Melatonin is a potential drug for the prevention of bone loss during space flight

Astronauts experience osteoporosis-like loss of bone mass because of microgravity conditions during space flight. To prevent bone loss, they need a riskless and antiresorptive drug. Melatonin is reported to suppress osteoclast function. However, no studies have examined the effects of melatonin on bone metabolism under microgravity conditions. We used goldfish scales as a bone model of coexisting osteoclasts and osteoblasts and demonstrated that mRNA expression level of acetylserotonin O-methyltransferase, an enzyme essential for melatonin synthesis, decreased significantly under microgravity. During space flight, microgravity stimulated osteoclastic activity and significantly increased gene expression for osteoclast differentiation and activation. Melatonin treatment significantly stimulated Calcitonin (an osteoclast-inhibiting hormone) mRNA expression and decreased the mRNA expression of receptor activator of nuclear factor κB ligand (a promoter of osteoclastogenesis), which coincided with suppressed gene expression levels for osteoclast functions. This is the first study to report the inhibitory effect of melatonin on osteoclastic activation by microgravity. We also observed a novel action pathway of melatonin on osteoclasts via an increase in CALCITONIN secretion. Melatonin could be the source of a potential novel drug to prevent bone loss during space flight.

Diminished nuclear RNA decay upon Salmonella infection upregulates antibacterial noncoding RNAs

Cytoplasmic mRNA degradation controls gene expression to help eliminate pathogens during infection. However, it has remained unclear whether such regulation also extends to nuclear RNA decay. Here, we show that 145 unstable nuclear RNAs, including enhancer RNAs (eRNAs) and long noncoding RNAs (lncRNAs) such as NEAT1v2, are stabilized upon Salmonella infection in HeLa cells. In uninfected cells, the RNA exosome, aided by the Nuclear EXosome Targeting (NEXT) complex, degrades these labile transcripts. Upon infection, the levels of the exosome/NEXT components, RRP6 and MTR4, dramatically decrease, resulting in transcript stabilization. Depletion of lncRNAs, NEAT1v2, or eRNA07573 in HeLa cells triggers increased susceptibility to Salmonella infection concomitant with the deregulated expression of a distinct class of immunity-related genes, indicating that the accumulation of unstable nuclear RNAs contributes to antibacterial defense. Our results highlight a fundamental role for regulated degradation of nuclear RNA in the response to pathogenic infection.

The endoglycosidase heparanase enters the nucleus of T lymphocytes and modulates H3 methylation at actively transcribed genes via the interplay with key chromatin modifying enzymes

The methylation of histones is a fundamental epigenetic process regulating gene expression programs in mammalian cells. Dysregulated patterns of histone methylation are directly implicated in malignant transformation. Here, we report the unexpected finding that the invasive extracellular matrix degrading endoglycosidase heparanase enters the nucleus of activated human T lymphocytes and regulates the transcription of a cohort of inducible immune response genes by controlling histone H3 methylation patterns. It was found that nuclear heparanase preferentially associates with euchromatin. Genome-wide ChIP-on-chip analyses showed that heparanase is recruited to both the promoter and transcribed regions of a distinct cohort of transcriptionally active genes. Knockdown and overexpression of the heparanase gene also showed that chromatin-bound heparanase is a prerequisite for the transcription of a subset of inducible immune response genes in activated T cells. Furthermore, the actions of heparanase seem to influence gene transcription by associating with the demethylase LSD1, preventing recruitment of the methylase MLL and thereby modifying histone H3 methylation patterns. These data indicate that heparanase belongs to an emerging class of proteins that play an important role in regulating transcription in addition to their well-recognized extra-nuclear functions.

Development of a novel microRNA promoter microarray for ChIP-on-chip assay to identify epigenetically regulated microRNAs

To gain a global view of epigenetic alterations around microRNA (miRNA) promoter regions, and to identify epigenetically regulated miRNAs, we developed a novel miRNA promoter microarray for chromatin immunoprecipitation (ChIP)-on-chip assay. We designed a custom oligo microarray covering regions spanning -10 to +2.5 kb of precursor miRNAs in the human genome. This microarray covers 541 miRNAs, each of which is covered by approximately 100 probes (60-mer) over its 12.5-kb genomic position, that includes predicted transcription start sites. Using this custom-made miRNA promoter microarray, we successfully performed ChIP-on-chip assay to identify miRNAs regulated by histone modification. Fifty-three miRNAs (9.8%) showed increased levels of both histone H3 acetylation and histone H3-K4 methylation in AGS gastric cancer cells treated with the DNA-methylation inhibitor 5-aza-2'-deoxycytidine and the histone deacetylase inhibitor 4-phenylbutyric acid. One of these miRNAs, miR-9, is downregulated in gastric cancer tissues and is activated by chromatin-modifying drugs, suggesting that it may be a potential target for epigenetic therapy of gastric cancer.

Array-based identification of common DNA methylation alterations in ulcerative colitis

Patients with long-standing ulcerative colitis (UC) have higher risk of developing colorectal cancer. Albeit the causes remain to be understood, epigenetic alterations have been suggested to play a role in the long-term cancer risk of these patients. In this work, we developed a novel microarray platform based on methylation-sensitive amplified fragment length polymorphism (MS-AFLP) DNA fingerprinting. The over 10,000 NotI sites of the human genome were used to generate synthetic primers covering these loci that are equally distributed into CpG rich regions (promoters and CpG islands) and outside the CpG islands, providing a panoramic view of the methylation alterations in the genome. The arrays were first tested using the colon cancer cell line CW-2 showing the reproducibility and sensitivity of the approach. We next investigated DNA methylation alterations in the colonic mucosa of 14 UC patients. We identified epigenetic alterations affecting genes putatively involved in UC disease, and in susceptibility to develop colorectal cancer. There was a strong concordance of methylation alterations (both hypermethylation and hypomethylation) shared by the cancer cells of the CW-2 cell line and the non-cancer UC samples. To the best of our knowledge, this work defines the first high-throughput aberrant DNA methylation profiles of the colonic mucosa of UC patients. These epigenetic profiles provide novel and relevant knowledge on the molecular alterations associated to the UC pathology. Some of the detected alterations could be exploited as cancer risk predictors underlying a field defect for cancerization in UC-associated carcinogenesis.

An integrative genomic analysis revealed the relevance of microRNA and gene expression for drug-resistance in human breast cancer cells

Background

Acquisition of drug-resistance in cancer has led to treatment failure, however, their mechanisms have not been clarified yet. Recent observations indicated that aberrant expressed microRNA (miRNA) caused by chromosomal alterations play a critical role in the initiation and progression of cancer. Here, we performed an integrated genomic analysis combined with array-based comparative hybridization, miRNA, and gene expression microarray to elucidate the mechanism of drug-resistance.

Results

Through genomic approaches in MCF7-ADR; a drug-resistant breast cancer cell line, our results reflect the unique features of drug-resistance, including MDR1 overexpression via genomic amplification and miRNA-mediated TP53INP1 down-regulation. Using a gain of function study with 12 miRNAs whose expressions were down-regulated and genome regions were deleted, we show that miR-505 is a novel tumor suppressive miRNA and inhibits cell proliferation by inducing apoptosis. We also find that Akt3, correlate inversely with miR-505, modulates drug sensitivity in MCF7-ADR.

Conclusion

These findings indicate that various genes and miRNAs orchestrate to temper the drug-resistance in cancer cells, and thus acquisition of drug-resistance is intricately controlled by genomic status, gene and miRNA expression changes.

Chromatin-associated protein kinase C-θ regulates an inducible gene expression program and microRNAs in human T lymphocytes

Studies in yeast demonstrate that signaling kinases have a surprisingly active role in the nucleus, where they tether to chromatin and modulate gene expression programs. Despite these seminal studies, the nuclear mechanism of how signaling kinases control transcription of mammalian genes is in its infancy. Here, we provide evidence for a hitherto unknown function of protein kinase C-theta (PKC-θ), which physically associates with the regulatory regions of inducible immune response genes in human T cells. Chromatin-anchored PKC-θ forms an active nuclear complex by interacting with RNA polymerase II, the histone kinase MSK-1, and the adaptor molecule 14-3-3ζ. ChIP-on-chip reveals that PKC-θ binds to promoters and transcribed regions of genes, as well as to microRNA promoters that are crucial for cytokine regulation. Our results provide a molecular explanation for the role of PKC-θ not only in normal T cell function, but also in circumstances of its ectopic expression in cancer.

Transcriptional profiling of genes responsive to abscisic acid and gibberellin in rice: phenotyping and comparative analysis between rice and Arabidopsis

We collected and completely sequenced 32,127 full-length complementary DNA clones from Oryza sativa L. ssp. japonica cv. "Nipponbare." Mapping of these clones to genomic DNA revealed approximately 20,500 transcriptional units (TUs) in the rice genome. For each TU, we selected 60-mers using an algorithm that took into account some DNA conditions such as base composition and sequence complexity. Using in situ synthesis technology, we constructed oligonucleotide arrays with these TUs on glass slides. We targeted RNAs prepared from normally grown rice callus and from callus treated with abscisic acid (ABA) or gibberellin (GA). We identified 200 ABA-responsive and 301 GA-responsive genes, many of which had never before been annotated as ABA or GA responsive in other expression analysis. Comparison of these genes revealed antagonistic regulation of almost all by both hormones; these had previously been annotated as being responsible for protein storage and defense against pathogens. Comparison of the cis-elements of genes responsive to one or antagonistic to both hormones revealed that the antagonistic genes had cis-elements related to ABA and GA responses. The genes responsive to only one hormone were rich in cis-elements that supported ABA and GA responses. In a search for the phenotypes of mutants in which a retrotransposon was inserted in these hormone-responsive genes, we identified phenotypes related to seed formation or plant height, including sterility, vivipary, and dwarfism. In comparison of cis-elements for hormone response genes between rice and Arabidopsis thaliana, we identified cis-elements for dehydration-stress response as Arabidopsis specific and for protein storage as rice specific.

Homogenous simultaneous detection of HCV RNA and internal control by two-color fluorescence real-time monitoring of isothermal sequence amplification with INAF probes

We demonstrated the homogenous simultaneous detection of HCV RNA and internal control by two-color fluorescence real-time monitoring of isothermal sequence amplification with INAF probes.

Homogeneous detection of a target nucleic acid sequence by combination of the intercalation activating fluorescence DNA probe and the isothermal sequence amplification

We demonstrated the homogeneous real-time detection of RNA produced during isothermal TRC amplification by INAF probe.

Cloning of a cDNA coding for porcine zona pellucida glycoprotein ZP1 and its genomic organization

The zona pellucida composed of three or four glycoproteins plays important roles in fertilization. Our previous study showed that porcine ZP1, one of the major glycoproteins of porcine zona pellucida, was divided into two components (porcine ZP4 and ZP2), and suggested it was a homologue of mouse ZP2. In this paper we report the cloning of a cDNA for porcine ZP1 and its genomic organization. The deduced amino acid sequence of porcine ZP1 shared a 54% and 63% identity with those of mouse and human ZP2, respectively. Genomic organization of porcine ZP1 was also similar to that of mouse ZP2. The transcript of porcine ZP1 gene was detected only in growing oocytes.

[Hyperthermic perfusion therapy using peplomycin for bladder cancer]

Hyperthermic intravesical perfusion therapy using peplomycin (40 micrograms/ml) in distilled water at 43 degrees C as a perfusate was performed for 2 to 3 hours in 18 patients with superficial bladder tumors and 2 with deep bladder tumors. The therapeutic efficacy was determined by cystoscopy, ultrasonography and/or CT scan. Complete and partial tumor regression was obtained in 1 and 3 of the 18 patients, respectively. There was no tumor regression in the 12 patients. Most of the patients studied had bladder discomfort such as irritation, urinary frequency and so on, during and/or after perfusion. None of the patients developed acute pyelonephritis.

Multiple regression analysis of the cholinesterase activity with certain physiochemical factors

Nineteen hundred sixteen agricultural workers who have been living in a rural area in central Japan were studied. Their age, blood pressure, Broca index, hemoglobin content, serum total cholesterol, and activity of serum cholinesterase and transaminase (GOT and GPT) were determined. The relation between the cholinesterase activity and certain physiochemical factors of the subjects was studied. Cholinesterase activity (ChE) is related to certain factors such as age, hemoglobin content (Hb), serum total cholesterol (TCh), transaminase activity (GPT), and Broca index (BI). A multiple regression equation exists between the cholinesterase activity and these factors: ln ChE = a (age) + b (Hb2) + c X ln GPT + d X ln TCh + e BI + f, where a, b, c, d, e, and f are constants. The estimated value of cholinesterase activity agrees with its measured activity. The partial correlation coefficients of the equation can be classified into the following three classes: (1) The partial correlation coefficients of total cholesterol and Broca index are nearly constant without distinction of sex and season. (2) The coefficient of hemoglobin content has a small seasonal and sexual difference. (3) The coefficients of age and GPT have a great seasonal and sexual difference. Using the equation, the most probable value of cholinesterase activity can be estimated. Therefore, the significant changes of its activity may be attributed to the toxic effects of insecticides or the abnormality of liver function.

[A double blind clinical trial of cefamandole and cefmetazole in complicated urinary tract infections]

We conducted a randomized double blind comparison of cefamandole (CMD) and cefmetazole (CMZ) in the treatment of 193 patients with complicated urinary tract infections. The patients received 1 gram of CMD or CMZ twice a day intravenously by drip infusion over 1 hour for 5 days. Pretreatment urinary leukocyte counts and urinary bacterial counts were at least 5 cells/hpf and 10(4) bacteria/ml, respectively. Each patient was randomly allocated either to CMD or CMZ group. There were 93 patients in CMD group and 100 patients in CMZ group. Clinical efficacy was evaluated based on the effect of treatment on bacteriuria and pyuria according to the criteria set by the UTI Committee, Japan. The response to CMD treatment was excellent in 18 cases (19.4%), moderate in 38 cases (40.9%) and poor in 37 cases (39.8%) with an overall effectiveness of 60.2%, whereas the response to CMZ was excellent in 19 cases (19.0%), moderate in 40 cases (40.0%) and poor in 41 cases (41.0%) with an overall effectiveness of 59.0%. No statistical significant difference was found between 2 treatment groups. Comparison of the bacteriological response between 2 groups showed that the eradication rate for strains of Gram-positive cocci were significantly higher in those patients treated with CMD. Gram-negative rods were eradicated from 68.4% of cases treated with CMD, and 78.0% of those with CMZ, but the difference was not significant. Adverse reactions were observed in 3 patients receiving CMD 1 case each of diarrhea, eruption and epigastric pain. Abnormality in laboratory tests was found in 6 patients in each treatment group. The results indicate that CMD is effective, safe and useful in the treatment of patients with complicated urinary tract infections, and its efficacy, safety and usefulness are comparable with those of CMZ.

Inhibitory effects of various drugs on dual asthmatic responses in wheat flour-sensitive subjects

In order to investigate the mechanism of late asthmatic response (LAR), inhibitory effects of various drugs for LAR were examined in two wheat flour-sensitive asthmatic subjects who showed immediate and late responses in the allergen provocation test and skin test. Antihistamines did not inhibit the LAR but totally or partially inhibited the immediate response. By contrast, corticosteroids inhibited the LAR but not the immediate response. Disodium cromoglycate inhibited both responses. Diethyl carbamazine citrate, an inhibitor of release of SRS-A, seemed to shorten the duration of the LAR, although it has no effect on the immediate response and/or on the severity of the LAR. Indomethacin and acetyl salicylate, which inhibit prostaglandin synthesis, had no significant effects on either the immediate or the LAR.