Inhibition of miR-1247 on cell proliferation and invasion in bladder cancer through its downstream target of RAB36

Identification of a glycolysis-related miRNA Signature for Predicting Breast cancer Survival

Breast cancer (BC) is a common type of cancer and has a poor prognosis. In this study, we collected the mRNA and miRNA expression profiles of BC patients were obtained from The Cancer Genome Atlas (TCGA) to explore a novel prognostic strategy for BC patients using bioinformatics tools. We found that six glycolysis-related miRNAs (GRmiRs, including hsa-mir-1247, hsa-mir148b, hsa-mir-133a-2, has-mir-1307, hsa-mir-195 and hsa-mir-1258) were correlated with prognosis of BC samples. The risk score model was established based on 6 prognosis-associated GRmiRs. The outcome of high risk group was significantly poorer. Cox regression analysis showed that risk score was an independent prognostic factor. Differentially expressed genes identified between high and low risk groups were mainly enriched in inflammation and immune-related signaling pathways. The proportion of infiltration of 12 kinds of immune cells in high and low risk groups were significantly different. Risk score was closely associated with many immune indexes. Multiple DEGRGs and miRNAs were associated with drugs. In conclusion, glycolysis-related miRNA signature effectively predicts BC prognosis.

Genome-wide Cas9-mediated screening of essential non-coding regulatory elements via libraries of paired single-guide RNAs

The functions of non-coding regulatory elements (NCREs), which constitute a major fraction of the human genome, have not been systematically studied. Here we report a method involving libraries of paired single-guide RNAs targeting both ends of an NCRE as a screening system for the Cas9-mediated deletion of thousands of NCREs genome-wide to study their functions in distinct biological contexts. By using K562 and 293T cell lines and human embryonic stem cells, we show that NCREs can have redundant functions, and that many ultra-conserved elements have silencer activity and play essential roles in cell growth and in cellular responses to drugs (notably, the ultra-conserved element PAX6_Tarzan may be critical for heart development, as removing it from human embryonic stem cells led to defects in cardiomyocyte differentiation). The high-throughput screen, which is compatible with single-cell sequencing, may allow for the identification of druggable NCREs.

Prognostic impact of MICALL1 and associates with immune infiltration in liver hepatocellular carcinoma patients

BACKGROUND

Liver hepatocellular carcinoma (LIHC) is one of the most malignancy over the world. Previous studies have proven that Molecules Interacting with CasL-Like 1 (MICALL1) participated in cellular trafficking cascades, while there has no study to explore the function and carcinogenic mechanism MICALL1 in LIHC.

METHODS

We aimed to investigate the relationship between MICALL1 mRNA expression and LIHC using TCGA database. The expression of MICALL1 protein in clinic samples were examined by UALCAN database. Kaplan-Meier method was used for survival analysis. Logistic regression and Cox regression were performed to evaluate the prognostic significance of MICALL1. The MICALL1-binding protein were built by the STRING tool. Enrichment analysis by GO, KEGG and GSEA was used to explore possible function of MICALL1. The ssGSEA method was used to investigate the association between MICALL1 expression and the immune infiltration level in LIHC.

RESULTS

The expression and prognostic value of different MICAL family members in LIHC were evaluated. The expression of MICALL1 was significantly increased at both the transcript and protein levels in LIHC tissues. Further, the LIHC patients with high MICALL1 levels showed a worse OS, DSS and PFI. Some clinicopathologic features were identified to be related to MICALL1 expression in LIHC included clinical T stage, pathologic stage, histologic grade and AFP concentration. Univariate and multivariate survival analysis showed that MICALL1 was an independent prognostic marker for OS and DSS. Further enrichment analysis revealed that the K-RAS, TNFα/NF-κB and inflammatory response were significantly enriched in the high MICALL1 expression group. Immune infiltration analysis showed that high MICALL1 expression was correlated with infiltration level of macrophage cells, Th2 cells and some other immune cell types, including TFH.

CONCLUSIONS

MICALL1 expression was significantly associated with immune cell infiltration and may regarded as a promising prognostic biomarker for LIHC patients.

Decoding pathogenesis factors involved in the progression of ATLL or HAM/TSP after infection by HTLV-1 through a systems virology study

Background

Human T-cell Leukemia Virus type-1 (HTLV-1) is a retrovirus that causes two diseases including Adult T-cell Leukemia/Lymphoma (ATLL cancer) and HTLV-1 Associated Myelopathy/Tropical Spastic Paraparesis (HAM/TSP, a neurodegenerative disease) after a long latency period as an asymptomatic carrier (AC). There are no obvious explanations about how each of the mentioned diseases develops in the AC carriers. Finding the discriminative molecular factors and pathways may clarify the destiny of the infection.

Methods

To shed light on the involved molecular players and activated pathways in each state, differentially co-expressed modules (DiffCoEx) algorithm was employed to identify the highly correlated genes which were co-expressed differently between normal and ACs, ACs and ATLL, as well as ACs and HAM/TSP samples. Through differential pathway analysis, the dysregulated pathways and the specific disease-genes-pathways were figured out. Moreover, the common genes between the member of DiffCoEx and differentially expressed genes were found and the specific genes in ATLL and HAM/TSP were introduced as possible biomarkers.

Results

The dysregulated genes in the ATLL were mostly enriched in immune and cancer-related pathways while the ones in the HAM/TSP were enriched in immune, inflammation, and neurological pathways. The differential pathway analysis clarified the differences between the gene players in the common activated pathways. Eventually, the final analysis revealed the involvement of specific dysregulated genes including KIRREL2, RAB36, and KANK1 in HAM/TSP as well as LTB4R2, HCN4, FZD9, GRIK5, CREB3L4, TACR2, FRMD1, LHB, FGF3, TEAD3, GRIN2D, GNRH2, PRLH, GPR156, and CRHR2 in ATLL.

Conclusion

The identified potential prognostic biomarkers and therapeutic targets are proposed as the most important platers in developing ATLL or HAM/TSP. Moreover, the proposed signaling network clarifies the differences between the functional players in the activated pathways in ACs, ATLL, and HAM/TSP.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12985-021-01643-8.

Bioinformatics analysis of long non-coding RNAs involved in nerve regeneration following sciatic nerve injury

Little is known about the role of epigenetic modification in axon regeneration following peripheral nerve injury. The purpose of the present study was to investigate the role of long non-coding RNAs (lncRNAs) in the regulation of axon regeneration. We used bioinformatics to perform microarray analysis and screened total 476 lncRNAs and 129 microRNAs (miRNAs) of differentially expressed genes after sciatic nerve injury in mice. lncRNA-GM4208 and lncRNA-GM30085 were examined, and the changes in lncRNA expression in the L4–L6 dorsal root ganglia (DRG) following sciatic nerve crush injury were analyzed by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). The expression of lncRNAs in the DRG changed, indicating that they might be related to nerve regeneration in the DRG following peripheral nerve injury.

MicroRNAs and target molecules in bladder cancer

Bladder cancer (BC) is considered as one of the most common malignant tumors in humans with complex pathogenesis including gene expression variation, protein degradation, and changes in signaling pathways. Many studies on involved miRNAs in BC have demonstrated that they could be used as potential biomarkers in the prognosis, response to treatment, and screening before the cancerous phenotype onset. MicroRNAs (miRNAs) regulate many cellular processes through their different effects on special targets along with modifying signaling pathways, apoptosis, cell growth, and differentiation. The diverse expression of miRNAs in cancerous tissues could mediate procedures leading to the oncogenic or suppressor behavior of certain genes in cancer cells. Since a specific miRNA may have multiple targets, an mRNA could also be regulated by multiple miRNAs which further demonstrates the actual role of miRNAs in cancer. In addition, miRNAs can be utilized as biomarkers in some cancers that cannot be screened in the early stages. Hence, finding blood, urine, or tissue miRNA biomarkers by novel or routine gene expression method could be an essential step in the prognosis and control of cancer. In the present review, we have thoroughly evaluated the recent findings on different miRNAs in BC which can provide comprehensive information on better understanding the role of diverse miRNAs and better decision making regarding the new approaches in the diagnosis, prognosis, prevention, and treatment of BC.

Cancer-driving mutations and variants of components of the membrane trafficking core machinery

The core machinery for vesicular membrane trafficking broadly comprises of coat proteins, RABs, tethering complexes and SNAREs. As cellular membrane traffic modulates key processes of mitogenic signaling, cell migration, cell death and autophagy, its dysregulation could potentially results in increased cell proliferation and survival, or enhanced migration and invasion. Changes in the levels of some components of the core machinery of vesicular membrane trafficking, likely due to gene amplifications and/or alterations in epigenetic factors (such as DNA methylation and micro RNA) have been extensively associated with human cancers. Here, we provide an overview of association of membrane trafficking with cancer, with a focus on mutations and variants of coat proteins, RABs, tethering complex components and SNAREs that have been uncovered in human cancer cells/tissues. The major cellular and molecular cancer-driving or suppression mechanisms associated with these components of the core membrane trafficking machinery shall be discussed.

OSlgg: An Online Prognostic Biomarker Analysis Tool for Low-Grade Glioma

Glioma is the most frequent primary brain tumor that causes high mortality and morbidity with poor prognosis. There are four grades of gliomas, I to IV, among which grade II and III are low-grade glioma (LGG). Although less aggressive, LGG almost universally progresses to high-grade glioma and eventual causes death if lacking of intervention. Current LGG treatment mainly depends on surgical resection followed by radiotherapy and chemotherapy, but the survival rates of LGG patients are low. Therefore, it is necessary to use prognostic biomarkers to classify patients into subgroups with different risks and guide clinical managements. Using gene expression profiling and long-term follow-up data, we established an Online consensus Survival analysis tool for LGG named OSlgg. OSlgg is comprised of 720 LGG cases from two independent cohorts. To evaluate the prognostic potency of genes, OSlgg employs the Kaplan-Meier plot with hazard ratio and p value to assess the prognostic significance of genes of interest. The reliability of OSlgg was verified by analyzing 86 previously published prognostic biomarkers of LGG. Using OSlgg, we discovered two novel potential prognostic biomarkers (CD302 and FABP5) of LGG, and patients with the elevated expression of either CD302 or FABP5 present the unfavorable survival outcome. These two genes may be novel risk predictors for LGG patients after further validation. OSlgg is public and free to the users at http://bioinfo.henu.edu.cn/LGG/LGGList.jsp.

A potential prognostic model based on miRNA expression profile in The Cancer Genome Atlas for bladder cancer patients

Background

This study aimed to construct prognostic model by screening prognostic miRNA signature of bladder cancer.

Methods

The miRNA expression profile data of bladder cancer (BC) in The Cancer Genome Atlas (TCGA) were obtained and randomly divided into the training set and the validation set. Differentially expressed miRNAs (DEMs) between BC and normal control samples in the training set were firstly identified, and DEMs related to prognosis were screened by Cox Regression analysis. Then, the MiR Score system was constructed using X-Tile based cutoff points and verified in the validation set. The prognostic clinical factors are selected out by univariate and multivariate Cox Regression analysis. Finally, the mRNAs related to prognosis were screened and the biological pathway analysis was carried out.

Results

We identified the 7-miRNA signature was significantly associated with the patient’s Overall Survival (OS). A prognostic model was constructed based on the prognostic 7-miRNA signature, and possessed a relative satisfying predicted ability both in the training set and validation set. In addition, univariate and multivariate Cox Regression analysis showed that age, lymphovascular invasion and MiR Score were considered as independent prognostic factors in BC patients. Furthermore, based on MiR Score prognostic model, several differentially expressed genes (DEGs), such as WISP3 and UNC5C, as well as their related biological pathway(s), including cell–cell adhesion and neuroactive ligand-receptor interaction, were considered to be related to BC prognosis.

Conclusion

The prognostic model which was constructed based on the prognostic 7-miRNA signature presented a high predictive ability for BC.

MicroRNA-1298-5p inhibits cell proliferation and the invasiveness of bladder cancer cells via down-regulation of connexin 43

MicroRNA (miR)-1298 is widely down-regulated in a variety of malignant tumors, which facilitates cell proliferation, invasiveness, and migration. However, the specific biological function of miR-1298 in bladder cancer (BC) is still unknown. Connexin 43 (Cx43) is often up-regulated in tumors. Identifying miRNAs that target Cx43 in the setting of BC will help to develop Cx43-based therapies for BC. In this study, the results demonstrated that the expression levels of miR-1298 and Cx43 were significantly down-regulated and up-regulated, respectively, in BC tissues. Overexpression of miR-1298 inhibited cell proliferation, migration, and invasiveness in two BC cell lines as determined using MTT assays, cell cycle assays, colony formation assays, Transwell assays, gelatin zymography, and Western blot. In addition, we found that miR-1298 decreased Cx43 expression by directly targeting the 3'-UTR. Further, we observed that the promotion of BC cell proliferation, migration, and invasiveness from Cx43 on could be partially attenuated by overexpressing miR-1298. Moreover, the protein expression of p-ERK was ameliorated after transfection with overexpressed-miR-1298. Knockdown of Cx43 reversed the promotion of cell migration and invasiveness due to decreased expression of miR-1298. All of the data from our study indicate that miR-1298 could be a diagnostic marker of BC and a potential therapeutic agent via inhibiting Cx43.

miR-1247-3p mediates apoptosis of cerebral neurons by targeting caspase-2 in stroke

Brain stroke is one of the leading causes of death worldwide. We explored a potential stroke-related role for a newly found microRNA, miR-1247-3p, and one of its target genes, caspase-2, predicted by TargetScanVert. In the present study, we found that miR-1247-3p was downregulated during ischemia/reperfusion (I/R) and that LV-miR-1247-3p overexpression attenuated brain impairment induced by I/R. Similar results were observed in neuro2a (N2a) cells treated with oxygen-glucose deprivation/reoxygenation (OGD/R). Caspase-2 was upregulated in the I/R and OGD/R model, while Z-VDVAD-FMK - the inhibitor of caspase-2-inhibited apoptosis of N2a cells induced by OGD/R. An miR-1247-3p mimic inhibited caspase-2 expression and attenuated apoptosis of N2a cells induced by OGD/R. Myocardin-related transcription factor-A (MRTF-A) overexpression upregulated miR-1247 and mature miR-1247-3p levels and attenuated apoptosis induced by OGD/R, whereas its anti-apoptotic function could be blocked by a miR-1247-3p inhibitor. Hence, we conclude that miR-1247-3p may protect cells during brain stroke. This study offers insights for the development of effective therapeutics for promoting the survival of cerebral neurons during brain I/R injury.

The relationship between microRNAs and Rab family GTPases in human cancers

microRNAs (miRNAs), as a group of noncoding RNAs, posttranscriptionally control gene expression by binding to 3'-untranslated region (3'-UTR). Ras-associated binding (Rab) proteins function as molecular switches for regulating vesicular transport, which mainly have oncogenic roles in cancer development and preventing the efficacy of chemotherapies. Increased evidence supported that miRNAs/Rabs interaction have been determined as potential therapeutics for cancer therapy. Nevertheless, instability and cross-targeting of miRNAs are main limitations of using miRNA-based therapeutic. The mutual interplay between Rabs and miRNAs has been poorly understood. In the present review, we focused on the essence and activity of these molecules in cancer pathogenesis. Also, numerous hindrances and potential methods in the expansion of miRNA as an anticancer therapeutics are mentioned.