Oncogenic KRAS Regulates Tumor Cell Signaling via Stromal Reciprocation.

Oncogenic mutations regulate signaling within both tumor cells and adjacent stromal cells. Here, we show that oncogenic KRAS (KRAS(G12D)) also regulates tumor cell signaling via stromal cells. By combining cell-specific proteome labeling with multivariate phosphoproteomics, we analyzed heterocellular KRAS(G12D) signaling in pancreatic ductal adenocarcinoma (PDA) cells. Tumor cell KRAS(G12D) engages heterotypic fibroblasts, which subsequently instigate reciprocal signaling in the tumor cells. Reciprocal signaling employs additional kinases and doubles the number of regulated signaling nodes from cell-autonomous KRAS(G12D). Consequently, reciprocal KRAS(G12D) produces a tumor cell phosphoproteome and total proteome that is distinct from cell-autonomous KRAS(G12D) alone. Reciprocal signaling regulates tumor cell proliferation and apoptosis and increases mitochondrial capacity via an IGF1R/AXL-AKT axis. These results demonstrate that oncogene signaling should be viewed as a heterocellular process and that our existing cell-autonomous perspective underrepresents the extent of oncogene signaling in cancer. VIDEO ABSTRACT.

Comprehensive analysis of immune subtypes reveals the prognostic value of cytotoxicity and FAP+ fibroblasts in stomach adenocarcinoma.

BACKGROUND: The heterogeneity limits the effective application of immune checkpoint inhibitors for patients with stomach adenocarcinoma (STAD). Precise immunotyping can help select people who may benefit from immunotherapy and guide postoperative management by describing the characteristics of tumor microenvironment. METHODS: Gene expression profiles and clinical information of patients were collected from ACRG and TCGA-STAD datasets. The immune subtypes (ISs) were identified by consensus clustering analysis. The tumor immune microenvironments (TIME) of each IS were characterized using a series of immunogenomics methods and further confirmed by multiplex immunohistochemistry (mIHC) staining in clinical samples. Two online datasets and one in-house dataset were utilized to construct and validate a prognostic immune-related gene (IRG) signature. RESULTS: STAD patients were stratified into five reproducible ISs. IS1 (immune deserve subtype) had low immune infiltration and the highest degree of HER2 gene mutation. With abundant CD8+ T cells infiltration and activated cytotoxicity reaction, patients in the IS2 (immune-activated subtype) had the best overall survival (OS). IS3 and IS4 subtypes were both in the reactive stroma state and indicated the worst prognosis. However, IS3 (immune-inhibited subtype) was characterized by enrichment of FAP+ fibroblasts and upregulated TGF-ß signaling pathway, while IS4 (activated stroma subtype) was characterized by enrichment of ACTA2+ fibroblasts. In addition, mIHC staining confirmed that TGF-ß upregulated FAP+ fibroblasts were independent risk factor of OS. IS5 (chronic inflammation subtype) displayed moderate immune cells infiltration and had a relatively good survival. Lastly, we developed a nine-IRG signature model with a robust performance on overall survival prognostication. CONCLUSIONS: The immunotyping is indicative for characterize the TIME heterogeneity and the prediction of tumor prognosis for STADs, which may provide valuable stratification for the design of future immunotherapy.

Cadmium-induced hormesis effect in medicinal herbs improves the efficiency of safe utilization for low cadmium-contaminated farmland soil.

Compared to other soil remediation technologies, Cd-contaminated farmland soil with low cadmium accumulation (LCA) plant-based safe utilization is more catered to developing countries with food in high demand. Hormesis, which describes the fortification of plant growth performance by a low level of environmental stress, can be innovatively used to achieve increases in crop yield and plant functional components, thus amplifying the safe utilization efficiency of low Cd-contaminated soil by LCA plants. In the present study, the growth and physiological responses of Polygonatum sibiricum, a traditional Chinese medicinal herb, were investigated under laboratory conditions of gradient Cd dosage concentrations and times. As a result, the growth performance of P. sibiricum reached the peak of an inverse U-shaped curve of hormesis under e0 mg kg-1 and 9 months of Cd stress, with elevations in tuber biomass (medicinal part), plant height and polysaccharide content (medicinal components) of 143%, 25% and 90%, respectively. Meanwhile, trace Cd accumulation (0.41 mg kg-1) in the tuber guaranteed medicinal edible safety. In addition, Cd-induced hormesis in P. sibiricum was verified to be overcompensated by antioxidation systems. In conclusion, such 'win-win' results, including low Cd accumulation and enhancement of plant pharmaceutical value, provided medicinal herbs with a possibility for safe soil utilization.

Metabolomics reveals the "Invisible" detoxification mechanisms of Amaranthus hypochondriacus at three ages upon exposure to different levels of cadmium.

To decipher the Cd hyperaccumulation and tolerance mechanisms of plants and increase phytoremediation efficiency, in this study, the physiological effects induced by environmentally relevant concentrations (0, 25 and 200 mg/kg) of Cd were characterized in Amaranthus hypochondriacus (K472) at three growth stages using LC/MS-based metabolomics. Metabolomic analysis identified 31, 29 and 30 significantly differential metabolites (SDMs) in K472 exposed to Cd at the early, intermediate and late stages of vegetative growth, respectively. These SDMs are involved in nine metabolic pathways responsible for antioxidation, osmotic balance regulation, energy supplementation and the promotion of metabolites that participate in phytochelatin (PC) synthesis. K472 at the intermediate stage of vegetative growth had the strongest tolerance to Cd with the combined action of Ala, Asp and Glu metabolism, purine metabolism, Gly, Ser and Thr metabolism and Pro and Arg metabolism. Among these crucial metabolic biomarkers, purine metabolism could be the primary regulatory target for increasing the Cd absorption of K472 for the restoration of Cd-contaminated soil.

[Comparison of therapeutic effect of moxibustion materials from different places and storage periods on knee osteoarthritis].

Osteoarthritis(OA) is a kind of osteoarticular degenerative disease. The most common joint involvement of OA is knee and hip joint. The incidence rate of OA increases with age. Meta analysis shows that moxibustion is superior to other therapies in treating knee osteoarthritis(KOA). In this study, the effects of moxibustion materials from different places of origin(Hubei Qichun, Henan Nanyang, Hunan) and storage periods(5, 3, 1 years) on knee osteoarthritis in rats were compared. The swelling degree of knee joint and the histopathology of knee joint cartilage were measured. The mechanism of moxibustion in the treatment of knee osteoarthritis was discussed from the perspective of Wnt/ß-catenin signaling pathway. The results showed that the swelling degree of knee joint in the moxibustion material group of Hubei Qichun and Henan Nanyang was significantly lower than that in the model group, the diffe-rence was statistically significant(P<0.05), and it was better than that in the moxibustion material group of Hunan Province; compared with the model group, the degeneration and pathological change of knee joint cartilage tissue in the moxibustion material group of different origins were alleviated to different degrees, the Mankin's score was significantly reduced, and that in the moxibustion material group of Qichun in Hubei Province and Nanyang in Henan Province was significantly reduced and better than Hunan moxibustion material group. The effect of moxibustion materials with different storage years on the swelling degree of osteoarthritis in rats was the earliest in Qichun 5-year group, and there was significant difference between Qichun 5-year group and model group after 3 days of treatment; the improvement of histopathological changes in Qichun 5-year and 3-year moxibustion materials group was better than that in Qichun 1-year moxibustion materials group. The study on the mechanism of action showed that moxibustion materials from different places could reduce the mRNA expression of ß-catenin, BMP-2, MMP-3, MMP-9 and MMP-13 genes in knee cartilage, suggesting that moxibustion could inhibit cartilage base by regulating Wnt/ß-catenin signal pathway. It may be one of the mechanisms of moxibustion in the treatment of OA.

Circulating extracellular vesicle-associated TGFß3 modulates response to cytotoxic therapy in head and neck squamous cell carcinoma.

Management of locally advanced head and neck squamous cell carcinoma (HNSCC) requires a multi-prong approach comprising surgery, radiation and/or chemotherapy, yet outcomes are limited. This is largely due to a paucity of biomarkers that can predict response to specific treatment modalities. Here, we evaluated TGFß3 protein levels in extracellular vesicles (EVs) released by HNSCC cells as a predictor for response to chemoradiation therapy (CRT). To this end, specific EV-fractions were isolated from cell lines or HNSCC patient plasma, and TGFß3 protein was quantified. In patients treated with CRT, TGFß3 levels were found to be significantly higher in plasma EV-fractions or non-responders compared with responders. High levels of TGFß3 levels in Annexin V-EVs were associated with the worst progression-free survival. In vitro experiments demonstrated that TGFß3 silencing sensitized HNSCC cells to cytotoxic therapies, and this phenotype could be rescued by treatment with exogenous. In addition, specific EV-fractions shed by cisplatin-resistant cells were sufficient to transfer the resistant phenotype to sensitive cells through activation of TGFß-signaling pathway. Therefore, our data show that TGFß3 transmitted through EV plays a significant role in response to cytotoxic therapy, which can be exploited as a potential biomarker for CRT response in HNSCC patients treated with curative intent.

CHARMM-GUI Glycan Modeler for modeling and simulation of carbohydrates and glycoconjugates.

Characterizing glycans and glycoconjugates in the context of three-dimensional structures is important in understanding their biological roles and developing efficient therapeutic agents. Computational modeling and molecular simulation have become an essential tool complementary to experimental methods. Here, we present a computational tool, Glycan Modeler for in silico N-/O-glycosylation of the target protein and generation of carbohydrate-only systems. In our previous study, we developed Glycan Reader, a web-based tool for detecting carbohydrate molecules from a PDB structure and generation of simulation system and input files. As integrated into Glycan Reader in CHARMM-GUI, Glycan Modeler (Glycan Reader & Modeler) enables to generate the structures of glycans and glycoconjugates for given glycan sequences and glycosylation sites using PDB glycan template structures from Glycan Fragment Database (http://glycanstructure.org/fragment-db). Our benchmark tests demonstrate the universal applicability of Glycan Reader & Modeler to various glycan sequences and target proteins. We also investigated the structural properties of modeled glycan structures by running 2-µs molecular dynamics simulations of HIV envelope protein. The simulations show that the modeled glycan structures built by Glycan Reader & Modeler have the similar structural features compared to the ones solved by X-ray crystallography. We also describe the representative examples of glycoconjugate modeling with video demos to illustrate the practical applications of Glycan Reader & Modeler. Glycan Reader & Modeler is freely available at http://charmm-gui.org/input/glycan.

Novel breeding approach for Japanese flounder using atmosphere and room temperature plasma mutagenesis tool.

BACKGROUND: Artificial induction of mutagenesis is effective for genetic resource innovation and breeding. However, the traditional mutation methods for fish breeding are not convenient or safe for daily use. Hence, development of a simple, safe and effective mutagenesis method with a high mutation rate and applicability to multiple fish species, is needed. RESULTS: We reported the first successful mutagenesis in a marine aquaculture fish species, Japanese flounder, Paralichthys olivaceus, using a novel atmosphere and room temperature plasma (ARTP) mutagenesis tool. ARTP treatment time was optimized for the fertilized eggs and sperm, respectively. Eggs fertilized for 60 min were treated by ARTP with a radio-frequency power input of 120 W, and the ARTP treatment time was 25 min. Under an ARTP radio-frequency power input of 200 W, the optimal treatment time for sperm diluted with Ringer's solution by 1:40 v/v was 10 min. The ARTP-treated group presented differences in morphological traits such as body height, total length among individuals at day 90 after hatching. Whole-genome sequencing was used to reveal the mutation features of ARTP-treated individuals collected at day 120 after hatching. In total, 69.25Gb clean data were obtained from three controls and eight randomly selected ARTP-treated individuals, revealing 240,722 to 322,978 SNPs and 82,149 to 86,798 InDels located in 17,394~18,457 and 12,907~13,333 genes, respectively. The average mutation rate reached 0.064% at the genome level. Gene ontology clustering indicated that genes associated with cell components, binding function, catalytic activity, cellular process, metabolic process and biological regulation processes had higher mutation rates. CONCLUSIONS: ARTP mutagenesis is a useful method for breeding of fish species to accelerate the selection of economically important traits that would benefit the aquaculture industry, given the variety of mutations detected.

Stalis: A Computational Method for Template-Based Ab Initio Ligand Design.

Proteins interact with small molecules through specific molecular recognition, which is central to essential biological functions in living systems. Therefore, understanding such interactions is crucial for basic sciences and drug discovery. Here, we present Structure template-based ab initio ligand design solution (Stalis), a knowledge-based approach that uses structure templates from the Protein Data Bank libraries of whole ligands and their fragments and generates a set of molecules (virtual ligands) whose structures represent the pocket shape and chemical features of a given target binding site. Our benchmark performance evaluation shows that ligand structure-based virtual screening using virtual ligands from Stalis outperforms a receptor structure-based virtual screening using AutoDock Vina, demonstrating reliable overall screening performance applicable to computational high-throughput screening. However, virtual ligands from Stalis are worse in recognizing active compounds at the small fraction of a rank-ordered list of screened library compounds than crystal ligands, due to the low resolution of the virtual ligand structures. In conclusion, Stalis can facilitate drug discovery research by designing virtual ligands that can be used for fast ligand structure-based virtual screening. Moreover, Stalis provides actual three-dimensional ligand structures that likely bind to a target protein, enabling to gain structural insight into potential ligands. Stalis can be an efficient computational platform for high-throughput ligand design for fundamental biological study and drug discovery research at the proteomic level. © 2019 Wiley Periodicals, Inc.

Mouse RUNX1C regulates premegakaryocytic/erythroid output and maintains survival of megakaryocyte progenitors.

RUNX1 is crucial for the regulation of megakaryocyte specification, maturation, and thrombopoiesis. Runx1 possesses 2 promoters: the distal P1 and proximal P2 promoters. The major protein isoforms generated by P1 and P2 are RUNX1C and RUNX1B, respectively, which differ solely in their N-terminal amino acid sequences. RUNX1C is the most abundantly expressed isoform in adult hematopoiesis, present in all RUNX1-expressing populations, including the cKit+ hematopoietic stem and progenitor cells. RUNX1B expression is more restricted, being highly expressed in the megakaryocyte lineage but downregulated during erythropoiesis. We generated a Runx1 P1 knock-in of RUNX1B, termed P1-MRIPV This mouse line lacks RUNX1C expression but has normal total RUNX1 levels, solely comprising RUNX1B. Using this mouse line, we establish a specific requirement for the P1-RUNX1C isoform in megakaryopoiesis, which cannot be entirely compensated for by RUNX1B overexpression. P1 knock-in megakaryocyte progenitors have reduced proliferative capacity and undergo increased cell death, resulting in thrombocytopenia. P1 knock-in premegakaryocyte/erythroid progenitors demonstrate an erythroid-specification bias, evident from increased erythroid colony-forming ability and decreased megakaryocyte output. At a transcriptional level, multiple erythroid-specific genes are upregulated and megakaryocyte-specific transcripts are downregulated. In addition, proapoptotic pathways are activated in P1 knock-in premegakaryocyte/erythroid progenitors, presumably accounting for the increased cell death in the megakaryocyte progenitor compartment. Unlike in the conditional adult Runx1 null models, megakaryocytic maturation is not affected in the P1 knock-in mice, suggesting that RUNX1B can regulate endomitosis and thrombopoiesis. Therefore, despite the high degree of structural similarity, RUNX1B and RUNX1C isoforms have distinct and specific roles in adult megakaryopoiesis.

Correction: RUNX1B Expression Is Highly Heterogeneous and Distinguishes Megakaryocytic and Erythroid Lineage Fate in Adult Mouse Hematopoiesis.

[This corrects the article DOI: 10.1371/journal.pgen.1005814.].

RUNX1B Expression Is Highly Heterogeneous and Distinguishes Megakaryocytic and Erythroid Lineage Fate in Adult Mouse Hematopoiesis.

The Core Binding Factor (CBF) protein RUNX1 is a master regulator of definitive hematopoiesis, crucial for hematopoietic stem cell (HSC) emergence during ontogeny. RUNX1 also plays vital roles in adult mice, in regulating the correct specification of numerous blood lineages. Akin to the other mammalian Runx genes, Runx1 has two promoters P1 (distal) and P2 (proximal) which generate distinct protein isoforms. The activities and specific relevance of these two promoters in adult hematopoiesis remain to be fully elucidated. Utilizing a dual reporter mouse model we demonstrate that the distal P1 promoter is broadly active in adult hematopoietic stem and progenitor cell (HSPC) populations. By contrast the activity of the proximal P2 promoter is more restricted and its upregulation, in both the immature Lineage- Sca1high cKithigh (LSK) and bipotential Pre-Megakaryocytic/Erythroid Progenitor (PreMegE) populations, coincides with a loss of erythroid (Ery) specification. Accordingly the PreMegE population can be prospectively separated into "pro-erythroid" and "pro-megakaryocyte" populations based on Runx1 P2 activity. Comparative gene expression analyses between Runx1 P2+ and P2- populations indicated that levels of CD34 expression could substitute for P2 activity to distinguish these two cell populations in wild type (WT) bone marrow (BM). Prospective isolation of these two populations will enable the further investigation of molecular mechanisms involved in megakaryocytic/erythroid (Mk/Ery) cell fate decisions. Having characterized the extensive activity of P1, we utilized a P1-GFP homozygous mouse model to analyze the impact of the complete absence of Runx1 P1 expression in adult mice and observed strong defects in the T cell lineage. Finally, we investigated how the leukemic fusion protein AML1-ETO9a might influence Runx1 promoter usage. Short-term AML1-ETO9a induction in BM resulted in preferential P2 upregulation, suggesting its expression may be important to establish a pre-leukemic environment.

Two-shift operation mode can improve the efficiency and comfort of flexible ureteroscopic holmium laser lithotripsy for the treatment of renal calculi larger than 1.5cm.

PURPOSE: To compare two-shift operation mode and single player mode different impact on surgical results and operator comfort in flexible ureteroscopic holmium laser lithotripsy for renal calculi larger than 1.5cm. MATERIALS AND METHODS: From december 2017 to december 2018, 92 patients with renal calculi admitted to Qilu Hospital and were treated through fl exible ureteroscopy. They were randomized in two-shift group (n=50) and single player group (n=42). The operative time, blood loss, hospitalization stay after operation, residual fragments (≥4mm) rate, fragmentation speed, postoperative complications and operator's fatigue score were compared. RESULTS: There was no significant difference between two groups regarding age, gender, illness side, stone size, blood loss, operative time, postoperative hospitalization stay, complications, etc (p >0.05). The fragmentation speed was 44.5±20.0mm3/min in two-shift group compared with 34.2±17.3mm3/min in single player group (p=0.037). Residual fragments (≥4mm) rate after fi rst surgery was 18% in two-shift group, while the residual fragments (≥4mm) rate was 40.5% after first surgery in single player group (p=0.017). The total fatigue score of two-shift group was 8.4 compared to 29.9 in single player group (p <0.001). CONCLUSION: In flexible ureteroscopic holmium laser lithotripsy for the treatment of renal calculi larger than 1.5cm, two-shift operation mode can raise the fragmentation speed and stone clearance rate, as well as signifi cantly lower operator's fatigue level and improve operator's comfort.

Glycan Reader is improved to recognize most sugar types and chemical modifications in the Protein Data Bank.

MOTIVATION: Glycans play a central role in many essential biological processes. Glycan Reader was originally developed to simplify the reading of Protein Data Bank (PDB) files containing glycans through the automatic detection and annotation of sugars and glycosidic linkages between sugar units and to proteins, all based on atomic coordinates and connectivity information. Carbohydrates can have various chemical modifications at different positions, making their chemical space much diverse. Unfortunately, current PDB files do not provide exact annotations for most carbohydrate derivatives and more than 50% of PDB glycan chains have at least one carbohydrate derivative that could not be correctly recognized by the original Glycan Reader. RESULTS: Glycan Reader has been improved and now identifies most sugar types and chemical modifications (including various glycolipids) in the PDB, and both PDB and PDBx/mmCIF formats are supported. CHARMM-GUI Glycan Reader is updated to generate the simulation system and input of various glycoconjugates with most sugar types and chemical modifications. It also offers a new functionality to edit the glycan structures through addition/deletion/modification of glycosylation types, sugar types, chemical modifications, glycosidic linkages, and anomeric states. The simulation system and input files can be used for CHARMM, NAMD, GROMACS, AMBER, GENESIS, LAMMPS, Desmond, OpenMM, and CHARMM/OpenMM. Glycan Fragment Database in GlycanStructure.Org is also updated to provide an intuitive glycan sequence search tool for complex glycan structures with various chemical modifications in the PDB. AVAILABILITY AND IMPLEMENTATION: http://www.charmm-gui.org/input/glycan and http://www.glycanstructure.org. CONTACT: wonpil@lehigh.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Aerosol delivery during spontaneous breathing with different types of nebulizers- in vitro/ex vivo models evaluation.

BACKGROUND: Nebulizers for spontaneous breathing have been evaluated through different study designs. There are limitations in simulated bench models related to patient and nebulizer factors. The aim of this study was to determine the correlation of inhaled drug mass between in vitro and ex vivo studies by testing aerosol deposition of various types of nebulizers. METHODS: Ten healthy subjects were recruited to receive aerosol therapy with five nebulizers in random order: 1) a jet nebulizer (JN); 2) a breath-enhanced nebulizer (BEN); 3) a manually triggered nebulizer (MTN), 4) a breath-actuated nebulizer (BAN), and 5) a vibrating mesh nebulizer (VMN) with valved-adapter. A unit dose of salbutamol containing 5 mg in 2.5 mL was placed into the nebulizer and administered for 10 min. For the ex vivo study, minute ventilation of healthy subjects was recorded for 1 min. For the in vitro study a breathing simulator was utilized with adult breathing patterns. Aerosolized drug from the nebulizers and the accessory tubes was captured using inspiratory and expiratory collecting filters. Captured drug was eluted, measured and expressed as inhaled and exhaled mass using spectrophotometry at a wavelength of 276 nm. RESULTS: 10 healthy subjects were recruited, aged 20.8 ±â€¯0.7 years old, with a mean height of 166.2 ±â€¯9.2 cm and weight of 64.7 ±â€¯12.4 kg. There was no significant difference in the inhaled drug dose between the JN and BEN (15.0 ±â€¯1.94% and 17.74 ±â€¯2.65%, respectively, p = .763), yet the inhaled doses were lower than the other three nebulizers (p < .001). The VMN delivered greater inhaled dose than the other four nebulizers (p < .01). The respiratory rate of the cohorts was significantly correlated with the inhaled drug dose. For the in vitro model, the JN delivered a lower inhaled dose (11.6 ±â€¯1.6, p < .001) than the other nebulizers, whereas the MTN and BAN deposited significantly lower exhaled doses (1.7 ±â€¯0.4 and 2.7 ±â€¯0.2, respectively, p < .001). The VMN demonstrated a greater drug dose with the in vitro study than the ex vivo model (44.0 ±â€¯0.9% and 35.5 ±â€¯6.3% respectively, p = .003), whereas the JN in the ex vivo model resulted in a greater inhaled drug dose (15.0 ±â€¯1.9% for ex vivo vs 11.6 ±â€¯1.6% for in vitro, p = .008). CONCLUSIONS: These in vitro/ex vivo model comparisons of nebulizers performance indicated that breath-related nebulizers can be estimated using an in vitro model; however, the JN and VMN delivered inhaled drug mass differed between models. There was a significant correlation between respiratory rate and inhaled mass, and the inhaled drug dose generated by VMN correlated with minute ventilation. This study demonstrated that the VMN produced greater inhaled drug dose and lowest residual dose, whereas the BEN, BAN, and MTN produced lower exhaled drug dose in both in vitro and ex vivo models.

Transmembrane motions of PglB induced by LLO are coupled with EL5 loop conformational changes necessary for OST activity.

N-linked glycosylation is an enzymatic reaction in which an oligosaccharide is transferred en bloc onto an asparagine residue of an acceptor polypeptide, catalyzed by oligosaccharyltransferase (OST). Despite the available crystal structures, the role of the external loop EL5, which is critical for the catalytic cycle, is enigmatic as EL5 in the crystal structures is partially absent or blocks a pathway of lipid-linked oligosaccharide to the active site. Here we report the molecular origin of EL5 conformational changes through a series of molecular dynamics simulations of a bacterial OST, Campylobacter lari PglB. The simulations reveal that the isoprenoid moiety of lipid-linked oligosaccharide favorably binds to a hydrophobic groove of the PglB transmembrane domain. This binding triggers the conformational changes of the transmembrane domain and subsequently impairs the structural stability of EL5, leading to disordered EL5 with open conformations that are required for correct placement of the oligosaccharide in the active site.

CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules.

Reading ligand structures into any simulation program is often nontrivial and time consuming, especially when the force field parameters and/or structure files of the corresponding molecules are not available. To address this problem, we have developed Ligand Reader & Modeler in CHARMM-GUI. Users can upload ligand structure information in various forms (using PDB ID, ligand ID, SMILES, MOL/MOL2/SDF file, or PDB/mmCIF file), and the uploaded structure is displayed on a sketchpad for verification and further modification. Based on the displayed structure, Ligand Reader & Modeler generates the ligand force field parameters and necessary structure files by searching for the ligand in the CHARMM force field library or using the CHARMM general force field (CGenFF). In addition, users can define chemical substitution sites and draw substituents in each site on the sketchpad to generate a set of combinatorial structure files and corresponding force field parameters for throughput or alchemical free energy simulations. Finally, the output from Ligand Reader & Modeler can be used in other CHARMM-GUI modules to build a protein-ligand simulation system for all supported simulation programs, such as CHARMM, NAMD, GROMACS, AMBER, GENESIS, LAMMPS, Desmond, OpenMM, and CHARMM/OpenMM. Ligand Reader & Modeler is available as a functional module of CHARMM-GUI at http://www.charmm-gui.org/input/ligandrm. © 2017 Wiley Periodicals, Inc.

CHARMM-GUI 10 years for biomolecular modeling and simulation.

CHARMM-GUI, http://www.charmm-gui.org, is a web-based graphical user interface that prepares complex biomolecular systems for molecular simulations. CHARMM-GUI creates input files for a number of programs including CHARMM, NAMD, GROMACS, AMBER, GENESIS, LAMMPS, Desmond, OpenMM, and CHARMM/OpenMM. Since its original development in 2006, CHARMM-GUI has been widely adopted for various purposes and now contains a number of different modules designed to set up a broad range of simulations: (1) PDB Reader & Manipulator, Glycan Reader, and Ligand Reader & Modeler for reading and modifying molecules; (2) Quick MD Simulator, Membrane Builder, Nanodisc Builder, HMMM Builder, Monolayer Builder, Micelle Builder, and Hex Phase Builder for building all-atom simulation systems in various environments; (3) PACE CG Builder and Martini Maker for building coarse-grained simulation systems; (4) DEER Facilitator and MDFF/xMDFF Utilizer for experimentally guided simulations; (5) Implicit Solvent Modeler, PBEQ-Solver, and GCMC/BD Ion Simulator for implicit solvent related calculations; (6) Ligand Binder for ligand solvation and binding free energy simulations; and (7) Drude Prepper for preparation of simulations with the CHARMM Drude polarizable force field. Recently, new modules have been integrated into CHARMM-GUI, such as Glycolipid Modeler for generation of various glycolipid structures, and LPS Modeler for generation of lipopolysaccharide structures from various Gram-negative bacteria. These new features together with existing modules are expected to facilitate advanced molecular modeling and simulation thereby leading to an improved understanding of the structure and dynamics of complex biomolecular systems. Here, we briefly review these capabilities and discuss potential future directions in the CHARMM-GUI development project. © 2016 Wiley Periodicals, Inc.

NFAT1 and JunB cooperatively regulate IL-31 gene expression in CD4+ T cells in health and disease.

IL-31 is a key mediator of itching in atopic dermatitis (AD) and is preferentially produced by activated CD4(+) T cells and Th2 cells. Although pathophysiological functions of IL-31 have been suggested in diverse immune disorders, the molecular events underlying IL-31 gene regulation are still unclear. In this study we identified the transcription start site and functional promoter involved in IL-31 gene regulation in mouse CD4(+) T cells. TCR stimulation-dependent IL-31 expression was found to be closely linked with in vivo binding of NFAT1 and JunB to the IL-31 promoter. Although NFAT1 alone enhanced IL-31 promoter activity, it was further enhanced in the presence of JunB. Conversely, knockdown of either NFAT1 or JunB resulted in reduced IL-31 expression. NFAT1-deficient CD4(+) T cells showed a significant defect in IL-31 expression compared with wild-type CD4(+) T cells. In agreement with these findings, mice subjected to atopic conditions showed much higher levels of IL-31, which were closely correlated with a significant increase in the number of infiltrated NFAT1(+)CD4(+) T cells into the AD ears. Amelioration of AD progression by cyclosporin A treatment was well correlated with downregulation of IL-31 expressions in CD4(+) T cells and total ear residual cells. In summary, our results suggest a functional cooperation between NFAT1 and JunB in mediating IL-31 gene expression in CD4(+) T cells and indicate that interference with this interaction or their activity has the potential of reducing IL-31-mediated AD symptoms.