Focal deletions of a promoter tether activate the IRX3 oncogene in T-cell acute lymphoblastic leukemia.

Oncogenes can be activated in cis through multiple mechanisms including enhancer hijacking events and noncoding mutations that create enhancers or promoters de novo. These paradigms have helped parse somatic variation of noncoding cancer genomes, thereby providing a rationale to identify noncanonical mechanisms of gene activation. Here we describe a novel mechanism of oncogene activation whereby focal copy number loss of an intronic element within the FTO gene leads to aberrant expression of IRX3, an oncogene in T cell acute lymphoblastic leukemia (T-ALL). Loss of this CTCF bound element downstream to IRX3 (+224 kb) leads to enhancer hijack of an upstream developmentally active super-enhancer of the CRNDE long noncoding RNA (-644 kb). Unexpectedly, the CRNDE super-enhancer interacts with the IRX3 promoter with no transcriptional output until it is untethered from the FTO intronic site. We propose that 'promoter tethering' of oncogenes to inert regions of the genome is a previously unappreciated biological mechanism preventing tumorigenesis.

Noncoding mutations drive persistence of a founder preleukemic clone which initiates late relapse in T-ALL.

ABSTRACT: T-ALL relapse usually occurs early but can occur much later, which has been suggested to represent a de novo leukemia. However, we conclusively demonstrate late relapse can evolve from a pre-leukemic subclone harbouring a non-coding mutation that evades initial chemotherapy.

Silica Microparticles from Sugarcane By-Products as an Encapsulation System for Retinoids Aimed at Topical Sustained Release.

The encapsulation of retinol within silica microparticles has emerged as a promising opportunity in the realm of cosmetic and pharmaceutical formulations, driven by the need to reinforce the photoprotection and oxidation stability of retinol. This work examines the process of encapsulating retinol into silica microparticles. The association efficiency, microparticle size, molecular structure, morphology, oxidation, and release profile, as well as biocompatibility and skin sensitization, were evaluated. Results showed that 0.03% of retinol and 9% of emulsifier leads to an association efficiency higher than 99% and a particle size with an average of 5.2 µm. FTIR results indicate that there is an association of retinol with the silica microparticles, and some may be on the surface. Microscopy indicates that when association happens, there is less aggregation of the particles. Oxidation occurs in two different phases, the first related to the retinol on the surface and the second to the associated retinol. In addition, a burst release of up to 3 h (30% free retinol, 17% associated retinol) was observed, as well as a sustained release of 44% of retinol up to 24 h. Encapsulation allowed an increase in the minimal skin cytotoxic concentrations of retinol from 0.04 µg/mL to 1.25 mg/mL without skin sensitization. Overall, retinol is protected when associated with silica microparticles, being safe to use in cosmetics and dermatology.

Enzymatic production of xylooligosaccharides from Brazilian Syrah grape pomace flour: a green alternative to conventional methods for adding value to agricultural by- products.

BACKGROUND: The aim of this work was to determine the most favorable conditions for the production of xylooligosaccharides (XOS) from Brazilian Syrah grape pomace. Chemical processes were performed using a rotatable central composite design where the concentration of sulfuric acid or sodium hydroxide and the grape pomace flour/solvent mass ratio were the dependent variables. Enzymatic production was also evaluated using xylanase produced by Aspergillus niger 3T5B8 and Viscozyme® enzymatic commercial cocktail. RESULTS: Chemical extraction allowed to recover 21.8-74.6% and 5.2-96.3% of total XOS for acidic and alkaline processes respectively. Enzymatic production extracted up to 88.68 ± 0.12% of total XOS using xylanase and up to 84.09 ± 2.40% with Viscozyme® . CONCLUSION: The present study demonstrated different feasible methods to produce high-added-value molecules, i.e. XOS, from Syrah grape pomace flour, valorizing this major by-product. The use of enzymatic cocktails demonstrated to be an alternative to the conventional methods, allowing to obtain an eco-friendly and sustainable grape pomace extract. © 2018 Society of Chemical Industry.

Benzobisthiazoles Represent a Novel Scaffold for Kinase Inhibitors of CLK Family Members.

Protein kinases are essential regulators of most cellular processes and are involved in the etiology and progression of multiple diseases. The cdc2-like kinases (CLKs) have been linked to various neurodegenerative disorders, metabolic regulation, and virus infection, and the kinases have been recognized as potential drug targets. Here, we have developed a screening workflow for the identification of potent CLK2 inhibitors and identified compounds with a novel chemical scaffold structure, the benzobisthiazoles, that has not been previously reported for kinase inhibitors. We propose models for binding of these compounds to CLK family proteins and key residues in CLK2 that are important for the compound interactions and the kinase activity. We identified structural elements within the benzobisthiazole that determine CLK2 and CLK3 inhibition, thus providing a rationale for selectivity assays. In summary, our results will inform structure-based design of CLK family inhibitors based on the novel benzobisthiazole scaffold.

Cell-type-specific transcriptional regulation of PIGM underpins the divergent hematologic phenotype in inherited GPl deficiency.

A rare point mutation in the core promoter -270GC-rich box of PIGM, a housekeeping gene, disrupts binding of the generic transcription factor (TF) Sp1 and causes inherited glycosylphosphatidylinositol (GPI) deficiency (IGD). We show that whereas PIGM messenger RNA levels and surface GPI expression in IGD B cells are low, GPI expression is near normal in IGD erythroid cells. This divergent phenotype results from differential promoter chromatin accessibility and binding of Sp1. Specifically, whereas PIGM transcription in B cells is dependent on Sp1 binding to the -270GC-rich box and is associated with lower promoter accessibility, in erythroid cells, Sp1 activates PIGM transcription by binding upstream of (but not to) the -270GC-rich box. These findings explain intact PIGM transcription in IGD erythroid cells and the lack of clinically significant intravascular hemolysis in patients with IGD. Furthermore, they provide novel insights into tissue-specific transcriptional control of a housekeeping gene by a generic TF.

Transcriptional and epigenetic basis for restoration of G6PD enzymatic activity in human G6PD-deficient cells.

HDAC inhibitors (HDACi) increase transcription of some genes through histone hyperacetylation. To test the hypothesis that HDACi-mediated enhanced transcription might be of therapeutic value for inherited enzyme deficiency disorders, we focused on the glycolytic and pentose phosphate pathways (GPPPs). We show that among the 16 genes of the GPPPs, HDACi selectively enhance transcription of glucose 6-phosphate dehydrogenase (G6PD). This requires enhanced recruitment of the generic transcription factor Sp1, with commensurate recruitment of histone acetyltransferases and deacetylases, increased histone acetylation, and polymerase II recruitment to G6PD. These G6PD-selective transcriptional and epigenetic events result in increased G6PD transcription and ultimately restored enzymatic activity in B cells and erythroid precursor cells from patients with G6PD deficiency, a disorder associated with acute or chronic hemolytic anemia. Therefore, restoration of enzymatic activity in G6PD-deficient nucleated cells is feasible through modulation of G6PD transcription. Our findings also suggest that clinical consequences of pathogenic missense mutations in proteins with enzymatic function can be overcome in some cases by enhancement of the transcriptional output of the affected gene.

Mechanism of Polycomb recruitment to CpG islands revealed by inherited disease-associated mutation.

How the transcription repressing complex Polycomb interacts with transcriptional regulators at housekeeping genes in somatic cells is not well understood. By exploiting a CpG island (CGI) point mutation causing a Mendelian disease, we show that DNA binding of activating transcription factor (TF) determines histone acetylation and nucleosomal depletion commensurate with Polycomb exclusion from the target promoter. Lack of TF binding leads to reversible transcriptional repression imposed by nucleosomal compaction and consolidated by Polycomb recruitment and establishment of bivalent chromatin status. Thus, within a functional hierarchy of transcriptional regulators, TF binding is the main determinant of Polycomb recruitment to the CGI of a housekeeping gene in somatic cells.

Sugarcane Straw as a Source of Arabinoxylans: Optimization and Economic Viability of a Two-Step Alkaline Extraction.

Sugarcane processing produces a significant amount of byproducts in the form of straw and bagasse, which are rich in cellulose, hemicellulose, and lignin. This work aims to provide a valorization approach to sugarcane straw by optimizing a two-step alkaline extraction of arabinoxylans by a response surface methodology to evaluate a potential industrial-scale production. Sugarcane straws were delignified using an alkaline-sulfite pretreatment, followed by alkaline extraction and precipitation of arabinoxylan, a two-step process optimized using a response surface methodology. A KOH concentration of (2.93-17.1%) and temperature (18.8-61.2 °C) were chosen as independent variables, and the arabinoxylan yield (%) as a response variable. The model application shows that KOH concentration, temperature, and the interaction between both independent variables are significant in extracting arabinoxylans from straw. The best-performing condition was further characterized by FTIR, DSC, and chemical and molecular weight evaluation. The straws arabinoxylans presented high purities levels, ca. 69.93%, and an average molecular weight of 231 kDa. The overall estimated production cost of arabinoxylan from straw was 0.239 €/g arabinoxylan. This work demonstrates a two-step alkaline extraction of the arabinoxylans method, as well as their chemical characterization and economic viability analysis, that can be used as a model for industrial scale-up production.

Biogenic silica microparticles as a new and sustainable cosmetic ingredient: Assessment of performance and quality parameters.

The demand for sustainable products is increasing worldwide and cosmetic industry is not an exception. Besides exploring nature as source of new ingredients, their production must be sustainable and should use environmentally friendly processes. In this work, biogenic silica microparticles were synthesized from sugarcane ash, and their potential application as cosmetic and skincare ingredient was evaluated. For such application, several properties were validated, including cytotoxicity in skin keratinocytes, potential sensitization effect on skin peptides, stimulation of pro-collagen I alpha 1, wound healing capacity, as well as the ingredient stability along a storage period. Biogenic silica showed to be non-cytotoxic on skin keratinocytes, at concentrations up to 5 wt%, and non-skin sensitizer. A positive effect on the stimulation of pro-collagen I alpha 1 suggests a potential anti-ageing activity, while the migration of fibroblasts to a wounded area suggests a regenerative capacity. Under an accelerated stability study, biogenic silica showed an increase on the loss on drying, but no changes were observed on its functional properties, mainly oil absorption capacity, as well the microbiological quality, which was maintained. Overall, novel biogenic silica microparticles produced from a sustainable source are safe, stable over time and have potential to be used as a cosmetic and skincare ingredient.

A Case of Late Diagnosis of Latent Autoimmune Diabetes in Adults.

Latent autoimmune diabetes of adults (LADA) is a type of autoimmune diabetes that begins in adulthood (usually after the age of 35 years); its main feature is the presence of diabetes-associated autoantibodies (most often autoantibody against glutamic acid decarboxylase), which leads to progressive destruction of the islets of Langerhans. This is a heterogeneous condition that presents with clinical and laboratory manifestations common to type 1 diabetes and type 2 diabetes. We report a case of a 71-year-old man diagnosed with type 2 diabetes two years ago, poorly controlled with oral antidiabetic therapy, and worsening in the third year. He had a positive family history of type 2 diabetes in two second-degree relatives (nephews). No pathologic findings at the physical examination were found. His body mass index was 23 kg/m2 and glycated hemoglobin was 10.6%. Laboratory workup revealed low basal C-peptide (<0.1 ng/mL) and positive glutamic acid decarboxylase antibodies, and the LADA diagnosis was confirmed. This case highlights the importance of being aware of this disease, especially in patients previously diagnosed with type 2 diabetes who remain uncontrolled with diet and oral hypoglycemic agents. LADA is often confused with type 2 diabetes, and therefore, the management is frequently inadequate. An early diagnosis and treatment are crucial to delaying disease progression.

Valorization of Sugarcane By-Products through Synthesis of Biogenic Amorphous Silica Microspheres for Sustainable Cosmetics.

Ashes from sugarcane by-product incineration were used to synthesize silica powders through alkaline hot extraction, followed by ethanol/acid precipitation or the sol-gel method. Both production methods allowed amorphous spherical silica microparticles with sizes ranging from 1-15 µm and 97% purity to be obtained. Water absorption ranged from 135-155 mL/100 g and 150-250 mL/100 g for precipitated silica and silica gel, respectively, while oil absorption ranged from 305 to 390 and from 250 to 350 mL/100 g. The precipitation with ethanol allowed the recovery of 178 g silica/kg ash, with a lab process cost of EUR 28.95/kg, while the sol-gel process showed a yield of 198 g silica/kg ash with a cost of EUR 10.89/kg. The experimental data suggest that ash from sugarcane by-products is a promising source to be converted into a competitive value-added product, minimizing the environmental impact of disposal problems.

Polymeric nanoparticles as oral delivery systems for a grape pomace extract towards the improvement of biological activities.

Grape pomace (GP) is a major by-product from the wine industry, known for its bioactive compounds and their impact upon gastrointestinal (GI) health. However, bioaccessibility is often poor due to their degradation during digestion. This work aimed to encapsulate bioactive GP extract (GPE) into chitosan (CS) and alginate (Alg) nanoparticles (NPs) to mitigate degradation in the GI tract. Alg and CS NPs were optimized using a rotatable central composite design and NPs were characterized for their size, polydispersity, zeta potential and total phenolics (TP) association efficiency. The best formulations showed sizes ranging 523-853 nm, polydispersity indexes of 0.11-0.36, zeta potential of -15.0-14.9 mV and TP association efficiencies of 68 and 65%. FTIR confirmed that there was no formation of new chemical groups after association of the polymers with GPE. Both formulations improved the bioaccessibility of different phenolics following in vitro GI digestion, leading to increased antioxidant and antimicrobial activities. Moreover, the permeability of bioactive compounds through a Caco-2/HT29-MTX co-culture was reduced, suggesting a higher residence time in the intestine. Cy5.5 was used for tracking the CS NPs, which did not affect the metabolic activity of Caco-2 and HT29-MTX cells. Confocal microscopy images confirmed the adsorption of NPs to the cellular layer and suggested a reduction of the tight junction protein occludin when cells were incubated with Cy5.5-CS in solution. This study suggests that encapsulation of GPE can offer protection against along the GI tract and improve its biological activity with significant impact for oral delivery applications, including functional foods.

Modulation of endothelial organelle size as an antithrombotic strategy.

BACKGROUND: It is long established that von Willebrand factor (VWF) is central to hemostasis and thrombosis. Endothelial VWF is stored in cell-specific secretory granules, Weibel-Palade bodies (WPBs), organelles generated in a wide range of lengths (0.5-5.0 µm). WPB size responds to physiological cues and pharmacological treatment, and VWF secretion from shortened WPBs dramatically reduces platelet and plasma VWF adhesion to an endothelial surface. OBJECTIVE: We hypothesized that WPB-shortening represented a novel target for antithrombotic therapy. Our objective was to determine whether compounds exhibiting this activity do exist. METHODS: Using a microscopy approach coupled to automated image analysis, we measured the size of WPB bodies in primary human endothelial cells treated with licensed compounds for 24 hours. RESULTS AND CONCLUSIONS: A novel approach to identification of antithrombotic compounds generated a significant number of candidates with the ability to shorten WPBs. In vitro assays of two selected compounds confirm that they inhibit the pro-hemostatic activity of secreted VWF. This set of compounds acting at a very early stage of the hemostatic process could well prove to be a useful adjunct to current antithrombotic therapeutics. Further, in the current SARS-CoV-2 pandemic, with a considerable fraction of critically ill COVID-19 patients affected by hypercoagulability, these WPB size-reducing drugs might also provide welcome therapeutic leads for frontline clinicians and researchers.

Doxorubicin activates FOXO3a to induce the expression of multidrug resistance gene ABCB1 (MDR1) in K562 leukemic cells.

Using the doxorubicin-sensitive K562 cell line and the resistant derivative lines KD30 and KD225 as models, we found that acquisition of multidrug resistance (MDR) is associated with enhanced FOXO3a activity and expression of ABCB1 (MDR1), a plasma membrane P-glycoprotein that functions as an efflux pump for various anticancer agents. Furthermore, induction of ABCB1 mRNA expression on doxorubicin treatment of naive K562 cells was also accompanied by increased FOXO3a activity. Analysis of transfected K562, KD30, and KD225 cells in which FOXO3a activity can be induced by 4-hydroxytamoxifen showed that FOXO3a up-regulates ABCB1 expression at protein, mRNA, and gene promoter levels. Conversely, silencing of endogenous FOXO3a expression in KD225 cells inhibited the expression of this transport protein. Promoter analysis and chromatin immunoprecipitation assays showed that FOXO3a regulation of ABCB1 expression involves binding of this transcription factor to the proximal promoter region. Moreover, activation of FOXO3a increased ABCB1 drug efflux potential in KD30 cells, whereas silencing of FOXO3a by siRNA significantly reduced ABCB1 drug efflux ability. Together, these findings suggest a novel mechanism that can contribute towards MDR, involving FOXO3a as sensor for the cytotoxic stress induced by anticancer drugs. Although FOXO3a may initially trigger a program of cell cycle arrest and cell death in response to doxorubicin, sustained FOXO3a activation promotes drug resistance and survival of cells by activating ABCB1 expression.

Impact of in vitro gastrointestinal digestion on the chemical composition, bioactive properties, and cytotoxicity of Vitis vinifera L. cv. Syrah grape pomace extract.

Grape pomace (GP) is a major byproduct worldwide, and it is well known for its bioactive compounds, such as fibers and phenolic compounds, that are popular for their impact upon human health, including gastrointestinal health. The objective of this work was to evaluate the chemical composition and biological activities of an enzymatic GP extract, as well as to investigate how gastrointestinal digestion (GID) modulates these properties. GP extract was previously produced using an enzymatic cocktail with xylanase activity and was then exposed to simulated conditions of GID, characterized for its chemical composition, and screened for antimicrobial, prebiotic, and antioxidant activities. The safety of this ingredient after GID was also assessed. GP extract presented high contents of dietary fiber and other carbohydrates, including xylooligosaccharides, in addition to minerals and phenolic compounds. In vitro simulated GID revealed that xylobiose was resistant to gastric conditions, unlike phenolic compounds. The use of 2% (w/v) of this ingredient proved to be a potential carbon source that could be fermented by Lactobacillus and Bifidobacterium spp, even after digestion. The extract also exhibited strong antioxidant and antimicrobial activities against Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa; however, after GID, the antioxidant capacity decreased, and the antimicrobial capacity was strongly reduced or lost. Furthermore, the extract safety was also guaranteed on Caco-2 intestinal cells. This novel and green GP extract proved to be composed of relevant bioactive molecules, including xylooligosaccharides, polyphenols, organic acids, and minerals, which provided different biological properties; it has potential applications in the food industry such that it can be used as an ingredient in the development of new functional foods.

Identification of Kinases and Phosphatases That Regulate ATG4B Activity by siRNA and Small Molecule Screening in Cells.

Autophagy protease ATG4B is a key regulator of the LC3/GABARAP conjugation system required for autophagosome formation, maturation and closure. Members of the ATG4 and the LC3/GABARAP family have been implicated in various diseases including cancer, and targeting the ATG4B protease has been suggested as a potential therapeutic anti-cancer strategy. Recently, it has been demonstrated that ATG4B is regulated by multiple post-translational modifications, including phosphorylation and de-phosphorylation. In order to identify regulators of ATG4B activity, we optimized a cell-based luciferase assay based on ATG4B-dependent release of Gaussia luciferase. We applied this assay in a proof-of-concept small molecule compound screen and identified activating compounds that increase cellular ATG4B activity. Next, we performed a high-throughput screen to identify kinases and phosphatases that regulate cellular ATG4B activity using siRNA mediated knockdown and cDNA overexpression. Of these, we provide preliminary evidence that the kinase AKT2 enhances ATG4B activity in cells. We provide all raw and processed data from the screens as a resource for further analysis. Overall, our findings provide novel insights into the regulation of ATG4B and highlight the importance of post-translational modifications of ATG4B.

Delivery Systems for Antimicrobial Peptides and Proteins: Towards Optimization of Bioavailability and Targeting.

Antimicrobial peptides (AMPs) and proteins are produced by a wide range of organisms as important elements of their defense mechanisms, forming a large number of antimicrobial compounds that can be used to treat several human infections. The potential for the use of AMPs and antimicrobial proteins in therapeutics is growing, but their application is often limited, due to their poor physical and/or chemical properties. In recent years, several drug delivery systems have been proposed to carry such molecules, in an attempt to overcome the difficulties regarding their properties. However, no review has yet systematized the most relevant information on this subject. Therefore, this review summarizes the work that has been conducted to develop delivery systems for the transport and protection of AMPs and antimicrobial proteins, including their description and potential applications, while highlighting the opportunities for future research in this field.

H3.3K27M Cooperates with Trp53 Loss and PDGFRA Gain in Mouse Embryonic Neural Progenitor Cells to Induce Invasive High-Grade Gliomas.

Gain-of-function mutations in histone 3 (H3) variants are found in a substantial proportion of pediatric high-grade gliomas (pHGG), often in association with TP53 loss and platelet-derived growth factor receptor alpha (PDGFRA) amplification. Here, we describe a somatic mouse model wherein H3.3K27M and Trp53 loss alone are sufficient for neoplastic transformation if introduced in utero. H3.3K27M-driven lesions are clonal, H3K27me3 depleted, Olig2 positive, highly proliferative, and diffusely spreading, thus recapitulating hallmark molecular and histopathological features of pHGG. Addition of wild-type PDGFRA decreases latency and increases tumor invasion, while ATRX knockdown is associated with more circumscribed tumors. H3.3K27M-tumor cells serially engraft in recipient mice, and preliminary drug screening reveals mutation-specific vulnerabilities. Overall, we provide a faithful H3.3K27M-pHGG model which enables insights into oncohistone pathogenesis and investigation of future therapies.