Mutations in the HPV16 genome induced by APOBEC3 are associated with viral clearance.

Abstract:

:HPV16 causes half of cervical cancers worldwide; for unknown reasons, most infections resolve within two years. Here, we analyze the viral genomes of 5,328 HPV16-positive case-control samples to investigate mutational signatures and the role of human APOBEC3-induced mutations in viral clearance and cervical carcinogenesis. We identify four de novo mutational signatures, one of which matches the COSMIC APOBEC-associated signature 2. The viral genomes of the precancer/cancer cases are less likely to contain within-host somatic HPV16 APOBEC3-induced mutations (Fisher's exact test, P = 6.2 x 10-14), and have a 30% lower nonsynonymous APOBEC3 mutation burden compared to controls. We replicate the low prevalence of HPV16 APOBEC3-induced mutations in 1,749 additional cases. APOBEC3 mutations also historically contribute to the evolution of HPV16 lineages. We demonstrate that cervical infections with a greater burden of somatic HPV16 APOBEC3-induced mutations are more likely to be benign or subsequently clear, suggesting they may reduce persistence, and thus progression, within the host.

journal_name

Nat Commun

journal_title

Nature communications

authors

Zhu B,Xiao Y,Yeager M,Clifford G,Wentzensen N,Cullen M,Boland JF,Bass S,Steinberg MK,Raine-Bennett T,Lee D,Burk RD,Pinheiro M,Song L,Dean M,Nelson CW,Burdett L,Yu K,Roberson D,Lorey T,Franceschi S,Castle PE,Wa

doi

10.1038/s41467-020-14730-1

subject

Has Abstract

pub_date

2020-02-14 00:00:00

pages

886

issue

1

issn

2041-1723

pii

10.1038/s41467-020-14730-1

journal_volume

11

pub_type

杂志文章
  • Anomalous X-ray diffraction studies of ion transport in K+ channels.

    abstract::Potassium ion channels utilize a highly selective filter to rapidly transport K+ ions across cellular membranes. This selectivity filter is composed of four binding sites which display almost equal electron density in crystal structures with high potassium ion concentrations. This electron density can be interpreted t...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-06957-w

    authors: Langan PS,Vandavasi VG,Weiss KL,Afonine PV,El Omari K,Duman R,Wagner A,Coates L

    更新日期:2018-10-31 00:00:00

  • Determining the rotation direction in pulsars.

    abstract::Pulsars are rotating neutron stars emitting lighthouse-like beams. Owing to their unique properties, pulsars are a unique astrophysical tool to test general relativity, inform on matter in extreme conditions, and probe galactic magnetic fields. Understanding pulsar physics and emission mechanisms is critical to these ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-11243-4

    authors: Gueroult R,Shi Y,Rax JM,Fisch NJ

    更新日期:2019-07-19 00:00:00

  • LATS-YAP/TAZ controls lineage specification by regulating TGFβ signaling and Hnf4α expression during liver development.

    abstract::The Hippo pathway regulates the self-renewal and differentiation of various adult stem cells, but its role in cell fate determination and differentiation during liver development remains unclear. Here we report that the Hippo pathway controls liver cell lineage specification and proliferation separately from Notch sig...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms11961

    authors: Lee DH,Park JO,Kim TS,Kim SK,Kim TH,Kim MC,Park GS,Kim JH,Kuninaka S,Olson EN,Saya H,Kim SY,Lee H,Lim DS

    更新日期:2016-06-30 00:00:00

  • Polymer physics indicates chromatin folding variability across single-cells results from state degeneracy in phase separation.

    abstract::The spatial organization of chromosomes has key functional roles, yet how chromosomes fold remains poorly understood at the single-molecule level. Here, we employ models of polymer physics to investigate DNA loci in human HCT116 and IMR90 wild-type and cohesin depleted cells. Model predictions on single-molecule struc...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-17141-4

    authors: Conte M,Fiorillo L,Bianco S,Chiariello AM,Esposito A,Nicodemi M

    更新日期:2020-07-03 00:00:00

  • Host STING-dependent MDSC mobilization drives extrinsic radiation resistance.

    abstract::Radiotherapy induces and promotes innate and adaptive immunity in which host STING plays an important role. However, radioresistance in irradiated tumors can also develop, resulting in relapse. Here we report a mechanism by which extrinsic resistance develops after local ablative radiation that relies on the immunosup...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-017-01566-5

    authors: Liang H,Deng L,Hou Y,Meng X,Huang X,Rao E,Zheng W,Mauceri H,Mack M,Xu M,Fu YX,Weichselbaum RR

    更新日期:2017-11-23 00:00:00

  • Molecular determinants for the strictly compartmentalized expression of kainate receptors in CA3 pyramidal cells.

    abstract::Distinct subtypes of ionotropic glutamate receptors can segregate to specific synaptic inputs in a given neuron. Using functional mapping by focal glutamate uncaging in CA3 pyramidal cells (PCs), we observe that kainate receptors (KARs) are strictly confined to the postsynaptic elements of mossy fibre (mf) synapses an...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms12738

    authors: Fièvre S,Carta M,Chamma I,Labrousse V,Thoumine O,Mulle C

    更新日期:2016-09-27 00:00:00

  • Observation of giant spin-split Fermi-arc with maximal Chern number in the chiral topological semimetal PtGa.

    abstract::Non-symmorphic chiral topological crystals host exotic multifold fermions, and their associated Fermi arcs helically wrap around and expand throughout the Brillouin zone between the high-symmetry center and surface-corner momenta. However, Fermi-arc splitting and realization of the theoretically proposed maximal Chern...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-15865-x

    authors: Yao M,Manna K,Yang Q,Fedorov A,Voroshnin V,Valentin Schwarze B,Hornung J,Chattopadhyay S,Sun Z,Guin SN,Wosnitza J,Borrmann H,Shekhar C,Kumar N,Fink J,Sun Y,Felser C

    更新日期:2020-04-27 00:00:00

  • The GEF Trio controls endothelial cell size and arterial remodeling downstream of Vegf signaling in both zebrafish and cell models.

    abstract::Arterial networks enlarge in response to increase in tissue metabolism to facilitate flow and nutrient delivery. Typically, the transition of a growing artery with a small diameter into a large caliber artery with a sizeable diameter occurs upon the blood flow driven change in number and shape of endothelial cells lin...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-19008-0

    authors: Klems A,van Rijssel J,Ramms AS,Wild R,Hammer J,Merkel M,Derenbach L,Préau L,Hinkel R,Suarez-Martinez I,Schulte-Merker S,Vidal R,Sauer S,Kivelä R,Alitalo K,Kupatt C,van Buul JD,le Noble F

    更新日期:2020-10-21 00:00:00

  • Tubular endocytosis drives remodelling of the apical surface during epithelial morphogenesis in Drosophila.

    abstract::During morphogenesis, remodelling of cell shape requires the expansion or contraction of plasma membrane domains. Here we identify a mechanism underlying the restructuring of the apical surface during epithelial morphogenesis in Drosophila. We show that the retraction of villous protrusions and subsequent apical plasm...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms3244

    authors: Fabrowski P,Necakov AS,Mumbauer S,Loeser E,Reversi A,Streichan S,Briggs JA,De Renzis S

    更新日期:2013-01-01 00:00:00

  • A novel method to test non-exclusive hypotheses applied to Arctic ice projections from dependent models.

    abstract::A major conundrum in climate science is how to account for dependence between climate models. This complicates interpretation of probabilistic projections derived from such models. Here we show that this problem can be addressed using a novel method to test multiple non-exclusive hypotheses, and to make predictions un...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-10561-x

    authors: Olson R,An SI,Fan Y,Chang W,Evans JP,Lee JY

    更新日期:2019-07-09 00:00:00

  • High protein copy number is required to suppress stochasticity in the cyanobacterial circadian clock.

    abstract::Circadian clocks generate reliable ~24-h rhythms despite being based on stochastic biochemical reactions. The circadian clock in Synechococcus elongatus uses a post-translational oscillator that cycles deterministically in a test tube. Because the volume of a single bacterial cell is much smaller than a macroscopic re...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-05109-4

    authors: Chew J,Leypunskiy E,Lin J,Murugan A,Rust MJ

    更新日期:2018-08-01 00:00:00

  • Smac mimetics synergize with immune checkpoint inhibitors to promote tumour immunity against glioblastoma.

    abstract::Small-molecule inhibitor of apoptosis (IAP) antagonists, called Smac mimetic compounds (SMCs), sensitize tumours to TNF-α-induced killing while simultaneously blocking TNF-α growth-promoting activities. SMCs also regulate several immunomodulatory properties within immune cells. We report that SMCs synergize with innat...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms14278

    authors: Beug ST,Beauregard CE,Healy C,Sanda T,St-Jean M,Chabot J,Walker DE,Mohan A,Earl N,Lun X,Senger DL,Robbins SM,Staeheli P,Forsyth PA,Alain T,LaCasse EC,Korneluk RG

    更新日期:2017-02-15 00:00:00

  • DNA copy number changes define spatial patterns of heterogeneity in colorectal cancer.

    abstract::Genetic heterogeneity between and within tumours is a major factor determining cancer progression and therapy response. Here we examined DNA sequence and DNA copy-number heterogeneity in colorectal cancer (CRC) by targeted high-depth sequencing of 100 most frequently altered genes. In 97 samples, with primary tumours ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms14093

    authors: Mamlouk S,Childs LH,Aust D,Heim D,Melching F,Oliveira C,Wolf T,Durek P,Schumacher D,Bläker H,von Winterfeld M,Gastl B,Möhr K,Menne A,Zeugner S,Redmer T,Lenze D,Tierling S,Möbs M,Weichert W,Folprecht G,Blanc E,

    更新日期:2017-01-25 00:00:00

  • Author Correction: Re-designing Interleukin-12 to enhance its safety and potential as an anti-tumor immunotherapeutic agent.

    abstract::The originally published version of this Article contained errors in Figure 4. In panel b, the square and diamond labels associated with the uppermost survival curve were incorrectly displayed as 'n' and 'u', respectively. These errors have now been corrected in both the PDF and HTML versions of the Article. ...

    journal_title:Nature communications

    pub_type: 杂志文章,已发布勘误

    doi:10.1038/s41467-017-02205-9

    authors: Wang P,Li X,Wang J,Gao D,Li Y,Li H,Chu Y,Zhang Z,Liu H,Jiang G,Cheng Z,Wang S,Dong J,Feng B,Chard LS,Lemoine NR,Wang Y

    更新日期:2018-01-10 00:00:00

  • Nuclear retention of the transcription factor NLP7 orchestrates the early response to nitrate in plants.

    abstract::Nitrate is both an important nutrient and a signalling molecule for plants. Although several components of the nitrate signalling pathway have been identified, their hierarchical organization remains unclear. Here we show that the localization of NLP7, a member of the RWP-RK transcription factor family, is regulated b...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms2650

    authors: Marchive C,Roudier F,Castaings L,Bréhaut V,Blondet E,Colot V,Meyer C,Krapp A

    更新日期:2013-01-01 00:00:00

  • Compositional boundary layers trigger liquid unmixing in a basaltic crystal mush.

    abstract::The separation of immiscible liquids has significant implications for magma evolution and the formation of magmatic ore deposits. We combine high-resolution imaging and electron probe microanalysis with the first use of atom probe tomography on tholeiitic basaltic glass from Hawaii, the Snake River Plain, and Iceland,...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-12694-5

    authors: Honour VC,Holness MB,Charlier B,Piazolo SC,Namur O,Prosa TJ,Martin I,Helz RT,Maclennan J,Jean MM

    更新日期:2019-10-23 00:00:00

  • Single-trial dynamics of motor cortex and their applications to brain-machine interfaces.

    abstract::Increasing evidence suggests that neural population responses have their own internal drive, or dynamics, that describe how the neural population evolves through time. An important prediction of neural dynamical models is that previously observed neural activity is informative of noisy yet-to-be-observed activity on s...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms8759

    authors: Kao JC,Nuyujukian P,Ryu SI,Churchland MM,Cunningham JP,Shenoy KV

    更新日期:2015-07-29 00:00:00

  • Achieving ultrahigh triboelectric charge density for efficient energy harvesting.

    abstract::With its light weight, low cost and high efficiency even at low operation frequency, the triboelectric nanogenerator is considered a potential solution for self-powered sensor networks and large-scale renewable blue energy. As an energy harvester, its output power density and efficiency are dictated by the triboelectr...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-017-00131-4

    authors: Wang J,Wu C,Dai Y,Zhao Z,Wang A,Zhang T,Wang ZL

    更新日期:2017-07-20 00:00:00

  • Synchronized conductivity modulation to realize broadband lossless magnetic-free non-reciprocity.

    abstract::Recent research has explored the spatiotemporal modulation of permittivity to break Lorentz reciprocity in a manner compatible with integrated-circuit fabrication. However, permittivity modulation is inherently weak and accompanied by loss due to carrier injection, particularly at higher frequencies, resulting in larg...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-017-00798-9

    authors: Dinc T,Tymchenko M,Nagulu A,Sounas D,Alu A,Krishnaswamy H

    更新日期:2017-10-06 00:00:00

  • Gaussian-preserved, non-volatile shape morphing in three-dimensional microstructures for dual-functional electronic devices.

    abstract::Motile plant structures such as Mimosa pudica leaves, Impatiens glandulifera seedpods, and Dionaea muscipula leaves exhibit fast nastic movements in a few seconds or less. This motion is stimuli-independent mechanical movement following theorema egregium rules. Artificial analogs of tropistic motion in plants are exem...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-20843-4

    authors: Tian Z,Xu B,Wan G,Han X,Di Z,Chen Z,Mei Y

    更新日期:2021-01-21 00:00:00

  • Modest CaV1.342-selective inhibition by compound 8 is β-subunit dependent.

    abstract::Two voltage-gated calcium channel subtypes-CaV1.2 and CaV1.3-underlie the major L-type Ca(2+) currents in the mammalian central nervous system. Owing to their high sequence homology, the two channel subtypes share similar pharmacological properties, and at high doses classic calcium channel blockers, such as dihydropy...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms5481

    authors: Huang H,Ng CY,Yu D,Zhai J,Lam Y,Soong TW

    更新日期:2014-07-24 00:00:00

  • JAM-A regulates cortical dynein localization through Cdc42 to control planar spindle orientation during mitosis.

    abstract::Planar spindle orientation in polarized epithelial cells depends on the precise localization of the dynein-dynactin motor protein complex at the lateral cortex. The contribution of cell adhesion molecules to the cortical localization of the dynein-dynactin complex is poorly understood. Here we find that junctional adh...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms9128

    authors: Tuncay H,Brinkmann BF,Steinbacher T,Schürmann A,Gerke V,Iden S,Ebnet K

    更新日期:2015-08-26 00:00:00

  • Publisher Correction: A quantitative sequencing framework for absolute abundance measurements of mucosal and lumenal microbial communities.

    abstract::An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...

    journal_title:Nature communications

    pub_type: 杂志文章,已发布勘误

    doi:10.1038/s41467-020-17055-1

    authors: Barlow JT,Bogatyrev SR,Ismagilov RF

    更新日期:2020-07-06 00:00:00

  • Controllable fatigue cracking mechanisms of copper bicrystals with a coherent twin boundary.

    abstract::High-angle grain boundaries are always the preferential fatigue cracking sites, while the intrinsic fatigue cracking mechanism of coherent twin boundary remains elusive. Here we systematically investigate the fatigue cracking behaviours of copper bicrystals with a coherent twin boundary as their sole internal boundary...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms4536

    authors: Li LL,Zhang ZJ,Zhang P,Wang ZG,Zhang ZF

    更新日期:2014-03-26 00:00:00

  • Mps1 kinase-dependent Sgo2 centromere localisation mediates cohesin protection in mouse oocyte meiosis I.

    abstract::A key feature of meiosis is the step-wise removal of cohesin, the protein complex holding sister chromatids together, first from arms in meiosis I and then from the centromere region in meiosis II. Centromeric cohesin is protected by Sgo2 from Separase-mediated cleavage, in order to maintain sister chromatids together...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-017-00774-3

    authors: El Yakoubi W,Buffin E,Cladière D,Gryaznova Y,Berenguer I,Touati SA,Gómez R,Suja JA,van Deursen JM,Wassmann K

    更新日期:2017-09-25 00:00:00

  • Protein kinase D regulates positive selection of CD4+ thymocytes through phosphorylation of SHP-1.

    abstract::Thymic selection shapes an appropriate T cell antigen receptor (TCR) repertoire during T cell development. Here, we show that a serine/threonine kinase, protein kinase D (PKD), is crucial for thymocyte positive selection. In T cell-specific PKD-deficient (PKD2/PKD3 double-deficient) mice, the generation of CD4 single ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms12756

    authors: Ishikawa E,Kosako H,Yasuda T,Ohmuraya M,Araki K,Kurosaki T,Saito T,Yamasaki S

    更新日期:2016-09-27 00:00:00

  • Dynamic self-stiffening in liquid crystal elastomers.

    abstract::Biological tissues have the remarkable ability to remodel and repair in response to disease, injury and mechanical stresses. Synthetic materials lack the complexity of biological tissues, and man-made materials that respond to external stresses through a permanent increase in stiffness are uncommon. Here we report tha...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms2772

    authors: Agrawal A,Chipara AC,Shamoo Y,Patra PK,Carey BJ,Ajayan PM,Chapman WG,Verduzco R

    更新日期:2013-01-01 00:00:00

  • The antiparasitic drug ivermectin is a novel FXR ligand that regulates metabolism.

    abstract::Farnesoid X receptor (FXR) has important roles in maintaining bile acid and cholesterol homeostasis. Here we report that the antiparasitic drug ivermectin is a ligand for nuclear FXR. We identify ivermectin using a high-throughput compound library screening and show that it induces the transcriptional activity of the ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms2924

    authors: Jin L,Feng X,Rong H,Pan Z,Inaba Y,Qiu L,Zheng W,Lin S,Wang R,Wang Z,Wang S,Liu H,Li S,Xie W,Li Y

    更新日期:2013-01-01 00:00:00

  • Dietary diversity and evolution of the earliest flying vertebrates revealed by dental microwear texture analysis.

    abstract::Pterosaurs, the first vertebrates to evolve active flight, lived between 210 and 66 million years ago. They were important components of Mesozoic ecosystems, and reconstructing pterosaur diets is vital for understanding their origins, their roles within Mesozoic food webs and the impact of other flying vertebrates (i....

    journal_title:Nature communications

    pub_type: 历史文章,杂志文章

    doi:10.1038/s41467-020-19022-2

    authors: Bestwick J,Unwin DM,Butler RJ,Purnell MA

    更新日期:2020-10-28 00:00:00

  • Unexpected seasonality in quantity and composition of Amazon rainforest air reactivity.

    abstract::The hydroxyl radical (OH) removes most atmospheric pollutants from air. The loss frequency of OH radicals due to the combined effect of all gas-phase OH reactive species is a measureable quantity termed total OH reactivity. Here we present total OH reactivity observations in pristine Amazon rainforest air, as a functi...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms10383

    authors: Nölscher AC,Yañez-Serrano AM,Wolff S,de Araujo AC,Lavrič JV,Kesselmeier J,Williams J

    更新日期:2016-01-22 00:00:00