Genetic Analysis of Yeast Sec24p Mutants Suggests Cargo Binding Is Not Co-operative during ER Export

Many eukaryotic secretory proteins are selected forexport from the endoplasmic reticulum (ER) through theirinteraction with the Sec24p subunit of the coat protein II(COPII) coat. Three distinct cargo-binding sites on yeastSec24p have been described by biochemical, genetic andstructural studies. Each site recognizes a limited set ofpeptide motifs or a folded structural domain, however,the breadth of cargo recognized by a given site and thedynamics of cargo engagement remain poorly under-stood. We aimed to gain further insight into the broadermolecular function of one of these cargo-binding sitesusing a non-biased genetic approach. We exploited thein vivolethality associated with mutation of the Sec24pB-site to identify genes that suppress this phenotypewhen overexpressed. We identifiedSMY2as a gen-eral suppressor that rescued multiple defects in Sec24p,andSEC22as a specific suppressor of two adjacentcargo-binding sites, raising the possibility of allostericregulation of these domains. We generated a novel setof mutations in Sec24p thatdistinguish these two sitesand examined the ability of Sec22p to rescue these muta-tions. Our findings suggest that co-operativity does notinfluence cargo capture at these sites, and that Sec22prescue occurs via its function as a retrograde SNARE

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

CD47 plays a critical role in T-cell recruitment by regulation of LFA-1 and VLA-4 integrin adhesive functions

CD47 plays an important but incompletely understood role in the innate and adaptive immune responses. CD47, also called integrin-associated protein, has been demonstrated to associate in cis with β1 and β3 integrins. Here we test the hypothesis that CD47 regulates adhesive functions of T-cell α4β1 (VLA-4) and αLβ2 (LFA-1) in in vivo and in vitro models of inflammation. Intravital microscopy studies reveal that CD47(−/−) Th1 cells exhibit reduced interactions with wild-type (WT) inflamed cremaster muscle microvessels. Similarly, murine CD47(−/−) Th1 cells, as compared with WT, showed defects in adhesion and transmigration across tumor necrosis factor-α (TNF-α)–activated murine endothelium and in adhesion to immobilized intercellular adhesion molecule 1 (ICAM-1) and vascular cell adhesion protein 1 (VCAM-1) under flow conditions. Human Jurkat T-cells lacking CD47 also showed reduced adhesion to TNF-α–activated endothelium and ICAM-1 and VCAM-1. In cis interactions between Jurkat T-cell β2 integrins and CD47 were detected by fluorescence lifetime imaging microscopy. Unexpectedly, Jurkat CD47 null cells exhibited a striking defect in β1 and β2 integrin activation in response to Mn(2+) or Mg(2+)/ethylene glycol tetraacetic acid treatment. Our results demonstrate that CD47 associates with β2 integrins and is necessary to induce high-affinity conformations of LFA-1 and VLA-4 that recognize their endothelial cell ligands and support leukocyte adhesion and transendothelial migration

Haptoglobin genotype is a determinant of survival and cardiac remodeling after myocardial infarction in diabetic mice

<p>Abstract</p> <p>Background</p> <p>We have recently demonstrated in man that a functional allelic polymorphism in the Haptoglobin (Hp) gene plays a major role in determining survival and congestive heart failure after myocardial infarction (MI). We sought to recapitulate the effect of Hp type on outcomes and cardiac remodeling after MI in transgenic mice.</p> <p>Methods</p> <p>The Hp 2 allele exists only in man. Wild type C57Bl/6 mice carry the Hp 1 allele with high homology to the human Hp 1 allele. We genetically engineered a murine Hp 2 allele and targeted its insertion by homologous recombination to the murine Hp locus to create Hp 2 mice. Diabetes Mellitus (DM) was induced with streptozotocin. MI was produced by occlusion of the left anterior descending artery in DM C57Bl/6 mice carrying the Hp 1 or Hp 2 allele. MI size was determined with TTC staining. Left ventricular (LV) function and dimensions were assessed by 2-dimensional echocardiography.</p> <p>Results</p> <p>In the absence of DM, Hp 1-1 and Hp 2-2 mice had similar LV dimensions and LV function. MI size was similar in DM Hp 1-1 and 2-2 mice 24 hours after MI (50.2 ± 2.1%and 46.9 ± 5.5%, respectively, p = 0.6). However, DM Hp 1-1 mice had a significantly lower mortality rate than DM Hp 2-2 mice 30 days after MI (HR 0.41, 95% CI (0.19–0.95), p = 0.037 by log rank). LV chamber dimensions were significantly increased in DM Hp 2-2 mice compared to DM Hp 1-1 mice 30 days after MI (0.196 ± 0.01 cm²vs. 0.163 ± 0.01 cm², respectively; p = 0.029).</p> <p>Conclusion</p> <p>In DM mice the Hp 2-2 genotype is associated with increased mortality and more severe cardiac remodeling 30 days after MI.</p

DYNAMO - I. A sample of H alpha-luminous galaxies with resolved kinematics

DYNAMO is a multiwavelength, spatially resolved survey of local (z ∼ 0.1) star-forming galaxies designed to study evolution through comparison with samples at z _ 2. Half of the sample has integrated Hα luminosities of >1042 erg s−1, the typical lower limit for resolved spectroscopy at z _ 2. The sample covers a range in stellar mass (109–1011M_) and star formation rate (0.2–100M_ yr−1). In this first paper of a series, we present integral-field spectroscopy of Hα emission for the sample of 67 galaxies. We infer gas fractions in our sample as high as _0.8, higher than typical for local galaxies. Gas fraction correlates with stellarmass in galaxies with star formation rates below 10M_ yr−1, as found by COLDGASS, but galaxies with higher star formation rates have higher than expected gas fractions. There is only a weak correlation, if any, between gas fraction and gas velocity dispersion. Galaxies in the sample visually classified as disc-like are offset from the local stellar mass Tully–Fisher relation to higher circular velocities, but this offset vanishes when both gas and stars are included in the baryonic Tully–Fisher relation. The mean gas velocity dispersion of the sample is_50 km s−1, and V/σ ranges from 2 to 10 for most of the discs, similar to ‘turbulent’ galaxies at high redshift. Half of our sample show disc-like rotation, while ∼20 per cent show no signs of rotation. The division between rotating and non-rotating is approximately equal for the sub-samples with either star formation rates >10M_ yr−1, or specific star formation rates typical of the star formation ‘main sequence’ at z _ 2. Across our whole sample, we find good correlation between the dominance of ‘turbulence’ in galaxy discs (as expressed by V/σ ) and gas fraction as has been predicted for marginally stable Toomre discs. Comparing our sample with many others at low- and high-redshift reveals a correlation between gas velocity dispersion and star formation rate. These findings suggest the DYNAMO discs are excellent candidates for local galaxies similar to turbulent z _ 2 disc galaxies

Genetic variants associated with subjective well-being, depressive symptoms, and neuroticism identified through genome-wide analyses

Very few genetic variants have been associated with depression and neuroticism, likely because of limitations on sample size in previous studies. Subjective well-being, a phenotype that is genetically correlated with both of these traits, has not yet been studied with genome-wide data. We conducted genome-wide association studies of three phenotypes: subjective well-being (n = 298,420), depressive symptoms (n = 161,460), and neuroticism (n = 170,911). We identify 3 variants associated with subjective well-being, 2 variants associated with depressive symptoms, and 11 variants associated with neuroticism, including 2 inversion polymorphisms. The two loci associated with depressive symptoms replicate in an independent depression sample. Joint analyses that exploit the high genetic correlations between the phenotypes (|ρ^| ≈ 0.8) strengthen the overall credibility of the findings and allow us to identify additional variants. Across our phenotypes, loci regulating expression in central nervous system and adrenal or pancreas tissues are strongly enriched for association.</p