Short-hairpin RNA library: identification of therapeutic partners for gefitinib-resistant non-small cell lung cancer.

Somatic mutations of the epidermal growth factor receptor often cause resistance to therapy with tyrosine kinase inhibitor in non-small cell lung cancer (NSCLC). In this study, we aimed to identify partner drugs and pathways that can induce cell death in combination with gefitinib in NSCLC cells. We undertook a genome-wide RNAi screen to identify synthetic lethality with gefitinib in tyrosine kinase inhibitor resistant cells. The screening data were utilized in different approaches. Firstly, we identified PRKCSH as a candidate gene, silencing of which induces apoptosis of NSCLC cells treated with gefitinib. Next, in an in silico gene signature pathway analysis of shRNA library data, a strong correlation of genes involved in the CD27 signaling cascade was observed. We showed that the combination of dasatinib (NF-κB pathway inhibitor) with gefitinib synergistically inhibited the growth of NSCLC cells. Lastly, utilizing the Connectivity Map, thioridazine was identified as a top pharmaceutical perturbagen. In our experiments, it synergized with gefitinib to reduce p-Akt levels and to induce apoptosis in NSCLC cells. Taken together, a pooled short-hairpin library screen identified several potential pathways and drugs that can be therapeutic targets for gefitinib resistant NSCLC

Divergence of male courtship displays between sympatric forms of anadromous threespine stickleback

Courtship displays are an important component of animal reproduction, and divergence in these displays can play an integral role in promoting or maintaining reproductive isolation between species. The courtship behaviour of the threespine stickleback (Gasterosteus aculeatus) has been extensively characterized. In Japan, there are two lineages of threespine stickleback that are genetically differentiated and reproductively isolated when found in regions of sympatry. We have previously shown that males of the Pacific Ocean lineage perform the zig-zag dance, while sympatric males of the Japan Sea lineage perform a different dance, which we have termed the rolling dance (Kitano et al., 2007, Biol. J. Linn. Soc. 91: 671-685). As a first step towards understanding the role of the courtship display in female mate choice and sexual isolation between this sympatric pair, we conducted a more detailed analysis of divergence between the courtship displays of the Pacific Ocean and Japan Sea males. Kinematic analysis revealed that the tempo of the zig-zag dance is two times faster than the tempo of the rolling dance. A detailed analysis of head movements during the courtship dance revealed that the Japan Sea males erect their gill covers, extend their red throats, and open their mouths more frequently during the rolling dance than the Pacific Ocean males do during the zig-zag dance. These results demonstrate that there is extensive divergence between sympatric Pacific Ocean and Japan Sea males in both the motor patterns and the tempo of their courtship displays. Thus, the Japanese sympatric stickleback pair provides a good system to study the role of courtship behaviour in speciation, as well as the genetic mechanisms that underlie the divergence of kinematics and motor patterns in courtship behaviour

Phenotypic divergence and reproductive isolation between sympatric forms of Japanese threespine sticklebacks

The threespine stickleback (Gasterosteus aculeatus) species complex is well suited for identifying the types of phenotypic divergence and isolating barriers that contribute to reproductive isolation at early stages of speciation. In the present study, we characterize the patterns of genetic and phenotypic divergence as well as the types of isolating barriers that are present between two sympatric pairs of threespine sticklebacks in Hokkaido, Japan. One sympatric pair consists of an anadromous and a resident freshwater form and shows divergence in body size between the forms, despite the lack of genetic differentiation between them. The second sympatric pair consists of two anadromous forms, which originated before the last glacial period and are currently reproductively isolated. These two anadromous forms have diverged in many morphological traits as well as in their reproductive behaviours. Both sexual isolation and hybrid male sterility contribute to reproductive isolation between the anadromous species pair. We discuss the shared and unique aspects of phenotypic divergence and reproductive isolation in the Japanese sympatric pairs compared with postglacial stickleback species pairs. Further studies of these divergent species pairs will provide a deeper understanding of the mechanisms of speciation in sticklebacks. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society, 2007, 91, 671–685

Utilization of Genomic Signatures to Identify Phenotype-Specific Drugs

Genetic and genomic studies highlight the substantial complexity and heterogeneity of human cancers and emphasize the general lack of therapeutics that can match this complexity. With the goal of expanding opportunities for drug discovery, we describe an approach that makes use of a phenotype-based screen combined with the use of multiple cancer cell lines. In particular, we have used the NCI-60 cancer cell line panel that includes drug sensitivity measures for over 40,000 compounds assayed on 59 independent cells lines. Targets are cancer-relevant phenotypes represented as gene expression signatures that are used to identify cells within the NCI-60 panel reflecting the signature phenotype and then connect to compounds that are selectively active against those cells. As a proof-of-concept, we show that this strategy effectively identifies compounds with selectivity to the RAS or PI3K pathways. We have then extended this strategy to identify compounds that have activity towards cells exhibiting the basal phenotype of breast cancer, a clinically-important breast cancer characterized as ER-, PR-, and Her2- that lacks viable therapeutic options. One of these compounds, Simvastatin, has previously been shown to inhibit breast cancer cell growth in vitro and importantly, has been associated with a reduction in ER-, PR- breast cancer in a clinical study. We suggest that this approach provides a novel strategy towards identification of therapeutic agents based on clinically relevant phenotypes that can augment the conventional strategies of target-based screens

Urinary adiponectin as a biomarker for DKD

We previously developed two immune complex transfer enzyme immunoassays (ICT-EIA) to measure total adiponectin (T-AN) and high molecular weight adiponectin (H-AN) in urine and have verified their usefulness as biomarkers for diabetic kidney disease. In this study, we developed T-AN and H-AN assays using the sandwich EIA (Sand-EIA). The reactivities of Sand-EIAs were compared with ICT-EIAs by measuring size exclusion chromatography (SEC) fractions of urine and adiponectin standard. As a result, ICT-EIAs showed higher macromolecular specificity. We then analyzed the molecular profile of adiponectin in the urine of 5 patients with different eGFR stages by measuring SEC fractions of urine. The results showed that smaller adiponectin correlated relatively well with eGFR stage. Finally, because SEC is time-consuming, we investigated that the ratio of T-ANs by Sand-EIA and ICT-EIA could be a good indicator of the monomer adiponectin. The ratio was evaluated using 77 urine samples from patients with diabetes and showed a significant decrease at an earlier stage compared with other biomarkers. In conclusion, we demonstrated a new index to estimate monomer adiponectin in urine by using Sand-EIA and ICT-EIA, and urinary monomer adiponectin can be a good early indicator of deterioration of renal function in diabetic patients

Regulation of Id2 expression by CCAAT/enhancer binding protein β

Mice deficient for Id2, a negative regulator of basic helix–loop–helix (bHLH) transcription factors, exhibit a defect in lactation due to impaired lobuloalveolar development during pregnancy, similar to the mice lacking the CCAAT enhancer binding protein (C/EBP) β. Here, we show that Id2 is a direct target of C/EBPβ. Translocation of C/EBPβ into the nucleus, which was achieved by using a system utilizing the fusion protein between C/EBPβ and the ligand-binding domain of the human estrogen receptor (C/EBPβ-ERT), demonstrated the rapid induction of endogenous Id2 expression. In reporter assays, transactivation of the Id2 promoter by C/EBPβ was observed and, among three potential C/EBPβ binding sites found in the 2.3 kb Id2 promoter region, the most proximal element was responsible for the transactivation. Electrophoretic mobility shift assay (EMSA) identified this element as a core sequence to which C/EBPβ binds. Chromatin immunoprecipitation (ChIP) furthermore confirmed the presence of C/EBPβ in the Id2 promoter region. Northern blotting showed that Id2 expression in C/EBPβ-deficient mammary glands was reduced at 10 days post coitus (d.p.c.), compared with that in wild-type mammary glands. Thus, our data demonstrate that Id2 is a direct target of C/EBPβ and provide insight into molecular mechanisms underlying mammary gland development during pregnancy

Reverse evolution of armor plates in the threespine stickleback.

Faced with sudden environmental changes, animals must either adapt to novel environments or go extinct. Thus, study of the mechanisms underlying rapid adaptation is crucial not only for the understanding of natural evolutionary processes but also for the understanding of human-induced evolutionary change, which is an increasingly important problem [1-8]. In the present study, we demonstrate that the frequency of completely plated threespine stickleback fish (Gasterosteus aculeatus) has increased in an urban freshwater lake (Lake Washington, Seattle, Washington) within the last 40 years. This is a dramatic example of "reverse evolution,"[9] because the general evolutionary trajectory is toward armor-plate reduction in freshwater sticklebacks [10]. On the basis of our genetic studies and simulations, we propose that the most likely cause of reverse evolution is increased selection for the completely plated morph, which we suggest could result from higher levels of trout predation after a sudden increase in water transparency during the early 1970s. Rapid evolution was facilitated by the existence of standing allelic variation in Ectodysplasin (Eda), the gene that underlies the major plate-morph locus [11]. The Lake Washington stickleback thus provides a novel example of reverse evolution, which is probably caused by a change in allele frequency at the major plate locus in response to a changing predation regime

Metabolomic Evaluation of the Quality of Leaf Lettuce Grown in Practical Plant Factory to Capture Metabolite Signature

Vegetables produce metabolites that affect their taste and nutritional value and compounds that contribute to human health. The quality of vegetables grown in plant factories under hydroponic cultivation, e.g., their sweetness and softness, can be improved by controlling growth factors including the temperature, humidity, light source, and fertilizer. However, soil is cheaper than hydroponic cultivation and the visual phenotype of vegetables grown under the two conditions is different. As it is not clear whether their metabolite composition is also different, we studied leaf lettuce raised under the hydroponic condition in practical plant factory and strictly controlled soil condition. We chose two representative cultivars, “black rose” (BR) and “red fire” (RF) because they are of high economic value. Metabolite profiling by comprehensive gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS) resulted in the annotation of 101 metabolites from 223 peaks detected by GC-MS; LC-MS yielded 95 peaks. The principal component analysis (PCA) scatter plot showed that the most distinct separation patterns on the first principal component (PC1) coincided with differences in the cultivation methods. There were no clear separations related to cultivar differences in the plot. PC1 loading revealed the discriminant metabolites for each cultivation method. The level of amino acids such as lysine, phenylalanine, tryptophan, and valine was significantly increased in hydroponically grown leaf lettuce, while soil-cultivation derived leaf lettuce samples contained significantly higher levels of fatty-acid derived alcohols (tetracosanol and hexacosanol) and lettuce-specific sesquiterpene lactones (lactucopicrin-15-oxalate and 15-deoxylactucin-8-sulfate). These findings suggest that the metabolite composition of leaf lettuce is primarily affected by its cultivation condition. As the discriminant metabolites reveal important factors that contribute to the nutritional value and taste characteristics of leaf lettuce, we performed comprehensive metabolite profiling to identify metabolite compositions, i.e., metabolite signature, that directly improve its quality and value

A Newly Established Cell Line from Normal Human Bone Responds to 1alpha, 25-Dihydroxyvitamin D3, Retinoic Acid and Transforming Growth Factor-beta1

We have recently established a new osteoblastic cell line, designated SV-HFO, from normal human bone by immortalization with simian virus 40. In the present study, we examined the effects of diffusive factors on the expression of osteoblastic phenotype in SV-HFO cell line. lα, 25-dihydroxyvitamin D? in-duced the expression of alkaline phosphatase (ALP) and osteocalcin. Retinoic acid down-regulated the expression of ALP, whereas it up-regulated the expres-sion of osteocalcin. Transforming growth factor-β?, reduced the expression of both osteoblastic properties. These effects were time- and dose-dependent. These results show that the SV-HFO cell line maintains responsiveness to these diffusive factors. This cell line is suitable model for studying both metabolism and multistep carcinogenesis of human bone