Synchronicity of genetic variants between primary sites and metastatic lymph nodes, and prognostic impact in nodal metastatic lung adenocarcinoma.

PURPOSE: Nodal positive lung adenocarcinoma includes wide range of survival. Several methods for the classification of nodal-positive lung cancer have been proposed. However, classification considering the impact of targetable genetic variants are lacking. The possibility of genetic variants for the better stratification of nodal positive lung adenocarcinoma was estimated. METHODS: Mutations of 36 genes between primary sites and metastatic lymph nodes (LNs) were compared using next-generation sequencing. Subsequently, mutations in EGFR and BRAF, rearrangements in ALK and ROS1 were evaluated in 69 resected pN1-2M0 adenocarcinoma cases. Recurrence-free survival (RFS), post-recurrence survival (PRS), and overall survival (OS) were evaluated with respect to targetable variants and tyrosine kinase inhibitor (TKI) therapy after recurrence. RESULTS: About 90% of variants were shared and allele frequencies were similar between primary and metastatic sites. In 69 pN1-2M0 cases, EGFR/ALK were positive in primary sites of 39 cases and same EGFR/ALK variants were confirmed in metastatic LNs of 96.7% tissue-available cases. Multivariate analyses indicated positive EGFR/ALK status was associated with worse RFS (HR 2.366; 95% CI 1.244-4.500; P = 0.009), and PRS was prolonged in cases receiving TKI therapy (no post-recurrence TKI therapies, HR 3.740; 95% CI 1.449-9.650; P = 0.006). OS did not differ with respect to targetable variants or TKI therapy. CONCLUSIONS: Cases harbouring targetable genetic variants had a higher risk of recurrence, but PRS was prolonged by TKI therapy. Classification according to the targetable genetic status provides a basis for predicting recurrence and determining treatment strategies after recurrence.

Inappropriate Expression of an NLP Effector in Colletotrichum orbiculare Impairs Infection on Cucurbitaceae Cultivars via Plant Recognition of the C-Terminal Region.

The hemibiotrophic pathogen Colletotrichum orbiculare preferentially expresses a necrosis and ethylene-inducing peptide 1 (Nep1)-like protein named NLP1 during the switch to necrotrophy. Here, we report that the constitutive expression of NLP1 in C. orbiculare blocks pathogen infection in multiple Cucurbitaceae cultivars via their enhanced defense responses. NLP1 has a cytotoxic activity that induces cell death in Nicotiana benthamiana. However, C. orbiculare transgenic lines constitutively expressing a mutant NLP1 lacking the cytotoxic activity still failed to infect cucumber, indicating no clear relationship between cytotoxic activity and the NLP1-dependent enhanced defense. NLP1 also possesses the microbe-associated molecular pattern (MAMP) sequence called nlp24, recognized by Arabidopsis thaliana at its central region, similar to NLPs of other pathogens. Surprisingly, inappropriate expression of a mutant NLP1 lacking the MAMP signature is also effective for blocking pathogen infection, uncoupling the infection block from the corresponding MAMP. Notably, the deletion analyses of NLP1 suggested that the C-terminal region of NLP1 is critical to enhance defense in cucumber. The expression of mCherry fused with the C-terminal 32 amino acids of NLP1 was enough to trigger the defense of cucurbits, revealing that the C-terminal region of the NLP1 protein is recognized by cucurbits and, then, terminates C. orbiculare infection.

Therapeutic strategies and genetic profile comparisons in small cell carcinoma and large cell neuroendocrine carcinoma of the lung using next-generation sequencing.

Small cell lung cancer (SCLC) and large cell neuroendocrine carcinoma (LCNEC) of the lung are classified as variants of endocrine carcinoma and subdivided into pure or combined type. Clinical benefit of target therapy has not been established in these tumors. This study aimed to compare genetic and clinicopathological features between SCLC and LCNEC or pure and combined types, and explore the possibility of target therapy using next-generation sequencing. In 13 SCLC and 22 LCNEC cases, 72 point mutations, 19 deletions, and 3 insertions were detected. As therapeutically targetable variants, mutations in EGFR (L858R), KRAS (G12D, G12A, G12V), and PIK3CA (E545K) were detected in 5 cases. The case harboring EGFR mutation showed response to EGFR-tyrosine kinase inhibitor. However, there are no clinicopathological features associated with therapeutically targetable cases. And there was no significant genetic feature between SCLC and LCNEC or pure and combined types. In conclusion, although patients with SCLC and LCNEC may benefit from target therapy, they were not identifiable by clinicopathologic background. And there was not significant genetic difference between SCLC and LCNEC, including between pure and combined types. Classifying SCLC and LCNEC in same category is reasonable. However, distinguishing the pure type from combined type was not validated. Comprehensive genetic analysis should be performed to detect targetable variants in any type of SCLC and LCNEC.

Comparative genomic and transcriptomic analyses reveal the hemibiotrophic stage shift of Colletotrichum fungi.

Hemibiotrophic fungal plant pathogens represent a group of agronomically significant disease-causing agents that grow first on living tissue and then cause host death in later, necrotrophic growth. Among these, Colletotrichum spp. are devastating pathogens of many crops. Identifying expanded classes of genes in the genomes of phytopathogenic Colletotrichum, especially those associated with specific stages of hemibiotrophy, can provide insights on how these pathogens infect a large number of hosts. The genomes of Colletotrichum orbiculare, which infects cucurbits and Nicotiana benthamiana, and C. gloeosporioides, which infects a wide range of crops, were sequenced and analyzed, focusing on features with potential roles in pathogenicity. Regulation of C. orbiculare gene expression was investigated during infection of N. benthamiana using a custom microarray. Genes expanded in both genomes compared to other fungi included sequences encoding small, secreted proteins (SSPs), secondary metabolite synthesis genes, proteases and carbohydrate-degrading enzymes. Many SSP and secondary metabolite synthesis genes were upregulated during initial stages of host colonization, whereas the necrotrophic stage of growth is characterized by upregulation of sequences encoding degradative enzymes. Hemibiotrophy in C. orbiculare is characterized by distinct stage-specific gene expression profiles of expanded classes of potential pathogenicity genes.

Large-scale gene disruption in Magnaporthe oryzae identifies MC69, a secreted protein required for infection by monocot and dicot fungal pathogens.

To search for virulence effector genes of the rice blast fungus, Magnaporthe oryzae, we carried out a large-scale targeted disruption of genes for 78 putative secreted proteins that are expressed during the early stages of infection of M. oryzae. Disruption of the majority of genes did not affect growth, conidiation, or pathogenicity of M. oryzae. One exception was the gene MC69. The mc69 mutant showed a severe reduction in blast symptoms on rice and barley, indicating the importance of MC69 for pathogenicity of M. oryzae. The mc69 mutant did not exhibit changes in saprophytic growth and conidiation. Microscopic analysis of infection behavior in the mc69 mutant revealed that MC69 is dispensable for appressorium formation. However, mc69 mutant failed to develop invasive hyphae after appressorium formation in rice leaf sheath, indicating a critical role of MC69 in interaction with host plants. MC69 encodes a hypothetical 54 amino acids protein with a signal peptide. Live-cell imaging suggested that fluorescently labeled MC69 was not translocated into rice cytoplasm. Site-directed mutagenesis of two conserved cysteine residues (Cys36 and Cys46) in the mature MC69 impaired function of MC69 without affecting its secretion, suggesting the importance of the disulfide bond in MC69 pathogenicity function. Furthermore, deletion of the MC69 orthologous gene reduced pathogenicity of the cucumber anthracnose fungus Colletotrichum orbiculare on both cucumber and Nicotiana benthamiana leaves. We conclude that MC69 is a secreted pathogenicity protein commonly required for infection of two different plant pathogenic fungi, M. oryzae and C. orbiculare pathogenic on monocot and dicot plants, respectively.

2,5-Dideoxy-2,5-imino-d-altritol as a new class of pharmacological chaperone for Fabry disease.

Chromatographic separation of the extract from roots of Adenophora triphylla resulted in the isolation of two pyrrolidines, six piperidines, and two piperidine glycosides. The structures of new iminosugars were elucidated by spectroscopic methods as 2,5-dideoxy-2,5-imino-d-altritol (DIA) (2), beta-1-C-butenyl-1-deoxygalactonojirimycin (8), 2,3-dideoxy-beta-1-C-ethyl-1-deoxygalactonojirimycin (9), and 6-O-beta-d-glucopyranosyl-2,3-dideoxy-beta-1-C-ethyl-1-deoxygalactonojirimycin (10). beta-1-C-Butyl-1-deoxygalactonojirimycin (7) and compound 8 were found to be better inhibitors of alpha-galactosidase than N-butyl-1-deoxygalactonojirimycin. The present work elucidated that DIA was a powerful competitive inhibitor of human lysosome alpha-galactosidase A (alpha-Gal A) with a K(i) value of 0.5muM. Furthermore, DIA improved the thermostability of alpha-Gal A in vitro and increased intracellular alpha-Gal A activity by 9.6-fold in Fabry R301Q lymphoblasts after incubation for 3days. These experimental results suggested that DIA would act as a specific pharmacological chaperone to promote the smooth escape from the endoplasmic reticulum (ER) quality control system and to accelerate transport and maturation of the mutant enzyme.

Traf2 interacts with Smad4 and regulates BMP signaling pathway in MC3T3-E1 osteoblasts.

Bone morphogenetic proteins (BMPs) play important roles in osteoblast differentiation and maturation. In mammals, the BMP-induced receptor-regulated Smads form complexes with Smad4. These complexes translocate and accumulate in the nucleus, where they regulate the transcription of various target genes. However, the function of Smad4 remains unclear. We performed a yeast two-hybrid screen using Smad4 as bait and a cDNA library derived from bone marrow, to indentify the proteins interacting with Smad4. cDNA clones for Tumor necrosis factor (TNF) receptor-associated factor 2 (Traf2) were identified, and the interaction between the endogenous proteins was confirmed in the mouse osteoblast cell line MC3T3-E1. To investigate the function of Traf2, we silenced it with siRNA. The level of BMP-2 protein in the medium, the expression levels of the Bmp2 gene and BMP-induced transcription factor genes, including Runx2, Dlx5, Msx2, and Sp7, and the phosphorylated-Smad1 protein level were increased in cells transfected with Traf2 siRNA. The nuclear accumulation of Smad1 increased with TNF-alpha stimulation for 30 min at Traf2 silencing. These results suggest that the TNF-alpha-stimulated nuclear accumulation of Smad1 may be dependent on Traf2. Thus, the interaction between Traf2 and Smad4 may play a role in the cross-talk between TNF-alpha and BMP signaling pathways.

Low-intensity pulsed ultrasound stimulates osteogenic differentiation in ROS 17/2.8 cells.

There have been no studies investigating the effects of the mechanical stimulation provided by Low-intensity pulsed ultrasound (LIPUS) treatment on periodontal disease accompanying bone loss. LIPUS is known to accelerate mineralization and bone regeneration, but the precise cellular mechanism is unclear. Here, we investigated the effect of LIPUS on osteogenesis by examining the effect of LIPUS stimulation on cell proliferation, alkaline phosphatase (ALPase) activity, osteogenesis-related gene expression, and mineralized nodule formation in a rat osteosarcoma cell line. The cells were cultured in medium with or without the addition of LIPUS stimulation. The ultrasound signal consisted of 1.5 MHz at an intensity of 30 mW/cm(2) for 20 min for all cultures. LIPUS stimulation did not affect the rate of cell proliferation. ALPase activity was increased at day 7 of culture after LIPUS stimulation. Real-time PCR analysis indicated that LIPUS significantly increased the expression of mRNA for the transcription factors Runx2, Msx2, Dlx5, and Osterix and for bone sialoprotein, whereas the mRNA expression of AJ18 was significantly reduced. The mineralized nodule formation and the calcium content in mineralized nodules were markedly increased on day 14 of culture after LIPUS stimulation. Our study demonstrates that LIPUS stimulation directly affects osteogenic cells, leading to mineralized nodule formation. In view of the widespread use of LIPUS for the clinical therapy of periodontal disease, it is likely that LIPUS has an important influence on key functional activities of osteoblasts in alveolar bone.

Effects of low-intensity pulsed ultrasound on the differentiation of C2C12 cells.

Low-intensity pulsed ultrasound (LIPUS) is known to accelerate bone regeneration, but the precise cellular mechanism is still unclear. The purpose of this study was to determine the effect of LIPUS on the differentiation of pluripotent mesenchymal cell line C2C12. The cells were cultured in differentiation medium with or without the addition of LIPUS stimulation. The ultrasound signal consisted of 1.5 MHz at an intensity of 70 mW/cm2 for 20 min for all cultures. To verify the cell lineage after LIPUS stimulation, mRNA expression of cellular phenotype-specific markers characterizing osteoblasts (Runx2, Msx2, Dlx5, AJ18), chondroblasts (Sox9), myoblasts (MyoD), and adipocytes (C/EBP, PPARgamma) was studied using real-time polymerase chain reaction analysis. The protein expression of Runx2 and activated phosphorylation of extracellular signal-regulated kinase 1/2 (ERK1/2) and p38 mitogen-activated protein kinase (p38 MAPK) were performed using Western blotting. The mRNA expression of Runx2, Msx2, Dlx5, AJ18, and Sox9 was increased markedly by the LIPUS stimulation, whereas the expression of MyoD, C/EBP, and PPARgamma was drastically decreased. In the Western blot analysis, LIPUS stimulation increased Runx2 protein expression and phosphorylation of ERK1/2 and p38 MAPK. Our study demonstrated that LIPUS stimulation converts the differentiation pathway of C2C12 cells into the osteoblast and/or chondroblast lineage via activated phosphorylation of ERK1/2 and p38 MAPK.

Inhibitory effect of dipeptide alcohol derivatives containing mercapto group on eukaryotic DNA polymerase alpha.

We reported previously that a novel dipeptide alcohol, L-homoserylaminoethanol (Hse-Gly-ol), is a selective inhibitor of eukaryotic DNA polymerase epsilon (pol epsilon). The discovery suggests that the dipeptide structure could be a chemical frame for a DNA polymerase inhibitor. Therefore, we chemically synthesized 14 different species of dipeptide alcohols and their derivatives, and tested this inhibitory capability. The mercapto group in the dipeptide alcohol was found to be important, and compound 4 (L-cysteinylaminoethanol, Cys-Gly-ol) was the strongest pol alpha inhibitor. Compound 4 did not influence the activities of other replicative DNA polymerases such as delta and epsilon, and had no effect on the activities of prokaryotic DNA polymerases, nor DNA metabolic enzymes such as human immunodeficiency virus type-1 reverse transcriptase, T7 RNA polymerase and bovine deoxyribonuclease I. The inhibitory effect of compound 4 on pol alpha was dose-dependent, and 50% inhibition was observed at a concentration of 14.8 microM. Compound 4-induced inhibition of pol alpha activity was non-competitive with both the DNA template-primer and the nucleotide substrate. The relationships between the structures of dipeptide alcohol and the inhibition of eukaryotic DNA polymerases are discussed.

Effects of the enamel matrix derivative and beta-tricalcium phosphate on bone augmentation within a titanium cap in rabbit calvarium.

In vitro studies suggest that enamel matrix derivative (EMD) affects the early stages of osteogenic maturation by stimulating bone cell proliferation. In the present study, we evaluated the effects of EMD and beta-tricalcium phosphate (beta-TCP) on bone augmentation within a titanium cap in rabbit calvaria, using 14 adult male Japanese white rabbits. The calvarium was exposed, a circular groove prepared, the marrow penetrated, and a standard hemispherical titanium cap placed in the groove. The cap was filled with a mixture of beta-TCP and EMD at the experimental site, and was filled with beta-TCP alone at the control site. At 1 and 3 months after cap implantation, animals were euthanized, and histological sections prepared. The sections were stained with basic fuchsin and methylene blue, and were examined using light microscopy. At 1 month, EMD tended to increase the amount of bone, but there was no significant difference in the amount of new tissue and mineralized bone between the experimental and control sites. The present findings indicate that the present mixture of EMD and beta-TCP does not accelerate bone formation, compared with beta-TCP alone.

Differential gene induction in macrophage-like human cells by two types of Porphyromonas gingivalis: a microarray study.

Several studies have provided clinical evidence that FimA clonal variation may contribute to the periodontopathogenicity of Porphyromonas gingivalis (P.g.). We studied the gene expression profiling of the macrophage-like human cell line U937 after infection of two types of P.g. (fimA type I; Pg-I and fimA type II; Pg-II) using microarray. Of 1088 genes examined, 394 genes were detectable. Bioinformatics algorithms were used to analyze the detectable genes. Hierarchical clustering analysis showed that gene expression patterns of Pg-II and the control (no infection) were grouped together. K-means clustering grouped 79 genes into Pg-II dominance and 88 genes into Pg-I dominance. A large number of genes related to cell signaling, extracellular communication proteins, cell receptors (by ligands), protein turnover and cell adhesion receptors/proteins were grouped into clusters of Pg-I dominance. Our results indicate that compared with Pg-I, Pg-II induces a low host response as measured by its weak induction of gene expression.

Relationship between Porphyromonas gingivalis, Epstein-Barr virus infection and reactivation in periodontitis.

The aim of this study was to assess the relationship-between Porphyromonas gingivalis, Epstein-Barr virus (EBV) infection and reactivation in periodontitis using real-time PCR. The mean proportion of P. gingivalis cells to total bacterial cells in the saliva from EBV-positive periodontitis patients was significantly higher than that in saliva from EBV-negative patients. An EBV-positive B-cell line was used to determine whether P. gingivalis sonicate induced reactivation of EBV, using real-time PCR to measure the virus genome in the culture medium. A significant increase in EBV numbers was observed after the stimulation with P. gingivalis sonicate. These findings suggest that the interaction between EBV and P. gingivalis is bi-directional, with EBV reactivation suppressing host defenses and permitting overgrowth of P. gingivalis, and P. gingivalis having the potential to induce EBV reactivation.