Implications of human genetic variation in CRISPR-based therapeutic genome editing

CRISPR-Cas genome-editing methods hold immense potential as therapeutic tools to fix disease-causing mutations at the level of DNA. In contrast to typical drug development strategies aimed at targets that are highly conserved among individual patients, treatment at the genomic level must contend with substantial inter-individual natural genetic variation. Here we analyze the recently released ExAC and 1000 Genomes data sets to determine how human genetic variation impacts target choice for Cas endonucleases in the context of therapeutic genome editing. We find that this genetic variation confounds the target sites of certain Cas endonucleases more than others, and we provide a compendium of guide RNAs predicted to have high efficacy in diverse patient populations. For further analysis, we focus on 12 therapeutically relevant genes and consider how genetic variation affects off-target candidates for these loci. Our analysis suggests that, in large populations of individuals, most candidate off-target sites will be rare, underscoring the need for prescreening of patients through whole-genome sequencing to ensure safety. This information can be integrated with empirical methods for guide RNA selection into a framework for designing CRISPR-based therapeutics that maximizes efficacy and safety across patient populations.

Genes Contributing to Porphyromonas gingivalis Fitness in Abscess and Epithelial Cell Colonization Environments

Porphyromonas gingivalis is an important cause of serious periodontal diseases, and is emerging as a pathogen in several systemic conditions including some forms of cancer. Initial colonization by P. gingivalis involves interaction with gingival epithelial cells, and the organism can also access host tissues and spread haematogenously. To better understand the mechanisms underlying these properties, we utilized a highly saturated transposon insertion library of P. gingivalis, and assessed the fitness of mutants during epithelial cell colonization and survival in a murine abscess model by high-throughput sequencing (Tn-Seq). Transposon insertions in many genes previously suspected as contributing to virulence showed significant fitness defects in both screening assays. In addition, a number of genes not previously associated with P. gingivalis virulence were identified as important for fitness. We further examined fitness defects of four such genes by generating defined mutations. Genes encoding a carbamoyl phosphate synthetase, a replication-associated recombination protein, a nitrosative stress responsive HcpR transcription regulator, and RNase Z, a zinc phosphodiesterase, showed a fitness phenotype in epithelial cell colonization and in a competitive abscess infection. This study verifies the importance of several well-characterized putative virulence factors of P. gingivalis and identifies novel fitness determinants of the organism.

Potent and Selective Covalent Quinazoline Inhibitors of KRAS G12C

Targeted covalent small molecules have shown promise for cancers driven by KRAS G12C. Allosteric compounds that access an inducible pocket formed by movement of a dynamic structural element in KRAS, switch II, have been reported, but these compounds require further optimization to enable their advancement into clinical development. We demonstrate that covalent quinazoline-based switch II pocket (SIIP) compounds effectively suppress GTP loading of KRAS G12C, MAPK phosphorylation, and the growth of cancer cells harboring G12C. Notably we find that adding an amide substituent to the quinazoline scaffold allows additional interactions with KRAS G12C, and remarkably increases the labeling efficiency, potency, and selectivity of KRAS G12C inhibitors. Structural studies using X-ray crystallography reveal a new conformation of SIIP and key interactions made by substituents located at the quinazoline 2-, 4-, and 7-positions. Optimized lead compounds in the quinazoline series selectively inhibit KRAS G12C-dependent signaling and cancer cell growth at sub-micromolar concentrations.

Abstract 2967: Pancreatic cancer cell growth requires lipids released by tumor-induced stroma autophagy

Pancreatic ductal adenocarcinoma (PDAC) is non-resectable in the majority of patients and highly resistant to chemotherapy, resulting in a poor survival. The tumor microenvironment and hypoxia are important modifiers of cancer progression in PDAC. Understanding the metabolic vulnerabilities of PDAC in the harsh tumor microenvironment may lead to novel therapeutic approaches with improved clinical efficacy. First, we found that PDAC cells showed beneficial effects of co-cultured stroma cells, but only under lipid-free serum conditions. To study the metabolic crosstalk between cancer cells and stroma in more detail, we performed an untargeted metabolomic screen of PDAC cells and fibroblasts co-cultured in normoxia and hypoxia, and performed RNA-seq profiling in parallel. We found that stromal cells are metabolically more responsive to co-culture than cancer cells. PDAC cells induce catabolic carbohydrate and protein metabolism in stromal cells, particularly in hypoxia. In contrast, 13C-based metabolic flux assays demonstrated that stromal cells display enhanced anabolic lipid metabolism in co-culture with PDAC cells. Furthermore, de novo synthesized 13C-labeled fatty acids in stromal cells were taken up by PDAC cells. In particular, PDAC cells showed extensive scavenging of lysophospholipids (lyso-PLs) from the culture medium, which was increased in co-culture under hypoxic conditions. These data were confirmed by analyzing portal vein plasma samples isolated from pancreatic cancer patients before and after surgery. In addition, we found metabolites and expression levels of metabolic enzymes from the glycerophospholipid pathway to be enriched in PDAC cells in co-culture and hypoxia. By using fibroblasts, human pancreatic stellate cells and patient-derived cancer-associated fibroblasts (CAFs), we demonstrate direct transfer of lyso-PLs from stromal to PDAC cells via lipid droplets. The transfer of lyso-PLs was abrogated by pharmacological inhibitors of autophagy, or by siRNA-mediated knockdown of autophagy genes in stromal and tumor cells. These data suggest that PDAC cells cause stroma cells to undergo autophagy, and reprogram stroma metabolism to obtain complex lipid species for their metabolic needs in the lipid-starved tumor microenvironment.

Citation Format: Petrus R. De Jong, Sean-Luc Shanahan, Morgan A. Brand, Alejandro D. Campos, Anagha Srirangam, Nikolas Marino, Claudia P. Miller, Olga Zagnitko, Adam D. Richardson, David A. Scott, Brian P. James, Andrew P. Hodges, Ally Perlina, Alexey M. Eroshin, Randall French, Malene Hansen, Sally A. Litherland, Andrew M. Lowy, J. Pablo Arnoletti, Garth Powis. Pancreatic cancer cell growth requires lipids released by tumor-induced stroma autophagy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2967. doi:10.1158/1538-7445.AM2017-2967

Molecular mechanisms of isocitrate dehydrogenase 1 (IDH1) mutations identified in tumors: The role of size and hydrophobicity at residue 132 on catalytic efficiency

Isocitrate dehydrogenase 1 (IDH1) catalyzes the reversible NADP⁺-dependent conversion of isocitrate (ICT) to α-ketoglutarate (αKG) in the cytosol and peroxisomes. Mutations in IDH1 have been implicated in >80% of lower grade gliomas and secondary glioblastomas and primarily affect residue 132, which helps coordinate substrate binding. However, other mutations found in the active site have also been identified in tumors. IDH1 mutations typically result in a loss of catalytic activity, but many also can catalyze a new reaction, the NADPH-dependent reduction of αKG to d-2-hydroxyglutarate (D2HG). D2HG is a proposed oncometabolite that can competitively inhibit αKG-dependent enzymes. Some kinetic parameters have been reported for several IDH1 mutations, and there is evidence that mutant IDH1 enzymes vary widely in their ability to produce D2HG. We report that most IDH1 mutations identified in tumors are severely deficient in catalyzing the normal oxidation reaction, but that D2HG production efficiency varies among mutant enzymes up to ∼640-fold. Common IDH1 mutations have moderate catalytic efficiencies for D2HG production, whereas rarer mutations exhibit either very low or very high efficiencies. We then designed a series of experimental IDH1 mutants to understand the features that support D2HG production. We show that this new catalytic activity observed in tumors is supported by mutations at residue 132 that have a smaller van der Waals volume and are more hydrophobic. We report that one mutation can support both the normal and neomorphic reactions. These studies illuminate catalytic features of mutations found in the majority of patients with lower grade gliomas.

Abstract P6-07-30: Identifying novel glycosylation markers in Her2+ breast cancer using MALDI mass spectrometry

Breast cancer characterized by human epidermal growth factor receptor 2 (HER2) overexpression represents approximately 25-30% of all breast cancer cases. Many patients acquire resistance to current chemotherapies, leading to a more aggressive disease state with severe clinical outcomes. Lapatinib, a first generation tyrosine kinase inhibitor of HER2 and EGFR (epidermal growth factor receptor), is commonly used to treat HER2+ breast cancer. Resistance to lapatinib is steadily increasing among HER2+ patients, highlighting the need for therapy development. Identifying markers that predict treatment response or potential drug targets could enhance treatment efficacy and patient survival. To investigate this, we have used MALDI mass spectrometry to identify N-linked glycans specific to human breast cancer cell lines with known resistance and sensitivity to lapatinib treatment, JIMT-1 (resistant) HER2+ and BT474 (sensitive) HER2+. After different lapatinib dose and time course experiments, N-linked glycans were isolated and comparatively profiled by high resolution MALDI mass spectrometry. Differences in the levels of fucosylation and sialylation of glycans from sensitive and resistant cell lines, before and after treatment, were evaluated. In addition, mouse xenograft tumor tissues derived from the same cell lines treated with and without lapatinib were processed for on-tissue imaging of N-glycans using a MALDI imaging mass spectrometry approach. Tissues from HER2+ human breast tumors were also imaged with the same MALDI imaging approach. Cumulatively, these preliminary studies have identified novel glycosylation patterns associated with lapatinib treatment sensitivity and resistance.

Citation Format: Scott DA, Angel P, Xu H, Drake R, Yeh E. Identifying novel glycosylation markers in Her2+ breast cancer using MALDI mass spectrometry [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P6-07-30.

Structure of RagB, a major immunodominant outer-membrane surface receptor antigen of Porphyromonas gingivalis

Porphyromonas gingivalis is the main causative agent of periodontitis. It deregulates the inflammatory and innate host immune responses through virulence factors, which include the immunodominant outer-membrane surface receptor antigens A (PgRagA) and B (PgRagB), co-transcribed from the rag pathogenicity island. The former is predicted to be a Ton-dependent porin-type translocator but the targets of this translocation and the molecular function of PgRagB are unknown. Phenomenologically, PgRagB has been linked with epithelial cell invasion and virulence according to murine models. It also acts as a Toll-like receptor agonist and promotes multiple mediators of inflammation. Hence, PgRagB is a candidate for the development of a periodontitis vaccine, which would be facilitated by the knowledge of its atomic structure. Here, we crystallized and solved the structure of 54-kDa PgRagB, which revealed a single domain centered on a curved helical scaffold. It consists of four tetratrico peptide repeats (TPR1-4), each arranged as two helices connected by a linker, plus two extra downstream capping helices. The concave surface bears four large intertwined irregular inserts (A-D), which contribute to an overall compact moiety. Overall, PgRagB shows substantial structural similarity with Bacteroides thetaiotaomicron SusD and Tannerella forsythia NanU, which are, respectively, engaged in binding and uptake of malto-oligosaccharide/starch and sialic acid. This suggests a similar sugar-binding function for PgRagB for uptake by the cognate PgRagA translocator, and, consistently, three potential monosaccharide-binding sites were tentatively assigned on the molecular surface.

ASPP2 deficiency causes features of 1q41q42 microdeletion syndrome

Chromosomal abnormalities are implicated in a substantial number of human developmental syndromes, but for many such disorders little is known about the causative genes. The recently described 1q41q42 microdeletion syndrome is characterized by characteristic dysmorphic features, intellectual disability and brain morphological abnormalities, but the precise genetic basis for these abnormalities remains unknown. Here, our detailed analysis of the genetic abnormalities of 1q41q42 microdeletion cases identified TP53BP2, which encodes apoptosis-stimulating protein of p53 2 (ASPP2), as a candidate gene for brain abnormalities. Consistent with this, Trp53bp2-deficient mice show dilation of lateral ventricles resembling the phenotype of 1q41q42 microdeletion patients. Trp53bp2 deficiency causes 100% neonatal lethality in the C57BL/6 background associated with a high incidence of neural tube defects and a range of developmental abnormalities such as congenital heart defects, coloboma, microphthalmia, urogenital and craniofacial abnormalities. Interestingly, abnormalities show a high degree of overlap with 1q41q42 microdeletion-associated abnormalities. These findings identify TP53BP2 as a strong candidate causative gene for central nervous system (CNS) defects in 1q41q42 microdeletion syndrome, and open new avenues for investigation of the mechanisms underlying CNS abnormalities.

Improved Direct Measurement of the 64.5 keV Resonance Strength in the ^{17}O(p,α)^{14}N Reaction at LUNA

The ^{17}O(p,α)^{14}N reaction plays a key role in various astrophysical scenarios, from asymptotic giant branch stars to classical novae. It affects the synthesis of rare isotopes such as ^{17}O and ^{18}F, which can provide constraints on astrophysical models. A new direct determination of the E_{R}=64.5  keV resonance strength performed at the Laboratory for Underground Nuclear Astrophysics (LUNA) accelerator has led to the most accurate value to date ωγ=10.0±1.4_{stat}±0.7_{syst}  neV, thanks to a significant background reduction underground and generally improved experimental conditions. The (bare) proton partial width of the corresponding state at E_{x}=5672  keV in ^{18}F is Γ_{p}=35±5_{stat}±3_{syst}  neV. This width is about a factor of 2 higher than previously estimated, thus leading to a factor of 2 increase in the ^{17}O(p, α)^{14}N reaction rate at astrophysical temperatures relevant to shell hydrogen burning in red giant and asymptotic giant branch stars. The new rate implies lower ^{17}O/^{16}O ratios, with important implications on the interpretation of astrophysical observables from these stars.

Differentiation of Chronic and Aggressive Periodontitis by FTIR Spectroscopy

Without longitudinal clinical data, it is difficult to differentiate some cases of chronic periodontitis (CP) and aggressive periodontitis (AgP). Furthermore, both forms of disease are exacerbated by tobacco use. Therefore, this cross-sectional study was planned, primarily, to determine the ability of Fourier-transform infrared (FTIR) spectroscopy to distinguish CP and AgP patients by analysis of human saliva samples and, secondarily, to assess the potential confounding influence of smoking on discriminating disease-specific spectral signatures. FTIR spectra were collected from patients with a clinical diagnosis of CP (n = 18; 7 smokers) or AgP (n = 23; 9 smokers). Self-reported smoking status, which may be unreliable, was confirmed by salivary cotinine analysis. Spectral band area analysis and hierarchical cluster analyses were performed to clarify if the 2 periodontitis groups as well as smoker and nonsmoker patients could be differentiated from each other. Significant variations in lipid, amino acid, lactic acid, and nucleic acid content were found between nonsmoker CP and AgP groups. Although significantly lower lipid, phospholipid, protein, amino acid, lactic acid, and nucleic acid content was noted in the smoker AgP group compared with the nonsmoker AgP group, in the CP group, phospholipid, protein, amino acid, and lactic acid content was significantly lower for smokers compared with the nonsmokers. Based on these variations, nonsmoker CP and AgP patients were discriminated from each other with high sensitivity and specificity. Successful differentiation was also obtained for the smoker CP and AgP groups. Thiocyanate levels successfully differentiated smokers from nonsmokers, irrespective of periodontal status, with 100% accuracy. Differentiation of AgP and CP forms, concomitant with determination of smoking status, may allow the dental health professional to tailor treatment accordingly.

Metabolic rewiring in melanoma

Oncogene-driven metabolic rewiring is an adaptation to low nutrient and oxygen conditions in the tumor microenvironment that enables cancer cells of diverse origin to hyperproliferate. Aerobic glycolysis and enhanced reliance on glutamine utilization are prime examples of such rewiring. However, tissue of origin as well as specific genetic and epigenetic changes determines gene expression profiles underlying these metabolic alterations in specific cancers. In melanoma, activation of the mitogen-activated protein kinase (MAPK) pathway driven by mutant BRAF or NRAS is a primary cause of malignant transformation. Activity of the MAPK pathway, as well as other factors, such as HIF1α, Myc and MITF, are among those that control the balance between non-oxidative and oxidative branches of central carbon metabolism. Here, we discuss the nature of metabolic alterations that underlie melanoma development and affect its response to therapy.

Glutamate and asparagine cataplerosis underlie glutamine addiction in melanoma

Glutamine dependence is a prominent feature of cancer metabolism, and here we show that melanoma cells, irrespective of their oncogenic background, depend on glutamine for growth. A quantitative audit of how carbon from glutamine is used showed that TCA-cycle-derived glutamate is, in most melanoma cells, the major glutamine-derived cataplerotic output and product of glutaminolysis. In the absence of glutamine, TCA cycle metabolites were liable to depletion through aminotransferase-mediated α-ketoglutarate-to-glutamate conversion and glutamate secretion. Aspartate was an essential cataplerotic output, as melanoma cells demonstrated a limited capacity to salvage external aspartate. Also, the absence of asparagine increased the glutamine requirement, pointing to vulnerability in the aspartate-asparagine biosynthetic pathway within melanoma metabolism. In contrast to melanoma cells, melanocytes could grow in the absence of glutamine. Melanocytes use more glutamine for protein synthesis rather than secreting it as glutamate and are less prone to loss of glutamate and TCA cycle metabolites when starved of glutamine.

Registered report: IDH mutation impairs histone demethylation and results in a block to cell differentiation

The Reproducibility Project: Cancer Biology seeks to address growing concerns about reproducibility in scientific research by conducting replications of selected experiments from a number of high-profile papers in the field of cancer biology. The papers, which were published between 2010 and 2012, were selected on the basis of citations and Altmetric scores (Errington et al., 2014). This Registered Report describes the proposed replication plan of key experiments from “IDH mutation impairs histone demethylation and results in a block to cell differentiation” by Lu and colleagues, published in Nature in 2012 (Lu et al., 2012). The experiments that will be replicated are those reported in Figures 1B, 2A, 2B, 2D and 4D. Lu and colleagues demonstrated that expression of mutant forms of IDH1 or IDH2 caused global increases in histone methylation and increased levels of 2 hydroxyglutarate (Figure 1B). This was correlated with a block in differentiation (Figures 2A, B and D). This effect appeared to be mediated by the histone demethylase KDM4C (Figure 4D). The Reproducibility Project: Cancer Biology is a collaboration between the Center for Open Scienceand Science Exchange, and the results of the replications will be published by eLife.

DOI:http://dx.doi.org/10.7554/eLife.10860.001

Resolvin D1, resolvin D2 and maresin 1 activate the GSK3β anti-inflammatory axis in TLR4-engaged human monocytes

Pro-resolving, docosahexaenoic acid-derived mediators have recently emerged as important potential therapeutic agents for the amelioration of complications arising from inflammation, such as vascular disease, asthma, acute lung injury and colitis. While resolvin D1 (RVD1), resolvin D2 (RVD2) and maresin 1 (MaR1) are established pro-resolvins, their mechanisms of action remain unclear. Here we show that, in LPS-stimulated primary human monocytes, RVD1, RVD2 and MaR1 each suppress the release of pro-inflammatory cytokines (TNF, IL-1β, IL-8) and the innate/adaptive bridging cytokine, IL-12 p40, while simultaneously augmenting the production of the anti-inflammatory cytokine, IL-10. Such resolving activity is accompanied by the increased phosphorylation (enhanced anti-inflammatory state) of glycogen synthase kinase 3β (GSK3β) along with increased phosphorylation (activation) of Akt, SGK1 and CREB but not MAPK-related molecules. Gain and loss of function experiments confirm a key role for GSK3β and CREB in the anti-inflammatory actions of resolvins. These results suggest that induction of the GSK3β anti-inflammatory axis is a common mechanism of action for RVD1, RVD2 and MaR1.

Presence of Porphyromonas gingivalis in esophagus and its association with the clinicopathological characteristics and survival in patients with esophageal cancer

Background

Mounting evidence suggests a causal relationship between specific bacterial infections and the development of certain malignancies. However, the possible role of the keystone periodontal pathogen, Porphyromonas gingivalis, in esophageal squamous cell carcinoma (ESCC) remains unknown. Therefore, we examined the presence of P. gingivalis in esophageal mucosa, and the relationship between P. gingivalis infection and the diagnosis and prognosis of ESCC.

Methods

The presence of P. gingivalis in the esophageal tissues from ESCC patients and normal controls was examined by immunohistochemistry using antibodies targeting whole bacteria and its unique secreted protease, the gingipain Kgp. qRT-PCR was used as a confirmatory approach to detect P. gingivalis 16S rDNA. Clinicopathologic characteristics were collected to analyze the relationship between P. gingivalis infection and development of ESCC.

Results

P. gingivalis was detected immunohistochemically in 61 % of cancerous tissues, 12 % of adjacent tissues and was undetected in normal esophageal mucosa. A similar distribution of lysine-specific gingipain, a catalytic endoprotease uniquely secreted by P. gingivalis, and P. gingivalis 16S rDNA was also observed. Moreover, statistic correlations showed P. gingivalis infection was positively associated with multiple clinicopathologic characteristics, including differentiation status, metastasis, and overall survival rate.

Conclusion

These findings demonstrate for the first time that P. gingivalis infects the epithelium of the esophagus of ESCC patients, establish an association between infection with P. gingivalis and the progression of ESCC, and suggest P. gingivalis infection could be a biomarker for this disease. More importantly, these data, if confirmed, indicate that eradication of a common oral pathogen could potentially contribute to a reduction in the overall ESCC burden.

Electronic supplementary material

The online version of this article (doi:10.1186/s13027-016-0049-x) contains supplementary material, which is available to authorized users.

The clinical effectiveness and cost-effectiveness of treatments for idiopathic pulmonary fibrosis: a systematic review and economic evaluation

BACKGROUND

Idiopathic pulmonary fibrosis (IPF) is a life-limiting lung disease that generally affects people over 60 years old. The main symptoms are shortness of breath and cough, and as the disease progresses there is a considerable impact on day-to-day life. Few treatments are currently available.

OBJECTIVES

To conduct a systematic review of clinical effectiveness and an analysis of cost-effectiveness of treatments for IPF based on an economic model informed by systematic reviews of cost-effectiveness and quality of life.

DATA SOURCES

Eleven electronic bibliographic databases, including MEDLINE, EMBASE, Web of Science, and The Cochrane Library and the Centre for Reviews and Dissemination databases, were searched from database inception to July 2013. Reference lists of relevant publications were also checked and experts consulted.

METHODS

Two reviewers independently screened references for the systematic reviews, extracted and checked data from the included studies and appraised their risk of bias. An advisory group was consulted about the choice of interventions until consensus was reached about eligibility. A narrative review with meta-analysis was undertaken, and a network meta-analysis (NMA) was performed. A decision-analytic Markov model was developed to estimate cost-effectiveness of pharmacological treatments for IPF. Parameter values were obtained from NMA and systematic reviews. Univariate and probabilistic sensitivity analyses were undertaken. The model perspective is NHS and Personal Social Services, and discount rate is 3.5% for costs and health benefits.

RESULTS

Fourteen studies were included in the review of clinical effectiveness, of which one evaluated azathioprine, three N-acetylcysteine (NAC) (alone or in combination), four pirfenidone, one BIBF 1120, one sildenafil, one thalidomide, two pulmonary rehabilitation, and one a disease management programme. Study quality was generally good, with a low risk of bias. The current evidence suggests that some treatments appear to be clinically effective. The model base-case results show increased survival for five pharmacological treatments, compared with best supportive care, at increased cost. General recommendations cannot be made of their cost-effectiveness owing to limitations in the evidence base.

LIMITATIONS

Few direct comparisons of treatments were identified. An indirect comparison through a NMA was performed; however, caution is recommended in the interpretation of these results. In relation to the economic model, there is an assumption that pharmacological treatments have a constant effect on the relative rate of per cent predicted forced vital capacity decline.

CONCLUSIONS

Few interventions have any statistically significant effect on IPF and a lack of studies on palliative care approaches was identified. Research is required into the effects of symptom control interventions, in particular pulmonary rehabilitation and thalidomide. Other research priorities include a well-conducted randomised controlled trial on inhaled NAC therapy and an updated evidence synthesis once the results of ongoing studies are reported.

STUDY REGISTRATION

This study is registered as PROSPERO CRD42012002116.

FUNDING

The National Institute for Health Research Health Technology Assessment programme.

Rationally engineered Cas9 nucleases with improved specificity

The RNA-guided endonuclease Cas9 is a versatile genome-editing tool with a broad range of applications from therapeutics to functional annotation of genes. Cas9 creates double-strand breaks (DSBs) at targeted genomic loci complementary to a short RNA guide. However, Cas9 can cleave off-target sites that are not fully complementary to the guide, which poses a major challenge for genome editing. Here, we use structure-guided protein engineering to improve the specificity of Streptococcus pyogenes Cas9 (SpCas9). Using targeted deep sequencing and unbiased whole-genome off-target analysis to assess Cas9-mediated DNA cleavage in human cells, we demonstrate that "enhanced specificity" SpCas9 (eSpCas9) variants reduce off-target effects and maintain robust on-target cleavage. Thus, eSpCas9 could be broadly useful for genome-editing applications requiring a high level of specificity.

Three New Low-Energy Resonances in the ^{22}Ne(p,γ)^{23}Na Reaction

The ^{22}Ne(p,γ)^{23}Na reaction takes part in the neon-sodium cycle of hydrogen burning. This cycle affects the synthesis of the elements between ^{20}Ne and ^{27}Al in asymptotic giant branch stars and novae. The ^{22}Ne(p,γ)^{23}Na reaction rate is very uncertain because of a large number of unobserved resonances lying in the Gamow window. At proton energies below 400 keV, only upper limits exist in the literature for the resonance strengths. Previous reaction rate evaluations differ by large factors. In the present work, the first direct observations of the ^{22}Ne(p,γ)^{23}Na resonances at 156.2, 189.5, and 259.7 keV are reported. Their resonance strengths are derived with 2%-7% uncertainty. In addition, upper limits for three other resonances are greatly reduced. Data are taken using a windowless ^{22}Ne gas target and high-purity germanium detectors at the Laboratory for Underground Nuclear Astrophysics in the Gran Sasso laboratory of the National Institute for Nuclear Physics, Italy, taking advantage of the ultralow background observed deep underground. The new reaction rate is a factor of 20 higher than the recent evaluation at a temperature of 0.1 GK, relevant to nucleosynthesis in asymptotic giant branch stars.

Syk negatively regulates TLR4-mediated IFNβ and IL-10 production and promotes inflammatory responses in dendritic cells

BACKGROUND

While Syk has been shown to associate with TLR4, the immune consequences of Syk-TLR interactions and related molecular mechanisms are unclear.

METHODS

Gain- and loss-of-function approaches were utilized to determine the regulatory function of Syk and elucidate the related molecular mechanisms in TLR4-mediated inflammatory responses. Cytokine production was measured by ELISA and phosphorylation of signaling molecules determined by Western blotting.

RESULTS

Syk deficiency in murine dendritic cells resulted in the enhancement of LPS-induced IFNβ and IL-10 but suppression of pro-inflammatory cytokines (TNFα, IL-6). Deficiency of Syk enhanced the activity of PI3K and elevated the phosphorylation of PI3K and Akt, which in turn, lead to the phospho-inactivation of the downstream, central gatekeeper of the innate response, GSK3β. Inhibition of PI3K or Akt abrogated the ability of Syk deficiency to enhance IFNβ and IL-10 in Syk deficient cells, confirmed by the overexpression of Akt (Myr-Akt) or constitutively active GSK3β (GSK3 S9A). Moreover, neither inhibition of PI3K-Akt signaling nor neutralization of de novo synthesized IFNβ could rescue TNFα and IL-6 production in LPS-stimulated Syk deficient cells. Syk deficiency resulted in decreased phosphorylation of IKKβ and the NF-κB p65 subunit, further suggesting a divergent influence of Syk on pro- and anti-inflammatory TLR responses.

CONCLUSIONS

Syk negatively regulates TLR4-mediated production of IFNβ and IL-10 and promotes inflammatory responses in dendritic cells through divergent regulation of downstream PI3K-Akt and NF-κB signaling pathways.

GENERAL SIGNIFICANCE

Syk may represent a novel target for manipulating the direction or intensity of the innate response, depending on clinical necessity.

'Arm-based' parameterization for network meta-analysis

We present an alternative to the contrast‐based parameterization used in a number of publications for network meta‐analysis. This alternative “arm‐based” parameterization offers a number of advantages: it allows for a “long” normalized data structure that remains constant regardless of the number of comparators; it can be used to directly incorporate individual patient data into the analysis; the incorporation of multi‐arm trials is straightforward and avoids the need to generate a multivariate distribution describing treatment effects; there is a direct mapping between the parameterization and the analysis script in languages such as WinBUGS and finally, the arm‐based parameterization allows simple extension to treatment‐specific random treatment effect variances.

We validated the parameterization using a published smoking cessation dataset. Network meta‐analysis using arm‐ and contrast‐based parameterizations produced comparable results (with means and standard deviations being within +/− 0.01) for both fixed and random effects models. We recommend that analysts consider using arm‐based parameterization when carrying out network meta‐analyses. © 2015 The Authors Research Synthesis Methods Published by John Wiley & Sons Ltd.

2-Amino-4-(3,4-(methylenedioxy)benzylamino)-6-(3-methoxyphenyl)pyrimidine is an anti-inflammatory TLR-2, -4 and -5 response mediator in human monocytes

OBJECTIVE AND DESIGN

To elucidate the influence of 2-amino-4-(3,4-(methylenedioxy)benzylamino)-6-(3-methoxyphenyl)pyrimidine (AMBMP), a canonical Wnt/β-catenin pathway activator, on the inflammatory response of TLR-engaged innate cells in vitro.

MATERIAL OR SUBJECT

Primary human monocytes.

TREATMENT

AMPMB (0-10 μM), LPS (0-1.0 μg/ml), Pam3CSK4, FSL-1, or S. typhimurium flagellin (0-0.25 μg/ml).

METHODS

TLR-induced cytokine release (TNF, IL-6, IL-12 p40) was monitored by ELISA while Wnt-related signals (GSK3β, p65, IκB, β-catenin) were assessed by Western blot, pharmaceutical inhibition and gene silencing.

RESULTS

AMBMP induced the rapid phosphorylation of NFκB p65 at Ser(536) and abrogated total IκB, accompanied by a subsequent increase in pro-inflammatory cytokine production (TNF, IL-6, IL-12 p40) in otherwise naive monocytes. However, in TLR2, -4 and -5-engaged monocytes, AMBMP-suppressed cytokine production. In the context of LPS stimulation, this occurred concomitant with the phosphorylative inactivation of GSK3β at Ser(9), β-catenin accumulation and abrogation of NFκB p65 phosphorylation. AMBMP-mediated suppression of the TLR4 -induced inflammatory response was reversed by two pharmaceutical Wnt/β-catenin pathway inhibitors, IWP-2 and PNU-74654 and by Wnt3a silencing.

CONCLUSIONS

Herein, we show that AMBMP induces canonical Wnt signaling events and acts as a suppressor of inflammation in surface TLR-engaged primary human monocytes.