Mitotic Cell Cycle Process Research Articles

An integrated analysis of prognostic and immune infiltrates for hub genes as potential survival indicators in patients with lung adenocarcinoma

ObjectiveLung adenocarcinoma (LUAD) is one of the major subtypes of lung cancer that is associated with poor prognosis. The aim of this study was to identify useful biomarkers to enhance the treatment and diagnosis of LUAD.MethodsGEO2R was used to identify common up-regulated differentially expressed genes (DEGs) in the GSE32863, GSE40791, and GSE75037 datasets. The DEGs were submitted to Metascape for gene ontology and pathway enrichment analysis as well as construction of the protein-protein interaction (PPI) network, while the molecular complex detection (MCODE) plug-in was employed to filter important subnetworks. The expression levels of the hub genes and their prognostic values were evaluated using the UALCAN, GEPIA2, and Kaplan-Meier plotter databases. The timer algorithm was utilized to determine the correlation between immune cell infiltration and the expression levels of hub genes in LUAD tissues. In addition, the hub gene mutation landscape and the correlation analysis with tumor mutational burden (TMB) score were evaluated using maftools package and ggstatsplot package in R software, respectively.ResultsWe identified 156 common up-regulated DEGs, with gene ontology and pathway enrichment analysis indicating that they were mostly enriched in mitotic cell cycle process and cell cycle pathway. DEGs in the subnetwork with the largest number of genes were AURKB, CCNB2, CDC20, CDCA5, CDCA8, CENPF, and KNTC1. The seven hub genes were highly expressed in LUAD tissues and were associated with poor prognosis. These hub genes were negatively correlated with most immune cells. The somatic mutation landscape showed that AURKB, CDC20, CENPF, and KNTC1 had mutations and were positively correlated with TMB scores.ConclusionsOur findings demonstrate that increased expression of seven hub genes is associated with poor prognosis for LUAD patients. Additionally, the TMB score indicates that the high expression of hub gene increases immune cell infiltration in patients with lung adenocarcinoma which may significantly improve response to immunotherapy.

Bioinformatics analysis and experimental validation of differentially expressed genes in mouse articular chondrocytes treated with IL-1β using microarray data.

Osteoarthritis (OA) is the most prevalent chronic degenerative disease that affects the health of the elderly. The present study aimed to identify significant genes involved in OA via bioinformatics analysis. A gene expression dataset (GSE104793) was downloaded from the Gene Expression Omnibus. Bioinformatics analysis was then performed in order to identify differentially expressed genes (DEGs) between untreated chondrocytes and chondrocytes cultured with interleukin-1β (IL-1β) for 24 h. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed using Metascape. A protein-protein interaction network of DEGs was constructed using the Search Tool for the Retrieval of Interacting Genes. Gene set enrichment analysis (GSEA) was performed using GSEA software. Furthermore, chondrocytes were extracted and treated with IL-1β (10 ng/ml) for 24 h, and reverse-transcription quantitative PCR was used to confirm differential expression of hub genes. Patient samples were also collected to verify the bioinformatic analysis results. Based on the cut-off criteria used for determination of the DEGs, a total of 844 DEGs, including 498 upregulated and 346 downregulated DEGs, were identified. The DEGs were mainly enriched in the GO terms and KEGG pathways ‘inflammatory response’, ‘negative regulation of cell proliferation’, ‘ossification’, ‘taxis’, ‘blood vessel morphogenesis’, ‘extracellular structure organization’, ‘mitotic cell cycle process’ and ‘TNF signaling pathway’. The majority of the PCR results, namely the differential expression of kininogen 2, complement C3, cyclin B1, cell division cycle 20, cyclin A2, 1-phosphatidylinositol 4-kinase, BUB1 mitotic checkpoint serine/threonine kinase, kinesin family member 11, cyclin B2 and BUB1 mitotic checkpoint serine/threonine kinase B were consistent with the bioinformatics results. Collectively, the present observations provided a regulation network of IL-1β-stimulated chondrocytes, which may provide potential targets of OA therapy.

Functional Genomics of PRUNE1 in Neurodevelopmental Disorders (NDDs) Tied to Medulloblastoma (MB) and Other Tumors.

We analyze the fundamental functions of Prune_1 in brain pathophysiology. We discuss the importance and maintenance of the function of Prune_1 and how its perturbation influences both brain pathological conditions, neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies (NMIHBA; OMIM: 617481), and tumorigenesis of medulloblastoma (MB) with functional correlations to other tumors. A therapeutic view underlying recent discoveries identified small molecules and cell penetrating peptides to impair the interaction of Prune_1 with protein partners (e.g., Nm23-H1), thus further impairing intracellular and extracellular signaling (i.e., canonical Wnt and TGF-β pathways). Identifying the mechanism of action of Prune_1 as responsible for neurodevelopmental disorders (NDDs), we have recognized other genes which are found overexpressed in brain tumors (e.g., MB) with functional implications in neurodevelopmental processes, as mainly linked to changes in mitotic cell cycle processes. Thus, with Prune_1 being a significant target in NDDs, we discuss how its network of action can be dysregulated during brain development, thus generating cancer and metastatic dissemination.

Testis transcriptome profiling identified lncRNAs involved in spermatogenic arrest of cattleyak

Cattleyaks are the crossbred offspring between cattle and yaks, exhibiting the prominent adaptability to the harsh environment as yaks and much higher growth performances than yaks around Qinghai-Tibet plateau. Unfortunately, cattleyak cannot be effectively used in yak breeding due to its male infertility resulted from spermatogenic arrest. In this study, we performed RNA sequencing (RNA-seq) and bioinformatics analysis to determine the expression profiles of long noncoding RNA (lncRNA) from cattleyak and yak testis. A total of 604 differentially expressed (DE) lncRNAs (135 upregulated and 469 downregulated) were identified in cattleyak with respect to yak. Through gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, we identified several DE lncRNAs regulating the mitotic cell cycle processes by targeting the genes significantly associated with the mitotic cell cycle checkpoint and DNA damage checkpoint term and also significantly involved in p53 signaling pathway, mismatch repair and homologous recombination pathway (P < 0.05). The reverse transcription PCR (RT-PCR) and quantitative Real-Time PCR (qRT-PCR) analysis of the randomly selected fourteen DE lncRNAs and the seven target genes validated the RNA-seq data and their true expressions during spermatogenesis in vivo. Molecular cloning and sequencing indicated that the testis lncRNAs NONBTAT012170 and NONBTAT010258 presented higher similarity among different cattleyak and yak individuals. The downregulation of these target genes in cattleyak contributed to the abnormal DNA replication and spermatogenic arrest during the S phase of mitotic cell cycle. This study provided a novel insight into lncRNA expression profile changes associated with spermatogenic arrest of cattleyak.

Applying cooperative module pair analysis to uncover compatibility mechanism of Fangjis: An example of Wenxin Keli decoction

Ethnopharmacological relevanceFangji is an ancient combinatorial formula. The compatibility mechanisms that how component herbs of Fangji work cooperatively to achieve the executive framework remain unexplored. Aim of the studyToexplore compatibility mechanism and systematical effects of Fangjis by taking Wenxin Keli decoction (WXKL), a classical Fangji constituted by Codonopsis Radix, PolygonatiRhizoma, Notoginseng Radix Et Rhizoma, Ambrum, and Nardostachyos Radix Et Rhizoma., as example. Main methodsHere, we employed bioinformatics approach, including cluster analysis, cooperative module pair analysis, primary module identification, and proximity examination among target profile of herbs, to investigate compatibility characterization and anti-arrhythmia mechanism of WXKL. Finally, core mechanisms of WXKL were validatedby in vivo experiments. ResultsAs a result, we identified 695 putative target proteins and 27 clusters (W-modules) inWXKL target network (W-network), in which W-module 1, 2, 4, 8, 10 were primary modules. The cooperative module pairs were W-module 2 and 4, W-module 2 and 8, and W-module 2 and 1, all of which existed in Codonopsis Radix- or Notoginseng Radix Et Rhizoma.-condition. And Nardostachyos Radix Et Rhizoma only yielded cooperation between W-module 1 and 2. The proximity of herbs’ target profiles of Codonopsis Radix and Notoginseng Radix Et Rhizoma were similar, and Nardostachyos Radix Et Rhizoma and Ambrum were similar. For the compatibility framework, Codonopsis Radix general regulated 70.67% targets and majority W-modules (81.48%) as sovereign herb, contributing to primary therapeutic effect, mainly involving neurohormonal regulation, vasomotor, inflammation and oxidative stress. Other herbs assisted Codonopsis Radix to enhance major outcomes through common modules, and acted as complementary roles through unique process including mitotic cell cycle, biosynthetic and catabolic process, etc. Furthermore, WXKL regulated 66.67% hub proteins of arrhythmia-network, 68.18% and 47.37% proteins in primary arrhythmia-module 1 and 2, mainly involving ion channel activity, neurohormonal regulation, and stress response processes, to constitute regulatory network focusing on cardiovascular, renal, nervous system, to reverse the pathological process of arrhythmia. In vivo experiments demonstrated WXKL can attenuate adrenergic activation induced sympathetic atrial fibrillation by inhibiting calmodulin expression (CaM) and ryanodine receptor 2 (RYR2) phosphorylation to regulate neurohormonal action. ConclusionThis strategy provided an overarching view of anti-arrhythmia mechanism of WXKL and its internal compatibility, and may facilitate the understanding of compatibility in Fangjis from the perspectives of modern biology.

Weighted Gene Co-Expression Network Analysis Reveals Key Genes and Potential Drugs in Abdominal Aortic Aneurysm.

Abdominal aortic aneurysm (AAA) is a prevalent aortic disease that causes high mortality due to asymptomatic gradual expansion and sudden rupture. The underlying molecular mechanisms and effective pharmaceutical therapy for preventing AAA progression have not been fully identified. In this study, we identified the key modules and hub genes involved in AAA growth from the GSE17901 dataset in the Gene Expression Omnibus (GEO) database through the weighted gene co-expression network analysis (WGCNA). Key genes were further selected and validated in the mouse dataset (GSE12591) and human datasets (GSE7084, GSE47472, and GSE57691). Finally, we predicted drug candidates targeting key genes using the Drug–Gene Interaction database. Overall, we identified key modules enriched in the mitotic cell cycle, GTPase activity, and several metabolic processes. Seven key genes (CCR5, ADCY5, ADCY3, ACACB, LPIN1, ACSL1, UCP3) related to AAA progression were identified. A total of 35 drugs/compounds targeting the key genes were predicted, which may have the potential to prevent AAA progression.

Identification of a five-gene signature in association with overall survival for hepatocellular carcinoma.

BackgroundHepatocellular carcinoma (HCC) is considered to be a malignant tumor with a high incidence and a high mortality. Accurate prognostic models are urgently needed. The present study was aimed at screening the critical genes for prognosis of HCC.MethodsThe GSE25097, GSE14520, GSE36376 and GSE76427 datasets were obtained from Gene Expression Omnibus (GEO). We used GEO2R to screen differentially expressed genes (DEGs). A protein-protein interaction network of the DEGs was constructed by Cytoscape in order to find hub genes by module analysis. The Metascape was performed to discover biological functions and pathway enrichment of DEGs. MCODE components were calculated to construct a module complex of DEGs. Then, gene set enrichment analysis (GSEA) was used for gene enrichment analysis. ONCOMINE was employed to assess the mRNA expression levels of key genes in HCC, and the survival analysis was conducted using the array from The Cancer Genome Atlas (TCGA) of HCC. Then, the LASSO Cox regression model was performed to establish and identify the prognostic gene signature. We validated the prognostic value of the gene signature in the TCGA cohort.ResultsWe screened out 10 hub genes which were all up-regulated in HCC tissue. They mainly enrich in mitotic cell cycle process. The GSEA results showed that these data sets had good enrichment score and significance in the cell cycle pathway. Each candidate gene may be an indicator of prognostic factors in the development of HCC. However, hub genes expression was weekly associated with overall survival in HCC patients. LASSO Cox regression analysis validated a five-gene signature (including CDC20, CCNB2, NCAPG, ASPM and NUSAP1). These results suggest that five-gene signature model may provide clues for clinical prognostic biomarker of HCC.

The strength and form of natural selection on transcript abundance in the wild.

Gene transcription variation is known to contribute to disease susceptibility and adaptation, but we currently know very little about how contemporary natural selection shapes transcript abundance. Here, we propose a novel analytical framework to quantify the strength and form of ongoing natural selection at the transcriptome level in a wild vertebrate. We estimated selection on transcript abundance in a cohort of a wild salmonid fish (Salmo trutta) affected by an extracellular myxozoan parasite (Tetracapsuloides bryosalmonae) through mark–recapture field sampling and the integration of RNA‐sequencing with classical regression‐based selection analysis. We show, based on fin transcriptomes of the host, that infection by the parasite and subsequent host survival is linked to upregulation of mitotic cell cycle process. We also detect a widespread signal of disruptive selection on transcripts linked to host immune defence, host–pathogen interactions, cellular repair and maintenance. Our results provide insights into how selection can be measured at the transcriptome level to dissect the molecular mechanisms of contemporary evolution driven by climate change and emerging anthropogenic threats. We anticipate that the approach described here will enable critical information on the molecular processes and targets of natural selection to be obtained in real time.

A Novel Therapeutic Strategy for Preferential Elimination of Multiple Myeloma Cells By Targeting Protein Disulfide Isomerase

Multiple myeloma (MM) is a genetically complex hematological disease which is characterized by clonal proliferation of plasma cells in the bone marrow and secretion of monoclonal antibodies and cytokines that can damage bone, bone marrow, and kidney function1. MM cells constantly operate at the limit of their unfolded protein response (UPR) in the face of a secretory load of immunoglobin (Ig) and cytokines that is unparalleled by any other mammalian cell 2,3 and microenvironmental factors that aggravate the degree of physiologic misfolding that occurs during synthesis of secreted proteins. The endoplasmic reticulum (ER) resident protein disulfide isomerases (PDIs) are indispensable for folding of secreted proteins that require intramolecular disulfide-bond arrangement 4 like antibodies and many cytokines. As the main PDI family member, near-complete function of PDIA1 is essential for survival of MM cells while its inhibition should be manageable by the UPR in normal cells creating an opportunity for a large therapeutic window for PDI inhibitors in MM. Previously, we discovered and characterized an irreversible PDI inhibitor (CCF642) that induced cell death in MM cells at doses that did not affect survival of normal bone marrow cells. However, CCF642 has poor solubility and suboptimal selectivity precluding clinical translation. Using structure guided medicinal chemistry, we developed and characterized a highly potent and selective PDI inhibitor, with 10-fold higher potency (Fig 1B) and selectivity. CCF642-34 showed remarkable selectivity against PDIA1 and off-target bindings were eliminated when compared to CCF642 (Fig 1C). In addition to improved selectivity and in vitro PDI inhibition, CCF642-34 demonstrated more than 3-fold higher potency compared to CCF642 against MM1.S and bortezomib resistant MM1.S cells remained sensitive to CCF642-34. Importantly, the novel analogue CCF642-34 has 18-fold better potency in restricting the colony forming abilities of RPMI1640 cells while at no effect on the clonogenic potential of CD34+ cells derived from healthy bone marrow was observed at equivalent doses. CCF642-34 induces ER stress in MM1.S cells as observed in dose and time dependent cleavage of XBP1, IRE1α oligomerization and the profound induction of programmed cell death reflected by PARP and caspase 3 cleavage. To further analyze the modes of action of CCF642-34 and CCF642 we performed RNAseq after treatment of MM1.S cells and found exclusive induction of genes associated with UPR and downstream cell cycle and apoptotic responses for CCF642-34 while additional genes affecting were detected after CCF642 treatment. There were 362 and 568 differentially expressed genes in CCF642-34 and CCF-642 (compared to controls) treated MM1.S cells, respectively. Among these differentially expressed genes 87 down regulated and 142 upregulated were common to both, including downregulation of cell division and mitotic cell cycle process, and upregulation of response to ER stress, unfolded protein response, and apoptotic process gene sets. Results confirm that both CCF642 and CCF642-34 treatment act by inducing lethal ER-stress with greater selectivity for CCF642-34. Accordingly, hierarchical clustering showed distinct gene expression profiles in 642-34 and 642 treated MM1S cells (Fig. 2). CCF642-34 is orally bioavailable and highly efficacious in against established multiple myeloma in a syngeneic 5TGM1-luc/C57BL/KaLwRij model of myeloma. All vehicle control animals were dead by 52 days while 3 out of 6 mice lived beyond 6 months with no sign of relapse. In summary, we synthesized and characterized a novel lead PDIA1 inhibitor based on structure-guided medicinal chemistry that has improved pharmacologic properties to act as novel lead for clinical translation.

Significant transcriptomic changes are associated with differentiation of bone marrow-derived mesenchymal stem cells into neural progenitor-like cells in the presence of bFGF and EGF

IntroductionMesenchymal stem cells (MSCs) isolated from bone marrow have different developmental origins, including neural crest. MSCs can differentiate into neural progenitor-like cells (NPCs) under the influence of bFGF and EGF. NPCs can terminally differentiate into neurons that express beta-III-tubulin and elicit action potential. The main aim of the study was to identify key genetic markers involved in differentiation of MSCs into NPCs through transcriptomic analysis.MethodTotal RNA was isolated from MSCs and MSCs-derived NPCs followed by cDNA library construction for transcriptomic analysis. Sample libraries that passed the quality and quantity assessments were subjected to high throughput mRNA sequencing using NextSeq®500. Differential gene expression analysis was performed using the DESeq2 R package with MSC samples being a reference group. The expression of eight differentially regulated genes was counter validated using real-time PCR.ResultsIn total, of the 3,252 differentially regulated genes between MSCs and NPCs with two or more folds, 1,771 were upregulated genes, whereas 1,481 were downregulated in NPCs. Amongst these differential genes, 104 transcription factors were upregulated, and 45 were downregulated in NPCs. Neurogenesis related genes were upregulated in NPCs and the main non-redundant gene ontology (GO) terms enriched in NPCs were the autonomic nervous system, cell surface receptor signalling pathways), extracellular structure organisation, and programmed cell death. The main non-redundant GO terms enriched in MSCs included cytoskeleton organisation cytoskeleton structural constituent, mitotic cell cycle), and the mitotic cell cycle process Gene set enrichment analysis also confirmed cell cycle regulated pathways as well as Biocarta integrin pathway were upregulated in MSCs. Transcription factors enrichment analysis by ChEA3 revealed Foxs1 and HEYL, amongst the top five transcription factors, inhibits and enhances, respectively, the NPCs differentiation of MSCs.ConclusionsThe vast differences in the transcriptomic profiles between NPCs and MSCs revealed a set of markers that can identify the differentiation stage of NPCs as well as provide new targets to enhance MSCs differentiation into NPCs.

Abstract 1678: Establishment and characterization by expression microarrays of a patient-derived xenograft biobank for human pancreatic adenocarcinoma

Abstract Pancreatic cancer survival rate is poor, with a 5-year survival rate of 7% in the Republic of Ireland. Over the last 40 years, pancreatic cancer is one of the only solid tumor types to have minimal improvement in patient outcome. In Ireland, pancreatic cancer surgical resection is limited to two hospitals: Cork University Hospital and St Vincent's University Hospital (SVUH) in Dublin. In collaboration with SVUH, we have established Ireland's only pancreatic cancer patient-derived xenograft (PDX) biobank program. Tumor material from candidate patients following surgical resection was cold transferred and implanted subcutaneously into CB17/Icr-Prkdcscid mice. At time of implant and continuation of generations, snap frozen material was collected. Using miRNA and mRNA microarray technology, matched adjacent normal tissue, original tumor material and first generation (F1) PDX tumor material was interrogated. Differential expression analysis was carried out on all samples with comparisons of normal, tumor and F1 generation. Across all comparisons there were approximately 4000 genes and miRNAs found to be differential expressed. In focusing on genes that were upregulated in tumor samples compared to normal and further upregulated in the PDX F1 samples compared to the tumor samples, we identified 88 genes of interest. Biological processes such as cell division, mitotic cell cycle processes and cell cycle processes characterized a significant number of these genes. Two of the key genes of interest in this analysis were TSPAN1 and TPX2. TSPAN1 was upregulated 9.5-fold in tumor-normal comparison and upregulated a further 2.3-fold in the PDX F1 compared to the patient tumor. TPX2 was upregulated 4.4-fold in the tumor-normal comparison and a further 3.9-fold increase in the PDX tumor compared to patient tumor. TSPAN1 has previously been shown to increase the metastatic and invasive potential of pancreatic ductal adenocarcinoma cell lines. TPX2, a microtubule-associated protein, has been shown to reduce tumor growth in vivo when silenced. The pancreatic PDX biobank represents a versatile, expandable patient cohort for preclinical investigation. Analysis of gene expression profiles of normal vs tumor and tumor Vs PDX showed genes with associated tumor proliferation and aggressiveness. Citation Format: Sandra Roche, Fiona O'Neill, Niall Swan, Ninfa L. Straubinger, Neil T. Conlon, Jean Murphy, Kevin Conlon, Ray McDermott, Justine Meiller, Justin Geoghegan, Michael Moriarty, Robert M. Straubinger, Martin Clynes. Establishment and characterization by expression microarrays of a patient-derived xenograft biobank for human pancreatic adenocarcinoma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1678.

Integrative analyses of gene expression profile reveal potential crucial roles of mitotic cell cycle and microtubule cytoskeleton in pulmonary artery hypertension

BackgroundPulmonary arterial hypertension (PAH) is a life-threatening condition. The aim of this study was to explore potential crucial genes and pathways associated with PAH based on integrative analyses of gene expression and to shed light on the identification of biomarker for PAH.MethodsGene expression profile of pulmonary tissues from 27 PAH patients and 22 normal controls were downloaded from public database (GSE53408 and GSE113439). After the identification of differentially expressed genes (DEGs), hub pathways and genes were identified based on the comprehensive evaluation of protein-protein interaction (PPI) network analysis, modular analysis and cytohubba’s analysis, and further validated in another PAH transcriptomic dataset (GSE33463). Potentially associated micro-RNAs (miRNAs) were also predicted.ResultsA total of 521 DEGs were found between PAH and normal controls, including 432 up-regulated DEGs and 89 down-regulated DEGs. Functional enrichment analysis showed that these DEGs were mainly enriched in mitotic cell cycle process, mitotic cell cycle and microtubule cytoskeleton organization. Moreover, five key genes (CDK1, SMC2, SMC4, KIF23, and CENPE) were identified and then further validated in another transcriptomic dataset associated with special phenotypes of PAH. Furthermore, these hub genes were mainly enriched in promoting mitotic cell cycle process, which may be closely associated with the pathogenesis of PAH. We also found that the predicted miRNAs targeting these hub genes were found to be enriched in TGF-β and Hippo signaling pathway.ConclusionThese findings are expected to gain a further insight into the development of PAH and provide a promising index for the detection of PAH.

De novo RNA sequencing analysis of Aeluropus littoralis halophyte plant under salinity stress

The study of salt tolerance mechanisms in halophyte plants can provide valuable information for crop breeding and plant engineering programs. The aim of the present study was to investigate whole transcriptome analysis of Aeluropus littoralis in response to salinity stress (200 and 400 mM NaCl) by de novo RNA-sequencing. To assemble the transcriptome, Trinity v2.4.0 and Bridger tools, were comparatively used with two k-mer sizes (25 and 32 bp). The de novo assembled transcriptome by Bridger (k-mer 32) was chosen as final assembly for subsequent analysis. In general, 103290 transcripts were obtained. The differential expression analysis (log2FC > 1 and FDR < 0.01) showed that 1861 transcripts expressed differentially, including169 up and 316 down-regulated transcripts in 200 mM NaCl treatment and 1035 up and 430 down-regulated transcripts in 400 mM NaCl treatment compared to control. In addition, 89 transcripts were common in both treatments. The most important over-represented terms in the GO analysis of differentially expressed genes (FDR < 0.05) were chitin response, response to abscisic acid, and regulation of jasmonic acid mediated signaling pathway under 400 mM NaCl treatment and cell cycle, cell division, and mitotic cell cycle process under 200 mM treatment. In addition, the phosphatidylcholine biosynthetic process term was common in both salt treatments. Interestingly, under 400 mM salt treatment, the PRC1 complex that contributes to chromatin remodeling was also enriched along with vacuole as a general salinity stress responsive cell component. Among enriched pathways, the MAPK signaling pathway (ko04016) and phytohormone signal transduction (ko04075) were significantly enriched in 400 mM NaCl treatment, whereas DNA replication (ko03032) was the only pathway that significantly enriched in 200 mM NaCl treatment. Finally, our findings indicate the salt-concentration depended responses of A. littoralis, which well-known salinity stress-related pathways are induced in 400 mM NaCl, while less considered pathways, e.g. cell cycle and DNA replication, are highlighted under 200 mM NaCl treatment.

Integrated Bioinformatics Analysis of the Clinical Value and Biological Function of ATAD2 in Hepatocellular Carcinoma.

ATPase family AAA domain-containing protein 2 (ATAD2), a chromatin regulator and an oncogenic transcription cofactor, is frequently overexpressed in many cancers, particularly in hepatocellular carcinoma (HCC). By integrating open-access online mRNA datasets and our institutional tissue data on HCC, the clinical role and functions of ATAD2 were analyzed by bioinformatic algorithms. We systematically examined ATAD2 expression in HCC based on a large sample population, integrating data from our institution and the GEO, Oncomine, and TCGA datasets. Aberrant ATAD2 expression related to pathways was identified by bioinformatic algorithms. The effects of ATAD2 downregulation on the cycle cell were also determined. A pooled analysis from 28 datasets indicated that ATAD2 overexpression was found in HCC (SMD = 8.88, 95% CI: 5.96–11.81, P < 0.001) and was correlated with poor survival. Subgroup analysis of Asian patients with a serum alpha-fetoprotein (AFP) concentration < 200 ng/ml in stage I + II showed that the ATAD2-high group had a more unfavorable overall survival (OS) rate than the ATAD2-low group. The receiver operating characteristic curve indicated that the efficiency of ATAD2 for HCC diagnosis was considerable (area under the curve = 0.89, 95% CI: 0.86–0.91). Functional analysis based on bioinformatic algorithms demonstrated that ATAD2 participates in cell division, mitotic nuclear division, DNA replication, repair, and cell cycle processes. ATAD2 knockout in HCC cells downregulated cyclin C and cyclin D1 protein levels and resulted in G1/S phase arrest in vitro. The kinesin family member C1 (KIFC1), shugoshin 1 (SGO1), GINS complex subunit 1 (GINS1), and TPX2 microtubule nucleation factor (TPX2) genes were closely related to ATAD2 upregulation. ATAD2 may interact with TTK protein kinase (TTK) to accelerate HCC carcinogenesis. ATAD2 plays a vital role in HCC carcinogenesis by disturbing the interaction between chromatin proteins and DNA. Targeting ATAD2 represents a promising method for the development of therapeutic treatments for cancer.

DNA methylation biomarkers for nasopharyngeal carcinoma

BackgroundAberrant methylation of DNA plays an important role in the pathogenesis of nasopharyngeal carcinoma (NPC). In the current study, we aimed to integrate three cohorts profile datasets to identify abnormally methylated-differentially expressed genes and pathways associated with NPC.MethodsData of gene expression microarrays (GSE53819, GSE412452) and gene methylation microarrays (GSE52068) obtained from the GEO database. Aberrantly methylated differentially expressed genes (DEGs) were obtained by GEO2R. The David database was utilized to perform enrichment and functional analysis regarding selected genes. To create a protein-protein interaction (PPI), STRING and Cytoscape software were utilized. The MCODE was used for module analysis of the PPI network.ResultsIn total, 181 hypomethylation-high expression genes were identified, which were enriched in the biological mechanisms involved in the differentiation of endodermal cell, mitotic nuclear division, mitotic cell cycle process, chromosome segregation and cell cycle phase transition, etc. Pathway enrichment showed ECM-receptor interaction, PI3K-Akt signaling pathway, Focal adhesion, Protein digestion and absorption and Amoebiasis, etc. The top 3 hub genes of PPI network were FANCI, POSTN, and IFIH1. Additionally, 210 hypermethylation-low expression genes were identified, and our data revealed enrichment in biological processes including axoneme assembly, micro tubular formation, assembly of axonemal dynein complex, cilium movement and cilium organization, etc. Pathway analysis indicated enrichment in B cell receptor signaling pathway, Hematopoietic cell lineage, Leukocyte transendothelial migration, Complement and coagulation cascades and Fc gamma R-mediated phagocytosis, etc. The ZMYND10, PACRG and POU2AF1 were identified as the top three hub genes of PPI network. After validation in TCGA and GEPIA database, most hub genes remained significant. Patients with high expression of POSTN found to have shorter overall survival, while in patients with high expression of ZMYND10 and POU2AF1 longer overall survival was identified.ConclusionsThe data revealed novel aberrantly methylated-differentially expressed genes and pathways in NPC by bioinformatics analysis, potentially providing novel insights for the molecular mechanisms governing NPC progression. Hub genes including FANCI, POSTN, IFIH1, ZMYND10, PACRG and POU2AF1 might serve as novel biomarkers for precision diagnosis and providing medical treatment for patient with NPC.

Identification of key genes and multiple molecular pathways of metastatic process in prostate cancer.

BackgroundCancer metastasis is well known as the most adverse outcome and the major cause of mortality in cancer patients, including prostate cancer (PCa). There are no credible predictors, to this day, that can reflect the metastatic ability of localized PCa. In the present study, we firstly identified the differentially expressed genes (DEGs) and molecular pathways involved in the metastaic process of PCa by comparing gene expressions of metastaic PCa with localized PCa directly, with the purpose of identifying potential markers or therapeutic targets.MethodsThe gene expression profiles (GSE6919 and GSE32269) were downloaded from the Gene Expression Omnibus database, which contained 141 tissue samples, including 87 primary localized PCa samples and 54 metastaic PCa samples. After data processing, DEGs were identified by R language using the Student’s t-test adjusted via the Beniamini–Hochberg method. Subsequently, the gene ontology functional and pathway enrichment analyses of DEGs were performed and the protein–protein interaction network was constructed. Hub genes were identified using the plug-in cytoHubba in Cytoscape software by MCC and degree. Furthermore, validation and prognostic significance analysis of the hub genes were performed by UALCAN and gene expression profiling interactive analysis (GEPIA).ResultsA total of 90 DEGs were identified between localized and metastaic PCa, which consisted of 47 upregulated and 43 downregulated genes. The enriched functions and pathways of the DEGs include catabolic process, cell cycle, response to steroid hormone, extracellular matrix (ECM)-receptor interaction and vascular smooth muscle contraction. A total of 10 genes were identified as hub genes and biological process analysis of hub genes showed that cell cycle phase, cell division, and mitotic cell cycle process were mainly enriched. The expression of hub genes were confirmed in metastaic PCa when compared with localized PCa tissues by The Cancer Genome Atlas database. Moreover, the disease-free survival analysis of hub genes revealed that these genes may play an important role in invasion, progression or recurrence. Therefore, these hub genes might be the key genes contributed to tumor progression or metastasis in PCa and provide candidate therapeutic targets for PCa.ConclusionsThe present study identified some DEGs between localized and metastaic PCa tissue samples. These key genes might be potential therapeutic targets and biomarkers for the metastaic process of PCa.

RAP-8 ameliorates liver fibrosis by modulating cell cycle and oxidative stress

AimsThe rapeseed protein derived peptide DHNNPQIR (named as RAP-8) has been previously reported to possess antioxidant activity and alleviate liver fibrosis. The purpose of the present study was to investigate the potential crucial pathways involved in ameliorating liver fibrosis of RAP-8. Main methodsNext-generation sequencing of messenger RNA (RNA-Seq) analysis of the fibrotic and RAP-8 treated mice was performed. Western blot, qPCR and flow cytometry detection analysis were conducted to measure cell cycle and oxidative stress in LX-2 cells and liver samples. Key findings588 overlapped differentially expressed genes were obtained from a batch of genes RAP-8 altered. Gene Ontology enrichment analysis revealed that changes in the most significant modules were mainly enriched in cell division, nuclear division and mitotic cell cycle process, while alterations in Kyoto Encyclopedia of Genes and Genomes were mainly enriched in cell cycle. Thereafter, according to the co-expression network analysis, the regulations of three core genes (Cenpp, Cyp2c55, Serpinh1) were verified that might be targets for treating liver fibrosis. Furthermore, through experimental verification, we demonstrated that RAP-8 induced cell cycle arrest and prevents oxidation stress. SignificanceAs a promising therapeutic candidate for hepatic fibrosis treating, RAP-8 exhibited anti-fibrotic effects via exerting cell cycle arrest and inhibiting oxidative stress.

Identification of key genes involved in the metastasis of clear cell renal cell carcinoma.

Clear cell renal cell carcinoma (ccRCC) is the most common and lethal renal malignant tumor in adults. The aim of the present study was to identify the key genes involved in ccRCC metastasis. Expression profiling data for ccRCC patients with metastasis and without metastasis were obtained from The Cancer Genome Atlas database. The datasets were used to identify differentially expressed genes (DEGs) between the metastasis group and the non-metastasis group using the DESeq2 package. Function enrichment analyses of DEGs were performed. The protein-protein interaction (PPI) network was constructed and analyzed using the Search Tool for the Retrieval of Interacting Genes and Cytoscape for further analysis of the identified hub genes. A total of 472 DEGs were identified, including 247 that were upregulated and 225 that were downregulated in the metastasis group. Gene Ontology enrichment analysis revealed that DEGs were mainly enriched in cell transmembrane movement and mitotic cell cycle process. Kyoto Encyclopedia of Genes Genomes pathway analysis revealed that the DEGs were mainly involved in the ‘cell cycle’ (hsa04110), ‘collecting duct acid secretion’ (hsa04966), ‘complement and coagulation cascades’ (hsa04610) and ‘aldosterone-regulated sodium reabsorption’ (hsa04960) pathways. Using the PPI network, 35 hub genes were identified, and the majority of them were upregulated in ccRCC tissue compared with normal kidney tissue. The expression levels of certain hub genes (CDKN3, TPX2, BUB1B, CDCA8, UBE2C, NDC80, RRM2, NCAPG, NCAPH, PTTG1, FAM64A, ANLN, KIF4A, CEP55, CENPF, KIF20A, ASPM and HJURP) were significantly associated with overall survival and recurrence-free survival in ccRCC. The present study has identified key genes associated with the metastasis of ccRCC.

Epigallocatechin‑3‑gallate modulates long non‑coding RNA and mRNA expression profiles in lung cancer cells.

(−)-Epigallocatechin-3-gallate (EGCG), a major constituent of green tea, is a potential anticancer agent, but the molecular mechanisms of its effects are not well-understood. The present study was conducted to examine the mechanism of EGCG in lung cancer cells. Alterations in long non-coding RNAs (lncRNAs) and mRNAs were investigated in lung cancer cells treated with EGCG by lncRNA microarray analysis. Furthermore, the functions and signaling pathways regulated by EGCG were predicted by bioinformatics analysis. A total of 960 lncRNAs and 1,434 mRNAs were significantly altered following EGCG treatment. These lncRNAs were distributed across nearly all human chromosomes and the mRNAs were involved in the cell cycle and the mitotic cell cycle process. Through a combination of microarray and bioinformatics analysis, 20 mRNAs predicted to serve a key role in the EGCG regulation were identified, and certain regulatory networks involving EGCG-regulated lncRNAs were predicted. In conclusion, EGCG affects the expression of various lncRNAs and mRNAs in the cells, therefore affecting cell functions. The results of the present study provide an insight into the mechanism of EGCG, which may be useful for therapeutic development.

Identification of Key Genes and Pathways in Cervical Cancer by Bioinformatics Analysis.

Cervical cancer is a common malignant tumour of the female reproductive system that seriously threatens the health of women. The aims of this study were to identify key genes and pathways and to illuminate new molecular mechanisms underlying cervical cancer. Altogether, 1829 DEGs were identified, including 794 significantly down-regulated DEGs and 1035 significantly up-regulated DEGs. GO analysis suggested that the up-regulated DEGs were mainly enriched in mitotic cell cycle processes, including DNA replication, organelle fission, chromosome segregation and cell cycle phase transition, and that the down-regulated DEGs were primarily enriched in development and differentiation processes, such as tissue development, epidermis development, skin development, keratinocyte differentiation, epidermal cell differentiation and epithelial cell differentiation. KEGG pathway analysis showed that the DEGs were significantly enriched in cell cycle, DNA replication, the p53 signalling pathway, pathways in cancer and oocyte meiosis. The top 9 hub genes with a high degree of connectivity (over 72 in the PPI network) were down-regulated TSPO, CCND1, and FOS and up-regulated CDK1, TOP2A, CCNB1, PCNA, BIRC5 and MAD2L1. Module analysis indicated that the top 3 modules were significantly enriched in mitotic cell cycle, DNA replication and regulation of cell cycle (P < 0.01). The heat map based on TCGA database preliminarily demonstrated the expression change of the key genes in cervical cancer. GSEA results were basically coincident with the front enrichment analysis results. By comprehensive analysis, we confirmed that cell cycle was a key biological process and a critical driver in cervical cancer. In conclusion, this study identified DEGs and screened the key genes and pathways closely related to cervical cancer by bioinformatics analysis, simultaneously deepening our understanding of the molecular mechanisms underlying the occurrence and progression of cervical cancer. These results might hold promise for finding potential therapeutic targets of cervical cancer.