Integrating transcription-factor abundance with chromatin accessibility in human erythroid lineage commitment.

Master transcription factors (TFs) directly regulate present and future cell states by binding DNA regulatory elements and driving gene-expression programs. Their abundance influences epigenetic priming to different cell fates at the chromatin level, especially in the context of differentiation. In order to link TF protein abundance to changes in TF motif accessibility and open chromatin, we developed InTAC-seq, a method for simultaneous quantification of genome-wide chromatin accessibility and intracellular protein abundance in fixed cells. Our method produces high-quality data and is a cost-effective alternative to single-cell techniques. We showcase our method by purifying bone marrow (BM) progenitor cells based on GATA-1 protein levels and establish high GATA-1-expressing BM cells as both epigenetically and functionally similar to erythroid-committed progenitors.

Microbial byproducts determine reproductive fitness of free-living and parasitic nematodes.

Trichuris nematodes reproduce within the microbiota-rich mammalian intestine and lay thousands of eggs daily, facilitating their sustained presence in the environment and hampering eradication efforts. Here, we show that bacterial byproducts facilitate the reproductive development of nematodes. First, we employed a pipeline using the well-characterized, free-living nematode C. elegans to identify microbial factors with conserved roles in nematode reproduction. A screen for E. coli mutants that impair C. elegans fertility identified genes in fatty acid biosynthesis and ethanolamine utilization pathways, including fabH and eutN. Additionally, Trichuris muris eggs displayed defective hatching in the presence of fabH- or eutN-deficient E. coli due to reduced arginine or elevated aldehydes, respectively. T. muris reared in gnotobiotic mice colonized with these E. coli mutants displayed morphological defects and failed to lay viable eggs. These findings indicate that microbial byproducts mediate evolutionarily conserved transkingdom interactions that impact the reproductive fitness of distantly related nematodes.

Control of RNA with quinone methide reversible acylating reagents.

Caging RNA by polyacylation (cloaking) has been developed recently as a simple and rapid method to control the function of RNAs. Previous approaches for chemical reversal of acylation (uncloaking) made use of azide reduction followed by amine cyclization, requiring ∼2-4 h for the completion of cyclization. In new studies aimed at improving reversal rates and yields, we have designed novel acylating reagents that utilize quinone methide (QM) elimination for reversal. The QM de-acylation reactions were tested with two bioorthogonally cleavable motifs, azide and vinyl ether, and their acylation and reversal efficiencies were assessed with NMR and mass spectrometry on model small-molecule substrates as well as on RNAs. Successful reversal both with phosphines and strained alkenes was documented. Among the compounds tested, the azido-QM compound A-3 displayed excellent de-acylation efficiency, with t1/2 for de-acylation of less than an hour using a phosphine trigger. To test its function in RNA caging, A-3 was successfully applied to control EGFP mRNA translation in vitro and in HeLa cells. We expect that this molecular caging strategy can serve as a valuable tool for biological investigation and control of RNAs both in vitro and in cells.

Trapping Transient RNA Complexes by Chemically Reversible Acylation.

RNA-RNA interactions are essential for biology, but they can be difficult to study due to their transient nature. While crosslinking strategies can in principle be used to trap such interactions, virtually all existing strategies for crosslinking are poorly reversible, chemically modifying the RNA and hindering molecular analysis. We describe a soluble crosslinker design (BINARI) that reacts with RNA through acylation. We show that it efficiently crosslinks noncovalent RNA complexes with mimimal sequence bias and establish that the crosslink can be reversed by phosphine reduction of azide trigger groups, thereby liberating the individual RNA components for further analysis. The utility of the new approach is demonstrated by reversible protection against nuclease degradation and trapping transient RNA complexes of E. coli DsrA-rpoS derived bulge-loop interactions, which underlines the potential of BINARI crosslinkers to probe RNA regulatory networks.

Simple alkanoyl acylating agents for reversible RNA functionalization and control.

We describe the synthesis and RNA acylation activity of a series of minimalist azidoalkanoyl imidazole reagents, with the aim of functionalizing RNA at 2'-hydroxyl groups at stoichiometric to superstoichiometric levels. We find marked effects of small structural changes on their ability to acylate and be reductively removed, and identify reagents and methods that enable efficient RNA functionalization and control.

Exceptionally rapid oxime and hydrazone formation promoted by catalytic amine buffers with low toxicity.

Hydrazone and oxime bond formation between α-nucleophiles (e.g. hydrazines, alkoxy-amines) and carbonyl compounds (aldehydes and ketones) is convenient and is widely applied in multiple fields of research. While the reactants are simple, a substantial drawback is the relatively slow reaction at neutral pH. Here we describe a novel molecular strategy for accelerating these reactions, using bifunctional buffer compounds that not only control pH but also catalyze the reaction. The buffers can be employed at pH 5-9 (5-50 mM) and accelerate reactions by several orders of magnitude, yielding second-order rate constants of >10 M-1 s-1. Effective bifunctional amines include 2-(aminomethyl)imidazoles and N,N-dimethylethylenediamine. Unlike previous diaminobenzene catalysts, the new buffer amines are found to have low toxicity to human cells, and can be used to promote reactions in cellular applications.

Aldehyde dehydrogenase 3A1 activation prevents radiation-induced xerostomia by protecting salivary stem cells from toxic aldehydes.

Xerostomia (dry mouth) is the most common side effect of radiation therapy in patients with head and neck cancer and causes difficulty speaking and swallowing. Since aldehyde dehydrogenase 3A1 (ALDH3A1) is highly expressed in mouse salivary stem/progenitor cells (SSPCs), we sought to determine the role of ALDH3A1 in SSPCs using genetic loss-of-function and pharmacologic gain-of-function studies. Using DarkZone dye to measure intracellular aldehydes, we observed higher aldehyde accumulation in irradiated Aldh3a1-/- adult murine salisphere cells and in situ in whole murine embryonic salivary glands enriched in SSPCs compared with wild-type glands. To identify a safe ALDH3A1 activator for potential clinical testing, we screened a traditional Chinese medicine library and isolated d-limonene, commonly used as a food-flavoring agent, as a single constituent activator. ALDH3A1 activation by d-limonene significantly reduced aldehyde accumulation in SSPCs and whole embryonic glands, increased sphere-forming ability, decreased apoptosis, and improved submandibular gland structure and function in vivo after radiation. A phase 0 study in patients with salivary gland tumors showed effective delivery of d-limonene into human salivary glands following daily oral dosing. Given its safety and bioavailability, d-limonene may be a good clinical candidate for mitigating xerostomia in patients with head and neck cancer receiving radiation therapy.

Tumorigenicity Evaluation of Umbilical Cord Blood-derived Mesenchymal Stem Cells.

Mesenchymal stem cells (MSCs) have been identified in multiple types of tissue and exhibit characteristic self-renewal and multi-lineage differentiation abilities. However, the possibility of oncogenic transformation after transplantation is concerning. In this study, we investigated the tumorigenic potential of umbilical cord blood-derived MSCs (hUCB-MSCs) relative to MRC-5 and HeLa cells (negative and positive controls, respectively) both in vitro and in vivo. To evaluate tumorigenicity in vitro, anchorage-independent growth was assessed using the soft agar colony formation assay. hUCB-MSCs and MRC-5 cells formed few colonies, while HeLa cells formed a greater number of larger colonies, indicating that hUCB-MSCs and MRC-5 cells do not have anchorage-independent proliferation potential. To detect tumorigenicity in vivo, hUCB-MSCs were implanted as a single subcutaneous injection into BALB/c-nu mice. No tumor formation was observed in mice transplanted with hUCB-MSCs or MRC-5 cells based on macroand microscopic examinations; however, all mice transplanted with HeLa cells developed tumors that stained positive for a human gene according to immunohistochemical analysis. In conclusion, hUCB-MSCs do not exhibit tumorigenic potential based on in vitro and in vivo assays under our experimental conditions, providing further evidence of their safety for clinical applications.

Dark Hydrazone Fluorescence Labeling Agents Enable Imaging of Cellular Aldehydic Load.

Aldehydes are key intermediates in many cellular processes, from endogenous metabolic pathways like glycolysis to undesired exogenously induced processes such as lipid peroxidation and DNA interstrand cross-linking. Alkyl aldehydes are well documented to be cytotoxic, affecting the functions of DNA and protein, and their levels are tightly regulated by the oxidative enzyme ALDH2. Mutations in this enzyme are associated with cardiac damage, diseases such as Fanconi anemia (FA), and cancer. Many attempts have been made to identify and quantify the overall level of these alkyl aldehydes inside cells, yet there are few practical methods available to detect and monitor these volatile aldehydes in real time. Here, we describe a multicolor fluorogenic hydrazone transfer ("DarkZone") system to label alkyl aldehydes, yielding up to 30-fold light-up response in vitro. A cell-permeant DarkZone dye design was applied to detect small-molecule aldehydes in the cellular environment. The new dye design also enabled the monitoring of cellular acetaldehyde production from ethanol over time by flow cytometry, demonstrating the utility of the DarkZone dyes for measuring and imaging the aldehydic load related to human disease.

Gel-type autologous chondrocyte (Chondron) implantation for treatment of articular cartilage defects of the knee.

BACKGROUND: Gel-type autologous chondrocyte (Chondron) implantations have been used for several years without using periosteum or membrane. This study involves evaluations of the clinical results of Chondron at many clinical centers at various time points during the postoperative patient follow-up. METHODS: Data from 98 patients with articular cartilage injury of the knee joint and who underwent Chondron implantation at ten Korean hospitals between January 2005 and November 2008, were included and were divided into two groups based on the patient follow-up period, i.e. 13~24-month follow-up and greater than 25-month follow-up. The telephone Knee Society Score obtained during telephone interviews with patients, was used as the evaluation tool. RESULTS: On the tKSS-A (telephone Knee Society Score-A), the score improved from 43.52 +/- 20.20 to 89.71 +/- 13.69 (P < 0.05), and on the tKSS-B (telephone Knee Society Score-B), the score improved from 50.66 +/- 20.05 to 89.38 +/- 15.76 (P < 0.05). The total improvement was from 94.18 +/- 31.43 to 179.10 +/- 24.69 (P < 0.05). CONCLUSION: Gel-type autologous chondrocyte implantation for chondral knee defects appears to be a safe and effective method for both decreasing pain and improving knee function.

Clinical spectrum of reflux esophagitis among 25,536 Koreans who underwent a health check-up: a nationwide multicenter prospective, endoscopy-based study.

BACKGROUND: Gastroesophageal reflux is a commonly encountered condition, but detailed data on reflux symptoms in Asian countries are lacking. GOALS: To evaluate the prevalence and to document the clinical spectrum of endoscopic reflux esophagitis (RE). STUDY: A total 25,536 subjects underwent an upper gastrointestinal endoscopic examination as part of a health check, and completed a gastroesophageal reflux questionnaire. Endoscopic findings classified according to the Los Angeles (LA) classification and the data from gastroesophageal reflux questionnaire were analyzed. RESULTS: On the basis of endoscopic findings, 2019 subjects (7.91%) were found to have RE: 5.87% in LA-A; 1.84% in LA-B; 0.18% in LA-C; and 0.02% in LA-D. Heartburn, acid regurgitation, chest pain, hoarseness, globus sensation, cough, and epigastric soreness were found to be associated with RE (P<0.05). Heartburn, acid regurgitation, and epigastric soreness were more frequent in LA-B than in LA-A (P<0.05). Epigastric soreness was most bothersome in LA-A and LA-B, and acid regurgitation was most bothersome in LA-C and LA-D (P<0.01). Heartburn, hoarseness, and globus sensation were more frequent in men with RE, and acid regurgitation was most common in women. CONCLUSIONS: The prevalence of RE was found to be 7.91% in Korea, and the profiles of reflux symptoms were found to depend on grade of RE and sex.

Metachronous gastric MALT lymphoma and early gastric cancer: a case report.

Metachronous association between gastric lymphoma and early gastric cancer is a rare event. Recent studies have suggested that a relationship exists between gastric mucosa-associated lymphoid tissue (MALT) lymphoma and gastric carcinoma although the mechanism is unknown. Herein, we report a 53-year-old man who visited to our hospital due to melena. Esophagogastroduodenoscopy (EGD) revealed a MALT lymphoma on the greater curvature of lower body. The patient received anti-Helicobacter pylori eradication therapy, followed by 6 cycles of chemotherapy and radiation therapy, and achieved complete remission 12 months after the therapy. Three years later, he revisited our hospital with epigastric pain. EGD revealed an early gastric cancer on the anterior wall of proximal antrum, nearly opposite to the previous lymphoma site, and a partial gastrectomy was performed. To the best of our knowledge, this is the first case report of metachronous MALT lymphoma and subsequent gastric carcinoma in Korea.

[Genetic polymorphisms of alcohol-metabolizing enzymes and cytokines in patients with alcohol induced pancreatitis and alcoholic liver cirrhosis].

BACKGROUND/AIMS: Susceptibility to organ damage induced by alcohol may be related to inherited variations (polymorphisms) in alcohol-metabolizing enzymes, or polymorphisms affecting cytokines. The aim of this study was to compare the genotype and allelic frequencies of ADH2, ADH3, ALDH2, cytochrome P450-2E1, IL-1, IL-6, IL-8 and tumor necrosis factor-alpha in patients with alcoholic pancreatitis and alcoholic liver cirrhosis with those of controls. METHODS: We determined the polymorphism of genes of the above-mentioned alcohol-metabolizing enzymes and cytokines in 29 alcoholic pancreatitis patients (AP), 22 alcoholic liver cirrhosis patients (LC) and 100 healthy blood donors (control). The genotypes were characterized by restriction fragment length polymorphism after amplification of genomic DNA by polymerase chain reaction. RESULTS: The allelic frequency of CYP2E1*c2 was significantly different in three groups (AP: LC: Control=0.224: 0.136: 0.320, p<0.05). There was no significant difference in the other genotypes or allelic frequencies of the three groups. The allelic frequencies of CYP2E1*c2 and ALDH2*2 were more frequent in the control than patients with alcoholic liver cirrhosis (LC: Control=0.136: 0.320, p<0.05, LC: Control= 0.114: 0.265, p<0.05). Allelic frequencies of ADH2 was statistically different between LC and control (ADH2*1; LC: Control=0.727: 0.495, ADH2*2; 0.227: 0.360, ADH2*3; 0.046: 0.145, p<0.05). CONCLUSIONS: There was no difference in the frequencies of genotype and allele of enzymes and cytokines among the three groups. However, frequency of ADH2*1 was significantly higher and those of CYP2E1*c2 and ALDH2*2 were significantly lower than LC group than control.