Genome editing demonstrates that the -5 kb Nanog enhancer regulates Nanog expression by modulating RNAPII initiation and/or recruitment.

Transcriptional enhancers have been defined by their ability to operate independent of distance and orientation in plasmid-based reporter assays of gene expression. At present, histone marks are used to identify and define enhancers but do not consider the endogenous role of an enhancer in the context of native chromatin. We employed a combination of genomic editing, single cell analyses, and sequencing approaches to investigate a Nanog-associated cis-regulatory element, which has been reported by others to be either an alternative promoter or a super-enhancer. We first demonstrate both distance and orientation independence in native chromatin, eliminating the issues raised with plasmid-based approaches. We next demonstrate that the dominant super-enhancer modulates Nanog globally and operates by recruiting and/or initiating RNA Polymerase II. Our studies have important implications to how transcriptional enhancers are defined and how they regulate gene expression.

Safety Evaluation of Soy Leghemoglobin Protein Preparation Derived From Pichia pastoris, Intended for Use as a Flavor Catalyst in Plant-Based Meat.

The leghemoglobin protein (LegH) from soy ( Glycine max) expressed in Pichia pastoris (LegH preparation, LegH Prep) imparts a meat-like flavor profile onto plant-based food products. The safety of LegH Prep was evaluated through a series of in vitro and in vivo tests. The genotoxic potential of LegH Prep was assessed using the bacterial reverse mutation assay (Ames test) and the in vitro chromosome aberration test. LegH Prep was nonmutagenic and nonclastogenic in each test, respectively. Systemic toxicity was assessed in a 28-day dietary study in male and female Sprague Dawley rats. There were no mortalities associated with the administration of LegH Prep. There were no clinical observations, body weight, ophthalmological, clinical pathology, or histopathological changes attributable to LegH Prep administration. There were no observed effects on male reproduction in this study, but the suggestion of a potential estrous cycle distribution effect in female rats prompted a second comprehensive 28-day dietary study in female Sprague Dawley rats. This study demonstrated that female reproductive parameters were comparable between rats treated with LegH Prep and concurrent control rats. These studies establish a no observed adverse effect level of 750 mg/kg/d LegH, which is over 100 times greater than the 90th percentile estimated daily intake. Collectively, the results of the studies presented raise no issues of toxicological concern with regard to LegH Prep under the conditions tested.

Embryonic expression of EphA receptor genes in mice supports their candidacy for involvement in cleft lip and palate.

BACKGROUND: Eph receptors, comprising the A- and B-subfamilies, are the largest family of receptor tyrosine kinases in the mammalian genome, and their function is critical for morphogenesis in a variety of contexts. Whereas signaling through B-type Ephs has been demonstrated to play a role in cleft lip and palate (CL/P), the involvement of A-type Ephs has not been examined in this context notwithstanding a recent genome-wide association study that identified the EPHA3 locus as a candidate for non-syndromic CL/P. RESULTS: Here, we present a systematic analysis of the gene expression patterns for the nine EphA receptors at progressive stages of mouse development and find that EphA3, EphA4, and EphA7 exhibit restricted overlapping patterns of expression during palate development. We find that homozygous mutation of EphA3 or compound homozygous mutation of EphA3 and EphA4 in mice does not result in defective midfacial development, supporting the possibility of redundant function with EphA7. We also document previously undescribed expression patterns in other tissues of the craniofacial complex including the lacrimal duct and salivary glands. CONCLUSIONS: Together, these results are consistent with the hypothesis that mutations in EPHA family genes may cause CL/P and also suggest that functional redundancy between family members may be at play.

The Safety of Soy Leghemoglobin Protein Preparation Derived from Pichia pastoris Expressing a Soy Leghemoglobin Gene from Glycine max: In Vitro and In Vivo Studies.

Soy leghemoglobin (LegH) protein derived from soy (Glycine max) produced in Pichia pastoris (reclassified as Komagataella phaffii) as LegH Prep is a novel food ingredient that provides meat-like flavor and aroma to plant-derived food products. The safety of LegH Prep has been previously assessed in a battery of in vivo and in vitro testing and found no adverse effects under the conditions tested. In this new work, we present the results of new in vivo and in vitro tests evaluating the safety of LegH Prep. LegH Prep was nonmutagenic in a bacterial reverse mutation assay and nonclastogenic in an in vitro micronucleus assay in human lymphocytes. Systemic toxicity was evaluated in the 90 day dietary study in male and female Sprague-Dawley® rats that included a 28 day recovery period. The study resulted in no animal deaths associated with the administration of LegH Prep at the highest dose (90,000 ppm). There were no significant adverse clinical or physical changes attributed to LegH Prep administration, and no observed adverse effects on either male or female rats over the course of the 28 day recovery phase study. The new 90 day dietary toxicity study established a no observed adverse effect level (NOAEL) of 4798.3 and 5761.5 mg/kg/day, the maximum level tested for male and female rats, respectively. Thus, the results of the studies demonstrate that under the conditions tested, LegH Prep is not toxic for consumption in meat analog products.

Super-Enhancers and CTCF in Early Embryonic Cell Fate Decisions.

Cell fate decisions are the backbone of many developmental and disease processes. In early mammalian development, precise gene expression changes underly the rapid division of a single cell that leads to the embryo and are critically dependent on autonomous cell changes in gene expression. To understand how these lineage specifications events are mediated, scientists have had to look past protein coding genes to the cis regulatory elements (CREs), including enhancers and insulators, that modulate gene expression. One class of enhancers, termed super-enhancers, is highly active and cell-type specific, implying their critical role in modulating cell-type specific gene expression. Deletion or mutations within these CREs adversely affect gene expression and development and can cause disease. In this mini-review we discuss recent studies describing the potential roles of two CREs, enhancers and binding sites for CTCF, in early mammalian development.

A cohesive look at leukemogenesis: The cohesin complex and other driving mutations in AML.

Acute myeloid leukemia (AML) affects tens of thousands of patients a year, yet survival rates are as low as 25% in certain populations. This poor survival rate is partially due to the vast genetic diversity of the disease. Rarely do 2 patients with AML have the same mutational profile, which makes the development of targeted therapies particularly challenging. However, a set of recurrent mutations in chromatin modifiers have been identified in many patients, including mutations in the cohesin complex, which have been identified in up to 20% of cases. Interestingly, the canonical function of the cohesin complex in establishing sister chromatid cohesin during mitosis is unlikely to be the affected role in leukemogenesis. Instead, the cohesin complex's role in DNA looping and gene regulation likely facilitates disease. The epigenetic mechanisms by which cohesin complex mutations promote leukemia are not completely elucidated, but alterations of enhancer-promoter interactions and differential histone modifications have been shown to drive oncogenic gene expression changes. Such changes commonly include HoxA upregulation, which may represent a common pathway that could be therapeutically targeted. As cohesin mutations rarely occur alone, examining the impact of common co-occurring mutations, including those in NPM1, the core-binding factor complex, FLT3, and ASXL1, will yield additional insight. While further study of these mutational interactions is required, current research suggests that the use of combinatorial genetics could be the key to uncovering new targets, allowing for the treatment of AML patients based on their individual genetic profiles.

Genome-Wide Maps of Transcription Regulatory Elements and Transcription Enhancers in Development and Disease.

Gene expression is regulated by numerous elements including enhancers, insulators, transcription factors, and architectural proteins. Regions of DNA distal to the transcriptional start site, called enhancers, play a central role in the temporal and tissue-specific regulation of gene expression through RNA polymerase II. The identification of enhancers and other cis regulatory elements has largely been possible due to advances in next generation sequencing technologies. Enhancers regulate gene expression through chromatin loops mediated by architectural proteins such as YY1, CTCF, the cohesin complex, and LDB1. Additionally, enhancers can be transcribed to produce noncoding RNAs termed enhancer RNAs that likely participate in transcriptional regulation. The central role of enhancers in regulating gene expression implicates them in both normal physiology but also many disease states. The importance of enhancers is evident by the suggested role of SNPs, duplications, and other alterations of enhancer function in many diseases, ranging from cancer to atherosclerosis to chronic kidney disease. Although much progress has been made in recent years, the field of enhancer biology and our knowledge of the cis regulome remains a work in progress. This review will highlight recent seminal studies which demonstrate the role of enhancers in normal physiology and disease pathogenesis. © 2019 American Physiological Society. Compr Physiol 9:439-455, 2019.

Antioxidant and protective effects of Amrit Nectar tablets on adriamycin- and cisplatin-induced toxicities.

OBJECTIVES: Maharishi herbal food supplements have been shown to inhibit the growth of mammary tumors and reduce free radical-mediated injuries. The purpose of this investigation is to evaluate the effects of aqueous and alcoholic extracts of Amrit Nectar tablets on rat liver microsomal lipid peroxidation and compare to other antioxidants. The protective effects of dietary Amrit Nectar tablets (MA-7; containing 38 herbs) on cisplatin-induced changes in glutathione (GSH) and glutathione-S-transferase (GST) activity in rat liver and kidney, and Adriamycin (Pharmacia S.p.A, Milan, Italy)-induced mortalities in mice were also investigated. RESULTS: Both aqueous and alcoholic extracts of MA-7 were more potent than other antioxidants tested under our experimental conditions. Adriamycin (15 mg/kg, intraperitoneally) caused 60% mortality during the period of 4 weeks in CDF1 mice. Dietary MA-7 (0.7%) treatment decreased the mortality to 20%. Dietary MA-7 (0.7%) supplementation with cisplatin treatment reversed the effects of cisplatin on liver and kidney GSH and GST activity. CONCLUSIONS: These results indicate that MA-7 is a powerful antioxidant. MA-7 supplementation with Adriamycin and cisplatin treatment may protect against their toxicities.

Naringin does not alter caffeine pharmacokinetics, energy expenditure, or cardiovascular haemodynamics in humans following caffeine consumption.

1. Naringin, a grapefruit constituent interacts with many medications including caffeine, a popular weight loss supplement. The purpose of the current study was to identify changes in caffeine pharmacokinetics, resting energy expenditure (REE), oxygen consumption (VO(2)) and respiratory exchange ratio (RER) after an acute dosage of caffeine and naringin. 2. Using a double-blinded, counterbalanced design, REE, VO(2), and RER were measured before and systematically for 8 h after a single dosage of caffeine (CAF, 200 mg) with and without naringin (100 mg (CN100) or 200 mg (CN200)) in 10 apparently healthy individuals. A standardized meal was provided following 240-minute measurements (400 kcals; 35 g carbohydrate; 27 g protein; 7 g fat). 3. Caffeine, CN100, CN200 did not alter VO(2) or VO(2) area under the curve (137 301 +/- 8318, 139 729 +/- 9300, 134 297 +/- 8318, mL/480 min). Resting energy expenditure (k/cals) was 10.0 +/- 1.4% higher with CAF versus CN200 (6.0 +/- 1.4%) and CN100 (6 +/- 1.5%) at 240 min (P = 0.07) which was then negated following a standardized meal. Percent change in RER from pre to 240 min and pre to 480 min was not different between the CAF, CN100, or CN200 (-0.2 +/- 1.7%, 1.7 +/- 1.7%, -2.8 +/- 1.9%). 4. Although caffeine alone suggests a trend of increased REE, the results of the present study indicate that concurrent consumption of caffeine with naringin in acute dosages does not affect RER, VO(2), and prevents the increase of REE in adult humans. The results suggest that the interaction of grapefruit juice and caffeine may be due to constituents of grapefruit juice other than naringin or in addition to naringin.

Acacetin inhibits cell growth and cell cycle progression, and induces apoptosis in human prostate cancer cells: structure-activity relationship with linarin and linarin acetate.

This study was carried out to assess the anticancer efficacy of linarin (LN), linarin acetate (LA) and acacetin (AC), the flavonoid compounds with the same flavone ring structure but different substitution, against human prostate cancer (PCA), LNCaP and DU145 cells. LN was isolated and purified from Chrysanthemum zawadskii; LA was chemically synthesized from LN, and AC obtained commercially. In each case, the cells were treated with these agents at 25-100 microM doses for 24-72 h. LN and LA showed moderate cell growth inhibition with different time kinetics as compared to AC. LN caused up to a 5-fold increase in cell death and LA enhanced cell death by up to 4-fold with the increase in treatment time in both cell lines. AC showed a time- as well as dose-dependent stronger cell growth inhibition (20-70%) accompanied by cell death as compared to LN and LA in both the cell lines. LN or LA did not show any profound effect on cell cycle arrest except for a moderate G1 arrest, whereas, AC showed a stronger G1 and/or G2-M arrest depending on the doses and treatment times. G1 arrest was associated with an increase in Cip1/p21 and a decrease in CDK2, CDK4 and CDK6 protein levels. G2-M arrest was associated with a decrease in Cdc25C, Cdc2/p34 and cyclin B1, which were more prominent in LNCaP compared to DU145 cells. LN, LA and AC induced cell death was associated with significant increase in apoptosis induction (up to 5-6-fold) accompanied by poly-(ADP-ribose) polymerase cleavage. Overall, AC showed more potent anticancer efficacy among these three flavonoids, which was diminished when its flavone ring was modified by disaccharide rhamnose substitution at C7 (LN) or acetylation of this substituted group (LA). These findings, for the first time, revealed the structural determinants in anticancer efficacy and mechanisms of these three flavonoids against human PCA cells.