health, and the information on the molecular mechanism of the progression of GC is still inadequate. Long noncoding RNA (LncRNA) has been confirmed to be widely involved in regulating the progression of GC. Our aim in this study was to explore the role and potential regulatory mechanism of lncRNA BBOX1-AS1 in GC. The expression levels of BBOX1-AS1, miR-361-3p, and MUC13 in GC tissues and cells were evaluated using quantitative real-time polymerase chain reaction and western blotting. The silencer of BBOX1 antisense RNA 1 (BBOX1-AS1) and mucin 13 (MUC13), the mimics and inhibitor of miR-361-3p, and their negative controls were used to alter the expression of these genes. Luciferase reporter, pull-down, and RNA immunoprecipitation assays were performed to verify the correlation between miR-361-3p, BBOX1-AS1, and MUC13. GC cell proliferation, invasion, and apoptosis were detected by cell counting kit-8, transwell, and flow cytometry assays, respectively. An in vivo functional experiment was performed to assess the effect of BBOX1-AS1 on GC. The results showed that BBOX1-AS1 was significantly upregulated in GC tissues. Silencing of BBOX1-AS1 inhibited GC cell proliferation and invasion and inhibited tumor growth in vivo, whereas it promoted apoptosis. MiR-361-3p was significantly downregulated in GC and counteracted the inhibitory effects of BBOX1-AS1 on GC progression. MUC13, which is targeted by miR-361-3p, is significantly upregulated in GC. MUC13 silencing inhibited GC progression was aborgated by miR-361-3p inhibitor. Collectively, BBOX1-AS1 silencing inhibits GC progression by regulating the miR-361-3p/MUC13 axis, providing a potential therapeutic biomarker for GC.

Identification of lncRNA Signature of Tumor-Infiltrating T Lymphocytes With Potential Implications for Prognosis and Chemotherapy of Head and Neck Squamous Cell Carcinoma

Purpose: We systematically analyzed HNSCC-infiltrating T lymphocytes lncRNAs (HILTlncRNAs) to assess their predictive value for the survival outcome and immunotherapy response of patients with anti-programmed death-1 (PD-1) therapy and to evaluate their predictive power to chemotherapeutic agents. Methods: HNSCC transcriptome and clinical information was obtained from The Cancer Genome Atlas (TCGA) database. Immunocell microarray data were obtained from the Gene Expression Omnibus (GEO) database. T-cell-specific lncRNAs were identified by differential expression analysis. Prognostic paired HILTlncRNAs (PHILTlncRNAs) were filtered and modeled by univariate cox, lasso and multivariate cox regression analysis. To construct lncRNA-miRNA-mRNA competitive endogenous RNA (ceRNA) regulatory networks, differentially expressed mRNAs in HNSCC patients were incorporated, microRNAs and differentially expressed mRNAs interacting with T-cell-specific lncRNAs were filtered out based on miRcode, miRDB, miRTarBase, and TargetScan databases. Results: 75 T-cell-specific lncRNAs and 9 prognostic PHILTlncRNAs were identified. Low-risk HNSCC patients had a better prognosis and significant immune cell infiltration, driving the immune response. Differential expression of RNA-binding proteins (RBPs), PD-1 and programmed cell death 1 ligand 1 (PD-L1) was demonstrated in the high and low risk groups of HNSCC patients. In the high risk group, high expression of PD-1 improved patient prognosis, whereas the opposite was observed in the low-risk group. The promoter methylation levels of two RBPs (DNMT1 and ZC3H12D) were decreased in HNSCC patients compared with normal samples, their expression levels were positively correlated with PD-1 and PD-L1 levels and T-cell infiltration. Finally, we screened the sensitivity of HNSCC patients to chemotherapeutic agents and found it differed between high and low risk groups. Conclusion: HILTlncRNAs provided a theoretical basis for immune targeted therapy and drug development.

Identification of a ZC3H12D-regulated competing endogenous RNA network for prognosis of lung adenocarcinoma at single-cell level

Background

To identify hub genes from the competing endogenous RNA (ceRNA) network of lung adenocarcinoma (LUAD) and to explore their potential functions on prognosis of patients from a single-cell perspective.

Methods

We performed RNA-sequencing of LUAD to construct ceRNA regulatory network, integrating with public databases to identify the vital pathways related to patients’ prognosis and to reveal the expression level of hub genes under different conditions, the functional enrichment of co-expressed genes and their potential immune-related mechanisms.

Results

ZC3H12D-hsa-miR-4443-ENST00000630242 axis was found to be related with LUAD. Lower ZC3H12D expression was significantly associated with shorter overall survival (OS) of patients (HR = 2.007, P < 0.05), and its expression was higher in early-stage patients, including T1 (P < 0.05) and N0 (P < 0.05). Additionally, ZC3H12D expression was higher in immune cells displayed by single-cell RNA-sequencing data, especially in Treg cells of lung cancer and CD8 T cells, B cells and CD4 T cells of LUAD. The functional enrichment analysis showed that the co-expressed genes mainly played a role in lymphocyte activation and cytokine-cytokine receptor interaction. In addition, ZC3H12D was associated with multiple immune cells and immune molecules, including immune checkpoints CTLA4, CD96 and TIGIT.

Conclusion

ZC3H12D-hsa-miR-4443-ENST00000630242 ceRNA network was identified in LUAD. ZC3H12D could affect prognosis of patients by regulating mRNA, miRNA, lncRNA, immune cells and immune molecules. Therefore, it may serve as a vital predictive marker and could be regarded as a potential therapeutic target for LUAD in the future.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12885-021-08992-1.

Analysis of microRNA expression in CD133 positive cancer stem‑like cells of human osteosarcoma cell line MG-63

Osteosarcoma (OS) is a primary malignant tumor of bone occurring in young adults. OS stem cells (OSCs) play an important role in the occurrence, growth, metastasis, drug resistance and recurrence of OS. CD133 is an integral membrane glycoprotein, which has been identified as an OSC marker. However, the mechanisms of metastasis, chemoresistance, and progression in CD133(+) OSCs need to be further explored. In this study, we aim to explore differences in miRNA levels between CD133(+) and CD133(-) cells from the MG-63 cell line. We found 20 differentially expressed miRNAs (DEmiRNAs) (16 upregulated and 4 downregulated) in CD133(+) cells compared with CD133(-) cells. Hsa-miR-4485-3p, hsa-miR-4284 and hsa-miR-3656 were the top three upregulated DEmiRNAs, while hsa-miR-487b-3p, hsa-miR-493-5p and hsa-miR-431-5p were the top three downregulated DEmiRNAs. In addition, RT-PCR analysis confirmed that the expression levels of hsa-miR-4284, hsa-miR-4485-3p and hsa-miR-3656 were significantly increased, while the expression levels of hsa-miR-487b-3p, hsa-miR-493-5p, and hsa-miR-431-5p were significantly decreased in CD133(+) cells compared with CD133(-) cells. Moreover, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that predicted or validated target genes for all 20 DEmiRNAs or the selected 6 DEmiRNAs participated in the "PI3K-Akt signaling pathway," "Wnt signaling pathway," "Rap1 signaling pathway," "Cell cycle" and "MAPK signaling pathway". Among the selected six DEmiRNAs, miR-4284 was especially interesting. MiR-4284 knockdown significantly reduced the sphere forming capacity of CD133(+) OS cells. The number of invasive CD133(+) OS cells was markedly decreased after miR-4284 knockdown. In addition, miR-4284 knockdown increased the p-β-catenin levels in CD133(+) OS cells. In conclusion, RNA-seq analysis revealed DEmiRNAs between CD133(+) and CD133(-) cells. MiRNAs might play significant roles in the function of OSCs and could serve as targets for OS treatment. MiR-4284 prompted the self-renewal and invasion of OSCs. The function of miR-4284 might be associated with the Wnt signaling pathway.