Regulation rewiring analysis reveals mutual regulation between STAT1 and miR-155-5p in tumor immunosurveillance in seven major cancers

Papain ameliorates monocyte-platelet aggregate formation-mediated inflammatory responses in monocytes by upregulating miRNA-146a transcription

BACKGROUND

MicroRNA-146a (miRNA-146a) is a nuclear factor κB (NF-κB)-inducible and inflammation-sensitive miRNA, while papain elicits anti-inflammatory effects by inhibiting monocyte-platelet aggregate (MPA)-mediated NF-κB pathway activation in monocytes. This study aimed to demonstrate the underlying effects of papain on MPA formation-initiated miRNA-146a expression and subsequent action in monocytes.

METHODS

THP-1 cells were exposed to papain, miRNA-146a mimic and inhibitor, NF-κB inhibitor (BAY11-7082), and platelets. Flow cytometry was used to measure the MPA formation-initiated monocyte activation. Levels of miRNA-146a, cyclooxygenase 2 (COX-2) mRNA and protein, and monocyte chemoattractant protein 1 (MCP-1) were analyzed in monocytes by RT-PCR, western blot, and ELISA.

RESULTS

The NF-κB inhibitor and miRNA-146a mimics upregulated miRNA-146a expression but suppressed subsequent monocyte activation and expression of COX-2 and MCP-1. Following exposure to papain, the enhanced miRNA-146a transcription induced by MPA-formation was found along with significant inhibition of monocyte activation in a dose-dependent manner. However, the inhibitory tendency was significantly reversed by miRNA-146a inhibitors. Expression of COX-2 mRNA and protein, as well as MCP-1, was inhibited in monocytes by papain, whereas miRNA-146a inhibitors promoted COX-2 and MCP-1 expression.

CONCLUSION

Our findings suggest that papain can inhibit MPA formation-mediated expression of inflammatory mediators in activated monocytes by upregulating miRNA-146a transcription.

MRNA Profiling Involved in Triggering of STAT1 with Regulatory Involvement of IRF7, PTPRF, and miR-145p in Patients Suffering from Gall Bladder Carcinoma

Background

Gall Bladder Cancer (GBC) is a type of extremely malignant tumor, which has high incidences of mortality. There is rare information about its mechanisms of invasion and gene expression regulations. microRNA-155 (miR-155) has mostly been reported to be over expressed in cases of solid tumors and hematopoietic malignancies. In this study, we have investigated the role and clinical significance of miR-155 in a Chinese population suffering from GBC and compared the results with nonneoplastic inflammation.

Methods

Tissue specimens were collected on 50 patients of Gall Bladder Carcinoma and 10 patients suffering from nonneoplastic inflammation who have undergone surgeries at the Department of Pathology, Renji Hospital, Shanghai, from January 2019 to January 2020. We performed profiling of miR-155 expression in both nonneoplastic and gall bladder carcinoma tissues by QRT-PCR.

Results

Expression levels of miR-155 were found to be extremely high in GBC patients in comparison to the nonneoplastic tissues (^∗P < 0.05), as high miRNA is correlated with TNM stages. Further results noted were that miR-145-5p expressed genes mimic the gene expression of STAT1, a downregulation of IRF7 was noted in the GBC, and an activation of STAT1 was significantly noted in carcinoma cells of the gallbladder. Downregulation of PTPRF was also noted during the expression of miR-145.

Conclusions

As downregulation of IRF7 is linked with low rates of survival, it was found that gall bladder carcinoma patients may face high mortality. The STAT-1 expression of unregulated in GBC patients was also noted.

Identification of novel prognostic biomarkers by integrating multi-omics data in gastric cancer

BACKGROUND

Gastric cancer is a fatal gastrointestinal cancer with high morbidity and poor prognosis. The dismal 5-year survival rate warrants reliable biomarkers to assess and improve the prognosis of gastric cancer. Distinguishing driver mutations that are required for the cancer phenotype from passenger mutations poses a formidable challenge for cancer genomics.

METHODS

We integrated the multi-omics data of 293 primary gastric cancer patients from The Cancer Genome Atlas (TCGA) to identify key driver genes by establishing a prognostic model of the patients. Analyzing both copy number alteration and somatic mutation data helped us to comprehensively reveal molecular markers of genomic variation. Integrating the transcription level of genes provided a unique perspective for us to discover dysregulated factors in transcriptional regulation.

RESULTS

We comprehensively identified 31 molecular markers of genomic variation. For instance, the copy number alteration of WASHC5 (also known as KIAA0196) frequently occurred in gastric cancer patients, which cannot be discovered using traditional methods based on significant mutations. Furthermore, we revealed that several dysregulation factors played a hub regulatory role in the process of biological metabolism based on dysregulation networks. Cancer hallmark and functional enrichment analysis showed that these key driver (KD) genes played a vital role in regulating programmed cell death. The drug response patterns and transcriptional signatures of KD genes reflected their clinical application value.

CONCLUSIONS

These findings indicated that KD genes could serve as novel prognostic biomarkers for further research on the pathogenesis of gastric cancers. Our study elucidated a multidimensional and comprehensive genomic landscape and highlighted the molecular complexity of GC.

ADAR1 Suppresses Interferon Signaling in Gastric Cancer Cells by MicroRNA-302a-Mediated IRF9/STAT1 Regulation

ADAR (adenosine deaminase acting on RNA) catalyzes the deamination of adenosine to generate inosine, through its binding to double-stranded RNA (dsRNA), a phenomenon known as RNA editing. One of the functions of ADAR1 is suppressing the type I interferon (IFN) response, but its mechanism in gastric cancer is not clearly understood. We analyzed changes in RNA editing and IFN signaling in ADAR1-depleted gastric cancer cells, to clarify how ADAR1 regulates IFN signaling. Interestingly, we observed a dramatic increase in the protein level of signal transducer and activator of transcription 1 (STAT1) and interferon regulatory factor 9 (IRF9) upon ADAR1 knockdown, in the absence of type I or type II IFN treatment. However, there were no changes in protein expression or localization of the mitochondrial antiviral signaling protein (MAVS) and interferon alpha and beta-receptor subunit 2 (IFNAR2), the two known mediators of IFN production. Instead, we found that miR-302a-3p binds to the untranslated region (UTR) of IRF9 and regulate its expression. The treatment of ADAR1-depleted AGS cells with an miR-302a mimic successfully restored IRF9 as well as STAT1 protein level. Hence, our results suggest that ADAR1 regulates IFN signaling in gastric cancer through the suppression of STAT1 and IRF9 via miR-302a, which is independent from the RNA editing of known IFN production pathway.

Bioinformatics Analysis of Evolution and Human Disease Related Transposable Element-Derived microRNAs

Transposable element (TE) has the ability to insert into certain parts of the genome, and due to this event, it is possible for TEs to generate new factors and one of these factors are microRNAs (miRNA). miRNAs are non-coding RNAs made up of 19 to 24 nucleotides and numerous miRNAs are derived from TE. In this study, to support general knowledge on TE and miRNAs derived from TE, several bioinformatics tools and databases were used to analyze miRNAs derived from TE in two aspects: evolution and human disease. The distribution of TEs in diverse species presents that almost half of the genome is covered with TE in mammalians and less than a half in other vertebrates and invertebrates. Based on selected evolution-related miRNAs studies, a total of 51 miRNAs derived from TE were found and analyzed. For the human disease-related miRNAs, total of 34 miRNAs derived from TE were organized from the previous studies. In summary, abundant miRNAs derived from TE are found, however, the function of miRNAs derived from TE is not informed either. Therefore, this study provides theoretical understanding of miRNAs derived from TE by using various bioinformatics tools.

Reciprocal regulations between miRNAs and HIF-1α in human cancers

Hypoxia inducible factor-1α (HIF-1α) is a central molecule involved in mediating cellular processes. Alterations of HIF-1α and hypoxically regulated microRNAs (miRNAs) are correlated with patients' outcome in various cancers, indicating their crucial roles on cancer development. Recently, an increasing number of studies have revealed the intricate regulations between miRNAs and HIF-1α in modulating a wide variety of processes, including proliferation, metastasis, apoptosis, and drug resistance, etc. miRNAs are a class of small noncoding RNAs which function as negative regulators by directly targeting mRNAs. Evidence shows that miRNAs can be regulated by HIF-1α at transcriptional level. In turn, HIF-1α itself can be modulated by many miRNAs whose alterations have been implicated in tumorigenesis, thus forming a reciprocal regulation network. These findings add a new layer of complexity to our understanding of HIF-1α regulatory networks. Here, we will provide a comprehensive overview of the current advances about the bidirectional interactions between HIF-1α and miRNAs in human cancers. Besides, the review will summarize the roles of miRNAs/HIF-1α crosstalk according to various cellular processes. Finally, the potential values of miRNAs/HIF-1α loops in clinical applications are discussed.

Downregulated NDR1 protein kinase inhibits innate immune response by initiating an miR146a-STAT1 feedback loop

Interferon (IFN)-stimulated genes (ISGs) play crucial roles in the antiviral immune response; however, IFNs also induce negative regulators that attenuate the antiviral response. Here, we show that both viral and bacterial invasion downregulate Nuclear Dbf2-related kinase 1 (NDR1) expression via the type I IFN signaling pathway. NDR1 promotes the virus-induced production of type I IFN, proinflammatory cytokines and ISGs in a kinase-independent manner. NDR1 deficiency also renders mice more susceptible to viral and bacterial infections. Mechanistically, NDR1 enhances STAT1 translation by directly binding to the intergenic region of miR146a, thereby inhibiting miR146a expression and liberating STAT1 from miR146a-mediated translational inhibition. Furthermore, STAT1 binds to the miR146a promoter, thus decreasing its expression. Together, our results suggest that NDR1 promotion of STAT1 translation is an important event for IFN-dependent antiviral immune response, and suggest that NDR1 has an important role in controlling viral infections.

The authors show that NDR1 promotion of STAT1 translation is an important event for IFN-dependent antiviral immune response. These data suggest that NDR1 has an important role in controlling viral infections.

The immune-related microRNA miR-146b is upregulated in glioblastoma recurrence

Background

Glioblastoma (GBM) has a high rate of local recurrence despite chemoradiotherapy (CRT). Genome-wide expression profiling was performed on patient tumors before and after chemoradiotherapy to identify genes and gene pathways associated with recurrence.

Results

Median time to recurrence was 8.9 months with median time to second surgery of 9.6 months. The microRNA (miRNA) analysis identified 9 oncologic and immune-related miRNAs to be differentially expressed, including the hypoxia-related miR-210 and the immune-modulatory miR-146b. More than 1200 differentially-expressed genes were identified with RNA-sequencing (RNA-seq). Gene set enrichment analysis (GSEA) identified p53 signaling, Notch, Wnt, VEGF, and MEK gene sets enriched in recurrent GBM. Consistent with the miRNA profiling data, the miR-146b target gene set from GSEA analysis was also associated with recurrence.

Methods

Fourteen patients with GBM recurrence after CRT who had available tumor tissue from the initial diagnosis as well as recurrence were selected. Total RNA was isolated from formalin-fixed paraffin-embedded (FFPE) tumor specimens. Genome-wide expression profiling using RT-PCR for miRNA analysis and RNA-seq for messenger RNA (mRNA) analysis were conducted to identify differentially-expressed genes. GSEA was performed on the differential expression data.

Conclusions

Genome-wide expression profiling identifies multiple oncologic and immune-related gene sets associated with GBM recurrence. In particular, immune-related miR-146b is upregulated in recurrence and deserves further investigation.

Macrophage MicroRNAs as Therapeutic Targets for Atherosclerosis, Metabolic Syndrome, and Cancer

Macrophages play a crucial role in the innate immune system and contribute to a broad spectrum of pathologies in chronic inflammatory diseases. MicroRNAs (miRNAs) have been demonstrated to play important roles in macrophage functions by regulating macrophage polarization, lipid metabolism and so on. Thus, miRNAs represent promising diagnostic and therapeutic targets in immune disorders. In this review, we will summarize the role of miRNAs in atherosclerosis, metabolic syndrome, and cancer by modulating macrophage phenotypes, which has been supported by in vivo evidence.

The miR-124-p63 feedback loop modulates colorectal cancer growth

Among the diverse co-regulatory relationships between transcription factors (TFs) and microRNAs (miRNAs), feedback loops have received the most extensive research attention. The co-regulation of TFs and miRNAs plays an important role in colorectal cancer (CRC) growth. Here, we show that miR-124 can regulate two isoforms of p63, TAp63 and ΔNp63, via iASPP, while p63 modulates signal transducers and activators of transcription 1 (STAT1) expression by targeting miR-155. Moreover, STAT1 acts as a regulator of CRC growth by targeting miR-124. Taken together, these results reveal a feedback loop between miRNAs and TFs. This feedback loop comprises miR-124, iASPP, STAT1, miR-155, TAp63 and ΔNp63, which are essential for CRC growth. Moreover, this feedback loop is perturbed in human colon carcinomas, which suggests that the manipulation of this microRNA-TF feedback loop has therapeutic potential for CRC.

Anti-inflammatory effects of curcumin are associated with down regulating microRNA-155 in LPS-treated macrophages and mice

CONTEXT

The natural polyphenolic compound curcumin has been proved to modulate innate immune responses and possess anti-inflammatory properties. Nevertheless, the mechanism remains poorly understood, particularly regarding curcumin-regulated miRNAs under inflammatory response.

OBJECTIVE

This study investigates the role of miRNA-155 in the effects of curcumin on inflammatory response in cell and a mouse model.

MATERIALS AND METHODS

The anti-inflammatory activity of curcumin (5, 10 and 15 μM, 2 h) in lipopolysaccharide (LPS, 200 ng/mL)-induced cells were measured by quantitative PCR. The animals were treated orally by 20 mg/kg curcumin for 3 days before an LPS intraperitoneal injection (10 mg/kg, 16 h). MicroRNA (miRNA) expression and the underlying molecular mechanisms were assessed using transfection technique and western blotting.

RESULTS AND DISCUSSION

Curcumin efficiently inhibited LPS-induced cytokines (TNF-α, IL-6) and microRNA-155 (miR-155) expression (p < 0.05) without affecting the normally growth of Raw264.7 and THP-1 cells (IC₅₀ 21.8 and 22.3 μM at 48 h, respectively). Moreover, the levels of cytokines were suppressed by curcumin in miR-155 mimics transfected cells (p < 0.05). A blockade of PI3K/AKT signalling pathways resulted in a decreased level of miR-155 (p < 0.05). Curcumin effectively protected mice from sepsis as evidenced by decreasing histological damage, reducing AST (352.0 vs 279.3 U/L), BUN (14.8 vs 10.8 mmol/L) levels and the proportion of macrophages in spleen (31.1% vs 13.5%). MicroRNA-155 level and cytokines were also reduced in curcumin-treated mice (p < 0.05).

CONCLUSIONS

Curcumin's ability to suppress LPS-induced inflammatory response may be due to the inhibition of miR-155.

MicroRNA-155 induction via TNF-α and IFN-γ suppresses expression of programmed death ligand-1 (PD-L1) in human primary cells

Programmed death ligand-1 (PD-L1) is a critical regulator of T cell function contributing to peripheral immune tolerance. Although it has been shown that posttranscriptional regulatory mechanisms control PD-L1 expression in cancer, it remains unknown whether such regulatory loops operate also in non-transformed cells. Here we studied PD-L1 expression in human dermal lymphatic endothelial cells (HDLECs), which play key roles in immunity and cancer. Treatment of HDLECs with the pro-inflammatory cytokines IFN-γ and TNF-α synergistically up-regulated PD-L1 expression. IFN-γ and TNF-α also affected expression of several microRNAs (miRNAs) that have the potential to suppress PD-L1 expression. The most highly up-regulated miRNA following IFN-γ and TNF-α treatment in HDLECs was miR-155, which has a central role in the immune system and cancer. Induction of miR-155 was driven by TNF-α, the effect of which was significantly enhanced by IFN-γ. The PD-L1 3′-UTR contains two functional miR-155-binding sites. Endogenous miR-155 controlled the kinetics and maximal levels of PD-L1 induction upon IFN-γ and TNF-α treatments. We obtained similar findings in dermal fibroblasts, demonstrating that the IFN-γ/TNF-α/miR-155/PD-L1 pathway is not restricted to HDLECs. These results reveal miR-155 as a critical component of an inflammation-induced regulatory loop controlling PD-L1 expression in primary cells.

The metastasis suppressor RARRES3 as an endogenous inhibitor of the immunoproteasome expression in breast cancer cells

In breast cancer metastasis, the dynamic continuum involving pro- and anti-inflammatory regulators can become compromised. Over 600 genes have been implicated in metastasis to bone, lung or brain but how these genes might contribute to perturbation of immune function is poorly understood. To gain insight, we adopted a gene co-expression network approach that draws on the functional parallels between naturally occurring bone marrow-derived mesenchymal stem cells (BM-MSCs) and cancer stem cells (CSCs). Our network analyses indicate a key role for metastasis suppressor RARRES3, including potential to regulate the immunoproteasome (IP), a specialized proteasome induced under inflammatory conditions. Knockdown of RARRES3 in near-normal mammary epithelial and breast cancer cell lines increases overall transcript and protein levels of the IP subunits, but not of their constitutively expressed counterparts. RARRES3 mRNA expression is controlled by interferon regulatory factor IRF1, an inducer of the IP, and is sensitive to depletion of the retinoid-related receptor RORA that regulates various physiological processes including immunity through modulation of gene expression. Collectively, these findings identify a novel regulatory role for RARRES3 as an endogenous inhibitor of IP expression, and contribute to our evolving understanding of potential pathways underlying breast cancer driven immune modulation.

The Emerging Role of miRNAs and Their Clinical Implication in Biliary Tract Cancer

Biliary tract cancers are aggressive malignancies that include gallbladder cancer and tumors of intra- and extrahepatic ducts and have a poor prognosis. Surgical resection remains the main curative therapy. Nevertheless, numerous patients experience recurrence even after radical surgery. This scenario drives the research to identify biliary tract cancer biomarkers despite the limited progress that has been made. Recently, a large number of studies have demonstrated that deregulated expression of microRNAs is closely associated with cancer development and progression. In this review, we highlight the role and importance of microRNAs in biliary tract cancers with an emphasis on utilizing circulating microRNAs as potential biomarkers. Additionally, we report several single-nucleotide polymorphisms in microRNA genes that are associated with the susceptibility of biliary tract tumors.

MicroRNA regulation of macrophages in human pathologies

Macrophages play a crucial role in the innate immune system and contribute to a broad spectrum of pathologies, like in the defence against infectious agents, in inflammation resolution, and wound repair. In the past several years, microRNAs (miRNAs) have been demonstrated to play important roles in immune diseases by regulating macrophage functions. In this review, we will summarize the role of miRNAs in the differentiation of monocytes into macrophages, in the classical and alternative activation of macrophages, and in the regulation of phagocytosis and apoptosis. Notably, miRNAs preferentially target genes related to the cellular cholesterol metabolism, which is of key importance for the inflammatory activation and phagocytic activity of macrophages. miRNAs functionally link various mechanisms involved in macrophage activation and contribute to initiation and resolution of inflammation. miRNAs represent promising diagnostic and therapeutic targets in different conditions, such as infectious diseases, atherosclerosis, and cancer.

Human Absorbable MicroRNA Prediction based on an Ensemble Manifold Ranking Model

MicroRNAs, a class of short non-coding RNAs, are able to regulate more than half of human genes and affect many fundamental biological processes. It has been long considered synthesized endogenously until very recent discoveries showing that human can absorb exogenous microRNAs from dietary resources. This finding has raised a challenge scientific question: which exogenous microRNAs can be integrated into human circulation and possibly exert functions in human? Here we present a well-designed ensemble manifold ranking model for identifying human absorbable exogenous miRNAs from 14 common dietary species. Specifically, we have analyzed 4,910 dietary microRNAs with 1,120 features derived based on the microRNA sequence and structure. In total, 70 discriminative features were selected to characterize the circulating microRNAs in human and have been used to infer the possibility of a certain exogenous microRNA getting integrated into human circulation. Finally, 461 dietary microRNAs have been identified as transportable exogenous microRNAs. To assess the performance of our ensemble model, we have validated the top predictions through a milk-feeding study. In addition, 26 microRNAs from two virus species were predicted as transportable and have been validated in two external experiments. The results demonstrate the data-driven computational model is highly promising to study transportable microRNAs while bypassing the complex mechanistic details.

A cross-cancer differential co-expression network reveals microRNA-regulated oncogenic functional modules

MicroRNAs (miRNAs) are small non-coding RNAs that can regulate their target gene expressions at the post-transcriptional level. Moreover, they have been reported as either oncomirs or tumor suppressors and possess therapeutic potential in cancer. In this study, we investigated differential co-expression of miRNAs across four cancer types. We observed that the loss of positive co-expressions among miRNAs frequently occurs in the studied cancer types. This observation suggests that the disruption of positive co-expressions among miRNAs may be prevalent during tumorigenesis. By systematically collecting these lost positive co-expressions among miRNAs in cancer, we constructed a cross-cancer miRNA differential co-expression network. We observed that the influential miRNAs in the proposed network, i.e., hubs or in larger cliques, tended to be involved in more cancer types than other miRNAs. Moreover, we found that miRNAs which lose their positive co-expressions in cancers might co-contribute to cancer development, and even could be used to predict the cancer types in which miRNAs were involved. Finally, we identified two potential miRNA-regulated onco-modules, mitosis and DNA replication, that are associated with poor survival outcomes in patients across multiple cancers. Collectively, our study suggested that the disruption of miRNA positive co-expression in cancer might contribute to cancer development. Our findings also form an important basis for identifying miRNAs with potential co-contribution to carcinogenesis.

MicroRNA-155 expression as a prognostic factor in patients with gallbladder carcinoma after surgical resection

BACKGROUND

MicroRNA-155 (miR-155) is over-expressed in both hematopoietic malignancies and solid tumors. In the present study, we investigated the clinical significance of miR-155 in gallbladder carcinoma among Chinese population.

METHODS

Tissue specimens were collected from 133 patients who had undergone surgical resection at Shandong Provincial Hospital, Shandong University between May 2008 and April 2014. We profiled miR- 155 expression in the gallbladder carcinoma tissues and normal gallbladder tissues by qRT-PCR. The Kaplan-Meier method was used to analyze the 5-year survival rate.

RESULTS

The expression levels of miR-155 were significantly higher in gallbladder carcinoma tissues than that in normal gallbladder tissues (P<0.001). High miR-155 expression was significantly associated with TNM stage (P=0.003), lymph node status (P=0.042), liver metastasis (P=0.010), and differentiated degree (P<0.001). We found that gallbladder carcinoma patients with high miR-155 expression level had distinctly shorter overall survival than patients with low miR-155 expression level (P=0.03). Multivariate analysis revealed that miR-155 expression level was independent prognostic factors for overall survival (HR=2.394, 95% CI: 1.568-10.034; P=0.009).

CONCLUSION

High miR-155 expression is a prognostic indicator for poor prognosis of patients with gallbladder carcinoma among Chinese population.