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Mechanisms that maintain transcriptional memory through cell division are important to maintain cell identity, and sequence-specific transcription factors that remain associated with mitotic chromatin are emerging as key players in transcriptional memory propagation. Here, we show that the major transcriptional effector of Notch signaling, RBPJ, is retained on mitotic chromatin, and that this mitotic chromatin association is mediated through the direct association of RBPJ with DNA. We further demonstrate that RBPJ binds directly to nucleosomal DNA in vitro, with a preference for sites close to the entry/exit position of the nucleosomal DNA. Genome-wide analysis in the murine embryonal-carcinoma cell line F9 revealed that roughly 60% of the sites occupied by RBPJ in asynchronous cells were also occupied in mitotic cells. Among them, we found that a fraction of RBPJ occupancy sites shifted between interphase and mitosis, suggesting that RBPJ can be retained on mitotic chromatin by sliding on DNA rather than disengaging from chromatin during mitotic chromatin condensation. We propose that RBPJ can function as a mitotic bookmark, marking genes for efficient transcriptional activation or repression upon mitotic exit. Strikingly, we found that sites of RBPJ occupancy were enriched for CTCF-binding motifs in addition to RBPJ-binding motifs, and that RBPJ and CTCF interact. Given that CTCF regulates transcription and bridges long-range chromatin interactions, our results raise the intriguing hypothesis that by collaborating with CTCF, RBPJ may participate in establishing chromatin domains and/or long-range chromatin interactions that could be propagated through cell division to maintain gene expression programs. [ABSTRACT FROM AUTHOR]

Background Sample size calculation is an important issue in the experimental design of biomedical research. For RNA-seq experiments, the sample size calculation method based on the Poisson model has been proposed; however, when there are biological replicates, RNA-seq data could exhibit variation significantly greater than the mean (i.e. over-dispersion). The Poisson model cannot appropriately model the over-dispersion, and in such cases, the negative binomial model has been used as a natural extension of the Poisson model. Because the field currently lacks a sample size calculation method based on the negative binomial model for assessing differential expression analysis of RNA-seq data, we propose a method to calculate the sample size. Results We propose a sample size calculation method based on the exact test for assessing differential expression analysis of RNA-seq data. Conclusions The proposed sample size calculation method is straightforward and not computationally intensive. Simulation studies to evaluate the performance of the proposed sample size method are presented; the results indicate our method works well, with achievement of desired power. [ABSTRACT FROM AUTHOR]

Lipopolysaccharide (LPS) triggers innate immunity mainly via TLR4 signaling. ATF3 is a negative regulator of TLR4 signaling. HMGB1 plays a critical role in the final step of sepsis. However, the mechanisms of ATF3 and the role of HMGB1 in regulating innate immunity-induced sepsis are incompletely understood. In this study, we found that serum HMGB1 levels were 10-fold higher in patients with sepsis than normal controls. We further demonstrated that ATF3 gene knockout in mice subjected to LPS-induced endotoxemia correlates with an increase in the mortality rate and the elevated expression of IL-6, TNF-α, NO, MCP-1, and HMGB1 in the lung tissues or serum. The biochemical effects of ATF3 were observed in in vitro macrophages and blocked by ATF3 siRNA treatment. We have also shown that adeno-associated virus-mediated ATF3 gene transfer protected ATF3 knockout mice from LPS-induced mortality. In addition, ATF3 knockdown increased LPS-induced release of HMGB1. In conclusion, upregulation of ATF3 contributes to the reduced release of inflammatory molecules, especially HMGB1, which induced lung injury and increased the survival rate of mice after LPS challenge. Therefore, suppressing LPS-induced inflammation with ATF3 induction or ATF3 mimetics may be an important strategy for sepsis therapy. [ABSTRACT FROM AUTHOR]

Background: Dealing with high dimensional markers, such as gene expression data obtained using microarray chip technology or genomics studies, is a key challenge because the numbers of features greatly exceeds the number of biological samples. After selecting biologically relevant genes, how to summarize the expression of selected genes and then further build predicted model is an important issue in medical applications. One intuitive method of addressing this challenge assigns different weights to different features, subsequently combining this information into a single score, named the compound covariate. Investigators commonly employ this score to assess whether an association exists between the compound covariate and clinical outcomes adjusted for baseline covariates. However, we found that some clinical papers concerned with such analysis report bias p-values based on flawed compound covariate in their training data set. Results: We correct this flaw in the analysis and we also propose treating the compound score as a random covariate, to achieve more appropriate results and significantly improve study power for survival outcomes. With this proposed method, we thoroughly assess the performance of two commonly used estimated gene weights through simulation studies. When the sample size is 100, and censoring rates are 50%, 30%, and 10%, power is increased by 10.6%, 3.5%, and 0.4%, respectively, by treating the compound score as a random covariate rather than a fixed covariate. Finally, we assess our proposed method using two publicly available microarray data sets. Conclusion: In this article, we correct this flaw in the analysis and the propose method, treating the compound score as a random covariate, can achieve more appropriate results and improve study power for survival outcomes. [ABSTRACT FROM AUTHOR]

Abstract: O6-Methylguanine-DNA methyltransferase (MGMT) is critical for repairing pro-mutagenic DNA bases and is correlated with response to alkylating agents in cancers. Since there is great interest in pursuing the potential role of temozolomide, a novel alkylating agent, in the treatment of brain metastases, this study aimed to evaluate MGMT expression as well as its prognostic value in this devastating disease. We studied the expression and methylation status of MGMT in 86 brain metastases of lung cancers. Twenty of them had matched primary lung tumor tissues available for direct comparison. MGMT expression was assessed by immunohistochemistry (IHC); the methylation status of MGMT promoter was analyzed by nested methylation-specific PCR (MSP) and validated by quantitative real-time PCR analysis. Positive nuclear MGMT expression was detected more frequently in brain metastases as compared with primary lung cancers (83% versus 50%, P =0.004). The discordance in MGMT expression persisted in the 20 paired primary and metastatic tumors (P =0.031). MGMT promoter hypermethylation was highly correlated with loss of MGMT expression. Both univariate and multivariate analyses showed that median overall survival was significantly longer in patients with positive MGMT expression in brain metastases (16.5 versus 3.5 months, P <0.001). In conclusion, MGMT expression was enhanced in brain metastases as compared with the primary lung cancers. MGMT expression in brain metastases was significantly correlated with better survival. [Copyright &y& Elsevier]

Background. Klebsiella pneumoniae has become the predominant pathogen causing primary pyogenic liver abscess (PLA). Methods. K. pneumoniae was stimulated by human serum, and gene expression was analyzed by microarray. Results. Three putative iron acquisition systems, Yersinia high-pathogenicity island (HPI), iucABCDiutA, and iroA(iroNDCB), that increased in expression and predominated in PLA-associated K. pneumoniae strains were identified. By use of siderophore uptake assays, these 3 systems were confirmed to be siderophore-dependent iron acquisition systems. Only the irp2-iuc-iroA triple mutant showed decreased virulence in mice. Full-genome analysis of K. pneumoniae strain NTUH-K2044 identified 10 putative iron uptake systems. Seven of these 10 systems were TonB dependent, including Yersinia HPI, iucABCDiutA, and iroA. A tonB deletion mutant was demonstrated to have profound attenuation of virulence. Immunization with the tonB mutant resulted in seroconversion of extracellular polysaccharide antibodies and protective efficacy against subsequent exposure to the parental strain. Conclusions. Iron uptake systems were the genes in K. pneumoniae that were highly up-regulated in response to sera. Although there are multiple iron transporter systems in NTUH-K2044, a mutation in all 3 loci (irp2, iuc, and iroA) is necessary to decrease virulence. The tonB mutant is a potential vaccine candidate because it can induce a significant protective immune response against challenge with a wild-type strain. [ABSTRACT FROM AUTHOR]

Resistin (Rstn) is known as an adipocyte-specific secretory factor that can cause insulin resistance and decrease adipocyte differentiation. Conversely, based on various studies, insulin-like growth factors (IGFs) can improve insulin resistance and stimulate adipocyte adipogenesis. Whether IGFs exert their effects through the control of Rstn' s production or modulation of Rstn' s action is unknown. This study was designed to examine the influence and the signaling of KIF-I on Rstn gene expression and protein secretion by 3T3-L1 adipocytes. We found that IGF-I suppressed Rstn mRNA expression and protein release in dose- and time-dependent manners. The IC50 of IGF-I was ∼1 nM for a range of 6-10 h of treatment. Treatment with cycloheximide, but not with actinomycin D, prevented IGF-I-suppressed Rstn mRNA expression, suggesting that IGF-I destabilizes Rstn mRNA and that IGF-I' s effect requires new protein, but not mRNA, synthesis. Pretreatment with IGF-1 receptor (IGF-IR) antibody blocked IGF-I-altered IUF-IR activity and Rstn mRNA levels. Neither PD-98059, SB-203580, nor LY-294002 changed the IGF-I-de creased levels of Rstn niRNA, but they inhibited IGF-I-stimulated activities of MEK1, p38 MAPK, and phosphoinositide 3-kinase, respectively. However, SB-203580 antag- onized the IGF-I-decreased Rstn protein release. These data demon- strate that IGF-1 downregulates Rstn gene expression via IGF-IR- dependent and MEKI -, p38 MAPK-, and phosphoinositide 3-kinase- independent pathways and likely modifies the distribution of Rstn protein between the intracellular and extracellular compartments via a p38 MAPK-dependent pathway. Decreases in Rstn production and secretion induced by IGF-I may be related to the mechanism by which IGF-1 modulates body weight and diabetes in animals. [ABSTRACT FROM AUTHOR]

Objectives: Chondrogenic differentiation of human dental pulp stem cells (hDPSCs) is highly promising for cartilage repair. The specific mechanism, however, still needs to be explicated. Materials and Methods: In this study, we isolated hDPSCs and transfected cells with lentiviruses containing an over‐expression, knock‐down, or negative control of miR‐20a‐5p. Three‐D pellet cultures of hDPSCs were used for the chondrogenic induction. Following the pellet culture period, chondrogenesis was assessed by histological and immunohistochemical analysis and expression of chondrogenic‐related genes. Dual‐luciferase report assay was performed to determine potential targeted genes of miR‐20a‐5p, and the phosphorylation levels of P65 and IκBα were explored. Animal experiments were performed to determine the effect of miR‐20a‐5p on cartilage regeneration. Results: miR‐20a‐5p was showed to repress the expression of SMAD6 to inhibit the chondrogenic differentiation of hDPSCs. Accordingly, the knock‐down of miR‐20a‐5p promoted cartilage regeneration in the osteochondral defects of rats. Mechanically, it is indicated that NF‐κB signaling is the potential down‐stream network of miR‐20a‐5p/Smad6 crosstalk during chondrogenic differentiation. Conclusions: miR‐20a‐5p could target SMAD6 to activate NF‐κB signaling pathway, and thus inhibit chondrogenesis of hDPSCs, which provided promising therapeutic target for cartilage defects clinically. [ABSTRACT FROM AUTHOR]

The association between human epidermal growth factor receptor-2 (HER2) amplification and brain metastasis (BM) in patients having colorectal cancer (CRC) has been suggested but not yet established. This study investigated the expression patterns of HER2, its association with BM, and its prognostic value in patients having CRC. We retrospectively identified 99 patients having metastatic CRC (mCRC) and BM (the BM cohort) and compared them with a cohort of 249 patients having mCRC and without BM (the stage IV cohort) by propensity score matching. Immunohistochemical studies of HER2 on all available paraffin-embedded tumour samples, either from the primary tumour, the metastasis (brain and/or extracranial sites) or both, were performed and analysed. HER2 fluorescent in situ hybridisation was applied when necessary. The expression of HER2 was compared and correlated with survival. HER2 amplifications were detected in 16 (18.4%) of 87 and 9 (3.6%) of 249 patients who had specimens available in the BM and stage IV cohorts, respectively (P <.001). After propensity score matching, HER2 amplification was significantly associated with BM (odds ratio: 5.38, P =.003). HER2 heterogeneity was frequently observed not only at the single tumour level but also in paired tumour samples. A marginally significant longer survival since BM was found in patients having HER2-amplified mCRC than in those without (P =.07). HER2 amplification was significantly associated with BM in patients having mCRC and might have prognostic value for survival since BM. Given the heterogeneity of HER2 expression, the testing of HER2 status on available tissues from both primary and metastatic tumours should be encouraged. • Propensity score matching examined HER2 amplification and brain metastases. • High frequency of HER2 amplification in patients having metastatic colorectal cancer and brain metastasis was demonstrated. • Intra-patient heterogeneities of HER2 amplification were observed. [ABSTRACT FROM AUTHOR]

Cockayne syndrome is an inherited premature aging disease associated with numerous developmental and neurological defects, and mutations in the gene encoding the CSB protein account for the majority of Cockayne syndrome cases. Accumulating evidence suggests that CSB functions in transcription regulation, in addition to its roles in DNA repair, and those defects in this transcriptional activity might contribute to the clinical features of Cockayne syndrome. Transcription profiling studies have so far uncovered CSB-dependent effects on gene expression; however, the direct targets of CSB's transcriptional activity remain largely unknown. In this paper, we report the first comprehensive analysis of CSB genomic occupancy during replicative cell growth. We found that CSB occupancy sites display a high correlation to regions with epigenetic features of promoters and enhancers. Furthermore, we found that CSB occupancy is enriched at sites containing the TPA-response element. Consistent with this binding site preference, we show that CSB and the transcription factor c-Jun can be found in the same protein-DNA complex, suggesting that c-Jun can target CSB to specific genomic regions. In support of this notion, we observed decreased CSB occupancy of TPA-response elements when c-Jun levels were diminished. By modulating CSB abundance, we found that CSB can influence the expression of nearby genes and impact nucleosome positioning in the vicinity of its binding site. These results indicate that CSB can be targeted to specific genomic loci by sequence-specific transcription factors to regulate transcription and local chromatin structure. Additionally, comparison of CSB occupancy sites with the MSigDB Pathways database suggests that CSB might function in peroxisome proliferation, EGF receptor transactivation, G protein signaling and NF-κB activation, shedding new light on the possible causes and mechanisms of Cockayne syndrome. [ABSTRACT FROM AUTHOR]

Background: Identification of expression alternations between early and late stage cancers is helpful for understanding cancer development and progression. Much research has been done focusing on stage-dependent gene expression profiles. In contrast, relatively fewer studies on isoform expression profiles have been performed due to the difficulty of quantification and noisy splicing. Here we conducted both gene- and isoform-level analysis on RNA-seq data of 234 stage I and 81 stage IV kidney renal clear cell carcinoma patients, aiming to uncover the stage-dependent expression signatures and investigate the advantage of isoform expression profiling for identifying advanced stage cancers and predicting clinical outcome. Results: Both gene and isoform expression signatures are useful for distinguishing cancer stages. They provide common and unique information associated with cancer progression and metastasis. Combining gene and isoform signatures even improves the classification performance and reveals additional important biological processes, such as angiogenesis and TGF-beta signaling pathway. Moreover, expression abundance of a number of genes and isoforms is predictive of the risk of cancer death in an independent dataset, such as gene and isoform expression of ITPKA, the expression of a functional important isoform of UPS19. Conclusion: Isoform expression profiling provides unique and important information which cannot be detected by gene expression profiles. Combining gene and isoform expression signatures helps to identify advanced stage cancers, predict clinical outcome, and present a comprehensive view of cancer development and progression. [ABSTRACT FROM AUTHOR]

Background: Community-acquired pyogenic liver abscess (PLA) complicated with meningitis and endophthalmitis caused by Klebsiella pneumoniae is an emerging infectious disease. To investigate the mechanisms and effects of biofilm formation of K. pneumoniae causing PLA, microtiter plate assays were used to determine the levels of biofilm formed by K. pneumoniae clinical isolates and to screen for biofilm-altered mutants from a transposon mutant library of a K. pneumoniae PLAassociated strain. Methodology/Principal Findings: The biofilm formation of K. pneumoniae was examined by microtiter plate assay. Higher levels of biofilm formation were demonstrated by K. pneumoniae strains associated with PLA. A total of 23 biofilm-decreased mutants and 4 biofilm-increased mutants were identified. Among these mutants, a biofilm-decreased treC mutant displayed less mucoviscosity and produced less capsular polysaccharide (CPS), whereas a biofilm-increased sugE mutant displayed higher mucoviscosity and produced more CPS. The biofilm phenotypes of treC and sugE mutants also were confirmed by glass slide culture. Deletion of treC, which encodes trehalose-6-phosphate hydrolase, impaired bacterial trehalose utilization. Addition of glucose to the culture medium restored the capsule production and biofilm formation in the treC mutant. Transcriptional profile analysis suggested that the increase of CPS production in DsugE may reflect elevated cps gene expression (upregulated through rmpA) in combination with increased treC expression. In vivo competition assays demonstrated that the treC mutant strain was attenuated in competitiveness during intragastric infection in mice. Conclusions/Significance: Genes important for biofilm formation by K. pneumoniae PLA strain were identified using an in vitro assay. Among the identified genes, treC and sugE affect biofilm formation by modulating CPS production. The importance of treC in gastrointestinal tract colonization suggests that biofilm formation contributes to the establishment and persistence of K. pneumoniae infection. [ABSTRACT FROM AUTHOR]

Resistin (Rstn) is known as an adipocyte-specific secretory hormone that can cause insulin resistance and decrease adipocyte differentiation. By contrast, green tea catechins, especially (-)-epigallocatechin gallate (EGCG), have been reported as body weight and diabetes chemopreventatives. Whether EGCG regulates production of Rstn is unknown. Using 3T3-L1 adipocytes, we found that EGCG at 20 and 100 μM suppressed Rstn mRNA levels by ∼35 and 50%, respectively, after 3 h. The basal half-life of Rstn mRNA induced by actinomycin D was >12 h but shifted to 3 h in the presence of EGCG. This suggests that EGCG regulates the stability of Rstn mRNA. Treatment with cycloheximide did not prevent EGCG-suppressed Rstn mRNA levels, which suggests that the effect of EGCG does not require new protein synthesis. Intracellular Rstn protein significantly decreased in the presence of 100 μM EGCG 3 h after treatment, whereas the release of the Rstn protein did not significantly change. This suggests that EGCG may modulate the distribution of Rstn protein between the intracellular and extracellular compartments. EGCG did not affect the amounts of extracellular signal-related kinase-1/2 (ERK1/2), phospho-JNK, phospho-p38, and phospho-Akt proteins but reduced the amounts of phospho-ERK1/2 proteins. Overexpression with MEK1 blocked EGCG-inhibited Rstn mRNA expression. These data suggest that EGCG downregulates Rstn expression via a pathway that is dependent on the ERK pathway. [ABSTRACT FROM AUTHOR]

Background: Wilms' tumor (WT) is one of the most common malignant neoplasms of the urinary tract in children. Anaplastic histology (unfavorable histology) accounts for about 10% of whole WTs, and it is the single most important histologic predictor of treatment response and survival in patients with WT; however, until now the molecular basis of this phenotype is not very clearly. Methods: A real-time polymerase chain reaction (PCR) array was designed and tested. Next, the gene expression profile of pediatric anaplastic histology WT and normal adjacent tissues were analyzed. These expression data were anlyzed with Multi Experiment View (MEV) cluster software further. Datasets representing genes with altered expression profiles derived from cluster analyses were imported into the Ingenuity Pathway Analysis Tool (IPA). Results: 88 real-time PCR primer pairs for quantitative gene expression analysis of key genes involved in pediatric anaplastic histology WT were designed and tested. The gene expression profile of pediatric anaplastic histology WT is significantly different from adjacent normal controls; we identified 15 genes that are up-regulated and 16 genes that are down-regulated in the former. To investigate biological interactions of these differently regulated genes, datasets representing genes with altered expression profiles were imported into the IPA for further analysis, which revealed three significant networks: Cancer, Hematological Disease, and Gene Expression, which included 27 focus molecules and a significance score of 43. The IPA analysis also grouped the differentially expressed genes into biological mechanisms related to Cell Death and Survival 1.15E-12, Cellular Development 2.84E-11, Cellular Growth and Proliferation 2.84E-11, Gene Expression 4.43E-10, and DNA Replication, Recombination, and Repair 1.39E-07. The important upstream regulators of pediatric anaplastic histology WT were TP53 and TGFβ1 signaling (P = 1.15E-14 and 3.79E-13, respectively). Conclusions: Our study demonstrates that the gene expression profile of pediatric anaplastic histology WT is significantly different from adjacent normal tissues with real-time PCR array. We identified some genes that are dysregulated in pediatric anaplastic histology WT for the first time, such as HDAC7, and IPA analysis showed the most important pathways for pediatric anaplastic histology WT are TP53 and TGFβ1 signaling. This work may provide new clues into the molecular mechanisms behind pediatric anaplastic histology WT. [ABSTRACT FROM AUTHOR]

Abstract: Collapsin response mediator protein (CRMP) family proteins are cytosolic phosphoproteins involved in semaphorin 3A-mediated neuronal cell growth cone collapse and cancer invasion. We identified a novel human isoform of CRMP family proteins named long form CRMP-1 (LCRMP-1), which was different from the known invasion suppressor, CRMP-1, in its molecular weight and the N-terminal exon-1. This study was aimed to elucidate the clinical significance of LCRMP-1 in non-small cell lung cancer (NSCLC) patients. Full-length human LCRMP-1 was cloned from lung adenocarcinoma based on the Expressed Sequence Tags (EST) database. We generated LCRMP-1 specific antibody and subsequent in vitro and in vivo invasion assays showed positive correlations between LCRMP-1 expression and lung cancer cell invasiveness. We further demonstrated that high LCRMP-1 mRNA expressions were associated with poor overall and disease-free survivals (P =0.004 and 0.006, respectively, log-rank test) in 72 NSCLC patients. The results were confirmed in an independent cohort of 54 NSCLC patients by immunohistochemistry (P =0.032, log-rank test). The metastatic lymph nodes showed higher LCRMP-1 expressions as compared with the paired primary lung tumors (P =0.012, McNemar''s test). In conclusion, LCRMP-1 was a cancer invasion enhancer that could be a novel prognostic biomarker in NSCLC. [Copyright &y& Elsevier]