Identification of mRNA and non-coding RNA hubs using network analysis in organ tropism regulated triple negative breast cancer metastasis

Advanced Insights into Competitive Endogenous RNAs (ceRNAs) Regulated Pathogenic Mechanisms in Metastatic Triple-Negative Breast Cancer (mTNBC)

Triple-negative breast cancer is aggressive and challenging to treat because of a lack of targets and heterogeneity among tumors. A paramount factor in the mortality from breast cancer is metastasis, which is driven by genetic and phenotypic alterations that drive epithelial-mesenchymal transition, stemness, survival, migration and invasion. Many genetic and epigenetic mechanisms have been identified in triple-negative breast cancer that drive these metastatic phenotypes; however, this knowledge has not yet led to the development of effective drugs for metastatic triple-negative breast cancer (mTNBC). One that may not have received enough attention in the literature is post-translational regulation of broad sets of cancer-related genes through inhibitory microRNAs and the complex competitive endogenous RNA (ceRNA) regulatory networks they are influenced by. This field of study and the resulting knowledge regarding alterations in these networks is coming of age, enabling translation into clinical benefit for patients. Herein, we review metastatic triple-negative breast cancer (mTNBC), the role of ceRNA network regulation in metastasis (and therefore clinical outcomes), potential approaches for therapeutic exploitation of these alterations, knowledge gaps and future directions in the field.

An integrated approach to understand the regulatory role of miR-27 family in breast cancer metastasis

One of the prime reasons of increasing breast cancer mortality is metastasizing cancer cells. Owing to the side effects of clinically available drugs to treat breast cancer metastasis, it is of utmost importance to understand the underlying biogenesis of breast cancer tumorigenesis. In-silico identification of potential RNAs might help in utilizing the miR-27 family as a therapeutic target in breast cancer. The experimentally verified common interacting mRNAs for miR27 family are retrieved from three publicly available databases- TargetScan, miRDB and miRTarBase. Finally on comparing the common genes with HCMDB and GEPIA data, four breast cancer-associated differentially expressed metastatic mRNAs (GATA3, ENAH, ITGA2 and SEMA4D) are obtained. Corresponding to the miR27 family and associated mRNAs, interacting drugs are retrieved from Sm2mir and CTDbase, respectively. The interaction network-based approach was utilized to obtain the hub RNAs and triad modules by employing the 'Cytohubba' and 'MClique' plugins, respectively in Cytoscape. Further, sample-, subclass- and promoter methylation-based expression analyses reveals GATA3 and ENAH to be the most significant mRNAs in breast cancer metastasis having >10% genetic alteration in both METABRIC Vs TCGA datasets as per their oncoprint analysis via cBioPortal. Additionally, survival analysis in Oncolnc reveals SEMA4D as survival biomarker. Interactions among the miR27 family, their target mRNAs and drugs interacting with miRNAs and mRNAs can be extensively explored in both in-vivo and in-vitro setups to assess their therapeutic potential in the diminution of breast cancer.

Multidimensional computational study to understand non-coding RNA interactions in breast cancer metastasis

Metastasis is a major breast cancer hallmark due to which tumor cells tend to relocate to regional or distant organs from their organ of origin. This study is aimed to decipher the interaction among 113 differentially expressed genes, interacting non-coding RNAs and drugs (614 miRNAs, 220 lncRNAs and 3241 interacting drugs) associated with metastasis in breast cancer. For an extensive understanding of genetic interactions in the diseased state, a backbone gene co-expression network was constructed. Further, the mRNA-miRNA-lncRNA-drug interaction network was constructed to identify the top hub RNAs, significant cliques and topological parameters associated with differentially expressed genes. Then, the mRNAs from the top two subnetworks constructed are considered for transcription factor (TF) analysis. 39 interacting miRNAs and 1641 corresponding TFs for the eight mRNAs from the subnetworks are also utilized to construct an mRNA-miRNA-TF interaction network. TF analysis revealed two TFs (EST1 and SP1) from the cliques to be significant. TCGA expression analysis of miRNAs and lncRNAs as well as subclass-based and promoter methylation-based expression, oncoprint and survival analysis of the mRNAs are also done. Finally, functional enrichment of mRNAs is also performed. Significant cliques identified in the study can be utilized for identification of newer therapeutic interventions for breast cancer. This work will also help to gain a deeper insight into the complicated molecular intricacies to reveal the potential biomarkers involved with breast cancer progression in future.

Identification of drug targets and prognosis projection for uterine carcinosarcoma based on alternative splicing events

BACKGROUND

Uterine carcinosarcoma (UCS) is an invasive variant of endometrial cancer. The complicated heterogeneity and low frequency of UCS suggest the relevant research is lack. There is an urgent need to further explore the pathogenic mechanism and identify new biomarkers of UCS from different angels to improve its diagnosis and prognosis.

OBJECTIVE

This study is to explore the importance of alternative splicing (AS) events in UCS, construct AS-based prognosis model and excavate key splicing factors (SFs).

METHOD

UCS related gene transcriptome data and AS events data were collected from The Cancer Genome Atlas (TCGA) and TCGA SpliceSeq database. The AS events related to survival were determined by Cox regression analysis, Least absolute shrinkage and selection operator (Lasso) regression analysis and optimal subset analysis. The corresponding risk score was calculated and its efficiency on prognosis was evaluated by Kaplan-Meier (K-M) survival estimate and validated by the receiver operating characteristic (ROC) curve. The prognosis model was constructed with risk score and clinic characters as independent variables to predict patients' survival. On the other hand, Kendall test was applied to inspect the correlation between the SFs and the prognosis-related AS events and a AS-SF network was constructed. Finally, the key SFs were screened through network nodes analysis and survival analysis.

RESULT

Seven AS events the most related to survival were detected and the risk score was obtained. K-M survival estimate and ROC curve validation suggested the risk score was effective. Then Cox model was constructed based on the risk score and a nomogram model was obtained which provided the highest prediction accuracy of 95%. Through the AS-SF network analysis, 16 SFs were screened, among which four survival-related SFs were eventually obtained.

CONCLUSION

The prognosis model could predict the survival rate of UCS patients by their clinical characters and AS-based risk score. And four newly discovered SFs could reveal the molecular mechanism of UCS and act as the potential drug targets and prognosis biomarkers.

An integrated approach to understand fluid shear stress-driven and reactive oxygen species-mediated metastasis of colon adenocarcinoma through mRNA-miRNA-lncRNA-circRNA networks

Development of colon adenocarcinoma (COAD) metastasis involves several mediators including fluid shear stress (FSS), intracellular ROS levels, and non-coding RNAs. In our present study, we identified and investigated the role of regulatory non-coding RNA molecules specifically involved in COAD metastasis and their association with FSS and ROS. Interactions between the mRNAs associated with FSS and ROS, the corresponding microRNAs (miRNAs), long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) in COAD metastasis were used to generate the mRNA-miRNA-lncRNA-circRNA network. Experimental validation of the identified RNA hubs using quantitative real-time PCR demonstrated a direct effect of the FSS on their expression levels in cancer cells. FSS resulted in the downregulation of HMGA1 and RAN, as well as the upregulation of HSP90AA1, PMAIP1 and BIRC5. Application of shear stress also led to downregulation of hsa-miR-26b-5p and hsa-miR-34a-5p levels in HCT116 cells. Further, functional enrichment and survival analysis of the significant miRNAs, as well as the OncoPrint and the survival analyses of the selected mRNAs were performed. Subsequently, their functional role was also corroborated with existing literature. Ten significant miRNA hubs were identified, out of which hsa-miR-17-5p and hsa-miR-20a-5p were found to interact with lncRNA (CCAT2) while hsa-miR-335 was found to interact with four circRNAs. Fifteen significant miRNAs were identified in 10 different modules suggesting their importance in FSS and ROS-mediated COAD metastasis. Finally, 10 miRNAs and 3 mRNAs associated with FSS and/or ROS were identified as significant overall survival markers; 33 mRNAs were also identified as metastasis-free survival markers whereas 15 mRNAs showed > 10% gene alterations in TCGA-COAD data and may serve as promising therapeutic biomarkers in the COAD metastasis.

miR-106b as an emerging therapeutic target in cancer

MicroRNAs (miRNAs) comprise short non-coding RNAs that function in regulating the expression of tumor suppressors or oncogenes and modulate oncogenic signaling pathways in cancer. miRNAs expression alters significantly in several tumor tissues and cancer cell lines. For example, miR-106b functions as an oncogene and increases in multiple cancers. The miR-106b directly targets genes involved in tumorigenesis, proliferation, invasion, migration, and metastases. This review has focused on the miR-106b function and its downstream target in different cancers and provide perspective into how miR-106 regulates cancer cell proliferation, migration, invasion, and metastases by regulating the tumor suppressor genes. Since miRNAs-based therapies are currently being developed to enhance cancer therapy outcomes, miR-106b could be an attractive and prospective candidate in different cancer types for detection, diagnosis, and prognosis assessment in the tumor.

Immunomodulatory Properties of Human Breast Milk: MicroRNA Contents and Potential Epigenetic Effects

Infants who are exclusively breastfed in the first six months of age receive adequate nutrients, achieving optimal immune protection and growth. In addition to the known nutritional components of human breast milk (HBM), i.e., water, carbohydrates, fats and proteins, it is also a rich source of microRNAs, which impact epigenetic mechanisms. This comprehensive work presents an up-to-date overview of the immunomodulatory constituents of HBM, highlighting its content of circulating microRNAs. The epigenetic effects of HBM are discussed, especially those regulated by miRNAs. HBM contains more than 1400 microRNAs. The majority of these microRNAs originate from the lactating gland and are based on the remodeling of cells in the gland during breastfeeding. These miRNAs can affect epigenetic patterns by several mechanisms, including DNA methylation, histone modifications and RNA regulation, which could ultimately result in alterations in gene expressions. Therefore, the unique microRNA profile of HBM, including exosomal microRNAs, is implicated in the regulation of the genes responsible for a variety of immunological and physiological functions, such as FTO, INS, IGF1, NRF2, GLUT1 and FOXP3 genes. Hence, studying the HBM miRNA composition is important for improving the nutritional approaches for pregnancy and infant's early life and preventing diseases that could occur in the future. Interestingly, the composition of miRNAs in HBM is affected by multiple factors, including diet, environmental and genetic factors.

iLncDA-LTR: Identification of lncRNA-disease associations by learning to rank

Identifying the associations between lncRNAs and diseases is helpful for the treatment and diagnosis of complex diseases. The existing computational methods mainly focus on the identification of associations between known lncRNAs and known diseases. However, with the application of high-throughput sequencing in lncRNA research, more and more lncRNAs have been detected. Predicting diseases related with newly detected lncRNAs has not been fully explored. Therefore, there is an urgent need for developing powerful computational methods to predict diseases related with newly detected lncRNAs. In this paper, we propose a Learning to Rank (LTR)-based method called iLncDA-LTR to predict diseases related with newly detected lncRNAs. iLncDA-LTR treats this task as an information retrieval task. The newly detected lncRNAs and diseases are considered as queries and documents, respectively. For a given newly detected lncRNA (query), iLncDA-LTR integrates multiple relevant information into LTR for predicting candidate diseases associated with query lncRNA. Experimental results show that iLncDA-LTR outperforms the other exiting state-of-the-art predictors on independent dataset. The corresponding web server of iLncDA-LTR has been constructed as well (http://bliulab.net/iLncDA-LTR/).

Evaluation of Diagnostic and Prognostic Value of hsa_circ_0084927 and Analysis of Associated ceRNA Network in Colorectal Cancer

Object

This study aims to analyze the differentially expressed circRNA in colon adenocarcinoma (COAD) and evaluate its diagnostic and prognostic value. Analyze associated circRNA-miRNA-mRNA network in COAD.

Methods and Materials

Real-time quantitative PCR (RT-PCR) was used to verify differentially expressed circRNA in COAD tissues and cells; Receiver operator characteristic (ROC) and Cox regression analysis were used to evaluating its diagnostic and prognostic value; Meanwhile we conducted CCK-8, invasion, and migration experiments in cell lines to explore the function of circRNA. In addition, a competitive endogenous RNA (ceRNA) network was established using bioinformatics methods to explore its prognostic value and potential functional mechanisms.

Results

Our study found that hsa_circ_0084927 is highly expressed in COAD tissues and cell lines. Plasma hsa_circ_0084927 can be used as a diagnostic marker for COAD patients; hsa_circ_0084927 can promote the proliferation, migration and invasion of COAD cells. In addition, we effectively constructed a ceRNA: network has_circ_0084927/miR-106b-5p/VEGFA. The ceRNA network indicates that hsa_circ_0084927 may affect the prognosis of COAD through the regulation of cell cycle, apoptosis and other pathways.

Conclusion

Our research results indicate that hsa_circ_0084927 has a cancer-promoting effect and may be used as a circulating tumor marker for COAD prognosis. In addition, this study proposes a new ceRNA network to provide new insights for the targeted therapy of COAD.

MILNP: Plant lncRNA-miRNA Interaction Prediction Based on Improved Linear Neighborhood Similarity and Label Propagation

Knowledge of the interactions between long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) is the basis of understanding various biological activities and designing new drugs. Previous computational methods for predicting lncRNA-miRNA interactions lacked for plants, and they suffer from various limitations that affect the prediction accuracy and their applicability. Research on plant lncRNA-miRNA interactions is still in its infancy. In this paper, we propose an accurate predictor, MILNP, for predicting plant lncRNA-miRNA interactions based on improved linear neighborhood similarity measurement and linear neighborhood propagation algorithm. Specifically, we propose a novel similarity measure based on linear neighborhood similarity from multiple similarity profiles of lncRNAs and miRNAs and derive more precise neighborhood ranges so as to escape the limits of the existing methods. We then simultaneously update the lncRNA-miRNA interactions predicted from both similarity matrices based on label propagation. We comprehensively evaluate MILNP on the latest plant lncRNA-miRNA interaction benchmark datasets. The results demonstrate the superior performance of MILNP than the most up-to-date methods. What's more, MILNP can be leveraged for isolated plant lncRNAs (or miRNAs). Case studies suggest that MILNP can identify novel plant lncRNA-miRNA interactions, which are confirmed by classical tools. The implementation is available on https://github.com/HerSwain/gra/tree/MILNP.

CASC7: a LncRNA with potential clinical application

AIM

To explore the novel lncRNA CASC7 and its potential clinical applications.Long non-coding RNAs (IncRNAs) are defined as non-coding genes with a length exceeding 200 nt. As transcripts of RNA polymerase Il, they have limited coding potential due to the lack of an open reading frame in the gene segment. Research has confirmed that lncRNAs are important biological factors that regulate many life processes in the human body through different mechanisms. This work focused on Cancer Susceptibility Candidate 7 (CASC7), a lncRNA with nuclear and cytoplasmic localization. Publicly available databases show that CASC7 is differentially expressed in human organs as well as in tumor tissues. A study confirmed that CASC7 is abnormally expressed in colorectal cancer, glioma, breast cancer, non-small cell lung cancer and thyroid cancer. In male infertility, asthma and heart failure, it may also be a potential therapeutic target and promising biomarker. CASC7 mainly plays a biological effect through direct or indirect effects of promoting or inhibiting the expression of related genes. Currently, only few studies have assessed CASC7, and its mechanisms are not clear. The main purpose of this review was to examine CASC7 and its possible molecular mechanisms and clinical significance in cancer.

CONCLUSION

We reviewed the recent research progress of CASC7 and its potential as a diagnostic marker and therapeutic target, and provide an outlook on its future application in terms of mechanism.Key points:CASC7 is a novel lncRNA, for which there are few reports.Aberrant expression of CASC7 may be associated with the emergence and treatment of many clinical diseases, including malignancy.

Construction of an HCC recurrence model based on the investigation of immune-related lncRNAs and related mechanisms

Long noncoding RNAs (lncRNAs) are emerging as critical regulators of gene expression and play fundamental roles in immune regulation. Growing evidence suggests that immune-related genes and lncRNAs can serve as markers to predict the prognosis of patients with cancers, including hepatocellular carcinoma (HCC). This study aimed to contract an immune-related lncRNA (IR-lncRNA) signature for prospective assessment to predict early recurrence of HCC. A total of 319 HCC samples under radical resection were randomly divided into a training cohort (161 samples) and a testing cohort (158 samples). In the training dataset, univariate, lasso, and multivariate Cox regression analyses identified a 9-IR-lncRNA signature closely related to disease-free survival. Kaplan-Meier analysis, principal component analysis, gene set enrichment analysis, and nomogram were used to evaluate the risk model. The results were further confirmed in the testing cohort. Furthermore, we constructed a competitive endogenous RNA regulatory network. The results of the present study indicated that this 9-IR-lncRNA signature has important clinical implications for improving predictive outcomes and guiding individualized treatment in HCC patients. These IR-lncRNAs and regulated genes may be potential biomarkers associated with the prognosis of HCC.

Long non-coding RNA CASC7 suppresses malignant behaviors of breast cancer by regulating miR-21-5p/FASLG axis

Recently, it has been increasingly proved that lncRNAs are functionally involved in a majority of tumor progression. LncRNA CASC7 has also been revealed to participate in the development of several cancers as a tumor promoter or suppressor. Herein, we focus on uncovering the role and underlying molecular mechanism of CASC7 in breast cancer. Tumor tissues and the paired paracancerous tissues from the breast cancer patients were used to evaluate the level of CASC7 in breast cancer. By analyzing the CASC7 expression in breast cancer cell lines, both the expression levels of CASC7 in cancer tissues and cell lines were obviously downregulated compared to those in paired paracancerous tissues and normal human epithelial MCF10A cells. Subsequently, the construction of lentivirus overexpression system (oe-CASC7 and oe-NC) was used to elevate the expression of CASC7. A series of functional experiments were conducted to show that the cell proliferation, migration, and invasion were inhibited when CASC7 overexpressed in breast cancer cells. Meanwhile, the apoptosis of oe-CASC7 cells was induced compared to the oe-NC breast cancer cells. We further confirmed that CASC7 functions by regulating miR-21-5p/FASLG axis. Finally, a xenograft model in nude mice verified that CASC7 was a tumor suppressor in breast cancer. These results suggest that lncRNA CASC7 suppresses to malignant behaviors of breast cancer by modulating miR-21-5p/FASLG axis. Abbreviations lncRNAs: long non-coding RNAs; ceRNA: competing endogenous RNA; CASC7: cancer susceptibility candidate 7; miRNAs: MicroRNAs; MAPK10: mitogen-activated protein kinase 10; FASLG: Tumor Necrosis Factor Ligand Superfamily Member 6; FAS: Tumor Necrosis Factor Receptor Superfamily Member 6.

Conditioned Medium of Bone Marrow Mesenchymal Stem Cells Involved in Acute Lung Injury by Regulating Epithelial Sodium Channels via miR-34c

Background

One of the characteristics of acute lung injury (ALI) is severe pulmonary edema, which is closely related to alveolar fluid clearance (AFC). Mesenchymal stem cells (MSCs) secrete a wide range of cytokines, growth factors, and microRNA (miRNAs) through paracrine action to participate in the mechanism of pulmonary inflammatory response, which increase the clearance of edema fluid and promote the repair process of ALI. The epithelial sodium channel (ENaC) is the rate-limiting step in the sodium–water transport and edema clearance in the alveolar cavity; the role of bone marrow-derived MSC-conditioned medium (BMSC-CM) in edema clearance and how miRNAs affect ENaC are still seldom known.

Methods

CCK-8 cell proliferation assay was used to detect the effect of BMSC-CM on the survival of alveolar type 2 epithelial (AT2) cells. Real-time polymerase chain reaction (RT-PCR) and western blot were used to detect the expression of ENaC in AT2 cells. The effects of miR-34c on lung fluid absorption were observed in LPS-treated mice in vivo, and the transepithelial short-circuit currents in the monolayer of H441 cells were examined by the Ussing chamber setup. Dual luciferase reporter gene assay was used to detect the target gene of miR-34c.

Results

BMSC-CM could increase the viability of mouse AT2 cells. RT-PCR and western blot results showed that BMSC-CM significantly increased the expression of the γ-ENaC subunit in mouse AT2 cells. MiR-34c could restore the AFC and lung wet/dry weight ratio in the ALI animal model, and Ussing chamber assay revealed that miR-34c enhanced the amiloride-sensitive currents associated with ENaC activity in intact H441 cell monolayers. In addition, we observed a higher expression of miR-34c in mouse AT2 cells administrated with BMSC-CM, and the overexpression or inhibition of miR-34c could regulate the expression of ENaC protein and alter the function of ENaC. Finally, we detected that myristoylated alanine-rich C kinase substrate (MARCKS) may be one of the target genes of miR-34c.

Conclusion

Our results indicate that BMSC-CM may alleviate LPS-induced ALI through miR-34c targeting MARCKS and regulate ENaC indirectly, which further explores the benefit of paracrine effects of bone marrow-derived MSCs on edematous ALI.

MicroRNAs Possibly Involved in the Development of Bone Metastasis in Clear-Cell Renal Cell Carcinoma

Simple Summary

Bone metastases cause substantial morbidity and implicate worse clinical outcomes for clear-cell renal cell carcinoma patients. MicroRNAs are small RNA molecules that modulate gene translation and are involved in the development of cancer and metastasis. We identified six microRNAs that are potentially specifically involved in metastasis to bone, of which two seem protective and four implicate a higher risk. This aids further understanding of the process of metastasizing to bone. Furthermore, these microRNA hold potential for biomarkers or therapeutic targets.

Abstract

Bone metastasis in clear-cell renal cell carcinoma (ccRCC) leads to substantial morbidity through skeletal related adverse events and implicates worse clinical outcomes. MicroRNAs (miRNA) are small non-protein coding RNA molecules with important regulatory functions in cancer development and metastasis. In this retrospective analysis we present dysregulated miRNA in ccRCC, which are associated with bone metastasis. In particular, miR-23a-3p, miR-27a-3p, miR-20a-5p, and miR-335-3p specifically correlated with the earlier appearance of bone metastasis, compared to metastasis in other organs. In contrast, miR-30b-3p and miR-139-3p were correlated with less occurrence of bone metastasis. These miRNAs are potential biomarkers and attractive targets for miRNA inhibitors or mimics, which could lead to novel therapeutic possibilities for bone targeted treatment in metastatic ccRCC.