A novel gain-of-function phosphorylation site modulates PTPN22 inhibition of TCR signaling.

Protein Tyrosine Phosphatase Non-receptor type 22 (PTPN22) is encoded by a major autoimmunity gene and is a known inhibitor of T cell receptor (TCR) signaling and drug target for cancer immunotherapy. However, little is known about PTPN22 post-translational regulation. Here we characterize a phosphorylation site at Ser325 situated C-terminal to the catalytic domain of PTPN22, and its roles in altering protein function. In human T cells, Ser325 is phosphorylated by Glycogen Synthase Kinase-3 (GSK3) following TCR stimulation, which promotes its TCR-inhibitory activity. Signaling through the major TCR-dependent pathway under PTPN22 control was enhanced by CRISPR/Cas9 mediated suppression of Ser325 phosphorylation and inhibited by mimicking it via glutamic acid substitution. Global phospho-mass spectrometry showed Ser325 phosphorylation state alters downstream transcriptional activity through enrichment of Swi3p, Rsc8p and Moira (SWIRM) domain binding proteins, and next-generation sequencing (NGS) revealed it differentially regulates the expression of chemokines and T cell activation pathways. Moreover, in vitro kinetic data suggest the modulation of activity depends on a cellular context. Finally, we begin to address the structural and mechanistic basis for the influence of Ser325 phosphorylation on the protein's properties by Deuterium Exchange Mass Spectrometry (DX/MS) and Nuclear Magnetic Resonance (NMR) spectroscopy. In conclusion, this study explores the function of a novel phosphorylation site of PTPN22 that is involved in complex regulation of TCR signaling and provides details that might inform the future development of allosteric modulators of PTPN22. Significance statement The tyrosine phosphatase PTPN22 serves as a negative regulator in T cells, and its phosphorylation is a major regulatory process for controlling its function. Here, we uncovered a novel phosphorylation site at Ser325 on PTPN22 that allosterically regulates its activity leading to impaired TCR-dependent pathways. Biophysical methods identify multiple regions affected upon Ser325 phosphorylation, which can be the basis for future mechanistic studies of PTPN22 activators or inhibitors.

Antipsychotic-induced epigenomic reorganization in frontal cortex of individuals with schizophrenia.

Genome-wide association studies have revealed >270 loci associated with schizophrenia risk, yet these genetic factors do not seem to be sufficient to fully explain the molecular determinants behind this psychiatric condition. Epigenetic marks such as post-translational histone modifications remain largely plastic during development and adulthood, allowing a dynamic impact of environmental factors, including antipsychotic medications, on access to genes and regulatory elements. However, few studies so far have profiled cell-specific genome-wide histone modifications in postmortem brain samples from schizophrenia subjects, or the effect of antipsychotic treatment on such epigenetic marks. Here, we conducted ChIP-seq analyses focusing on histone marks indicative of active enhancers (H3K27ac) and active promoters (H3K4me3), alongside RNA-seq, using frontal cortex samples from antipsychotic-free (AF) and antipsychotic-treated (AT) individuals with schizophrenia, as well as individually matched controls (n=58). Schizophrenia subjects exhibited thousands of neuronal and non-neuronal epigenetic differences at regions that included several susceptibility genetic loci, such as NRG1, DISC1, and DRD3. By analyzing the AF and AT cohorts separately, we identified schizophrenia-associated alterations in specific transcription factors, their regulatees, and epigenomic and transcriptomic features that were reversed by antipsychotic treatment; as well as those that represented a consequence of antipsychotic medication rather than a hallmark of schizophrenia in postmortem human brain samples. Notably, we also found that the effect of age on epigenomic landscapes was more pronounced in frontal cortex of AT-schizophrenics, as compared to AF-schizophrenics and controls. Together, these data provide important evidence of epigenetic alterations in the frontal cortex of individuals with schizophrenia, and remark for the first time on the impact of age and antipsychotic treatment on chromatin organization.

Systems-biology analysis of rheumatoid arthritis fibroblast-like synoviocytes implicates cell line-specific transcription factor function.

Rheumatoid arthritis (RA) is an immune-mediated disease affecting diarthrodial joints that remains an unmet medical need despite improved therapy. This limitation likely reflects the diversity of pathogenic pathways in RA, with individual patients demonstrating variable responses to targeted therapies. Better understanding of RA pathogenesis would be aided by a more complete characterization of the disease. To tackle this challenge, we develop and apply a systems biology approach to identify important transcription factors (TFs) in individual RA fibroblast-like synoviocyte (FLS) cell lines by integrating transcriptomic and epigenomic information. Based on the relative importance of the identified TFs, we stratify the RA FLS cell lines into two subtypes with distinct phenotypes and predicted active pathways. We biologically validate these predictions for the top subtype-specific TF RARα and demonstrate differential regulation of TGFß signaling in the two subtypes. This study characterizes clusters of RA cell lines with distinctive TF biology by integrating transcriptomic and epigenomic data, which could pave the way towards a greater understanding of disease heterogeneity.

Caspase-8 Variant G Regulates Rheumatoid Arthritis Fibroblast-Like Synoviocyte Aggressive Behavior.

OBJECTIVE: Fibroblast-like synoviocytes (FLS) play a pivotal role in rheumatoid arthritis (RA) by contributing to synovial inflammation and progressive joint damage. An imprinted epigenetic state is associated with the FLS aggressive phenotype. We identified CASP8 (encoding for caspase-8) as a differentially marked gene and evaluated its pathogenic role in RA FLSs. METHODS: RA FLS lines were obtained from synovial tissues at arthroplasty and used at passage 5-8. Caspase-8 was silenced using small interfering RNA, and its effect was determined in cell adhesion, migration and invasion assays. Quantitative reverse transcription PCR and western blot were used to assess gene and protein expression, respectively. A caspase-8 selective inhibitor was used determine the role of enzymatic activity on FLS migration and invasion. Caspase-8 isoform transcripts and epigenetic marks in FLSs were analyzed in FLS public databases. Crystal structures of caspase-8B and G were determined. RESULTS: Caspase-8 deficiency in RA FLSs reduced cell adhesion, migration, and invasion independent of its catalytic activity. Epigenetic and transcriptomic analyses of RA FLSs revealed that a specific caspase-8 isoform, variant G, is the dominant isoform expressed (~80% of total caspase-8) and induced by PDGF. The crystal structures of caspase-8 variant G and B were identical except for a unique unstructured 59 amino acid N-terminal domain in variant G. Selective knockdown of caspase-8G was solely responsible for the effects of caspase-8 on calpain activity and cell invasion in FLS. CONCLUSION: Blocking caspase-8 variant G could decrease cell invasion in diseases like RA without the potential deleterious effects of nonspecific caspase-8 inhibition.

Engineering a Histone Reader Protein by Combining Directed Evolution, Sequencing, and Neural Network Based Ordinal Regression.

Directed evolution is a powerful approach for engineering proteins with enhanced affinity or specificity for a ligand of interest but typically requires many rounds of screening/library mutagenesis to obtain mutants with desired properties. Furthermore, mutant libraries generally only cover a small fraction of the available sequence space. Here, for the first time, we use ordinal regression to model protein sequence data generated through successive rounds of sorting and amplification of a protein-ligand system. We show that the ordinal regression model trained on only two sorts successfully predicts chromodomain CBX1 mutants that would have stronger binding affinity with the H3K9me3 peptide. Furthermore, we can extract the predictive features using contextual regression, a method to interpret nonlinear models, which successfully guides identification of strong binders not even present in the original library. We have demonstrated the power of this approach by experimentally confirming that we were able to achieve the same improvement in binding affinity previously achieved through a more laborious directed evolution process. This study presents an approach that reduces the number of rounds of selection required to isolate strong binders and facilitates the identification of strong binders not present in the original library.

Bayesian Networks Predict Neuronal Transdifferentiation.

We employ the language of Bayesian networks to systematically construct gene-regulation topologies from deep-sequencing single-nucleus RNA-Seq data for human neurons. From the perspective of the cell-state potential landscape, we identify attractors that correspond closely to different neuron subtypes. Attractors are also recovered for cell states from an independent data set confirming our models accurate description of global genetic regulations across differing cell types of the neocortex (not included in the training data). Our model recovers experimentally confirmed genetic regulations and community analysis reveals genetic associations in common pathways. Via a comprehensive scan of all theoretical three-gene perturbations of gene knockout and overexpression, we discover novel neuronal trans-differrentiation recipes (including perturbations of SATB2, GAD1, POU6F2 and ADARB2) for excitatory projection neuron and inhibitory interneuron subtypes.

Comprehensive epigenetic landscape of rheumatoid arthritis fibroblast-like synoviocytes.

Epigenetics contributes to the pathogenesis of immune-mediated diseases like rheumatoid arthritis (RA). Here we show the first comprehensive epigenomic characterization of RA fibroblast-like synoviocytes (FLS), including histone modifications (H3K27ac, H3K4me1, H3K4me3, H3K36me3, H3K27me3, and H3K9me3), open chromatin, RNA expression and whole-genome DNA methylation. To address complex multidimensional relationship and reveal epigenetic regulation of RA, we perform integrative analyses using a novel unbiased method to identify genomic regions with similar profiles. Epigenomically similar regions exist in RA cells and are associated with active enhancers and promoters and specific transcription factor binding motifs. Differentially marked genes are enriched for immunological and unexpected pathways, with "Huntington's Disease Signaling" identified as particularly prominent. We validate the relevance of this pathway to RA by showing that Huntingtin-interacting protein-1 regulates FLS invasion into matrix. This work establishes a high-resolution epigenomic landscape of RA and demonstrates the potential for integrative analyses to identify unanticipated therapeutic targets.

Structures and properties of phosphate-based bioactive glasses from computer simulation: a review.

Phosphate-based bioactive glasses (PBGs) dissolve harmlessly in the body with a dissolution rate which depends sensitively on composition. This makes them proposed vectors for e.g. drug delivery, or other applications where an active component needs to be delivered at a therapeutically appropriate rate. Molecular dynamics (MD) simulations provide atomic-level structural information about PBG compositions. We review recent work to show that MD is an excellent tool to unravel the connections between the PBG glass composition, its atomic structure, and its dissolution rate, which can help to optimise PBGs for specific medical applications.

Systematic identification of protein combinations mediating chromatin looping.

Chromatin looping plays a pivotal role in gene expression and other biological processes through bringing distal regulatory elements into spatial proximity. The formation of chromatin loops is mainly mediated by DNA-binding proteins (DBPs) that bind to the interacting sites and form complexes in three-dimensional (3D) space. Previously, identification of DBP cooperation has been limited to those binding to neighbouring regions in the proximal linear genome (1D cooperation). Here we present the first study that integrates protein ChIP-seq and Hi-C data to systematically identify both the 1D- and 3D-cooperation between DBPs. We develop a new network model that allows identification of cooperation between multiple DBPs and reveals cell-type-specific and -independent regulations. Using this framework, we retrieve many known and previously unknown 3D-cooperations between DBPs in chromosomal loops that may be a key factor in influencing the 3D organization of chromatin.

MIEC-SVM: automated pipeline for protein peptide/ligand interaction prediction.

MOTIVATION: MIEC-SVM is a structure-based method for predicting protein recognition specificity. Here, we present an automated MIEC-SVM pipeline providing an integrated and user-friendly workflow for construction and application of the MIEC-SVM models. This pipeline can handle standard amino acids and those with post-translational modifications (PTMs) or small molecules. Moreover, multi-threading and support to Sun Grid Engine (SGE) are implemented to significantly boost the computational efficiency. AVAILABILITY AND IMPLEMENTATION: The program is available at http://wanglab.ucsd.edu/MIEC-SVM CONTACT: : wei-wang@ucsd.edu SUPPLEMENTARY INFORMATION: Supplementary data available at Bioinformatics online.

Using Hierarchical Virtual Screening To Combat Drug Resistance of the HIV-1 Protease.

Human immunodeficiency virus (HIV) protease inhibitors (PIs) are important components of highly active anti-retroviral therapy (HAART) that block the catalytic site of HIV protease, thus preventing maturation of the HIV virion. However, with two decades of PI prescriptions in clinical practice, drug-resistant HIV mutants have now been found for all of the PI drugs. Therefore, the continuous development of new PI drugs is crucial both to combat the existing drug-resistant HIV strains and to provide treatments for future patients. Here we purpose an HIV PI drug design strategy to select candidate PIs with binding energy distributions dominated by interactions with conserved protease residues in both wild-type and various drug-resistant mutants. On the basis of this strategy, we have constructed a virtual screening pipeline including combinatorial library construction, combinatorial docking, MM/GBSA-based rescoring, and reranking on the basis of the binding energy distribution. We have tested our strategy on lopinavir by modifying its two functional groups. From an initial 751 689 candidate molecules, 18 candidate inhibitors were selected using the pipeline for experimental validation. IC50 measurements and drug resistance predictions successfully identified two ligands with both HIV protease inhibitor activity and an improved drug resistance profile on 2382 HIV mutants. This study provides a proof of concept for the integration of MM/GBSA energy analysis and drug resistance information at the stage of virtual screening and sheds light on future HIV drug design and the use of virtual screening to combat drug resistance.

On the structure of biomedical silver-doped phosphate-based glasses from molecular dynamics simulations.

First-principles and classical molecular dynamics simulations of undoped and silver-doped phosphate-based glasses with 50 mol% P2O5, 0-20 mol% Ag2O, and varying amounts of Na2O and CaO have been carried out. Ag occupies a distorted local coordination with a mean Ag-O bond length of 2.5 Šand an ill-defined first coordination shell. This environment is shown to be distorted octahedral/trigonal bipyramidal. Ag-O coordination numbers of 5.42 and 5.54-5.71 are calculated for first-principles and classical methodologies respectively. A disproportionation in the medium-range phosphorus Q(n) distribution is explicitly displayed upon silver-doping via CaO substitution, approximating 2Q(2)→Q(1) + Q(3), but not on silver-doping via Na2O substitution. An accompanying increase in FWHM of the phosphorus to bridging oxygen partial pair-correlation function is strong evidence for a bulk structural mechanism associated with decreased dissolution rates with increased silver content. Experimentally, Ag2O ↔ Na2O substitution is known to decrease dissolution and we show this to be a result of Ag's local bonding.

Ab initio molecular dynamics simulations of structural changes associated with the incorporation of fluorine in bioactive phosphate glasses.

Phosphate-based bioactive glasses containing fluoride ions offer the potential of a biomaterial which combines the bioactive properties of the phosphate glass and the protection from dental caries by fluoride. We conduct accurate first-principles molecular dynamics simulations of two compositions of fluorinated phosphate-based glass to assess its suitability as a biomaterial. There is a substantial amount of F-P bonding and as a result the glass network will be structurally homogeneous on medium-range length scales, without the inhomogeneities which reduce the bioactivity of other fluorinated bioactive glasses. We observe a decrease in the network connectivity with increasing F content, caused by the replacement of bridging oxygen atoms by non-bridging fluorine atoms, but this decrease is small and can be opposed by an increase in the phosphate content. We conclude that the structural changes caused by the incorporation of fluoride into phosphate-based glasses will not adversely affect their bioactivity, suggesting that fluorinated phosphate glasses offer a superior alternative to their silicate-based counterparts.

Nanoscale chains control the solubility of phosphate glasses for biomedical applications.

Bioactive phosphate-based glasses (PBGs) have several possible biomedical applications because of the chemical reactions they undergo with their surroundings when implanted into the body. The dissolution rate of PBGs in physiological conditions is a crucial parameter for these applications, to ensure, e.g., delivery of drugs or nutrients to the body at the correct rate. While it has been well-known that increasing the CaO content of these glasses at the expense of Na2O slows the dissolution rate, this paper provides an atomistic explanation of this for the first time. In this work, molecular dynamics simulations of five ternary P2O5-CaO-Na2O glasses reveal the structural properties at the atomic level that enhance the durability of PBGs as more Ca is added: (i) Ca binds together more fragments of the phosphate glass network than Na, (ii) Ca binds together more PO4 tetrahedra than Na, and (iii) Ca has a lower concentration of intratetrahedral phosphate bonding than Na. This behavior is rooted in the calcium ion's higher charge and field strength. These results open the path to precise control and optimization of the PBG dissolution rate for specific biomedical applications.

Modelling the structural evolution of ternary phosphate glasses from melts to solid amorphous materials.

The local and medium-range structural properties of phosphate-based melts and glasses have been characterized by means of first principles (density functional theory) and classical (shell-model) molecular dynamics simulations. The structure of glasses with biomedically active molecular compositions, (P2O5)0.45(CaO)x(Na2O)0.55-x (x = 0.30, 0.35 and 0.40), have been generated using first principles molecular dynamics simulations for the full melt-and-quench procedure and the changes in the structural properties as the 3000 K melt is cooled down to room temperature have been compared extensively with those of the final glasses. The melts are characterized by a significant fraction of threefold (P3c) and fivefold (P5c) phosphorus atoms, but structural defects rapidly decrease during the cooling phase and for temperatures lower than 1800 K the system is free of under- and over-coordinated species. The analysis of the structures of the glasses at 300 K shows a prevalence of the metaphosphate Q2 and pyrophosphate Q1 species, whereas the number of Q3 units, which constitute the three-dimensional phosphate network, significantly decreases with the increase of calcium content in the glass. The radial and angular distribution functions indicate that higher calcium concentration in the glass leads to an increase of the rigidity of the phosphate tetrahedral network, which has been explained in terms of the calcium's higher field strength compared to that of sodium. The structural characterization of the melts and glasses obtained from first principles simulations was used to assess and validate a recently developed interatomic shell-model forcefield for phosphate-based materials. For all three compositions, our potential model is in good agreement with the first principles data. In the glass network, the forcefield provides a very good description of the split between the shorter distances of phosphorus to non-bonded oxygen and the longer distances of the phosphorus to bonded oxygen; the phosphorus-phosphorus medium-range distribution; and the coordination environment around the Na and Ca glass modifiers. Moreover, the distribution of the Qn species in the melts and glasses is in excellent agreement with the values extracted from the first principles simulations. In contrast, simulations using standard rigid ion potentials do not provide a satisfactory description of the local short-range structure of phosphate-based glasses and are therefore less suitable to model this class of multicomponent amorphous system.

Polarizable force field development and molecular dynamics study of phosphate-based glasses.

Molecular dynamics simulations of phosphate-based glasses P(2)O(5)-CaO-Na(2)O have been carried out, using an interatomic force field that has been parameterized to reproduce the structural and mechanical properties of crystalline phosphorus pentoxide, o(')(P(2)O(5))(∞) orthorhombic phase. Polarization effects have been included through the shell-model potential and formal charges have been used to aid transferability. A modification to the DL_POLY code (version 2.20) was used to model the high temperature shell dynamics. Structural characterizations of three biomedically applicative molar compositions, (P(2)O(5))(0.45)(CaO)(x)(Na(2)O)(0.55-x) (x = 0.30, 0.35, and 0.40), have been undertaken. Good agreement with available experimental and ab initio data is obtained. The simulations show that, dependent on composition, the phosphorus atoms are primarily bonded to two or three oxygens that in turn bridge to neighbouring phosphorus atoms. Na(+) and Ca(2+) modifiers are found to occupy a pseudo-octahedral bonding environment with mean oxygen coordination numbers of 6.55 and 6.85, respectively, across all compositions studied.

A density functional theory study of structural, mechanical and electronic properties of crystalline phosphorus pentoxide.

Quantum mechanical calculations of single crystal phosphorus pentoxide (P(2)O(5)) have been conducted using the plane-wave ultrasoft pseudopotential technique based on the density functional theory (DFT), in the generalized gradient approximation, with dispersive correction (DFT-D). The implementation of the dispersive correction is shown to improve significantly the structural agreement with experiment, compared to standard plane-wave DFT. The second order elastic constants for the o'(P(2)O(5))(∞) and o(P(2)O(5)) orthorhombic phases were obtained from a polynomial fit to the calculated energy-strain relation. Both phases are shown to be highly elastically anisotropic due to structural features. Polycrystalline aggregate properties have been evaluated to give complete mechanical descriptions. Further investigation of the electronic band structure and density of states has been completed. Analysis of the complex chemical bonding has been carried out using Löwdin atomic charge and valence charge density data showing mixed ionic and covalent character in both phases.