Evaluation of Collection and Processing Conditions for Gene Expression Analysis Using Human Myeloid Cells.

Background: The population of blast cells among peripheral blood mononuclear cells (PBMCs) obtained from patients is a desirable specimen for analyzing gene expression in diseases including acute myeloid leukemia. Although the enrichment of blast cells often needs to be performed at a central laboratory, acceptable conditions for sample transport from clinical sites remain to be established. Methods: We evaluated storage temperature, duration, and tube type before initiating sample processing for the analysis of cluster of differentiation (CD)33+ myeloid cells among PBMCs as an alternative to CD34+/CD33+ blast cells. Results: CD33+ myeloid cells were successfully purified by MACS. The cell viability and the RNA integrity were sustained during storage up to 48 hours before sample processing. Storage at 4°C had minimal effects on gene expression, whereas storage at room temperature induced the senescence pathway, characterized by the expression of stress-inducible genes. A CPT tube was also better than an ethylenediaminetetraacetic acid tube for minimizing gene expression change. Conclusions: Our study provided important clues for establishing a sample handling approach for gene expression analysis with purified cell fractions from human PBMCs. To keep the variation of gene expression to a minimum, samples should be delivered at 4°C within 48 hours before processing.

An exploratory assessment of the applicability of direct-to-consumer genetic testing to translational research in Japan.

OBJECTIVE: In order to assess the applicability of a direct-to-consumer (DTC) genetic testing to translational research for obtaining new knowledge on relationships between drug target genes and diseases, we examined possibility of these data by associating SNPs and disease related phenotype information collected from healthy individuals. RESULTS: A total of 12,598 saliva samples were collected from the customers of commercial service for SNPs analysis and web survey were conducted to collect phenotype information. The collected dataset revealed similarity to the Japanese data but distinguished differences to other populations of all dataset of the 1000 Genomes Project. After confirmation of a well-known relationship between ALDH2 and alcohol-sensitivity, Phenome-Wide Association Study (PheWAS) was performed to find association between pre-selected drug target genes and all the phenotypes. Association was found between GRIN2B and multiple phenotypes related to depression, which is considered reliable based on previous reports on the biological function of GRIN2B protein and its relationship with depression. These results suggest possibility of using SNPs and phenotype information collected from healthy individuals as a translational research tool for drug discovery to find relationship between a gene and a disease if it is possible to extract individuals in pre-disease states by properly designed questionnaire.

Multicomponent Coupling Reaction Using Arynes: Synthesis of Xanthene Derivatives.

One-pot synthesis of xanthene derivatives was achieved by a route involving the cascade three-component coupling reaction of arynes with DMF and active methylenes followed by the SN2' reaction of three-component coupling products with thiols. The reactivity of three-component coupling products toward nucleophiles and the further conversion of oxygen heterocycles allowing facile incorporation of structural variety were studied.

Characterization and thermal isomerization of (all-E)-lycopene.

A large amount of (all-E)-lycopene was successfully purified from tomato paste using an improved method that included a procedure to wash crystalline powder with acetone. The total yield of the pure (all-E) form was at least 30%. The melting point of (all-E)-lycopene was determined to be 176.35 °C by differential scanning calorimetry (DSC) measurements. Bathochromic shifts were observed in the absorption maxima of all solvents tested (at most a 36 nm shift for λ2 in carbon disulfide, as was observed in hexane) and were accompanied by absorbance decreases, namely, a hypochromic effect, showing a higher correlation between the position and the intensity of the main absorption bands. This bathochromic shift was dependent upon the polarizability of the solvent rather than its polarity. The structure of (all-E)-lycopene in CDCl3 and C6D6 was identified on the basis of one- and two-dimensional nuclear magnetic resonance (NMR) spectra, including (1)H and (13)C NMR, homonuclear correlation spectroscopy ((1)H-(1)H COSY), heteronuclear multiple-quantum coherence (HMQC), and heteronuclear multiple-bond connectivity (HMBC). The rate constants of the decrease in (all-E)-lycopene with hexane and benzene were calculated to be 3.19 × 10(-5) and 3.55 × 10(-5) s(-1), respectively. The equilibrium constants between (all-E) and (13Z) isomers were estimated to be 0.29 in hexane and 0.31 in benzene, respectively, from the point at which the amount of (13Z)-lycopene reached its maximum.

Sex and circadian modulatory effects on rat liver as assessed by transcriptome analyses.

The present study was designed to fully uncover sex and circadian modulatory effects on rat liver. Hepatic transcriptome analyses were performed at 4 hr intervals of a day-night cycle using young adult male and female rats. Sexually dimorphic genes, which were identified by a cross-sex comparison of time series data, included representative sex-predominant genes such as male- or female-predominant cytochrome P450 subfamilies (Cyp2c11, Cyp2c12, Cyp2c13, and Cyp3a2), sulfotransferases, and glutathione S-transferase Yc2. The identified sexually dimorphic genes were over-represented in the metabolism of retinols, xenobiotics, linoleic acids, or androgen and estrogen, or bile acid biosynthesis. Furthermore, transcription factor targets modeling suggested that transcription factors SP1, hepatocyte nuclear factor 4-alpha (HNF4-alpha), and signal transducer and activator of transcription 5b (STAT5b) serve as core nodes in the regulatory networks. On the other hand, Fourier transform analyses extracted universal circadian-regulated genes in both sexes. The circadian-regulated genes included clock or clock-controlled genes such as aryl hydrocarbon receptor nuclear translocator-like (Arntl), period homolog 2 (Per2), and D site albumin promoter binding protein (Dbp). The extracted cyclic genes were over-represented in major tissue activities, e.g. the urea cycle and the metabolism of amino acids, fatty acids, or glucose, indicating that the major liver functions are under circadian control. The transcription factor targets modeling suggested that transcription factors SP1, HNF4-alpha, and c-Myc proto-oncogene protein (c-MYC) serve as major hubs in the circadian-regulatory gene networks. Interestingly, transcription factors SP1 and HNF4-alpha are likely to orchestrate not only sexually dimorphic, but also circadian-regulated genes even though each criterion was rather mutually exclusive. This suggests the cross-talk between those regulations. Sexual dimorphism is likely to interact with circadian rhythmicity via overlapping gene regulatory networks on rat liver.