Non-coding RNAs: regulators of disease

Potential Biomarker and Therapeutic LncRNAs in Multiple Sclerosis Through Targeting Memory B Cells

Multiple sclerosis (MS) is a chronic autoimmune disease that degenerates the central nervous system (CNS). B cells exacerbate the progression of CNS lesions in MS by producing auto-antibodies, pro-inflammatory cytokines, and presenting auto-antigens to activated T cells. Long non-coding RNAs (lncRNAs) play a crucial role in complex biological processes and their stability in body fluids combined with their tissue specificity make these biomolecules promising biomarker candidates for MS diagnosis. In the current study, we investigated memory B cell-specific lncRNAs located, on average, less than 50 kb from differentially expressed protein-coding genes in MS patients compared to healthy individuals. Moreover, we included in our selection criteria lncRNA transcripts predicted to interact with microRNAs with established involvement in MS. To assess the expression levels of lncRNAs and their adjacent protein-coding genes, quantitative reverse transcription PCR was performed on peripheral blood mononuclear cells samples of 50 MS patients compared to 25 controls. Our results showed that in relapsing MS patients, compared to remitting MS patients and healthy controls, lncRNA RP11-530C5.1 was up-regulated while AL928742.12 was down-regulated. Pearson's correlation tests showed positive correlations between the expression levels of RP11-530C5.1 and AL928742.12 with PAWR and IGHA2, respectively. The results of the ROC curve test demonstrated the potential biomarker roles of AL928742.12 and RP11-530C5.1. We conclude that these lncRNAs are potential markers for detection of relapsing MS patients.

Identification of hsa_circ_0001821 as a Novel Diagnostic Biomarker in Gastric Cancer via Comprehensive Circular RNA Profiling

Background: The morbidity and mortality of gastric cancer (GC) remain high worldwide. With the advent of the Human Genome Sequencing Project, circular RNAs (circRNAs) have attracted widespread attention in cancer research due to their stable ring structure. Our aim was to identify differentially expressed circRNAs in GC and explore their potential roles in GC diagnosis, treatment, and prognostic prediction.

Methods: Large-scale gene screening was performed in three pairs of GC tissues and adjacent noncancerous tissues using high-throughput sequencing. The expression of hsa_circ_0001821 was detected in 80 pairs of tissue samples by quantitative real-time PCR (qRT-PCR). Stability of the ring structure of hsa_circ_0001821 RNA was verified by exonuclease digestion assay, and its diagnostic value was evaluated by receiver operating characteristic (ROC) analysis. In addition, the location of hsa_circ_0001821 in GC cells was detected by nucleoplasm separation assay.

Results: A total of 25,303 circRNAs were identified, among which 2,007 circRNAs were differentially expressed (fold change > 2.0, P < 0.05). Further validation disclosed that hsa_circ_0001821 was significantly downregulated in the 80 pairs of GC tissues and 30 whole-blood specimens obtained from the GC patients. The specificity of hsa_circ_0001821 in GC was higher than that in other solid tumors. In addition, hsa_circ_0001821 was relatively stable after RNA exonuclease digestion. Clinicopathological parameter analysis showed that hsa_circ_0001821 was negatively correlated with tumor depth (r = −0.255, P = 0.022) and lymph node metastasis (r = −0.235, P = 0.036). Area under the curve (AUC) analysis showed that the diagnostic efficiency of circulating hsa_circ_0001821 in distinguishing GC patients was higher than that in GC tissues (0.872, 95%CI: 0.767–0.977 vs. 0.792, 95%CI: 0.723–0.861). Combined use of circulating hsa_circ_0001821 with the existing tumor markers yielded the largest AUC of 0.933. Finally, hsa_circ_0001821 was demonstrated to mainly locate in the cytoplasm, implying that it played a potential regulatory role in GC at the posttranscriptional level.

Conclusion: Hsa_circ_0001821 may prove to be a new and promising potential biomarker for GC diagnosis.

Molecular mechanisms of circular RNAs, transforming growth factor-β, and long noncoding RNAs in hepatocellular carcinoma

At the heart of hepatocellular carcinoma (HCC) lies disruption of signaling pathways at the level of molecules, genes, and cells. Non‐coding RNAs (ncRNAs) have been implicated in the disease progression of HCC. For instance, dysregulated expression of circular RNAs (circRNAs) has been observed in patients with HCC. As such, these RNAs are potential therapeutic targets and diagnostic markers for HCC. Long non‐coding RNAs (lncRNAs), a type of ncRNA, have also been recognized to participate in the initiation and progression of HCC. Transforming growth factor‐beta (TGF‐β) is another element which is now recognized to play crucial roles in HCC. It has been implicated in many biological processes such as survival, immune surveillance, and cell proliferation. In HCC, TGF‐β promotes disease progression by two mechanisms: an intrinsic signaling pathway and the extrinsic pathway. Through these pathways, it modulates various microenvironment factors such as inflammatory mediators and fibroblasts. An interesting yet‐to‐be resolved concept is whether the HCC‐promoting role of TGF‐β pathways is limited to a subset of HCC patients or it is involved in the whole process of HCC development. This review summarizes recent advancements to highlight the roles of circRNAs, lncRNAs, and TGF‐β in HCC.

Non-Coding RNAs in Cartilage Development: An Updated Review

In the development of the skeleton, the long bones are arising from the process of endochondral ossification (EO) in which cartilage is replaced by bone. This complex process is regulated by various factors including genetic, epigenetic, and environmental elements. It is recognized that DNA methylation, higher-order chromatin structure, and post-translational modifications of histones regulate the EO. With emerging understanding, non-coding RNAs (ncRNAs) have been identified as another mode of EO regulation, which is consist of microRNAs (miRNAs or miRs) and long non-coding RNAs (lncRNAs). There is expanding experimental evidence to unlock the role of ncRNAs in the differentiation of cartilage cells, as well as the pathogenesis of several skeletal disorders including osteoarthritis. Cutting-edge technologies such as epigenome-wide association studies have been employed to reveal disease-specific patterns regarding ncRNAs. This opens a new avenue of our understanding of skeletal cell biology, and may also identify potential epigenetic-based biomarkers. In this review, we provide an updated overview of recent advances in the role of ncRNAs especially focus on miRNA and lncRNA in the development of bone from cartilage, as well as their roles in skeletal pathophysiology.

LDAPred: A Method Based on Information Flow Propagation and a Convolutional Neural Network for the Prediction of Disease-Associated lncRNAs

Long non-coding RNAs (lncRNAs) play a crucial role in the pathogenesis and development of complex diseases. Predicting potential lncRNA-disease associations can improve our understanding of the molecular mechanisms of human diseases and help identify biomarkers for disease diagnosis, treatment, and prevention. Previous research methods have mostly integrated the similarity and association information of lncRNAs and diseases, without considering the topological structure information among these nodes, which is important for predicting lncRNA-disease associations. We propose a method based on information flow propagation and convolutional neural networks, called LDAPred, to predict disease-related lncRNAs. LDAPred not only integrates the similarities, associations, and interactions among lncRNAs, diseases, and miRNAs, but also exploits the topological structures formed by them. In this study, we construct a dual convolutional neural network-based framework that comprises the left and right sides. The embedding layer on the left side is established by utilizing lncRNA, miRNA, and disease-related biological premises. On the right side of the frame, multiple types of similarity, association, and interaction relationships among lncRNAs, diseases, and miRNAs are calculated based on information flow propagation on the bi-layer networks, such as the lncRNA-disease network. They contain the network topological structure and they are learned by the right side of the framework. The experimental results based on five-fold cross-validation indicate that LDAPred performs better than several state-of-the-art methods. Case studies on breast cancer, colon cancer, and osteosarcoma further demonstrate LDAPred's ability to discover potential lncRNA-disease associations.

lncRNA SPRY4-IT1 Regulates Cell Proliferation and Migration by Sponging miR-101-3p and Regulating AMPK Expression in Gastric Cancer

Increasing evidence indicates that long noncoding RNA SPRY4 intronic transcript 1 (lncRNA SPRY4-IT1) has been reported to be associated with the progression of several cancers, but its expression level and the function of SPRY4-IT1 in the progression of gastric cancer (GC) have been rarely reported. Here we found that SPRY4-IT1 was upregulated in GC. In vitro experiments revealed that SPRY4-IT1 knockdown significantly inhibited GC cell proliferation by causing G1 arrest and promoting apoptosis, whereas SPRY4-IT1 overexpression promoted cell growth. Further functional assays indicated that SPRY4-IT1 overexpression significantly promoted cell migration and invasion. Bioinformatics analysis predicted that there is a SPRY4-IT1/miR-101-3p/AMPK axis in GC progression. A dual-luciferase reporter system validated the direct interaction of SPRY4-IT1, miR-101-3p, and AMPK. Western blot verified that the inhibition of SPRY4-IT1 decreased AMPK expression. Furthermore, silencing SPRY4-IT1 suppressed GC growth in vivo. Importantly, we demonstrated that SPRY4-IT1 was upregulated in serum exosomes from GC patients and correlated with cancer metastasis. Altogether, silencing SPRY4-IT1 suppresses the progression of GC by interacting with miR-101-3p and decreasing inhibiting AMPK expression. Taken together, our study demonstrates that SPRY4-IT1 could act as a potential therapeutic target for GC patients.

MicroRNAs and complex diseases: from experimental results to computational models

Plenty of microRNAs (miRNAs) were discovered at a rapid pace in plants, green algae, viruses and animals. As one of the most important components in the cell, miRNAs play a growing important role in various essential and important biological processes. For the recent few decades, amounts of experimental methods and computational models have been designed and implemented to identify novel miRNA-disease associations. In this review, the functions of miRNAs, miRNA-target interactions, miRNA-disease associations and some important publicly available miRNA-related databases were discussed in detail. Specially, considering the important fact that an increasing number of miRNA-disease associations have been experimentally confirmed, we selected five important miRNA-related human diseases and five crucial disease-related miRNAs and provided corresponding introductions. Identifying disease-related miRNAs has become an important goal of biomedical research, which will accelerate the understanding of disease pathogenesis at the molecular level and molecular tools design for disease diagnosis, treatment and prevention. Computational models have become an important means for novel miRNA-disease association identification, which could select the most promising miRNA-disease pairs for experimental validation and significantly reduce the time and cost of the biological experiments. Here, we reviewed 20 state-of-the-art computational models of predicting miRNA-disease associations from different perspectives. Finally, we summarized four important factors for the difficulties of predicting potential disease-related miRNAs, the framework of constructing powerful computational models to predict potential miRNA-disease associations including five feasible and important research schemas, and future directions for further development of computational models.

MiR-27a-3p downregulation contributes to the development of occlusive bronchiolitis

The only effective clinical treatment for many end-stage lung diseases is lung transplantation. However, chronic rejection of transplanted lung affects the long-term efficacy of lung transplantation to a large extent, thereby limiting the clinical application of lung transplantation. Occlusive bronchiolitis (OB) is a major cause of chronic functional loss of the transplanted lung. However, the OB pathogenesis remains unclear. Therefore, studying the OB pathogenesis and finding effective intervention methods are highly important. This study analyzed changes in the expression profile of microRNAs and transcription factors in mice with OB after orthotopic tracheal transplantation. miR-27a-3p was upregulated in lung tissue 20 days after transplantation. Transcription factor microarray analysis revealed that Smad3 was significantly downregulated. A miRNA-mRNA interaction network was constructed, and specific regulatory effects of miR-27a-3p on Smad3 were found. Smad3 was strongly associated with tumorigenesis and organ fibrosis. Compared with the control group, miR-27a-3p inhibited the epithelial-mesenchymal transformation (EMT) of lung epithelial cells. In addition, miR-27a-3p inhibition promoted the invasion and migration of lung epithelial cells. Dual luciferase reporter gene assay showed that miR-27a-3p can regulate the promoter activity of Smad3. MiR-27a-3p also inhibited the expression of inflammatory cytokines. Western blot results showed that miR-27a-3p can upregulate the E-cadherin expression and downregulate the expression of vimentin, fibronectin, and α-SMA. By studying the OB pathogenesis, we found that inhibition or alteration of the occurrence of EMT may reduce the proportion of chronic rejection of lung transplantation. MiR-27a-3p may also be developed as a new drug for the OB therapy. This finding will provide many possibilities for OB treatment and improve the prognosis of patients with OB.

Graph Convolutional Network and Convolutional Neural Network Based Method for Predicting lncRNA-Disease Associations

Aberrant expressions of long non-coding RNAs (lncRNAs) are often associated with diseases and identification of disease-related lncRNAs is helpful for elucidating complex pathogenesis. Recent methods for predicting associations between lncRNAs and diseases integrate their pertinent heterogeneous data. However, they failed to deeply integrate topological information of heterogeneous network comprising lncRNAs, diseases, and miRNAs. We proposed a novel method based on the graph convolutional network and convolutional neural network, referred to as GCNLDA, to infer disease-related lncRNA candidates. The heterogeneous network containing the lncRNA, disease, and miRNA nodes, is constructed firstly. The embedding matrix of a lncRNA-disease node pair was constructed according to various biological premises about lncRNAs, diseases, and miRNAs. A new framework based on a graph convolutional network and a convolutional neural network was developed to learn network and local representations of the lncRNA-disease pair. On the left side of the framework, the autoencoder based on graph convolution deeply integrated topological information within the heterogeneous lncRNA-disease-miRNA network. Moreover, as different node features have discriminative contributions to the association prediction, an attention mechanism at node feature level is constructed. The left side learnt the network representation of the lncRNA-disease pair. The convolutional neural networks on the right side of the framework learnt the local representation of the lncRNA-disease pair by focusing on the similarities, associations, and interactions that are only related to the pair. Compared to several state-of-the-art prediction methods, GCNLDA had superior performance. Case studies on stomach cancer, osteosarcoma, and lung cancer confirmed that GCNLDA effectively discovers the potential lncRNA-disease associations.

LncRNA-Disease Associations Prediction Using Bipartite Local Model With Nearest Profile-Based Association Inferring

There is much evidence that long non-coding RNA (lncRNA) is associated with many diseases. However, it is time-consuming and expensive to identify meaningful lncRNA-disease associations (LDAs) through medical or biological experiments. Therefore, investigating how to identify more meaningful LDAs is necessary, and at the same time it is conducive to the prevention, diagnosis and treatment of complex diseases. Considering the limitations of some current prediction models, a novel model based on bipartite local model with nearest profile-based association inferring, BLM-NPAI, is developed for predicting LDAs. This model predicts novel LDAs from the lncRNA side and the disease side, respectively. More importantly, for some lncRNAs and diseases without any association, the model can also be predicted by their nearest neighbors. Leave-one-out cross validation (LOOCV) and 5-fold cross validation are implemented for BLM-NPAI to evaluate the performance of this model. Our model is superior to current advanced methods in most cases. In addition, to verify the validity and reliability of BLM-NPAI, three disease cases and three lncRNA cases are analyzed to further evaluate BLM-NPAI. Finally, these predicted novel LDAs are confirmed by using the LncRNA-disease database.

Long noncoding RNA NORAD regulates MPP+-induced Parkinson's disease model cells

BACKGROUND

Long non-coding RNAs (lncRNAs) have been demonstrated to play important roles in human diseases. Yet, the functions of lncRNAs in neurodegenerative disorders, such as Parkinson's disease (PD) are poorly understood. In this study, we used human neuroblastoma SH-SY5Y cell line as a cell-basedin vitro PD model, and investigated the role of lncRNA, Non-Coding RNA Activated By DNA Damage (NORAD) in 1-methyl-4-phenylpyridinium (MPP+)-induced PD-like cytotoxicity.

METHODS

SH-SY5Y cells were culturedin vitro, and treated with MPP + at various concentrations, or of various durations of times to induce PD-like cytotoxic events. qRT-PCR was used to measure MPP+-induced NORAD expression changes. Lentiviral transduction was applied to stably upregulate or downregulate NORAD in SH-SY5Y cells. The effects of NORAD upregulation or downregulation on MPP+-induced cytotoxic events, including dose-dependent and time-dependent cell death, apoptosis, caspase 3/7, reactive Oxygen Species (ROS) and lactate dehydrogenase (LDH) activities, were quantitatively investigated.

RESULTS

MPP + induced cytotoxicity, and downregulated NORAD in both dose- and time- dependent manners in SH-SY5Y cells. Lentiviral-induced NORAD upregulation was found to protect against MPP+-induced cytotoxicity in SH-SY5Y cells, as it rescued MPP+-induced cellular destruction and apoptosis, as well as decreased MPP+-induced caspase 3/7, ROS and LDH activities. Alternatively, NORAD downregulation was found to significantly deteriorate MPP+-induced cytotoxicity in SH-SY5Y cells.

CONCLUSION

We presented a novel functional role of lncRNA NORAD in regulating human Parkinson's disease.

DNILMF-LDA: Prediction of lncRNA-Disease Associations by Dual-Network Integrated Logistic Matrix Factorization and Bayesian Optimization

Identifying associations between lncRNAs and diseases can help understand disease-related lncRNAs and facilitate disease diagnosis and treatment. The dual-network integrated logistic matrix factorization (DNILMF) model has been used for drug-target interaction prediction, and good results have been achieved. We firstly applied DNILMF to lncRNA-disease association prediction (DNILMF-LDA). We combined different similarity kernel matrices of lncRNAs and diseases by using nonlinear fusion to extract the most important information in fused matrices. Then, lncRNA-disease association networks and similarity networks were built simultaneously. Finally, the Gaussian process mutual information (GP-MI) algorithm of Bayesian optimization was adopted to optimize the model parameters. The 10-fold cross-validation result showed that the area under receiving operating characteristic (ROC) curve (AUC) value of DNILMF-LDA was 0.9202, and the area under precision-recall (PR) curve (AUPR) was 0.5610. Compared with LRLSLDA, SIMCLDA, BiwalkLDA, and TPGLDA, the AUC value of our method increased by 38.81%, 13.07%, 8.35%, and 6.75%, respectively. The AUPR value of our method increased by 52.66%, 40.05%, 37.01%, and 44.25%. These results indicate that DNILMF-LDA is an effective method for predicting the associations between lncRNAs and diseases.

Transgenerational inheritance: how impacts to the epigenetic and genetic information of parents affect offspring health

BACKGROUND

A defining feature of sexual reproduction is the transmission of genomic information from both parents to the offspring. There is now compelling evidence that the inheritance of such genetic information is accompanied by additional epigenetic marks, or stable heritable information that is not accounted for by variations in DNA sequence. The reversible nature of epigenetic marks coupled with multiple rounds of epigenetic reprogramming that erase the majority of existing patterns have made the investigation of this phenomenon challenging. However, continual advances in molecular methods are allowing closer examination of the dynamic alterations to histone composition and DNA methylation patterns that accompany development and, in particular, how these modifications can occur in an individual’s germline and be transmitted to the following generation. While the underlying mechanisms that permit this form of transgenerational inheritance remain unclear, it is increasingly apparent that a combination of genetic and epigenetic modifications plays major roles in determining the phenotypes of individuals and their offspring.

OBJECTIVE AND RATIONALE

Information pertaining to transgenerational inheritance was systematically reviewed focusing primarily on mammalian cells to the exclusion of inheritance in plants, due to inherent differences in the means by which information is transmitted between generations. The effects of environmental factors and biological processes on both epigenetic and genetic information were reviewed to determine their contribution to modulating inheritable phenotypes.

SEARCH METHODS

Articles indexed in PubMed were searched using keywords related to transgenerational inheritance, epigenetic modifications, paternal and maternal inheritable traits and environmental and biological factors influencing transgenerational modifications. We sought to clarify the role of epigenetic reprogramming events during the life cycle of mammals and provide a comprehensive review of how the genomic and epigenomic make-up of progenitors may determine the phenotype of its descendants.

OUTCOMES

We found strong evidence supporting the role of DNA methylation patterns, histone modifications and even non-protein-coding RNA in altering the epigenetic composition of individuals and producing stable epigenetic effects that were transmitted from parents to offspring, in both humans and rodent species. Multiple genomic domains and several histone modification sites were found to resist demethylation and endure genome-wide reprogramming events. Epigenetic modifications integrated into the genome of individuals were shown to modulate gene expression and activity at enhancer and promoter domains, while genetic mutations were shown to alter sequence availability for methylation and histone binding. Fundamentally, alterations to the nuclear composition of the germline in response to environmental factors, ageing, diet and toxicant exposure have the potential to become hereditably transmitted.

WIDER IMPLICATIONS

The environment influences the health and well-being of progeny by working through the germline to introduce spontaneous genetic mutations as well as a variety of epigenetic changes, including alterations in DNA methylation status and the post-translational modification of histones. In evolutionary terms, these changes create the phenotypic diversity that fuels the fires of natural selection. However, rather than being adaptive, such variation may also generate a plethora of pathological disease states ranging from dominant genetic disorders to neurological conditions, including spontaneous schizophrenia and autism.

Minireview: The Epigenetic Modulation of KISS1 in Reproduction and Cancer

Epigenetics describes how both lifestyle and environment may affect human health through the modulation of genome functions and without any change to the DNA nucleotide sequence. The discovery of several epigenetic mechanisms and the possibility to deliver epigenetic marks in cells, gametes, and biological fluids has opened up new perspectives in the prevention, diagnosis, and treatment of human diseases. In this respect, the depth of knowledge of epigenetic mechanisms is fundamental to preserving health status and to developing targeted interventions. In this minireview, we summarize the epigenetic modulation of the KISS1 gene in order to provide an example of epigenetic regulation in health and disease.

MiR-6872 host gene SEMA3B and its antisense lncRNA SEMA3B-AS1 function synergistically to suppress gastric cardia adenocarcinoma progression

BACKGROUND

Semaphorin 3B (SEMA3B) is frequently inactivated in several carcinomas. However, as the host gene of miR-6872, the roles of SEMA3B, antisense lncRNA SEMA3B-AS1, and miR-6872 in gastric cardia adenocarcinoma (GCA) tumorigenesis have not been clarified.

METHODS

The expression levels of SEMA3B, SEMA3B-AS1, and miR-6872 were respectively detected by qRT-PCR, western blot, or immunohistochemical staining assays. The methylation status was determined by BGS and BS-MSP methods. In vitro assays were preformed to explore the biological effects of SEMA3B, SEMA3B-AS1, and miR-6872-5p in gastric cancer cells. Chromatin immunoprecipitation assay was used to detect the binding of protein to DNA. The interaction of SEMA3B-AS1 with MLL4 was identified by RNA immunoprecipitation and RNA pull-down assays.

RESULTS

Frequent downregulation of SEMA3B, SEMA3B-AS1, and miR-6872 was detected in GCA tissues and gastric cancer cells. Aberrant hypermethylation of the promoter region was more tumor specific and was negatively correlated with the expression level of SEMA3B, SEMA3B-AS1, and miR-6872-5p. Transcription factor Sp1 activated SEMA3B or SEMA3B-AS1 transcription and CpG sites hypermethylation within promoter region eliminated Sp1 binding ability. Overexpression of SEMA3B and SEMA3B-AS1 inhibited gastric cancer cell proliferation, migration, and invasion in vitro. SEMA3B-AS1 induced the expression of SEMA3B by interacting with MLL4. ZNF143 might be the target gene of miR-6872-5p and miR-6872-5p functioning synergistically with SEMA3B to suppress cell invasion. Furthermore, SEMA3B, SEMA3B-AS1, and miR-6872-5p expression levels were associated with GCA patients' survival.

CONCLUSIONS

SEMA3B, SEMA3B-AS1, and miR-6872 may act as tumor suppressors and may serve as potential targets for antitumor therapy.

lncRNA mortal obligate RNA transcript was downregulated in ovarian carcinoma and inhibits cancer cell proliferation by downregulating miRNA-21

microRNA-21 (miRNA-21) is a well-characterized oncogenic miRNA in human cancers. In the present study, we found that miRNA-21 was upregulated, while long noncoding RNA Mortal Obligate RNA Transcript (lncRNA MORT), which has been reported to be silenced in 16 types of cancers, was downregulated in tumor tissues than in adjacent healthy tissues of patients with ovarian carcinoma. Expression of lncRNA MORT in tumor tissues was found to be significantly affected by tumor size but not by tumor metastasis. Expression levels of lncRNA MORT and miRNA-21 were significantly and inversely correlated in both tumor tissues and adjacent healthy tissues. Overexpression of lncRNA MORT inhibited miRNA-21, while miRNA-21 overexpression failed to significantly affect lncRNA MORT expression. Overexpression of lncRNA MORT inhibited, while miRNA-21 overexpression promoted the proliferation of cells of ovarian cancer cell lines. In addition, miRNA-21 overexpression partially reversed the inhibitory effects of lncRNA MORT overexpression on cancer cell proliferation. However, overexpression of lncRNA MORT showed no significant effects on cancer cell migration and invasion. Therefore, lncRNA MORT was downregulated in ovarian carcinoma and lncRNA MORT overexpression inhibited cancer cell proliferation, possibly by downregulating miRNA-21.

miR-23b and miR-27b are oncogenic microRNAs in breast cancer: evidence from a CRISPR/Cas9 deletion study

BACKGROUND

Altered expression of microRNAs (miRNAs) is known to contribute to cancer progression. miR-23b and miR-27b, encoded within the same miRNA cluster, are reported to have both tumor suppressive and oncogenic activity across human cancers, including breast cancer.

METHODS

To clarify this dichotomous role in breast cancer, miR-23b and miR-27b were knocked out using CRISPR/Cas9 gene knockout technology, and the role of endogenous miR-23b and miR-27b was examined in a breast cancer model system in vitro and in vivo.

RESULTS

Characterization of the knockout cells in vitro demonstrated that miR-23b and miR-27b are indeed oncogenic miRNAs in MCF7 breast cancer cells. miR-23b and miR-27b knockout reduced tumor growth in xenograft nude mice fed a standard diet, supporting their oncogenic role in vivo. However, when xenograft mice were provided a fish-oil diet, miR-27b depletion, but not miR-23b depletion, compromised fish-oil-induced suppression of xenograft growth, indicating a context-dependent nature of miR-27b oncogenic activity.

CONCLUSIONS

Our results demonstrate that miR-23b and miR-27b are primarily oncogenic in MCF7 breast cancer cells and that miR-27b may have tumor suppressive activity under certain circumstances.

The Long Non-Coding RNA (lncRNA) AGAP2-AS1 is Upregulated in Ovarian Carcinoma and Negatively Regulates lncRNA MEG3

Background

lncRNA AGAP2-AS1 has been reported to promote several types of cancers, but its involvement in ovarian carcinoma (OC) is unknown. Our study was carried out to investigate the potential involvement of AGAP2-AS1 in OC.

Material/Methods

We enrolled 82 patients with ovarian carcinoma. Quantitative real-time PCR (qRT-PCR) was performed to analyze lncRNA AGAP2-AS1 expression in ovarian carcinoma and proliferation assays were performed.

Results

We found AGAP2-AS1 was upregulated in OC tissues compared to adjacent healthy tissues, and expression levels of AGAP2-AS1 increased with increased clinical stages. lncRNA MEG3 was downregulated in OC tissues and was inversely correlated with AGAP2-AS1. AGAP2-AS1 overexpression led to downregulation of MEG3, while MEG3 overexpression failed to affect AGAP2-AS1. AGAP2-AS1 overexpression promoted proliferation of OC cells, while MEG3 overexpression inhibited proliferation of OC cells. In addition, MEG3 overexpression attenuated the effects of AGAP2-AS1 overexpression on cancer cell proliferation, but AGAP2-AS1 overexpression did not obviously affect cancer cell invasion and migration.

Conclusions

lncRNA AGAP2-AS1 is upregulated in ovarian carcinoma and negatively regulates lncRNA MEG3 to participate in the regulation of cancer cell proliferation.

LncRNA FOXP4-AS1 is activated by PAX5 and promotes the growth of prostate cancer by sequestering miR-3184-5p to upregulate FOXP4

Prostate cancer (PCa) is one of the major men malignancies worldwide. Long noncoding RNAs (lncRNAs) have been reported as essential regulators in human cancers, including PCa. In the present study, lncRNA forkhead box P4 antisense RNA 1 (FOXP4-AS1) was found to be highly expressed in TCGA PCa samples. Upregulation of FOXP4-AS1 was further validated in 64 PCa tissues and predicted poor prognosis in patients with PCa. Functionally, high FOXP4-AS1 level was associated with increased cell proliferation and decreased cell apoptosis, indicating that FOXP4-AS1 exerted oncogenic functions in the tumorigenesis of PCa. Furthermore, FOXP4-AS1 was located in the cytoplasm of PCa cell lines and positively regulated FOXP4. LncRNAs can exert their functions by cooperating with their nearby genes. Mechanistically, FOXP4-AS1 post-transcriptionally regulated FOXP4 by acting as a competing endogenous RNA (ceRNA) in PCa to sponge miR-3184-5p. Considering the upregulation of both FOXP4-AS1 and its nearby gene FOXP4, we further detected the coactivator of FOXP4-AS1 and FOXP4. Mechanism analysis indicated that paired box 5 (PAX5) transcriptionally activated FOXP4-AS1 and FOXP4 in PCa. Collectively, we determined that PAX5-induced upregulation of FOXP4-AS1/FOXP4 axis promoted tumorigenesis of PCa.

Phytochemicals as Modulators of Long Non-Coding RNAs and Inhibitors of Cancer-Related Carbonic Anhydrases

Long non-coding RNAs (lncRNAs) are classified as a group of transcripts which regulate various biological processes, such as RNA processing, epigenetic control, and signaling pathways. According to recent studies, lncRNAs are dysregulated in cancer and play an important role in cancer incidence and spreading. There is also an association between lncRNAs and the overexpression of some tumor-associated proteins, including carbonic anhydrases II, IX, and XII (CA II, CA IX, and CA XII). Therefore, not only CA inhibition, but also lncRNA modulation, could represent an attractive strategy for cancer prevention and therapy. Experimental studies have suggested that herbal compounds regulate the expression of many lncRNAs involved in cancer, such as HOTAIR (HOX transcript antisense RNA), H19, MALAT1 (metastasis-associated lung adenocarcinoma transcript 1), PCGEM1 (Prostate cancer gene expression marker 1), PVT1, etc. These plant-derived drugs or phytochemicals include resveratrol, curcumin, genistein, quercetin, epigallocatechin-3-galate, camptothcin, and 3,3'-diindolylmethane. More comprehensive information about lncRNA modulation via phytochemicals would be helpful for the administration of new herbal derivatives in cancer therapy. In this review, we describe the state-of-the-art and potential of phytochemicals as modulators of lncRNAs in different types of cancers.

Loss of lncRNA-SNHG7 Promotes the Suppression of Hepatic Stellate Cell Activation via miR-378a-3p and DVL2

Small nuclear RNA host gene 7 (SNHG7), a novel long non-coding RNA (lncRNA), acts as an oncogene in cancers. However, whether SNHG7 is involved in hepatic stellate cell (HSC) activation during liver fibrosis is still unclear. In this study, upregulation of SNHG7 was found in vivo and in vitro during liver fibrosis. Silencing of SNHG7 led to the suppression of HSC activation, with a reduction in cell proliferation and collagen expression. SNHG7 knockdown also resulted in the suppression of liver fibrosis in vivo. Interestingly, miR-378a-3p was a target of SNHG7. SNHG7 and miR-378a-3p were co-located in the cytoplasm. Downregulation of miR-378a-3p blocked down the effects of loss of SNHG7 on HSC activation. Notably, SNHG7 could enhance Wnt/β-catenin pathway activation to contribute to liver fibrosis, with an increase in T cell factor (TCF) activity and a reduction in P-β-catenin level. It was found that miR-378a-mediated dishevelled segment polarity protein 2 (DVL2) was responsible for SNHG7-activated Wnt/β-catenin pathway. DVL2 was confirmed as a target of miR-378a-3p. SNHG7-induced HSC activation was almost blocked down by DVL2 knockdown. Accordingly, enhanced Wnt/β-catenin by SNHG7 was suppressed by loss of DVL2. Collectively, we demonstrate that SNHG7 reduces miR-378a-3p and attenuates its control on DVL2, leading to aberrant Wnt/β-catenin activity, which contributes to liver fibrosis progression.

Construction and analysis of a lncRNA‑miRNA‑mRNA network based on competitive endogenous RNA reveals functional lncRNAs in diabetic cardiomyopathy

Diabetic cardiomyopathy (DCM) is a major cause of mortality in patients with diabetes, particularly those with type 2 diabetes. Long non‑coding RNAs (lncRNAs), including terminal differentiation‑induced lncRNA (TINCR), myocardial infarction‑associated transcript (MIAT) and H19, serve a key role in the regulation of DCM. MicroRNAs (miRNAs/miRs) can inhibit the expression of mRNA at the post‑transcriptional level, whereas lncRNAs can mask the inhibitory effects of miRNAs on mRNA. Together, miRNAs and lncRNAs form a competitive endogenous non‑coding RNA (ceRNA) network that regulates the occurrence and development of various diseases. However, the regulatory role of lncRNAs in DCM is unclear. In this study, a background network containing mRNAs, miRNAs and lncRNAs was constructed using starBase and a regulatory network of DCM was screened using Cytoscape. A functional lncRNA, X‑inactive specific transcript (XIST), was identified in the disease network and the main miRNAs (miR‑424‑5p and miR‑497‑5p) that are regulated by XIST were further screened to obtain the ceRNA regulatory network of DCM. In conclusion, the results of this study revealed that lncRNAs may serve an important role in DCM and provided novel insights into the pathogenesis of DCM.

Circulating cell-free nucleic acids as biomarkers in colorectal cancer screening and diagnosis - an update

Introduction: Screening methods for one of the most frequently diagnosed malignancy, colorectal cancer (CRC), have limitations. Circulating cell-free nucleic acids (cfNA) hold clinical relevance as screening, prognostic and therapy monitoring markers. Area covered: In this review, we summarize potential CRC-specific cfNA biomarkers, the recently developed sample preparation techniques, their applications, and pitfalls. Expert opinion: Automated extraction of cfDNA is highly reproducible, however, cfDNA yield is less compared to manual isolation. Quantitative and highly sensitive detection techniques (e.g. digital PCR, NGS) can be applied to analyze genetic and epigenetic changes. Detection of DNA mutations or methylation in cfDNA and related altered levels of mRNA, miRNA, and lncRNA may improve early cancer recognition, based on specific, CRC-related patterns. Detection of cfDNA mutations (e.g. TP53, KRAS, APC) has limited diagnostic sensitivity (40-60%), however, methylated DNA including SEPT9, SFRP1, SDC2 can be applied with higher sensitivity (up to 90%) for CRC. Circulating miRNAs (e.g. miR-21, miR-92, miR-141) provide comparably high sensitivity for CRC as the circulating tumor cell mRNA markers (e.g. EGFR, CK19, CK20, CEA). Automation of cfNA isolation coupled with quantitative analysis of CRC-related, highly sensitive biomarkers may enhance CRC screening and early detection in the future.

MicroRNA-145 inhibits proliferation and induces apoptosis in human prostate carcinoma by upregulating long non-coding RNA GAS5

MicroRNA-145 (miR-145) and long non-coding RNA (lncRNA) growth arrest specific 5 (GAS5) function as tumor suppressors in prostate carcinoma. The aim of the present study was to investigate the role of miR-145 and lncRNA GAS5 in prostate carcinoma. In the present study, miR-145 and lncRNA GAS5 expression levels were demonstrated to be downregulated in tumor tissues compared with adjacent healthy tissues of patients with prostate carcinoma. miR-145 and lncRNA GAS5 expression levels were found to be positively and significantly correlated in tumor tissues, but not in adjacent healthy tissues. A follow-up study revealed that low miR-145 and lncRNA GAS5 expression levels were associated with poor survival. Overexpression of miR-145 resulted in upregulated lncRNA GAS5, whereas lncRNA GAS5 overexpression or silencing did not affect miR-145 expression. Overexpression of miR-145 and lncRNA GAS5 promoted apoptosis and inhibited cell proliferation in prostate carcinoma cell lines, whereas lncRNA GAS5 knockdown had an opposite effect. In addition, lncRNA GAS5 knockdown partially attenuated the effect of miR-145 overexpression of cancer cell proliferation and apoptosis. Therefore, miR-145 may inhibit cell proliferation and induce apoptosis in human prostate carcinoma by upregulating lncRNA GAS5.

LncRNA-Disease Association Prediction Using Two-Side Sparse Self-Representation

Evidences increasingly indicate the involvement of long non-coding RNAs (lncRNAs) in various biological processes. As the mutations and abnormalities of lncRNAs are closely related to the progression of complex diseases, the identification of lncRNA-disease associations has become an important step toward the understanding and treatment of diseases. Since only a limited number of lncRNA-disease associations have been validated, an increasing number of computational approaches have been developed for predicting potential lncRNA-disease associations. However, how to predict potential associations precisely through computational approaches remains challenging. In this study, we propose a novel two-side sparse self-representation (TSSR) algorithm for lncRNA-disease association prediction. By learning the self-representations of lncRNAs and diseases from known lncRNA-disease associations adaptively, and leveraging the information provided by known lncRNA-disease associations and the intra-associations among lncRNAs and diseases derived from other existing databases, our model could effectively utilize the estimated representations of lncRNAs and diseases to predict potential lncRNA-disease associations. The experiment results on three real data sets demonstrate that our TSSR outperforms other competing methods significantly. Moreover, to further evaluate the effectiveness of TSSR in predicting potential lncRNAs-disease associations, case studies of Melanoma, Glioblastoma, and Glioma are carried out in this paper. The results demonstrate that TSSR can effectively identify some candidate lncRNAs associated with these three diseases.

Circular RNAs as potential biomarkers and therapeutics for cardiovascular disease

Circular RNAs (circRNAs) are genetic regulators that were earlier considered as "junk". In contrast to linear RNAs, they have covalently linked ends with no polyadenylated tails. CircRNAs can act as RNA-binding proteins, sequestering agents, transcriptional regulators, as well as microRNA sponges. In addition, it is reported that some selected circRNAs are transformed into functional proteins. These RNA molecules always circularize through covalent bonds, and their presence has been demonstrated across species. They are usually abundant and stable as well as evolutionarily conserved in tissues (liver, lung, stomach), saliva, exosomes, and blood. Therefore, they have been proposed as the "next big thing" in molecular biomarkers for several diseases, particularly in cancer. Recently, circRNAs have been investigated in cardiovascular diseases (CVD) and reported to play important roles in heart failure, coronary artery disease, and myocardial infarction. Here, we review the recent literature and discuss the impact and the diagnostic and prognostic values of circRNAs in CVD.

RNA Regulatory Networks as a Control of Stochasticity in Biological Systems

The discovery that the non-protein coding part of human genome, dismissed as "junk DNA," is actively transcripted and carries out crucial functions is probably one of the most important discoveries of the past decades. These transcripts are becoming the rising stars of modern biology. In this review, we have casted a new light on RNAs. We have placed these molecules in the context of life origins, evolution with a big emphasize on the "RNA networks" concept. We discuss how this view can help us to understand the global role of RNA networks in modern cells, and can change our perception of the cell biology and therapy. Finally, although high-throughput methods as well as traditional case-to-case studies have laid the groundwork for our current knowledge of transcriptomes, we would like to discuss new strategies that are better suited to uncover and tackle these integrated and complex RNA networks.

Systems biology in inflammatory bowel diseases: on the way to precision medicine

Inflammatory bowel diseases (IBD) are chronic and recurrent inflammatory disorders of the gastrointestinal tract. The elucidation of their etiopathology requires complex and multiple approaches. Systems biology has come to fulfill this need in approaching the pathogenetic mechanisms of IBD and its etiopathology, in a comprehensive way, by combining data from different scientific sources. In combination with bioinformatics and network medicine, it uses principles from computer science, mathematics, physics, chemistry, biology, medicine and computational tools to achieve its purposes. Systems biology utilizes scientific sources that provide data from omics studies (e.g., genomics, transcriptomics, etc.) and clinical observations, whose combined analysis leads to network formation and ultimately to a more integrative image of disease etiopathogenesis. In this review, we analyze the current literature on the methods and the tools utilized by systems biology in order to cover an innovative and exciting field: IBD-omics.

Non-coding RNAs as potential therapeutic targets in breast cancer

Paradigm shifting studies especially involving non-coding RNAs (ncRNAs) during last few decades have significantly changed the scientific perspectives regarding the complexity of cellular signalling pathways. Several studies have shown that the non-coding RNAs, initially ignored as transcriptional noise or products of erroneous transcription; actually regulate plethora of biological phenomena ranging from developmental processes to various diseases including cancer. Current strategies that are employed for the management of various cancers including that of breast fall short when their undesired side effects like Cancer Stem Cells (CSC) enrichment, low recurrence-free survival and development of drug resistance are taken into consideration. This review aims at exploring the potential role of ncRNAs as therapeutics in breast cancer, by providing a comprehensive understanding of their mechanism of action and function and their crucial contribution in regulating various aspects of breast cancer progression such as cell proliferation, angiogenesis, EMT, CSCs, drug resistance and metastasis. In addition, we also provide information about various strategies that can be employed or are under development to explore them as potential moieties that may be used for therapeutic intervention in breast cancer.

Long non-coding RNA00882 contributes to platelet-derived growth factor-induced proliferation of human fetal airway smooth muscle cells by enhancing Wnt/β-catenin signaling via sponging miR-3619-5p

Long non-coding RNAs (lncRNAs) are emerging as novel and critical regulators in the pathogenesis of asthma. However, the precise role of lncRNAs in pediatric asthma remains largely unknown. In this study, we aimed to investigate the biological function of lncRNA00882 (LINC00882) in regulating the proliferation of fetal airway smooth muscle (ASM) cells, which play an important role in airway remodeling during asthma development. Herein, we found that LINC00882 expression was significantly up-regulated in ASM cells stimulated with platelet-derived growth factor (PDGF). Functional experiments showed that the knockdown of LINC00882 markedly reduced the proliferation of fetal ASM cells induced by PDGF, while the overexpression of LINC00882 exhibited the opposite effect. Bioinformatics analysis, the luciferase reporter assay and the RNA pull-down assay revealed that LINC00882 directly interacted with microRNA-3619-5p (miR-3619-5p). LINC00882 negatively regulated miR-3619-5p expression in fetal ASM cells. Notably, β-catenin was identified as a target gene of miR-3619-5p. miR-3619-5p overexpression restricted PDGF-induced cell proliferation through inhibiting Wnt/β-catenin signaling. Moreover, miR-3619-5p overexpression significantly attenuated the LINC00882-induced promotion effect on PDGF-induced cell proliferation and Wnt/β-catenin signaling in fetal ASM cells. In contrast, miR-3619-5p inhibition significantly reversed the LINC00882 knockdown-mediated inhibitory effect on PDGF-induced cell proliferation and Wnt/β-catenin signaling. Taken together, our results demonstrate that LINC00882 promotes PDGF-induced cell proliferation of ASM cells by enhancing Wnt/β-catenin signaling via sponging miR-3619-5p, suggesting a potential role for LINC00882 in airway remodeling in pediatric asthma.

lncRNA-NEF is downregulated in osteosarcoma and inhibits cancer cell migration and invasion by downregulating miRNA-21

Long non-coding RNA (lncRNA)-NEF inhibits cancer metastasis in hepatocellular carcinoma; however, its role in other malignancies is unknown. The present study revealed that plasma lncRNA-NEF was downregulated, while miRNA-21 was upregulated in patients with osteosarcoma compared with healthy controls. Plasma lncRNA-NEF and miRNA-21 were negatively correlated in patients with osteosarcoma and healthy controls. Downregulation of lncRNA-NEF and upregulation of miRNA-21 distinguished patients with osteosarcoma from healthy controls. lncRNA-NEF overexpression mediated the inhibition of miRNA-21 expression in osteosarcoma cell lines, while miRNA-21 overexpression did not significantly affect the expression of lncRNA-NEF. lncRNA-NEF overexpression inhibited, while miRNA-21 overexpression promoted, migration and invasion of osteosarcoma cell lines in vitro. miRNA-21 overexpression partially compensated the inhibitory effects of lncRNA-NEF overexpression on osteosarcoma cell migration and invasion. Therefore, lncRNA-NEF may inhibit cancer cell migration and invasion in osteosarcoma by downregulating miRNA-21.

MiR-34b-5p Mediates the Proliferation and Differentiation of Myoblasts by Targeting IGFBP2

As key post-transcriptional regulators, microRNAs (miRNAs) play an indispensable role in skeletal muscle development. Our previous study suggested that miR-34b-5p and IGFBP2 could have a potential role in skeletal muscle growth. Our goal in this study is to explore the function and regulatory mechanism of miR-34b-5p and IGFBP2 in myogenesis. In this study, the dual-luciferase reporter assay and Western blot analysis showed that IGFBP2 is a direct target of miR-34b-5p. Flow cytometric analysis and EdU assay showed that miR-34b-5p could repress the cell cycle progression of myoblasts, and miR-34b-5p could promote the formation of myotubes by promoting the expression of MyHC. On the contrary, the overexpression of IGFBP2 significantly facilitated the proliferation of myoblasts and hampered the formation of myotubes. Together, our results indicate that miR-34b-5p could mediate the proliferation and differentiation of myoblasts by targeting IGFBP2.

LncRNA MIR100HG promotes cancer cell proliferation, migration and invasion in laryngeal squamous cell carcinoma through the downregulation of miR-204-5p

Purpose: LncRNA MIR100HG promotes several types of malignancies, while its involvement in other human diseases is unknown.

Patients and methods: Our study included 70 patients with LSCC who were diagnosed and treated in the First Affiliated Hospital and College of Clinical Medicine of Henan University of Science and Technology from January 2016 to July 2018. qRT-PCR, cell transfection, in vitro cell proliferation assay, cell migration and invasion assay were applied for the research.

Results: In the present study we found that MIR100HG was upregulated, while miR-204-5p was downregulated in tumor tissues than in adjacent healthy tissues of laryngeal squamous cell carcinoma (LSCC) patients. Expression of MIR100HG was significantly affected by AJCC stage. A significant and inverse correlation between MIR100HG and miR-204-5p was found in tumor tissues but not in adjacent healthy tissues of LSCC patients. Overexpression of MIR100HG resulted in the downregulation of miR-204-5p in LSCC cells, while miR-204-5p overexpression failed to significantly affect MIR100HG expression. Overexpression of MIR100HG led to promoted, while miR-204-5p, overexpression led to inhibited proliferation, migration and invasion of LSCC cells. In addition, miR-204-5p overexpression attenuated the enhancing effects of MIR100HG overexpression on cancer cell proliferation, migration and invasion.

Conclusion: Therefore, lncRNA MIR100HG promoted cancer cell proliferation, migration and invasion in LSCC possibly through the downregulation of miR-204-5p.

MicroRNAs and Long Non-coding RNAs in Genetic Diseases

Since the discovery and classification of non-coding RNAs, their roles have gained great attention. In this respect, microRNAs and long non-coding RNAs have been firmly demonstrated to be linked to regulation of gene expression and onset of human diseases, including rare genetic diseases; therefore they are suitable targets for therapeutic intervention. This issue, in the context of rare genetic diseases, is being considered by an increasing number of research groups and is of key interest to the health community. In the case of rare genetic diseases, the possibility of developing personalized therapy in precision medicine has attracted the attention of researchers and clinicians involved in developing "orphan medicinal products" and proposing these to the European Medicines Agency (EMA) and to the Food and Drug Administration (FDA) Office of Orphan Products Development (OOPD) in the United States. The major focuses of these activities are the evaluation and development of products (drugs, biologics, devices, or medical foods) considered to be promising for diagnosis and/or treatment of rare diseases or conditions, including rare genetic diseases. In an increasing number of rare genetic diseases, analysis of microRNAs and long non-coding RNAs has been proven a promising strategy. These diseases include, but are not limited to, Duchenne muscular dystrophy, cystic fibrosis, Rett syndrome, and β-thalassemia. In conclusion, a large number of approaches based on targeting microRNAs and long non-coding RNAs are expected in the field of molecular diagnosis and therapy, with a facilitated technological transfer in the case of rare genetic diseases, in virtue of the existing regulation concerning these diseases.

Microarray-based differential expression profiling of long noncoding RNAs and messenger RNAs in formalin-fixed paraffin-embedded human papillary thyroid carcinoma samples

BACKGROUND

Long noncoding RNAs (lncRNAs) can regulate the expression of genes at almost every level. The altered expression of lncRNAs was observed in many kinds of cancers. Until recently, few studies have focused on the function of lncRNAs in the context of papillary thyroid carcinoma (PTC).

METHODS

In the current study, we collected seven PTC and nodular goiter tissue samples and explored mRNA and lncRNA expression patterns in these samples by microarray.

RESULTS

We observed aberrant expression of 94 lncRNAs and 99 mRNAs in the seven PTC samples as compared to the nodular goiter tissue [fold change (FC) ≥2.0; P<0.01]. To confirm these microarray results, quantitative polymerase chain reaction (q-PCR) was performed to assess the expression of three randomly selected differentially expressed mRNAs and lncRNAs, confirming our microarray findings significantly. We then performed gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) analyses to systematically characterize the twelve significantly differential genes. A co-expression analysis revealed that the lncRNAs n382996, n342483, and n409114 were closely related to the regulation of MT1G, MT1H, and MT1F.

CONCLUSIONS

In the present study a string of novel lncRNAs associated with PTC were identified. Further study of these lncRNAs should be performed to identify novel target molecules which may improve diagnosis and treatment of PTC.

Promoter hypermethylation-mediated downregulation of tumor suppressor gene SEMA3B and lncRNA SEMA3B-AS1 correlates with progression and prognosis of esophageal squamous cell carcinoma

Frequent deletions of tumor-suppressor genes at chromosome 3p21.3 have been detected in esophageal squamous cell carcinoma (ESCC). As a candidate tumor suppressor gene, semaphorin 3B (SEMA3B) is located at 3p21.3 and is frequently inactivated in several tumors. However, the role and inactivation mechanisms of SEMA3B and its antisense long non-coding RNA (lncRNA) SEMA3B-AS1 in the carcinogenesis of ESCC have not been fully elucidated. The present study was conducted to investigate the role, epigenetic inactivation mechanisms, and prognostic value of SEMA3B and SEMA3B-AS1 in ESCC tumorigenesis and prognosis. Frequent downregulation of SEMA3B and SEMA3B-AS1 was detected in esophageal cancer cells and ESCC tissues, and the expression level of SEMA3B and SEMA3B-AS1 in ESCC tissues was correlated with TNM stage and lymph node metastasis. SEMA3B and SEMA3B-AS1 shared the same CpG island in the promoter region and the expression of both genes might be regulated by the promoter methylation status. Furthermore, transcription factor Sp1 activated SEMA3B or SEMA3B-AS1 transcription and the promoter hypermethylation of SEMA3B and SEMA3B-AS1 influenced Sp1 binding ability. Moreover, over-expression of SEMA3B and SEMA3B-AS1 suppressed the viability and invasion of esophageal cancer cells in vitro. SEMA3B-AS1 influenced the protein expression of SEMA3B. SEMA3B or SEMA3B-AS1 expression and promoter methylation status were correlated with ESCC patients' survival. Thus, these findings suggest that SEMA3B and SEMA3B-AS1 may act as tumor suppressors and may serve as potential targets for antitumor therapy.

Long non-coding RNA NEAT1 confers oncogenic role in triple-negative breast cancer through modulating chemoresistance and cancer stemness

Triple-negative breast cancer (TNBC) is a malignant subtype of breast cancer with the absence of targeted therapy, resulting in poor prognosis in patients. Chemotherapy remains the mainstay of treatment for TNBC; however, development of drug resistance is the main obstacle for successful treatments. In recent years, long non-coding RNA (lncRNA) has been implicated in multiple biological functions in various diseases, particularly cancers. Accumulating evidence suggested that lncRNA nuclear paraspeckle assembly transcript 1 (NEAT1) expression is dysregulated in many human cancers and thus is a useful prognostic marker for cancer patients. Nevertheless, the mechanism of how NEAT1 confers drug resistance in TNBC is still largely unknown. We performed lncRNA profiling by the LncRNA Profiler qPCR Array Kit in normal control (NC) and breast cancers (BC) blood samples and further validated in a larger cohort of samples by qRT-PCR. Gene expression level and localization were investigated by qRT-PCR, western blotting, and immunofluorescence staining. Flow cytometric analysis was carried out to detect cancer stem cells. Functional studies were performed both in vitro and in vivo xenograft model. Among 90 lncRNAs, NEAT1 was highly expressed in the blood samples of breast cancer patients than in NC. In particular, the expression of NEAT1 was higher in TNBC tissues than other subgroups. Functional studies revealed that NEAT1 conferred oncogenic role by regulating apoptosis and cell cycle progression in TNBC cells. We identified that knockdown of NEAT1 sensitized cells to chemotherapy, indicating the involvement in chemoresistance. Importantly, shNEAT1 reduced stem cell populations such as CD44+/CD24−, ALDH+, and SOX2+, implicating that NEAT1 was closely related to cancer stemness in TNBC. Our data highlighted the roles of NEAT1 chemoresistance and cancer stemness, suggesting that it could be used as a new clinical therapeutic target for treating TNBC patients especially those with drug resistance.

Role of epigenomic mechanisms in the onset and management of insulin resistance

The prevalence of insulin resistance (IR) is increasing rapidly worldwide and it is a relevant health problem because it is associated with several diseases, such as type 2 diabetes, cardiovascular disorders and cancer. Understanding the mechanisms involved in IR onset and progression will open new avenues for identifying biomarkers for preventing and treating IR and its co-diseases. Epigenetic mechanisms such as DNA methylation are important factors that mediate the environmental effect in the genome by regulating gene expression and consequently its effect on the phenotype and the development of disease. Taking into account that IR results from a complex interplay between genes and the environment and that epigenetic marks are reversible, disentangling the relationship between IR and epigenetics will provide new tools to improve the management and prevention of IR. Here, we review the current scientific evidence regarding the association between IR and epigenetic markers as mechanisms involved in IR development and potential management.

A Novel Method for LncRNA-Disease Association Prediction Based on an lncRNA-Disease Association Network

An increasing number of studies have indicated that long-non-coding RNAs (lncRNAs) play critical roles in many important biological processes. Predicting potential lncRNA-disease associations can improve our understanding of the molecular mechanisms of human diseases and aid in finding biomarkers for disease diagnosis, treatment, and prevention. In this paper, we constructed a bipartite network based on known lncRNA-disease associations; based on this work, we proposed a novel model for inferring potential lncRNA-disease associations. Specifically, we analyzed the properties of the bipartite network and found that it closely followed a power-law distribution. Moreover, to evaluate the performance of our model, a leave-one-out cross-validation (LOOCV) framework was implemented, and the simulation results showed that our computational model significantly outperformed previous state-of-the-art models, with AUCs of 0.8825, 0.9004, and 0.9292 for known lncRNA-disease associations obtained from the LncRNADisease database, Lnc2Cancer database, and MNDR database, respectively. Thus, our approach may be an excellent addition to the biomedical research field in the future.

The long non-coding RNA LINC00460 predicts the prognosis and promotes the proliferation and migration of cells in bladder urothelial carcinoma

Long non-coding RNAs (lncRNAs) may serve an important role in cancer development and may also be suitable for use as prognostic biomarkers. At present, the role of lncRNAs in bladder cancer remains unclear. The present study examined the potential involvement of lncRNA LINC00460 in bladder urothelial carcinoma using data from The Caner Genome Atlas (TCGA) and cell line experiments. The results indicated that LINC00460 expression levels were increased in bladder urothelial carcinoma tissues and bladder cancer 5637 and T24 cell lines compared with corresponding normal controls (P<0.05). TCGA data indicated that LINC00460 expression was negatively correlated with a positive prognosis in patients with bladder urothelial carcinoma (P<0.05). Consistently, the downregulation of LINC00460 with short hairpin RNA significantly suppressed 5637 and T24 cell proliferation and migration. Therefore, it was suggested that strategies that target LINC00460 may be developed as novel therapeutic approaches for the treatment of bladder cancer. In addition, the expression level of androgen receptor (AR) was downregulated in bladder urothelial carcinoma tissues and exhibited a negative correlation with the expression level of LINC00460 (r=−0.43; P<0.0001), based on the data from TCGA. We hypothesized that LINC00460 may serve an oncogenic role by regulating the expression of AR.

Long non-coding antisense RNA GAS6-AS1 supports gastric cancer progression via increasing GAS6 expression

OBJECTIVE

As one broader class of non-coding RNAs (lncRNAs), non-coding antisense (AS) transcripts are functionally characterized to play pivotal roles in various pathophysiological processes, including tumor biology.

METHODS

In this study, the exact biological functions and regulation mechanisms of GAS6-AS1 in gastric cancer (GC) was examined.

RESULTS

The expression of GAS6-AS1 was markedly upregulated in GC tissues and is associated with advanced stage (III + IV) of GC patients. Gain-of-function and loss-of-function experiments showed that GAS6-AS1 promoted cell proliferation, migration, invasion ability in vitro and xenograft tumor growth in vivo by promoting entry into S-phase. The mechanistic investigations showed that GAS6-AS1 can control the expression of its cognate sense gene GAS6 at the transcriptional or translational levels by forming a RNA-RNA duplex, consequently inducing an increase of AXL level and driveling AXL signaling pathway activation.

CONCLUSIONS

Taken together, our studies indicate that GAS6-AS1 significantly driving the aggressive phenotype in GC through activating its cognate sense gene GAS6, and provides a more complete understanding of GAS6-AS1 as a potential therapeutic target for GC.

Deciphering DMET genetic data: comprehensive assessment of Northwestern Han, Tibetan, Uyghur populations and their comparison to eleven 1000 genome populations

We investigated the allele frequencies of drug absorption, distribution, metabolism and elimination (ADME)-related drug-metabolizing enzymes and transporters (DMET) genes in the Northwestern Han, Tibetan and Uyghur populations and compared the related genes in these three populations with those in eleven 1000 Genome populations. We examined 1936 single nucleotide polymorphisms of 225 DMET genes involved in ADME processes and found 732, 679 and 804 sites were polymorphic in Han, Tibetan and Uyghur. Tibetan differed from Han in only four sites (p < .05), whereas Uyghur differed from Han and Tibetan in 24 and 21 sites, respectively (p < .05). The distributions of 1058 genotyping data of 245 individuals from Han, Tibetan and Uyghur were compared with 1207 other individuals from the eleven 1000 Genomes populations. The top four populations in Han that exhibited the smallest pairwise Fst values were CHB, Tibetan, CHD and JPT; those in Tibetan were Han, CHB, Uyghur and CHD; and those in Uyghur were Han, Tibetan, GIH and CEU. MEGA results revealed that CHB, CHD, JPT, Han, Tibetan and Uyghur were grouped in cluster 1. GIH, MEX, CEU and TSI were grouped in cluster 2. MKK, ASW, LWK and YRI were grouped in cluster 3.

Epitranscriptomic Signatures in lncRNAs and Their Possible Roles in Cancer

In contrast to the amazing exponential growth in knowledge related to long non-coding RNAs (lncRNAs) involved in cell homeostasis or dysregulated pathological states, little is known so far about the links between the chemical modifications occurring in lncRNAs and their function. Generally, ncRNAs are post-transcriptional regulators of gene expression, but RNA modifications occurring in lncRNAs generate an additional layer of gene expression control. Chemical modifications that have been reported in correlation with lncRNAs include m⁶A, m⁵C and pseudouridylation. Up to date, several chemically modified long non-coding transcripts have been identified and associated with different pathologies, including cancers. This review presents the current level of knowledge on the most studied cancer-related lncRNAs, such as the metastasis associated lung adenocarcinoma transcript 1 (MALAT1), the Hox transcript antisense intergenic RNA (HOTAIR), or the X-inactive specific transcript (XIST), as well as more recently discovered forms, and their potential roles in different types of cancer. Understanding how these RNA modifications occur, and the correlation between lncRNA changes in structure and function, may open up new therapeutic possibilities in cancer.

Role of non-coding RNAs in liver disease progression to hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is a tumor with poor prognosis and frequently aggressive. The development of HCC is associated with fibrosis and cirrhosis, which mainly results from nonalcoholic fatty liver disease, excessive alcohol consumption, and viral infections. Non-coding RNAs (ncRNAs) are RNAs transcribed from the genome, but are not translated into proteins. Recently, ncRNAs emerged as key contributors to tumor development and progression because of their abilities to regulate various targets and modulate cell proliferation, differentiation, apoptosis, and development. In this review, we summarize the frequently activated pathways in HCC and discuss the pathological implications of ncRNAs in the context of human liver disease progression, in particular HCC development and progression. This review aims to summarize the role of ncRNA dysregulation in the diseases and discuss the diagnostic and therapeutic potentials of ncRNAs.