Related Regulatory Networks Research Articles

Integrative analysis of miRNAs and mRNAs revealed regulation of lipid metabolism in dairy cattle.

Lipid metabolism in bovine mammary epithelial cells has been the primary focus of the research of milk fat percentage of dairy cattle. Functional microRNAs can affect lipid metabolism by regulating the expression of candidate genes. The purpose of the study was to screen and identify differentially expressed miRNAs, candidate genes, and co-regulatory pathways related to the metabolism of milk fat. To achieve this aim, we used miRNA and transcriptome data from the mammary epithelial cells of dairy cattle with high (H, 4.85%) and low milk fat percentages (L, 3.41%) during mid-lactation. One hundred ninety differentially expressed genes and 33 differentially expressed miRNAs were significantly enriched in related regulatory networks, of which 27 candidate genes regulated by 18 differentially expressed miRNAs significantly enriched in pathways related to lipid metabolism (p < 0.05). Target relationships between PDE4D and bta-miR-148a, PEG10 and bta-miR-877, SOD3 and bta-miR-2382-5p, and ADAMTS1 and bta-miR-2425-5p were verified using luciferase reporter assays and quantitative RT-PCR. The detection of triglyceride production in BMECs showed that bta-miR-21-3p and bta-miR-148a promote triglyceride synthesis, whereas bta-miR-124a, bta-miR-877, bta-miR-2382-5p, and bta-miR-2425-5p inhibit triglyceride synthesis. The conjoint analysis could identify functional miRNAs and regulatory candidate genes involved in lipid metabolism within the co-expression networks of the dairy cattle mammary system, which contributes to the understanding of potential regulatory mechanisms of genetic element and gene signaling networks involved in milk fat metabolism.

Identification of crucial long non-coding RNAs and mRNAs along with related regulatory networks through microarray analysis in esophageal carcinoma.

Esophageal carcinoma (EC) is a tremendous threat to human health and life worldwide. Long non-coding RNAs (lncRNAs) have been identified as crucial players in carcinomas including EC. An in-depth understanding on regulatory networks of lncRNAs contributes to the better management of EC. In this text, 2052 lncRNAs and 3240 mRNAs were found to be differentially expressed in 5 EC tumor tissues versus adjacent normal tissues by microarray analysis. Moreover, 297 carcinoma-related genes were screened out according to pathway and disease annotation analyses. In addition, 410 potential lncRNA-mRNA cis-regulation pairs and 395 lncRNA-mRNA trans-regulation pairs were screened out. Among these genes, 14 trans-regulated and 19 cis-regulated genes were found to be related with carcinomas. Additionally, 42 possible lncRNA-mRNA trans-regulation pairs and 26 cis-regulation pairs were found to be related with carcinomas. Also, 4 differentially expressed transcription factors in EC and lncRNAs possibly regulated by these transcription factors were screened out. Moreover, plenty of common upregulated or downregulated lncRNAs and mRNAs in EC were identified by comparative analysis for our microarray outcomes and previous high-throughput data. Furthermore, we demonstrated that ENST00000437781.1 knockdown inhibited cell proliferation and facilitated cell apoptosis by downregulating SIX homeobox 4 (SIX4) and ENST00000524987.1 knockdown had no influence on anoctamin 1 calcium activated chloride channel (ANO1) expression in EC cells. In conclusion, we identified some crucial lncRNAs and genes along with potential regulatory networks of lncRNAs/genes, deepening our understanding on pathogenesis of EC.

Research advances in plant fructokinases

Sugars are essential to the fundamental processes required for plant growth and development. The hexose sugars glucose and fructose are central to most metabolic pathways and serve as the raw material for organic matter in plants. Fructose accounts for half of the hexose generated by sucrose cleavage, and it can be phosphorylated either by fructokinase (FRK) or hexokinase (HXK). FRKs are the main fructose phosphorylating enzymes because their substrate specificity and affinity for fructose are much higher than those of the HXK, and thereby regulate fructose concentration and the distribution and flow of organic carbon in cells. Therefore, FRKs are considered to be of critical importance for all metabolic pathways and the formation of organic matter in plants. To date, all plant FRKs have been assigned to the phosphofructokinase type B subfamily, a large group within the sugar kinase family. Unlike mammalian FRKs, which phosphorylate fructose to form fructose 1-phosphate (F1P), plant FRKs, similar to bacterial FRKs, phosphorylate fructose to form fructose 6-phosphate (F6P). Moreover, there are both cytosolic and plastidic FRKs in plants, indicating that they play roles in different cellular compartments. Phylogenetic analysis shows that most of the FRK genes that are located on similar branches encode proteins with similar subcellular localizations, suggesting that they may perform similar functions. A large number of studies have implicated plant FRKs in vascular tissue development, and in recent years, it has been found that FRK is related to seed, fruit, and pollen development. FRK can also interact with the plant FLOWERING LOCUS T protein to co-regulate flowering. Additionally, a large number of experiments have shown that FRK affects chloroplast development mainly by affecting chloroplast gene expression, thus affecting photosynthesis and the source-sink relationship. Beyond these functions, FRK, as an important carbon flux-regulated kinase in plants, also plays an important role in plant stress response and can be used as an early marker of stress response signaling. Despite the fact that numerous studies have highlighted the functions and importance of FRK, detailed studies on the physiological and metabolic functions of this enzyme and the underlying regulatory mechanisms are lacking. Most research on FRK has been focused on model plants such as Arabidopsis thaliana , and limited progress has been made studying FRK functions in crops. With the aim of systematically summarizing the characteristics of FRKs and their important roles in plant life activities, this paper reviews their roles in regulating plant growth and development, responding to stress, and regulating photosynthetic and metabolic pathways. In addition, several scientific questions about FRKs are discussed, including whether they act as sugar-sensing signals, whether they are involved in plant defense processes, how they regulate plant source-sink metabolism, whether they are involved in regulating the phase transitions from the vegetative to reproductive growth, and whether there is redundancy in function among family members. Recently developed omics and gene editing technologies are expected to be applied toward answering these questions and discovering the related regulatory networks in order to fully understand the role of FRKs in plant sugar metabolism.

Role of ATF3 as a prognostic biomarker and correlation of ATF3 expression with macrophage infiltration in hepatocellular carcinoma

BackgroundThe abnormal expression of activating transcription factor 3 (ATF3), a member of the basic leucine zipper (bZIP) family of transcription factors, is associated with carcinogenesis. However, the expression pattern and exact role of ATF3 in the development and progression of hepatocellular carcinoma (HCC) remain unclear.MethodsWe used UALCAN, ONCOMINE, Kaplan–Meier plotter, and cBioPortal databases to investigate the prognostic value of ATF3 expression in HCC.ResultsATF3 was found to be expressed at low levels in multiple HCC tumor tissues. Moreover, low ATF3 expression was significantly associated with clinical cancer stage and pathological tumor grade in patients with HCC. Therefore, low expression of ATF3 was significantly associated with poor overall survival in patients with HCC. Functional network analysis showed that ATF3 regulates cytokine receptors and signaling pathways via various cancer-related kinases, miRNAs, and transcription factors. ATF3 expression was found to be correlated with macrophage infiltration levels and with macrophage immune marker sets in HCC patients.ConclusionsUsing data mining methods, we clarified the role of ATF3 expression and related regulatory networks in HCC, laying a foundation for further functional research. Future research will validate our findings and establish clinical applications of ATF3 in the diagnosis and treatment of HCC.

The role of RNA m5C modification in cancer metastasis.

Epigenetic modification plays a crucial regulatory role in the biological processes of eukaryotic cells. The recent characterization of DNA and RNA methylation is still ongoing. Tumor metastasis has long been an unconquerable feature in the fight against cancer. As an inevitable component of the epigenetic regulatory network, 5-methylcytosine is associated with multifarious cellular processes and systemic diseases, including cell migration and cancer metastasis. Recently, gratifying progress has been achieved in determining the molecular interactions between m5C writers (DNMTs and NSUNs), demethylases (TETs), readers (YTHDF2, ALYREF and YBX1) and RNAs. However, the underlying mechanism of RNA m5C methylation in cell mobility and metastasis remains unclear. The functions of m5C writers and readers are believed to regulate gene expression at the post-transcription level and are involved in cellular metabolism and movement. In this review, we emphatically summarize the recent updates on m5C components and related regulatory networks. The content will be focused on writers and readers of the RNA m5C modification and potential mechanisms in diseases. We will discuss relevant upstream and downstream interacting molecules and their associations with cell migration and metastasis.

Immune gene prognostic signature for disease free survival of gastric cancer: Translational research of an artificial intelligence survival predictive system

The progress of artificial intelligence algorithms and massive data provide new ideas and choices for individual mortality risk prediction for cancer patients. The current research focused on depict immune gene related regulatory network and develop an artificial intelligence survival predictive system for disease free survival of gastric cancer.Multi-task logistic regression algorithm, Cox survival regression algorithm, and Random survival forest algorithm were used to develop the artificial intelligence survival predictive system.Nineteen transcription factors and seventy immune genes were identified to construct a transcription factor regulatory network of immune genes. Multivariate Cox regression identified fourteen immune genes as prognostic markers. These immune genes were used to construct a prognostic signature for gastric cancer. Concordance indexes were 0.800, 0.809, and 0.856 for 1-, 3- and 5- year survival. An interesting artificial intelligence survival predictive system was developed based on three artificial intelligence algorithms for gastric cancer. Gastric cancer patients with high risk score have poor survival than patients with low risk score.The current study constructed a transcription factor regulatory network and developed two artificial intelligence survival prediction tools for disease free survival of gastric cancer patients. These artificial intelligence survival prediction tools are helpful for individualized treatment decision.

Clinical and biological impact of LINC02544 expression in breast cancer after neoadjuvant chemotherapy.

Analysis of breast cancer and cancer tissue after neoadjuvant chemotherapy (nCT) may be helpful to find new biomarkers. It is known that long non-coding RNAs (lncRNAs) are involved in the carcinogenic pathway and drug resistance of breast cancer. Our aim was to determine the role of LINC02544 in the behavior and outcome of post-nCT breast cancer. The expression level of LINC02544 in breast cancer and its effect on the survival time of patients were predicted by lnCAR database. In vitro, EdU, Wound-healing and transwell assays were used to detect the effects of LINC02544 on the proliferation, migration and invasion of MCF-7 cells, and the related regulatory networks were analyzed by the database. Quantitative Reverse Transcriptase-Polymerase Chain Reaction (QRT-PCR) was used to detect the expression of LINC02544 in 147 cases of nCT before and after treatment, and the relationship between the expression of LINC02544 and survival time and clinicopathological features was analyzed. LINC02544 was highly expressed in breast cancer and led to poor prognosis. Overexpression of LINC02544 promoted proliferation, invasion and migration of breast cancer cells. Compared with the residual tumor after nCT with low expression of LINC02544, the high expression of LINC02544 in the residual tumor after nCT was significantly correlated with overall survival and disease-free survival. In this study, it is suggested that LINC02544 has a potential application prospect as a biomarker and therapeutic target for breast cancer patients and neoadjuvant therapy patients.

Long non-coding RNA expression profiles and related regulatory networks in areca nut chewing-induced tongue squamous cell carcinoma.

Areca nut chewing is an important risk factor for developing tongue squamous cell carcinoma (TSCC), although the underlying molecular mechanism is unknown. To determine the potential molecular mechanisms of areca nut chewing-induced TSCC, the present study performed whole-genome detection with five pairs of TSCC and adjacent normal tissues, via mRNA- and long non-coding (lnc)RNA-gene chip analysis. A total of 3,860 differentially expressed genes were identified, including 2,193 lncRNAs and 1,667 mRNAs. Gene set-enrichment analysis revealed that the differentially expressed mRNAs were enriched in chromosome 22q13, 8p21 and 3p21 regions, and were regulated by nuclear factor kappa B (NF-κB) and interferon regulatory factors (IRFs). The results of ingenuity pathway analysis revealed that these mRNAs were significantly enriched for inflammatory immune-related signaling pathways. A co-expression network of mRNAs and lncRNAs was constructed by performing weighted gene co-expression network analysis. The present study focused on NF-κB-, IRF- and Th cell-signaling pathway-related lncRNAs and the corresponding mRNA-lncRNA regulatory networks. To the best of our knowledge, the present study was the first to investigate differential mRNA- and lncRNA-expression profiles in TSCCs induced by areca nut chewing. Inflammation-related mRNA-lncRNA regulatory networks driven by IRFs and NF-κB were identified, as well as the Th cell-related signaling pathways that play important carcinogenic roles in areca nut chewing-induced TSCC. These differentially expressed mRNAs and lncRNAs, and their regulatory networks provide insight for further analysis on the molecular mechanism of areca nut chewing-induced TSCC, candidate molecular markers and targets for further clinical intervention.

SmMYC2b Enhances Tanshinone Accumulation in Salvia miltiorrhiza by Activating Pathway Genes and Promoting Lateral Root Development.

Salvia miltiorrhiza Bunge (Lamiaceae) is an economically important medicinal plant as well as an emerging model plant. Our previous studies indicate that SmMYC2b is a positive transcription factor that can affect the biosynthesis of phenolic acids and tanshinones in S. miltiorrhiza. Moreover, MYC2s are well known to induce the development of lateral roots. As tanshinones are mainly distributed in the periderm, the promotion of lateral root development probably leads to increased accumulation of tanshinones. In this paper, we firstly discovered that SmMYC2b played a dual regulatory role in effectively enhancing the tanshinone accumulation by activating tanshinone biosynthetic pathway and promoting lateral root development. The expression levels of the previously studied pathway genes SmCPS1, SmKSL1, SmCYP76AH1, SmCYP76AH3, and SmCYP76AK1 dramatically increased. In addition, SmMYC2b was proved to exhibit a similar function as other homologs in promoting lateral root development, which increased the tanshinone produced tissue and further enhanced the biosynthesis of tanshinones. RNA-seq assays revealed that SmMYC2b-regulated genes comprised 30.6% (1,901 of 6,210) of JA-responsive genes, confirming that SmMYC2b played a crucial role in transcriptional regulation of JA-regulated genes. Overall, we concluded that SmMYC2b could enhance tanshinone accumulation by activating the tanshinone biosynthetic pathway and promoting lateral root development. Our study provides an effective approach to enhance the production of desired tanshinones and enriches our knowledge of the related regulatory network.

Develop a circular RNA-related regulatory network associated with prognosis of gastric cancer.

BackgroundIn gastric cancer (GC), circular RNAs (circRNAs) mainly play an important role in miRNA sponge, which not only indicate long‐term survival and prognosis but also increase resistance to the apoptosis. The purpose of the study is to explore new circRNAs and their underlying mechanisms in GC.MethodThrough rigorous retrieval strategies, we used the sva package to analyze and identify differentially expressed circRNAs (DECs) from three Gene Expression Omnibus microarray datasets (GSE83521, GSE89143, and GSE78092). Online website CSCD and CircInteractome were used to reveal the binding sites between miRNAs and DECs. The possible target miRNAs of the DECs identified based on miRNAs, and Cytoscape was used to create a regulatory network of circRNA‐miRNA‐mRNA and identified the hub genes which were further validated using The Cancer Genome Atlas database and Human Protein Atlas.ResultsTwenty‐eight DECs were obtained using the sva package. A regulatory network of circRNA‐miRNA‐mRNA (competing endogenous RNA) containing 15 circRNAs, 24 miRNAs, and 158 genes was identified. A protein‐protein interaction network based on the 158 genes was established, and further determined that 10 hub genes (SKA1, ANLN, CHEK1, SKA3, TOP2A, BIRC5, RRM2, NCAPG2, FANCI, and RAD51) were associated with some cancer‐related pathways based on the functional enrichment analysis. Finally, six hub genes (BIRC5, TOP2A, FANCI, NCAPG2, RAD51, and RRM2) were proven to influence the overall survival of GC.ConclusionOur study established a circRNA‐miRNA‐mRNA regulatory network and defined six circRNA‐related hub genes in GC, which could serve as potential therapeutic targets or prognostic biomarker for GC treatment.

The Transcription Factor TCF1 in T Cell Differentiation and Aging.

The transcription factor T cell factor 1 (TCF1), a pioneer transcription factor as well as a downstream effector of WNT/β-catenin signaling, is indispensable for T cell development in the thymus. Recent studies have highlighted the additional critical role of TCF1 in peripheral T cell responses to acute and chronic infections as well as cancer. Here, we review the regulatory functions of TCF1 in the differentiation of T follicular helper cells, memory T cells and recently described stem-like exhausted T cells, where TCF1 promotes less differentiated stem-like cell states by controlling common gene-regulatory networks. These studies also provide insights into the mechanisms of defective T cell responses in older individuals. We discuss alterations in TCF1 expression and related regulatory networks with age and their consequences for T cell responses to infections and vaccination. The increasing understanding of the pathways regulating TCF1 expression and function in aged T cells holds the promise of enabling the design of therapeutic interventions aiming at improving T cell responses in older individuals.

The Actionable Genomic Landscape in Glioblastoma

The standard treatment for glioblastoma involves a combination of surgery, radiation and chemotherapy but have limited impact on survival. The recent exponential increase in targeted agents directed at pivotal oncogenic pathways now provide new therapeutic opportunities for this tumor type. However, lack of precision oncology testing at diagnosis means such therapeutic opportunities are missed. To address this unmet clinical need we established Oncofocus®, a clinically validated precision oncology test for solid tumors, detecting actionable genetic variants in 505 genes linked to 764 anti-cancer targeted agents/combinations and immunotherapies. Analysis of trending data in relation to a cohort of 55 glioblastoma cases has revealed a complex and rich actionable mutational landscape in which 166 actionable mutations were detected across 36 genes. The majority of patients harbored three or more actionable mutations (median 3, range 1-9) affecting key cancer related regulatory networks including the PI3K/AKT/MTOR and RAS/RAF/MEK/MAPK signaling pathways, DNA-damage repair pathways and cell cycle checkpoints. Oncogenic fusion genes were identified at high frequency (23.6%), including two novel fusions in glioblastoma, namely TBL1XR1-PIK3CA and FIP1L1–PDGFRA. Linkage with anti-PD-L1/PD-1 immunotherapy was also identified in 63.6% of glioblastoma patients as a consequence of either elevated PD-L1 levels or mutations in DNA-damage repair genes. Despite the commonly held perception that treatment options for glioblastoma are limited, we have shown here that glioblastoma harbors a diverse actionable mutational landscape providing a broad therapeutic armamentarium of targeted therapies and immunotherapies. Our data indicates that precision oncology testing should be considered as part of the standard molecular diagnostic work up for glioblastoma.

The actionable genomic mutational landscape in solid tumours.

e13642 Background: The recent exponential increase in targeted agents and immunotherapies provide new therapeutic opportunities for patients with advanced cancers who have failed first line therapy. However, lack of comprehensive precision oncology testing as part of routine pathology assessment means potential therapeutic opportunities are difficult to identify or remain undiscovered for many patients. Methods: To address this unmet clinical need we established Oncofocus, a clinically validated, ISO15189/2012 and CLIA accredited, precision oncology test optimized for analysis of small diagnostic PWET clinical biopsy samples (sample acceptance 94%). Oncofocus detects actionable genetic variants in 505 genes linked to 764 anti-cancer targeted therapy protocols, either on-market FDA and EMA approved, carrying ESMO and NCCN guideline references or currently in clinical trials. Oncofocus trending data was analyzed for a real-life cohort of 1111 patients with the aim of determining the frequency of actionable mutations in this population. This cohort represent patients with advanced stage disease who underwent Oncofocus testing having failed first line treatment protocols. Results: Analysis of trending data revealed a complex mutational landscape in which 90% of solid tumors harbored actionable mutations. The majority of patients harbored one or more actionable mutations (median 2, range 0-13) affecting key cancer related regulatory networks including the PI3K/AKT/MTOR and RAS/RAF/MEK/MAPK signaling pathways, DNA-damage repair pathways and cell cycle checkpoints. Actionable genetic variants across 33 DNA Damage and Repair (DDR) genes were identified in 30% of tumors. Using a defined predictive cut point of &gt; 10% for tumor proportion score, PD-L1 expression levels were significantly raised in 19% of cases. Abrogation of DDR function and elevated PD-L1 levels were identified in 5% of patients, a subpopulation potentially more responsive to immunotherapy. Notably, many of the actionable mutations identified did not show linkage with histological type or site of origin. Conclusions: Our data indicates that comprehensive precision oncology testing should be strongly considered as part of the diagnostic work up for all patients with advanced cancers, independent of tumor type, thereby ensuring capture of all targeted therapy opportunities and accelerating “site agnostic” molecular basket clinical trials. Comprehensive precision oncology testing was performed successfully on routine biopsy samples circumventing the requirement for fresh tissue or large sample specimens.

Construction of differentially expressed Her-2 related lncRNA-mRNA-miRNA ceRNA network in Her-2 positive breast cancer.

BackgroundHer-2 positive subtype breast cancer is characterized as Her-2 gene amplification with poor survival and increased invasiveness accounting for 20–30% of invasive infiltrated breast cancer. A lncRNA-miRNA-mRNA competing endogenous RNA (ceRNA) network is constructed to detect Her-2 specific RNAs in the development and progression of HER-2 positive breast cancer which may overcoming the anti-HER-2 therapy resistance of breast cancer cells.MethodsOne thousand one hundred and nine breast cancer samples obtained from The Cancer Genome Atlas (TCGA) database were classified into two cohorts including ER+/PR+ (n=461) and ER-/PR- breast cancer (n=152). Differently expressed mRNAs, lncRNAs and miRNAs were screened in ER+/PR+ and ER-/PR- breast cancer cohorts, respectively. lncRNA-miRNA interactions were preformed to predicted and verified by miRcode. miRNA-mRNA interactions were selected to predict targeted mRNAs of miRNAs by miRanda, Targetscan and miRTarBase.ResultslncRNA-miRNA-mRNA ceRNA network was constructed by retained lncRNAs, miRNAs and mRNAs. Fifteen DEmiRNAs, 129 DElncRNAs and 269 DEmRNAs were retained in ER+/PR+ cohort after intersection with DEmiRNAs, DElncRNAs and DEmRNAs between breast cancer and normal tissues. Six hundred and ninety-three DEmRNAs, 25 DEmiRNAs and 364 DElncRNAs were retained in ER-/PR- cohort. ceRNA network in ER+/PR+ breast cancer cohort was constructed of the interactions of 4 DElncRNA–DEmiRNA pairs and 2 DEmiRNA–DEmRNA pairs included 4 DElncRNAs, 1 DEmiRNAs, and 2 DEmRNAs. ceRNA network in ER-/PR- breast cancer cohort was constructed of the interactions of 24 DElncRNA–DEmiRNA pairs and 1 DEmiRNA–DEmRNA pairs included 19 DElncRNAs, 4 DEmiRNAs, and 1 DEmRNA. MIR7-3HG- hsa-mir-204-NTRK2 axis was identified in both ER+/PR+ and ER-/PR- cohort in our study.ConclusionsBased on the ceRNA hypothesis, a potential Her-2 related regulatory ceRNA networks are constructed which may provide novel insights into the mechanism underlying the biological processes of Her-2 positive breast cancer.

Hematopoietic stem cell metabolism and stemness.

Hematopoietic stem cells (HSCs) are considered to originate from the aorta-gonad-mesonephros, migrate into fetal liver for a rapid expansion, and eventually reside into a unique hypoxic bone marrow niche, where they maintain their homeostasis throughout their life span. HSCs have been widely used for the treatment of many begin or malignant hematopoietic disorders. However, the unavailability of sufficient amount of HSCs still impedes their applications in the clinic. It is urgent to understand how HSC stemness or cell fates are determined at different developmental stages. Although many intrinsic and extrinsic factors (niche components) have been identified in the regulation of HSC origination, expansion, migration, and localization, the underlying mechanisms remain largely unknown. In this article, we summarize current views on the metabolic profiles of HSCs and related regulatory networks, which shows that intrinsic metabolic regulation may be critical for the cell fate determinations of HSCs: HSCs utilize glycolysis as their major energy sources; mitochondrial respiration is also required for the homeostasis of HSCs; amino acids, lipids, or other nutrient metabolisms also have unique roles in sustaining HSC activities. Mechanistically, many important regulatory pathways, such as MEIS1/HIF1A, MYC, PPM1K/CDC20, and ROS signals, are identified to fine-tune the nutrient metabolisms and cell fate commitments in HSCs. Nevertheless, more effort is required for the optimization or establishment of sensitive and specific metabolic techniques/systems for the metabolism studies in HSCs with limited cell numbers and exploring the metabolic profiles and fundamental regulatory mechanisms of different types of nutrients at each developmental stage of HSCs.

Transcriptome and Gene Coexpression Network Analyses of Two Wild Populations Provides Insight into the High-Salinity Adaptation Mechanisms of Crassostrea ariakensis.

Crassostrea ariakensis naturally distributes in the intertidal and estuary region with relative low salinity ranging from 10 to 25‰. To understand the adaptive capacity of oysters to salinity stress, we conducted transcriptome analysis to investigate the metabolic pathways of salinity stress effectors in oysters from two different geographical sites, namely at salinities of 16, 23, and 30‰. We completed transcriptome sequencing of 18 samples and a total of 52,392 unigenes were obtained after assembly. Differentially expressed gene (DEG) analysis and weighted gene correlation network analysis (WGCNA) were performed using RNA-Seq transcriptomic data from eye-spot larvae at different salinities and from different populations. The results showed that at moderately high salinities (23 and 30‰), genes related to osmotic agents, oxidation-reduction processes, and related regulatory networks of complex transcriptional regulation and signal transduction pathways dominated to counteract the salinity stress. Moreover, there were adaptive differences in salinity response mechanisms, especially at high salinity, in oyster larvae from different populations. These results provide a framework for understanding the interactions of multiple pathways at the system level and for elucidating the complex cellular processes involved in responding to osmotic stress and maintaining growth. Furthermore, the results facilitate further research into the biological processes underlying physiological adaptations to hypertonic stress in marine invertebrates and provide a molecular basis for our subsequent search for high salinity-tolerant populations.

NEAT1_2-SFPQ axis mediates cisplatin resistance in liver cancer cells in vitro.

BackgroundLiver cancer is a type of malignant tumor with high morbidity and mortality in People’s Republic of China. Its occurrence and development involve the variation and expression changes of multiple genes, and the pathogenesis and related regulatory networks are complex.PurposeIn the present research, we investigate the involvement of NEAT1_2 and SFPQ in cisplatin resistance in liver cancer. The effects of LncRNA NEAT1 and SFPQ expression on the chemotherapeutic resistance of liver cancer cells were analyzed.MethodsThe expression level of NEAT1_2 and SFPQ mRNA in tissue specimens or cell lines were examined by RT-qPCR and western blotting. CCK-8 assay was performed to evaluate cell viability. Cell proliferation was performed using the EdU cell proliferation assay.ResultsOur data showed that increase NEAT1_2 and SFPQ expressions in liver cancer specimens were associated with the development of cisplatin resistance; high SFPQ expression level impaired patients’ survival from liver cancer. Gain-and loss-of function assay using NEAT1_2 knock-in and knock-out cells constructed using CRISPER/Cas9 system revealed that NEAT1_2 is essential for liver cancer cell survival and mediates cisplatin resistance in liver cancer cells at least partially through SFPQ. Artificial change in NEAT1_2 expression level didn’t significantly influence SFPQ transcription or translation level.ConclusionOur data revealed NEAT1_2—SFPQ axis as a novel cisplatin resistance mechanism in liver cancer cells in vitro.

RECTA: Regulon Identification Based on Comparative Genomics and Transcriptomics Analysis.

Regulons, which serve as co-regulated gene groups contributing to the transcriptional regulation of microbial genomes, have the potential to aid in understanding of underlying regulatory mechanisms. In this study, we designed a novel computational pipeline, regulon identification based on comparative genomics and transcriptomics analysis (RECTA), for regulon prediction related to the gene regulatory network under certain conditions. To demonstrate the effectiveness of this tool, we implemented RECTA on Lactococcus lactis MG1363 data to elucidate acid-response regulons. A total of 51 regulons were identified, 14 of which have computational-verified significance. Among these 14 regulons, five of them were computationally predicted to be connected with acid stress response. Validated by literature, 33 genes in Lactococcus lactis MG1363 were found to have orthologous genes which were associated with six regulons. An acid response related regulatory network was constructed, involving two trans-membrane proteins, eight regulons (llrA, llrC, hllA, ccpA, NHP6A, rcfB, regulons #8 and #39), nine functional modules, and 33 genes with orthologous genes known to be associated with acid stress. The predicted response pathways could serve as promising candidates for better acid tolerance engineering in Lactococcus lactis. Our RECTA pipeline provides an effective way to construct a reliable gene regulatory network through regulon elucidation, and has strong application power and can be effectively applied to other bacterial genomes where the elucidation of the transcriptional regulation network is needed.

Identification of miR-24 and miR-137 as novel candidate multiple sclerosis miRNA biomarkers using multi-staged data analysis protocol.

Many studies have investigated misregulation of miRNAs relevant to multiple sclerosis (MS) pathogenesis. Abnormal miRNAs can be used both as candidate biomarker for MS diagnosis and understanding the disease miRNA-mRNA regulatory network. In this comprehensive study, misregulated miRNAs related to MS were collected from existing literature, databases and via in silico prediction. A multi-staged data integration strategy (including the construction of miRNA-mRNA regulatory network and systematic data analysis) was conducted in order to investigate MS related miRNAs and their regulatory networks. The final outcome was a bi-layer MS related regulatory network constructed with 27 miRNAs (seven of them were novel) and 59 mRNA targets. To verify the accuracy of the bioinformatics strategy three novel and five previously reported miRNAs from the network model were selected for experimental validation using the real-time PCR assay. The obtained results proved the accuracy of the network. The expression of themiR-24 and miR-137(as novel MS candidate biomarker) and miR-16, and miR-181 (as previously reported MS candidate biomarker) showed significant deregulation in 33 MS patients compared to the control. The optimized data integration strategy conducted in this study found two miRNAs (miR-24and miR-16)that can be considered as candidate biomarkers for MS and also has the potential to generate a regulatory network to aid in further understanding the mechanisms underlying this disease.

AtCircDB: a tissue-specific database for Arabidopsis circular RNAs.

Circular RNAs are widely existing in eukaryotes. However, there is as yet no tissue-specific Arabidopsis circular RNA database, which hinders the study of circular RNA in plants. Here, we used 622 Arabidopsis RNA sequencing data sets from 87 independent studies hosted at NCBI SRA and developed AtCircDB to systematically identify, store and retrieve circular RNAs. By analyzing back-splicing sites, we characterized 84 685 circular RNAs, 30 648 tissue-specific circular RNAs and 3486 microRNA-circular RNA interactions. In addition, we used a metric (detection score) to measure the detection ability of the circular RNAs using a big-data approach. By experimental validation, we demonstrate that this metric improves the accuracy of the detection algorithm. We also defined the regions hosting enriched circular RNAs as super circular RNA regions. The results suggest that these regions are highly related to alternative splicing and chloroplast. Finally, we developed a comprehensive tissue-specific database (AtCircDB) to help the community store, retrieve, visualize and download Arabidopsis circular RNAs. This database will greatly expand our understanding of circular RNAs and their related regulatory networks. AtCircDB is freely available at http://genome.sdau.edu.cn/circRNA.