Loss of miR-146b-5p promotes T cell acute lymphoblastic leukemia migration and invasion via the IL-17A pathway

The potential role of miRNAs and regulation of their expression in the development of mare endometrial fibrosis

Mare endometrial fibrosis (endometrosis), is one of the main causes of equine infertility. Despite the high prevalence, both ethology, pathogenesis and the nature of its progression remain poorly understood. Recent studies have shown that microRNAs (miRNAs) are important regulators in multiple cellular processes and functions under physiological and pathological circumstances. In this article, we reported changes in miRNA expression at different stages of endometrosis and the effect of transforming growth factor (TGF)-β1 on the expression of the most dysregulated miRNAs. We identified 1, 26, and 5 differentially expressed miRNAs (DEmiRs), in categories IIA (mild fibrosis), IIB (moderate fibrosis), and III (severe fibrosis) groups compared to category I (no fibrosis) endometria group, respectively (Padjusted < 0.05, log2FC ≥ 1.0/log2FC ≤  - 1.0). This study indicated the potential involvement of miRNAs in the regulation of the process associated to the development and progression of endometrosis. The functional enrichment analysis revealed, that DEmiRs target genes involved in the mitogen-activated protein kinases, Hippo, and phosphoinositide-3-kinase (PI3K)-Akt signalling pathways, focal adhesion, and extracellular matrix-receptor interaction. Moreover, we demonstrated that the most potent profibrotic cytokine-TGF-β1-downregulated novel-eca-miR-42 (P < 0.05) expression in fibroblasts derived from endometria at early-stage endometrosis (category IIA).

Immune-epigenetic crosstalk in haematological malignancies

Haematological malignancies comprise a diverse set of lymphoid and myeloid neoplasms which can arise during any stage of haematopoiesis in the bone marrow. Accumulating evidence suggests that chronic inflammation generated by inflammatory cytokines secreted by tumour and the tumour-associated cells within the bone marrow microenvironment initiates signalling pathways in malignant cells, resulting in activation of master transcription factors including Smads, STAT3, and NF-κB which confer cancer stem cell phenotypes and drive disease progression. Deciphering the molecular mechanisms for how immune cells interact with malignant cells to induce such epigenetic modifications, specifically DNA methylation, histone modification, expression of miRNAs and lnRNAs to perturbate haematopoiesis could provide new avenues for developing novel targeted therapies for haematological malignancies. Here, the complex positive and negative feedback loops involved in inflammatory cytokine-induced cancer stem cell generation and drug resistance are reviewed to highlight the clinical importance of immune-epigenetic crosstalk in haematological malignancies.

Identification of an immune-related 6-lncRNA panel with a good performance for prognostic prediction in hepatocellular carcinoma by integrated bioinformatics analysis

Hepatocellular carcinoma (HCC) is one of the most malignant tumors with a poor prognosis. The long non-coding RNA (lncRNA) has been found to have great potential as a prognostic biomarker or therapeutic target for cancer patients. However, the prognostic value and tumor immune infiltration of lncRNAs in HCC has yet to be fully elucidated. To identify prognostic biomarkers of lncRNA in HCC by integrated bioinformatics analysis and explore their functions and relationship with tumor immune infiltration. The prognostic risk assessment model for HCC was constructed by comprehensively using univariate/multivariate Cox regression analysis, Kaplan-Meier survival analysis, and the least absolute shrinkage and selection operator regression analysis. Subsequently, the accuracy, independence, and sensitivity of our model were evaluated, and a nomogram for individual prediction in the clinic was constructed. Tumor immune microenvironment (TIME), immune checkpoints, and human leukocyte antigen alleles were compared in high- and low-risk patients. Finally, the functions of our lncRNA signature were examined using Gene Ontology, Kyoto Encyclopedia of Genes and Genomes enrichment analysis, and gene set enrichment analysis. A 6-lncRNA panel of HCC consisting of RHPN1-AS1, LINC01224, CTD-2510F5.4, RP1-228H13.5, LINC01011, and RP11-324I22.4 was eventually identified, and show good performance in predicting the survivals of patients with HCC and distinguishing the immunomodulation of TIME of high- and low-risk patients. Functional analysis also suggested that this 6-lncRNA panel may play an essential role in promoting tumor progression and immune regulation of TIME. In this study, 6 potential lncRNAs were identified as the prognostic biomarkers in HCC, and the regulatory mechanisms involved in HCC were initially explored.

GRN is a prognostic biomarker and correlated with immune infiltration in glioma: A study based on TCGA data

Background

Among primary brain tumors, gliomas are associated with a poor prognosis and a median survival that varies depending on the tumor grade and subtype. As the most malignant form of glioma, glioblastoma (GBM) constitutes a significant health concern. Alteration in granulin(GRN) has been proved to be accountable for several diseases. However, the relationship between GRN and GBM remains unclear. We evaluated the role of GRN in GBM through The Cancer Genome Atlas (TCGA) database

Methods

First, we assessed the relationship between GRN and GBM through the GEPIA database. Next, the relationship between GRN and GBM prognosis was analyzed by logistic regression and multivariate cox methods. Using CIBERSORT and the GEPIA correlation module, we also investigated the link between GRN and immune infiltrates in cancer. Using the TCGA data, a gene set enrichment analysis (GSEA) was performed. We also employed Tumor Immune Estimation Resource (TIMER) to examine the data set of GRN expression and immune infiltration level in GBM and investigate the cumulative survival in GBM. We also validated tissues from GBM patients by Western blotting, RT-qPCR, and immunohistochemistry.

Results

Increased GRN expression was shown to have a significant relationship to tumor grade in a univariate study utilizing logistic regression. Furthermore, multivariate analysis disclosed that GRN expression down-regulation is an independent predictive factor for a favorable outcome. GRN expression level positively correlates with the number of CD4+ T cells, neutrophils, macrophages, and dendritic cells (DCs) that infiltrate a GBM. The GSEA also found that the high GRN expression phenotype pathway was enriched for genes involved in immune response molecular mediator production, lymphocyte-mediated immunity, cytokine-mediated signaling pathway, leukocyte proliferation, cell chemotaxis, and CD4+ alpha beta T cell activation. Differentially enriched pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG) include lysosome, apoptosis, primary immunodeficiency, chemokine signaling pathway, natural killer cell-mediated cytotoxicity, and B cell receptor signaling pathway. Validated result showed that GRN was upregulated in GBM tissues. These results suggested that GRN was a potential indicator for the status of GBM.

Conclusion

GRN is a prognostic biomarker and correlated with immune infiltrates in GBM.

Implication of microRNAs in Carcinogenesis with Emphasis on Hematological Malignancies and Clinical Translation

MicroRNAs (miRNAs) are evolutionarily conserved small non-coding RNAs, that are involved in the multistep process of carcinogenesis, contributing to all established hallmarks of cancer. In this review, implications of miRNAs in hematological malignancies and their clinical utilization fields are discussed. As components of the complex regulatory network of gene expression, influenced by the tissue microenvironment and epigenetic modifiers, miRNAs are “micromanagers” of all physiological processes including the regulation of hematopoiesis and metabolic pathways. Dysregulated miRNA expression levels contribute to both the initiation and progression of acute leukemias, the metabolic reprogramming of malignantly transformed hematopoietic precursors, and to the development of chemoresistance. Since they are highly stable and can be easily quantified in body fluids and tissue specimens, miRNAs are promising biomarkers for the early detection of hematological malignancies. Besides novel opportunities for differential diagnosis, miRNAs can contribute to advanced chemoresistance prediction and prognostic stratification of acute leukemias. Synthetic oligonucleotides and delivery vehicles aim the therapeutic modulation of miRNA expression levels. However, major challenges such as efficient delivery to specific locations, differences of miRNA expression patterns between pediatric and adult hematological malignancies, and potential side effects of miRNA-based therapies should be considered.

Characterization of the microRNA transcriptomes and proteomics of cochlear tissue-derived small extracellular vesicles from mice of different ages after birth

The cochlea is an important sensory organ for both balance and sound perception, and the formation of the cochlea is a complex developmental process. The development of the mouse cochlea begins on embryonic day (E)9 and continues until postnatal day (P)21 when the hearing system is considered mature. Small extracellular vesicles (sEVs), with a diameter ranging from 30 to 200 nm, have been considered a significant medium for information communication in both physiological and pathological processes. However, there are no studies exploring the role of sEVs in the development of the cochlea. Here, we isolated tissue-derived sEVs from the cochleae of FVB mice at P3, P7, P14, and P21 by ultracentrifugation. These sEVs were first characterized by transmission electron microscopy, nanoparticle tracking analysis, and western blotting. Next, we used small RNA-seq and mass spectrometry to characterize the microRNA transcriptomes and proteomes of cochlear sEVs from mice at different ages. Many microRNAs and proteins were discovered to be related to inner ear development, anatomical structure development, and auditory nervous system development. These results all suggest that sEVs exist in the cochlea and are likely to be essential for the normal development of the auditory system. Our findings provide many sEV microRNA and protein targets for future studies of the roles of cochlear sEVs.

Tumor Endothelial Marker TEM7 is a Prognostic Biomarker and Correlating with Immune Infiltrates in Gastric Cancer

Introduction

Tumor endothelial marker 7 (TEM7) is included in the endothelial cells of tumors as a greatly expressed protein. In previous studies, it has been confirmed that TEM7 is highly expressed in gastric cancer (GC) cells and related to tumor invasion and migration. However, the relationship between TEM7 gene expressions, prognostic and tumor-infiltrating lymphocyte in GC is still unclear.

Methods

We obtained the expression of TEM7 in GC tissues using Oncomine and TIMER databases and validated it using qRT-PCR. The effect of TEM7 on survival in patients with GC was explored through the Kaplan–Meier Plotter database. Univariate and multifactorial analyses of the TCGA (The Cancer Genome Atlas) database were performed to explore the association of TEM7 expression with clinical traits. TIMER and GEPIA databases were used to analyze the relationship between TEM7 expression and immune infiltration. GSEA pathway enrichment in Kyoto Encyclopedia of Genes and Genomes (KEGG) exposed possible ways.

Results

An expression level of TEM7 was significantly increased in gastric cancer tissues and related with unfavorable survival in GC. Univariate analysis of TCGA (The Cancer Genome Atlas) database indicated that excessive level of TEM7 expression was linked with age, tumor grade and TMN classification, and multivariate analysis indicated that age and level of TEM7 expression were independent prognostic factors for a poor prognosis. The level of expression of TEM7 was positively related to tumor-infiltrating CD4+ and CD8+ T cells, neutrophils, macrophages, and dendritic cells other than B cells in GC. In the end, GSEA pathway enrichment exposed possible ways related to immunity.

Discussion

Our study indicates that TEM7 is a prognostic biomarker that makes the decision that the progression of GC and is connected with tumor immune infiltrates in GC.

One Omics Approach Does Not Rule Them All: The Metabolome and the Epigenome Join Forces in Haematological Malignancies

Aberrant DNA methylation, dysregulation of chromatin-modifying enzymes, and microRNAs (miRNAs) play a crucial role in haematological malignancies. These epimutations, with an impact on chromatin accessibility and transcriptional output, are often associated with genomic instability and the emergence of drug resistance, disease progression, and poor survival. In order to exert their functions, epigenetic enzymes utilize cellular metabolites as co-factors and are highly dependent on their availability. By affecting the expression of metabolic enzymes, epigenetic modifiers may aid the generation of metabolite signatures that could be utilized as targets and biomarkers in cancer. This interdependency remains often neglected and poorly represented in studies, despite well-established methods to study the cellular metabolome. This review critically summarizes the current knowledge in the field to provide an integral picture of the interplay between epigenomic alterations and the cellular metabolome in haematological malignancies. Our recent findings defining a distinct metabolic signature upon response to enhancer of zeste homolog 2 (EZH2) inhibition in multiple myeloma (MM) highlight how a shift of preferred metabolic pathways may potentiate novel treatments. The suggested link between the epigenome and the metabolome in haematopoietic tumours holds promise for the use of metabolic signatures as possible biomarkers of response to treatment.

MicroRNA as a Prognostic and Diagnostic Marker in T-Cell Acute Lymphoblastic Leukemia

T cell acute lymphoblastic leukemia (T-ALL) is a biologically and genetically heterogeneous disease with a poor prognosis overall and several subtypes. The neoplastic transformation takes place through the accumulation of numerous genetic and epigenetic abnormalities. There are only a few prognostic factors in comparison to B cell precursor acute lymphoblastic leukemia, which is characterized by a lower variability and more homogeneous course. The microarray and next-generation sequencing (NGS) technologies exploring the coding and non-coding part of the genome allow us to reveal the complexity of the genomic and transcriptomic background of T-ALL. miRNAs are a class of non-coding RNAs that are involved in the regulation of cellular functions: cell proliferations, apoptosis, migrations, and many other processes. No miRNA has become a significant prognostic and diagnostic factor in T-ALL to date; therefore, this topic of investigation is extremely important, and T-ALL is the subject of intensive research among scientists. The altered expression of many genes in T-ALL might also be caused by wide miRNA dysregulation. The following review focuses on summarizing and characterizing the microRNAs of pediatric patients with T-ALL diagnosis and their potential future use as predictive factors.

DNA methylation-mediated silencing of microRNA-204 enhances T cell acute lymphoblastic leukemia by up-regulating MMP-2 and MMP-9 via NF-κB

T cell acute lymphoblastic leukaemia (T‐ALL) is a highly aggressive haematological cancer of the bone marrow. The abnormal expression of microRNAs (miRNAs) is reportedly involved in T‐ALL development and progression. Thus, we aimed to decipher the involvement of miR‐204 silencing mediated by DNA methylation in the occurrence of T cell acute lymphoblastic leukaemia (T‐ALL). miR‐204 expression was determined in bone marrow and peripheral blood samples from T‐ALL patients by real‐time quantitative PCR (RT‐qPCR) with its effect on cell proliferation evaluated by functional assays. In addition, bisulphite sequencing PCR was employed to detect the DNA methylation level of the miR‐204 promoter region, and the binding site between miR‐204 and IRAK1 was detected by luciferase assay. We found that miR‐204 was down‐regulated in T cells of T‐ALL patients, which was caused by the increased DNA methylation in the promoter region of miR‐204. Moreover, overexpression of miR‐204 inhibited T‐ALL cell proliferation while enhancing their apoptosis through interleukin receptor‐associated kinase 1 (IRAK1), which enhanced the expression of matrix metalloproteinase‐2 (MMP‐2) and MMP‐9 through activation of p‐p65. Thus, miR‐204 modulated MMP‐2 and MMP‐9 through IRAK1/NF‐κB signalling pathway, which was confirmed by in vivo assay. Taken together, DNA methylation‐mediated miR‐204 silencing increased the transcription of IRAK1, thus activating the NF‐κB signalling pathway and up‐regulating the downstream targets MMP‐2/MMP‐9.

miR-146b correlates with increased disease activity and psoriatic tissue inflammation and promotes keratinocyte proliferation in psoriasis

The present study aimed to investigate the expression of microRNA (miR)-146b in psoriatic tissue and its correlation with psoriasis activity and inflammation. The effect of miR-146b overexpression on keratinocyte proliferation and apoptosis was also explored. The expression of miR-146b in the psoriasis-affected tissue and non-affected tissue of 110 patients was determined via reverse transcription-quantitative (RT-q)PCR. The psoriasis-affected body surface area and psoriasis area severity index (PASI) score were recorded for evaluating disease activity. The expression of various inflammatory cytokines in psoriasis-affected tissue was also detected via RT-qPCR. miR-146b overexpression and control plasmids were constructed and transfected into HaCaT cells in vitro. Subsequently, cell proliferation, apoptosis and tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL)-induced cell apoptosis were determined. The results revealed that the expression of miR-146b was increased in psoriasis-affected tissue compared with that in unaffected tissue. The results obtained from a receiver operating characteristic curve analysis demonstrated that miR-146b levels were able to discriminate between psoriasis-affected tissue and unaffected tissue, with an area under the curve value of 0.781 (95% CI: 0.720-0.843). In addition, miR-146b expression in psoriatic tissue was correlated with an increased PASI score in patients with psoriasis. miR-146b expression in psoriatic tissue was positively correlated with TNF-α, interleukin (IL)-6 and IL-17 mRNA levels. In vitro, miR-146b overexpression enhanced HaCaT cell proliferation and suppressed apoptosis as well as TRAIL-induced apoptosis when compared with that in control-transfected HaCaT cells. In conclusion, miR-146b was positively correlated with disease activity and psoriatic tissue inflammation. Keratinocyte proliferation was also promoted in psoriasis.

Protective effect of FOXP3-mediated miR-146b-5p/Robo1/NF-κB system on lipopolysaccharide-induced acute lung injury in mice

Background

As a key transcription factor, forkhead box protein 3 (FOXP3) plays an important role in the development and function of natural cluster of differentiation 4 [CD4 (+)] regulatory T cells (Treg cells). However, the function of FOXP3 in Lipopolysaccharide (LPS)-induced acute lung injury (ALI) through regulating miR-146b-5p is unclear. This research aimed to disclose the regulatory effect of the FOXP3-mediated miR-146b-5p/Roundabout 1 (Robo1)/NF-κB system on LPS-induced ALI in mice.

Methods

The mice were subjected to 5 mg/kg of LPS via intratracheal instillation to induce ALI and generate the ALI model. Mice was divided into five group, including control group, ALI group, ALI + FOXP3 group, the ALI + miR antagomir group and ALI + miR antagomir+ FOXP3 group. Lung tissue injury were detected by hematoxylin and eosin (HE) staining. Lung wet/dry weight ratio, total cells in bronchoalveolar lavage fluid (BALF), total protein in BALF and the polymorphonuclear leukocyte (PMN) in BALF were detected. The levels of tumor necrosis factor-α (TNF-α), Interleukin 6 (IL-6) and IL-1β were detected by enzyme-linked immunosorbent assay (ELISA) kit. The dual-luciferase reporter assay were used to detect the target relationship between FOXP3 and Robo1. Mice was divided into five group, including control group, ALI group, ALI + FOXP3 group, ALI + Robo1 group and ALI + FOXP3+ Robo1 group. The protein levels of FOXP3, Robo1 and p-p65 were detected by western bolt. The mRNA levels of miR-146b-5p and Robo1 were detected by quantitative reverse transcription polymerase chain reaction (qRT-PCR).

Results

Although protein expression levels of FOXP3 were significantly down-regulated in the ALI model, the increased FOXP3 levels promoted an increase in miR-146b-5p. Compared with the control group, the ALI model group exhibited severe histopathologic injury, such as thickening of the alveolar wall, pulmonary congestion, and decreased alveolar numbers. By mediating the overexpression of miR-146b-5p, FOXP3 also increased alveolar clearance and inhibited inflammatory responses in the ALI model. Importantly, Robo1 is a potential target of miR-146b-5p.

Conclusions

FOXP3 could inhibit NF-κB activation, reduce lung pathological damage, and inhibit inflammatory responses by mediating the miR-146b-5p/Robo1/NF-κB system in the ALI model. These results may provide a new potential target for the treatment of ALI disease.

Intestinal Epithelium-Derived Luminally Released Extracellular Vesicles in Sepsis Exhibit the Ability to Suppress TNF-a and IL-17A Expression in Mucosal Inflammation

Sepsis is a systemic inflammatory disorder induced by a dysregulated immune response to infection resulting in dysfunction of multiple critical organs, including the intestines. Previous studies have reported contrasting results regarding the abilities of exosomes circulating in the blood of sepsis mice and patients to either promote or suppress inflammation. Little is known about how the gut epithelial cell-derived exosomes released in the intestinal luminal space during sepsis affect mucosal inflammation. To study this question, we isolated extracellular vesicles (EVs) from intestinal lavage of septic mice. The EVs expressed typical exosomal (CD63 and CD9) and epithelial (EpCAM) markers, which were further increased by sepsis. Moreover, septic-EV injection into inflamed gut induced a significant reduction in the messaging of pro-inflammatory cytokines TNF-α and IL-17A. MicroRNA (miRNA) profiling and reverse transcription and quantitative polymerase chain reaction (RT-qPCR) revealed a sepsis-induced exosomal increase in multiple miRNAs, which putatively target TNF-α and IL-17A. These results imply that intestinal epithelial cell (IEC)-derived luminal EVs carry miRNAs that mitigate pro-inflammatory responses. Taken together, our study proposes a novel mechanism by which IEC EVs released during sepsis transfer regulatory miRNAs to cells, possibly contributing to the amelioration of gut inflammation.

SYT16 is a prognostic biomarker and correlated with immune infiltrates in glioma: A study based on TCGA data

BACKGROUND

Glioma is the most lethal primary brain tumor. Lower-grade glioma (LGG) is the crucial pathological type of Glioma. Immune-infiltration of the tumor microenvironment positively associated with overall survival in LGG. SYT16 is a gene has not been reported in cancer. We assess the role of SYT16 in LGG, via the publicly available TCGA database.

METHODS

Gene Expression Profiling Interactive Analysis (GEPIA) was used to analyze the expression of SYT16 in LGG. We evaluated the influence of SYT16 on survival of LGG patients by survival module. Then, datasets of LGG were downloaded from TCGA. The correlations between the clinical information and SYT16 expression were analyzed using logistic regression. Univariable survival and Multivariate Cox analysis was used to compare several clinical characteristics with survival. we also explore the correlation between SYT16 and cancer immune infiltrates using CIBERSORT and correlation module of GEPIA. Gene set enrichment analysis (GSEA) was performed using the TCGA dataset. In addition, we use TIMER to explore the collection of SYT16 Expression and Immune Infiltration Level in LGG and to explore cumulative survival in LGG.

RESULTS

The univariate analysis using logistic regression, indicated that increased SYT16 expression significantly correlated with the tumor grade. Moreover, multivariate analysis revealed that the up-regulated SYT16 expression is an independent prognostic factor for good prognosis. Specifically, SYT16 expression level has significant negative correlations with infiltrating levels of B cell, CD4+ T cells, Macrophages, Neutrophils and DCs in LGG. In addition, GSEA identified ingle organism behavior, gated channel activity, cognition, transporter complex and ligand gated channel activity  in Gene Ontology (GO) were differentially enriched in the high SYT16 expression phenotype pathway. Neuroactive ligand receptor interaction, calcium signaling pathway, long term potentiation, type II diabetes mellitus and long term depression were identified as differentially enriched  pathway in Kyoto Encyclopedia of Genes and Genomes (KEGG).

CONCLUSION

SYT16 is a Prognostic Biomarker and Correlated with Immune Infiltrates in LGG.

MicroRNAs and their involvement in T-ALL: A brief overview

T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy in which the transformed clone is arrested during T-cell development. Several genetic and epigenetic events have been implicated in this transformation. MicroRNAs (miRNAs) are small, non-coding RNAs that primarily function as endogenous translational repressors of protein-coding genes. The involvement of miRNAs in the regulation of cancer progression is well-established, namely by down-regulating the expression of key oncogenes or tumor suppressors and thereby preventing or promoting tumorigenesis, respectively. Similar to other cancers, several miRNA genes have been identified and implicated in the context of T-ALL. In this review we focused on the most studied microRNAs associated with T-ALL pathogenesis.