Co-active receptor tyrosine kinases mitigate the effect of FGFR inhibitors in FGFR1-amplified lung cancers with low FGFR1 protein expression.

Targeted therapies are effective in subsets of lung cancers with EGFR mutations and anaplastic lymphoma kinase (ALK) translocations. Large-scale genomics have recently expanded the lung cancer landscape with FGFR1 amplification found in 10-20% of squamous cell carcinomas (SCCs). However, the response rates have been low for biomarker-directed fibroblast growth factor receptor (FGFR) inhibitor therapy in SCC, which contrasts to the relatively high rates of response seen in EGFR mutant and ALK-translocated lung cancers treated with epidermal growth factor receptor (EGFR) inhibitors and ALK inhibitors, respectively. In order to better understand the low response rates of FGFR1-amplified lung cancers to FGFR inhibitors, relationships between gene copy number, mRNA expression and protein expression of FGFR1 were assessed in cell lines, tumor specimens and data from The Cancer Genome Atlas. The importance of these factors for the sensitivity to FGFR inhibitors was determined by analyzing drug screen data and conducting in vitro and in vivo experiments. We report that there was a discrepancy between FGFR1 amplification level and FGFR1 protein expression in a number of these cell lines, and the cancers with unexpectedly low FGFR1 expression were uniformly resistant to the different FGFR inhibitors. Further interrogation of the receptor tyrosine kinase activity in these discordant cell lines revealed co-activation of HER2 and platelet-derived growth factor receptor-α (PDGFRα) caused by gene amplification or ligand overexpression maintained phosphoinositide 3-kinase (PI3K) and MEK/ERK signaling even in the presence of FGFR inhibitor. Accordingly, co-inhibition of FGFR1 and HER2 or PDGFRα led to enhanced drug responses. In contrast, FGFR1-amplified high FGFR1 protein-expressing lung cancers are sensitive to FGFR inhibitor monotherapy by downregulating ERK signaling. Addition of a PI3K inhibitor to these high FGFR1 protein-expressing cancers further sensitized them to FGFR inhibitor. These data reveal that biomarker-directed trials for FGFR1-amplified SCC require assessment of FGFR1 protein expression and uncover novel therapeutic strategies for FGFR1-amplified SCC with low FGFR1 protein expression.

Increased plasma LIGHT levels in patients with atopic dermatitis.

LIGHT [the name of which is derived from 'homologous to lymphotoxins, exhibits inducible expression, competes with herpes simplex virus glycoprotein D for herpes simplex virus entry mediator (HVEM), and expressed by T lymphocytes'], is a member of the tumour necrosis factor superfamily that is involved in various inflammatory diseases. We aimed to estimate the relevance of plasma LIGHT levels as a biomarker for atopic dermatitis (AD). In order to understand the putative role of LIGHT in AD pathogenesis, we also investigate the effects of LIGHT on a monocytic cell line, human acute monocytic leukaemia cell line (THP-1). We examined plasma LIGHT levels, total serum IgE, serum value of CCL17 and peripheral blood eosinophil counts in patients with AD and healthy subjects. The effects of LIGHT on activation and apoptosis in THP-1 cells were also investigated. The plasma concentrations of LIGHT in AD patients were significantly higher than those in healthy individuals and the concentrations decreased as the symptoms were improved by treatment. The LIGHT plasma concentrations correlated with IgE levels and the Severity Scoring of AD (SCORAD) index. In addition, LIGHT stimulation increased expression of CD86 and induced production of interleukin-1ß in THP-1 cells. Apoptosis was inhibited, the Bcl-2 level increased and the caspase-3 level decreased in THP-1 cells stimulated with LIGHT, compared to unstimulated control cells. These results suggest that plasma LIGHT levels may be one of the promising biomarkers for AD.

Influence of leukotriene pathway polymorphisms on clinical responses to montelukast in Japanese patients with asthma.

WHAT IS KNOWN AND OBJECTIVE: Montelukast, a cysteinyl leukotriene receptor 1 antagonist, is safe and efficacious in patients with asthma. The mechanisms underlying the significant interpatient variability in response to montelukast are not clear but are believed to be, in part, because of genetic variability. METHODS: To examine the associations between polymorphisms in candidate genes in the leukotriene pathway and outcomes in patients with asthma on montelukast for 4-8 weeks, we evaluated the changes in peak expiratory flow (PEF), forced expiratory volume in 1 s (FEV(1·0) ) and patients' subjective symptom before and after montelukast treatment. DNA was collected from 252 Japanese participants. RESULTS AND DISCUSSION: Two single-nucleotide polymorphisms (SNPs) in the ALOX5 (rs2115819) and LTA4H (rs2660845) genes were successfully typed. There was no difference between members of the general population (n = 200) and patients (n = 52) in each genotype frequency. Significant associations were found between SNP genotypes in the LTA4H gene and changes in PEF and FEV(1·0) . The PEF and FEV(1·0) responses to montelukast in the A/A genotypes (n = 4) for the LTA4H SNP were significantly higher than those in the G allele carriers (A/G+G/G) (n = 17). WHAT IS NEW AND CONCLUSION: Despite the small sample size, our results suggest that genetic variation in leukotriene pathway candidate genes contributes to variability in clinical responses to montelukast in Japanese patients with asthma.

Gene expression-based pharmacodynamic biomarkers: the beginning of a new era in biomarker-driven anti-tumor drug development.

Pharmacodynamic (PD) biomarkers play a pivotal role in anti-tumor drug development as a biochemical measurement to estimate the level of drug interaction with the target, or to assess the downstream impact of its interaction with the target. Although immunohistochemistry (IHC)-based protein biomarkers have been conventionally used as PD biomarkers, gene expression-based PD biomarkers have recently emerged as quantitative biomarkers. This review introduces examples of gene expression-based mRNA biomarkers that have been validated in preclinical or clinical studies of several anti-tumor agents including HDAC, mTOR, and B-RAF inhibitors. The measurement of PD biomarker levels in tumors has proven to be ideal; however, in clinical studies, easily accessible surrogate tissues have been used for analysis. In the present review, we also discuss the advantages and disadvantages in using surrogate tissues, such as peripheral blood mononuclear cells (PBMCs), skin tissue, and circulating tumor cells, in the assessment of PD biomarkers. PD biomarkers are generally classified into two categories: 1) target engagement biomarkers and 2) early efficacy biomarkers. This classification depends on their respective distance from target intervention. The strategies used to identify and distinguish between these two types of PD biomarkers via expression profiling are also discussed. Finally, we propose two novel approaches for PD marker identification. One approach utilizes mRNA expression profiling of tumors prior to drug treatment rather than post-treatment samples. The second method involves the application of microRNA expression profiles to determine PD effects. In conclusion, the recent advances in mRNA and microRNA profiling and the identification of gene expression-based PD biomarkers may aid investigators to drive drug development through the establishment of quantitative PD effects.

Renal complications in two patients with dentatorubral-pallidoluysian atrophy.

Dentatorubral-pallidoluysian atrophy (DRPLA) is an autosomal dominant neurodegenerative disorder characterized by various combinations of myoclonus epilepsy, ataxia, choreoathetosis and dementia. No specific therapy has been established and renal complication is rare. We report two cases of DRPLA with renal complications. Hematuria and proteinuria had gradually progressed for 2 and 13 years in these patients. Renal biopsy findings revealed focal glomerulosclerosis in one case and end-stage kidney disease in the other case. Angiotensin-converting enzyme inhibitor and angiotensin receptor II antagonist were administered to both patients, resulting in improved proteinuria and preserved renal function in one patient, while renal function continued to deteriorate in the other patient. Although renal complication is rare in patients with DRPLA, the presence of renal disease has to be suspected in patients with persistent proteinuria.

RB silencing compromises the DNA damage-induced G2/M checkpoint and causes deregulated expression of the ECT2 oncogene.

As alterations in retinoblastoma (RB)/E2F pathway are commonly found in human cancers, the molecular mechanism underlying cell cycle deregulation caused by the mutations in the RB/E2F pathway needs to be investigated extensively. Compared with good understanding of RB/E2F functions in G1-S cell cycle progression, it is not fully understood how an abrogated RB pathway affects the G2-M phase of the cell cycle. Here, we report that disruption of RB accelerated G2-M progression in the presence of DNA damage by elevating the expression of a set of mitotic regulatory genes. We generated RB(+)- and (-)-matched cells using short hairpin RNA. In the RB(-) cells, the G2/M checkpoint mediated by a DNA-damaging agent was over-ridden. With microarray analysis, we found that the expression of key G2-M regulatory genes was upregulated in RB(-) cells. In particular, we demonstrated that the proto-oncogene ECT2 was directly regulated by E2Fs. Furthermore, suppression of ECT2 expression by small interfering RNA in RB(-) cells resulted in cytokinesis arrest, suggesting that RB(-) cells lack the regulation of E2F-mediated cytokinesis. These results indicate that aberrant ECT2 expression, observed in various human tumors, could be the direct result of RB/E2F pathway deficiency, thereby contributing to cell division in cancers.

Effect of serotonin on the differentiation of human monocytes into dendritic cells.

The local cytokine environment and presence of stimulatory signals determine whether monocytes acquire dendritic cell (DC) or macrophage characteristics and functions. Because enhanced platelet activation is reported in patients with many allergic disorders, such as atopic dermatitis, platelet-derived factors may influence monocytic differentiation into DC. In this study we examined the effect of serotonin, a prototypic mediator of allergic inflammation released mainly by activated platelets at the inflammatory site, on the granulocyte-macrophage colony-stimulating factor (GM-CSF) and interleukin (IL)-4-driven differentiation of monocytes into monocyte-derived DC. Monocytes from healthy adult donors were cultured with GM-CSF and IL-4 in the presence or absence of serotonin, and the phenotypes and function of these cells were analysed. In the presence of serotonin, monocytes differentiated into DC with reduced expression of co-stimulatory molecules and CD1a, whereas expression of CD14 was increased. These serotonin-treated DC exhibited significantly reduced stimulatory activity toward allogeneic T cells. However, these cells showed enhanced cytokine-producing capacity, including IL-10 but not IL-12. There was no significant difference between both types of DC in phagocytic activity. Experiments using agonists and antagonists indicated that serotonin 5-hydroxytryptamine (5-HT) induced the alteration of their phenotype and reduction in antigen-presenting capacity were mediated via 5-HTR(1/7). It is therefore suggested that serotonin-driven DC may have a regulatory function in the inflammatory process.

Advances in isolation and characterization of homogeneous cell populations using laser microdissection.

The isolation and characterization of homogeneous cell populations are of great importance for the analysis of gene expression, because normal tissues contain various types of cells, and the differences in the populations of isolated cells exert significant effects on gene expression analysis. Researchers have attempted to develop methods for the isolation of homogeneous cell populations, such as flow cytometry and mechanical dissection. However, the recent emergence of laser-assisted microdissection has revolutionized the isolation of single-cell populations from solid tissues. With the help of a cutting laser, laser microdissection can isolate tissues (cells) of interest without contamination from surrounding tissues with the microscopic visualization field. By combining laser microdissection and subsequent microarray technology, several studies have resulted in the identification of disease-related genes. In this review, we summarize the principle of laser microdissection and provide several successful examples of target-gene identification using the conventional method combining laser microdissection and microarray. Next, we discuss the practical drawbacks of the combinational method, such as the need for a large number of cells and the disturbance of the relative abundance of transcripts during RNA amplification. We introduce our modifications to combined laser microdissection and microarray for detection of disease-related genes; the technique is simple, yet practical and accurate. Finally, versatile applications of laser microdissection, not only to transcript expression analysis, but also to other genomics and proteomics analyses are, also presented.

Genomic localization of endogenous mobile CACTA family transposons in natural variants of Arabidopsis thaliana.

The differentiation between gene-rich and transposon-rich (gene-poor) regions is a common feature of plant genomes. This may be due to preferential integration of transposons into gene-poor regions or may be due to purifying selection against transposon insertion into gene-rich regions. We examined the distribution of a low-copy-number mobile subfamily of Arabidopsis CACTA transposons in the genomes of 19 natural variants (ecotypes) of A. thaliana, and compared that to the pattern of integrations induced in the laboratory by mutation of the DDM1 (Decrease in DNA Methylation) gene. Sequences similar to mobile CACTA1 copies were distributed among the ecotypes and showed high degrees of polymorphism in genomic localization. Despite the high level of polymorphism, the copy number was low in all the ecotypes examined, and the elements were localized preferentially in pericentromeric and transposon-rich regions. This contrasts with the pattern of transposition induced by the ddm1 mutation, in which the range of integration sites is less biased and the copy number frequently increases. Based on these observations, we discuss the possible contribution of natural selection and chromatin structure to the distribution of transposons.

Prevalence of positive anticardiolipin antibody in benign infantile convulsion.

We report six anticardiolipin antibody (aCL)-positive cases among 18 children with epilepsy showing various seizure types in our initial study. These six cases revealed normal coagulation tests. As three of these six cases involved benign infantile convulsion (BIC), we further investigated the high frequency of positive aCL-Immunoglobulin (Ig) G in BIC in our subsequent study of nine cases that included three cases from the previous study and an additional six BIC cases followed and/or diagnosed by co-author (T.K.). As a result, eight of nine BIC cases were positive for aCL-IgG and the values of aCL-IgG decreased over long-term observation in three of these cases. The frequency of positivity for aCL-IgG in BIC was obviously higher than that of controls. Based on these results, we suggest that some immunological responses may be responsible for the pathogenesis of BIC.

Vertical profiles of temperature and contaminant concentration in rooms ventilated by displacement with heat loss through room envelopes.

The purpose of this study is to examine the effect of heat loss through walls upon the gradients of temperature and contaminant concentration in room with displacement ventilation. It is known that conduction heat loss is governed by outside temperature, heat load inside the room, supply air temperature and overall heat transfer coefficient of walls. Experiments were conducted to measure the temperature gradient and the ventilation efficiency in the room ventilated by displacement ventilation with various combinations of heat load and temperature difference between supply air and outside air. In order to simulate the change of seasons, the supply air temperature was changed instead of the outside air temperature. The effect of supply air temperature and heat generation inside the room on the temperature gradient and the concentration of tracer gas were investigated through the experiments. As a result, it turned out that the higher the heat generation rate and the lower the supply temperature, the stronger the temperature stratification and the lower the concentration in the lower zone. Additionally, ventilation heat loss turned out to be a good index for assessing the concentration in the lower zone. Temperature differences of around 3 degrees C between supply air temperature and exhaust temperature are at least needed for displacement ventilation under the conditions of the experiment presented in this paper.

Identification of breast cancer resistant protein/mitoxantrone resistance/placenta-specific, ATP-binding cassette transporter as a transporter of NB-506 and J-107088, topoisomerase I inhibitors with an indolocarbazole structure.

The antitumor drugs NB-506 and J-107088 are potent topoisomerase I inhibitors with an indolocarbazole structure. To clarify the factors involved in resistance to these drugs, we established two NB-506-resistant mouse fibroblast cell lines (LY/NR1 and LY/NR2), a human colon carcinoma cell line (HCT116/NR1), and a lung cancer cell line (PC13/NR1). These cell lines were highly resistant to NB-506 and J-107088, and LY/NR2 cells showed markedly reduced accumulation and strong efflux of NB-506, suggesting activation of a drug efflux pump in the resistant cells. To identify the molecules responsible for efflux of NB-506, we compared the gene expressions of the mouse resistant LY/NR1 cells, LY/NR2 cells, and their parental cells by oligonucleotide microarray. Of 34,020 genes analyzed, we found that an ATP-binding cassette transporter BCRP/MXR/ABCP (BCRP) gene showed the highest increase in the expression, 31-fold higher in the LY/NR2-resistant cells than in their parental cells. The selective overexpression of this gene was also detected in the two human resistant cell lines, suggesting the involvement of breast cancer resistant protein (BCRP) in the resistance and efflux of these drugs. Finally, a PC-13 cell line transfected with BCRP expression vector displayed 22- and 17-fold resistance to NB-506 and J-107088 and enhanced efflux activity of J-107088. However, the transfectants were not resistant to mitoxantrone or topotecan, the drugs previously thought to be the substrates of BCRP. Thus, our study presents a novel mechanism of drug resistance mediated by BCRP.

The size and sequence organization of the centromeric region of Arabidopsis thaliana chromosome 4.

We have determined the genome structure of the centromeric region of Arabidopsis thaliana chromosome 4 by sequence analysis of BAC clones obtained by genome walking, followed by construction of a physical map using DNA of a hypomethylated strain. The total size of the centromeric region, corresponding to the recombinant inbred (RI) markers between mi87 and mi167, was approximately 5.3 megabases (Mb). This value is over 3 Mb longer than that previously estimated by the Arabidopsis Genome Initiative (Nature, 408, 796-815, 2000). Although we could not cover the entire centromeric region by BAC clones because of the presence of highly repetitive sequences in the middle (2.7 Mb), the cloned regions spanning approximately 1 Mb at both sides of the gap were newly sequenced. These results together with the reported sequences in the adjacent regions suggest that the centromeric region is principally composed of a central domain of 2.7 Mb, consisting of mainly 180-bp repeats and Athila elements, and upper and lower flanking regions of 1.55 Mb and 1 Mb, respectively. The flanking regions were predominantly composed of various types of transposable elements, except for the upper end moiety in which a large 5S rDNA array (0.65 Mb) and central domain-like sequence are present. Such an organization is essentially identical to the centromeric region of chromosome 5 reported previously.

Increased resistance to collagen-induced arthritis in CD44-deficient DBA/1 mice.

OBJECTIVE: To study the role of CD44, the principal hyaluronan (HA) receptor, in experimental arthritis. METHODS: We generated CD44 gene deficiency in arthritis-susceptible DBA/1LacJ mice to study the role of CD44 directly in collagen-induced arthritis (CIA). Wild-type and CD44-deficient mice were immunized with chicken type II collagen, and the onset and severity of CIA were monitored up to day 64. The immune status of immunized mice was determined at the end of the experiments. Cell transfer experiments were performed to monitor lymphocyte traffic to the inflamed joints. RESULTS: Mice homozygous for the CD44 mutation developed normally and showed no phenotypic defects. Although they showed a normal response to immunization with type II collagen and had Th1/Th2 ratios comparable with those in wild-type animals, CD44-deficient mice exhibited significant reductions in both the incidence and severity of CIA. This was accompanied by altered serum levels of HA, reduced expression of L-selectin, and a delayed entry of intravenously injected CD44-deficient donor lymphocytes into the arthritic joints of recipient mice. CONCLUSION: While CD44 is not essential for morphogenesis and autoimmunity, this cell surface receptor seems to play an important role in the development of arthritis, most likely by directing leukocyte traffic to the site of inflammation.

Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.

The genome of the model plant Arabidopsis thaliana has been sequenced by an international collaboration, The Arabidopsis Genome Initiative. Here we report the complete sequence of chromosome 5. This chromosome is 26 megabases long; it is the second largest Arabidopsis chromosome and represents 21% of the sequenced regions of the genome. The sequence of chromosomes 2 and 4 have been reported previously and that of chromosomes 1 and 3, together with an analysis of the complete genome sequence, are reported in this issue. Analysis of the sequence of chromosome 5 yields further insights into centromere structure and the sequence determinants of heterochromatin condensation. The 5,874 genes encoded on chromosome 5 reveal several new functions in plants, and the patterns of gene organization provide insights into the mechanisms and extent of genome evolution in plants.