当前位置： SCI文献检索 > Scientific Reports期刊下所有文献 > Differentially Methylated Super-Enhancers Regulate Target Gene Expression in Human Cancer.

Differentially Methylated Super-Enhancers Regulate Target Gene Expression in Human Cancer.

Abstract：

:Current literature suggests that epigenetically regulated super-enhancers (SEs) are drivers of aberrant gene expression in cancers. Many tumor types are still missing chromatin data to define cancer-specific SEs and their role in carcinogenesis. In this work, we develop a simple pipeline, which can utilize chromatin data from etiologically similar tumors to discover tissue-specific SEs and their target genes using gene expression and DNA methylation data. As an example, we applied our pipeline to human papillomavirus-related oropharyngeal squamous cell carcinoma (HPV + OPSCC). This tumor type is characterized by abundant gene expression changes, which cannot be explained by genetic alterations alone. Chromatin data are still limited for this disease, so we used 3627 SE elements from public domain data for closely related tissues, including normal and tumor lung, and cervical cancer cell lines. We integrated the available DNA methylation and gene expression data for HPV + OPSCC samples to filter the candidate SEs to identify functional SEs and their affected targets, which are essential for cancer development. Overall, we found 159 differentially methylated SEs, including 87 SEs that actively regulate expression of 150 nearby genes (211 SE-gene pairs) in HPV + OPSCC. Of these, 132 SE-gene pairs were validated in a related TCGA cohort. Pathway analysis revealed that the SE-regulated genes were associated with pathways known to regulate nasopharyngeal, breast, melanoma, and bladder carcinogenesis and are regulated by the epigenetic landscape in those cancers. Thus, we propose that gene expression in HPV + OPSCC may be controlled by epigenetic alterations in SE elements, which are common between related tissues. Our pipeline can utilize a diversity of data inputs and can be further adapted to SE analysis of diseased and non-diseased tissues from different organisms.

journal_name

Sci Rep

journal_title

Scientific reports

authors

Flam EL,Danilova L,Kelley DZ,Stavrovskaya E,Guo T,Considine M,Qian J,Califano JA,Favorov A,Fertig EJ,Gaykalova DA

doi

10.1038/s41598-019-51018-x

subject

Has Abstract

pub_date

2019-10-21 00:00:00

pages

15034

issue

1

issn

2045-2322

pii

10.1038/s41598-019-51018-x

journal_volume

9

pub_type

杂志文章

相关文献

Scientific Reports文献大全
  • Gauss's law for networks directly reveals community boundaries.

    abstract：:The study of network topology provides insight into the function and behavior of physical, social, and biological systems. A natural step towards discovering the organizing principles of these complex topologies is to identify a reduced network representation using cohesive subgroups or communities. This procedure oft...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-018-30401-0

    authors： Sinha A,Gleich DF,Ramani K

    更新日期：2018-08-09 00:00:00

  • Identification of key genes involved in the biosynthesis of triterpenic acids in the mint family.

    abstract：:Triterpenic acids (TAs), a large group of natural compounds with diverse biological activity, are produced by several plant taxa. Betulinic, oleanolic, and ursolic acids are the most medicinally important TAs and are mainly found in plants of the mint family. Metabolic engineering is strongly dependent on identifying ...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-019-52090-z

    authors： Aminfar Z,Rabiei B,Tohidfar M,Mirjalili MH

    更新日期：2019-11-01 00:00:00

  • Test-photostability of pulsed laser deposited amorphous thin films from Ge-As-Te system.

    abstract：:Amorphous thin films from Ge-As-Te system were prepared by pulsed laser deposition to study their intrinsic photostability, morphology, chemical composition, structure and optical properties. Photostability of fabricated layers was studied by spectroscopic ellipsometry within as-deposited as well as relaxed (annealed)...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep09310

    authors： Hawlová P,Verger F,Nazabal V,Boidin R,Němec P

    更新日期：2015-03-23 00:00:00

  • Analysis of Corneal Spherical Aberrations in Cataract Patients with High Myopia.

    abstract：:To evaluate the corneal spherical aberrations in cataract patients with and without high myopia, we conducted a retrospective case series of 502 cataract eyes with high myopia and 1500 age-related cataract eyes and measure their corneal biometric data and axial length using Pentacam and IOLMaster. Both the anterior an...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-018-36539-1

    authors： Zhang M,Qian D,Jing Q,Chen J,Jiang Y

    更新日期：2019-02-05 00:00:00

  • Quantum Search on Encrypted Data Based on Quantum Homomorphic Encryption.

    abstract：:We propose a homomorphic search protocol based on quantum homomorphic encryption, in which a client Alice with limited quantum ability can give her encrypted data to a powerful but untrusted quantum server and let the server search for her without decryption. By outsourcing the interactive key-update process to a trus...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-61791-9

    authors： Zhou Q,Lu S,Cui Y,Li L,Sun J

    更新日期：2020-03-20 00:00:00

  • Fast cooling in dispersively and dissipatively coupled optomechanics.

    abstract：:The cooling performance of an optomechanical system comprising both dispersive and dissipative coupling is studied. Here, we present a scheme to cool a mechanical resonator to its ground state in finite time using a chirped pulse. We show that there is distinct advantage in using the chirp-pulse scheme to cool a reson...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep07745

    authors： Chen T,Wang XB

    更新日期：2015-01-13 00:00:00

  • Identification and molecular characterization of the first complete genome sequence of Human Parechovirus type 15.

    abstract：:Using a metagenomics approach, we have determined the first full-length genome sequence of a human parechovirus type 15 (HPeV15) strain, isolated from a child with acute flaccid paralysis and co-infected with EV-A71. HPeV15 is a rarely reported type. To date, no full-length genome sequence of HPeV15 is available in th...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-63467-w

    authors： Fernandez-Garcia MD,Simon-Loriere E,Kebe O,Sakuntabhai A,Ndiaye K

    更新日期：2020-04-21 00:00:00

  • Intravenous C16 and angiopoietin-1 improve the efficacy of placenta-derived mesenchymal stem cell therapy for EAE.

    abstract：:The placenta has emerged as an attractive source of mesenchymal stem cells (MSCs) because of the absence of ethical issues, non-invasive access, and abundant yield. However, inflammatory cell invasion into grafts negatively impacts the survival and efficacy of transplanted cells. Previous studies have shown that synth...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-018-22867-9

    authors： Tian KW,Zhang YY,Jiang H,Han S

    更新日期：2018-03-15 00:00:00

  • Photonic transistor and router using a single quantum-dot-confined spin in a single-sided optical microcavity.

    abstract：:The future Internet is very likely the mixture of all-optical Internet with low power consumption and quantum Internet with absolute security guaranteed by the laws of quantum mechanics. Photons would be used for processing, routing and com-munication of data, and photonic transistor using a weak light to control a st...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep45582

    authors： Hu CY

    更新日期：2017-03-28 00:00:00

  • Reflection type metasurface designed for high efficiency vectorial field generation.

    abstract：:We propose a reflection type metal-insulator-metal (MIM) metasurface composed of hybrid nano-antennas for comprehensive spatial engineering of the properties of optical fields. The capability of such structure is illustrated in the design of a device that can be used to produce a radially polarized vectorial beam for ...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep29626

    authors： Wang S,Zhan Q

    更新日期：2016-07-15 00:00:00

  • Rapidly discriminate commercial medicinal Pulsatilla chinensis (Bge.) Regel from its adulterants using ITS2 barcoding and specific PCR-RFLP assay.

    abstract：:Pulsatillae radix is a conventional traditional Chinese medicine (TCM) with common name Baitouweng, and has notable effects on inflammation and dysentery. Pulsatilla chinensis (Bge.) Regel is the only source plant of Baitouweng recorded in Chinese Pharmacopoeia, but its adulteration often occurs in the market that pos...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep40000

    authors： Shi Y,Zhao M,Yao H,Yang P,Xin T,Li B,Sun W,Chen S

    更新日期：2017-01-06 00:00:00

  • Multi-Channel 3D Deep Feature Learning for Survival Time Prediction of Brain Tumor Patients Using Multi-Modal Neuroimages.

    abstract：:High-grade gliomas are the most aggressive malignant brain tumors. Accurate pre-operative prognosis for this cohort can lead to better treatment planning. Conventional survival prediction based on clinical information is subjective and could be inaccurate. Recent radiomics studies have shown better prognosis by using ...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-018-37387-9

    authors： Nie D,Lu J,Zhang H,Adeli E,Wang J,Yu Z,Liu L,Wang Q,Wu J,Shen D

    更新日期：2019-01-31 00:00:00

  • Constructing the magnetic bifunctional graphene/titania nanosheet-based composite photocatalysts for enhanced visible-light photodegradation of MB and electrochemical ORR from polluted water.

    abstract：:Photocatalysis is a promising strategy to address the global environmental and energy challenges. However, the studies on the application of the photocatalytically degraded dye-polluted water and the multi-purpose use of one type of catalyst have remained sparse. In this report, we try to demonstrate a concept of mult...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-017-12504-2

    authors： Zhang Q,Zhang Y,Meng Z,Tong W,Yu X,An Q

    更新日期：2017-09-25 00:00:00

  • Reprogramming Escherichia coli for the production of prenylated indole diketopiperazine alkaloids.

    abstract：:Prenylated indole diketopiperazine (DKP) alkaloids are important bioactive molecules or their precursors. In the context of synthetic biology, efficient means for their biological production would increase their chemical diversification and the discovery of novel bioactive compounds. Here, we prove the suitability of ...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-019-45519-y

    authors： Dubois P,Correia I,Le Chevalier F,Dubois S,Jacques I,Canu N,Moutiez M,Thai R,Gondry M,Lequin O,Belin P

    更新日期：2019-06-25 00:00:00

  • Basal protein phosphatase 2A activity restrains cytokine expression: role for MAPKs and tristetraprolin.

    abstract：:PP2A is a master controller of multiple inflammatory signaling pathways. It is a target in asthma; however the molecular mechanisms by which PP2A controls inflammation warrant further investigation. In A549 lung epithelial cells in vitro we show that inhibition of basal PP2A activity by okadaic acid (OA) releases rest...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep10063

    authors： Rahman MM,Rumzhum NN,Morris JC,Clark AR,Verrills NM,Ammit AJ

    更新日期：2015-05-18 00:00:00

  • Exploring the biological role of postzygotic and germinal de novo mutations in ASD.

    abstract：:De novo mutations (DNMs), including germinal and postzygotic mutations (PZMs), are a strong source of causality for Autism Spectrum Disorder (ASD). However, the biological processes involved behind them remain unexplored. Our aim was to detect DNMs (germinal and PZMs) in a Spanish ASD cohort (360 trios) and to explore...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-79412-w

    authors： Alonso-Gonzalez A,Calaza M,Amigo J,González-Peñas J,Martínez-Regueiro R,Fernández-Prieto M,Parellada M,Arango C,Rodriguez-Fontenla C,Carracedo A

    更新日期：2021-01-11 00:00:00

  • Non-reliance of metazoans on stromatolite-forming microbial mats as a food resource.

    abstract：:Grazing and burrowing organisms usually homogenise microalgal mats that form on benthic sediments of many aquatic ecosystems. In the absence of this disruption, microalgal mats can accrete laminated deposits (stromatolites). Stromatolites are rare in modern coastal ecosystems, but persist at locations where metazoans ...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep42614

    authors： Rishworth GM,Perissinotto R,Bird MS,Strydom NA,Peer N,Miranda NA,Raw JL

    更新日期：2017-02-16 00:00:00

  • Dual targeting of ANGPT1 and TGFBR2 genes by miR-204 controls angiogenesis in breast cancer.

    abstract：:Deregulated expression of microRNAs has been associated with angiogenesis. Studying the miRNome of locally advanced breast tumors we unsuspectedly found a dramatically repression of miR-204, a small non-coding RNA with no previous involvement in tumor angiogenesis. Downregulation of miR-204 was confirmed in an indepen...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep34504

    authors： Flores-Pérez A,Marchat LA,Rodríguez-Cuevas S,Bautista-Piña V,Hidalgo-Miranda A,Ocampo EA,Martínez MS,Palma-Flores C,Fonseca-Sánchez MA,Astudillo-de la Vega H,Ruíz-García E,González-Barrios JA,Pérez-Plasencia C,Streber ML,Lópe

    更新日期：2016-10-05 00:00:00

  • Ferroelectric control of a Mott insulator.

    abstract：:The electric field control of functional properties is an important goal in oxide-based electronics. To endow devices with memory, ferroelectric gating is interesting, but usually weak compared to volatile electrolyte gating. Here, we report a very large ferroelectric field-effect in perovskite heterostructures combin...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep02834

    authors： Yamada H,Marinova M,Altuntas P,Crassous A,Bégon-Lours L,Fusil S,Jacquet E,Garcia V,Bouzehouane K,Gloter A,Villegas JE,Barthélémy A,Bibes M

    更新日期：2013-10-03 00:00:00

  • Replication of results from a cervical cancer genome-wide association study in Taiwanese women.

    abstract：:Genetic epidemiological studies show that genetic factors contribute significantly to cervical cancer carcinogenesis. Several genome-wide association studies (GWAS) have revealed novel genetic variants associated with cervical cancer susceptibility. We aim to replicate 4 GWAS-identified single nucleotide polymorphisms...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-018-33430-x

    authors： Yang YC,Chang TY,Chen TC,Lin WS,Lin CL,Lee YJ

    更新日期：2018-10-17 00:00:00

  • Genome-level identification of targets of Hox protein Ultrabithorax in Drosophila: novel mechanisms for target selection.

    abstract：:Hox proteins are transcription factors and key regulators of segmental identity along the anterior posterior axis across all bilaterian animals. Despite decades of research, the mechanisms by which Hox proteins select and regulate their targets remain elusive. We have carried out whole-genome ChIP-chip experiments to ...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep00205

    authors： Agrawal P,Habib F,Yelagandula R,Shashidhara LS

    更新日期：2011-01-01 00:00:00

  • Reversible inactivation of a peptidoglycan transpeptidase by a β-lactam antibiotic mediated by β-lactam-ring recyclization in the enzyme active site.

    abstract：:β-lactam antibiotics act as suicide substrates of transpeptidases responsible for the last cross-linking step of peptidoglycan synthesis in the bacterial cell wall. Nucleophilic attack of the β-lactam carbonyl by the catalytic residue (Ser or Cys) of transpeptidases results in the opening of the β-lactam ring and in t...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-017-09341-8

    authors： Edoo Z,Arthur M,Hugonnet JE

    更新日期：2017-08-22 00:00:00

  • Peritumoral and intratumoral radiomic features predict survival outcomes among patients diagnosed in lung cancer screening.

    abstract：:The National Lung Screening Trial (NLST) demonstrated that screening with low-dose computed tomography (LDCT) is associated with a 20% reduction in lung cancer mortality. One potential limitation of LDCT screening is overdiagnosis of slow growing and indolent cancers. In this study, peritumoral and intratumoral radiom...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-67378-8

    authors： Pérez-Morales J,Tunali I,Stringfield O,Eschrich SA,Balagurunathan Y,Gillies RJ,Schabath MB

    更新日期：2020-06-29 00:00:00

  • β-barrel Oligomers as Common Intermediates of Peptides Self-Assembling into Cross-β Aggregates.

    abstract：:Oligomers populated during the early amyloid aggregation process are more toxic than mature fibrils, but pinpointing the exact toxic species among highly dynamic and heterogeneous aggregation intermediates remains a major challenge. β-barrel oligomers, structurally-determined recently for a slow-aggregating peptide de...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-018-28649-7

    authors： Sun Y,Ge X,Xing Y,Wang B,Ding F

    更新日期：2018-07-09 00:00:00

  • In vivo Real-Time Mass Spectrometry for Guided Surgery Application.

    abstract：:Here we describe a new instrument (SpiderMass) designed for in vivo and real-time analysis. In this instrument ion production is performed remotely from the MS instrument and the generated ions are transported in real-time to the MS analyzer. Ion production is promoted by Resonant Infrared Laser Ablation (RIR-LA) base...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep25919

    authors： Fatou B,Saudemont P,Leblanc E,Vinatier D,Mesdag V,Wisztorski M,Focsa C,Salzet M,Ziskind M,Fournier I

    更新日期：2016-05-18 00:00:00

  • Rotating edge-field driven processing of chiral spin textures in racetrack devices.

    abstract：:Topologically distinct magnetic structures like skyrmions, domain walls, and the uniformly magnetized state have multiple applications in logic devices, sensors, and as bits of information. One of the most promising concepts for applying these bits is the racetrack architecture controlled by electric currents or magne...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-77337-y

    authors： Schäffer AF,Siegl P,Stier M,Posske T,Berakdar J,Thorwart M,Wiesendanger R,Vedmedenko EY

    更新日期：2020-11-23 00:00:00

  • Bark and wood tissues of American elm exhibit distinct responses to Dutch elm disease.

    abstract：:Tolerance to Dutch elm disease (DED) has been linked to the rapid and/or high induction of disease-responsive genes after infection with the fungus Ophiostoma novo-ulmi. Although the fungal infection by O. novo-ulmi primarily takes places in xylem vessels, it is still unclear how xylem contributes to the defense again...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-017-07779-4

    authors： Sherif SM,Erland LA,Shukla MR,Saxena PK

    更新日期：2017-08-02 00:00:00

  • Differential proteomics profiling of the ova between healthy and Rice stripe virus-infected female insects of Laodelphax striatellus.

    abstract：:Rice stripe virus-infected females of the small brown planthopper (SBPH, Laodelphax striatellus) usually lay fewer eggs with a longer hatch period, low hatchability, malformation and retarded or defective development compared with healthy females. To explore the molecular mechanism of those phenomena, we analyzed the ...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep27216

    authors： Liu B,Qin F,Liu W,Wang X

    更新日期：2016-06-09 00:00:00

  • In Silico Models of DNA Damage and Repair in Proton Treatment Planning: A Proof of Concept.

    abstract：:There is strong in vitro cell survival evidence that the relative biological effectiveness (RBE) of protons is variable, with dependence on factors such as linear energy transfer (LET) and dose. This is coupled with the growing in vivo evidence, from post-treatment image change analysis, of a variable RBE. Despite thi...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-019-56258-5

    authors： Smith EAK,Henthorn NT,Warmenhoven JW,Ingram SP,Aitkenhead AH,Richardson JC,Sitch P,Chadwick AL,Underwood TSA,Merchant MJ,Burnet NG,Kirkby NF,Kirkby KJ,Mackay RI

    更新日期：2019-12-27 00:00:00

  • Forecasting Events in the Complex Dynamics of a Semiconductor Laser with Optical Feedback.

    abstract：:Complex systems performing spiking dynamics are widespread in Nature. They cover from earthquakes, to neurons, variable stars, social networks, or stock markets. Understanding and characterizing their dynamics is relevant in order to detect transitions, or to predict unwanted extreme events. Here we study, under an or...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-018-29110-5

    authors： Colet M,Aragoneses A

    更新日期：2018-07-16 00:00:00