Virus-induced translational arrest through 4EBP1/2-dependent decay of 5'-TOP mRNAs restricts viral infection

The mosquito-transmitted bunyavirus, Rift Valley fever virus (RVFV), is a highly successful pathogen for which there are no vaccines or therapeutics. Translational arrest is a common antiviral strategy used by hosts. In response, RVFV inhibits two well-known antiviral pathways that attenuate translation during infection, PKR and type I IFN signaling. Despite this, translational arrest occurs during RVFV infection by unknown mechanisms. Here, we find that RVFV infection triggers the decay of core translation machinery mRNAs that possess a 5'-terminal oligopyrimidine (5'-TOP) motif in their 5'-UTR, including mRNAs encoding ribosomal proteins, which leads to a decrease in overall ribosomal protein levels. We find that the RNA decapping enzyme NUDT16 selectively degrades 5'-TOP mRNAs during RVFV infection and this decay is triggered in response to mTOR attenuation via the translational repressor 4EBP1/2 axis. Translational arrest of 5'-TOPs via 4EBP1/2 restricts RVFV replication, and this increased RNA decay results in the loss of visible RNA granules, including P bodies and stress granules. Because RVFV cap-snatches in RNA granules, the increased level of 5'-TOP mRNAs in this compartment leads to snatching of these targets, which are translationally suppressed during infection. Therefore, translation of RVFV mRNAs is compromised by multiple mechanisms during infection. Together, these data present a previously unknown mechanism for translational shutdown in response to viral infection and identify mTOR attenuation as a potential therapeutic avenue against bunyaviral infection

Saint: a lightweight integration environment for model annotation

Summary: Saint is a web application which provides a lightweight annotation integration environment for quantitative biological models. The system enables modellers to rapidly mark up models with biological information derived from a range of data sources

Hematopoietic stem and progenitor cells are a distinct HIV reservoir that contributes to persistent viremia in suppressed patients

Long-lived reservoirs of persistent HIV are a major barrier to a cure. CD4+ hematopoietic stem and progenitor cells (HSPCs) have the capacity for lifelong survival, self-renewal, and the generation of daughter cells. Recent evidence shows that they are also susceptible to HIV infection in vitro and in vivo. Whether HSPCs harbor infectious virus or contribute to plasma virus (PV) is unknown. Here, we provide strong evidence that clusters of identical proviruses from HSPCs and their likely progeny often match residual PV. A higher proportion of these sequences match residual PV than proviral genomes from bone marrow and peripheral blood mononuclear cells that are observed only once. Furthermore, an analysis of near-full-length genomes isolated from HSPCs provides evidence that HSPCs harbor functional HIV proviral genomes that often match residual PV. These results support the conclusion that HIV-infected HSPCs form a distinct and functionally significant reservoir of persistent HIV in infected people

Gas sensors based on localized surface plasmon resonances: synthesis of oxide films with embedded metal nanoparticles, theory and simulation, and sensitivity enhancement strategies

This work presents a comprehensive review on gas sensors based on localized surface plasmon resonance (LSPR) phenomenon, including the theory of LSPR, the synthesis of nanoparticle-embedded oxide thin films, and strategies to enhance the sensitivity of these optical sensors, supported by simulations of the electromagnetic properties. The LSPR phenomenon is known to be responsible for the unique colour effects observed in the ancient Roman Lycurgus Cup and at the windows of the medieval cathedrals. In both cases, the optical effects result from the interaction of the visible light (scattering and absorption) with the conduction band electrons of noble metal nanoparticles (gold, silver, and gold–silver alloys). These nanoparticles are dispersed in a dielectric matrix with a relatively high refractive index in order to push the resonance to the visible spectral range. At the same time, they have to be located at the surface to make LSPR sensitive to changes in the local dielectric environment, the property that is very attractive for sensing applications. Hence, an overview of gas sensors is presented, including electronic-nose systems, followed by a description of the surface plasmons that arise in noble metal thin films and nanoparticles. Afterwards, metal oxides are explored as robust and sensitive materials to host nanoparticles, followed by preparation methods of nanocomposite plasmonic thin films with sustainable techniques. Finally, several optical properties simulation methods are described, and the optical LSPR sensitivity of gold nanoparticles with different shapes, sensing volumes, and surroundings is calculated using the discrete dipole approximation method.This research was funded by the Portuguese Foundation for Science and Technology (FCT) in the framework of the Strategic Funding UIDB/04650/2020; and by the project NANO4BIO POCI-01-0145-FEDER-032299, with FCT reference PTDC/FISMAC/32299/2017. Marco S. Rodrigues acknowledges FCT for his PhD Scholarship, SFRH/BD/118684/2016

Quantitative Fitness Analysis Shows That NMD Proteins and Many Other Protein Complexes Suppress or Enhance Distinct Telomere Cap Defects

To better understand telomere biology in budding yeast, we have performed systematic suppressor/enhancer analyses on yeast strains containing a point mutation in the essential telomere capping gene CDC13 (cdc13-1) or containing a null mutation in the DNA damage response and telomere capping gene YKU70 (yku70Δ). We performed Quantitative Fitness Analysis (QFA) on thousands of yeast strains containing mutations affecting telomere-capping proteins in combination with a library of systematic gene deletion mutations. To perform QFA, we typically inoculate 384 separate cultures onto solid agar plates and monitor growth of each culture by photography over time. The data are fitted to a logistic population growth model; and growth parameters, such as maximum growth rate and maximum doubling potential, are deduced. QFA reveals that as many as 5% of systematic gene deletions, affecting numerous functional classes, strongly interact with telomere capping defects. We show that, while Cdc13 and Yku70 perform complementary roles in telomere capping, their genetic interaction profiles differ significantly. At least 19 different classes of functionally or physically related proteins can be identified as interacting with cdc13-1, yku70Δ, or both. Each specific genetic interaction informs the roles of individual gene products in telomere biology. One striking example is with genes of the nonsense-mediated RNA decay (NMD) pathway which, when disabled, suppress the conditional cdc13-1 mutation but enhance the null yku70Δ mutation. We show that the suppressing/enhancing role of the NMD pathway at uncapped telomeres is mediated through the levels of Stn1, an essential telomere capping protein, which interacts with Cdc13 and recruitment of telomerase to telomeres. We show that increased Stn1 levels affect growth of cells with telomere capping defects due to cdc13-1 and yku70Δ. QFA is a sensitive, high-throughput method that will also be useful to understand other aspects of microbial cell biology

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

Chromothripsis is a mutational phenomenon characterized by massive, clustered genomic rearrangements that occurs in cancer and other diseases. Recent studies in selected cancer types have suggested that chromothripsis may be more common than initially inferred from low-resolution copy-number data. Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), we analyze patterns of chromothripsis across 2,658 tumors from 38 cancer types using whole-genome sequencing data. We find that chromothripsis events are pervasive across cancers, with a frequency of more than 50% in several cancer types. Whereas canonical chromothripsis profiles display oscillations between two copy-number states, a considerable fraction of events involve multiple chromosomes and additional structural alterations. In addition to non-homologous end joining, we detect signatures of replication-associated processes and templated insertions. Chromothripsis contributes to oncogene amplification and to inactivation of genes such as mismatch-repair-related genes. These findings show that chromothripsis is a major process that drives genome evolution in human cancer

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

Antiviral Activities of Dead-Box RNA Helicases

Arthropod-borne RNA viruses pose a threat to human health throughout the world, but few treatments are available. A better understanding of the interactions between viruses and host cells will enable the development of new ways to combat these infections. During entry and replication, viral RNAs are exposed to host RNA-binding proteins with diverse functions. Some of these interactions have been studied, but many remain undefined. To understand how host RNA-binding proteins contribute to cellular defenses, we sought to characterize the antiviral functions of conserved DEAD-box helicase proteins identified by targeted screening in insect and mammalian host cells. Focusing on alphavirus and flavivirus infection, we assessed the effect of siRNA silencing of DDX23, DDX24, and DDX56 on infection by a panel of RNA viruses, and used CLIP-Seq to assess binding interactions of DDX56 on CHIKV and DENV RNAs during infection of human cells. We found a specific enrichment of DDX56 binding within the CHIKV nsP4 gene encoding the viral RNA-dependent RNA polymerase, which led us to investigate the role of DDX56 on initial steps of viral RNA translation and replication as an entering CHIKV genome launches replication within a host cell. We found that depletion of DDX56 improves stability of CHIKV genomes and increases levels of viral proteins, suggesting that DDX56 is capable of exerting an antiviral effect at the earliest stages of infection. The region of the CHIKV nsP4 gene bound by DDX56 is adjacent to a known structural element, and RNA folding algorithms predict structure in the DDX56 binding region as well. Taken together, these results suggest that DDX56 control of alphavirus infection likely involves recognition of a structural element that results in the CHIKV genome being targeted for degradation rather than launching replication. In contrast, CLIP-Seq analysis of DDX56 interactions with DENV RNA revealed lower and more uniform binding along the length of the viral genome, suggesting a less specific interaction and possibly a distinct antiviral mechanism. Together, these studies highlight the sensitivity of viral RNA to cellular factors shortly after entry and uncover additional virus-host interactions contributing to the control of infection