Abstract:
:Noncoding RNAs (ncRNAs) are emerging as key molecules in human cancer, with the potential to serve as novel markers of disease and to reveal uncharacterized aspects of tumor biology. Here we discover 121 unannotated prostate cancer-associated ncRNA transcripts (PCATs) by ab initio assembly of high-throughput sequencing of polyA(+) RNA (RNA-Seq) from a cohort of 102 prostate tissues and cells lines. We characterized one ncRNA, PCAT-1, as a prostate-specific regulator of cell proliferation and show that it is a target of the Polycomb Repressive Complex 2 (PRC2). We further found that patterns of PCAT-1 and PRC2 expression stratified patient tissues into molecular subtypes distinguished by expression signatures of PCAT-1-repressed target genes. Taken together, our findings suggest that PCAT-1 is a transcriptional repressor implicated in a subset of prostate cancer patients. These findings establish the utility of RNA-Seq to identify disease-associated ncRNAs that may improve the stratification of cancer subtypes.
journal_name
Nat Biotechnoljournal_title
Nature biotechnologyauthors
Prensner JR,Iyer MK,Balbin OA,Dhanasekaran SM,Cao Q,Brenner JC,Laxman B,Asangani IA,Grasso CS,Kominsky HD,Cao X,Jing X,Wang X,Siddiqui J,Wei JT,Robinson D,Iyer HK,Palanisamy N,Maher CA,Chinnaiyan AMdoi
10.1038/nbt.1914subject
Has Abstractpub_date
2011-07-31 00:00:00pages
742-9issue
8eissn
1087-0156issn
1546-1696pii
nbt.1914journal_volume
29pub_type
杂志文章abstract::Pluripotent stem cell-derived cardiomyocyte grafts can remuscularize substantial amounts of infarcted myocardium and beat in synchrony with the heart, but in some settings cause ventricular arrhythmias. It is unknown whether human cardiomyocytes can restore cardiac function in a physiologically relevant large animal m...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt.4162
更新日期:2018-08-01 00:00:00
abstract::Droplet single-cell RNA-sequencing (dscRNA-seq) has enabled rapid, massively parallel profiling of transcriptomes. However, assessing differential expression across multiple individuals has been hampered by inefficient sample processing and technical batch effects. Here we describe a computational tool, demuxlet, that...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt.4042
更新日期:2018-01-01 00:00:00
abstract::Purging of tumor cells and selection of stem cells are key technologies for enabling stem cell transplantation and stem cell gene therapy. Here we report a strategy for cell selection based on physical properties of the cells. Exposing cells to an external pulsed electric field (PEF) increases the natural potential di...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/78504
更新日期:2000-08-01 00:00:00
abstract::The excitement and controversy surrounding the potential role of human embryonic stem (ES) cells in transplantation therapy have often overshadowed their potentially more important use as a basic research tool for understanding the development and function of human tissues. Human ES cells can proliferate without a kno...
journal_title:Nature biotechnology
pub_type:
doi:10.1038/nbt761
更新日期:2002-12-01 00:00:00
abstract::Massively parallel sequencing of cDNA has enabled deep and efficient probing of transcriptomes. Current approaches for transcript reconstruction from such data often rely on aligning reads to a reference genome, and are thus unsuitable for samples with a partial or missing reference genome. Here we present the Trinity...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt.1883
更新日期:2011-05-15 00:00:00
abstract::Analyzing patent data from 1995-2005 show the increasing importance of patenting by small and medium-sized biotech companies. ...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt0606-643
更新日期:2006-06-01 00:00:00
abstract::New cultivars with very erect leaves, which increase light capture for photosynthesis and nitrogen storage for grain filling, may have increased grain yields. Here we show that the erect leaf phenotype of a rice brassinosteroid-deficient mutant, osdwarf4-1, is associated with enhanced grain yields under conditions of ...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt1173
更新日期:2006-01-01 00:00:00
abstract::RNA interference (RNAi) induced by short interfering RNA (siRNA) allows for discovery research and large-scale screening; however, owing to their size and anionic charge, siRNAs do not readily enter cells. Current approaches do not deliver siRNAs into a high percentage of primary cells without cytotoxicity. Here we re...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt.1541
更新日期:2009-06-01 00:00:00
abstract::While the use of enzymes as biocatalysts to assist in the industrial manufacture of fine chemicals and pharmaceuticals has enormous potential, application is frequently limited by evolution-led catalyst traits. The advent of designer biocatalysts, produced by informed selection and mutation through recombinant DNA tec...
journal_title:Nature biotechnology
pub_type: 杂志文章,评审
doi:10.1038/nbt0102-37
更新日期:2002-01-01 00:00:00
abstract::Despite developments in targeted gene sequencing and whole-genome analysis techniques, the robust detection of all genetic variation, including structural variants, in and around genes of interest and in an allele-specific manner remains a challenge. Here we present targeted locus amplification (TLA), a strategy to se...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt.2959
更新日期:2014-10-01 00:00:00
abstract::Nitrile hydratase (NHase), which catalyzes the hydration of nitriles to amides, has been used in the industrial production of acrylamide and nicotinamide. Recent studies on NHases, which are roughly classified into iron and cobalt types according to the metal involved, have clarified the photoactivation mechanism, the...
journal_title:Nature biotechnology
pub_type: 杂志文章,评审
doi:10.1038/nbt0898-733
更新日期:1998-08-01 00:00:00
abstract::Isoflavones have drawn much attention because of their benefits to human health. These compounds, which are produced almost exclusively in legumes, have natural roles in plant defense and root nodulation. Isoflavone synthase catalyzes the first committed step of isoflavone biosynthesis, a branch of the phenylpropanoid...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/72671
更新日期:2000-02-01 00:00:00
abstract::New high-dimensional, single-cell technologies offer unprecedented resolution in the analysis of heterogeneous tissues. However, because these technologies can measure dozens of parameters simultaneously in individual cells, data interpretation can be challenging. Here we present viSNE, a tool that allows one to map h...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt.2594
更新日期:2013-06-01 00:00:00
abstract::Complex interactions among genetic components often result in variable systemic performance in designed multigene systems. Using the bacterial clustered regularly interspaced short palindromic repeat (CRISPR) pathway we develop a synthetic RNA-processing platform, and show that efficient and specific cleavage of precu...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt.2355
更新日期:2012-10-01 00:00:00
abstract::Recent therapeutic successes have renewed interest in drug combinations, but experimental screening approaches are costly and often identify only small numbers of synergistic combinations. The DREAM consortium launched an open challenge to foster the development of in silico methods to computationally rank 91 compound...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt.3052
更新日期:2014-12-01 00:00:00
abstract::Detection of mutations and damaged DNA bases is important for the early diagnosis of genetic disease. Here we describe an electrocatalytic method for the detection of single-base mismatches as well as DNA base lesions in fully hybridized duplexes, based on charge transport through DNA films. Gold electrodes modified w...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/80301
更新日期:2000-10-01 00:00:00
abstract::For the past five decades, the need for new antibiotics has been met largely by semisynthetic tailoring of natural product scaffolds discovered in the middle of the 20(th) century. More recently, however, advances in technology have sparked a resurgence in the discovery of natural product antibiotics from bacterial so...
journal_title:Nature biotechnology
pub_type: 杂志文章,评审
doi:10.1038/nbt1266
更新日期:2006-12-01 00:00:00
abstract::A fibrinolytic agent consisting of a tissue-type plasminogen activator (tPA) coupled to the surface of red blood cells (RBCs) can dissolve nascent clots from within the clot, in a Trojan horse-like strategy, while having minimal effects on preexisting hemostatic clots or extravascular tissue. After intravenous injecti...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt846
更新日期:2003-08-01 00:00:00
abstract::Calcium (Ca(2+)) signals that are precisely modulated in space and time mediate a myriad of cellular processes, including contraction, excitation, growth, differentiation and apoptosis. However, study of Ca(2+) responses has been hampered by technological limitations of existing Ca(2+)-modulating tools. Here we presen...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt.3350
更新日期:2015-10-01 00:00:00
abstract::Although bile duct disorders are well-recognized causes of liver disease, the molecular and cellular events leading to biliary dysfunction are poorly understood. To enable modeling and drug discovery for biliary disease, we describe a protocol that achieves efficient differentiation of biliary epithelial cells (cholan...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt.3294
更新日期:2015-08-01 00:00:00
abstract::Debates on patenting DNA must evolve to reflect the global decline in filings and regional disparities in patenting activity. ...
journal_title:Nature biotechnology
pub_type: 杂志文章,评审
doi:10.1038/nbt0207-185
更新日期:2007-02-01 00:00:00
abstract::High-throughput genetic screens have become essential tools for studying a wide variety of biological processes. Here we experimentally compare systems based on clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) or its transcriptionally repressive variant, CRISPR-inter...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt.3536
更新日期:2016-06-01 00:00:00
abstract::Can new approaches for deriving human stem cells circumnavigate existing patents that dominate embryonic stem cell intellectual property? ...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt0406-411
更新日期:2006-04-01 00:00:00
abstract::Transplantation of oligodendrocyte precursor cells (OPCs) is a promising potential therapeutic strategy for diseases affecting myelin. However, the derivation of engraftable OPCs from human pluripotent stem cells has proven difficult and primary OPCs are not readily available. Here we report the generation of induced ...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt.2564
更新日期:2013-05-01 00:00:00
abstract::We compared bona fide human induced pluripotent stem cells (iPSCs) derived from umbilical cord blood (CB) cells and neonatal keratinocytes (K). As a consequence of both incomplete erasure of tissue-specific methylation and aberrant de novo methylation, CB-iPSCs and K-iPSCs were distinct in genome-wide DNA methylation ...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt.2052
更新日期:2011-11-27 00:00:00
abstract::A protocol was established for the introduction of DNA into embryogenic suspension-derived tissues of cassava via microparticle bombardment, for the selection of genetically transformed cells, and for the regeneration of fully transgenic plants from these cells. The plasmid DNA used for bombardment contained a gene en...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt0696-731
更新日期:1996-06-01 00:00:00
abstract::Single-molecule long-read DNA sequencing with biological nanopores is fast and high-throughput but suffers reduced accuracy in homonucleotide stretches. We now combine the CsgG nanopore with the 35-residue N-terminal region of its extracellular interaction partner CsgF to produce a dual-constriction pore with improved...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/s41587-020-0570-8
更新日期:2020-12-01 00:00:00
abstract::Colorectal cancer (CRC) is a leading cause of death in the developed world, yet facile preclinical models that mimic the natural stages of CRC progression are lacking. Through the orthotopic engraftment of colon organoids we describe a broadly usable immunocompetent CRC model that recapitulates the entire adenoma-aden...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt.3837
更新日期:2017-06-01 00:00:00
abstract::Engineered T cells are effective therapies against a range of malignancies, but current approaches rely on autologous T cells, which are difficult and expensive to manufacture. Efforts to develop potent allogeneic T cells that are not rejected by the recipient's immune system require abrogating both T- and natural kil...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/s41587-020-0601-5
更新日期:2021-01-01 00:00:00
abstract::Correct reconstruction of macromolecular structure by cryo-electron microscopy (cryo-EM) relies on accurate determination of the orientation of single-particle images. For small (<100 kDa) DNA-binding proteins, obtaining particle images with sufficiently asymmetric features to correctly guide alignment is challenging....
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/s41587-020-0716-8
更新日期:2020-10-19 00:00:00