IgG-Immune Complexes Promote B Cell Memory by Inducing BAFF

Memory B cell responses are vital for protection against infections, but must also be regulated to prevent autoimmunity. Cognate T cell help, somatic hypermutation, and affinity maturation within germinal centers (GCs) are required for high affinity memory B cell formation; however, the signals that commit GC B cells to the memory pool remain unclear. In this study, we identify a role for IgG immune complexes (ICs), FcγRs, and BAFF during the formation of memory B cells in mice. We found that early secretion of IgG in response to immunization with a T-dependent antigen leads to IC-FcγR interactions that induce DCs to secrete BAFF which acts at or upstream of Bcl-6 in activated B cells. Loss of CD16, hematopoietic cell-derived BAFF, or blocking IC:FcγR regions in vivo diminished the expression of Bcl-6, the frequency of GC and memory B cells, and secondary antibody responses. BAFF also contributed to the maintenance and/or expansion of the Tfh population, although it was dispensable for their formation. Thus, early antibody responses contribute to the optimal formation of B cell memory through IgG-ICs and BAFF. Our work defines a new role for FcγRs in GC and memory B cell responses

High-Throughput Sequencing of mGluR Signaling Pathway Genes Reveals Enrichment of Rare Variants in Autism

Identification of common molecular pathways affected by genetic variation in autism is important for understanding disease pathogenesis and devising effective therapies. Here, we test the hypothesis that rare genetic variation in the metabotropic glutamate-receptor (mGluR) signaling pathway contributes to autism susceptibility. Single-nucleotide variants in genes encoding components of the mGluR signaling pathway were identified by high-throughput multiplex sequencing of pooled samples from 290 non-syndromic autism cases and 300 ethnically matched controls on two independent next-generation platforms. This analysis revealed significant enrichment of rare functional variants in the mGluR pathway in autism cases. Higher burdens of rare, potentially deleterious variants were identified in autism cases for three pathway genes previously implicated in syndromic autism spectrum disorder, TSC1, TSC2, and SHANK3, suggesting that genetic variation in these genes also contributes to risk for non-syndromic autism. In addition, our analysis identified HOMER1, which encodes a postsynaptic density-localized scaffolding protein that interacts with Shank3 to regulate mGluR activity, as a novel autism-risk gene. Rare, potentially deleterious HOMER1 variants identified uniquely in the autism population affected functionally important protein regions or regulatory sequences and co-segregated closely with autism among children of affected families. We also identified rare ASD-associated coding variants predicted to have damaging effects on components of the Ras/MAPK cascade. Collectively, these findings suggest that altered signaling downstream of mGluRs contributes to the pathogenesis of non-syndromic autism

Co-operation, Contestation and Complexity in Post-Conflict Security Sector Reform

Security Sector Reform (SSR) remains a key feature of peacebuilding interventions and is usually undertaken by a state alongside national and international partners. External actors engaged in SSR tend to follow a normative agenda that often has little regard for the context in post-conflict societies. Despite recurrent criticism, SSR practices of international organisations and bilateral donors often remain focused on state institutions, and often do not sufficiently attend to alternative providers of security or existing normative frameworks of security. This article provides a critical overview of existing research and introduces the special issue on “Co-operation, Contestation and Complexity in Post-Conflict Security Sector Reform”. We explore three aspects that add an important piece to the puzzle of what constitutes effective SSR. First, the variation of norm adoption, norm contestation and norm imposition in post-conflict countries that might explain the mixed results in terms of peacebuilding. Second, the multitude of different security actors within and beyond the state which often leads to multiple patterns of co-operation and contestation within reform programmes. And third, how both the multiplicity of and tension between norms and actors further complicate efforts to build peace or, as complexity theory would posit, influence the complex and non-linear social system that is the conflict-affected environment

Comprehensive molecular characterization of gastric adenocarcinoma

Gastric cancer is a leading cause of cancer deaths, but analysis of its molecular and clinical characteristics has been complicated by histological and aetiological heterogeneity. Here we describe a comprehensive molecular evaluation of 295 primary gastric adenocarcinomas as part of The Cancer Genome Atlas (TCGA) project. We propose a molecular classification dividing gastric cancer into four subtypes: tumours positive for Epstein–Barr virus, which display recurrent PIK3CA mutations, extreme DNA hypermethylation, and amplification of JAK2, CD274 (also known as PD-L1) and PDCD1LG2 (also knownasPD-L2); microsatellite unstable tumours, which show elevated mutation rates, including mutations of genes encoding targetable oncogenic signalling proteins; genomically stable tumours, which are enriched for the diffuse histological variant and mutations of RHOA or fusions involving RHO-family GTPase-activating proteins; and tumours with chromosomal instability, which show marked aneuploidy and focal amplification of receptor tyrosine kinases. Identification of these subtypes provides a roadmap for patient stratification and trials of targeted therapies

The Somatic Genomic Landscape of Chromophobe Renal Cell Carcinoma

We describe the landscape of somatic genomic alterations of 66 chromophobe renal cell carcinomas (ChRCCs) based on multidimensional and comprehensive characterization, including mitochondrial DNA (mtDNA) and whole genome sequencing. The result is consistent that ChRCC originates from the distal nephron compared to other kidney cancers with more proximal origins. Combined mtDNA and gene expression analysis implicates changes in mitochondrial function as a component of the disease biology, while suggesting alternative roles for mtDNA mutations in cancers relying on oxidative phosphorylation. Genomic rearrangements lead to recurrent structural breakpoints within TERT promoter region, which correlates with highly elevated TERT expression and manifestation of kataegis, representing a mechanism of TERT up-regulation in cancer distinct from previously-observed amplifications and point mutations

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

The mGluR pathway coupling synaptic activity to synaptic protein synthesis.

<p>The diagram illustrates components and interactions in the mGluR pathway <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035003#pone.0035003-KelleherRJ1" target="_blank">[4]</a>. Genes encoding proteins highlighted in yellow were sequenced in this study. Activation of postsynaptic group 1 mGluRs (mGluR1, mGluR5) stimulates protein synthesis by signaling through the Ras/ERK and PI3K/mTOR pathways. Group 1 mGluR function is modulated by interaction with Homer1, which interacts in turn with Shank3 and links mGluRs to the network of postsynaptic density-localized proteins. FMRP regulates synaptic protein synthesis by binding to target mRNAs and repressing their translation. Arc regulates mGluR-dependent synaptic plasticity, and its levels are regulated by FMRP-dependent translation and Ube3a-dependent degradation. The activity of the mGluR pathway is regulated by several pathway components responsible for syndromic ASDs (indicated by asterisks), including NF1 (neurofibromatosis type 1), Ras/ERK cascade members (cardiofaciocutaneous/Noonan syndromes), PTEN (ASD with microcephaly), TSC1 and TSC2 (tuberous sclerosis complex), FMRP (fragile X mental retardation syndrome), and Ube3a (Angelman's syndrome). Mutations in Shank3, Nrxn1, Nlgn3, and Nlgn4 cause rare non-syndromic ASDs, and structural variants in SynGAP1 and DLGAP2/SAPAP2 have been associated with autism (indicated by asterisks) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035003#pone.0035003-Pinto1" target="_blank">[7]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035003#pone.0035003-Durand1" target="_blank">[23]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035003#pone.0035003-Jamain1" target="_blank">[43]</a>.</p

Rare, potentially deleterious variants identified in mGluR pathway genes in autism cases.

<p><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035003#pone-0035003-t002" target="_blank">Table 2</a> summarizes the 58 rare, potentially deleterious SNVs that were identified in mGluR pathway genes only in autism cases. For each variant, the nucleotide substitution is shown, and the corresponding amino acid substitution is indicated parenthetically.</p

SNV detection and classification.

<p>(A) The flow diagram depicts the experimental strategy for SNV discovery and confirmation. For the AGRE and control cohorts, orthogonal multiplexing was performed to prepare two distinct sets of sample pools (15 pools of 20 samples each, or 20 pools of 15 samples each). Following enrichment of exonic target regions for all 18 mGluR pathway genes, SNVs were identified and confirmed by deep resequencing of orthogonal pools on two independent NGS platforms (Illumina GAII and the Helicos HeliScope). SNVs concordantly detected on both platforms were then analyzed as shown in panel B. (B) The flow diagram depicts the procedure used to classify the presumptive functional effects of identified variants. SNVs concordantly detected on both NGS platforms were classified as common or rare using a minor allele frequency (maf) threshold of 1%. Common SNVs, rare SNVs occurring in both autism and control populations, and rare synonymous (silent) SNVs were considered likely to be benign. Rare SNVs in intronic sequences flanking exons that did not affect conserved splice donor or acceptor sites or in 5′ untranslated regions were classified as not benign but of unknown significance. Rare SNVs causing missense substitutions or occurring in mRNA 3′ untranslated regions (and therefore possibly affecting mRNA stability or translation <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035003#pone.0035003-Chen1" target="_blank">[28]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035003#pone.0035003-Conne1" target="_blank">[29]</a>) were considered possibly deleterious, and rare SNVs causing nonsense mutations or affecting conserved splice donor or acceptor sequences were considered probably deleterious. These latter two categories of SNVs were together considered potentially deleterious.</p