Integrating genomic alterations in diffuse large B-cell lymphoma identifies new relevant pathways and potential therapeutic targets

Genome studies of diffuse large B-cell lymphoma (DLBCL) have revealed a large number of somatic mutations and structural alterations. However, the clinical significance of these alterations is still not well defined. In this study, we have integrated the analysis of targeted next-generation sequencing of 106 genes and genomic copy number alterations (CNA) in 150 DLBCL. The clinically significant findings were validated in an independent cohort of 111 patients. Germinal center B-cell and activated B-cell DLBCL had a differential profile of mutations, altered pathogenic pathways and CNA. Mutations in genes of the NOTCH pathway and tumor suppressor genes (TP53/CDKN2A), but not individual genes, conferred an unfavorable prognosis, confirmed in the independent validation cohort. A gene expression profiling analysis showed that tumors with NOTCH pathway mutations had a significant modulation of downstream target genes, emphasizing the relevance of this pathway in DLBCL. An in silico drug discovery analysis recognized 69 (46%) cases carrying at least one genomic alteration considered a potential target of drug response according to early clinical trials or preclinical assays in DLBCL or other lymphomas. In conclusion, this study identifies relevant pathways and mutated genes in DLBCL and recognizes potential targets for new intervention strategies.

The association of genetic variants in Krüppel-like factor 11 and Type 2 diabetes in the Japanese population

AIMS

Krüppel-like factor 11 (KLF11) is a transcriptional factor of the zinc finger domain family that regulates the expression of insulin. In North European populations, its common functional variant Q62R (rs35927125) is a strong genetic factor for Type 2 diabetes (P = 0.00033, odds ratio for G allele = 1.29, 95% CI 1.12-1.49). We examined the contribution of KLF11 variants to the susceptibility to Type 2 diabetes in a Japanese population.

METHODS

By re-sequencing Japanese individuals (n = 24, partly 96), we screened all four exons, exon/intron boundaries and flanking regions of KLF11. Verified single nucleotide polymorphisms (SNPs) were genotyped in 731 initial samples (369 control and 362 case subjects). Subsequently, we tested for association in 1087 samples (524 control and 563 case subjects), which were collected in different districts of Japan from the initial samples.

RESULTS

We identified eight variants, including a novel A/C variant on intron 3, but no mis-sense mutations. In an association study, we failed to find any significant result of SNPs (minor allele frequency 8.2-46.2%) after correcting for multiple testing. Similarly, no haplotypes were associated with Type 2 diabetes. It is notable that the G allele in rs35927125 was completely absent in 1818 Japanese individuals.

CONCLUSIONS

Genetic variants in KLF11 are unlikely to have a major effect of Type 2 diabetes in the Japanese population, although they were significantly associated in North European populations. These observations might help to determine the role of KLF11 variants in Type 2 diabetes in different populations.

Three-dimensional structures of canine senile plaques

In this study, the three-dimensional structures of two types of canine senile plaques (SP), diffuse plaques (DP) and mature plaques (MP), were compared using a confocal laser scanning microscope. The three-dimensional observation revealed that canine DP were uneven nebula-like assemblies of amyloid-beta (Abeta), while MP were comparatively uniform assemblies of membrane-like or fibrous Abeta materials with some differences among subtypes (primitive, classic and compact). We also noticed the presence of areas with low-density Abeta deposition inside DP and MP, indicating degradation of Abeta. Double staining for Abeta and other SP constituents was also conducted. Amyloid precursor protein (APP) was mainly deposited as rough granules around Abeta assemblies in DP and both inside and around Abeta assemblies in MP. The patten of ubiquitin deposition was quite similar to that of APP. Glial fibrillary acidic protein-positive astroglial projections were found around and inside Abeta assemblies in both types of SP, but were more prominent in MP than DP. DP were often invaded by neurofilament-positive neuronal processes (neurites), while no such neurites were observed inside MP. Dystrophic neurites were, however, frequently detected around MP. These results clearly showed that canine DP and MP have completely different three-dimensional structures, consistent with different processes of DP and MP formation.

Transdermal drug delivery by electroporation applied on the stratum corneum of rat using stamp-type electrode and frog-type electrode in vitro

Transdermal enhancement effects of electroporation applied only on the stratum corneum by two electrode types, the stamp-type electrode and the frog-type electrode, were investigated in vitro using excised rat skin. Carboxyfluorescein (CF) was selected as a model compound. The excised skin was set in a Franz type diffusion cell and a square wave electric pulse was applied to the stratum corneum under various electric pulse conditions. We determined the permeability of CF to the receptor compartment under these conditions. Voltage, electric pulse length, and number of electric pulses, were varied from 10 to 1000 V, 50 micros to 15 ms and 5 to 30 pulses, respectively. Flux rate was enhanced as the electric pulse condition strengthened. However, the maximum value was attained in the flux rate, above which no increase was observed despite strengthening of the electric pulse. Although at low electric pulses, the enhancement effect of the frog-type electrode was superior to that of the stamp-type electrode, the maximum flux rates were the same. These results indicate that electroporation on the stratum corneum using the stamp-type electrode or frog-type electrode, is useful for transdermal drug delivery.

Fractal analysis of senile plaque observed in various animal species

In the present study, the fractal dimension (FD), a concept to determine morphological complexity, was applied to morphological estimation of animal and human senile plaque using a computer-aided method. The FDs of mature plaque in a 17-year-old dog were significantly higher than those of diffuse plaque in 11- to 16-year-old dogs. In both types of plaque, the FD tended to increase as the size expanded and there was a significant difference between the slope values of the approximate line for diffuse and mature plaque. In humans, there was also a significant difference in FD value between diffuse and mature plaque. No significant differences were observed between the two types of plaque in a bear or a cynomolgus monkey. The FD of feline diffuse plaque was significantly lower than that of a camel, bear and monkey. These results indicated that the diffuse and mature plaque of the dog might form in a different manner, and similar events may occur in human senile plaque formation. In addition, specific shapes and different FD values of the diffuse plaque among animals suggested that the original conditions for plaque formation would be different.

Activating transcription factor-2 is a positive regulator in CaM kinase IV-induced human insulin gene expression

Insulin plays a crucial role in the regulation of glucose-homeostasis, and its synthesis is regulated by several stimuli. The transcription of the human insulin gene, enhanced by an elevated intracellular concentration of calcium ions, was completely blocked by Ca2+/calmodulin-dependent protein kinase inhibitor. The activity of the transcription factor activating transcription factor-2 (ATF-2), which binds to the cAMP responsive elements of the human insulin gene, was enhanced by Ca2+/calmodulin-dependent protein kinase IV (CaMKIV). Mutagenesis studies showed that Thr69, Thr71, and Thr73 of ATF-2 are all required for activation by CaMKIV. CaMKIV-induced ATF-2 transcriptional activity was not altered by activation of cJun NH2-terminal protein kinase (JNK) or p38 mitogen-activated protein (MAP) kinase. Furthermore, when transfected into rat primary cultured islets, ATF-2 enhanced glucose-induced insulin promoter activity, whereas cAMP response element-binding protein (CREB) repressed it. These results suggest a mechanism in which ATF-2 regulates insulin gene expression in pancreatic beta-cells, with the transcriptional activity of ATF-2 being increased by an elevated concentration of calcium ions.

Use of electroporation to accelerate the skin permeability enhancing action of oleic acid

Rat skin permeability after treatment by electroporation (newly developed frog type electrode, 100V, 10 pulses), oleic acid/propylene glycol (PG) and a combination of both were investigated using Fourier transformed infrared attenuated total reflectance (FT-IR/ATR) analysis. Electroporation immediately disordered the stratum corneum lipid structure up to a certain threshold level. This action lasted throughout the experiment. This may be attributed to the formation of long lifetime of metastable lipid structures, which may allow molecules to pass to the inside of the stratum corneum due to the electroporation-induced fluidized lipid membranes. Electroporation also altered the protein structure of the stratum corneum. When electroporation was combined with 0.05 M oleic acid/PG, uptake of oleic acid and PG into the stratum corneum was remarkably accelerated compared to the application of only 0.05 M oleic acid/PG to the skin. This indicates that electroporation enables oleic acid and PG to penetrate the stratum corneum easily by disrupting the structure of the latter. PG transfer into the dermis from the epidermis was accelerated, not because of the direct action of electroporation on the dermis, but because electroporation induced the rapidly disordering action of oleic acid on the stratum corneum. Lipid-soluble indomethacin permeated the skin more rapidly when the skin was treated with electroporation plus oleic acid/PG than with 0.05 M oleic acid/PG in vitro.

Antioxidant alpha-tocopherol ameliorates glycemic control of GK rats, a model of type 2 diabetes

We have shown recently that oxidative stress by chronic hyperglycemia damages the pancreatic beta-cells of GK rats, a model of non-obese type 2 diabetes, which may worsen diabetic condition and suggested the administration of antioxidants as a supportive therapy. To determine if natural antioxidant alpha-tocopherol (vitamin E) has beneficial effects on the glycemic control of type 2 diabetes, GK rats were fed a diet containing 0, 20 or 500 mg/kg diet alpha-tocopherol. Intraperitoneal glucose tolerance test revealed a significant increment of insulin secretion at 30 min and a significant decrement of blood glucose levels at 30 and 120 min after glucose loading in the GK rats fed with high alpha-tocopherol diet. The levels of glycated hemoglobin A1c, an indicator of glycemic control, were also reduced. Vitamin E supplementation clearly ameliorated diabetic control of GK rats, suggesting the importance of not only dietary supplementation of natural antioxidants but also other antioxidative intervention as a supportive therapy of type 2 diabetic patients.

Cycloaromatization and DNA cleavage of novel non-conjugated aromatic enetetrayne systems

The novel, non-conjugated aromatic enetetrayne (2) underwent thermal cycloaromatization reaction to give polyphenylene derivative 6, forming a methyl cation as an active intermediate, and showed DNA-cleaving activity.

Glucose intolerance caused by a defect in the entero-insular axis: a study in gastric inhibitory polypeptide receptor knockout mice

Mice with a targeted mutation of the gastric inhibitory polypeptide (GIP) receptor gene (GIPR) were generated to determine the role of GIP as a mediator of signals from the gut to pancreatic beta cells. GIPR-/- mice have higher blood glucose levels with impaired initial insulin response after oral glucose load. Although blood glucose levels after meal ingestion are not increased by high-fat diet in GIPR+/+ mice because of compensatory higher insulin secretion, they are significantly increased in GIPR-/- mice because of the lack of such enhancement. Accordingly, early insulin secretion mediated by GIP determines glucose tolerance after oral glucose load in vivo, and because GIP plays an important role in the compensatory enhancement of insulin secretion produced by a high insulin demand, a defect in this entero-insular axis may contribute to the pathogenesis of diabetes.

The MH1 domains of smad2 and smad3 are involved in the regulation of the ALK7 signals

The biological responses of the transforming growth factor beta (TGF-beta) superfamily are induced by activation of a receptor complex and Smad proteins. We surveyed the TGF-beta superfamily receptors using the degenerate PCR strategy, and found activin receptor-like kinase 7 (ALK7) to be abundantly expressed in fetal rat pancreatic islets. ALK7 is also expressed in adult rat islets and pancreatic beta-cell-derived MIN6 cells. The constitutively active form of ALK7, ALK7(T194D), activated Smad3 and a chimeric Smad protein, Smad3-2, containing the MH1 domain of Smad3 and the MH2 domain of Smad2, and translocated them to nuclei and then induced activation of the human PAI-1 promoter. However, neither Smad2 nor Smad2-3 protein, containing the MH1 domain of Smad2 and the MH2 domain of Smad3 were activated. These results indicate that the ALK7 signal regulates nuclear localization and activation of Smad2 and Smad3, and the MH1 domain of Smad2 has inhibitory effects on the nuclear localization.

Cerebral amyloid angiopathy in an aged great spotted woodpecker (Picoides major)

A male great spotted woodpecker (Picoides major), which was at least 16 years old, died due to general weakening. Cerebral vascular walls, including capillaries, were positively stained with Congo red with green-gold birefringence, and some of which showed a severe deposition of the Congophilic materials resulting in a corona-like fibrillar radiating structure. The Congophilic materials were positive for beta amyloid protein, but negative for prion protein. Only a few senile plaque-like structures were observed in the cortex by PAM stain and beta amyloid immunostain. The present case is the first observation of cerebral amyloid angiopathy in avian species and will indicate the presence of such age-related cerebral lesions also in birds.

Chronic electrical stimulation of the left ventrointermediate (Vim) thalamic nucleus for the treatment of pharmacotherapy-resistant Parkinson's disease: a differential impact on access to semantic and episodic memory?

Thalamotomy for medically refractory Parkinson's disease (PD) is considered to be efficacious and relatively safe. Because a minority of patients experience decrements in language and memory (often mild and transient) after thalamotomy, chronic thalamic deep brain stimulation (DBS) might be a safer treatment given its reversibility and the modifiability of stimulation parameters. Two preliminary studies support the relative cognitive safety of unilateral DBS of the ventral intermediate (Vim) thalamic nucleus, but it is unclear whether possibly subtle changes in language and memory represent effects of "microthalamotomy" or of stimulation per se. This report provides preliminary data concerning effects of left thalamic stimulation on information processing speed, semantic memory (verbal fluency and visual confrontation naming), and verbal episodic memory in a patient with PD. In addition to being evaluated before and 3 and 6 months after surgery, the patient was tested 18 months after surgery either on or off medications and with the stimulator turned either on or off (order counterbalanced across medication conditions). Test performance differences between the stimulation conditions were attenuated "off" as compared to "on" medication. Vim stimulation consistently, albeit subtly, improved semantic verbal fluency but interfered with immediate recall of word lists. Parallels to findings from acute, intraoperative thalamic stimulation studies are explored. The hypothesis is offered that left Vim stimulation might facilitate access to semantic memory, but interfere with episodic memory processes.

Skin penetration enhancing action of cis-unsaturated fatty acids with omega-9, and omega-12-chain lengths

The skin penetrative action of high purity cis-omega-12-octadecenoic acid (petroselinic acid, HP-PSA) on rat skin was compared with that of high purity cis-omega-9-octadecenoic acid (oleic acid, HP-OA), following treatment of rat intact skin surface with either 0.05 M HP-PSA or HP-OA in propylene glycol (PG), using Fourier transform/attenuated total reflection (FT-IR/ATR) analysis. Both HP-PSA and HP-OA disordered the lipid structures of the stratum corneum region to a similar extent. Removal of the extractable lipids of the stratum corneum region was marked with HP-PSA/PG but was very slight upon HP-OA/PG treatment. The spectra of the amide II region which originated from proteins suggests that HP-PSA/PG more rapidly disordered the protein structures of both the stratum corneum and the dermis than HP-OA/PG. However, the extent of disordering of the protein structures was presumed to be similar between these two skin penetration enhancers at the maximum level. Enhancement of PG flux in the dermis showed strong positive correlation with the degree of dermis-disordering action of HP-PSA/PG and HP-OA/PG. These results demonstrate that HP-PSA, which has a double bond at an even numbered position (omega-12), more rapidly affects the perturbation of the structures of both the stratum corneum and the dermis than HP-OA, which has the double bond at an odd numbered position (omega-9). Differences in the physicochemical properties of HP-PSA and HP-OA which originate from differences in the double bond position most likely determine the efficacy of these compounds as skin penetration enhancers.

Succinimide and isoaspartate residues in the crystal structures of hen egg-white lysozyme complexed with tri-N-acetylchitotriose

The isomerization of Asp101 to isoaspartate autocatalytically proceeds via a succinimide intermediate in hen egg-white lysozyme at a mildly acidic condition. The crystal structures of succinimide and isoaspartate forms of the lysozyme proteins, each complexed with a tri-N-acetylchitotriose ligand, have been determined at 1.8 A resolution, and distinctively elucidate coplanar cyclic aminosuccinyl and beta-linked isoaspartyl residues. Compared with the liganded native protein with normal Asp101, succinimide 101 protrudes toward the ligand, and isoaspartate 101 extends away from the ligand. The formations of these residues caused the loss of three hydrogen-bonds between the ligand and the side-chains of Asp101 and Asn103 along with 0.5 A displacement of the ligand location.

An evaluation of crystal structure of mannan I by X-ray powder diffraction and molecular mechanics studies

The present study reports the re-examination of the crystal structure of mannan I by the X-ray powder diffraction study combined with the miniature crystal model simulation. A primary objective of this study was to investigate an adequate chain staggering position along the fiber axis. Among the several crystal structure models proposed for mannan I, that derived from the electron diffraction study of the single crystals was adopted as a starting model. The X-ray crystallographic residuals were calculated for the single crystal structure at different chain staggering positions, while the ab projection was kept invariant. In a similar fashion, the miniature crystal models consisting of seven mannotetraoses were constructed, each having different chain staggering values and the three-dimensional structures of all the models were subsequently optimized by using the MM3(92) program without introducing any constraint. Both the X-ray residual and lattice energy plots with respect to the chain staggering position showed the common minima around the -0.25 x c chain staggering. The minimum models were subjected to a search for preferred orientations of O2 and O6 hydroxyl groups. It was found that the hydroxyl groups present inside the minicrystal tended to rotate into particular orientations during the structure optimizations to form the O5-H-O2 and O3-H-O6 intermolecular hydrogen bonds between the adjacent oligomers in an alternative direction.