Modeling microRNA-transcription factor networks in cancer

Gene dosage compensation: Origins, criteria to identify compensated genes, and mechanisms including sensor loops as an emerging systems-level property in cancer

The gene dosage compensation hypothesis presents a mechanism through which the expression of certain genes is modulated to compensate for differences in the dose of genes when additional chromosomes are present. It is one of the means through which cancer cells actively cope with the potential damaging effects of aneuploidy, a hallmark of most cancers. Dosage compensation arises through several processes, including downregulation or overexpression of specific genes and the relocation of dosage-sensitive genes. In cancer, a majority of compensated genes are generally thought to be regulated at the translational or post-translational level, and include the basic components of a compensation loop, including sensors of gene dosage and modulators of gene expression. Post-translational regulation is mostly undertaken by a general degradation or aggregation of remaining protein subunits of macromolecular complexes. An increasingly important role has also been observed for transcriptional level regulation. This article reviews the process of targeted gene dosage compensation in cancer and other biological conditions, along with the mechanisms by which cells regulate specific genes to restore cellular homeostasis. These mechanisms represent potential targets for the inhibition of dosage compensation of specific genes in aneuploid cancers. This article critically examines the process of targeted gene dosage compensation in cancer and other biological contexts, alongside the criteria for identifying genes subject to dosage compensation and the intricate mechanisms by which cells orchestrate the regulation of specific genes to reinstate cellular homeostasis. Ultimately, our aim is to gain a comprehensive understanding of the intricate nature of a systems-level property. This property hinges upon the kinetic parameters of regulatory motifs, which we have termed "gene dosage sensor loops." These loops have the potential to operate at both the transcriptional and translational levels, thus emerging as promising candidates for the inhibition of dosage compensation in specific genes. Additionally, they represent novel and highly specific therapeutic targets in the context of aneuploid cancer.

hsa-mir-(4328, 4422, 548z and -628-5p) in diabetic retinopathy: diagnosis, prediction and linking a new therapeutic target

AIMS

Growing evidence suggests that microRNAs (miRNAs) are crucial in controlling how diabetic retinopathy (DR) develops. We intend to mine miRNAs with diagnostic and predictive value for DR and to investigate new drug therapeutic targets.

METHODS

After performing a differential analysis on the miRNA and mRNA datasets for DR and neovascularization (NEO), miRNA-mRNA networks were created. Combine the results of enrichment analysis, Protein-Protein Interaction Networks (PPI), and Cytoscape to identify key miRNAs. DrugBank was used to find drugs that interacted with transcription factors (TF) predicted by TransmiR. Finally, whole blood and clinical data were collected from 58 patients with type 2 diabetes mellitus (T2DM), and RT-qPCR, logistic analysis, and ROC were used to verify the value of key miRNAs.

RESULTS

Differential analysis indicated the presence of genes and miRNAs that co-regulate DR and NEO. Enrichment analysis showed that key genes are inextricably linked to neovascularization. Combining the results of PPI and Cytoscape identified four key miRNAs, namely hsa-mir-(4328, 4422, 548z and -628-5p). RT-qPCR, logistic, and ROC results showed that decreased expression levels of hsa-mir-(4328, 4422, 548z and -628-5p) signal the risk of evolution to DR in T2DM patients. Finally, we constructed a TF-miRNA network to find the 15 TFs and the 35 drugs that interact with these TFs.

CONCLUSION

hsa-mir-(4328, 4422, 548z and -628-5p) in whole blood are protective factors for DR as novel biomarkers for diagnosis and prediction. In addition, our research provides new drug directions for the treatment of DR, such as Diosmin, Atorvastatin, and so on.

MYC dosage compensation is mediated by miRNA-transcription factor interactions in aneuploid cancer

We hypothesize that dosage compensation of critical genes arises from systems-level properties for cancer cells to withstand the negative effects of aneuploidy. We identified several candidate genes in cancer multiomics data and developed a biocomputational platform to construct a mathematical model of their interaction network with micro-RNAs and transcription factors, where the property of dosage compensation emerged for MYC and was dependent on the kinetic parameters of its feedback interactions with three micro-RNAs. These circuits were experimentally validated using a genetic tug-of-war technique to overexpress an exogenous MYC, leading to overexpression of the three microRNAs involved and downregulation of endogenous MYC. In addition, MYC overexpression or inhibition of its compensating miRNAs led to dosage-dependent cytotoxicity in MYC-amplified colon cancer cells. Finally, we identified negative correlation of MYC dosage compensation with patient survival in TCGA breast cancer patients, highlighting the potential of this mechanism to prevent aneuploid cancer progression.

miR-4486 reverses cisplatin-resistance of colon cancer cells via targeting ATG7 to inhibiting autophagy

Cisplatin (DDP) resistance is one of the main causes of treatment failure in patients with colon cancer (CC). Autophagy is a key mechanism of resistance to chemotherapy. Since autophagy-related 7 (ATG7) has been reported to be involved in the regulation of autophagy and DDP resistance for lung and esophageal cancer, the present study aimed to explore the functions of microRNA (miR)-4486 in the autophagy-mediated DDP resistance of CC. The expression level of miR-4486 in HCT116, DDP-resistant HCT116 cells (HCT116/DDP), SW480 and DDP-resistant SW480 cells (SW480/DDP) was quantified by reverse transcription-quantitative PCR. Western blotting was utilized to analyze the expression of ATG7, autophagy-related proteins Beclin 1 and LC3-I/II, as well as apoptosis-related proteins Bcl-2, Bax and cleaved-caspase 3 in HCT116/DDP and SW480/DDP cells. The half maximal inhibitory concentration of DDP on all cell lines and the cell viability of HCT116/DDP and SW480/DDP cells were measured using Cell Counting Kit 8 assay. Luciferase assay was used to examine the potential targets of miR-4486 and ATG7. The effects of upregulating mimic miR-4486 expression on the apoptosis and autophagy of HCT116/DDP and SW480/DDP cells were determined by flow cytometry and electron microscopy, respectively. It was found that miR-4486 expression was significantly decreased in HCT116/DDP and SW480/DDP cells compared with that in HCT116 and SW480 cells. Overexpression of miR-4486 could increase the sensitivity of HCT116/DDP and SW480/DDP cells to DDP by reducing cell viability, promoting apoptosis and inhibiting autophagy through downregulating Beclin 1 expression and the LC3-II/LC3-I ratio. Additionally, ATG7 was identified to be a target gene of miR-4486, where ATG7 overexpression could partially reverse the effects of miR-4486 on cell viability and apoptosis by promoting the formation of autophagosomes. In conclusion, the present results demonstrated that miR-4486 could reverse DDP resistance in HCT116/DDP and SW480/DDP cells by targeting ATG7 to inhibit autophagy.

Regulatory role of the transforming growth factor-β signaling pathway in the drug resistance of gastrointestinal cancers

Gastrointestinal (GI) cancer, including esophageal, gastric, and colorectal cancer, is one of the most prevalent types of malignant carcinoma and the leading cause of cancer-related deaths. Despite significant advances in therapeutic strategies for GI cancers in recent decades, drug resistance with various mechanisms remains the prevailing cause of therapy failure in GI cancers. Accumulating evidence has demonstrated that the transforming growth factor (TGF)-β signaling pathway has crucial, complex roles in many cellular functions related to drug resistance. This review summarizes current knowledge regarding the role of the TGF-β signaling pathway in the resistance of GI cancers to conventional chemotherapy, targeted therapy, immunotherapy, and traditional medicine. Various processes, including epithelial-mesenchymal transition, cancer stem cell development, tumor microenvironment alteration, and microRNA biogenesis, are proposed as the main mechanisms of TGF-β-mediated drug resistance in GI cancers. Several studies have already indicated the benefit of combining antitumor drugs with agents that suppress the TGF-β signaling pathway, but this approach needs to be verified in additional clinical studies. Moreover, the identification of potential biological markers that can be used to predict the response to TGF-β signaling pathway inhibitors during anticancer treatments will have important clinical implications in the future.

Roles of microRNAs in tumorigenesis and metastasis of esophageal squamous cell carcinoma

Esophageal squamous cell carcinoma (ESCC) is the major subtype of esophageal cancer that is prevalent in Eastern Asia. Despite recent advances in therapy, the outcome of ESCC patients is still dismal. MicroRNAs (miRNAs) are non-coding RNAs which can negatively modulate gene expression at the post-transcriptional level. The involvement and roles of miRNAs have become one of the hot topics of cancer research in recent years. In ESCC, genetic variations within miRNA coding genes were found to have distinct epidemiological significance in different populations. Dysregulated expression of several miRNAs was reported to be associated with therapeutic response. Functionally, miRNAs can act either in an oncogenic or a tumor-suppressive manner during tumorigenesis of ESCC by interrupting signaling pathways associated with cell proliferation, metabolism, cancer stemness, and resistance to chemo- or radiotherapy. Moreover, miRNAs modulate metastasis of ESCC by targeting genes that regulate cytoskeleton dynamics, extracellular matrix remodeling, epithelial-mesenchymal transition, and tumor microenvironment. Most importantly, mounting evidence suggests that inhibiting oncogenic miRNAs or restoring the loss of tumor-suppressive miRNAs has therapeutic potential in the treatment of ESCC. Here, we review and discuss recent studies on the significance, biological functions, and therapeutic potential of miRNAs in tumorigenesis and metastasis of ESCC.

Molecular mechanisms of the microRNA-132 during tumor progressions

Cancer as one of the leading causes of human deaths has always been one of the main health challenges in the world. Despite recent advances in therapeutic and diagnostic methods, there is still a high mortality rate among cancer patients. Late diagnosis is one of the main reasons for the high ratio of cancer related deaths. Therefore, it is required to introduce novel early detection methods. Various molecular mechanisms are associated with the tumor progression and metastasis. MicroRNAs (miRNAs) are a class of non-coding RNAs (ncRNAs) family that has important functions in regulation of the cellular processes such as cell proliferation, apoptosis, and tumor progression. Moreover, they have higher stability in body fluids compared with mRNAs which can be introduced as non-invasive diagnostic markers in cancer patients. MiR-132 has important functions as tumor suppressor or oncogene in different cancers. In the present review, we have summarized all of the studies which have been reported the role of miR-132 during tumor progressions. We categorized the miR-132 target genes based on their cell and molecular functions. Although, it has been reported that the miR-132 mainly functions as a tumor suppressor, it has also oncogenic functions especially in pancreatic tumors. MiR-132 mainly exerts its roles during tumor progressions by regulation of the transcription factors and signaling pathways. Present review clarifies the tumor specific molecular mechanisms of miR-132 to introduce that as an efficient non-invasive diagnostic marker in various cancers.

rSjP40 suppresses hepatic stellate cell activation by promoting microRNA-155 expression and inhibiting STAT5 and FOXO3a expression

Activation of hepatic stellate cells (HSCs) is the central event of the evolution of hepatic fibrosis. Schistosomiasis is one of the pathogenic factors which could induce hepatic fibrosis. Previous studies have shown that recombinant Schistosoma japonicum egg antigen P40 (rSjP40) can inhibit the activation and proliferation of HSCs. MicroRNA‐155 is one of the multifunctional noncoding RNA, which is involved in a series of important biological processes including cell development, proliferation, differentiation and apoptosis. Here, we try to observe the role of microRNA‐155 in rSjP40‐inhibited HSC activation and explore its potential mechanisms. We found that microRNA‐155 was raised in rSjP40‐treated HSCs, and further studies have shown that rSjP40 enhanced microRNA‐155 expression by inhibiting STAT5 transcription. Up‐regulated microRNA‐155 can down‐regulate the expression of FOXO3a and then participate in rSjP40‐inhibited expression of α‐smooth muscle actin (α‐SMA) and collagen I. Furthermore, we observed microRNA‐155 inhibitor could partially restore the down‐regulation of FOXO3a, α‐SMA and collagen I expression in LX‐2 cells induced by rSjP40. Therefore, our research provides further insight into the mechanism by which rSjP40 could inhibit HSC activation via miR‐155.

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.

miR-192 targeting IL-1RI regulates the immune response in miiuy croaker after pathogen infection in vitro and in vivo

Activation of innate and acquired immune responses is regulated by detailed mechanisms to control their onset and termination. MicroRNAs have been implicated as negative regulators controlling the diverse of biophysical and biochemical processes at the post-transcriptional level. However, the physiological roles of miRNAs in aquatic organisms are largely unclear. In this study, we explored the potential roles of mmi-miR-192 in regulating interleukin 1 receptor type I (IL-1RI) involved in immune and inflammatory response in miiuy croakers. This was further evaluated by negative expression profiles in both LPS exposure macrophages and Vibrio anguillarum challenged miiuy croaker. By means of promoter analysis, mmi-miR-192 was found to be an AP-1 dependent gene. Importantly, the dual luciferase reporter assay presented the regulation between mmi-miR-192 and IL-1RI. The result of miiuy croaker miR-192 reduced the wild-type IL-1RI but not the mutant one luciferase levels suggested that mmi-miR-192 modulated IL-1RI expression by directly targeting the 3'UTR of IL-1RI mRNA. Overall, our study revealed the mechanism that the miR-192-IL1RI pathway regulated bacteria infection in miiuy croakers.

Time-Delayed Models of Gene Regulatory Networks

We discuss different mathematical models of gene regulatory networks as relevant to the onset and development of cancer. After discussion of alternative modelling approaches, we use a paradigmatic two-gene network to focus on the role played by time delays in the dynamics of gene regulatory networks. We contrast the dynamics of the reduced model arising in the limit of fast mRNA dynamics with that of the full model. The review concludes with the discussion of some open problems.

Acinar cell reprogramming: a clinically important target in pancreatic disease

Acinar cells of the pancreas produce the majority of enzymes required for digestion and make up >90% of the cells within the pancreas. Due to a common developmental origin and the plastic nature of the acinar cell phenotype, these cells have been identified as a possible source of β cells as a therapeutic option for Type I diabetes. However, recent evidence indicates that acinar cells are the main source of pancreatic intraepithelial neoplasias (PanINs), the predecessor of pancreatic ductal adenocarcinoma (PDAC). The conversion of acinar cells to either β cells or precursors to PDAC is dependent on reprogramming of the cells to a more primitive, progenitor-like phenotype, which involves changes in transcription factor expression and activity, and changes in their epigenetic program. This review will focus on the mechanisms that promote acinar cell reprogramming, as well as the factors that may affect these mechanisms.

Regulatory networks in retinal ischemia-reperfusion injury

BACKGROUND

Retinal function is ordered by interactions between transcriptional and posttranscriptional regulators at the molecular level. These regulators include transcription factors (TFs) and posttranscriptional factors such as microRNAs (miRs). Some studies propose that miRs predominantly target the TFs rather than other types of protein coding genes and such studies suggest a possible interconnection of these two regulators in co-regulatory networks.

RESULTS

Our lab has generated mRNA and miRNA microarray expression data to investigate time-dependent changes in gene expression, following induction of ischemia-reperfusion (IR) injury in the rat retina. Data from different reperfusion time points following retinal IR-injury were analyzed. Paired expression data for miRNA-target gene (TG), TF-TG, miRNA-TF were used to identify regulatory loop motifs whose expressions were altered by the IR injury paradigm. These loops were subsequently integrated into larger regulatory networks and biological functions were assayed. Systematic analyses of the networks have provided new insights into retinal gene regulation in the early and late periods of IR. We found both overlapping and unique patterns of molecular expression at the two time points. These patterns can be defined by their characteristic molecular motifs as well as their associated biological processes. We highlighted the regulatory elements of miRs and TFs associated with biological processes in the early and late phases of ischemia-reperfusion injury.

CONCLUSIONS

The etiology of retinal ischemia-reperfusion injury is orchestrated by complex and still not well understood gene networks. This work represents the first large network analysis to integrate miRNA and mRNA expression profiles in context of retinal ischemia. It is likely that an appreciation of such regulatory networks will have prognostic potential. In addition, the computational framework described in this study can be used to construct miRNA-TF interactive systems networks for various diseases/disorders of the retina and other tissues.

MicroRNA-1 in Cardiac Diseases and Cancers

MicroRNAs (miRs) are endogenous ≈22-nt non-coding RNAs that participate in the regulation of gene expression at post-transcriptional level. MiR-1 is one of the muscle-specific miRs, aberrant expression of miR-1 plays important roles in many physiological and pathological processes. In this review, we focus on the recent studies about miR-1 in cardiac diseases and cancers. The findings indicate that miR-1 may be a novel, important biomarker, and a potential therapeutic target in cardiac diseases and cancers.

Multiple targets of the microRNA miR-8 contribute to immune homeostasis in Drosophila

MicroRNAs (miRNAs) are noncoding, around 22-nucleotide-long RNAs that exert significant modulatory roles in gene expression throughout the genome. As such, miRNAs take part in and modulate almost all biological processes like cell growth, development, and immunity. We previously showed that miR-8 miRNA plays a role in maintaining immune homeostasis in Drosophila. Here, we further discovered that targeting of multiple coding genes by miR-8 contributes to the maintenance of immune homeostasis. Toll and Dorsal, respectively the receptor and transcription factor in the Toll immune pathway, were found to be miR-8 targets, as shown by reporter assays and miR-8 null flies. Moreover, U-shaped (Ush), a previously verified miR-8 target, was seen to mediate miR-8 regulation of immune homeostasis. Consistently, overexpression of either Dorsal or Ush in the fat body led to increased Drosomycin expression, mimicking that induced by deletion of miR-8. Furthermore, mutation in Toll immune pathway or Ush rescues the abnormal expression of Drosomycin and lethality in miR-8 mutant. Thus, miR-8 regulates Drosophila immune homeostasis by targeting multiple immune genes, thereby contributing to survival.

miRNome of Italian Large White pig subcutaneous fat tissue: new miRNAs, isomiRs and moRNAs

Small RNAs, such as micro-RNAs (miRNAs), are decisive regulators of gene expression, and they could determine adipose tissue traits. A better knowledge of porcine fat genomics is relevant given that the pig is a biomedical model for metabolic and cardiovascular human pathologies. Adipose tissue is particularly important for the meat industry. We explored the miRNome of two adult Italian Large White pig backfat samples by Illumina RNA-Seq. Using custom bioinformatic methods, the expressed miRNAs were identified and quantified and the nucleotide sequence variability of miRNA isoforms were analysed. We detected 222 known miRNAs, 68 new miRNAs and 17 miRNA-offset RNAs (moRNAs) expressed from known hairpins, and 312 new miRNAs expressed from 253 new hairpins. Porcine transcripts targeted by the most expressed miRNAs were predicted, showing that these miRNAs may have an impact on Wnt, insulin signalling and axon guidance pathways. The expression of five small RNAs, including moRNA ssc-5'-moR-21 and a miRNA from a new hairpin, was validated by a qRT-PCR assay, thus confirming the robustness of our results. The depicted miRNome complexity suggests that quantitative and qualitative features of miRNAs and non-canonical products of their precursors are worthy of further investigation to clarify their roles in the adipose tissue biology.

Downregulated miR-646 in clear cell renal carcinoma correlated with tumour metastasis by targeting the nin one binding protein (NOB1)

Background:

Nin one binding protein (NOB1) was identified as a potential oncogene in human glioma and miR-646 plays an important role in human growth and development. However, the underlying molecular mechanisms of NOB1 in tumorigenicity and its correlation with miR-646 in renal cell carcinoma (RCC) have not been investigated.

Methods:

We performed bioinformatic analysis to explore miRNA targeting NOB1. The expression of NOB1 and miR-646 from 100 cases of clear cell RCC (ccRCC) and 30 cases of adjacent non-tumour tissues were detected by quantitative real-time PCR. The expression of miR-646 was correlated with NOB1 expression, tumour features and patient metastasis-free survival. The effect of overexpression of mir-646 on renal cancer cell proliferation was detected by colony formation in soft agar. Using a xenograft tumour model, we observed the in vivo tumorigenesis effect of miR-646 and NOB1.

Results:

miR-646 negatively regulated NOB1 and inhibited the proliferation and migration of renal cancer cells. There was a significant upregulation of NOB1 in ccRCC and it was further increased in metastatic cases, while miR-646 was downregulated in tumour tissues and further decreased in metastatic ccRCC. Additionally, expression of miR-646 was inversely correlated with the expression of NOB1. The downregulation of miR-646 also indicated a higher probability of developing metastasis. Most importantly, miR-646 expression was an independent predictor of ccRCC metastasis by the univariate analysis and binary logistic regression model (both P<0.05). Colony formation in soft agar and xenograft tumour model suggested that miR-646 and NOB1 are required for tumorigenesis in vitro and in vivo. Furthermore, suppression of NOB1 increased the phosphorylation of several proteins in MAPK pathway.

Conclusions:

Downregulated miR-646 in ccRCC was associated with tumour metastasis through MAPK pathway by targeting NOB1. miR-646 and NOB1 may play an important role in the development of ccRCC.

MicroRNA-24 modulates aflatoxin B1-related hepatocellular carcinoma prognosis and tumorigenesis

MicroRNA-24 (miR-24) may be involved in neoplastic process; however, the role of this microRNA in the hepatocellular carcinoma (HCC) related to aflatoxin B1 (AFB1) has not been well elaborated. Here, we tested miR-24 expression in 207 pathology-diagnosed HCC cases from high AFB1 exposure areas and HCC cells. We found that miR-24 was upregulated in HCC tumor tissues relative to adjacent noncancerous tissue samples, and that the high expression of miR-24 was significantly correlated with larger tumor size, higher microvessel density, and tumor dedifferentiation. Additionally, this microRNA overexpression modified the recurrence-free survival (relative hazard ratio [HR], 4.75; 95% confidence interval [CI], 2.66-8.47) and overall survival (HR = 3.58, 95% CI = 2.34-5.46) of HCC patients. Furthermore, we observed some evidence of joint effects between miR-24 and AFB1 exposure on HCC prognosis. Functionally, miR-24 overexpression progressed tumor cells proliferation, inhibited cell apoptosis, and developed the formation of AFB1-DNA adducts. These results indicate for the first time that miR-24 may modify AFB1-related HCC prognosis and tumorigenesis.

MicroRNAs in gastrointestinal cancer: prognostic significance and potential role in chemoresistance

INTRODUCTION

Although chemotherapy is an important therapeutic strategy for gastrointestinal cancer, its clinical effect remains unsatisfied due to drug resistance. Drug resistance is a complex multistep process resulting from deregulated expression of many molecules, including tumor suppressor genes, oncogenes and microRNAs (miRNAs). A better understanding of drug resistance-related miRNAs may eventually lead to optimized therapeutic strategies for cancer patients.

AREAS COVERED

This review summarizes the recent advances of drug resistance-related miRNAs in esophageal, gastric and colorectal cancer. Furthermore, this study envisages future developments toward the clinical applications of these miRNAs to cancer therapy.

EXPERT OPINION

Drug resistance-related miRNAs may be potentially predicting biomarkers that help guide individualized chemotherapy. Specific miRNAs and their target genes can be used as therapeutic targets by reversing drug resistance. More investigations should be performed to promote the translational bridging of the latest research into clinical application.

Studying the system-level involvement of microRNAs in Parkinson's disease

Background

Parkinson's Disease (PD) is a progressive neurologic disorder that affects movement and balance. Recent studies have revealed the importance of microRNA (miR) in PD. However, the detailed role of miR and its regulation by Transcription Factor (TF) remain unexplored. In this work for the first time we have studied TF-miR-mRNA regulatory network as well as miR co-expression network in PD.

Result

We compared the 204 differentially expressed miRs from microarray data with 73 PD related miRs obtained from literature, Human MicroRNA Disease Database and found a significant overlap of 47 PD related miRs (p-value<0.05). Functional enrichment analyses of these 47 common (Group1) miRs and the remaining 157 (Group2) miRs revealed similar kinds of over-representative GO Biological Processes and KEGG pathways. This strengthens the possibility that some of the Group 2 miRs can have functional roles in PD progression, hitherto unidentified in any study. In order to explore the cross talk between TF, miR and target mRNA, regulatory networks were constructed. Study of these networks resulted in 14 Inter-Regulatory hub miRs whereas miR co-expression network revealed 18 co-expressed hub miRs. Of these 32 hub miRs, 23 miRs were previously unidentified with respect to their association with PD. Hierarchical clustering analysis further strengthens the roles of these novel miRs in different PD pathways. Furthermore hsa-miR-92a appeared as novel hub miR in both regulatory and co-expression network indicating its strong functional role in PD. High conservation patterns were observed for most of these 23 novel hub miRs across different species including human. Thus these 23 novel hub miRs can be considered as potential biomarkers for PD.

Conclusion

Our study identified 23 novel miR markers which can open up new avenues for future studies and shed lights on potential therapeutic targets for PD.

Differentiation therapy for solid tumors

Differentiation therapy for tumors refers to treating malignant tumors via the induction of cell differentiation. The best characterized clinical application of differentiation therapy is the use of all-trans retinoic acid in the treatment of acute promyelocytic leukemia (APL), which markedly improved the outcome of this disease. Unlike the situation with APL, the development of differentiation therapy for solid tumors is far from satisfactory. To date, no differentiation-inducing agents have been demonstrated to exert a curative effect on solid tumors. However, over the past decade progress in understanding the differentiation pathways and the development of differentiation-inducing agents might shed new light on the differentiation therapy for solid tumors.

Prognosis-related microRNAs in esophageal cancer

INTRODUCTION

Despite improvements in detection, surgical resection and adjuvant therapy, the prognosis of esophageal cancer (EC) patients is dismal. A number of microRNAs (miRNAs) are related with the prognosis of EC.

AREAS COVERED

This review summarises the recent advances in prognosis-related miRNAs in EC and also analyses the molecular functions that they provide. This study further envisages future developments in the potential clinical applications of these miRNAs.

EXPERT OPINION

Altered miRNA expression of cancer tissues is useful for predicting the prognosis of EC patients. Individual circulating miRNAs have the potential to be used as novel biomarkers. Continued basic studies are warranted to gain more mechanistic insights into the functional effect of prognosis-related miRNAs on EC. More clinical trials should be performed to promote the clinical use of prognosis-related miRNAs.

Reconstruction and analysis of transcription factor-miRNA co-regulatory feed-forward loops in human cancers using filter-wrapper feature selection

BACKGROUND

As one of the most common types of co-regulatory motifs, feed-forward loops (FFLs) control many cell functions and play an important role in human cancers. Therefore, it is crucial to reconstruct and analyze cancer-related FFLs that are controlled by transcription factor (TF) and microRNA (miRNA) simultaneously, in order to find out how miRNAs and TFs cooperate with each other in cancer cells and how they contribute to carcinogenesis. Current FFL studies rely on predicted regulation information and therefore suffer the false positive issue in prediction results. More critically, FFLs generated by existing approaches cannot represent the dynamic and conditional regulation relationship under different experimental conditions.

METHODOLOGY/PRINCIPAL FINDINGS

In this study, we proposed a novel filter-wrapper feature selection method to accurately identify co-regulatory mechanism by incorporating prior information from predicted regulatory interactions with parallel miRNA/mRNA expression datasets. By applying this method, we reconstructed 208 and 110 TF-miRNA co-regulatory FFLs from human pan-cancer and prostate datasets, respectively. Further analysis of these cancer-related FFLs showed that the top-ranking TF STAT3 and miRNA hsa-let-7e are key regulators implicated in human cancers, which have regulated targets significantly enriched in cellular process regulations and signaling pathways that are involved in carcinogenesis.

CONCLUSIONS/SIGNIFICANCE

In this study, we introduced an efficient computational approach to reconstruct co-regulatory FFLs by accurately identifying gene co-regulatory interactions. The strength of the proposed feature selection method lies in the fact it can precisely filter out false positives in predicted regulatory interactions by quantitatively modeling the complex co-regulation of target genes mediated by TFs and miRNAs simultaneously. Moreover, the proposed feature selection method can be generally applied to other gene regulation studies using parallel expression data with respect to different biological contexts.

MicroRNA-429 Modulates Hepatocellular Carcinoma Prognosis and Tumorigenesis

MicroRNA-429 (miR-429) may modify the development and progression of cancers; however, the role of this microRNA in the hepatocellular carcinoma (HCC) has not been well elaborated. Here, we tested miR-429 expression in 138 pathology-diagnosed HCC cases and SMMC-7721 cells. We found that miR-429 was upregulated in HCC tumor tissues and that the high expression of miR-429 was significantly correlated with larger tumor size (odd ratio (OR), 2.70; 95% confidence interval (CI), 1.28–5.56) and higher aflatoxin B1-DNA adducts (OR = 3.13, 95% CI = 1.47–6.67). Furthermore, this microRNA overexpression modified the recurrence-free survival and overall survival of HCC patients. Functionally, miR-429 overexpression progressed tumor cells proliferation and inhibited cell apoptosis. These results indicate for the first time that miR-429 may modify HCC prognosis and tumorigenesis and may be a potential tumor therapeutic target.