Competing endogenous RNAs (ceRNAs): new entrants to the intricacies of gene regulation

CircRNA Expression Profile during Yak Adipocyte Differentiation and Screen Potential circRNAs for Adipocyte Differentiation

The yak (Bos grunniens) is subjected to nutritional deficiency during the whole winter grazing season; deciphering the adipose metabolism and energy homeostasis under cold and nutrients stress conditions could be a novel way to understand the specific mechanism of energy metabolism. Circular RNAs (circRNAs) have elucidated that they play a key role in many biological events, but the regulatory function of adipose development remains mostly unknown. Therefore, the expression pattern of circRNAs were identified for the first time during yak adipocyte differentiation to gain insight into their potential functional involvement in bovine adipogenesis. We detected 7203 circRNA candidates, most of them contained at least two exons, and multiple circRNA isoforms could be generated from one parental gene. Analysis of differential expression circRNAs displayed that 136 circRNAs were differentially expressed at day 12 (Ad) after adipocyte differentiation, compared with the control at day 0 (Pread 0), while 7 circRNAs were detected on day 2. Sanger sequencing validated that six circRNAs had head-to-tail junction, and quantitative real-time PCR (qPCR) results revealed that the expression patterns of ten circRNAs were consistent with their expression levels from RNA-sequencing (RNA-seq) data. We further predicted the networks of circRNA-miRNA-gene based on miRNAs sponging by circRNAs, in which genes were participated in the adipocyte differentiation-related signaling pathways. After that, we constructed several adipocyte differentiation-related ceRNAs and revealed six circRNAs (novel_circ_0009127, novel_circ_0000628, novel_circ_0011513, novel_circ_0010775, novel_circ_0006981 and novel_circ_0001494) were related to adipogenesis. Furthermore, we analyzed the homology among yak, human and mouse circRNAs and found that 3536 yak circRNAs were homologous to human and mouse circRNAs. In conclusion, these findings provide a solid basis for the investigation of yak adipocyte differentiation-related circRNAs and serve as a great reference to study the energy metabolism of high-altitude animals.

Knockdown of lncRNA PCAT6 Enhances Radiosensitivity in Triple-Negative Breast Cancer Cells by Regulating miR-185-5p/TPD52 Axis

Background

Long non-coding RNAs (lncRNAs) have been reported to play essential roles in regulating the radiosensitivity of cancers. Prostate cancer-associated transcript 6 (PCAT6) exerts oncogenic roles in several tumors. However, the roles of PCAT6 and its underlying mechanism in regulating the radiosensitivity of triple-negative breast cancer (TNBC) have not been investigated.

Methods

The expression levels of PCAT6, microRNA-185-5p (miR-185-5p) and tumor protein D52 (TPD52) were determined by quantitative real-time polymerase chain reaction (qRT-PCR). Cell viability, apoptosis and colony formation were assessed by Cell Counting Kit-8 (CCK-8) assay, flow cytometry and colony formation assay, respectively. The interaction between miR-185-5p and PCAT6 or TPD52 was predicted by bioinformatics analysis and verified by dual-luciferase reporter assay. Western blot was carried out to detect the protein level of TPD52.

Results

PCAT6 and TPD52 were highly expressed and miR-185-5p was lowly expressed in TNBC tissues and cells, which was associated with an aggressive tumor phenotype in patients, affecting lymph node metastasis and clinical stage. PCAT6 or TPD52 knockdown or miR-185-5p overexpression enhanced the radiosensitivity of TNBC cells via inhibiting proliferation and inducing apoptosis. PCAT6 directly interacted with miR-185-5p and negatively regulated miR-185-5p expression. Moreover, TPD52 was confirmed as a target of miR-185-5p. Besides, PCAT6 regulated the radiosensitivity of TNBC cells through acting as a molecular sponge of miR-185-5p to modulate TPD52 expression.

Conclusion

Knockdown of PCAT6 promoted the radiosensitivity of TNBC cells through regulating miR-185-5p/TPD52 axis, providing a vital theoretical basis to improve the radiotherapy efficiency of TNBC.

LncRNA ZFAS1 confers inflammatory responses and reduces cholesterol efflux in atherosclerosis through regulating miR-654-3p-ADAM10/RAB22A axis

PURPOSE

Atherosclerosis is the leading cause of cardiovascular diseases (CVD) with high incidence rate and mortality rate. Long non-coding RNAs (lncRNAs) are important functional molecules in atherosclerosis. Present study aimed to explore the functional role and underlying mechanism of ZFAS1 in atherosclerosis.

METHODS

The in-vitro cell model of atherosclerosis was established by using oxidized low-density lipoprotein (ox-LDL) to induce THP-1 macrophage-derived foam cells. qRT-PCR measured the mRNA levels of ZFAS1, miR-654-3p, ADAM10 and RAB22A. Western blot detected the protein levels of ADAM10 and RAB22A. The levels of IL-1β, IL-6 and TNF-ɑ (inflammatory biomarkers) were tested with ELISA assay. Detection of cholesterol efflux rate was experimented. The interaction between RNAs was affirmed with luciferase reporter and RNA pull-down experiments.

RESULTS

The expression of ZFAS1 was significantly up-regulated in in-vitro cell model of atherosclerosis at a dose- and time-dependent manner. Knockdown of ZFAS1 impaired inflammatory responses and promoted cholesterol efflux rate. Overexpression of ZFAS1 accelerated inflammatory responses and hampered cholesterol efflux rate. Then, the cytoplasmic role of ZFAS1 was revealed. By bio-informatics analysis and mechanism assays, miR-654-3p was identified to bind with ZFAS1. Moreover, ADAM10 and RAB22A were targeted and suppressed by miR-654-3p. ZFAS1 served as a ceRNA to positively regulate ADAM10 and RAB22A expression through endogenously sponging miR-654-3p.

CONCLUSION

In conclusion, ZFAS1 elevated ADAM10/RAB22A expression to reduce cholesterol efflux rate and facilitate inflammatory responses in atherosclerosis at a miR-654-3p-dependent way, suggesting a prospective treatment method for amelioration of atherosclerosis.

Circ_0038467 regulates lipopolysaccharide-induced inflammatory injury in human bronchial epithelial cells through sponging miR-338-3p

Background

Pneumonia is a common acute lower respiratory infection in children and elders. Circular RNAs (circRNAs) have recently been uncovered to play important roles in pneumonia. However, the function and mechanism of circ_0038467 in pneumonia remain elusive.

Methods

Cell viability and apoptosis were determined using the Cell Counting Kit‐8 (CCK‐8) assay and flow cytometry, respectively. The levels of interleukin 6 (IL‐6), IL‐8 and IL‐1β were detected by enzyme‐linked immunosorbent assay (ELISA). Western blot analysis was performed to assess the expression of related proteins. Circ_0038467 was characterized by Ribonuclease R (RNase) digestion and subcellular localization assays. The levels of circ_0038467 and miR‐338‐3p were evaluated by quantitative real‐time polymerase chain reaction (qRT‐PCR). The direct interaction between circ_0038467 and miR‐338‐3p was validated by the dual‐luciferase reporter and RNA immunoprecipitation (RIP) assays.

Results

Our data indicated that lipopolysaccharide (LPS) induced an inflammatory injury in 16HBE cells by repressing cell viability and enhancing cell apoptosis and proinflammatory cytokines production. Circ_0038467 was upregulated and miR‐338‐3p was downregulated in LPS‐treated 16HBE cells. Circ_0038467 knockdown or miR‐338‐3p overexpression attenuated LPS‐induced 16HBE cell inflammatory injury. Moreover, circ_0038467 acted as a sponge of miR‐338‐3p in 16HBE cells. MiR‐338‐3p mediated the alleviated effect of circ_0038467 knockdown on LPS‐induced 16HBE cell inflammatory injury. Additionally, the Janus kinase/ signal transducer and activator of transcription 3 (JAK/STAT3) signaling pathway was involved in the circ_0038467/miR‐338‐3p axis‐mediated regulation in LPS‐induced 16HBE cell inflammatory injury.

Conclusions

The current work had led to the identification of circ_0038467 knockdown that alleviated LPS‐induced inflammatory injury in 16HBE cells at least partly through sponging miR‐338‐3p and regulating JAK/STAT3 pathway, highlighting novel molecular targets for the treatment of pneumonia.

Unique miRNAs and their targets in tomato leaf responding to combined drought and heat stress

BACKGROUND

Both drought and heat stress are serious global problems, leading to agricultural production loss. MicroRNAs (miRNAs) play important roles in plant species responding to individual drought and heat stress. However, the miRNAs and mRNAs in association with combined drought and heat in crops like tomato remains unclear.

RESULTS

We studied the crosstalk of miRNAs and their target genes in tomato plants grown under simultaneous drought and heat stress that frequently happen in field conditions. In total, 335 known miRNAs representing 55 miRNA families and 430 potential novel miRNAs were identified in Solanum lycopersicum L. using small RNA deep sequencing. Through expression analysis, miRNAs in association with drought, heat and the combination of these were investigated. In total, 61, 74 and 37 miRNAs were differentially regulated for combination (of both stresses) vs control, combination vs drought and combination vs heat, respectively. Target genes with different expression levels were found using degradome sequencing, which were mainly involved in transcription factor activity, sequence-specific DNA binding, transcription, regulation of transcription, nucleus, DNA binding etc. The quantitative real-time polymerase chain reaction (qRT-PCR) results confirmed the accuracy of sequencing.

CONCLUSIONS

Our study serves as valuable knowledge on how crop adapted to combined drought and heat stress by regulating miRNAs and mRNAs, which provide information for crop improvement to deal with future climate changes.

The novel long noncoding RNA CRART16 confers cetuximab resistance in colorectal cancer cells by enhancing ERBB3 expression via miR-371a-5p

Background

Long noncoding RNAs (lncRNAs) have been shown to participate in multiple biological processes and confer drug resistance. However, it remains unclear whether lncRNAs are involved in conferring cetuximab resistance in colorectal cancer (CRC) cells.

Methods

Cell Counting Kit-8 (CCK-8) assays were performed to assess the sensitivity of CRC cell lines to cetuximab treatment. We incubated Caco-2 cells, which are partially responsive to cetuximab, with increasing concentrations of cetuximab for approximately 6 months to generate Caco-2 cetuximab-resistant (Caco-2 CR) cells. Microarray analysis comparing Caco-2 CR with Caco-2 cells was used to identify lncRNAs that were potentially related to cetuximab resistance. Caco-2 cells were stably transduced with cetuximab resistance-associated RNA transcript 16 (CRART16) or an empty vector using lentiviral infection; the cells were designated Caco-2-CRART16 and Caco-2-NC, respectively, and were analyzed with RNA sequencing (RNA-seq). Quantitative real-time PCR (qRT-PCR) was performed to investigate RNA expression. Flow cytometry and TUNEL assays were used to assess apoptosis levels induced by cetuximab. The cell cycle, stemness biomarkers and membrane proteins of CRC cells were assessed via flow cytometry. RNA fluorescence in situ hybridization (FISH) was used to examine CRART16 localization and expression. Bioinformatics analysis was performed to predict the potential mechanism of CRART16, which was further validated by a dual-luciferase reporter assay. Differences in measurement data were compared using Student’s t test, one-way ANOVA followed by Dunnett’s test and two-way ANOVA.

Results

The novel lncRNA CRART16 was upregulated in Caco-2 CR cells. CRART16 overexpression reversed the effects of cetuximab on cell viability and reduced cetuximab-induced apoptosis. Meanwhile, CRART16 overexpression led to increases in the proportion of CD44⁺/CD133⁺ cells. In addition, CRART16 acts as a competing endogenous RNA (ceRNA) for miR-371a-5p to regulate V-Erb-B2 Erythroblastic Leukemia Viral Oncogene Homolog 3 (ERBB3) expression. MiR-371a-5p mimics counteracted the cetuximab resistance induced by CRART16 overexpression. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that after CRART16 was overexpressed, the resulting differentially expressed mRNAs were mainly enriched in the MAPK signaling pathway.

Conclusions

CRART16 overexpression may contribute to cetuximab resistance through the miR-371a-5p/ERBB3/MAPK pathway. Additionally, CRART16 contributes to the acquisition of stemness properties.

LncRNA LOXL1-AS1 promotes endometrial cancer progression by sponging miR-28-5p to upregulate RAP1B expression

BACKGROUND

Increasing lncRNAs are found to be involved in the biological process of multiple cancer types. Herein, we aimed to reveal the role of LOXL1-AS1 in endometrial cancer (EC) progression.

METHODS

Tumor and corresponding normal tissues were obtained from EC patients. Si-LOXL1-AS1 and miR-28-5p inhibitor were transfected to downregulate the expressions of LOXL1-AS1 and miR-28-5p, while miR-28-5p mimics were used to upregulate the miR-28-5p expression. CCK-8 and colony assays were applied to estimate the cell proliferation. Flow cytometry was performed to measure the cell apoptosis. Wound healing and transwell assays were conducted to assess the cell migration and invasion abilities. Informatics analysis was used to explore the relationship among LOXL1-AS1, miR-28-5p and RAP1B.

RESULTS

LOXL1-AS1 was found markedly up-regulated in EC tissues and cell lines. LOXL1-AS1 knockdown displayed evident suppression in cell proliferation, migration and invasion, as well as promotion in cell apoptosis. Moreover, the LOXL1-AS1 induced regulatory effects on EC cells were partially reversed by miR-28-5p inhibitor. Mechanistically, LOXL1-AS1 competitively bond to miR-28-5p, resulting in upregulation of RAP1B. Additionally, in vivo study confirmed the findings discovered in vitro.

CONCLUSIONS

In summary, LOXL1-AS1 exerted oncogenic roles in EC progression by sponging miR-28-5p and thereby upregulating RAP1B. This finding might provide potential targets for EC therapy.

lncRNA KLF3-AS1 Suppresses Cell Migration and Invasion in ESCC by Impairing miR-185-5p-Targeted KLF3 Inhibition

Esophageal squamous cell carcinoma (ESCC) is a common cancer occurring in males and females worldwide. Accumulating evidence continues to highlight the crucial roles of long non-coding RNAs (lncRNAs) in the process of tumorigenesis. However, the regulatory mechanism of lncRNAs in ESCC remains unclear. The aim of this study is to elucidate the role of lncRNA Krüppel-like factor 3 antisense RNA 1 (KLF3-AS1) in ESCC by regulating miR-185-5p and KLF3. Initially, ESCC cell spheres with stem cell-like properties were prepared by suspension culture, and subsequently characterized by assessing colony formation ability and stem cell markers. LncRNA KLF3-AS1 was found to be poorly expressed in ESCC and could upregulate the expression of KLF3 by binding to miR-185-5p. lncRNA KLF3-AS1 upregulation was observed to inhibit miR-185-5p, thereby contributing to decreased expression of SOX2 and Oct4 (octamer-binding transcription factor 4). Furthermore, enhancement of lncRNA KLF3-AS1 resulted in reduced colony formation ability, cell invasion and migration, and tumor volume in vivo while promoting cell apoptosis in ESCC through downregulation of miR-185-5p. Collectively, this study indicated that lncRNA KLF3-AS1 inhibited ESCC cell invasion and migration by impairing miR-185-5p-mediated inhibition of KLF3, highlighting a promising novel potential target for ESCC treatment.

Pentoxifylline alleviated cardiac injury via modulating the cardiac expression of lncRNA-00654-miR-133a-SOX5 mRNA in the rat model of ischemia-reperfusion

Pentoxifylline (PTX) protects from many cardiovascular complications. It plays a critical role in stem cell proliferation and differentiation. Here, the effect of PTX administration on cardiac ischemia and dysfunction was explored. PTX in 3 doses (20, 30, and 40 mg/kg), was administered in vivo 5 min before a 45 min occlusion of the left anterior descending artery, followed by a 120 min reperfusion in male Wistar rats. The left ventricular end-diastolic pressure and dP/dt_max were assessed. Blood and cardiac tissue samples were collected for measuring the levels of cardiac enzymes and the expression of lncRNA-00654-miR-133a-SOX5. Samples of left ventricles were collected and processed for light microscopic, immunohistochemical staining for c-kit (a marker for cardiac progenitor cells) and transmission electron microscopic examination. PTX administration showed improvements in cardiac function tests, enzymes, and myocytes. Microscopic features showed minimal cardiac edema, hemorrhage, cellular inflammatory infiltration and fibrosis in addition to increased c-kit + cells in cardiac tissue samples. Notably, this treatment also produced a dose-dependent decrease in lncRNA-00654 with an increase in SOX5 mRNA and miRNA-133a-3p expressions. In conclusion, PTX has the potential to alleviate cardiac injury and increase the number of c-kit + cells following ischemia-reperfusion in the rat model via modulation of lncRNA-00654 and miR-133a-SOX5 mRNA expressions.

The Long Non-Coding RNA NEAT1 Promotes Gastric Cancer Cell Proliferation and Invasion by Regulating miR-103a/ STAMBPL1 Axis

BACKGROUND

Gastric cancer (GC) is a common malignancy with high morbidity. Long non-coding RNAs (LncRNAs) have been demonstrated to be critical post-transcriptional regulators in tumorigenesis. This study aimed to investigate the effect of LncRNA NEAT1 on the proliferation and metastasis of GC.

MATERIAL AND METHODS

The expression of LncRNA NEAT1 was examined in clinical samples and GC cell lines. GC cell lines (SGC-7901 and BGC-823) and human normal gastric epithelial cell line (GES-1) were employed. The correlation between NEAT1, miR-103a and STAMBPL1 was determined by luciferase reporter assay. Cell viability was determined by CCK8 assay. Cell invasion capacity was examined by Transwell assay. The protein level of STAMBPL1 was analyzed by western blotting.

RESULTS

LncRNA NEAT1 was found to be up-regulated in GC cell lines. Further studies identified LncRNA NEAT1 as a direct target of miR-103a. Moreover, NEAT1 knockdown and miR-103a overexpression inhibited cell proliferation and cell invasion. NEAT1 knockdown and miR-103a overexpression also decreased STAMBPL1 levels.

CONCLUSION

Our study indicated that LncRNA NEAT1 was up-regulated in GC cells and tissues. NEAT1 was targeted and inhibited by miR-103a and acted as an oncogene, which promoted the malignant behavior of GC cells. This regulatory effect of NEAT1 may be associated with STAMBPL1. Therefore, NEAT1 could be used as a biomarker for predicting the progression of GC.

Unravelling the role of long non-coding RNA - LINC01087 in breast cancer

Apoptosis is a 'programmed fate' of all cells participating in diverse physiological and pathological conditions. The role of critical regulators and their involvement in this complex multi-stage process of apoptosis weaved around non-coding RNAs (ncRNAs) is poorly deciphered in breast carcinoma (BC). Aberrant expression patterns of the ncRNAs and their interacting partners, either ncRNAs or coding RNAs or proteins at any point along these pathways, may lead to the malignant transformation of the affected cells, tumour metastasis and resistance to anticancer drugs. Longest non-coding type of ncRNAs (lncRNAs) have been considered as critical factors for the development and progression of breast cancer. The aim of our study was to identify set of novel lncRNAs interacting with microRNAs (miRNAs) or proteins that were significantly dysregulated in breast cancer using RNA-Sequencing (RNA-Seq) technique in different samples acting as oncogenic drivers contributing to cancerous phenotype involved in post-transcriptional processing of RNAs. Four lncRNAs; LINC01087, lnc-CLSTN2-1:1, lnc-c7orf65-3:3 and LINC01559:2 were selected for further analysis. Gene expression analysis of over-expressed LINC01087 in vitro reduced both cell viability and apoptosis. We integrated miRNA and mRNA (hsa-miR-548 and AKT1) expression profiles with curated regulations with lncRNA (LINC01087) which has not been previously associated with any breast cancer type, using different computational tools. The network (lncRNA→ miRNA→ mRNA) is promising for the identification of carcinoma associated genes and apoptosis signaling path highlighting the potential roles of LINC01087, hsa-miR548n, AKT1 gene which may play crucial role in proliferation.

lncRNA LINC00460 Silencing Represses EMT in Colon Cancer through Downregulation of ANXA2 via Upregulating miR-433-3p

Colon cancer (CC), one of the major causes of tumor-associated death, is often presented with a heterogenic pool of cells with unique differentiation patterns. This study explored the functions that LINC00460 displayed in CC by regulating microRNA-433-3p (miR-433-3p) and Annexin A2 (ANXA2). LINC00460 expression was either silenced or overexpressed in HCT-116 and LOVO cells to explore the functional roles of LINC00460 in CC. The relationship between miR-433-3p and LINC00460/ANXA2 was analyzed using dual-luciferase reporter assay, RNA-pull down, and RNA immunoprecipitation (RIP) assays. Cell proliferation, metastasis, invasion, and apoptosis were examined in vitro, and tumorigenicity was evaluated in vivo following LINC00460 silencing. Additionally, the regulatory mechanisms were investigated using LINC00460 and ANXA2 gain- or loss-of-function experiments. We found that LINC00460 was expressed highly in CC. Downregulation of LINC00460 inhibited cell invasion and proliferation in vitro and restrained tumor growth in vivo. Moreover, LINC00460 was able to specifically bind to miR-433-3p to increase the expression of ANXA2. Furthermore, LINC00460 downregulated the E-cadherin expression and upregulated the vimentin and N-cadherin expression by upregulating ANXA2, therefore inducing epithelial-mesenchymal transition. These findings suggested that LINC00460 might function as an oncogenic long non-coding RNA (lncRNA) in CC development and could be explored as a potential biomarker and therapeutic target for CC.

FBXL19-AS1 promotes cell proliferation and inhibits cell apoptosis via miR-876-5p/FOXM1 axis in breast cancer

As the most common cancer and one of the leading causes of cancer-associated mortality, breast cancer continues to need more key molecules to regulate its progression. F-box and leucine-rich repeat protein 19 antisense RNA 1 (known as FBXL19-AS1) is a long non-coding RNA (lncRNA) which has been reported as an oncogene in several types of human cancers. However, the specific downstream targets of FBXL19-AS1 remain unknown. In this study, we set out to find more reliable downstream molecules of FBXL19-AS1 in breast cancer. FBXL19-AS1 was expressed at a high level in breast cancer cells. Loss-of-function experiments revealed that silencing FBXL19-AS1 could impair cell proliferation and induce cell apoptosis in breast cancer. In addition, the location of FBXL19-AS1 in the cytoplasm was detected by fluorescent in situ hybridization assay, while FBXL19-AS1 regulated the expression of Forkhead box M1 (FOXM1) by directly absorbing miR-876-5p. Through rescue assays, it was observed that FOXM1 overexpression recovered the inhibited tumor growth caused by FBXL19-AS1 downregulation. We affirmed the function of FBXL19-AS1 in breast cancer and described the mechanism of the FBXL19-AS1/miR-876-5p/FOXM1 axis. The current work presents the molecular mechanism which underlies FBXL19-AS1 in breast cancer and suggests a comprehensive, feasible FBXL19-AS1-mediated therapeutic approach for treating breast cancer.

TMPO-AS1 promotes cervical cancer progression by upregulating RAB14 via sponging miR-577

BACKGROUND

Accumulating evidence has shown that long non-coding RNAs play a key role in cancer initiation and development. However, the effect of TMPO antisense RNA 1 (TMPO-AS1) on the progression of cervical cancer (CC) remains to be determined.

METHODS

The mRNA expression of TMPO-AS1, miR-577 and RAB14 was measured by a quantitative reverse transcriptase-polymerase chain reaction. The protein level of RAB14 was detected by western blotting. The function of TMPO-AS1 in CC was measured via Cell Counting Kit-8, 5-ethynyl-2'-deoxyuridine and transwell assays, as well as by flow cytometry analysis. Nuclear-cytoplasmic fractionation and RNA-fluorescence in situ hybridization validated the subcellular position of TMPO-AS1. An interaction between miR-577 and TMPO-AS1 or RAB14 was confirmed by luciferase reporter, RNA pull-down and RNA immunoprecipitation assays.

RESULTS

TMPO-AS1 was highly expressed in CC. In addition, TMPO-AS1 knockdown inhibited proliferation and migration, and also induced apoptosis. TMPO-AS1 located in the cytoplasm and promoted RAB14 expression by absorbing miR-577. RAB14 overexpression or miR-577 knockdown restored the suppressing effect of TMPO-AS1 knockdown on the biological behavior of CC cells.

CONCLUSIONS

The present study has revealed a novel TMPO-AS1/miR-577/RAB14 regulatory axis in the pathogenesis of CC, highlighting TMPO-AS1 as a promising therapeutic target for CC patients.

A Novel Long Noncoding RNA, lncR-125b, Promotes the Differentiation of Goat Skeletal Muscle Satellite Cells by Sponging miR-125b

Long noncoding RNAs (lncRNAs) have emerged as essential regulators of skeletal myogenesis, but few myogenesis-associated lncRNAs have been identified and our understanding of their regulatory mechanisms remains limited, particularly in goat. Here, we identified a novel lncRNA, TCONS_00006810 (named lncR-125b), from our previous lncRNA sequencing data on fetal (45, 60, and 105 days of gestation, three biological replicates for each point) and postnatal (3 days after birth, n = 3) goat skeletal muscle, and found that it is highly expressed in skeletal muscle and gradually upregulated during skeletal muscle satellite cell (SMSC) differentiation in goat. Notably, overexpression of lncR-125b accelerated the expression of myogenic differentiation 1 (MyoD 1) and myogenin (MyoG), and the formation of myotubes, and knockdown of lncR-125b showed opposite effects in SMSCs. Results of dual-luciferase assay and quantitative real-time polymerase chain reaction revealed that lncR-125b acts as a molecular sponge for miR-125b and that insulin-like growth factor 2 (IGF2), a critical regulator of skeletal myogenesis, is a direct target gene of miR-125b. Further analyses showed that lncR-125b negatively regulates miR-125b expression and positively regulates IGF2 expression in SMSCs. Mechanistically, lncR-125b promotes SMSC differentiation by functioning as a competing endogenous RNA (ceRNA) for miR-125b to control IGF2 expression. These findings identify lncR-125b as a novel noncoding regulator of muscle cell differentiation and skeletal muscle development in goat.

Competitive endogenous RNA (ceRNA) regulation network of lncRNA-miRNA-mRNA during the process of the nickel-induced steroidogenesis disturbance in rat Leydig cells

Nickel (Ni) is a ubiquitous environmental pollutant, which can disrupt the production of steroid in rat Leydig cells. Steroidogenesis can be affected by non-coding RNAs (ncRNAs), which operate in normal physiological processes. To date, however, very few studies have focused on whether ncRNAs are involved in Ni-induced steroidogenesis disturbance. The present study was designed to investigate the impact of NiSO₄ on the regulation of RNA networks including long non-coding RNA (lncRNA), microRNA (miRNA), and mRNA in rat Leydig cells. After treatment with 1000 μmol/L NiSO₄ for 24 h, 372 lncRNAs, 27 miRNAs (fold change>2, p < .05) and 3666 mRNAs (fold change>2, p < .01, and FDR < 0.01) were identified to be markedly altered by high-throughput sequencing analysis in rat Leydig cells. Functional analysis showed that the differentially expressed mRNAs were annotated into some steroid-related pathways. A dysregulated competing endogenous RNA (ceRNA) network of lncRNA-miRNA-mRNA was constructed based on bioinformatic analysis. Furthermore, a ceRNA network related to steroidogenesis was selected to analyze further and after the validation by qRT-PCR. The LOC102549726/miR-760-3p/Atf6, LOC102549726/miR-760-3p/Ets1, LOC102549726/miR-760-3p/Sik1 and AABR07037489.1/miR-708-5p/MAPK14 ceRNA networks were eventually confirmed. Collectively, our study provided a systematic perspective on the potential role of ncRNAs in steroidogenesis disturbance induced by Ni in rat Leydig cells.

LncRNA HULC promotes the progression of gastric cancer by regulating miR-9-5p/MYH9 axis

Long non-coding RNAs (lncRNAs) highly upregulated in liver cancer (HULC) has been identified as an oncogene involved in many human cancers. Herein, we aimed to further explore the role and molecular mechanism of HULC in gastric cancer (GC) progression. The levels of HULC, miR-9-5p and myosin heavy chain 9 (MYH9) mRNA were detected by qRT-PCR. The targeted interaction between HULC and miR-9-5p was verified by dual-luciferase reporter and RNA pull-down assays. Cell proliferation assay, cell colony formation, flow cytometry and transwell assay were used to determine cell proliferation, colony formation, apoptosis and migration and invasion, respectively. Xenograft assay was used to observe the effect of HULC on GC growth in vivo. Our results revealed that HULC was upregulated and miR-9-5p was downregulated in GC, and both were associated with clinicopathologic features of GC patients. A positive correlation was found between HULC expression and epithelial-to-mesenchymal transition (EMT) of GC tissues. Moreover, HULC repressed miR-9-5p expression by binding to miR-9-5p. The regulatory effects of HULC knockdown on GC cell proliferation, migration, invasion, EMT and apoptosis were reversed by introduction of anti-miR-9-5p. HULC regulated MYH9 expression by acting as a molecular sponge of miR-9-5p in GC cells. HULC knockdown inhibited tumor growth in vivo. In conclusion, our data demonstrated that HULC knockdown repressed GC progression at least partly by regulating miR-9-5p/MYH9 axis.

Competing Endogenous RNA Networks Underlying Anatomical and Physiological Characteristics of Poplar Wood in Acclimation to Low Nitrogen Availability

Although poplar plantations are often established on nitrogen (N)-poor soil, the physiological and molecular mechanisms underlying wood properties of poplars in acclimation to low N availability remain largely unknown. To investigate wood properties of poplars in acclimation to low N, Populus � canescens saplings were exposed to either 50 (low N) or 500 (normal N) �M NH4NO3 for 2 months. Low N resulted in decreased xylem width and cell layers of the xylem (the number of cells counted along the ray parenchyma on the stem cross section), narrower lumina of vessels and fibers, greater thickness of double fiber walls (the walls between two adjacent fiber cells), more hemicellulose and lignin deposition, and reduced cellulose accumulation in poplar wood. Consistently, concentrations of gibberellins involved in cell size determination and the abundance of various metabolites including amino acids, carbohydrates and precursors for cell wall biosynthesis were decreased in low N-supplied wood. In line with these anatomical and physiological changes, a number of mRNAs, long noncoding RNAs (lncRNAs) and microRNAs (miRNAs) were significantly differentially expressed. Competing endogenous RNA regulatory networks were identified in the wood of low N-treated poplars. Overall, these results indicate that miRNAs-lncRNAs-mRNAs networks are involved in regulating wood properties and physiological processes of poplars in acclimation to low N availability.

LncRNA NORAD Promotes Proliferation And Inhibits Apoptosis Of Gastric Cancer By Regulating miR-214/Akt/mTOR Axis

PURPOSE

In previous studies, we confirmed that the overexpression of lncRNA NORAD was associated with the occurrence and development of gastric cancer (GC). The aim of the present study was to explore the molecular mechanism of lncRNA NORAD on GC cell proliferation and apoptosis in vitro and in vivo.

PATIENTS AND METHODS

The quantitative Real-Time PCR (qRT-PCR) was used to determine the expression levels of lncRNA NORAD and miR-214 in GC tissues and cells. The interaction between lncRNA NORAD and miR-214 was investigated by biological information and Dual-Luciferase gene reporter assay. Effect of lncRNA NORAD on GC tumor growth in vivo was studied in tumor xenograft model mice. The apoptosis of GC cells was determined by flow cytometry. The proliferation of GC cells was determined by 5-ethynyl-2´-deoxyuridine (EDU) and colony formation assays. Western Blot was used to determine the expressions of caspase-3, Akt and mTOR in GC tissues and cells.

RESULTS

The qRT-PCR results showed that lncRNA NORAD was highly expressed in human GC tissues and cell lines, while miR-214 was significantly down-regulated. Meanwhile, there was a direct interaction between lncRNA NORAD and miR-214. In addition, lncRNA NORAD could promote the growth and proliferation of GC cells both in vivo and in vitro. NOARD could also inhibit the apoptosis of GC cells by down-regulating caspase-3; however, miR-214 overexpression attenuated this effect. Moreover, lncRNA NORAD promoted the phosphorylation of Akt and mTOR in mouse GC tissues and GC cell lines, while miR-214 mimics inhibited that promotion.

CONCLUSION

These results suggested that NORAD could promote the development of GC by inhibiting miR-214 expression and activating the Akt/mTOR signaling pathway.

The MicroRNA Centrism in the Orchestration of Neuroinflammation in Neurodegenerative Diseases

MicroRNAs (miRNAs) are small non-coding RNAs with a unique ability to regulate the transcriptomic profile by binding to complementary regulatory RNA sequences. The ability of miRNAs to enhance (proinflammatory miRNAs) or restrict (anti-inflammatory miRNAs) inflammatory signalling within the central nervous system is an area of ongoing research, particularly in the context of disorders that feature neuroinflammation, including neurodegenerative diseases (NDDs). Furthermore, the discovery of competing endogenous RNAs (ceRNAs) has led to an increase in the complexity of miRNA-mediated gene regulation, with a paradigm shift from a unidirectional to a bidirectional regulation, where miRNA acts as both a regulator and is regulated by ceRNAs. Increasing evidence has revealed that ceRNAs, including long non-coding RNAs, circular RNAs, and pseudogenes, can act as miRNA sponges to regulate neuroinflammation in NDDs within complex cross-talk regulatory machinery, which is referred to as ceRNA network (ceRNET). In this review, we discuss the role of miRNAs in neuroinflammatory regulation and the manner in which cellular and vesicular ceRNETs could influence neuroinflammatory dynamics in complex multifactorial diseases, such as NDDs.

Vitamin D (1,25-(OH)2D3) regulates the gene expression through competing endogenous RNAs networks in high glucose-treated endothelial progenitor cells

Vitamin D (vit-D) supplementation can improve endothelial cell function in type 2 diabetes mellitus patients with vit-D insufficiency or deficiency. In the present study, we aimed to compare the expression profiles of circRNAs, lncRNAs, miRNAs, and mRNAs between 1,25-(OH)₂D₃-treated endothelial progenitor cells (EPCs) and control cells, and to further construct the 1,25-(OH)₂D₃-regulated ceRNA networks in EPCs. RNA sequencing was performed on the 1,25-(OH)₂D₃-treated EPCs and control cells derived from the bone marrow (BM). Bioinformatics analyses were performed to identify differentially expressed (DE) microRNAs (miRNAs), circular RNAs (circRNAs), mRNAs, and long non-coding RNAs (lncRNAs). Then Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted to predict the function of genes. Competing endogenous RNA (ceRNA) networks were constructed with Cytoscape software. 1,25-(OH)₂D₃ application induced changes in the expression profiles of 1791 mRNAs, 2726 lncRNAs, 205 circRNAs, and 45 miRNAs in EPCs treated with high levels of glucose. These DE RNAs were associated with MMP and GTPase activities, specific signaling pathways, and components of actin, extracellular matrix, or adherens junction. DE circRNAs, which functioned independently of their linear host genes, interacted with miRNAs to serve as miRNA sponges in complex ceRNA networks. The data indicated that circRNAs and lncRNAs comprised ceRNAs to sponge effects of miRNAs on the expressions of mRNAs following 1,25-(OH)₂D₃ application in EPCs. 1,25-(OH)₂D₃ improved the function of EPCs via associated ceRNA interaction networks in diabetes patients.

Identification of messenger and long noncoding RNAs associated with gallbladder cancer via gene expression profile analysis

The present study aimed to investigate the long noncoding RNAs (lncRNAs) and messenger RNAs (mRNAs) involved in the progression of gallbladder cancer and explore the potential physiopathologic mechanisms of gallbladder cancer in terms of competing endogenous RNAs (ceRNAs). The original lncRNA and mRNA expression profile data (nine gallbladder cancer tissues samples and nine normal gallbladder samples) in GSE76633 was downloaded from the Gene Expression Omnibus database. Differentially expressed mRNAs and lncRNAs between gallbladder cancer tissue and normal control were selected and the pathways in which they are involved were analyzed using bioinformatics analyses. MicroRNAs (miRNAs) were also predicted based on the differentially expressed mRNAs. Finally, the co-expression relation between lncRNA and mRNA was analyzed and the ceRNA network was constructed by combining the lncRNA-miRNA, miRNA-mRNA, and lncRNA-mRNA pairs. Overall, 373 significantly differentially expressed mRNAs and 47 lncRNAs were identified between cancer and normal tissue samples. The upregulated genes were significantly enriched in the extracellular matrix (ECM)-receptor interaction pathway, while the downregulated genes were involved in the complement and coagulation cascades. Altogether, 128 co-expression relations between lncRNA and mRNA were obtained. In addition, 196 miRNA-mRNA regulatory relations and 145 miRNA-lncRNA relation pairs were predicted. Finally, the lncRNA-miRNA-gene ceRNA network was constructed by combining the three types of relation pairs, such as XLOC_011309-miR-548c-3p-SPOCK1 and XLOC_012588-miR-765-CEACAM6. mRNAs and lncRNAs may be involved in gallbladder cancer progression via ECM-receptor interaction pathways and the complement and coagulation cascades. Moreover, ceRNAs such as XLOC_011309-miR-548c-3p-SPOCK1 and XLOC_012588-miR-765-CEACAM6 can also be implicated in the pathogenesis of gallbladder cancer.

Gene Regulatory Networks in Peripheral Mononuclear Cells Reveals Critical Regulatory Modules and Regulators of Multiple Sclerosis

Multiple sclerosis (MS) is a complex, demyelinating disease with the involvement of autoimmunity and neurodegeneration. Increasing efforts have been made towards identifying the diagnostic markers to differentiate the classes of MS from other similar neurological conditions. Using a systems biology approach, we constructed four types of gene regulatory networks (GRNs) involved in peripheral blood mononuclear cells (PBMCs). The regulatory strength of each GRN across primary progressive MS (PPMS), relapsing-remitting MS (RRMS), secondary progressive MS (SPMS), and control were evaluated by an integrity algorithm. Among the constructed GRNs (referred as TF_gene_miRNA), POU3F2_CDK6_hsa-miR-590-3p, MEIS1_CASC3_hsa-miR-1261, STAT3_OGG1_hsa-miR-298, and TCF4_FMR1_hsa-miR-301b were top-ranked and differentially regulated in all classes of MS compared to control. These GRNs showed potential involvement in regulating various molecular pathways such as interleukin, integrin, glypican, sphingosine phosphate, androgen, and Wnt signaling pathways. For validation, the qPCR analysis of the GRN components (TFs, gene, and miRNAs) in PBMCs of healthy controls (n = 30), RRMS (n = 14), PPMS (n = 13) and SPMS (n = 12) were carried out. Real-time expression analysis of GRNs showed a similar regulatory pattern as derived from our systems biology approach. Also, our study provided several novel GRNs that regulate unique and common molecular mechanisms between MS conditions. Hence, these regulatory components of GRNs will help to understand the disease mechanism across MS classes and further insight may though light towards diagnosis.

LincRNA-SLC20A1 (SLC20A1) promotes extracellular matrix degradation in nucleus pulposus cells in human intervertebral disc degeneration by targeting the miR-31-5p/MMP3 axis

Long non-coding RNAs (lncRNAs) are novel players in intervertebral disc degeneration (IDD) and show multiple functions. LncRNA lincRNA-SLC20A1 (SLC20A1) is aberrantly expressed in IDD. However, the role of SLC20A1 in degenerative nucleus pulposus (NP) cells and its underlying mechanism are unclear. The expressions of SLC20A1, miR-31-5p, and MMP3 were determined using RT-qPCR and western blotting. Extracellular matrix (ECM) degradation was evaluated by ECM-related genes collagen II, aggrecan, and ADAMTS4 using western blotting and an enzyme-linked immunosorbent assay (ELISA). The target binding between miR-31-5p and SLC20A1 or matrix metalloproteinase (MMP3) was predicted based on the miRcode or starBase websites and confirmed using a luciferase reporter assay and an RNA pull-down assay. SLC20A1 expression is upregulated in NP tissues from IDD patients, and this expression promotes ADAMTS5 expression and represses collagen II and aggrecan expression in degenerative NP cells derived from IDD patients. Mechanically, SLC20A1 acts as a competing endogenous RNA (ceRNA) to negatively regulate miRNA-31-5p (miR-31-5p) expression. Moreover, MMP3 is a downstream target for miR-31-5p and is positively modulated by SLC20A1 in degenerative NP cells. Similar to the SLC20A1 effect in human NP cells, the downregulation of miR-31-5p facilitates ECM degradation as well. On the contrary, miR-31-5p upregulation abolishes the promoting role of SLC20A1 in degenerative NP cells, the effect of which is then blocked by the ectopic expression of MMP3. The upregulation of SLC20A1 aggravates ECM degradation in degenerative human NP cells by targeting the miR-31-5p/MMP3 axis, suggesting that the SLC20A1/miR-31-5p/MMP3 pathway can contribute to IDD progression.

Bufalin suppresses the migration and invasion of prostate cancer cells through HOTAIR, the sponge of miR-520b

Bufalin, the major active component of the traditional Chinese medicine ChanSu obtained from the skin and parotid venom glands of toads, has long been known as an anticancer agent. Recent studies show that microRNAs (miRs) are involved in the anticancer activities of bufalin, while long non-coding RNAs (lncRNAs) are known to interact with miRNAs to regulate various biological functions. In this paper, we investigated the possible network related to the antimetastatic effect of bufalin in prostate cancer (PCa) cells. We demonstrated that bufalin (0.05-10 µM) dose-dependently suppressed the proliferation of prostate cancer DU145 and PC3 cells with IC50 values of 0.89 and 1.28 µM, respectively. Furthermore, bufalin treatment significantly suppressed the cell migration and invasion. To explore the role of lncRNAs in the antimetastatic activity of bufalin, we used an lncRNA microarray and found that HOX transcript antisense RNA (HOTAIR) was the most markedly downregulated lncRNA in bufalin-treated PCa cells. Overexpression of HOTAIR counteracted the suppressing effects of bufalin on DU145 and PC3 cells. We then predicted and verified that HOTAIR upregulated FGFR1 expression by sponging miR-520b in PCa cells. In 40 patients with PCa bone metastasis, we used in situ hybridization or immunohistochemical assay to assess the HOTAIR and FGFR1 expression, which revealed that both HOTAIR and FGFR1 expression were significantly higher in bone metastasis tissues than in the primary PCa tissues. In addition, the level of serum HOTAIR was positively associated with the levels of serum bone metabolic markers (CTx, OST, B-ALP and PINP) and may serve as a reasonable biomarker for PCa bone metastasis. Taken together, this is the first study revealing that HOTAIR promotes PCa bone metastasis, and bufalin may be a promising candidate for the treatment of this disease.

Silencing of GAS5 represses the malignant progression of atherosclerosis through upregulation of miR-135a

Long non-coding RNA growth arrest-specific 5 (GAS5) has been demonstrated to be involved in the pathogenesis of atherosclerosis (AS). The purpose of the present study was to investigate the underlying mechanisms of GAS5 on the inflammation and lipid metabolic disorders of AS. ApoE^-/- mice were fed on a high fat diet (HFD) and THP-1 macrophages were treated with ox-LDL to construct AS model in vivo and in vitro, respectively. The detections of blood lipids and inflammatory cytokines were performed using corresponding assay kits. qRT-PCR was used to assess the expression of GAS5 and miR-135a. Western blot was performed to detect PPARα and CPT1 levels. The targeted interaction between GAS5 and miR-135a was determined by dual-luciferase reporter assay and RNA immunoprecipitation assay. Our data revealed that GAS5 was upregulated in AS mice model and ox-LDL-treated macrophages. GAS5 silencing alleviated lipid metabolic disorders and inflammation in AS mice and ox-LDL-treated macrophages. Moreover, GAS5 directly targeted miR-135a and repressed miR-135a expression. MiR-135a expression restoration abrogated the alleviative effects of GAS5 silencing on inflammation and lipid metabolic disorders in ox-LDL-treated macrophages. In conclusion, our study suggested that GAS5 silencing repressed the malignant progression of AS at least partly through upregulation of miR-135a. Targeting GAS5 might be a promising treatment strategy for AS management.

Long non-coding RNA HOTTIP promotes hypoxia-induced glycolysis through targeting miR-615-3p/HMGB3 axis in non-small cell lung cancer cells

Increased glycolysis under hypoxic stress is a fundamentally important feature of non-small cell lung cancer (NSCLC) cells, but molecular mechanisms of hypoxia on glycolysis remain elusive. Herein, we aimed to explore whether lncRNAs and miRNAs are involved in the glycolytic reprogramming under hypoxic conditions. The levels of HOXA transcript at the distal tip (HOTTIP), miR-615-3p and high mobility group box 3 (HMGB3) mRNA were assessed by qRT-PCR. Western blot was performed to determine the protein expression of hexokinase 2 (HK-2) and HMGB3. Glucose consumption and lactate production were analyzed using a respective assay kit. The targeted correlation between miR-615-3p and HOTTIP or HMGB3 was verified using dual-luciferase reporter and RNA immunoprecipition assays. Our data revealed that HOTTIP was upregulated and miR-615-3p was downregulated in NSCLC tissues and cells. Hypoxia induced glycolysis, increased HOTTIP and HMGB3 mRNA levels and repressed miR-615-3p expression in NSCLC cells. HOTTIP deficiency or miR-615-3p expression restoration repressed hypoxia-induced glycolysis. Moreover, HOTTIP acted as a molecular sponge for miR-615-3p and HMGB3 was a direct target of miR-615-3p. The inhibitory effect of HOTTIP deficiency on glycolysis under hypoxic exposure was reversed by miR-615-3p restoration. Additionally, HOTTIP regulated HMGB3 expression by acting as a molecular sponge of miR-615-3p in NSCLC cells. In conclusion, our study suggested that HOTTIP might promote glycolysis under hypoxic conditions at least partly through regulating miR-615-3p/HMGB3 axis in NSCLC cells. Targeting HOTTIP might be a promising therapeutic strategy for NSCLC treatment.

Long noncoding RNA FOXD2-AS1 promotes glioma cell cycle progression and proliferation through the FOXD2-AS1/miR-31/CDK1 pathway

Long noncoding RNAs (lncRNAs) are vital mediators involved in cancer progression. Previous studies confirmed that FOXD2 adjacent opposite strand RNA 1 (FOXD2-AS1) is upregulated in tumor diseases. The potential influence of FOXD2-AS1 in glioma progression, however, remains unknown. In this paper, FOXD2-AS1 was found to be upregulated in glioma tissues. Its level was linked with glioma stage. Moreover, glioma patients expressing high level of FOXD2-AS1 suffered worse prognosis. Biological functions of FOXD2-AS1 in glioma cells were analyzed through integrative bioinformatics and TCGA RNA sequencing data analysis. Pathway enrichment analysis uncovered that FOXD2-AS1 was mainly linked with cell cycle regulation in both low-grade glioma and glioblastoma. Further experiments demonstrated that silence of FOXD2-AS1 inhibited proliferation, arrested cell cycle and downregulated cyclin-dependent kinase 1 (CDK1) in human glioma cells. Dual-luciferase reporter assay confirmed that FOXD2-AS1 upregulated CDK1 by sponging miR-31. Rescue assays were performed and confirmed the regulatory loop FOXD2-AS1/miR-31/CDK1 in glioma. Collectively, our results indicated that the FOXD2-AS1/miR-31/CDK1 axis influenced glioma progression, providing a potential new target for glioma patients.

LncRNA FOXD2-AS1 induces chondrocyte proliferation through sponging miR-27a-3p in osteoarthritis

Osteoarthritis (OA) is a common degenerative joint disease worldwide. Long non-coding RNAs (lncRNAs) have been widely confirmed to involve in the modulation of OA progression. However, the underlying mechanisms of lncRNA FOXD2-AS1 in OA remain unclear. In the present study, we showed FOXD2-AS1 expression was upregulated and positively associated with the severity of OA patients. IL-1β and/or TNF-α treatment could increase FOXD2-AS1 expression in chondrocytes. FOXD2-AS1 overexpression induced cell proliferation, inflammation and extracellular matrix (ECM) degradation in chondrocytes. Mechanistically, we found that FOXD2-AS1 upregulated the expression level of TLR4 by sponging miR-27a-3p. In addition, we revealed that miR-27a-3p mimics could abolish the effects of FOXD2-AS1 overexpression on cell proliferation, inflammation, and ECM degradation in chondrocytes. Therefore, we demonstrated that FOXD2-AS1 could play a crucial role in the progression of OA, at least partially, by regulating miR-27a-3p/TLR4 axis.

SNHG14 silencing suppresses the progression and promotes cisplatin sensitivity in non-small cell lung cancer

Long non-coding RNAs (lncRNAs) small nucleolar RNA host gene 14 (SNHG14) has been identified as an oncogene involved in the progression of various human cancers. Nevertheless, the functional role and molecular mechanism of SNHG14 on NSCLC remain largely elusive. qRT-PCR assay was performed to detect the levels of SNHG14, miR-34a and high mobility group box 1 (HMGB1) mRNA. HMGB1 protein level was assessed by western blot analysis. CCK-8 assay was used to determine the IC50 value of cisplatin (CDDP), and transwell assays were employed to detect cell migration and invasion abilities. Cell apoptosis was determined by flow cytometric analysis. Dual-luciferase reporter assay, RNA immuoprecipitation assay and RNA pull-down assay were performed to confirm the interaction between SNHG14 and miR-34a, or miR-34a and HMGB1. Our data demonstrated that SNHG14 was upregulated in NSCLC cells, and SNHG14 silencing repressed the migration, invasion while accelerated the apoptosis of NSCLC cells. Moreover, we manifested that SNHG14 silencing promoted NSCLC cell sensitivity to CDDP. SNHG14 repressed miR-34a expression by binding to miR-34a. Additionally, SNHG14 regulated HMGB1 expression by sponging miR-34a. SNHG14 silencing exerted its regulatory effect by miR-34a and HMGB1 mediated the regulatory effect of miR-34a on NSCLC cells. In conclusion, SNHG14 silencing suppressed NSCLC progression at least partly by miR-34a/HMGB1 axis in vitroand promoted NSCLC cell sensitivity to CDDP, highlighting that SNHG14 might be a potential target for NSCLC therapy.

Network-Based Methods and Other Approaches for Predicting lncRNA Functions and Disease Associations

The discovery that a considerable portion of eukaryotic genomes is transcribed and gives rise to long noncoding RNAs (lncRNAs) provides an important new perspective on the transcriptome and raises questions about the centrality of these lncRNAs in gene-regulatory processes and diseases. The rapidly increasing number of mechanistically investigated lncRNAs has provided evidence for distinct functional classes, such as enhancer-like lncRNAs, which modulate gene expression via chromatin looping, and noncoding competing endogenous RNAs (ceRNAs), which act as microRNA decoys. Despite great progress in the last years, the majority of lncRNAs are functionally uncharacterized and their implication for disease biogenesis and progression is unknown. Here, we summarize recent developments in lncRNA function prediction in general and lncRNA-disease associations in particular, with emphasis on in silico methods based on network analysis and on ceRNA function prediction. We believe that such computational techniques provide a valuable aid to prioritize functional lncRNAs or disease-relevant lncRNAs for targeted, experimental follow-up studies.

CircRNA expression profile of bovine placentas in late gestation with aberrant SCNT fetus

BACKGROUNDS

One of the limitations of somatic cell nuclear transfer (SCNT) strategy to generate genetically modified offspring is the low birth rate. Placental dysfunction is one of the causes of abortion. Circular RNA (circRNA) is noncoding RNA which functions as microRNA (miRNA) sponges in biological processes.

METHODS

Two aberrant pregnant placenta (aberrant group, AG) and three normal pregnant placenta (normal group, NG) during late gestation (180-210 days) with bovine SCNT fetus were collected for high-throughput sequencing and analyzed. The host genes of differentially expressed (DE) circRNAs were predicted. And the microRNAs (miRNAs) which could interact with DE circRNAs were analyzed. Then, the expressional level of partial DE circRNAs and corresponding host genes was verified through qRT-PCR. At last, the function of host genes was analyzed through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG).

RESULTS

Altogether 123 differentially expressed circRNAs between two groups were identified, which were found related to 60 host genes and 32 miRNAs. The top 10 upregulated circRNAs were bta_circ_0012985, bta_circ_0013071, bta_circ_0013074, bta_circ_0016024, bta_circ_0013068, bta_circ_0008816, bta_circ_0012982, bta_circ_0013072, bta_circ_0019285, and bta_circ_0013067. The top 10 downregulated circRNAs were bta_circ_0024234, bta_circ_0017528, bta_circ_0008077, bta_circ_0003222, bta_circ_0007500, bta_circ_0020328, bta_circ_0011001, bta_circ_0016364, bta_circ_0008839, and bta_circ_0016049. The qRT-PCR results showed consistent trend with sequencing analysis result, while host genes had no statistic difference. The GO and KEGG analyses of the host genes suggested that abnormal circRNA expression may play multiple roles in placental structure and dysfunction.

CONCLUSION

The abnormal circRNA expression may be one of reasons of placental dysfunction, leads to abortion of bovine SCNT fetus.

The role of dietary phytochemicals in the carcinogenesis via the modulation of miRNA expression

PURPOSE

Phytochemicals are naturally occurring plant-derived compounds and some of them have the potential to serve as anticancer drugs. Based on recent evidence, aberrantly regulated expression of microRNAs (miRNAs) is closely associated with malignancy. MicroRNAs are characterized as small non-coding RNAs functioning as posttranscriptional regulators of gene expression. Accordingly, miRNAs regulate various target genes, some of which are involved in the process of carcinogenesis.

RESULTS

This comprehensive review emphasizes the anticancer potential of phytochemicals, either isolated or in combination, mediated by miRNAs. The ability to modulate the expression of miRNAs demonstrates their importance as regulators of tumorigenesis. Phytochemicals as anticancer agents targeting miRNAs are widely studied in preclinical in vitro and in vivo research. Unfortunately, their anticancer efficacy in targeting miRNAs is less investigated in clinical research.

CONCLUSIONS

Significant anticancer properties of phytochemicals as regulators of miRNA expression have been proven, but more studies investigating their clinical relevance are needed.

LncRNA RMRP/miR-613 axis is associated with poor prognosis and enhances the tumorigenesis of hepatocellular carcinoma by impacting oncogenic phenotypes

Increasing evidences demonstrate that long noncoding RNAs (lncRNAs) play an important role in the tumorigenesis of hepatocellular carcinoma (HCC). LncRNA RMRP (RNA component of mitochondrial RNA processing endoribonuclease) has been proved to involve in the tumorigenesis of several human cancers. However, the role and molecular mechanism of RMRP in HCC remain largely unknown. In current study, we compared the expression profiles of RMRP in 52 paired HCC specimens and corresponding adjacent non-tumor tissues. The clinicopathological characteristics of HCC patients in relation to RMRP expression were analyzed, and the prognostic value of RMRP expression was examined. RNAi technology was performed to knockdown RMRP expression in HCC cells, and the effects of RMRP on cell proliferation, cell cycle, migration and invasion of HCC cells were assessed by using MTT, flow cytometry, wound scratch and transwell invasion assays. The potential binding site of RMRP to miR-613 was confirmed by using dual luciferase reporter gene and qRT-PCR assays. Here, we found that RMRP expression was significantly upregulated in the HCC tissues and cells, and high RMRP expression was positively correlated with tumor aggressive phenotypes and poor overall survival of patients with HCC. Furthermore, RMRP knockdown suppressed cell proliferation, migration, invasion and induced cell cycle arrest at G0/G1 phase. The expression of miR-613 was dramatically down-regulated in HCC tissues and cells, and RMRP could negatively regulate miR-613 expression by acting as a ceRNA. In mechanism, RMRP exerted an oncogenic role in HCC via downregulation of miR-613. In vivo experiment also revealed that RMRP knockdown inhibited HCC tumorigenesis, while miR-613 silencing could partly reversed the inhibitory effect of RMRP knockdown on HCC tumorigenesis. In conclusion, our data demonstrated that RMRP plays an oncogenic role in regulating HCC tumorigenesis by acting as a ceRNA of miR-613, indicating RMRP/miR-613 axis may serve as a novel molecular target for the treatment of HCC.

LncRNA SNHG6 promotes the migration, invasion, and epithelial-mesenchymal transition of colorectal cancer cells by miR-26a/EZH2 axis

Objective: Colorectal cancer (CRC) is a leading cause of cancer-related deaths worldwide. Small nucleolar RNA host gene 6 (SNHG6) was reported to function as an oncogene in a number of cancers. Here, we aimed to further explore the roles and molecular mechanism of SNHG6 in CRC metastasis.

Methods: The expression levels of SNHG6, miR-26a, and enhancer of zeste homolog 2 (EZH2) mRNA were assessed by quantification real-time PCR in CRC tissues and cell lines. Western blot analysis was performed to determine the levels of E-cadherin, Snail, Vimentin, N-cadherin, and EZH2. Cell migration and invasion capacities were detected by transwell assay. Dual-luciferase reporter assay or RNA Immunoprecipitation assay was employed to verify the interaction between SNHG6 and miR-26a, or EZH2 and miR-26a.

Results: Our data indicated that SNHG6 and EZH2 mRNA were upregulated, and miR-26a was downregulated in CRC tissues and cell lines. SNHG6 knockdown suppressed the migration, invasion, and epithelial-mesenchymal transition (EMT) of CRC cells. Moreover, SNHG6 binded to miR-26a and repressed miR-26a expression. EZH2 was a direct target of miR-26a, and it was regulated by SNHG6/miR-26a. MiR-26a inhibitor undermined the effect of SNHG6 knockdown on cell migration, invasion, and EMT. Additionally, EZH2 antagonized the effect of miR-26a on cell migration, invasion, and EMT in CRC cells.

Conclusion: SNHG6 knockdown suppressed cell migration, invasion, and EMT at least partly by sponging miR-26a and regulating EZH2 expression in CRC cells, providing a strategy for blocking CRC metastasis.

circRNAs (hsa_circ_00156, hsa_circ _000224, and hsa_circ _000520) are novel potential biomarkers in hepatocellular carcinoma

Circular RNAs (circRNAs) are a newly validated type of noncoding RNAs recently found to be deregulated in several human cancers. More accurate and specific noninvasive biomarkers are strongly needed for better diagnosis and prognosis of hepatocellular carcinoma (HCC). We performed a bioinformatics analysis to retrieve a novel panel of circRNAs potentially relevant to HCC. We examined their expression in the sera of 68 patients with HCC, 60 patients with chronic hepatitis C, and 36 healthy controls using quantitative polymerase chain reaction. We examined the performance characteristics of the selected circRNA biomarker panel in comparison with alpha-fetoprotein (AFP). In addition, we performed a survival analysis to correlate between their expression levels and patient survival. The circRNAs hsa_circ _00224 and hsa_circ _00520 showed a strong biomarker potential with relatively high sensitivities and specificities compared with AFP. The combined panel including the three circRNAs showed superior performance characteristics relative to those of AFP. The median follow-up period was 26 months. hsa_circ_00520 expression has been shown to be associated with relapse-free survival (P < 0.005). circRNAs hsa_circ_00156, hsa_circ_000224, and hsa_circ_000520 are novel potential biomarkers of high sensitivity and specificity, which could potentially be used in the diagnosis of HCC.

lncRNA CADM1-AS1 inhibits cell-cycle progression and invasion via PTEN/AKT/GSK-3β axis in hepatocellular carcinoma

Purpose: CADM1-AS1 (cell adhesion molecule 1 antisense RNA 1, long non-coding RNA), was firstly characterized in renal clear cell carcinoma, and exhibits a tumor suppressor role. However, its clinical relevance and exact effects in hepatocellular carcinoma (HCC) remain unknown. Therefore, in this study, we aimed to assess the clinical significance and function of CADM1-AS1 in HCC. Methods: We detected CADM1-AS1 expression in liver cancer tissue samples and cell lines, and analyzed the association between CADM1-AS1 expression and clinical parameters in 90 liver cancer patients. Moreover, we conducted gain-of-function and loss-of-function studies in liver cancer cell to explore the biological function and molecular mechanism of CADM1-AS1. Results: CADM1-AS1 expression was reduced in HCC. Clinical data showed that this downregulation was associated with advanced tumor stage, high TNM stage and reduced survival in HCC patients. CADM1-AS1 overexpression inhibited HCC cells proliferation, migration and invasion, while inducing G0/G1 phase arrest. Meanwhile, we revealed that CADM1-AS1 inhibited the phosphorylation of AKT and GSK-3β. Furthermore, our study showed that CADM1-AS1 decreased the cell cycle associated proteins expression of cyclinD, cyclinE, CDK2 CDK4, CDK6, and enhanced the levels of p15, p21 and p27. More importantly, SC79, a specific activator for AKT;, apparently attenuated the effects of CADM1-AS1 on above cell-cycle associated proteins, confirming that CADM1-AS1 inhibited cell cycles through the AKT signaling pathway. And we also found the CADM1-AS1 has antitumor effect in vivo by a xenograft HCC mouse model. In conclusion, the present findings show that the CADM1-AS1 inhibits proliferation of HCC by inhibiting AKT/GSK-3β signaling pathway, then upregulate p15, p21, p27 expression and downregulate cyclin, CDK expression to inhibit the G0/G1 to S phase transition both in vitro and in vivo. Conclusion: CADM1-AS1 functions as a tumor-suppressive lncRNA. This study reveals a molecular pathway involving PTEN/AKT/GSK-3β which regulates HCC cell-cycle progression.

The LncRNA LINC00963 facilitates osteosarcoma proliferation and invasion by suppressing miR-204-3p/FN1 axis

Purpose: It remains unclear that long noncoding RNAs' role in cancer initiation and progression, including osteosarcoma. Long noncoding RNA LINC00963 was found to be participated in carcinogenesis and progression of osteosarcoma. However, the molecular mechanisms of LINC00963 engaged in osteosarcoma (OS) still needs to be explored. Methods: LINC00963 and miR-204-3p RNA expression levels were quantified by PCR in OS tissues and cells. CCK 8 assay, wound healing assay and transwell migration and invasion assay were chosen to assess cell growth, viability, migration, and invasion. Luciferase reporter assays were performed to verify direct interaction between LINC00963 and miR-204-3p and miR-204-3p and Fibronectin-1. Western blot was conducted to evaluate Fibronectin-1 expression in OS cells. Results: LINC00963 was verified to be highly expressed in OS samples and cells. Specifically, elevated expression of LINC00963 was correlated with poor prognosis in patients. Furthermore, LINC00963 overexpression was found to promote proliferation, migration, and invasion in vitro. The luciferase reporter assay showed that LINC00963 can suppress miR-204-3p by directly binding miR-204-3p. Rescue experiment results indicated that function of LINC00963 in osteosarcoma was miR-204-3p dependant. Besides, we initially explored Fibronectin-1 (FN1) as the target of LINC00963/miR-204-3p axis in osteosarcoma. Conclusions: Our findings implied that LINC00963/miR-204-3p/FN1 can play an important role in proliferation and progression in osteosarcoma. LINC00963 has the potential to be a therapeutic target for osteosarcoma treatment.

Long noncoding RNA: a crosslink in biological regulatory network

Long noncoding RNAs (lncRNAs) had been defined as a novel class of functional RNAs longer than 200 nucleotides around a decade ago. It is widely acknowledged that lncRNAs play a significant role in regulation of gene expression, but the biological and molecular mechanisms are diverse and complex, and remain to be determined. Especially, the regulatory network of lncRNAs associated with other biological molecules is still a controversial matter, thus becoming a new frontier of the studies on transcriptome. Recent advance in high-throughput sequencing technologies and bioinformatics approaches may be an accelerator to lift the mysterious veil. In this review, we will outline well-known associations between lncRNAs and other biological molecules, demonstrate the diverse bioinformatics approaches applied in prediction and analysis of lncRNA interaction and perform a case study for lncRNA linc00460 to concretely decipher the lncRNA regulatory network.

Characteristics of the competition among RNAs for the binding of shared miRNAs

Competing endogenous RNAs (ceRNAs) are RNAs that share common miRNA binding sites and compete with each other for the miRNA association at these sites. The observation of this phenomenon in the cells altered the view of the miRNA target RNAs from molecules that are passively controlled by miRNAs to molecules that also modulate the miRNAs activity. In this review, we build a general profile of ceRNAS characteristics in order to facilitate ceRNAs identification by researchers. The information summarized here contains an actualized list of previously reported ceRNAs and classes of RNAs that can participate in this type of interaction, the expression behavior and characteristics of ceRNAs and miRNAs in the context of competition, the influence of the shared MREs/miRNAs numbers and the miRNA binding strength on the competition, reports on competition between RNAs in different subcellular localizations and the concept that ceRNAs may form a huge regulatory network in the cell.

Prediction of Recurrence in Cervical Cancer Using a Nine-lncRNA Signature

Background and Objective

As a common cancer type in women, cervical cancer remains one of the leading causes of cancer-associated mortalities word wide. Recent evidence has demonstrated the regulatory role of a large number of long non-coding RNAs (lncRNAs) in cervical cancer. Here, we aimed to identify new biomarkers that related with the recurrence through comprehensive bioinformatics analysis.

Methods

Firstly, we collected online lncRNA expression data of cervical cancer patients which were divided into training, validation, and test set. Then we developed a nine-lncRNA signature from training set by conducting LASSO Cox regression model along with 10-fold cross validation. The prognostic value of this risk score was validated in all the three sets using Kaplan–Meier analysis, C-index, time-dependent ROC curves and dynamic AUC. Biological function of these lncRNAs in cervical cancer cells were evaluated by performing gene ontology biological process enrichment and Kyoto Encyclopedia of Genes and Genomes signaling pathways analysis.

Results

According to the results, a higher predict accuracy was observed in the nine-lncRNA signature than that of FIGO stage in all the three sets. Stratified analysis also demonstrated that the nine-lncRNA signature can predict the recurrence of cervical cancer within FIGO stage. The potential mechanisms underlying the nine-lncRNAs from the signature were also identified according to the gene enrichment analysis.

Conclusion

In the present article, we provided a reliable prognostic tool to facilitate the individual management of patients with cervical cancer after treatment.

Dysregulation of long non-coding RNA SNHG12 alters the viability, apoptosis, and autophagy of prostate cancer cells by regulating miR-195/CCNE1 axis

This study aimed to explore the role and mechanism of lncRNA small nucleolar RNA host gene 12 (SNHG12) in the development of prostate cancer (PCa). The expression of SNHG12 in the serum of PCa patients as well as PCa cells was determined, and then we investigated whether SNHG12 could act as a competing endogenous RNA (ceRNA) to mediate the development of PCa. Furthermore, the association between SNHG12 and activation of the PI3K/AKT/mTOR pathway was explored. SNHG12 expression was up-regulated in the serum of PCa patients as well as PCa cells. High expression of SNHG12 resulted in a poor prognosis of PCa patients. Moreover, suppression of SNHG12 inhibited viability and promoted apoptosis and autophagy of LNCaP cells. Furthermore, SNHG12 was found to act as a ceRNA to regulate the expression of Cyclin E1 (CCNE1) by sponging miR-195. Lastly, suppression of SNHG12 inhibited the activation of PI3K/AKT/mTOR pathway. Our results revealed that up-regulation of SNHG12 promoted the viability and inhibited apoptosis and autophagy of PCa cells by regulating CCNE1 expression by sponging miR-195. Moreover, activation of PI3K/AKT/mTOR pathway is a key downstream mechanism regulating SNHG12-mediated the development of PCa. Our findings provide an experimental basis for targeted therapy of PCa.

MicroRNAs, Hypoxia and the Stem-Like State as Contributors to Cancer Aggressiveness

MicroRNAs (miRNAs) are small non-coding RNA molecules that play key regulatory roles in cancer acting as both oncogenes and tumor suppressors. Due to their potential roles in improving cancer prognostic, predictive, diagnostic and therapeutic approaches, they have become an area of intense research focus in recent years. Several studies have demonstrated an altered expression of several miRNAs under hypoxic condition and even shown that the hypoxic microenvironment drives the selection of a more aggressive cancer cell population through cellular adaptations referred as the cancer stem-like cell. These minor fractions of cells are characterized by their self-renewal abilities and their ability to maintain the tumor mass, suggesting their crucial roles in cancer development. This review aims to highlight the interconnected role between miRNAs, hypoxia and the stem-like state in contributing to the cancer aggressiveness as opposed to their independent contributions, and it is based in four aggressive tumors, namely glioblastoma, cervical, prostate, and breast cancers.

The Interaction Between lncRNA SNHG1 and miR-140 in Regulating Growth and Tumorigenesis via the TLR4/NF-κB Pathway in Cholangiocarcinoma

Cholangiocarcinoma (CCA) is the second most common primary hepatobiliary carcinoma. The long noncoding RNA (lncRNA) small nucleolar RNA host gene 1 (SNHG1) has been reported to contribute to the progression of multiple cancers. Nonetheless, the functions and hidden mechanism of SNHG1 remain unclear in CCA. In this study, the SNHG1 levels were boosted in CCA cell lines, and knockdown of SNHG1 repressed CCA cell proliferation and invasion in vitro. The data also demonstrated that miR-140 could act as a target of SNHG1 in CCA and inhibited CCA cell proliferation and invasion, whereas the inhibition effects were relieved by overexpression of SNHG1. In addition, Toll-like receptor 4 (TLR4), an NF-κB-activating signal, was identified to be a target of miR-140. SNHG1, as a competing endogenous RNA (ceRNA) for miR-140, enhanced TLR4 expression and activated NF-κB signaling, thereby regulating growth and tumorigenesis in CCA. Animal experiments further confirmed this conclusion. Collectively, these findings not only uncovered a key role of SNHG1/miR-140/TLR4/NF-κB signaling axis in CCA tumorigenesis and progression but also denoted the probable utilization of SNHG1 as a therapeutic target for CCA.

Identification of a 26-lncRNAs Risk Model for Predicting Overall Survival of Cervical Squamous Cell Carcinoma Based on Integrated Bioinformatics Analysis

As a common malignancy in women, cervical squamous cell carcinoma is a major cause of cancer-related mortality globally. Recent studies have demonstrated that long non-coding RNA (lncRNA) can function as potential biomarkers in cancer prognosis; however, little is known about its role in cervical cancer. In this study, we downloaded the gene expression profiles along with the clinical data of patients with cervical squamous cell carcinoma from The Cancer Genome Atlas. By applying bioinformatics analysis including random forest selection and Least Absolute Shrinkage and Selection Operator (LASSO) cox regression model along with 10-fold cross-validation, we constructed a 26-lncRNAs risk model that can be used to predict the overall survival of cervical squamous cell carcinoma. After that, Kaplan-Meier analysis combined with log-rank p test was applied to assess the predictive accuracy of the 26-lncRNAs risk model. Further analysis showed that the prognostic value of 26-lncRNAs risk model was independent of other clinicopathological factors. At last, lncRNAs in the model were put into gene ontology biological process enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathways analysis, which suggested that these lncRNAs might contribute to cancer-associated processes such as cell cycle and apoptosis. This study indicated that lncRNAs signature could be a useful marker to predict the prognosis of cervical squamous cell carcinoma.