DTox: A deep neural network-based in visio lens for large scale toxicogenomics data.

With the advancement of large-scale omics technologies, particularly transcriptomics data sets on drug and treatment response repositories available in public domain, toxicogenomics has emerged as a key field in safety pharmacology and chemical risk assessment. Traditional statistics-based bioinformatics analysis poses challenges in its application across multidimensional toxicogenomic data, including administration time, dosage, and gene expression levels. Motivated by the visual inspection workflow of field experts to augment their efficiency of screening significant genes to derive meaningful insights, together with the ability of deep neural architectures to learn the image signals, we developed DTox, a deep neural network-based in visio approach. Using the Percellome toxicogenomics database, instead of utilizing the numerical gene expression values of the transcripts (gene probes of the microarray) for dose-time combinations, DTox learned the image representation of 3D surface plots of distinct time and dosage data points to train the classifier on the experts' labels of gene probe significance. DTox outperformed statistical threshold-based bioinformatics and machine learning approaches based on numerical expression values. This result shows the ability of image-driven neural networks to overcome the limitations of classical numeric value-based approaches. Further, by augmenting the model with explainability modules, our study showed the potential to reveal the visual analysis process of human experts in toxicogenomics through the model weights. While the current work demonstrates the application of the DTox model in toxicogenomic studies, it can be further generalized as an in visio approach for multi-dimensional numeric data with applications in various fields in medical data sciences.

[Percellome Project: research on molecular mechanisms of toxicological responses based on transcriptomics and epigenetics].

We are constructing the "Percellome Database" containing many transcriptomes of mice exposed to a series of chemicals to elucidate the molecular mechanism of toxicity and to develop toxicity prediction technology. Acute toxicity of a chemical can be predicted to a certain extent by searching the similarity of the transcriptomes obtained by the single-dose exposure experiments. In addition, we are analyzing the relation between the transcriptome and the epigenome i.e. histone modification and genomic DNA methylation to understand the molecular mechanism of the repeated dose toxicity. We are attempting to expand the scale and improve the efficiency of the analysis by introducing artificial intelligence technologies. This approach should maximize the use of toxicogenomics technology for optimizing the experimental protocols for repeated dose toxicity studies towards 3Rs principle, and optimizing the process of in silico toxicity prediction by combining the available big data.

A Geometric Clustering Tool (AGCT) to robustly unravel the inner cluster structures of time-series gene expressions.

Systems biology aims at holistically understanding the complexity of biological systems. In particular, nowadays with the broad availability of gene expression measurements, systems biology challenges the deciphering of the genetic cell machinery from them. In order to help researchers, reverse engineer the genetic cell machinery from these noisy datasets, interactive exploratory clustering methods, pipelines and gene clustering tools have to be specifically developed. Prior methods/tools for time series data, however, do not have the following four major ingredients in analytic and methodological view point: (i) principled time-series feature extraction methods, (ii) variety of manifold learning methods for capturing high-level view of the dataset, (iii) high-end automatic structure extraction, and (iv) friendliness to the biological user community. With a view to meet the requirements, we present AGCT (A Geometric Clustering Tool), a software package used to unravel the complex architecture of large-scale, non-necessarily synchronized time-series gene expression data. AGCT capture signals on exhaustive wavelet expansions of the data, which are then embedded on a low-dimensional non-linear map using manifold learning algorithms, where geometric proximity captures potential interactions. Post-processing techniques, including hard and soft information geometric clustering algorithms, facilitate the summarizing of the complete map as a smaller number of principal factors which can then be formally identified using embedded statistical inference techniques. Three-dimension interactive visualization and scenario recording over the processing helps to reproduce data analysis results without additional time. Analysis of the whole-cell Yeast Metabolic Cycle (YMC) moreover, Yeast Cell Cycle (YCC) datasets demonstrate AGCT's ability to accurately dissect all stages of metabolism and the cell cycle progression, independently of the time course and the number of patterns related to the signal. Analysis of Pentachlorophenol iduced dataset demonstrat how AGCT dissects data to identify two networks: Interferon signaling and NRF2-signaling networks.

Exosome-mediated horizontal gene transfer occurs in double-strand break repair during genome editing.

The CRISPR-Cas9 system has been successfully applied in many organisms as a powerful genome-editing tool. Undoubtedly, it will soon be applied to human genome editing, including gene therapy. We have previously reported that unintentional DNA sequences derived from retrotransposons, genomic DNA, mRNA and vectors are captured at double-strand breaks (DSBs) sites when DSBs are introduced by the CRISPR-Cas9 system. Therefore, it is possible that unintentional insertions associated with DSB repair represent a potential risk for human genome editing gene therapies. To address this possibility, comprehensive sequencing of DSB sites was performed. Here, we report that exosome-mediated horizontal gene transfer occurs in DSB repair during genome editing. Exosomes are present in all fluids from living animals, including seawater and breathing mammals, suggesting that exosome-mediated horizontal gene transfer is the driving force behind mammalian genome evolution. The findings of this study highlight an emerging new risk for this leading-edge technology.

Learning and Memory Deficits in Male Adult Mice Treated with a Benzodiazepine Sleep-Inducing Drug during the Juvenile Period.

Gamma-aminobutyric acid (GABA), the major inhibitory neurotransmitter in the mammalian central nervous system, is also known to be important for brain development. Therefore, disturbances of GABA receptor (GABA-R) mediated signaling (GABA-R signal) during brain development may influence normal brain maturation and cause late-onset brain malfunctions. In this study, we examined whether the stimulation of the GABA-R signal during brain development induces late-onset adverse effects on the brain in adult male mice. To stimulate the GABA-R signal, we used either the benzodiazepine sleep-inducing drug triazolam (TZ) or the non-benzodiazepine drug zolpidem (ZP). We detected learning and memory deficits in mice treated with TZ during the juvenile period, as seen in the fear conditioning test. On the other hand, ZP administration during the juvenile period had little effect. In addition, decreased protein expression of GluR1 and GluR4, which are excitatory neurotransmitter receptors, was detected in the hippocampi of mice treated with TZ during the juvenile period. We measured mRNA expression of the immediate early genes (IEGs), which are neuronal activity markers, in the hippocampus shortly after the administration of TZ or ZP to juvenile mice. Decreased IEG expression was detected in mice with juvenile TZ administration, but not in mice with juvenile ZP administration. Our findings demonstrate that TZ administration during the juvenile period can induce irreversible learning and memory deficits in adult mice. It may need to take an extra care for the prescription of benzodiazepine sleep-inducing drugs to juveniles because it might cause learning and memory deficits.

Ewing's sarcoma precursors are highly enriched in embryonic osteochondrogenic progenitors.

Ewing's sarcoma is a highly malignant bone tumor found in children and adolescents, and the origin of this malignancy is not well understood. Here, we introduced a Ewing's sarcoma-associated genetic fusion of the genes encoding the RNA-binding protein EWS and the transcription factor ETS (EWS-ETS) into a fraction of cells enriched for osteochondrogenic progenitors derived from the embryonic superficial zone (eSZ) of long bones collected from late gestational murine embryos. EWS-ETS fusions efficiently induced Ewing's sarcoma-like small round cell sarcoma formation by these cells. Analysis of the eSZ revealed a fraction of a precursor cells that express growth/differentiation factor 5 (Gdf5), the transcription factor Erg, and parathyroid hormone-like hormone (Pthlh), and selection of the Pthlh-positive fraction alone further enhanced EWS-ETS-dependent tumor induction. Genes downstream of the EWS-ETS fusion protein were quite transcriptionally active in eSZ cells, especially in regions in which the chromatin structure of the ETS-responsive locus was open. Inhibition of ß-catenin, poly (ADP-ribose) polymerase 1 (PARP1), or enhancer of zeste homolog 2 (EZH2) suppressed cell growth in a murine model of Ewing's sarcoma, suggesting the utility of the current system as a preclinical model. These results indicate that eSZ cells are highly enriched in precursors to Ewing's sarcoma and provide clues to the histogenesis of Ewing's sarcoma in bone.

Active repression by RARγ signaling is required for vertebrate axial elongation.

Retinoic acid receptor gamma 2 (RARγ2) is the major RAR isoform expressed throughout the caudal axial progenitor domain in vertebrates. During a microarray screen to identify RAR targets, we identified a subset of genes that pattern caudal structures or promote axial elongation and are upregulated by increased RAR-mediated repression. Previous studies have suggested that RAR is present in the caudal domain, but is quiescent until its activation in late stage embryos terminates axial elongation. By contrast, we show here that RARγ2 is engaged in all stages of axial elongation, not solely as a terminator of axial growth. In the absence of RA, RARγ2 represses transcriptional activity in vivo and maintains the pool of caudal progenitor cells and presomitic mesoderm. In the presence of RA, RARγ2 serves as an activator, facilitating somite differentiation. Treatment with an RARγ-selective inverse agonist (NRX205099) or overexpression of dominant-negative RARγ increases the expression of posterior Hox genes and that of marker genes for presomitic mesoderm and the chordoneural hinge. Conversely, when RAR-mediated repression is reduced by overexpressing a dominant-negative co-repressor (c-SMRT), a constitutively active RAR (VP16-RARγ2), or by treatment with an RARγ-selective agonist (NRX204647), expression of caudal genes is diminished and extension of the body axis is prematurely terminated. Hence, gene repression mediated by the unliganded RARγ2-co-repressor complex constitutes a novel mechanism to regulate and facilitate the correct expression levels and spatial restriction of key genes that maintain the caudal progenitor pool during axial elongation in Xenopus embryos.

Gene expression response to EWS-FLI1 in mouse embryonic cartilage.

Ewing's sarcoma is a rare bone tumor that affects children and adolescents. We have recently succeeded to induce Ewing's sarcoma-like small round cell tumor in mice by expression of EWS-ETS fusion genes in murine embryonic osteochondrogenic progenitors. The Ewing's sarcoma precursors are enriched in embryonic superficial zone (eSZ) cells of long bone. To get insights into the mechanisms of Ewing's sarcoma development, gene expression profiles between EWS-FLI1-sensitive eSZ cells and EWS-FLI1-resistant embryonic growth plate (eGP) cells were compared using DNA microarrays. Gene expression of eSZ and eGP cells (total, 30 samples) was evaluated with or without EWS-FLI1 expression 0, 8 or 48 h after gene transduction. Our data provide useful information for gene expression responses to fusion oncogenes in human sarcoma.

Oral administration of pentachlorophenol induces interferon signaling mRNAs in C57BL/6 male mouse liver.

Pentachlorophenol (PCP) was monitored for transcriptome responses in adult mouse liver at 2, 4, 8 and 24 hr after a single oral administration at four dose levels, 0, 10, 30 and 100 mg/kg. The expression data obtained using Affymetrix GeneChip MOE430 2.0 were absolutized by the Percellome method and expressed as three dimensional (3D) surface graphs with axes of time, dose and copy numbers of mRNA per cell. We developed the programs RSort, for comprehensive screening of the 3D surface data and PercellomeExploror for cross-referencing and confirmed the significant responses by visual inspection. In the first 8 hr, approximately 100 probe sets (PSs) related to PXR/SXR and Cyp2a4 and other metabolic enzymes were induced whereas Fos and JunB were suppressed. At 24 hr, about 1,200 PSs were strongly induced. We cross-referenced the Percellome database consisting of 111 chemicals on the liver transcriptome and found that about half of the PSs belonged to the metabolic pathways including Nrf2-mediated oxidative stress response networks shared with some of the 111 chemicals. The other half of the induced genes were interferon signaling network genes (ISG) and their induction was unique to PCP. Toll like receptors and other pattern recognition receptors, interferon regulatory factors and interferon alpha itself were included but inflammatory cytokines were not induced. In summary, these data indicated that functional symptoms of PCP treatment, such as hyperthermia and profuse sweating might be mediated by the ISG rather than the previously documented mitochondrial uncoupling mechanism. PCP might become a hint for developing low molecular weight orally available interferon mimetic drugs following imiquimod and RO4948191 as agonists of toll-like receptor and interferon receptor.

Minichromosome maintenance 2 bound with retroviral Gp70 is localized to cytoplasm and enhances DNA-damage-induced apoptosis.

The interaction of viral proteins with host-cellular proteins elicits the activation of cellular signal transduction pathways and possibly leads to viral pathogenesis as well as cellular biological events. Apoptotic signals induced by DNA-damage are remarkably up-regulated by Friend leukemia virus (FLV) exclusively in C3H hosts; however, the mechanisms underlying the apoptosis enhancement and host-specificity are unknown. Here, we show that C3H mouse-derived hematopoietic cells originally express higher levels of the minichromosome maintenance (MCM) 2 protein than BALB/c- or C57BL/6-deriverd cells, and undergo more frequent apoptosis following doxorubicin-induced DNA-damage in the presence of the FLV envelope protein gp70. Dual transfection with gp70/Mcm2 reproduced doxorubicin-induced apoptosis even in BALB/c-derived 3T3 cells. Immunoprecipitation assays using various deletion mutants of MCM2 revealed that gp70 bound to the nuclear localization signal (NLS) 1 (amino acids 18-24) of MCM2, interfered with the function of NLS2 (amino acids 132-152), and suppressed the normal nuclear-import of MCM2. Cytoplasmic MCM2 reduced the activity of protein phosphatase 2A (PP2A) leading to the subsequent hyperphosphorylation of DNA-dependent protein kinase (DNA-PK). Phosphorylated DNA-PK exhibited elevated kinase activity to phosphorylate P53, thereby up-regulating p53-dependent apoptosis. An apoptosis-enhancing domain was identified in the C-terminal portion (amino acids 703-904) of MCM2. Furthermore, simultaneous treatment with FLV and doxorubicin extended the survival of SCID mice bearing 8047 leukemia cells expressing high levels of MCM2. Thus, depending on its subcellular localization, MCM2 plays different roles. It participates in DNA replication in the nucleus as shown previously, and enhances apoptosis in the cytoplasm.

Development of humanized steroid and xenobiotic receptor mouse by homologous knock-in of the human steroid and xenobiotic receptor ligand binding domain sequence.

The human steroid and xenobiotic receptor (SXR), (also known as pregnane X receptor PXR, and NR1I2) is a low affinity sensor that responds to a variety of endobiotic, nutritional and xenobiotic ligands. SXR activates transcription of Cytochrome P450, family 3, subfamily A (CYP3A) and other important metabolic enzymes to up-regulate catabolic pathways mediating xenobiotic elimination. One key feature that demarcates SXR from other nuclear receptors is that the human and rodent orthologues exhibit different ligand preference for a subset of toxicologically important chemicals. This difference leads to a profound problem for rodent studies to predict toxicity in humans. The objective of this study is to generate a new humanized mouse line, which responds systemically to human-specific ligands in order to better predict systemic toxicity in humans. For this purpose, the ligand binding domain (LBD) of the human SXR was homologously knocked-in to the murine gene replacing the endogenous LBD. The LBD-humanized chimeric gene was expressed in all ten organs examined, including liver, small intestine, stomach, kidney and lung in a pattern similar to the endogenous gene expressed in the wild-type (WT) mouse. Quantitative reverse transcription-polymerase chain reaction (RT-PCR) analysis showed that the human-selective ligand, rifampicin induced Cyp3a11 and Carboxylesterase 6 (Ces6) mRNA expression in liver and intestine, whereas the murine-selective ligand, pregnenolone-16-carbonitrile did not. This new humanized mouse line should provide a useful tool for assessing whole body toxicity, whether acute, chronic or developmental, induced by human selective ligands themselves and subsequently generated metabolites that can trigger further toxic responses mediated secondarily by other receptors distributed body-wide.

Genistein promotes DNA demethylation of the steroidogenic factor 1 (SF-1) promoter in endometrial stromal cells.

It has recently been demonstrated that genistein (GEN), a phytoestrogen in soy products, is an epigenetic modulator in various types of cells; but its effect on endometrium has not yet been determined. We investigated the effects of GEN on mouse uterine cells, in vivo and in vitro. Oral administration of GEN for 1 week induced mild proliferation of the endometrium in ovariectomized (OVX) mice, which was accompanied by the induction of steroidogenic factor 1 (SF-1) gene expression. GEN administration induced demethylation of multiple CpG sites in the SF-1 promoter; these sites are extensively methylated and thus silenced in normal endometrium. The GEN-mediated promoter demethylation occurred predominantly on the luminal side, as opposed to myometrium side, indicating that the epigenetic change was mainly shown in regenerated cells. Primary cultures of endometrial stromal cell colonies were screened for GEN-mediated alterations of DNA methylation by a high-resolution melting (HRM) method. One out of 20 colony-forming cell clones showed GEN-induced demethylation of SF-1. This clone exhibited a high proliferation capacity with continuous colony formation activity through multiple serial clonings. We propose that only a portion of endometrial cells are capable of receiving epigenetic modulation by GEN.

CITED2 is activated in ulcerative colitis and induces p53-dependent apoptosis in response to butyric acid.

BACKGROUND: In ulcerative colitis (UC), Fusobacterium varium is significantly detected in patients' mucosa, and butyric acid (BA), abundantly produced by the bacterium, activates the p53 system and induces epithelial apoptosis, as we previously reported. However, factors active in the link between BA and p53 have yet to be clarified. Here, we identified a gene activated by BA specifically in UC-associated cancer cell lines and ascertained the mechanism of its activation of p53. METHODS: cDNA microarray analysis based on the Percellome (per cell normalization) method was performed on BA-stimulated UC-associated cancers and sporadic colorectal cancer cell lines under conditions mimicking colonic epithelium UC. For validation of microarray results, molecular, biochemical, and histopathological analyses were performed. RESULTS: We found the CBP/p300-interacting transactivator with glutamic acid/asparagine-rich carboxy-terminal domain 2 (CITED2) to be specifically upregulated in UC-associated cancer cell lines by BA treatment, at both mRNA and protein expression levels. CITED2 could be shown to induce p53 acetylation and p53-dependent apoptosis, accompanied by binding of CBP/p300. BA-dependent apoptosis was suppressed by an inhibitor of monocarboxylate transporter-1 and an siRNA for p53. In inflammatory foci of UC, histologically evident inflammatory activity and CITED2 expression were significantly correlated. CONCLUSIONS: CITED2 was identified as UC-associated protein by cDNA microarray based on the Percellome method under UC-mimicking conditions in vitro. CITED2 activation may induce mucosal apoptosis and erosion by activating p53 and thus play a critical role in linking enteric bacteria with mucosal inflammation in UC.

NANOS2 interacts with the CCR4-NOT deadenylation complex and leads to suppression of specific RNAs.

Nanos is one of the evolutionarily conserved proteins implicated in germ cell development. We have previously shown that NANOS2 plays an important role in both the maintenance and sexual development of germ cells. However, the molecular mechanisms underlying these events have remained elusive. In our present study, we found that NANOS2 localizes to the P-bodies, known centers of RNA degradation that are abundantly accumulated in male gonocytes. We further identified by immunoprecipitation that the components of the CCR4-NOT deadenylation complex are NANOS2-interacting proteins and found that NANOS2 promotes the localization of CNOT proteins to P-bodies in vivo. We also elucidated that the NANOS2/CCR4-NOT complex has deadenylase activity in vitro, and that some of the RNAs implicated in meiosis interact with NANOS2 and are accumulated in its absence. Our current data thus indicate that the expression of these RNA molecules is normally suppressed via a NANOS2-mediated mechanism. We propose from our current findings that NANOS2-interacting RNAs may be recruited to P-bodies and degraded by the enzymes contained therein through NANOS2-mediated deadenylation.

Intrauterine environment-genome interaction and children's development (2): Brain structure impairment and behavioral disturbance induced in male mice offspring by a single intraperitoneal administration of domoic acid (DA) to their dams.

To demonstrate induction of delayed central nervous toxicity by disturbing neuronal activities in the developing brain, we administered a single intraperitoneal dose of domoic acid (DA; 1 mg/kg), a potent glutamate receptor agonist, to pregnant female mice at the gestational day of 11.5, 14.5 or 17.5. The dams had recovered from acute symptoms within 24 hr, followed by normal delivery, feeding and weaning. All male offspring mice after weaning were apparently normal in response to handlers during cage maintenance, body weight measurement and to mate mice in group housing conditions. At the age of 11 weeks, our neurobehavior testing battery revealed severe impairment of learning and memory with serious deviances of anxiety-related behaviors. The developed brain of prenatally exposed mice showed myelination failure and the overgrowth of neuronal processes of the limbic cortex neurons. This study indicates that the temporal disturbance of neurotransmission of the developing brain induces irreversible structural and functional damage to offspring which becomes monitorable in their adulthood by a proper battery of neurobehavioral tests.

Glycolytic inhibition by mutation of pyruvate kinase gene increases oxidative stress and causes apoptosis of a pyruvate kinase deficient cell line.

OBJECTIVE: SLC3 is a Friend erythroleukemic cell line established from the Pk-1(slc) mouse, a mouse model of red blood cell type-pyruvate kinase (R-PK) deficiency. This study was aimed to elucidate the mechanisms attributing to apoptosis induced by R-PK deficiency. MATERIALS AND METHODS: SLC3 and a control Friend cell line, CBA2, were cultured in a condition of glucose deprivation or supplementation with 2-deoxyglucose, and apoptosis was detected by annexin V. We established two stable transfectants of SLC3 cells with human R-PK cDNA, and examined the effect of R-PK on an apoptotic feature by cell cycle analysis. Intracellular oxidation was measured with 2',7'-dichlorofluorescin diacetate. DNA microarray analysis was performed to examine gene-expression profiles between the two transfectants and parental SLC3. RESULTS: SLC3 was more susceptible than CBA2 to apoptosis induced by glycolytic inhibition. The forced expression of R-PK significantly decreased cells at the sub G0/G1 stage in an expression-level dependent manner. Microarray analysis showed that proapoptotic genes, such as Bad, Bnip3, and Bnip3l, were downregulated in the transfectants. In addition, peroxiredoxin 1 (Prdx1) and other antioxidant genes, such as Cat, Txnrd1, and Glrx1 were also downregulated. A significant decrease of dichlorofluorescein fluorescence was observed by R-PK expression. Preincubation with a glutathione precursor showed a significant decrease of apoptosis. CONCLUSION: These results indicated that glycolytic inhibition by R-PK gene mutation augmented oxidative stress in the Friend erythroleukemia cell, leading to activation of hypoxia-inducible factor-1 as well as downstream proapoptotic gene expression. Thus, R-PK plays an important role as an antioxidant during erythroid differentiation.

Transgenic rescue of hemolytic anemia due to red blood cell pyruvate kinase deficiency.

BACKGROUND AND OBJECTIVES: Red blood cell pyruvate kinase (R-PK) deficiency is the most common glycolytic enzyme defect associated with hereditary non-spherocytic hemolytic anemia. Cases with the most severe deficiency die in the peri- or neonatal period and no specific therapy exists at present. To test whether the targeted overexpression of the normal R-PK gene in erythroid cells could reduce hemolysis in R-PK mutant mice, we performed a genetic rescue study using human R-PK transgenic mice. DESIGN AND METHODS: Human R-PK promoter driven with human mLCR of the human b-globin locus was used for the erythroid-specific expression of human R-PK in murine erythrocytes. The transgenic lines were mated with homozygous R-PK mutant mice and subsequently backcrossed. Mutant homozygotes with the mLCR-R-PK transgene were examined for any therapeutic effects of transgene expression. RESULTS: Two PK transgenic lines, hRPK_lo and hRPK_hi, were obtained. R-PK activity of the transgenic mice reached as high as three times that of the animals with the endogenous PK gene. Overexpression of human R-PK in the homozygous mutant mice successfully reduced hemolytic anemia. Improvements of hemolysis were evaluated by hemoglobin concentration, reticulocyte count, and spleen weight, which showed significant correlations with the levels of expression of the transgene. Recovery from metabolic disturbance in mutant red blood cells was shown as normalized concentrations of the glycolytic intermediates upstream of PK. In addition, there was a remarkable negative correlation between R-PK activity and the number of TUNEL-positive erythroid progenitors in the spleen. INTERPRETATION AND CONCLUSIONS: These results indicate that overexpression of the wild-type PK gene in mutant erythroid cells ameliorates both erythroid apoptosis and the shortened red blood cell lifespan observed in PK mutant mice. It is likely that the level of transgene expression required to achieve evident therapeutic effects should be equivalent to or more than that of the endogenous PK gene. This gene-addition strategy may be suitable for clinical application if there is a high level of transgene expression of R-PK in erythroid progenitors/red blood cells.

Gene expression profiles in T24 human bladder carcinoma cells by inhibiting an L-type amino acid transporter, LAT1.

Inhibition of LAT1 (L-type amino acid transporter 1) activity in tumor cells could be effective in the inhibition of tumor cell growth by depriving tumor cells of essential amino acids. Because of the high level of expression of LAT1 in tumor cells, LAT1 inhibitors would be useful for anticancer therapy in suppressing tumor growth without affecting normal tissues. In recent years, cDNA microarray technique is useful technology for anticancer drug development. It allows identifying and characterizing new targets for developments in cancer drug therapy through the understanding genes involved in drug action. The present study was designed to investigate gene expression profile induced by LAT1 inhibitor using gene chip technology. Human bladder carcinoma cells (T24 cells) were treated with classical system L inhibitor 2-aminobicyclo-(2, 2, 1)-heptane-2-carboxylic acid (BCH). Gene chip experiment was applied for treated and untreated cells after 3 and 12 h. Two independent experiments with a high degree of concordance identified the altered expression of 151 and 200 genes after 3 and 12 h BCH treatment. Among these genes, 132 and 13 were up-regulated and 19 and 187 were down-regulated by 3 and 12 h BCH treatment respectively. We found that BCH affected the expression of a large number of genes that are related to the control of cell survival and physiologic behaviors. These data are useful for understanding of intracellular signaling of cell growth inhibition induced by LAT1 inhibitors as candidate for anticancer drug therapy.

Activation of Notch1 signaling in cardiogenic mesoderm induces abnormal heart morphogenesis in mouse.

Notch signaling is implicated in many developmental processes. In our current study, we have employed a transgenic strategy to investigate the role of Notch signaling during cardiac development in the mouse. Cre recombinase-mediated Notch1 (NICD1) activation in the mesodermal cell lineage leads to abnormal heart morphogenesis, which is characterized by deformities of the ventricles and atrioventricular (AV) canal. The major defects observed include impaired ventricular myocardial differentiation, the ectopic appearance of cell masses in the AV cushion, the right-shifted interventricular septum (IVS) and impaired myocardium of the AV canal. However, the fates of the endocardium and myocardium were not disrupted in NICD1-activated hearts. One of the Notch target genes, Hesr1, was found to be strongly induced in both the ventricle and the AV canal of NICD1-activated hearts. However, a knockout of the Hesr1 gene from NICD-activated hearts rescues only the abnormality of the AV myocardium. We searched for additional possible targets of NICD1 activation by GeneChip analysis and found that Wnt2, Bmp6, jagged 1 and Tnni2 are strongly upregulated in NICD1-activated hearts, and that the activation of these genes was also observed in the absence of Hesr1. Our present study thus indicates that the Notch1 signaling pathway plays a suppressive role both in AV myocardial differentiation and the maturation of the ventricular myocardium.