Genome-wide discovery of somatic regulatory variants in diffuse large B-cell lymphoma.

Abstract:

:Diffuse large B-cell lymphoma (DLBCL) is an aggressive cancer originating from mature B-cells. Prognosis is strongly associated with molecular subgroup, although the driver mutations that distinguish the two main subgroups remain poorly defined. Through an integrative analysis of whole genomes, exomes, and transcriptomes, we have uncovered genes and non-coding loci that are commonly mutated in DLBCL. Our analysis has identified novel cis-regulatory sites, and implicates recurrent mutations in the 3' UTR of NFKBIZ as a novel mechanism of oncogene deregulation and NF-κB pathway activation in the activated B-cell (ABC) subgroup. Small amplifications associated with over-expression of FCGR2B (the Fcγ receptor protein IIB), primarily in the germinal centre B-cell (GCB) subgroup, correlate with poor patient outcomes suggestive of a novel oncogene. These results expand the list of subgroup driver mutations that may facilitate implementation of improved diagnostic assays and could offer new avenues for the development of targeted therapeutics.

journal_name

Nat Commun

journal_title

Nature communications

authors

Arthur SE,Jiang A,Grande BM,Alcaide M,Cojocaru R,Rushton CK,Mottok A,Hilton LK,Lat PK,Zhao EY,Culibrk L,Ennishi D,Jessa S,Chong L,Thomas N,Pararajalingam P,Meissner B,Boyle M,Davidson J,Bushell KR,Lai D,Farinha

doi

10.1038/s41467-018-06354-3

subject

Has Abstract

pub_date

2018-10-01 00:00:00

pages

4001

issue

1

issn

2041-1723

pii

10.1038/s41467-018-06354-3

journal_volume

9

pub_type

杂志文章
  • Faster phonological processing and right occipito-temporal coupling in deaf adults signal poor cochlear implant outcome.

    abstract::The outcome of adult cochlear implantation is predicted positively by the involvement of visual cortex in speech processing, and negatively by the cross-modal recruitment of the right temporal cortex during and after deafness. How these two neurofunctional predictors concur to modulate cochlear implant (CI) performanc...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms14872

    authors: Lazard DS,Giraud AL

    更新日期:2017-03-28 00:00:00

  • Retinoic acid signalling regulates the development of tonotopically patterned hair cells in the chicken cochlea.

    abstract::Precise frequency discrimination is a hallmark of auditory function in birds and mammals and is required for distinguishing similar sounding words, like 'bat,' 'cat' and 'hat.' In the cochlea, tuning and spectral separation result from longitudinal differences in basilar membrane stiffness and numerous individual grad...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms4840

    authors: Thiede BR,Mann ZF,Chang W,Ku YC,Son YK,Lovett M,Kelley MW,Corwin JT

    更新日期:2014-05-20 00:00:00

  • LFA-1 activates focal adhesion kinases FAK1/PYK2 to generate LAT-GRB2-SKAP1 complexes that terminate T-cell conjugate formation.

    abstract::Lymphocyte function-associated antigen 1 (LFA-1) affinity and avidity changes have been assumed to mediate adhesion to intercellular adhesion molecule-1 for T-cell conjugation to dendritic cells (DC). Although the T-cell receptor (TCR) and LFA-1 can generate intracellular signals, the immune cell adaptor protein linke...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms16001

    authors: Raab M,Lu Y,Kohler K,Smith X,Strebhardt K,Rudd CE

    更新日期:2017-07-12 00:00:00

  • MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA-DNA triplex structures.

    abstract::Long noncoding RNAs (lncRNAs) regulate gene expression by association with chromatin, but how they target chromatin remains poorly understood. We have used chromatin RNA immunoprecipitation-coupled high-throughput sequencing to identify 276 lncRNAs enriched in repressive chromatin from breast cancer cells. Using one o...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms8743

    authors: Mondal T,Subhash S,Vaid R,Enroth S,Uday S,Reinius B,Mitra S,Mohammed A,James AR,Hoberg E,Moustakas A,Gyllensten U,Jones SJ,Gustafsson CM,Sims AH,Westerlund F,Gorab E,Kanduri C

    更新日期:2015-07-24 00:00:00

  • Selective isolation of gold facilitated by second-sphere coordination with α-cyclodextrin.

    abstract::Gold recovery using environmentally benign chemistry is imperative from an environmental perspective. Here we report the spontaneous assembly of a one-dimensional supramolecular complex with an extended {[K(OH₂)₆][AuBr₄](α-cyclodextrin)₂}n chain superstructure formed during the rapid co-precipitation of α-cyclodextrin...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms2891

    authors: Liu Z,Frasconi M,Lei J,Brown ZJ,Zhu Z,Cao D,Iehl J,Liu G,Fahrenbach AC,Botros YY,Farha OK,Hupp JT,Mirkin CA,Fraser Stoddart J

    更新日期:2013-01-01 00:00:00

  • AutoMap is a high performance homozygosity mapping tool using next-generation sequencing data.

    abstract::Homozygosity mapping is a powerful method for identifying mutations in patients with recessive conditions, especially in consanguineous families or isolated populations. Historically, it has been used in conjunction with genotypes from highly polymorphic markers, such as DNA microsatellites or common SNPs. Traditional...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-20584-4

    authors: Quinodoz M,Peter VG,Bedoni N,Royer Bertrand B,Cisarova K,Salmaninejad A,Sepahi N,Rodrigues R,Piran M,Mojarrad M,Pasdar A,Ghanbari Asad A,Sousa AB,Coutinho Santos L,Superti-Furga A,Rivolta C

    更新日期:2021-01-22 00:00:00

  • Genome-wide rare variant analysis for thousands of phenotypes in over 70,000 exomes from two cohorts.

    abstract::Understanding the impact of rare variants is essential to understanding human health. We analyze rare (MAF < 0.1%) variants against 4264 phenotypes in 49,960 exome-sequenced individuals from the UK Biobank and 1934 phenotypes (1821 overlapping with UK Biobank) in 21,866 members of the Healthy Nevada Project (HNP) coho...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-14288-y

    authors: Cirulli ET,White S,Read RW,Elhanan G,Metcalf WJ,Tanudjaja F,Fath DM,Sandoval E,Isaksson M,Schlauch KA,Grzymski JJ,Lu JT,Washington NL

    更新日期:2020-01-28 00:00:00

  • Glutamine metabolism regulates autophagy-dependent mTORC1 reactivation during amino acid starvation.

    abstract::Activation of autophagy and elevation of glutamine synthesis represent key adaptations to maintain amino acid balance during starvation. In this study, we investigate the role of autophagy and glutamine on the regulation of mTORC1, a critical kinase that regulates cell growth and proliferation. We report that suppleme...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-017-00369-y

    authors: Tan HWS,Sim AYL,Long YC

    更新日期:2017-08-24 00:00:00

  • Atomically flat single-crystalline gold nanostructures for plasmonic nanocircuitry.

    abstract::Deep subwavelength integration of high-definition plasmonic nanostructures is of key importance in the development of future optical nanocircuitry for high-speed communication, quantum computation and lab-on-a-chip applications. To date, the experimental realization of proposed extended plasmonic networks consisting o...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms1143

    authors: Huang JS,Callegari V,Geisler P,Brüning C,Kern J,Prangsma JC,Wu X,Feichtner T,Ziegler J,Weinmann P,Kamp M,Forchel A,Biagioni P,Sennhauser U,Hecht B

    更新日期:2010-01-01 00:00:00

  • Dual nature of magnetic dopants and competing trends in topological insulators.

    abstract::Topological insulators interacting with magnetic impurities have been reported to host several unconventional effects. These phenomena are described within the framework of gapping Dirac quasiparticles due to broken time-reversal symmetry. However, the overwhelming majority of studies demonstrate the presence of a fin...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms12027

    authors: Sessi P,Biswas RR,Bathon T,Storz O,Wilfert S,Barla A,Kokh KA,Tereshchenko OE,Fauth K,Bode M,Balatsky AV

    更新日期:2016-06-27 00:00:00

  • Electrically tunable optical polarization rotation on a silicon chip using Berry's phase.

    abstract::The continued convergence of electronics and photonics on the chip scale can benefit from the voltage control of optical polarization for applications in communications, signal processing and sensing. It is challenging, however, to electrically manipulate the polarization state of light in planar optical waveguides. H...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms6337

    authors: Xu Q,Chen L,Wood MG,Sun P,Reano RM

    更新日期:2014-11-12 00:00:00

  • All-optical observation and reconstruction of spin wave dispersion.

    abstract::To know the properties of a particle or a wave, one should measure how its energy changes with its momentum. The relation between them is called the dispersion relation, which encodes essential information of the kinetics. In a magnet, the wave motion of atomic spins serves as an elementary excitation, called a spin w...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms15859

    authors: Hashimoto Y,Daimon S,Iguchi R,Oikawa Y,Shen K,Sato K,Bossini D,Tabuchi Y,Satoh T,Hillebrands B,Bauer GEW,Johansen TH,Kirilyuk A,Rasing T,Saitoh E

    更新日期:2017-06-12 00:00:00

  • Ballistic interferences in suspended graphene.

    abstract::The low-energy electronic excitations in graphene are described by massless Dirac fermions that have a linear dispersion relation. Taking advantage of this 'optics-like' electron dynamics, generic optical elements like lenses and wave guides have been proposed for electrons in graphene. Tuning of these elements relies...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms3342

    authors: Rickhaus P,Maurand R,Liu MH,Weiss M,Richter K,Schönenberger C

    更新日期:2013-01-01 00:00:00

  • Initial pulse of Siberian Traps sills as the trigger of the end-Permian mass extinction.

    abstract::Mass extinction events are short-lived and characterized by catastrophic biosphere collapse and subsequent reorganization. Their abrupt nature necessitates a similarly short-lived trigger, and large igneous province magmatism is often implicated. However, large igneous provinces are long-lived compared to mass extinct...

    journal_title:Nature communications

    pub_type: 历史文章,杂志文章

    doi:10.1038/s41467-017-00083-9

    authors: Burgess SD,Muirhead JD,Bowring SA

    更新日期:2017-07-31 00:00:00

  • Low-frequency vibrational modes of stable glasses.

    abstract::Unusual features of the vibrational density of states D(ω) of glasses allow one to rationalize their peculiar low-temperature properties. Simulational studies of D(ω) have been restricted to studying poorly annealed glasses that may not be relevant to experiments. Here we report on D(ω) of zero-temperature glasses wit...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-07978-1

    authors: Wang L,Ninarello A,Guan P,Berthier L,Szamel G,Flenner E

    更新日期:2019-01-03 00:00:00

  • Rapid host strain improvement by in vivo rearrangement of a synthetic yeast chromosome.

    abstract::Synthetic biology tools, such as modular parts and combinatorial DNA assembly, are routinely used to optimise the productivity of heterologous metabolic pathways for biosynthesis or substrate utilisation, yet it is well established that host strain background is just as important for determining productivity. Here we ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-03143-w

    authors: Blount BA,Gowers GF,Ho JCH,Ledesma-Amaro R,Jovicevic D,McKiernan RM,Xie ZX,Li BZ,Yuan YJ,Ellis T

    更新日期:2018-05-22 00:00:00

  • Skin-inspired hydrogel-elastomer hybrids with robust interfaces and functional microstructures.

    abstract::Inspired by mammalian skins, soft hybrids integrating the merits of elastomers and hydrogels have potential applications in diverse areas including stretchable and bio-integrated electronics, microfluidics, tissue engineering, soft robotics and biomedical devices. However, existing hydrogel-elastomer hybrids have limi...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms12028

    authors: Yuk H,Zhang T,Parada GA,Liu X,Zhao X

    更新日期:2016-06-27 00:00:00

  • Male-female communication triggers calcium signatures during fertilization in Arabidopsis.

    abstract::Cell-cell communication and interaction is critical during fertilization and triggers free cytosolic calcium ([Ca2+]cyto) as a key signal for egg activation and a polyspermy block in animal oocytes. Fertilization in flowering plants is more complex, involving interaction of a pollen tube with egg adjoining synergid ce...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms5645

    authors: Denninger P,Bleckmann A,Lausser A,Vogler F,Ott T,Ehrhardt DW,Frommer WB,Sprunck S,Dresselhaus T,Grossmann G

    更新日期:2014-08-22 00:00:00

  • Postsynaptic current bursts instruct action potential firing at a graded synapse.

    abstract::Nematode neurons generally produce graded potentials instead of action potentials. It is unclear how the graded potentials control postsynaptic cells under physiological conditions. Here we show that postsynaptic currents frequently occur in bursts at the neuromuscular junction of Caenorhabditis elegans. Cholinergic b...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms2925

    authors: Liu P,Chen B,Wang ZW

    更新日期:2013-01-01 00:00:00

  • Multi-ancestry GWAS of the electrocardiographic PR interval identifies 202 loci underlying cardiac conduction.

    abstract::The electrocardiographic PR interval reflects atrioventricular conduction, and is associated with conduction abnormalities, pacemaker implantation, atrial fibrillation (AF), and cardiovascular mortality. Here we report a multi-ancestry (N = 293,051) genome-wide association meta-analysis for the PR interval, discoverin...

    journal_title:Nature communications

    pub_type: 杂志文章,meta分析

    doi:10.1038/s41467-020-15706-x

    authors: Ntalla I,Weng LC,Cartwright JH,Hall AW,Sveinbjornsson G,Tucker NR,Choi SH,Chaffin MD,Roselli C,Barnes MR,Mifsud B,Warren HR,Hayward C,Marten J,Cranley JJ,Concas MP,Gasparini P,Boutin T,Kolcic I,Polasek O,Rudan I,

    更新日期:2020-05-21 00:00:00

  • Critical roles of nardilysin in the maintenance of body temperature homoeostasis.

    abstract::Body temperature homoeostasis in mammals is governed centrally through the regulation of shivering and non-shivering thermogenesis and cutaneous vasomotion. Non-shivering thermogenesis in brown adipose tissue (BAT) is mediated by sympathetic activation, followed by PGC-1α induction, which drives UCP1. Here we identify...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms4224

    authors: Hiraoka Y,Matsuoka T,Ohno M,Nakamura K,Saijo S,Matsumura S,Nishi K,Sakamoto J,Chen PM,Inoue K,Fushiki T,Kita T,Kimura T,Nishi E

    更新日期:2014-01-01 00:00:00

  • Evolution of separate predation- and defence-evoked venoms in carnivorous cone snails.

    abstract::Venomous animals are thought to inject the same combination of toxins for both predation and defence, presumably exploiting conserved target pharmacology across prey and predators. Remarkably, cone snails can rapidly switch between distinct venoms in response to predatory or defensive stimuli. Here, we show that the d...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms4521

    authors: Dutertre S,Jin AH,Vetter I,Hamilton B,Sunagar K,Lavergne V,Dutertre V,Fry BG,Antunes A,Venter DJ,Alewood PF,Lewis RJ

    更新日期:2014-03-24 00:00:00

  • The NMDA receptor regulates competition of epithelial cells in the Drosophila wing.

    abstract::Cell competition is an emerging principle that eliminates suboptimal or potentially dangerous cells. For 'unfit' cells to be detected, their competitive status needs to be compared to the collective fitness of cells within a tissue. Here we report that the NMDA receptor controls cell competition of epithelial cells an...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-16070-6

    authors: Banreti AR,Meier P

    更新日期:2020-05-06 00:00:00

  • The structural basis of promiscuity in small multidrug resistance transporters.

    abstract::By providing broad resistance to environmental biocides, transporters from the small multidrug resistance (SMR) family drive the spread of multidrug resistance cassettes among bacterial populations. A fundamental understanding of substrate selectivity by SMR transporters is needed to identify the types of selective pr...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-19820-8

    authors: Kermani AA,Macdonald CB,Burata OE,Ben Koff B,Koide A,Denbaum E,Koide S,Stockbridge RB

    更新日期:2020-11-27 00:00:00

  • The photospheric origin of the Yonetoku relation in gamma-ray bursts.

    abstract::Long duration gamma-ray bursts (GRBs), the brightest events since the Big Bang itself, are believed to originate in an ultra-relativistic jet breaking out from a massive stellar envelope. Despite decades of study, there is still no consensus on their emission mechanism. One unresolved question is the origin of the tig...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-09281-z

    authors: Ito H,Matsumoto J,Nagataki S,Warren DC,Barkov MV,Yonetoku D

    更新日期:2019-04-03 00:00:00

  • Ultra-fast self-assembly and stabilization of reactive nanoparticles in reduced graphene oxide films.

    abstract::Nanoparticles hosted in conductive matrices are ubiquitous in electrochemical energy storage, catalysis and energetic devices. However, agglomeration and surface oxidation remain as two major challenges towards their ultimate utility, especially for highly reactive materials. Here we report uniformly distributed nanop...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms12332

    authors: Chen Y,Egan GC,Wan J,Zhu S,Jacob RJ,Zhou W,Dai J,Wang Y,Danner VA,Yao Y,Fu K,Wang Y,Bao W,Li T,Zachariah MR,Hu L

    更新日期:2016-08-12 00:00:00

  • Budding-like division of all-aqueous emulsion droplets modulated by networks of protein nanofibrils.

    abstract::Networks of natural protein nanofibrils, such as cytoskeletal filaments, control the shape and the division of cells, yet mimicking this functionality in a synthetic setting has proved challenging. Here, we demonstrate that artificial networks of protein nanofibrils can induce controlled deformation and division of al...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-04510-3

    authors: Song Y,Michaels TCT,Ma Q,Liu Z,Yuan H,Takayama S,Knowles TPJ,Shum HC

    更新日期:2018-05-29 00:00:00

  • Plasmonic antenna coupling to hyperbolic phonon-polaritons for sensitive and fast mid-infrared photodetection with graphene.

    abstract::Integrating and manipulating the nano-optoelectronic properties of Van der Waals heterostructures can enable unprecedented platforms for photodetection and sensing. The main challenge of infrared photodetectors is to funnel the light into a small nanoscale active area and efficiently convert it into an electrical sign...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-18544-z

    authors: Castilla S,Vangelidis I,Pusapati VV,Goldstein J,Autore M,Slipchenko T,Rajendran K,Kim S,Watanabe K,Taniguchi T,Martín-Moreno L,Englund D,Tielrooij KJ,Hillenbrand R,Lidorikis E,Koppens FHL

    更新日期:2020-09-25 00:00:00

  • A regulatory circuit of miR-125b/miR-20b and Wnt signalling controls glioblastoma phenotypes through FZD6-modulated pathways.

    abstract::Molecularly defined subclassification is associated with phenotypic malignancy of glioblastoma (GBM). However, current understanding of the molecular basis of subclass conversion that is often involved in GBM recurrence remain rudimentary at best. Here we report that canonical Wnt signalling that is active in proneura...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms12885

    authors: Huang T,Alvarez AA,Pangeni RP,Horbinski CM,Lu S,Kim SH,James CD,J Raizer J,A Kessler J,Brenann CW,Sulman EP,Finocchiaro G,Tan M,Nishikawa R,Lu X,Nakano I,Hu B,Cheng SY

    更新日期:2016-10-04 00:00:00

  • Backmapping triangulated surfaces to coarse-grained membrane models.

    abstract::Many biological processes involve large-scale changes in membrane shape. Computer simulations of these processes are challenging since they occur across a wide range of spatiotemporal scales that cannot be investigated in full by any single current simulation technique. A potential solution is to combine different lev...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-16094-y

    authors: Pezeshkian W,König M,Wassenaar TA,Marrink SJ

    更新日期:2020-05-08 00:00:00