Computational Analysis of miR-140 and miR-135 as Potential Targets to Develop Combinatorial Therapeutics for Degenerative Tendinopathy.

Background: Degenerative tendinopathy, a condition causing movement restriction due to high pain, highly impacts productivity and quality of life. The healing process is a complex phenomenon and involves a series of intra-cellular and inter-cellular processes. Proliferation and differentiation of the tenocyte is a major and essential process to heal degenerative tendinopathy. The recent development in microRNA (miRNA)-mediated reprogramming of the cellular function through specific pathways opened door for the development of new regenerative therapeutics. Based on information about gene expression and regulation of tendon injury and healing, we attempted to evaluate the combinatorial effect of selected miRNAs for better healing of degenerative tendinopathy. Methods: The present study was designed to evaluate the combinatorial effect of two miRNAs (has-miR-140 and has-miR-135) in the healing process of the tendon. Publicly available information/data were retrieved from appropriate platforms such as PubMed. Only molecular data, directly associated with tendinopathies, including genes/proteins and miRNAs, were used in this study. The miRNAs involved in tendinopathy were analyzed by a Bioinformatics tools (e.g., TargetScan, miRDB, and the RNA22v2). Interactive involvement of the miRNAs with key proteins involved in tendinopathy was predicted by the Insilco approach. Results: Based on information available in the public domain, tendon healing-associated miRNAs were predicted to explore their therapeutic potentials. Based on computation analysis, focusing on the potential regulatory effect on tendon healing, the miR-135 and miR-140 were selected for this study. These miRNAs were found as key players in tendon healing through Rho-associated coiled-coil containing protein kinase 1 (ROCK1), IGF-1/PI3K/Akt, PIN, and Wnt signaling pathways. It was also predicted that these miRNAs may reprogram the cells to induce proliferation and differentiation activity. Many miRNAs are likely to regulate genes important for the tendinopathy healing process, and the result of this study allows an approach for miRNA-mediated regeneration of the tenocyte for tendon healing. Based on computational analysis, the role of these miRNAs in different pathways was established, and the results provided insights into the combinatorial approach of miRNA-mediated cell reprogramming. Conclusions: In this study, the association between miRNAs and the disease was evaluated to correlate the tendinopathy genes and the relevant role of different miRNAs in their regulation. Through this study, it was established that the synergistic effect of more than one miRNA on directed reprogramming of the cell could be helpful in the regeneration of damaged tissue. It is anticipated that this study will be helpful for the design of miRNA cocktails for the orchestration of cellular reprogramming events.

Effect of Ammonia and Indole-3-acetic Acid Producing Endophytic Klebsiella pneumoniae YNA12 as a Bio-Herbicide for Weed Inhibition: Special Reference with Evening Primroses.

Information on the use of endophytic bacteria as a bio-herbicide for the management of weed control in agricultural fields is limited. The current study aimed to isolate endophytic bacteria from evening primroses and to screen them for their bio-herbicidal activity. Two isolated endophytic bacteria (Pantoea dispersa YNA11 and Klebsiella pneumoniae YNA12) were initially screened for citrate utilization and for indole-3-acetic acid (IAA) and catalase production. The preliminary biochemical assessment showed YNA12 as a positive strain. Ammonia, catalase, and IAA in its culture filtrate were quantified. Gas Chromatography/Mass Spectroscopy- Selective Ion Monitoring (GC/MS-SIM) analysis revealed the production of IAA by YNA12 in a time-dependent manner. YNA12 also exhibited significant ammonia-producing potential and catalase activity against hydrogen peroxide. The YNA12 culture filtrate significantly inhibited the germination rate of evening primrose seeds, resulting in a marked reduction in seedling length and biomass compared with those of the control seeds. Moreover, the culture filtrate of YNA12 significantly accelerated the endogenous abscisic acid (ABA) production and catalase activity of evening primrose seedlings. Macronutrient regulation was adversely affected in the seedlings exposed to the culture filtrate of YNA12, leading to inhibition of seed germination. The current results suggest that endophytic YNA12 may be used as a potent bio-herbicidal agent for controlling weed growth and development.

Autophagy Suppresses Toll-Like Receptor 3-Mediated Inflammatory Reaction in Human Epidermal Keratinocytes.

Autophagy, one mechanism of programmed cell death, is fundamental to cellular homeostasis. Previous studies have identified autophagy as a novel mechanism by which cytokines control the immune response. However, its precise role in immune-related inflammatory skin diseases such as psoriasis remains unclear. Thus, this study explored the functional role of autophagy in psoriatic inflammation of epidermal keratinocytes. Strong light chain 3 immunoreactivity was observed in epidermal keratinocytes of both human psoriatic lesions and imiquimod-induced mice psoriatic model, and it was readily induced by polycytidylic acid (poly (I:C)), which stimulates Toll-like receptor 3 (TLR3), in human epidermal keratinocytes in vitro. Rapamycin-induced activation of autophagy significantly reduced poly (I:C)-induced inflammatory reaction, whereas, inhibition of autophagy by 3-methyladeine increased that. Our results indicate that the induction of autophagy may attenuate TLR3-mediated immune responses in human epidermal keratinocytes, thus providing novel insights into the mechanisms underlying the development of inflammatory skin diseases including psoriasis.

NNMT depletion contributes to liver cancer cell survival by enhancing autophagy under nutrient starvation.

Nicotinamide N-methyl transferase (NNMT) transfers a methyl group from S-adenosyl-L-methionine (SAM) to nicotinamide (NAM), producing 1-methylnicotinamide (1MNA). NNMT has been implicated in several cancer types and recently in metabolism, but its role in autophagy regulation has not yet been investigated. In this study, we determined that NNMT negatively regulated autophagy at the stage of ULK1 activation through protein phosphatase 2A (PP2A) activity. Specifically, NNMT knockdown increased PP2A methylation and subsequently enhanced phosphatase activity. Consequent p-ULK1 (S638) dephosphorylation derepressed ULK1 activity, resulting in autophagy induction. Accordingly, NNMT downregulation rescued tumor cells under nutrient deficiency in vivo, which was alleviated by ULK1 inhibitor treatment. In summary, our results suggest a novel mechanism by which tumor cells protect themselves against nutrient deprivation through NNMT suppression to accelerate autophagy.

Detecting primary drug-resistant mutations in Korean HIV patients using ultradeep pyrosequencing.

HIV primary resistance, drug resistance in treatment-naïve patients, is an emerging public health issue. The prevalence of HIV primary resistance mutations down to the level of 1% minor variants was investigated using ultradeep pyrosequencing (UDPS) in HIV-positive Korean blood donors and in treatment naïve chronic patients for the comparison. The entire pol region was sequenced from 25 HIV-positive blood donors, and 18 treatment-naïve chronic HIV patients. UDPS was successful in 19 blood donors and 18 chronic patients. In total, 1,011,338 sequence reads were aligned, and 28,093 sequence reads were aligned on average per sample. The prevalence of HIV primary resistance mutations in the HIV-positive blood donors and chronic HIV patients were 63.2% and 44.4% according to UDPS, respectively. Protease inhibitor (PI) drugs demonstrated different patterns in HIV-positive blood donors and chronic HIV patients, whereas non-nucleoside reverse transcriptase inhibitors (NNRTI), nucleoside reverse transcriptase inhibitors (NRTI), and integrase inhibitor (INI) drugs showed similar patterns between the two groups. Higher level of primary resistance prevalence was observed mainly because UDPS method could detect mutations in minor variants with 1-10% frequency. The higher resistance prevalence was observed in HIV-positive blood donors than in chronic patients. Considering that treatments for HIV-infected patients were recently amended to start at an earlier stage, information about degree of drug resistance to each drug between the two groups would help to establish future policies, design additional clinical trials, assess HIV patient care in Korea.

Comparison of quasispecies diversity of HCV between chronic hepatitis c and hepatocellular carcinoma by Ultradeep pyrosequencing.

BACKGROUNDS: Hepatitis C virus (HCV) exists as population of closely related genetic variants known as quasispecies. HCV quasispecies diversity is strongly influenced by host immune pressure on virus. Quasispecies diversity is expected to decline as host immune response to HCV decreases over natural course of progressing from chronic hepatitis C (CHC) to hepatocellular carcinoma (HCC). METHODS: Ultradeep pyrosequencing (UDPS) was used to evaluate degree of quasispecies diversity in 49 patients infected with HCV including 26 with CHC and 23 with HCC. Whole structural protein of HCV genome was subjected to UDPS. RESULTS: Shannon's indices for quasispecies diversity in HCV E1 were significantly lower in patients with HCC than in those with CHC. 14 amino acid positions differed significantly between two groups. Area under curve of ROC analysis for differentiating HCC from CHC was >0.8 for all of 14 amino acid positions. CONCLUSION: HCV quasispecies diversity as indicator of declining host immune functions was easily assessed by UDPS technology. Shannon's indices in 14 amino acid positions were found to differentiate between patients with CHC and those with HCC. Our data propose that degree of HCV quasispecies measured by UDPS might be useful to predict progression of HCC in chronic HCV patients.

Updates in bacteriological epidemiology of community-acquired severe acute cholangitis and the effectiveness of metronidazole added routinely to the first-line antimicrobial regimen.

Prompt antimicrobial therapy, together with subsequent biliary drainage, is crucial to prevent the rapidly deteriorating course of severe acute cholangitis. Therefore, updates in bacteriological epidemiology and resistance profile are important for management of this critical disease. Also, because the routine addition of metronidazole to the first-line regimen is controversial, we intended this prospective study with historical controls. Patients with severe acute cholangitis who fulfilled the definition of severity by the Tokyo Guidelines and underwent biliary drainage within 24 h from presentation were enrolled prospectively from January 2010 to December 2011. During that period, metronidazole was not added to third-generation cephalosporins, which were used as the initial antimicrobials except for patients who were allergic to penicillin and received ciprofloxacin instead (no metronidazole group). Outcomes were compared with a historical cohort from March 2007 to December 2009 when metronidazole was added routinely (metronidazole group). A unified strategy was maintained throughout the whole period excepting the use of metronidazole. Outcomes between the metronidazole group (n = 338) and the no metronidazole group (n = 338) did not differ in terms of the rate of successful biliary drainage by interventional procedures (93.2% vs. 94.7%, p = 0.88), time elapsed for cholangitis to be controlled (10.4 ± 0.6 vs. 8.9 ± 1.2 days, p = 0.38), and mortality (1.2% vs. 0.6% with p = 0.34 for all causes and 0.9% vs. 0% with p = 0.15 for cholangitis-related, respectively). As the routine addition of metronidazole did not improve outcomes, it can be excluded from the first-line regimen if emergent biliary drainage can be performed efficiently.

BNIP3 is degraded by ULK1-dependent autophagy via MTORC1 and AMPK.

BNIP3 (BCL2/adenovirus E1B 19 kDa interacting protein 3) is an atypical BH3-only protein that is induced by hypoxia-inducible factor 1 (HIF1) under hypoxia. BNIP3 is primarily regulated at the transcriptional level. However, little is known about the underlying mechanism of BNIP3 degradation. In this study, we found that BNIP3 was downregulated when hypoxia was accompanied by amino acid starvation. The BNIP3 downregulation did not occur at the transcription level and was independent of HIF1A. BNIP3 was primarily degraded by the proteasome, but BNIP3 was subjected to both proteasomal and autophagic degradation in response to starvation. The autophagic degradation of BNIP3 was dependent on ATG7 and MAP1LC3. We determined that autophagic degradation of BNIP3 was specifically regulated by ULK1 via the MTOR-AMPK pathway. Moreover, we confirmed that BNIP3 could play a protective role in tumor cells under hypoxia, and the treatment with Torin1, an MTOR inhibitor, decreased the BNIP3 level and enhanced the death of hypoxic tumor cells.

Rapamycin inhibits both motility through down-regulation of p-STAT3 (S727) by disrupting the mTORC2 assembly and peritoneal dissemination in sarcomatoid cholangiocarcinoma.

Cholangiocarcinoma (CC) is a malignant epithelium neoplasm that originates from the bile epithelium and for which there are few therapeutic strategies. The mTOR pathway involved in many cellular processes was reported to be up-regulated in various cancers. We investigated the activation of the AKT/mTOR pathway in CC cell lines with different degrees of dedifferentiation and found that rapamycin could suppress the motility and the peritoneal dissemination of sarcomatoid SCK cells. Inhibition of the mTOR pathway with rapamycin decreased significantly the number of tumor nodules and prolonged the survival rates of nude mice inoculated with sarcomatoid CC cells. Prolonged treatments with rapamycin were found to disrupt the mTORC2 assembly and to reduce the phosphorylation of STAT3 at Ser 727. Rapamycin decreased both mRNA and protein levels of MMP2 and Twist1, which are regulated by STAT3 and associated with cancer metastasis. The overexpression of STAT3 S727A lacking the phosphorylation site resulted in significantly less sensitivity to rapamycin than the overexpression of STAT3 WT. Taken together, our results suggest that rapamycin could suppress the motility of sarcomatoid CC by down-regulating p-STAT3 (S727) through the impairment of mTORC2 assembly.

REST-dependent expression of TRF2 renders non-neuronal cancer cells resistant to DNA damage during oxidative stress.

REST is a neuronal gene silencing factor ubiquitously expressed in non-neuronal tissues. REST is additionally believed to serve as a tumor suppressor in non-neuronal cancers. Conversely, recent findings on REST-dependent tumorigenesis in non-neuronal cells consistently suggest a potential role of REST as a tumor promoter. Here, we have uncovered for the first time the mechanism by which REST contributes to cancer cell survival in non-neuronal cancers. We observed abundant expression of REST in various types of non-neuronal cancer cells compared to normal tissues. The delicate roles of REST were further evaluated in HCT116 and HeLa, non-neuronal cancer cell lines expressing REST. REST silencing resulted in decreased cell survival and activation of the DNA damage response (DDR) through a decrease in the level of TRF2, a telomere-binding protein. These responses were correlated with reduced colony formation ability and accelerated telomere shortening in cancer cells upon the stable knockdown of REST. Interestingly, REST was down-regulated under oxidative stress conditions via ubiquitin proteasome system, suggesting that sustainability of REST expression is critical to determine cell survival during oxidative stress in a tumor microenvironment. Our results collectively indicate that REST-dependent TRF2 expression renders cancer cells resistant to DNA damage during oxidative stress, and mechanisms to overcome oxidative stress, such as high levels of REST or the stress-resistant REST mutants found in specific human cancers, may account for REST-dependent tumorigenesis.

Response failure to the treatment of Clostridium difficile infection and its impact on 30-day mortality.

BACKGROUND/AIMS: Few data are available on response failure and hospital mortality. This study aimed to evaluate the association between response failure to the treatment of CDI and 30-day mortality. METHODS: Medical records of patients diagnosed with CDI between March 2005 and March 2010 were reviewed. CDI diagnosis was considered in patients with diarrhea when the stool toxins assay was positive or pseudomembranous colitis (PMC) was confirmed by endoscopy. If there were no symptomatic improvements during 10 days of treatment, the case was regarded as response failure. Patients were stratified into a mild or severe disease group based on clinical criteria. RESULTS: Among 536 subjects (age 64±14.12, mild 266, severe 270), 26 (4.9%) showed response failure, which occurred more frequently in the severe disease than mild disease group. Forty-eight (9%) patients died within 1 month and mortality rate in the failure group was higher than in the response group (42.3% vs. 7.3%, p<0.001). Malignancy, albumin <2.5 mg/dL, WBC >15,000 cells/mm3, ICU admission and response failure were independent risk factors associated with 30-day mortality after CDI. CONCLUSIONS: Response failure to the treatment negatively affects a patients' survival within 30 days after CDI.

A case of Sweet's syndrome in a patient with liver cirrhosis caused by chronic hepatitis B.

Sweet's syndrome (SS), also known as acute febrile neutrophilic dermatosis, is characterized by the sudden onset of painful erythematous skin lesions together with fever and neutrophilia. SS can be associated with several disorders, such as malignancy, autoimmune disease, and infections. However, SS associated with liver cirrhosis is uncommon. We report a case of SS in a patient who was diagnosed with liver cirrhosis caused by chronic hepatitis B.

Effects of lateral spacing on enzymatic on-chip DNA polymerization.

Enzymatic on-chip DNA polymerization can be utilized to elongate surface-bound primers with DNA polymerase and to enhance the signal in the detection of target DNAs on the solid support. In order to investigate the steric effect of the enzymatic reaction on the solid support, we compared the efficiency of on-chip DNA polymerization on a high-density surface with that on a spacing-controlled surface. The spacing-controlled, 9-acid dendron-coated surface exhibited approximately 8-fold higher efficiency of on-chip DNA polymerization compared with the high-density surface. The increase in fluorescence intensity during the on-chip DNA polymerization could be fit to an exponential equation, and the saturation level of the 9-acid dendron slide was 7 times higher than that of the high-density slide. The on-chip DNA polymerization was employed to measure the transcription level of nine genes related to epithelial-to-mesenchymal transition in hepatocellular carcinoma cells. Compared to the high-density surface, the dendron-coated surface exhibited a lower detection limit in the on-chip DNA polymerization and higher correlation with transcription levels as determined by quantitative real-time PCR. Our results suggest that control of the lateral spacing of DNA strands on the solid support should significantly enhance the accessibility of DNA polymerase and the efficiency of the on-chip DNA polymerization.

Endoscopic treatments of gastric mucosal lesions are not riskier in patients with chronic renal failure or liver cirrhosis.

BACKGROUND: Little is known about the feasibility of endoscopic submucosal dissection (ESD) and endoscopic mucosal resection (EMR) for patients with chronic renal failure (CRF) or liver cirrhosis (LC). This study aimed to assess the safety, efficacy, and clinical outcomes of EMR or ESD in patients with CRF or LC compared to those in patients without. METHODS: Between February 2003 and November 2009, a total of 1016 gastric neoplastic lesions in 928 patients were treated by using EMR or ESD. Among them, 18 patients had LC and 17 patients had CRF. Their medical records were reviewed retrospectively. En bloc resection rate, histological complete resection rate, operation time, and complications were compared between patients with CRF or LC and those without (control group). RESULTS: Baseline characteristics were not significantly different between the CRF, LC, and control groups except for a high rate of comorbidities in the CRF group and prolonged prothrombin time in the LC group. Operation time and therapeutic outcomes such as en bloc and complete resection rates did not differ significantly between the groups. Immediate bleeding tended to occur more frequently in the CRF+LC group than in controls (47.5 vs. 33.9%, p=0.077). There was no significant difference in the incidence of perforation between the CRF, LC, and control groups. The hospital stay was longer in the CRF+LC group than in the control group (6.4±3.53 vs. 4.9±3.15 days, p=0.012). CONCLUSIONS: EMR and ESD for the treatment of early gastric neoplasia may be equally effective and tolerable in the CRF or the LC group compared to the control group, although patients with CRF or LC might need the longer admission period than the control group.

Overexpression of high-mobility group box 2 is associated with tumor aggressiveness and prognosis of hepatocellular carcinoma.

PURPOSE: We investigated the expression of high-mobility group box 2 (HMGB2) in patients with hepatocellular carcinoma (HCC) and its clinical effects with underlying mechanisms. EXPERIMENTAL DESIGN: HMGB2 mRNA levels were measured in 334 HCC patients by real-time reverse transcription-PCR and HMGB2 protein levels in 173 HCC patients by immunohistochemical studies. The HMGB2 expression level was measured by Western blotting for three HCC cell lines. To clarify the precise role of HMGB2 on cell proliferation, we did in vitro analysis with expression vectors and small interfering RNAs. RESULTS: HMGB2 mRNA and protein expression were significantly higher in HCC than in noncancerous surrounding tissues (P < 0.0001) and showed a positive correlation (ρ = 0.35, P < 0.001). HMGB2 overexpression was significantly correlated with shorter overall survival time, both at mRNA (P = 0.0054) and protein level (P = 0.023). Moreover, HMGB2 mRNA level was an independent prognostic factor for overall survival in a multivariate analysis (P = 0.0037). HMGB2 knockdown by small interfering RNAs decreased cell proliferation, and overexpression of HMGB2 by expression vectors diminished cisplatin- and etoposide-induced cell death. CONCLUSIONS: Our clinical and in vitro data suggest that HMGB2 plays a significant role in tumor development and prognosis of HCC. These results can partly be explained by altered cell proliferations by HMGB2 associated with the antiapoptotic pathway.

Apoptosis-related mRNA expression profiles of ovarian cancer cell lines following cisplatin treatment.

OBJECTIVE: The aim of this study was to identify apoptosis-related genes of ovarian cancer cell lines following cisplatin treatment. METHODS: We used IC(50) values and fluorescence-activated cell sorting analysis to compare cell death in 2 ovarian cancer cell lines, namely, SKOV-3 and OVCAR-3, upon treatment with cisplatin. Moreover, the change in transcriptional levels of apoptosis-associated genes was measured with a dendron-modified DNA microarray. RESULTS: The protein levels for the up-regulated genes in each cell line were validated to identify the molecules that may determine the cellular behavior of cisplatin resistance. Eight genes were over-expressed in the 2 cell lines. The cisplatin-induced up-regulation of DAD1 in transcriptional and protein levels contributed to the cisplatin resistance of OVCAR-3, and the up-regulation of FASTK and TNFRSF11A in SKOV-3 resulted in its higher sensitivity to cisplatin than that of OVCAR-3. CONCLUSION: In the present study, we have identified a set of genes responsible for apoptosis following cisplatin treatment in ovarian cancer cell lines. These genes may give information about the understanding of cisplatin-induced apoptosis in ovarian cancer.

The modification of alpha-synuclein by dicarbonyl compounds inhibits its fibril-forming process.

Oxidative modification of alpha-synuclein (alphaSyn) was reported to have significant effects on its amyloidogenic properties. Dicarbonyl compounds are metabolites accumulated by various oxidative processes in the intracellular environment. In this study, two dicarbonyl compounds, methylglyoxal (MGO) and glyoxal (GO), were investigated for their effects on the structural and fibril-forming properties of alphaSyn. Both compounds were found to induce the oligomerization of alphaSyn. By adding substoichiometric amounts of alphaSyn modified by MGO or GO, the fibrillization of alphaSyn was substantially inhibited. The heterogeneously-modified alphaSyns were separated into three fractions: monomers, oligomers, and high molecular mass oligomers. When each modified alphaSyn species was used to seed fibril formation, protein fibrillization was significantly suppressed. Temperature scanning and interactions with liposomes revealed that both MGO- and GO-modified monomers were not as susceptible as the unmodified alphaSyn to conformational changes into partially folded intermediates and alpha-helixes. Our observations suggest that dicarbonyl modification of alphaSyn reduces conformational flexibility of the protein, thereby contributing to a reduction in the ability of alphaSyn to form fibrils, and the modified protein inhibits the fibrillization of the unmodified alphaSyn.