Spontaneous histone exchange between nucleosomes.

The nucleosome is the fundamental gene-packing unit in eukaryotes. Nucleosomes comprise ∼147 bp DNA wrapped around an octameric histone protein core composed of two H2A-H2B dimers and one (H3-H4)2 tetramer. The strong yet flexible DNA-histone interactions are the physical basis of the dynamic regulation of genes packaged in chromatin. The dynamic nature of DNA-histone interactions also implies that nucleosomes dissociate DNA-histone contacts both transiently and repeatedly. This kinetic instability may lead to spontaneous nucleosome disassembly or histone exchange between nucleosomes. At high nucleosome concentrations, nucleosome-nucleosome collisions and subsequent histone exchange would be a more likely event, where nucleosomes could act as their own histone chaperone. This spontaneous histone exchange could serve as a mechanism for maintaining overall chromatin stability, although it has never been reported. Here we employed three-color single-molecule FRET (smFRET) to demonstrate that histone H2A-H2B dimers are exchanged spontaneously between nucleosomes on a time scale of a few tens of seconds at a physiological nucleosome concentration. We show that the rate of histone exchange increases at a higher monovalent salt concentration, with histone-acetylated nucleosomes, and in the presence of histone chaperone Nap1, while it remains unchanged at a higher temperature, and decreases upon DNA methylation. These results support the notion of histone exchange via transient and repetitive partial disassembly of the nucleosome and corroborate spontaneous histone diffusion in a compact chromatin context, modulating the local concentrations of histone modifications and variants.

Methods to investigate nucleosome structure and dynamics with single-molecule FRET.

The nucleosome is the fundamental building block of chromatin. Changes taking place at the nucleosome level are the molecular basis of chromatin transactions with various enzymes and factors. These changes are directly and indirectly regulated by chromatin modifications such as DNA methylation and histone post-translational modifications including acetylation, methylation, and ubiquitylation. Nucleosomal changes are often stochastic, unsynchronized, and heterogeneous, making it very difficult to monitor with traditional ensemble averaging methods. Diverse single-molecule fluorescence approaches have been employed to investigate the structure and structural changes of the nucleosome in the context of its interactions with various enzymes such as RNA Polymerase II, histone chaperones, transcription factors, and chromatin remodelers. We utilize diverse single-molecule fluorescence methods to study the nucleosomal changes accompanying these processes, elucidate the kinetics of these processes, and eventually learn the implications of various chromatin modifications in directly regulating these processes. The methods include two- and three-color single-molecule fluorescence resonance energy transfer (FRET), single-molecule fluorescence correlation spectroscopy, and fluorescence (co-)localization. Here we report the details of the two- and three-color single-molecule FRET methods we currently use. This report will help researchers design their single-molecule FRET approaches to investigating chromatin regulation at the nucleosome level.

Endoscopic resection and laparoscopic lymph node dissection for early gastric cancer beyond conventional endoscopic treatment indications: a 10-year outcome study.

BACKGROUND: Endoscopic full-thickness gastric resection (EFTGR) with laparoscopic regional lymph node dissection (LLND) and endoscopic submucosal dissection (ESD) with LLND have been investigated as treatment options for early gastric cancer beyond the absolute indications for ESD. However, comparative studies on the long-term outcomes of these procedures are lacking. This study aimed to analyze and compare the 10-year outcomes of both procedures in a real clinical setting. METHODS: Between January 2009 and December 2013, 28 and 37 patients diagnosed with EGC beyond the absolute indications for ESD were treated with EFTGR with LLND and ESD with LLND, respectively. In both procedures, the dye was injected into the tumor. However, after injection and LLND, EFTGR was performed immediately in the EFTGR with LLND group, whereas LLND was followed by ESD in the ESD with LLND group. The primary endpoint was the 10-year survival rate. RESULTS: The EFTGR with LLND group had one case of local recurrence (3.6%) and mortality (3.6%) each, while the ESD with LLND group had none (0.0% for both); however, the differences were not statistically significant (P = 0.247 for each). Furthermore, there was no significant difference in complications such as ischemia and anastomosis leakage between the groups (P = 0.247). CONCLUSIONS: When the procedures were properly applied, EFTGR with LLND and ESD with LLND did not increase the 10-year mortality in patients with EGC beyond the absolute ESD indications compared with conventional radical gastrectomy.

Da Vinci robot-assisted endoscopic full-thickness gastric resection with regional lymph node dissection using a 3D near-infrared video system: a single-center 5-year clinical outcome.

BACKGROUND: Endoscopic full-thickness gastric resection (EFTGR) with regional lymph node dissection (LND) has been used for early gastric cancer (EGC) exceeding the indications for endoscopic submucosal dissection (ESD). The extent of the dissected lymph nodes is crucial. A 3D near-infrared (NIR) video robot system significantly enhances visualization of the lymphatic system. However, this system has not been used in EFTGR with LND. Thus, this study assessed the benefits of the 3D NIR video robot system in a clinical setting. METHODS: Between February 2015 and September 2018, 24 patients with EGC exceeding the indications for ESD were treated with EFTGR and LND using a 3D NIR video system with the da Vinci surgical robot. Indocyanine green (ICG) was injected endoscopically around the tumor, and basin node (BN) dissection around the nodes was examined using the 3D NIR video system of the da Vinci Si surgical robot. Subsequently, robot-assisted EFTGR was performed. The primary outcome was the 5-year survival rate. RESULT: During a 5-year follow-up of all 24 patients, an 80-year-old patient with an ulcer and T2 invasion was lost to follow-up. Among the remaining 23 patients, no mortality or recurrence was observed. CONCLUSION: No metastasis or mortality occurred using the da Vinci robot-assisted EFTGR with LLND and a 3D NIR video system for patients who required radical gastrectomy for EGC in over 5 years. Hence, this may be a safe and effective method for radical gastrectomy; further studies are required confirming its effectiveness.

CT-based Hounsfield unit values reflect the degree of steatohepatitis in patients with low-grade fatty liver disease.

BACKGROUND/AIMS: Nonalcoholic fatty liver disease (NAFLD) is the most common liver disease worldwide. Ultrasound, the most used tool for diagnosing NAFLD, is operator-dependent and shows suboptimal performance in patients with mild steatosis. However, few studies have been conducted on whether alternative noninvasive methods are useful for diagnosing mild hepatic steatosis. Also, little is known about whether noninvasive tests are useful for grading the severity of hepatic steatosis or the degree of intrahepatic inflammation. Therefore, we aimed to evaluate whether the HSI, the FLI and HU values in CT could be used to discriminate mild hepatic steatosis and to evaluate the severity of hepatic steatosis or the degree of intrahepatic inflammation in patients with low-grade fatty liver disease using liver biopsy as a reference standard. METHODS: Demographic, laboratory, CT imaging, and histological data of patients who underwent liver resection or biopsy were analyzed. The performance of the HSI, HU values and the FLI for diagnosing mild hepatic steatosis was evaluated by calculating the area under the receiver operating characteristic curve. Whether the degree of hepatic steatosis and intrahepatic inflammation could be predicted using the HSI, HU values or the FLI was also analyzed. Moreover, we validate the results using magnetic resonance imaging proton density fat fraction as an another reference standard. RESULTS: The AUROC for diagnosing mild hepatic steatosis was 0.810 (p < 0.001) for the HSI, 0.732 (p < 0.001) for liver HU value, 0.802 (p < 0.001) for the difference between liver and spleen HU value (L-S HU value) and 0.813 (p < 0.001) for the FLI. Liver HU and L-S HU values were negatively correlated with the percentage of hepatic steatosis and NAFLD activity score (NAS) and significantly different between steatosis grades and between NAS grades. The L-S HU value was demonstrated the good performance for grading the severity of hepatic steatosis and the degree of intrahepatic inflammation. CONCLUSIONS: The HU values on CT are feasible for stratifying hepatic fat content and evaluating the degree of intrahepatic inflammation, and the HSI and the FLI demonstrated good performance with high sensitivity and specificity in diagnosing mild hepatic steatosis.

The Effects of Histone H2B Ubiquitylations on the Nucleosome Structure and Internucleosomal Interactions.

Eukaryotic gene compaction takes place at multiple levels to package DNA to chromatin and chromosomes. Two of the most fundamental levels of DNA packaging are at the nucleosome and dinucleosome stacks. The nucleosome is the basic gene-packing unit and is composed of DNA wrapped around a histone core. Nucleosomes stack with one another for further compaction of DNA. The first stacking step leads to dinucleosome formation, which is driven by internucleosomal interactions between various parts of two nucleosomes. Histone proteins are rich targets for post-translational modifications, some of which affect the structure of the nucleosome and the interactions between nucleosomes. These effects are often implicated in the regulation of various genomic transactions. In particular, histone H2B ubiquitylation has been associated with facilitated transcription and hexasome formation. Here, we employed semi-synthetically ubiquitylated histone H2B and single-molecule FRET to investigate the effects of H2B ubiquitylations at lysine 34 (H2BK34) and lysine 120 (H2BK120) on the structure of the nucleosome and the interactions between two nucleosomes. Our results suggest that H2BK34 ubiquitylation widens the DNA gyre gap in the nucleosome and stabilizes long- and short-range internucleosomal interactions while H2BK120 ubiquitylation does not affect the nucleosome structure or internucleosomal interactions. These results suggest potential roles for H2B ubiquitylations in facilitated transcription and hexasome formation while maintaining the structural integrity of chromatin.

Selective production of retinol by engineered Saccharomyces cerevisiae through the expression of retinol dehydrogenase.

Retinol is a fat-soluble vitamin A that is widely used in the food and pharmaceutical industries. Currently, retinol is commercially produced by chemical synthesis. Microbial production of retinol has been alternatively explored but restricted to a mixture of retinoids including retinol, retinal, and retinoic acid. Thus, we introduced heterologous retinol dehydrogenase into retinoids mixture-producing Saccharomyces cerevisiae for the selective production of retinol using xylose. Expression of human RDH10 and Escherichia coli ybbO led to increase in retinol production, but retinal remained as a major product. In contrast, S. cerevisiae harboring human RDH12 produced retinol selectively with negligible production of retinal. The resulting strain (SR8A-RDH12) produced retinol only. However, more glycerol was accumulated due to intracellular redox imbalance. Therefore, Lactococcus lactis noxE coding for H2 O-forming NADH oxidase was additionally introduced to resolve the redox imbalance. The resulting strain produced 52% less glycerol and more retinol with a 30% higher yield than a parental strain. As the produced retinol was not stable, we examined culture and storage conditions including temperature, light, and antioxidants for the optimal production of retinol. In conclusion, we achieved selective production of retinol efficiently from xylose by introducing human RDH12 and NADH oxidase into S. cerevisiae.

Association between long-term exposure to particulate matter and childhood cancer: A retrospective cohort study.

BACKGROUND: Although particulate matter is a known carcinogen, its association with childhood cancer is inconclusive. The present study aimed to examine the association between long-term exposure to particulate matter and childhood cancer. METHODS: A retrospective cohort was constructed from the claims database of the Korea National Health Insurance Service, including children born in seven metropolitan cities in Korea between 2002 and 2012. Monthly mean concentrations of particulate matter with aerodynamic diameter <10 µm (PM10) and other air pollutants (NO2, SO2, CO, and O3) were calculated using data from the AirKorea. Monthly mean concentrations of particulate matter with aerodynamic diameter <2.5 µm (PM2.5) were estimated based on a data fusion approach. Cumulative exposure was assessed by averaging the monthly concentrations accounting for the residential mobility of the children. The occurrence of cancer was identified by the appearance of diagnosis codes in the claims database. Hazard ratios (HR) and 95% confidence intervals (95% CI) were calculated using Cox proportional regression, adjusting for potential confounders and O3 concentrations. RESULTS: During the study period, 1,725 patients were newly diagnosed with cancer among 1,261,855 children. HR of all cancers per 10 µg/m3 increment in annual mean concentrations of PM2.5 and PM10 were 3.02 (95% CI: 1.63, 5.59) and 1.04 (0.74, 1.45), respectively. CONCLUSION: PM2.5 exposure was positively associated with childhood cancer in a large retrospective cohort with exposure assessment accounting for residential mobility.

Safety of Gastrointestinal Endoscopy in Korea: A Nationwide Survey and Population-Based Study.

BACKGROUND: Attention should be paid to endoscopy-related complications and safety-related accidents that may occur in the endoscopy unit. This study investigated the current status of complications associated with diagnostic and therapeutic endoscopy in Korea. METHODS: A questionnaire survey on endoscopy-related complications was conducted in a total of 50 tertiary or general hospitals in Korea. The results were compared to the population-level claims data from the Health Insurance Review & Assessment Service (HIRA), which analyzed endoscopy procedures conducted in 2017 in Korea. RESULTS: The incidences of bleeding associated with diagnostic and therapeutic esophagogastroduodenoscopy (EGD) and with diagnostic and therapeutic colonoscopy were 0.224% and 3.155% and 0.198% and 0.356%, respectively, in the 2017 HIRA claims data, compared to 0.012% and 1.857%, and 0.024% and 0.717%, in the 50 hospitals surveyed. The incidences of perforation associated with diagnostic and therapeutic EGD and with diagnostic and therapeutic colonoscopy were 0.023% and 0.613%, and 0.007% and 0.013%, respectively, in the 2017 HIRA claims data compared to 0.001% and 0.325%, and 0.017% and 0.206%, in the 50 hospitals surveyed. In the HIRA claims data, the incidence of bleeding/perforation after diagnostic colonoscopy in clinics, community hospitals, general hospitals, and tertiary hospitals was 0.129%/0.000%, 0.088%/0.004%, 0.262%/0.009%, and 0.479%/0.030% respectively, and the corresponding incidence of bleeding/perforation after therapeutic colonoscopy was 0.258%/0.004%, 0.401%/0.007%, 0.408%/0.024%, and 0.731%/0.055%. CONCLUSION: The incidences of complications associated with diagnostic and therapeutic EGD or colonoscopy tended to increase with the hospital volume in Korea. TRIAL REGISTRATION: Clinical Research Information Service Identifier: KCT0001728.

Alertness during working hours among eight-hour rotating-shift nurses: An observational study.

PURPOSE: The aim of this study was to identify the patterns of the decline in the alertness of rotating-shift nurses during working hours across different shift types (day, evening, and night) using an objective measure. DESIGN: An observational study using ReadiBand wrist actigraphs was conducted. METHODS: Data were collected from June 2019 to February 2020. Participants were rotating-shift nurses (N = 82) who provided direct nursing care for patients in acute care hospitals in South Korea. Nurses wore actigraphs continuously for 14 days on their non-dominant hand to identify sleep-wake cycles and predict their alertness scores hourly. All participants completed a sleep diary. FINDINGS: Nurses working during night shifts had lower average alertness scores (mean = 77.12) than nurses working during day (mean = 79.05) and evening (mean = 91.21). Overall, alertness showed a declining trend and the specific patterns of decline differed across shifts. Participants with alertness scores less than 70 or 80 demonstrated a significant decline in alertness across all shifts. CONCLUSIONS: Distinct patterns of decline in alertness per nursing shift were revealed. Each shift feature should be considered when developing interventions to increase nurses' alertness, promote high-quality care provision, and ensure patient safety. CLINICAL RELEVANCE: The implementation of interventions to increase alertness among shift nurses is needed at the organizational level, and the cooperation of nursing managers and administrators is required.

Enzyme aggregation and fragmentation induced by catalysis relevant species.

It is usually assumed that enzymes retain their native structure during catalysis. However, the aggregation and fragmentation of proteins can be difficult to detect and sometimes conclusions are drawn based on the assumption that the protein is in its native form. We have examined three model enzymes, alkaline phosphatase (AkP), hexokinase (HK) and glucose oxidase (GOx). We find that these enzymes aggregate or fragment after addition of chemical species directly related to their catalysis. We used several independent techniques to study this behavior. Specifically, we found that glucose oxidase and hexokinase fragment in the presence of D-glucose but not L-glucose, while hexokinase aggregates in the presence of Mg2+ ion and either ATP or ADP at low pH. Alkaline phosphatase aggregates in the presence of Zn2+ ion and inorganic phosphate. The aggregation of hexokinase and alkaline phosphatase does not appear to attenuate their catalytic activity. Our study indicates that specific multimeric structures of native enzymes may not be retained during catalysis and suggests pathways for different enzymes to associate or separate over the course of substrate turnover.

PCNA Monoubiquitination Is Regulated by Diffusion of Rad6/Rad18 Complexes along RPA Filaments.

Translesion DNA synthesis (TLS) enables DNA replication through damaging modifications to template DNA and requires monoubiquitination of the proliferating cell nuclear antigen (PCNA) sliding clamp by the Rad6/Rad18 complex. This posttranslational modification is critical to cell survival following exposure to DNA-damaging agents and is tightly regulated to restrict TLS to damaged DNA. Replication protein A (RPA), the major single-strand DNA (ssDNA) binding protein complex, forms filaments on ssDNA exposed at TLS sites and plays critical yet undefined roles in regulating PCNA monoubiquitination. Here, we utilize kinetic assays and single-molecule FRET microscopy to monitor PCNA monoubiquitination and Rad6/Rad18 complex dynamics on RPA filaments, respectively. Results reveal that a Rad6/Rad18 complex is recruited to an RPA filament via Rad18·RPA interactions and randomly translocates along the filament. These translocations promote productive interactions between the Rad6/Rad18 complex and the resident PCNA, significantly enhancing monoubiquitination. These results illuminate critical roles of RPA in the specificity and efficiency of PCNA monoubiquitination and represent, to the best of our knowledge, the first example of ATP-independent translocation of a protein complex along a protein filament.

Single-molecule FRET method to investigate the dynamics of transcription elongation through the nucleosome by RNA polymerase II.

Transcription elongation through the nucleosome is a precisely coordinated activity to ensure timely production of RNA and accurate regulation of co-transcriptional histone modifications. Nucleosomes actively participate in transcription regulation at various levels and impose physical barriers to RNA polymerase II (RNAPII) during transcription elongation. Despite its high significance, the detailed dynamics of how RNAPII translocates along nucleosomal DNA during transcription elongation and how the nucleosome structure dynamically conforms to the changes necessary for RNAPII progression remain poorly understood. Transcription elongation through the nucleosome is a complex process and investigating the changes of the nucleosome structure during this process by ensemble measurements is daunting. This is because it is nearly impossible to synchronize elongation complexes within a nucleosome or a sub-nucleosome to a designated location at a high enough efficiency for desired sample homogeneity. Here we review our recently developed single-molecule FRET experimental system and method that has fulfilled this deficiency. With our method, one can follow the changes in the structure of individual nucleosomes during transcription elongation. We demonstrated that this method enables the detailed measurements of the kinetics of transcription elongation through the nucleosome and its regulation by a transcription factor, which can be easily extended to investigations of the roles of environmental variables and histone post-translational modifications in regulating transcription elongation.

Super-Resolution Optical Lithography with DNA.

We developed an efficient, versatile, and accessible super-resolution microscopy method to construct a nanoparticle assembly at a spatial resolution below the optical diffraction limit. The method utilizes DNA and a photoactivated DNA cross-linker. Super-resolution optical techniques have been used only as a means to make measurements below the light diffraction limit. Furthermore, no optical technique is currently available to construct nanoparticle assemblies with a precisely designed shape and internal structure at a resolution of a few tens of nanometers (nm). Here we demonstrate that we can fulfill this deficiency by utilizing spontaneous structural dynamics of DNA hairpins combined with single-molecule fluorescence resonance energy transfer (smFRET) microscopy and a photoactivated DNA cross-linker. The stochastic fluorescence blinking due to the spontaneous folding and unfolding motions of DNA hairpins enables us to precisely localize a folded hairpin and solidify it only when it is within a predesigned target area whose size is below the diffraction limit. As the method is based on an optical microscope and an easily clickable DNA cross-linking reagent, it will provide an efficient means to create large nanoparticle assemblies with a shape and internal structure at an optical super-resolution, opening a wide window of opportunities toward investigating their photophysical and optoelectronic properties and developing novel devices.

Clinical significance of atypical protein kinase C (PKCι and PKCζ) and its relationship with yes-associated protein in lung adenocarcinoma.

BACKGROUND: Protein kinase C iota (PKCι) and protein kinase C zeta (PKCζ) are two atypical protein kinase (aPKC) enzymes that contribute to cell proliferation and cancer development. The Hippo/YAP pathway is commonly disrupted and upregulated in cancers. Herein, the expression patterns and clinical relevance of PKCι and PKCζ are evaluated in relation to YAP, a downstream effector of Hippo, in lung adenocarcinoma (LAC). The protein and mRNA expression levels of PKCι, PKCζ, YAP, and their phosphorylated forms, namely p-PKCι, p-PKCζ and p-YAP, are evaluated in relation to clinicopathological factors, including patient survival. METHODS: A total of 200 primary LAC tissue samples were examined by immunohistochemistry for PKCι, p-PKCι, PKCζ, p-PKCζ, YAP, and p-YAP protein expression. Sixty pairs of LAC and non-neoplastic lung tissue samples were assessed for PRKCI, PRKCZ, and YAP mRNA levels. PKCι, p-PKCι, PKCζ, and p-PKCζ protein expression were evaluated by Western blot analysis in the PC9 and PC9/GR LAC cell lines with YAP modulation. RESULTS: LAC demonstrated cytoplasmic PKCι, p-PKCι, PKCζ, and p-PKCζ immunostaining patterns. Positive aPKC protein expressions were related with poor patient survival. Especially, increased p-PKCι protein expression was significantly correlated with higher pathological stage and shortened overall survival. YAP overexpression contributes phosphorylation of PKCι and PKCζ protein expression in the LAC cell line. CONCLUSIONS: PKCι and PKCζ are related to YAP in LAC. PKCι and PKCζ play distinct roles in LAC; specifically, p-PKCι overexpression is suggested to underlie factors that indicate a poor prognosis.

Therapeutic Outcome of Achalasia Based on High-Resolution Manometry: A Korean Multicenter Study.

BACKGROUND: Because achalasia subtype is associated with therapeutic response, it is possible that regional differences in subtype distribution could lead to differences in therapeutic outcomes. STUDY QUESTION: We aimed to evaluate and compare high-resolution manometry (HRM) profiles among the different subtypes of achalasia and to elucidate predictive factors associated with treatment outcomes. STUDY DESIGN: Patients who were diagnosed with achalasia using HRM at 4 Korean university hospitals were retrospectively identified and analyzed. Sixty-four patients with untreated achalasia were divided into 3 subtypes using the Chicago classification system. MEASURES AND OUTCOMES: Clinical characteristics, manometric features, and treatment outcomes were compared. RESULTS: Among 64 patients diagnosed with achalasia, 31 patients were classified as type I, 27 as type II, and 6 as type III. Regarding HRM parameters, there were statistically significant differences in basal lower esophageal sphincter pressure, 4-second-integrated relaxation pressure, residual upper esophageal sphincter pressure, body amplitude, and maximal intrabolus pressure between subtypes. Regarding therapeutic outcome, type II patients (overall success rate of 80.0%) were more likely to respond than type I (55.2%) or type III (33.2%) patients. Multivariate analysis demonstrated that achalasia subtype (type I vs. III, P = 0.072; type II vs. III, P = 0.005), therapeutic modality (dilation vs. pharmacologic, P = 0.013; laparoscopic Heller's myotomy vs. pharmacologic, P = 0.006), and HRM-measured esophageal length (<27.5 vs. ≥27.5 cm, P = 0.014) are independent predictive factors for therapeutic failure. CONCLUSIONS: Patients with type II achalasia had better treatment outcomes than patients with other achalasia subtypes. Achalasia subtype, therapeutic modality, and esophageal length are independent predictive factors of therapeutic outcome.

Efficacy and Safety of Tenofovir Disoproxil Fumarate in Treatment-Naïve Patients with Chronic Hepatitis B in Korea.

AIMS: To evaluate the efficacy and safety of 144-week tenofovir disoproxil fumarate (TDF) therapy in treatment-naïve chronic hepatitis B (CHB) patients in Korean. METHODS: In total, 579 treatment-naïve CHB patients at 11 medical centers were enrolled retrospective and prospective from September 2015 to January 2016 by design (NCT02533544). We evaluated the complete virologic response (CVR) rate and the renal safety of TDF. RESULTS: The overall CVR rate was 69.4%, 87.0%, and 89.7% at weeks 48, 96, and 144, respectively. In the HBeAg-positive CHB patients, the CVR rate at weeks 48, 96, and 144 was 61.4%, 83.1%, and 89.6%, respectively. The rates of HBeAg loss and seroconversion at weeks 48, 96, and 144 were 16.6%, 23.5%, 34.1%, and 7.6%, 8.9%, 13.3%, respectively. In HBeAg-negative CHB patients, the CVR rate at weeks 48, 96, and 144 was 82.5%, 93.2%, and 90.0%, respectively. The rate of alanine aminotransferase normalization was 36.9%, 45.4%, and 46.8% at weeks 48, 96, and 144, respectively. Of the CHB patients, 0.9% showed an elevated creatinine (> 0.5 mg/dL from baseline). Age (≥ 60 years) was significantly associated with a decline in renal function at week 144 (P < 0.0001). Comorbidities (diabetes or hypertension) showed the tendency to reduce renal function (P = 0.0624). Hepatocellular carcinoma developed in 10 (1.7%) patients and was related to cirrhosis. CONCLUSIONS: TDF therapy induced sustained viral suppression and had a favorable safety profile over a 3-year period. However, close monitoring of renal function should be mandatory in treating CHB patients receiving TDF, particularly older patients.

Human Placenta Hydrolysate Promotes Liver Regeneration via Activation of the Cytokine/Growth Factor-Mediated Pathway and Anti-oxidative Effect.

Liver regeneration is a very complex process and is regulated by several cytokines and growth factors. It is also known that liver transplantation and the regeneration process cause massive oxidative stress, which interferes with liver regeneration. The placenta is known to contain various physiologically active ingredients such as cytokines, growth factors, and amino acids. In particular, human placenta hydrolysate (hPH) has been found to contain many amino acids. Most of the growth factors found in the placenta are known to be closely related to liver regeneration. Therefore, in this study, we investigated whether hPH is effective in promoting liver regeneration in rats undergoing partial hepatectomy. We confirmed that cell proliferation was significantly increased in HepG2 and human primary cells. Hepatocyte proliferation was also promoted in partial hepatectomized rats by hPH treatment. hPH increased liver regeneration rate, double nucleic cell ratio, mitotic cell ratio, proliferating cell nuclear antigen (PCNA), and Ki-67 positive cells in vivo as well as interleukin (IL)-6, tumor necrosis factor alpha (TNF-α), and hepatocyte growth factor (HGF). Moreover, Kupffer cells secreting IL-6 and TNF-α were activated by hPH treatment. In addition, hPH reduced thiobarbituric acid reactive substances (TBARs) and significantly increased glutathione (GSH), glutathione peroxidase (GPx), and superoxide dismutase (SOD). Taken together, these results suggest that hPH promotes liver regeneration by activating cytokines and growth factors associated with liver regeneration and eliminating oxidative stress.

The elongation factor Spt4/5 regulates RNA polymerase II transcription through the nucleosome.

RNA polymerase II (RNAPII) passes through the nucleosome in a coordinated manner, generating several intermediate nucleosomal states as it breaks and then reforms histone-DNA contacts ahead of and behind it, respectively. Several studies have defined transcription-induced nucleosome intermediates using only RNA Polymerase. However, RNAPII is decorated with elongation factors as it transcribes the genome. One such factor, Spt4/5, becomes an integral component of the elongation complex, making direct contact with the 'jaws' of RNAPII and nucleic acids in the transcription scaffold. We have characterized the effect of incorporating Spt4/5 into the elongation complex on transcription through the 601R nucleosome. Spt4/5 suppressed RNAPII pausing at the major H3/H4-induced arrest point, resulting in downstream re-positioning of RNAPII further into the nucleosome. Using a novel single molecule FRET system, we found that Spt4/5 affected the kinetics of DNA re-wrapping and stabilized a nucleosomal intermediate with partially unwrapped DNA behind RNAPII. Comparison of nucleosomes of different sequence polarities suggest that the strength of the DNA-histone interactions behind RNAPII specifies the Spt4/5 requirement. We propose that Spt4/5 may be important to coordinate the mechanical movement of RNAPII through the nucleosome with co-transcriptional chromatin modifications during transcription, which is affected by the strength of histone-DNA interactions.

DNA Oxidation and Excision Repair Pathways.

The physiological impact of the aberrant oxidation products on genomic DNA were demonstrated by embryonic lethality or the cancer susceptibility and/or neurological symptoms of animal impaired in the base excision repair (BER); the major pathway to maintain genomic integrity against non-bulky DNA oxidation. However, growing evidence suggests that other DNA repair pathways or factors that are not primarily associated with the classical BER pathway are also actively involved in the mitigation of oxidative assaults on the genomic DNA, according to the corresponding types of DNA oxidation. Among others, factors dedicated to lesion recognition in the nucleotide excision repair (NER) pathway have been shown to play eminent roles in the process of lesion recognition and stimulation of the enzyme activity of some sets of BER factors. Besides, substantial bulky DNA oxidation can be preferentially removed by a canonical NER mechanism; therefore, loss of function in the NER pathway shares common features arising from BER defects, including cancer predisposition and neurological disorders, although NER defects generally are nonlethal. Here we discuss recent achievements for delineating newly arising roles of NER lesion recognition factors to facilitate the BER process, and cooperative works of BER and NER pathways in response to the genotoxic oxidative stress.