Proteomic maps of breast cancer subtypes.

Abstract:

:Systems-wide profiling of breast cancer has almost always entailed RNA and DNA analysis by microarray and sequencing techniques. Marked developments in proteomic technologies now enable very deep profiling of clinical samples, with high identification and quantification accuracy. We analysed 40 oestrogen receptor positive (luminal), Her2 positive and triple negative breast tumours and reached a quantitative depth of >10,000 proteins. These proteomic profiles identified functional differences between breast cancer subtypes, related to energy metabolism, cell growth, mRNA translation and cell-cell communication. Furthermore, we derived a signature of 19 proteins, which differ between the breast cancer subtypes, through support vector machine (SVM)-based classification and feature selection. Remarkably, only three proteins of the signature were associated with gene copy number variations and eleven were also reflected on the mRNA level. These breast cancer features revealed by our work provide novel insights that may ultimately translate to development of subtype-specific therapeutics.

journal_name

Nat Commun

journal_title

Nature communications

authors

Tyanova S,Albrechtsen R,Kronqvist P,Cox J,Mann M,Geiger T

doi

10.1038/ncomms10259

subject

Has Abstract

pub_date

2016-01-04 00:00:00

pages

10259

issn

2041-1723

pii

ncomms10259

journal_volume

7

pub_type

杂志文章
  • Genome engineering empowers the diatom Phaeodactylum tricornutum for biotechnology.

    abstract::Diatoms, a major group of photosynthetic microalgae, have a high biotechnological potential that has not been fully exploited because of the paucity of available genetic tools. Here we demonstrate targeted and stable modifications of the genome of the marine diatom Phaeodactylum tricornutum, using both meganucleases a...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms4831

    authors: Daboussi F,Leduc S,Maréchal A,Dubois G,Guyot V,Perez-Michaut C,Amato A,Falciatore A,Juillerat A,Beurdeley M,Voytas DF,Cavarec L,Duchateau P

    更新日期:2014-05-29 00:00:00

  • Precise allele-specific genome editing by spatiotemporal control of CRISPR-Cas9 via pronuclear transplantation.

    abstract::Gene-targeted animal models that are generated by injecting Cas9 and sgRNAs into zygotes are often accompanied by undesired double-strand break (DSB)-induced byproducts and random biallelic targeting due to uncontrollable Cas9 targeting activity. Here, we establish a parental allele-specific gene-targeting (Past-CRISP...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-18391-y

    authors: Li Y,Weng Y,Bai D,Jia Y,Liu Y,Zhang Y,Kou X,Zhao Y,Ruan J,Chen J,Yin J,Wang H,Teng X,Wang Z,Liu W,Gao S

    更新日期:2020-09-14 00:00:00

  • Prediction of the strength and timing of sunspot cycle 25 reveal decadal-scale space environmental conditions.

    abstract::The Sun's activity cycle governs the radiation, particle and magnetic flux in the heliosphere creating hazardous space weather. Decadal-scale variations define space climate and force the Earth's atmosphere. However, predicting the solar cycle is challenging. Current understanding indicates a short window for predicti...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-07690-0

    authors: Bhowmik P,Nandy D

    更新日期:2018-12-06 00:00:00

  • Using the president's tweets to understand political diversion in the age of social media.

    abstract::Social media has arguably shifted political agenda-setting power away from mainstream media onto politicians. Current U.S. President Trump's reliance on Twitter is unprecedented, but the underlying implications for agenda setting are poorly understood. Using the president as a case study, we present evidence suggestin...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-19644-6

    authors: Lewandowsky S,Jetter M,Ecker UKH

    更新日期:2020-11-10 00:00:00

  • Selective inhibition of the kinase DYRK1A by targeting its folding process.

    abstract::Autophosphorylation of amino-acid residues is part of the folding process of various protein kinases. Conventional chemical screening of mature kinases has missed inhibitors that selectively interfere with the folding process. Here we report a cell-based assay that evaluates inhibition of a kinase at a transitional st...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms11391

    authors: Kii I,Sumida Y,Goto T,Sonamoto R,Okuno Y,Yoshida S,Kato-Sumida T,Koike Y,Abe M,Nonaka Y,Ikura T,Ito N,Shibuya H,Hosoya T,Hagiwara M

    更新日期:2016-04-22 00:00:00

  • A distinct sodium channel voltage-sensor locus determines insect selectivity of the spider toxin Dc1a.

    abstract::β-Diguetoxin-Dc1a (Dc1a) is a toxin from the desert bush spider Diguetia canities that incapacitates insects at concentrations that are non-toxic to mammals. Dc1a promotes opening of German cockroach voltage-gated sodium (Nav) channels (BgNav1), whereas human Nav channels are insensitive. Here, by transplanting common...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms5350

    authors: Bende NS,Dziemborowicz S,Mobli M,Herzig V,Gilchrist J,Wagner J,Nicholson GM,King GF,Bosmans F

    更新日期:2014-07-11 00:00:00

  • Corrigendum: Contribution of classical end-joining to PTEN inactivation in p53-mediated glioblastoma formation and drug-resistant survival.

    abstract::This corrects the article DOI: 10.1038/ncomms14013. ...

    journal_title:Nature communications

    pub_type: 杂志文章,已发布勘误

    doi:10.1038/ncomms15795

    authors: Kang YJ,Balter B,Csizmadia E,Haas B,Sharma H,Bronson R,Yan CT

    更新日期:2017-08-14 00:00:00

  • Transposable element expression in tumors is associated with immune infiltration and increased antigenicity.

    abstract::Profound global loss of DNA methylation is a hallmark of many cancers. One potential consequence of this is the reactivation of transposable elements (TEs) which could stimulate the immune system via cell-intrinsic antiviral responses. Here, we develop REdiscoverTE, a computational method for quantifying genome-wide T...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-13035-2

    authors: Kong Y,Rose CM,Cass AA,Williams AG,Darwish M,Lianoglou S,Haverty PM,Tong AJ,Blanchette C,Albert ML,Mellman I,Bourgon R,Greally J,Jhunjhunwala S,Chen-Harris H

    更新日期:2019-11-19 00:00:00

  • A CD36 ectodomain mediates insect pheromone detection via a putative tunnelling mechanism.

    abstract::CD36 transmembrane proteins have diverse roles in lipid uptake, cell adhesion and pathogen sensing. Despite numerous in vitro studies, how they act in native cellular contexts is poorly understood. A Drosophila CD36 homologue, sensory neuron membrane protein 1 (SNMP1), was previously shown to facilitate detection of l...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms11866

    authors: Gomez-Diaz C,Bargeton B,Abuin L,Bukar N,Reina JH,Bartoi T,Graf M,Ong H,Ulbrich MH,Masson JF,Benton R

    更新日期:2016-06-15 00:00:00

  • Reconstructing plate-motion changes in the presence of finite-rotations noise.

    abstract::Understanding lithospheric plate motions is of paramount importance to geodynamicists. Much effort is going into kinematic reconstructions featuring progressively finer temporal resolution. However, the challenge of precisely identifying ocean-floor magnetic lineations, and uncertainties in geomagnetic reversal timesc...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms2051

    authors: Iaffaldano G,Bodin T,Sambridge M

    更新日期:2012-01-01 00:00:00

  • Identification and characterization of N9-methyltransferase involved in converting caffeine into non-stimulatory theacrine in tea.

    abstract::Caffeine is a major component of xanthine alkaloids and commonly consumed in many popular beverages. Due to its occasional side effects, reduction of caffeine in a natural way is of great importance and economic significance. Recent studies reveal that caffeine can be converted into non-stimulatory theacrine in the ra...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-15324-7

    authors: Zhang YH,Li YF,Wang Y,Tan L,Cao ZQ,Xie C,Xie G,Gong HB,Sun WY,Ouyang SH,Duan WJ,Lu X,Ding K,Kurihara H,Hu D,Zhang ZM,Abe I,He RR

    更新日期:2020-03-19 00:00:00

  • An enrichment method based on synergistic and reversible covalent interactions for large-scale analysis of glycoproteins.

    abstract::Protein glycosylation is ubiquitous in biological systems and essential for cell survival. However, the heterogeneity of glycans and the low abundance of many glycoproteins complicate their global analysis. Chemical methods based on reversible covalent interactions between boronic acid and glycans have great potential...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-04081-3

    authors: Xiao H,Chen W,Smeekens JM,Wu R

    更新日期:2018-04-27 00:00:00

  • Optical molecular imaging can differentiate metastatic from benign lymph nodes in head and neck cancer.

    abstract::Identification of lymph node (LN) metastasis is essential for staging of solid tumors, and as a result, surgeons focus on harvesting significant numbers of LNs during ablative procedures for pathological evaluation. Isolating those LNs most likely to harbor metastatic disease can allow for a more rigorous evaluation o...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-13076-7

    authors: Nishio N,van den Berg NS,van Keulen S,Martin BA,Fakurnejad S,Teraphongphom N,Chirita SU,Oberhelman NJ,Lu G,Horton CE,Kaplan MJ,Divi V,Colevas AD,Rosenthal EL

    更新日期:2019-11-06 00:00:00

  • Energetics of activation of GTP hydrolysis on the ribosome.

    abstract::Several of the steps in protein synthesis on the ribosome utilize hydrolysis of guanosine triphosphate (GTP) as the driving force. This reaction is catalyzed by translation factors that become activated upon binding to the ribosome. The recently determined crystal structure of an elongation factor-Tu ternary complex b...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms2741

    authors: Wallin G,Kamerlin SC,Aqvist J

    更新日期:2013-01-01 00:00:00

  • Zero-temperature glass transition in two dimensions.

    abstract::Liquids cooled towards the glass transition temperature transform into amorphous solids that have a wide range of applications. While the nature of this transformation is understood rigorously in the mean-field limit of infinite spatial dimensions, the problem remains wide open in physical dimensions. Nontrivial finit...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-09512-3

    authors: Berthier L,Charbonneau P,Ninarello A,Ozawa M,Yaida S

    更新日期:2019-04-03 00:00:00

  • Characterization of the hemodynamic response function in white matter tracts for event-related fMRI.

    abstract::Accurate estimates of the BOLD hemodynamic response function (HRF) are crucial for the interpretation and analysis of event-related functional MRI data. To date, however, there have been no comprehensive measurements of the HRF in white matter (WM) despite increasing evidence that BOLD signals in WM change after a sti...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-09076-2

    authors: Li M,Newton AT,Anderson AW,Ding Z,Gore JC

    更新日期:2019-03-08 00:00:00

  • Nuclear membrane protein Lem2 regulates nuclear size through membrane flow.

    abstract::The size of the membrane-bound nucleus scales with cell size in a wide range of cell types but the mechanisms determining overall nuclear size remain largely unknown. Here we investigate the role of fission yeast inner nuclear membrane proteins in determining nuclear size, and propose that the Lap2-Emerin-Man1 domain ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-09623-x

    authors: Kume K,Cantwell H,Burrell A,Nurse P

    更新日期:2019-04-23 00:00:00

  • Cas9-AAV6-engineered human mesenchymal stromal cells improved cutaneous wound healing in diabetic mice.

    abstract::Human mesenchymal stromal cells (hMSCs) are a promising source for engineered cell-based therapies in which genetic engineering could enhance therapeutic efficacy and install novel cellular functions. Here, we describe an optimized Cas9-AAV6-based genome editing tool platform for site-specific mutagenesis and integrat...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-16065-3

    authors: Srifa W,Kosaric N,Amorin A,Jadi O,Park Y,Mantri S,Camarena J,Gurtner GC,Porteus M

    更新日期:2020-05-18 00:00:00

  • Surface oxygenation of multicomponent nanoparticles toward active and stable oxidation catalysts.

    abstract::The need for active and stable oxidation catalysts is driven by the demands in production of valuable chemicals, remediation of hydrocarbon pollutants and energy sustainability. Traditional approaches focus on oxygen-activating oxides as support which provides the oxygen activation at the catalyst-support peripheral i...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-18017-3

    authors: Shan S,Li J,Maswadeh Y,O'Brien C,Kareem H,Tran DT,Lee IC,Wu ZP,Wang S,Yan S,Cronk H,Mott D,Yang L,Luo J,Petkov V,Zhong CJ

    更新日期:2020-08-21 00:00:00

  • Transcription errors induce proteotoxic stress and shorten cellular lifespan.

    abstract::Transcription errors occur in all living cells; however, it is unknown how these errors affect cellular health. To answer this question, we monitor yeast cells that are genetically engineered to display error-prone transcription. We discover that these cells suffer from a profound loss in proteostasis, which sensitize...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms9065

    authors: Vermulst M,Denney AS,Lang MJ,Hung CW,Moore S,Moseley MA,Thompson JW,Madden V,Gauer J,Wolfe KJ,Summers DW,Schleit J,Sutphin GL,Haroon S,Holczbauer A,Caine J,Jorgenson J,Cyr D,Kaeberlein M,Strathern JN,Duncan MC,E

    更新日期:2015-08-25 00:00:00

  • Arctic-Eurasian climate linkage induced by tropical ocean variability.

    abstract::Eurasian continent has experienced cold winters over the past two decades in contrast with Arctic warming. Previous studies have suggested that the cold Eurasian winters are associated with Arctic sea-ice loss, while others attributed them to atmospheric internal variability. However, here we show that the Arctic and ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-11359-7

    authors: Matsumura S,Kosaka Y

    更新日期:2019-08-01 00:00:00

  • Somatic Trp53 mutations differentially drive breast cancer and evolution of metastases.

    abstract::TP53 mutations are the most frequent genetic alterations in breast cancer and are associated with more aggressive disease and worse overall survival. We have created two conditional mutant Trp53 alleles in the mouse that allow expression of Trp53R172H or Trp53R245W missense mutations in single cells surrounded by a no...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-06146-9

    authors: Zhang Y,Xiong S,Liu B,Pant V,Celii F,Chau G,Elizondo-Fraire AC,Yang P,You MJ,El-Naggar AK,Navin NE,Lozano G

    更新日期:2018-09-27 00:00:00

  • Formation of nitrogen-doped graphene nanoscrolls by adsorption of magnetic γ-Fe2O3 nanoparticles.

    abstract::Graphene nanoscrolls are Archimedean-type spirals formed by rolling single-layer graphene sheets. Their unique structure makes them conceptually interesting and understanding their formation gives important information on the manipulation and characteristics of various carbon nanostructures. Here we report a 100% effi...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms3319

    authors: Sharifi T,Gracia-Espino E,Barzegar HR,Jia X,Nitze F,Hu G,Nordblad P,Tai CW,Wågberg T

    更新日期:2013-01-01 00:00:00

  • MNKs act as a regulatory switch for eIF4E1 and eIF4E3 driven mRNA translation in DLBCL.

    abstract::The phosphorylation of eIF4E1 at serine 209 by MNK1 or MNK2 has been shown to initiate oncogenic mRNA translation, a process that favours cancer development and maintenance. Here, we interrogate the MNK-eIF4E axis in diffuse large B-cell lymphoma (DLBCL) and show a distinct distribution of MNK1 and MNK2 in germinal ce...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms6413

    authors: Landon AL,Muniandy PA,Shetty AC,Lehrmann E,Volpon L,Houng S,Zhang Y,Dai B,Peroutka R,Mazan-Mamczarz K,Steinhardt J,Mahurkar A,Becker KG,Borden KL,Gartenhaus RB

    更新日期:2014-11-18 00:00:00

  • Photonic integrated field-programmable disk array signal processor.

    abstract::Thanks to the nature of strong programmability, field-programmable gate arrays (FPGAs) have been playing a significant role in signal processing and control. With the explosive growth in digital data, big data analytics becomes an important emerging field, in which FPGAs are a major player. However, the computational ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-14249-0

    authors: Zhang W,Yao J

    更新日期:2020-01-21 00:00:00

  • Variant surface glycoprotein density defines an immune evasion threshold for African trypanosomes undergoing antigenic variation.

    abstract::Trypanosoma brucei is a protozoan parasite that evades its host's adaptive immune response by repeatedly replacing its dense variant surface glycoprotein (VSG) coat from its large genomic VSG repertoire. While the mechanisms regulating VSG gene expression and diversification have been examined extensively, the dynamic...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-017-00959-w

    authors: Pinger J,Chowdhury S,Papavasiliou FN

    更新日期:2017-10-10 00:00:00

  • Computational identification of mutually exclusive transcriptional drivers dysregulating metastatic microRNAs in prostate cancer.

    abstract::Androgen-ablation therapies, which are the standard treatment for metastatic prostate cancer, invariably lead to acquired resistance. Hence, a systematic identification of additional drivers may provide useful insights into the development of effective therapies. Numerous microRNAs that are critical for metastasis are...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms14917

    authors: Xue M,Liu H,Zhang L,Chang H,Liu Y,Du S,Yang Y,Wang P

    更新日期:2017-04-11 00:00:00

  • ERG induces taxane resistance in castration-resistant prostate cancer.

    abstract::Taxanes are the only chemotherapies used to treat patients with metastatic castration-resistant prostate cancer (CRPC). Despite the initial efficacy of taxanes in treating CRPC, all patients ultimately fail due to the development of drug resistance. In this study, we show that ERG overexpression in in vitro and in viv...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms6548

    authors: Galletti G,Matov A,Beltran H,Fontugne J,Miguel Mosquera J,Cheung C,MacDonald TY,Sung M,O'Toole S,Kench JG,Suk Chae S,Kimovski D,Tagawa ST,Nanus DM,Rubin MA,Horvath LG,Giannakakou P,Rickman DS

    更新日期:2014-11-25 00:00:00

  • Identification and characterization of a novel botulinum neurotoxin.

    abstract::Botulinum neurotoxins are known to have seven serotypes (BoNT/A-G). Here we report a new BoNT serotype, tentatively named BoNT/X, which has the lowest sequence identity with other BoNTs and is not recognized by antisera against known BoNTs. Similar to BoNT/B/D/F/G, BoNT/X cleaves vesicle-associated membrane proteins (...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms14130

    authors: Zhang S,Masuyer G,Zhang J,Shen Y,Lundin D,Henriksson L,Miyashita SI,Martínez-Carranza M,Dong M,Stenmark P

    更新日期:2017-08-03 00:00:00

  • Postmitotic control of sensory area specification during neocortical development.

    abstract::The mammalian neocortex is subdivided into cytoarchitectural areas with distinct connectivity, gene expression and neural functions. Areal identity is initially specified by rostrocaudal and mediolateral gene expression gradients in neuroepithelial and radial glial progenitors (the 'protomap'). On further differentiat...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms6632

    authors: Alfano C,Magrinelli E,Harb K,Hevner RF,Studer M

    更新日期:2014-12-05 00:00:00