Multiple Bioinformatics Analyses Research Articles

Network-Based Approach to Identify the Antiproliferative Mechanisms of Bruceine D in Breast Cancer From the Cancer Genome Atlas.

Bruceine D (BD) is a natural compound extracted from a Chinese herb Brucea javanica that has been used for anti-inflammatory and anti-cancer treatment. However, little is reported about BD's effects in breast cancer tumorigenesis. In this paper, we aimed to investigate the effect of BD in breast cancer and elucidate the potential mechanism of BD by integrated multiple databases. Our data suggested BD inhibited MCF-7 and MDA-MB-231 cells proliferation and promoted cells apoptosis. We integrated multiple bioinformatics analysis strategies to identify genes, hub modules and pathways associated with BD treatment. Three key pathways, including AMIT_SERUM_RESPONSE_40_MCF10A, BILD_HRAS_ONCOGENIC_SIGNATURE, and NAGASHIMA_NRG1_SIGNALING_UP were identified to be associated with therapeutic effects of BD in breast cancer. Additionally, we validated the key genes by using quantitative real-time PCR and western blot. In conclusion, these findings revealed potential molecular mechanisms of BD to treat breast cancer by affecting AMIT_SERUM_RESPONSE_40_MCF10A, BILD_HRAS_ONCOGENIC_SIGNATURE, and NAGASHIMA_NRG1_SIGNALING_UP pathways and regulating expression of ZFP36, EGR1, and FOS.

Evaluation of the genetic association between early-onset primary angle-closure glaucoma and retinitis pigmentosa

Primary angle-closure glaucoma (PACG) and retinitis pigmentosa (RP) can co-occur, but the mechanism of their association is not yet established. The purpose of this study was to investigate the differences in ocular biometry parameters and molecular genetics in patients with PACG with or without RP, and to determine the association between PACG and RP. Patients with early-onset PACG (age of onset <45 years) with or without RP were selected from the glaucoma outpatient department after full ocular examinations by the same glaucoma specialist (LX). Ocular biometry parameters were statistically analyzed. Blood samples were collected from the probands, and genomic DNA was sent out for whole exome sequencing. Variants in 326 selected genes, were extracted from the whole exome sequencing data and filtered using multiple bioinformatics analysis. The 326 genes included 10 PACG-associated genes from two genome wide association studies; 45 genes associated with anterior segment dysgenesis, microcornea, and microphthalmia; and 271 RetNet genes. Potential pathogenic variants (PPV) were obtained and underwent further genotype–phenotype analysis. As a result, a total of 32 probands with early-onset PACG were collected; nine had accompanying RP. No significant differences were noted for ocular biometry parameters between patients with PACG with RP and with PACG alone. Systematic analysis of the variants revealed that 16 of 32 probands (50%) carried PPV in 15 of 326 genes, including 14 RetNet genes and one anterior segment dysgenesis-associated gene. Of these 16 probands with PPV, five (55.56%) were from the group of nine probands with both had PACG and RP and 11 (47.83%) were from the group of 23 probands with PACG alone. Of the 15 genes, five genes, CRB1, COL2A1, RHO, RP1L1, and PAX6, were reported to cause phenotypes including glaucoma. The variants in RetNet genes appeared to be associated with a significant proportion of PACG, especially in probands with both PACG and RP. These findings enrich the phenotype spectrum of RetNet genes and provide clues for genetic screening for glaucoma. Our study suggests a genetic association between PACG and RP, although the cause-effect relationship between them needs further validation.

An Anti-Cancer Peptide LVTX-8 Inhibits the Proliferation and Migration of Lung Tumor Cells by Regulating Causal Genes' Expression in p53-Related Pathways.

Spider venom has been found to show its anticancer activity in a variety of human malignancies, including lung cancer. In this study, we investigated the anti-cancer peptide toxin LVTX-8, with linear amphipathic alpha-helical conformation, designed and synthesized from the cDNA library of spider Lycosa vittata. Multiple cellular methods, such as CCK-8 assay, flow cytometry, colony formation assay, Transwell invasion and migration assay, were performed to detect peptide-induced cell growth inhibition and anti-metastasis in lung cancer cells. Our results demonstrated that LVTX-8 displayed strong cytotoxicity and anti-metastasis towards lung cancer in vitro. Furthermore, LVTX-8 could suppress the growth and metastasis of lung cancer cells (A549 and H460) in nude mouse models. Transcriptomics, integrated with multiple bioinformatics analysis, suggested that the molecular basis of the LVTX-8-mediated inhibition of cancer cell growth and metastasis manifested in two aspects: Firstly, it could restrain the activity of cancer cell division and migration through the functional pathways, including “p53 hypoxia pathway” and “integrin signaling”. Secondly, it could regulate the expression level of apoptotic-related proteins, which may account for programmed apoptosis of cancer cells. Taken together, as an anticancer peptide with high efficiency and acceptable specificity, LVTX-8 may become a potential precursor of a therapeutic agent for lung cancer in the future.

Multiple Bioinformatics Analyses of Integrated Gene Expression Profiling Data and Verification of Hub Genes Associated with Diabetic Retinopathy.

BackgroundDiabetic retinopathy (DR) is a serious complication of diabetes that can lead to blindness. This study aimed to identify the core genes and molecular functions involved in DR through multiple bioinformatics analyses.Material/MethodsThe mRNA gene profiles of human DR tissues from the GSE60436 and GSE53257 datasets were assessed with R software and integrated to identify the co-expressed differentially expressed genes (DEGs). Multiple bioinformatics analyses were used: Gene Ontology (GO) analysis, signaling pathway analysis, and hub gene prediction. Quantitative reverse transcription-PCR (qRT-PCR) was used to verify the hub genes.ResultsThe Database for Annotation, Visualization and Integrated Discovery (DAVID) online tool suggested that the biological processes of the DEGs focused on mitochondrial transport, the cellular components focused on mitochondria, and molecular functions focused on catalytic activity. The results provided by DAVID were consistent with those provided by STRING and the GeneMANIA online database. All the DEGs function in metabolic pathways, consistent with the g: Profiler online analysis results. The protein-protein interaction (PPI) networks forecasted by STRING and GeneMANIA were entered into Cytoscape for cytoHubba degree analysis. The hub genes predicted by cytoHubba suggested that fumarate hydratase (FH) might be relevant to DR. qRT-PCR suggested that the expression of FH was higher in DR retinal tissues than in normal control tissues.ConclusionsMultiple bioinformatics analyses verified that FH could be used as a potential diagnostic marker and new therapeutic target of DR.

Comprehensive Analysis of CDC27 Related to Peritoneal Metastasis by Whole Exome Sequencing in Gastric Cancer.

IntroductionThe peritoneum is the most common metastatic site of gastric cancer and is associated with a dismal prognosis. However, there is no reliable biomarker for predicting peritoneal metastasis (PM).Materials and MethodsWhole-exome sequencing (WES) was performed on formalin-fixed, paraffin-embedded (FFPE) samples from 63 patients with stage I–III gastric cancer and circulating tumor DNA (ctDNA) samples from 10 patients with stage IV gastric cancer. Differentially expressed genes (DEGs) were identified between the PM and non-PM groups and analyzed by multiple bioinformatics analyses. Univariate and multivariate Cox regression analyses were used to identify the risk factors for PM and a risk score model was developed.ResultsThe number of mutant genes and the tumor mutation burden (TMB) in the PM group were higher than those in the non-PM group (p < 0.05). There was a significant positive correlation between the number of mutant genes and the TMB (R2 = 0.9997). The risk of PM was significantly higher in the high TMB group than in the low TMB group (p = 0.045). Forty-nine DEGs were identified as associated with PM in gastric cancer. CDC27 mutations were associated with a higher risk for PM and poor survival. The CDC27 mutations were located in the Apc3 region, the TPR region, and the phosphorylation region, and new mutation sites were not included in the TCGA database. Multivariable Cox regression analysis demonstrated that pathological T stage, poor tumor differentiation, Borrmann type, and CDC27 mutations were independent predictive factors of PM. A risk score model was constructed that demonstrated good performance.ConclusionThrough WES, we identified 49 DEGs relevant to PM in gastric cancer. CDC27 mutations were independently associated with PM by statistical and bioinformatics analyses. A risk score model was built and was demonstrated to effectively discriminate gastric cancer patients with and without PM.

Deduced Roles of Cardiac 14‐3‐3 Protein Interactome in Heart Metabolism, Protein Synthesis and Proteostasis

The 14‐3‐3 protein family is known to interact with many proteins in non‐cardiac cell types to regulate multiple signaling pathways, particularly those relating to energy and protein homeostasis, and the 14‐3‐3 network is a therapeutic target of critical metabolic and proteostatic signalings in cancer and neurological diseases. Although the heart is critically sensitive to nutrient and energy alterations, and multiple signaling pathways coordinate to maintain the cardiac cell homeostasis, neither the structure of cardiac 14‐3‐3 protein interactome nor potential functional roles of 14‐3‐3 protein‐protein interactions (PPIs) has been explored in heart. Here, we evaluated both RNA expression and protein abundance of 14‐3‐3 isoforms in mouse left ventricle, followed by co‐immunoprecipitation of 14‐3‐3 proteins and mass spectrometry in left ventricle. We identified 594 proteins comprising the cardiac 14‐3‐3 interactome. Immunofluorescence assays indicated that 14‐3‐3 proteins localize in mitochondria and ribosome. Multiple bioinformatic analyses indicated that more than half of proteins bound to 14‐3‐3 are related to mitochondria, and the deduced functions of the mitochondrial 14‐3‐3 network are to regulate cardiac ATP production via interactions with mitochondrial inner membrane proteins, especially those in mitochondrial complex I and V, and to regulate cardiac fatty acid metabolism via interactions with enzymes within mitochondrial matrix. 14‐3‐3 protein binding to ribosomal proteins may triage energy production to coordinate protein synthesis and protein quality control. In summary, we establish the comprehensive landscape of cardiac 14‐3‐3 PPIs, dissecting its structure, deducing its function to have a major role to regulate cardiac metabolic homeostasis and proteostasis. Because 14‐3‐3 binds to proteins that are crucial to cardiac functions and heart health, the cardiac 14‐3‐3 interactome may be a potential therapeutic target in cardiovascular metabolic and proteostatic disease states, as it already is in cancer therapy.Support or Funding InformationIntramural Research Program, National Institute on Aging, National Institutes of HealthConduction of 14‐3‐3 interactomeFigure 1Deduced roles of 14‐3‐3 protein‐protein interactions in metabolism and maintenance of cardiac homeostasisFigure 2

MAFA-AS1, a long non-coding RNA, predicts for poor survival of hepatocellular carcinoma.

BackgroundHepatocellular carcinoma (HCC) is a common cancer with high morbidity and mortality, especially in East Asia. Reliable biomarkers for HCC are indispensible given the absence of capable prediction of prognosis. Long non-coding RNAs (lncRNAs) are the most abundant products of transcription, which might serve as robust markers for diagnosis or treatment.MethodsMultiple bioinformatics tools were utilized to screen indicative lncRNAs for HCC concurrently with the underlying mechanism of its role in tumorigenesis and development. We analyzed the genome-wide alterations and transcriptomics profiles of HCC and non-tumor samples from The Cancer Genome Atlas (TCGA). Survival analyses were also applied. Integrated bioinformatics analyses were applied to identify co-expressed genes along with chromosome loci, predictive RNA binding proteins (RBPs) and co-expressed miRNAs.ResultsCombining copy number variations (CNVs) with expressions of lncRNAs, 20 most aberrant lncRNAs were identified. MAFA-AS1 was identified as a prognostic indicator of HCC poor overall survival (OS) and disease-free survival (DFS). Multiple bioinformatics analyses suggest that MAFA-AS1 is involved in HCC progression via interacting with SRSF1/SRSF9 and coordinating with miR210.ConclusionsMAFA-AS1is a prognostic biomarker for poor OS and DFS of patients with HCC. It is involved in HCC progression.

Proteomic Analysis of Mucopolysaccharidosis IIIB Mouse Brain.

Mucopolysaccharidosis IIIB (MPS IIIB) is an inherited metabolic disease due to deficiency of α-N-Acetylglucosaminidase (NAGLU) enzyme with subsequent storage of undegraded heparan sulfate (HS). The main clinical manifestations of the disease are profound intellectual disability and neurodegeneration. A label-free quantitative proteomic approach was applied to compare the proteome profile of brains from MPS IIIB and control mice to identify altered neuropathological pathways of MPS IIIB. Proteins were identified through a bottom up analysis and 130 were significantly under-represented and 74 over-represented in MPS IIIB mouse brains compared to wild type (WT). Multiple bioinformatic analyses allowed to identify three major clusters of the differentially abundant proteins: proteins involved in cytoskeletal regulation, synaptic vesicle trafficking, and energy metabolism. The proteome profile of NAGLU−/− mouse brain could pave the way for further studies aimed at identifying novel therapeutic targets for the MPS IIIB. Data are available via ProteomeXchange with the identifier PXD017363.

Deduced Roles of the Cardiac 14-3-3 Protein Interactome in Heart Metabolism, Protein Synthesis and Proteostasis

The 14-3-3 protein family is known to interact with many proteins in non-cardiac cell types to regulate multiple signaling pathways, particularly those relating to energy and protein homeostasis, and the 14-3-3 network is a therapeutic target of critical metabolic and proteostatic signalings in cancer and neurological diseases. Although the heart is critically sensitive to nutrient and energy alterations, and multiple signaling pathways coordinate to maintain the cardiac cell homeostasis, neither the structure of cardiac 14-3-3 protein interactome nor potential functional roles of 14-3-3 protein-protein interactions (PPIs) has been explored in heart. Here, we evaluated both RNA expression and protein abundance of 14-3-3 isoforms in mouse left ventricle, followed by co-immunoprecipitation of 14-3-3 proteins and mass spectrometry in left ventricle. We identified 594 proteins comprising the cardiac 14-3-3 interactome. Immunofluorescence assays indicated that 14-3-3 proteins localize in mitochondria and ribosome. Multiple bioinformatic analyses indicated that more than half of proteins bound to 14-3-3 are related to mitochondria, and the deduced functions of the mitochondrial 14-3-3 network are to regulate cardiac ATP production via interactions with mitochondrial inner membrane proteins, especially those in mitochondrial complex I and V, and to regulate cardiac fatty acid metabolism via interactions with enzymes within mitochondrial matrix. 14-3-3 protein binding to ribosomal proteins may triage energy production to coordinate protein synthesis and protein quality control. In summary, we establish the comprehensive landscape of cardiac 14-3-3 PPIs, dissecting its structure, deducing its function to have a major role to regulate cardiac metabolic homeostasis and proteostasis. Because 14-3-3 binds to proteins that are crucial to cardiac functions and heart health, the cardiac 14-3-3 interactome may be a potential therapeutic target in cardiovascular metabolic and proteostatic disease states, as it already is in cancer therapy.

Occurrence of potentially pathogenic bacteria on shared bicycles.

Shared bicycles offer the potential to be sources for interindividual bacterial community transfer. However, the overall ecology of the bacterial community persisting on the shared bicycles is still unknown. We used 16S rRNA sequencing techniques in combination with multiple bioinformatic analyses to profile bacterial communities on shared bicycle handles and saddles in selected five locations in a metropolitan area (Chengdu, China). Samples of air around shared bicycles were collected as a control. We demonstrate that the species richness and diversity of samples from shared bicycles are significantly higher than those of surrounding air samples. Taxonomical composition indicates that community structure of shared bicycle handles and saddles are also different. Additionally, high occurrence of pathogenic or potentially pathogenic genera is found on the surfaces of shared bicycles, including Sphingomonas, Acinetobacter, Staphylococcus, and Cutibacterium. Moreover, PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) further verifies that bacteria involved in signaling pathways related to human diseases are at significantly higher levels in shared bicycle samples, while bacteria associated with environmental information processing pathways are at significantly higher levels in the air samples. Our results reveal the profiles of bacterial communities on shared bicycles, and suggest that potentially pathogenic bacteria may impair human health through shared bicycles, especially in susceptible individuals. Notably, this investigation will prompt the public to pay more attention to the management of bicycle sharing programs worldwide, and it also provides research basis for the government to formulate corresponding public health policies.

Identification and Expression of NAC Transcription Factors of Vaccinium corymbosum L. in Response to Drought Stress

Research Highlights: Phenotypic changes and expression profiles, phylogeny, conserved motifs, and expression correlations of NAC (NAM, ATAF1, ATAF2 and CUC2) transcription factors (TFs) in blueberry genome were detected under drought stress, and the expression patterns and functions of 12 NACs were analyzed. Background and Objectives: Blueberry is an important shrub species with a high level of flavonoids in fruit, which are implicated in a broad range of health benefits. However, the molecular mechanism of this shrub species in response to drought stress still remains elusive. NAC TFs widely participate in stress tolerance in many plant species. The characterization and expression profiles of NAC TFs were analyzed on the basis of genome data in blueberry when subjected to drought stress. Materials and Methods: Combined with the analysis of chlorophyll a fluorescence and endogenous phytohormones, the phenotypic changes of blueberry under drought stress were observed. The phylogenetic tree, conserved motifs, differently expressed genes, and expression correlation were determined by means of multiple bioinformatics analysis. The expression profiles of NACs in different organs were examined and compared through RNA-seq and qRT-PCR assay. Results: The chlorophyll a fluorescence parameters φPo, φEo, φRo, and PIabs of leaves were significantly inhibited under drought stress. ABA (abscisic acid) content noticeably increased over the duration of drought, whereas GA3 (gibberellic acid) and IAA (indole acetic acid) content decreased continuously. A total of 158 NACs were identified in blueberry genome and 62 NACs were differently expressed in leaf and root of blueberry under drought stress. Among them, 14 NACs were significantly correlated with the expression of other NAC genes. Conclusions: Our results revealed the phenotypic changes of this shrub under drought stress and linked them with NAC TFs, which are potentially involved in the process of response to drought stress.

Detection of Ancestry Information of Urumqi Mongolians Based on the AIM-InDels Loci Multiplex System.

Objective To explore the genetic background and structure of Urumqi Mongolians, the previously developed 39-AIM-InDels panel for ancestry inference was utilized in the present study. Methods The blood samples of 145 unrelated healthy Urumqi Mongolian individuals were collected and genotyped. The compositions of ancestry information of Urumqi Mongolians were studied with 17 different populations from three continents （East Asia, Europe and Africa） as reference populations. Then, multiple population genetics and bioinformatics analysis methods were applied, the Fst and DA values between matched populations were compared and analyzed, PCA analysis was performed and a phylogenetic tree was constructed. The proportions of ancestry information components of Urumqi Mongolians were analyzed with Structure software, etc. Results The ancestry information components of Urumqi Mongolian group in different intercontinental populations accounted for 89%, 7%, and 3% of East Asian, European, and African populations, respectively. Compared with other intercontinental populations, Urumqi Mongolian group and East Asian populations have lower Fst and DA values, and they were in the same cluster in PCA analysis as well. In a phylogenetic tree, the Urumqi Mongolian group was in the same branch as East Asian populations. Conclusion Urumqi Mongolian group had relatively close genetic relationships with East Asian populations, and the proportion of its East Asian ancestry was about 89%.

Genome-wide investigation of the clinical significance and prospective molecular mechanism of minichromosome maintenance protein family genes in patients with Lung Adenocarcinoma.

Our current study is to identify clinical significance of minichromosome maintenance (MCM) gene expression in Lung Adenocarcinoma (LUAD) using genome-wide RNA sequencing (RNA-seq) dataset and bioinformatics analysis tools. The biological function and potential process for function of the MCM1-10 were identified by multiple bioinformatics analysis tools. Clinical significance and molecular mechanism of the MCM1-10 were investigated by the RNA-seq dataset of LUAD from The Cancer Genome Atlas. Functional assessment substantiated involvement of MCM1-10 in cell cycle progression and DNA replication, and co-expressed with each other. We also observed that the MCM1-10 were dysregulation in LUAD tumor tissues, and may be have diagnostic implications in LUAD. Prognosis analysis in TCGA and KM plotter cohorts suggest that high abundance of MCM5, MCM8 and MCM4 notably correlated to poor LUAD overall survival. Mechanistic exploration of MCM4, MCM5, and MCM8 by gene set enrichment analysis suggests that these genes may influence the LUAD prognosis by regulating the cell cycle, DNA replication and other multiple biological processes and pathways. In comclusion, our study suggests that MCM1-10 can serve as diagnostic biomarkers for LUAD patients. Of them, MCM4, MCM5, and MCM8 may act as potential prognostic indicators for LUAD.

Abstract 3517: Establishing reference samples for universal benchmarking study of NGS technologies

Abstract Regulatory authorities including the FDA are well aware of the crucial role Next Generation Sequencing (NGS) plays in precision medicine. However, the lack of thoroughly-characterized and community-validated reference samples creates a challenge for the development and review of NGS applications in precision oncology. Over 200 members from over 60 institutions have formed the Somatic Mutation Working Group within the FDA-led Sequencing Quality Control Phase II (SEQC-II) Consortium to address this challenge. We have developed strategies to establish a community standard reference samples. We used multiple orthogonal sequencing technologies, sequencing replicates, sequencing centers, and bioinformatics analysis pipelines for mutation detection, thus minimizing biaes related to any particular sequencing platform, assay, or informatics software. Combining with targeted sequencing and microarray technologies, we established a high-confidence mutation call set (Gold Set). Here, we present our initial reference samples: a human triple-negative breast cancer cell line (HCC1395), and matched B lymphocyte derived normal cell line (HCC1395BL). The first public release of the Gold Set includes the fully phased germline variants, high-confidence somatic single nucleotide variants (SNV), small insertion and deletions (InDel), copy number variations (CNV), and structural variations (SV). For variant discovery, we have performed whole genome sequencing (WGS) for each of the tumor-normal genomes to combined depths of 650X from 12 replicates on Illumina HiSeq sequencers, 380X from 9 replicates on Illumina NovaSeq sequencer, 1000X from 11 replicates on 10X Genomics platform, and 50X on PacBio sequencer. In addition, we have also performed Hi-C sequencing to 34X. For variant validation, we have performed WGS to 300X for seven different tumor purities in a tumor-normal titration series, whole exome sequencing (WES) to a total of 12000X from 14 replicates, AmpliSeq targeted sequencing to 1000X, RNASeq to 186 million reads, Affymetrix GeneChip array to 2.1 million probes, and Cytogenetic arrays to 4.3 million probes. HCC1395 has a highly rearranged near-triploid genome with 66 chromosomes. The confidence levels of somatic mutations in the Gold Set were obtained based on the cross-institution and cross-aligner reproducibility of each mutation call. There are approximately 40,000 and 2,000 high-confidence somatic SNVs and InDels, with variant allele frequencies (VAF) ranging between 2% and 100%. The VAFs of both somatic and germline variants are consistent with our CNV calls. We will continuously accept input from the community to advance accuracy and completeness of our Gold Set for the reference samples in order to serve as a community standard well into the future. Citation Format: Li Tai Fang, Wenming Xiao, Somatic Mutation Working Group of the SEQC-II Consortium. Establishing reference samples for universal benchmarking study of NGS technologies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3517.

Metagenomic insights into functional traits variation and coupling effects on the anammox community during reactor start-up

Anammox technology is an energy-efficient wastewater treatment process and anammox community structure has gained extensive attention. However, the dynamics of community functional traits are still elusive. Here, we combined the long-term reactor operation and metagenomic, multiple bioinformatic and network analyses to reveal the succession of anammox community and function traits during reactor start-up. We found the cooperation of denitrifiers that affiliated to the phylum Proteobacteria could reduce nitrite to dinitrogen gas. These organisms and genes had higher abundance after the inhibition phase, which could contribute to nitrite consuming and reactor performance recovery. Importantly, the Terrimonas and Anaerolinea organisms had ability of extracellular polymers secretion or aggregate formation. They had the highest abundance at the end of the lag phase, which could benefit for promoting the nitrogen removal rate (NRR). Meanwhile, Terrimonas and Anaerolinea bacteria could cooperate with methanogenic and nitrite-denitrifying methanotrophic organisms based on H2 and CH4, respectively. Since these organisms also had higher abundance after the inhibition phase, their cooperation could prevent anammox bacteria from nitrite inhibiting when the influent nitrite concentration was higher. The analysis of community and function shift is expected to emphasize the importance of functional bacteria in anammox process and provides a potential control strategy for nitrogen-containing wastewater treatment process.

Use of Genome-Scale Integrated Analysis to Identify Key Genes and Potential Molecular Mechanisms in Recurrence of Lower-Grade Brain Glioma.

BackgroundThe aim of this study was to identify gene signals for lower-grade glioma (LGG) and to assess their potential as recurrence biomarkers.Material/MethodsAn LGG-related mRNA sequencing dataset was downloaded from The Cancer Genome Atlas (TCGA) Informix. Multiple bioinformatics analysis methods were used to identify key genes and potential molecular mechanisms in recurrence of LGG.ResultsA total of 326 differentially-expressed genes (DEGs), were identified from 511 primary LGG tumor and 18 recurrent samples. Gene ontology (GO) analysis revealed that the DEGs were implicated in cell differentiation, neuron differentiation, negative regulation of neuron differentiation, and cell proliferation in the forebrain. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database suggests that DEGs are associated with proteoglycans in cancer, the Wnt signaling pathway, ECM-receptor interaction, the PI3K-Akt signaling pathway, transcriptional deregulation in cancer, and the Hippo signaling pathway. The hub DEGs in the protein–protein interaction network are apolipoprotein A2 (APOA2), collagen type III alpha 1 chain (COL3A1), collagen type I alpha 1 chain (COL1A1), tyrosinase (TYR), collagen type I alpha 2 chain (COL1A2), neurotensin (NTS), collagen type V alpha 1 chain (COL5A1), poly(A) polymerase beta (PAPOLB), insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1), and anomalous homeobox (ANHX). GSEA revealed that the following biological processes may associated with LGG recurrence: cell cycle, DNA replication and repair, regulation of apoptosis, neuronal differentiation, and Wnt signaling pathway.ConclusionsOur study demonstrated that hub DEGs may assist in the molecular understanding of LGG recurrence. These findings still need further molecular studies to identify the assignment of DEGs in LGG.

LncRNA SNHG1 contributes to sorafenib resistance by activating the Akt pathway and is positively regulated by miR-21 in hepatocellular carcinoma cells

BackgroundAcquired resistance to sorafenib greatly limits its therapeutic efficiency in the treatment of hepatocellular carcinoma (HCC). Increasing evidence indicates that long noncoding RNAs (lncRNAs) play important roles in the resistance to anti-cancer drugs. The present study aims to explore the involvement of lncRNA SNHG1 (small nucleolar RNA host gene 1) in sorafenib resistance and how SNHG1 is associated with overexpressed microRNA-21 (miR-21) and the activated Akt pathway, which have been demonstrated to mediate this resistance in HCC cells.MethodsSorafenib-resistant HCC (SR-HCC) cells were generated and their sorafenib-resistant properties were confirmed by cell viability and apoptosis assays. Potential lncRNAs were screened by using multiple bioinformatics analyses and databases. The expression of genes and proteins was detected by qRT-PCR, Western blot and in situ hybridization. Gene silencing was achieved by specific siRNA or lncRNA Smart Silencer. The effects of anti-SNHG1 were evaluated in vitro and in experimental animals by using quantitative measures of cell proliferation, apoptosis and autophagy. The binding sites of miR-21 and SNHG1 were predicted by using the RNAhybrid algorithm and their interaction was verified by luciferase assays.ResultsThe Akt pathway was highly activated by overexpressed miR-21 in SR-HCC cells compared with parental HCC cells. Among ten screened candidates, SNHG1 showed the largest folds of alteration between SR-HCC and parental cells and between vehicle- and sorafenib-treated cells. Overexpressed SNHG1 contributes to sorafenib resistance by activating the Akt pathway via regulating SLC3A2. Depletion of SNHG1 enhanced the efficacy of sorafenib to induce apoptosis and autophagy of SR-HCC cells by inhibiting the activation of Akt pathway. Sorafenib induced translocation of miR-21 to the nucleus, where it promoted the expression of SNHG1, resulting in upregulation of SLC3A2, leading to the activation of Akt pathway. In contrast, SNHG1 was shown to have little effect on the expression of miR-21, which downregulated the expression of PTEN, leading to the activation of the Akt pathway independently of SNHG1.ConclusionsThe present study has demonstrated that lncRNA SNHG1 contributes to sorafenib resistance by activating the Akt pathway and its nuclear expression is promoted by miR-21, whose nuclear translocation is induced by sorafenib. These results indicate that SNHG1 may represent a potentially valuable target for overcoming sorafenib resistance for HCC.

Region-resolved proteomics profiling of monkey heart.

Nonhuman primates (NHPs) play an indispensable role in biomedical research because of their similarities in genetics, physiological, and neurological function to humans. Proteomics profiling of monkey heart could reveal significant cardiac biomarkers and help us to gain a better understanding of the pathogenesis of heart disease. However, the proteomic study of monkey heart is relatively lacking. Here, we performed the proteomics profiling of the normal monkey heart by measuring three major anatomical regions (vessels, valves, and chambers) based on iTRAQ‐coupled LC‐MS/MS analysis. Over 3,200 proteins were identified and quantified from three heart tissue samples. Furthermore, multiple bioinformatics analyses such as gene ontology analysis, protein–protein interaction analysis, and gene‐diseases association were used to investigate biological network of those proteins from each area. More than 60 genes in three heart regions are implicated with heart diseases such as hypertrophic cardiomyopathy, heart failure, and myocardial infarction. These genes associated with heart disease are mainly enriched in citrate cycle, amino acid degradation, and glycolysis pathway. At the anatomical level, the revelation of molecular characteristics of the healthy monkey heart would be an important starting point to investigate heart disease. As a unique resource, this study can serve as a reference map for future in‐depth research on cardiac disease‐related NHP model and novel biomarkers of cardiac injury.

The regulatory network of miR-141 in the inhibition of angiogenesis.

The miR-200 family, consisting of miR-200a/b/c, miR-141, and miR-429, is well known to inhibit epithelial-to-mesenchymal transition (EMT) in cancer invasion and metastasis. Among the miR-200 family members, miR-200a/b/c and miR-429 have been reported to inhibit angiogenesis. However, the role of miR-141 in angiogenesis remains elusive, as contradicting results have been found in different cancer types and tumor models. Particularly, the effect of miR-141 in vascular endothelial cells has not been defined. In this study, we used several in vitro and in vivo models to demonstrate that miR-141 in endothelial cells inhibits angiogenesis. Additional mechanistic studies showed that miR-141 suppresses angiogenesis through multiple targets, including NRP1, GAB1, CXCL12β, TGFβ2, and GATA6, and bioinformatics analysis indicated that miR-141 and its targets comprise a powerful and precise regulatory network to modulate angiogenesis. Taken together, these data not only demonstrate an anti-angiogenic effect of miR-141, further strengthening the critical role of miR-200 family in the process of angiogenesis, but also provides a valuable cancer therapeutic target to control both angiogenesis and EMT, two essential steps in tumor growth and metastasis.

Gene profiles to characterize the combined toxicity induced by low level co-exposure of silica nanoparticles and benzo[a]pyrene using whole genome microarrays in zebrafish embryos

Several studies have suggested that air pollutants combine exposure have greater adverse effects. However, limited studies were available on the combined toxicity of silica nanoparticles (SiNPs) and benzo[a]pyrene (B[a]P). The study was to evaluate the toxic effect and mechanisms of low-dose exposure of SiNPs, B[a]P and co-exposure in zebrafish embryos. In this study, zebrafish embryos received intravenous microinjection of SiNPs and B[a]P, and then was used to select differentially expressed genes by microarray analysis. Multiple bioinformatics analyses and STC analysis were done to identify key genes, pathways and biological processes and the expression trend of genes in each group. 1) 3065 differentially expressed genes were identified in zebrafish embryos. 2) These differentially expressed genes were involved in multiple biological processes and cellular processes such as immunity, response to stimuli, cell proliferation, adhesion, signaling transduction, and embryonic development. 3) Dynamic Gene Network analysis was used to identify a subgroup of 26 core genes that involved in multiple biological processes and cellular processes. 4) Pathway analysis and Signal-net analysis indicated that the MAPK signaling pathway, calcium signaling pathway, p53 signaling pathway, PI3k/Akt signaling pathway, and several pathways associated with immune response were the most prominent significant pathways induced by co-exposure of SiNPs and B[a]P in zebrafish embryos. Our study demonstrated that the molecular actions of co-treated with SiNPs and B[a]P on the immune system, inflammatory process and cardiovascular development had more severe toxicity than single exposure.