Abstract:
BACKGROUND:Diffuse large B-cell lymphoma (DLBCL) is an aggressive disease, with 30% to 40% of patients failing to be cured with available primary therapy. microRNAs (miRNAs) are RNA molecules that attenuate expression of their mRNA targets. To characterize the DLBCL miRNome, we sequenced miRNAs from 92 DLBCL and 15 benign centroblast fresh frozen samples and from 140 DLBCL formalin-fixed, paraffin-embedded tissue samples for validation. RESULTS:We identify known and candidate novel miRNAs, 25 of which are associated with survival independently of cell-of-origin and International Prognostic Index scores, which are established indicators of outcome. Of these 25 miRNAs, six miRNAs are significantly associated with survival in our validation cohort. Abundant expression of miR-28-5p, miR-214-5p, miR-339-3p, and miR-5586-5p is associated with superior outcome, while abundant expression of miR-324-5p and NOVELM00203M is associated with inferior outcome. Comparison of DLBCL miRNA-seq expression profiles with those from other cancer types identifies miRNAs that were more abundant in B-cell contexts. Unsupervised clustering of miRNAs identifies two clusters of patients that have distinct differences in their outcomes. Our integrative miRNA and mRNA expression analyses reveal that miRNAs increased in abundance in DLBCL appear to regulate the expression of genes involved in metabolism, cell cycle, and protein modification. Additionally, these miRNAs, including one candidate novel miRNA, miR-10393-3p, appear to target chromatin modification genes that are frequent targets of somatic mutation in non-Hodgkin lymphomas. CONCLUSIONS:Our comprehensive sequence analysis of the DLBCL miRNome identifies candidate novel miRNAs and miRNAs associated with survival, reinforces results from previous mutational analyses, and reveals regulatory networks of significance for lymphomagenesis.
journal_name
Genome Bioljournal_title
Genome biologyauthors
Lim EL,Trinh DL,Scott DW,Chu A,Krzywinski M,Zhao Y,Robertson AG,Mungall AJ,Schein J,Boyle M,Mottok A,Ennishi D,Johnson NA,Steidl C,Connors JM,Morin RD,Gascoyne RD,Marra MAdoi
10.1186/s13059-014-0568-ysubject
Has Abstractpub_date
2015-01-29 00:00:00pages
18eissn
1474-7596issn
1474-760Xpii
s13059-014-0568-yjournal_volume
16pub_type
杂志文章相关文献
GENOME BIOLOGY文献大全abstract:BACKGROUND:Gene expression signatures indicative of tumor proliferative capacity and tumor-immune cell interactions have emerged as principal biology-driven predictors of breast cancer outcomes. How these signatures relate to one another in biological and prognostic contexts remains to be clarified. RESULTS:To investi...
journal_title:Genome biology
pub_type: 杂志文章,随机对照试验
doi:10.1186/gb-2013-14-4-r34
更新日期:2013-04-29 00:00:00
abstract:BACKGROUND:Despite the biological and economic significance of scleractinian reef-building corals, the lack of large molecular datasets for a representative range of species limits understanding of many aspects of their biology. Within the Scleractinia, based on molecular evidence, it is generally recognised that there...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-018-1552-8
更新日期:2018-11-02 00:00:00
abstract:BACKGROUND:The draft genome sequence of the ascidian Ciona intestinalis, along with associated gene models, has been a valuable research resource. However, recently accumulated expressed sequence tag (EST)/cDNA data have revealed numerous inconsistencies with the gene models due in part to intrinsic limitations in gene...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2008-9-10-r152
更新日期:2008-10-14 00:00:00
abstract:BACKGROUND:The lifelong accumulation of somatic mutations underlies age-related phenotypes and cancer. Mutagenic forces are thought to shape the genome of aging cells in a tissue-specific way. Whole genome analyses of somatic mutation patterns, based on both types and genomic distribution of variants, can shed light on...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1892-z
更新日期:2019-12-18 00:00:00
abstract::The Network of Cancer Genes (NCG) is a manually curated repository of 2372 genes whose somatic modifications have known or predicted cancer driver roles. These genes were collected from 275 publications, including two sources of known cancer genes and 273 cancer sequencing screens of more than 100 cancer types from 34...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-018-1612-0
更新日期:2019-01-03 00:00:00
abstract::Tissues are complex milieus consisting of numerous cell types. Several recent methods have attempted to enumerate cell subsets from transcriptomes. However, the available methods have used limited sources for training and give only a partial portrayal of the full cellular landscape. Here we present xCell, a novel gene...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-017-1349-1
更新日期:2017-11-15 00:00:00
abstract:BACKGROUND:Reconstruction of ancestral karyotypes is critical for our understanding of genome evolution, allowing for the identification of the gross changes that shaped extant genomes. The identification of such changes and their time of occurrence can shed light on the biology of each species, clade and their evoluti...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-018-1544-8
更新日期:2018-10-05 00:00:00
abstract::The accuracy of base calls produced by Illumina sequencers is adversely affected by several processes, with laser cross-talk and cluster phasing being prominent. We introduce an explicit statistical model of the sequencing process that generalizes current models of phasing and cross-talk and forms the basis of a base ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2012-13-2-r13
更新日期:2012-02-29 00:00:00
abstract::Although chromosomal deletions and inversions are important in cancer, conventional methods for detecting DNA rearrangements require laborious indirect assays. Here we develop fluorescent reporters to rapidly quantify CRISPR/Cas9-mediated deletions and inversions. We find that inversion depends on the non-homologous e...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-015-0680-7
更新日期:2015-05-28 00:00:00
abstract:BACKGROUND:Seed germination involves progression from complete metabolic dormancy to a highly active, growing seedling. Many factors regulate germination and these interact extensively, forming a complex network of inputs that control the seed-to-seedling transition. Our understanding of the direct regulation of gene e...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-017-1302-3
更新日期:2017-09-15 00:00:00
abstract::Genetic mapping and determination of the organization of the wheat genome are changing the wheat-breeding process. New initiatives to analyze the expressed portion of the wheat genome and structural analysis of the genomes of Arabidopsis and rice are increasing our knowledge of the genes that are linked to key agronom...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2002-3-5-reviews1013
更新日期:2002-01-01 00:00:00
abstract:BACKGROUND:Gene duplication followed by divergence is one of the main sources of metabolic versatility. The patchwork and stepwise models of metabolic evolution help us to understand these processes, but their assumptions are relatively simplistic. We used a network-based approach to determine the influence of metaboli...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2007-8-2-r26
更新日期:2007-01-01 00:00:00
abstract::A report on the 11th Cold Spring Harbor Laboratory/Wellcome Trust conference on Genome Informatics, Cold Spring Harbor Laboratories, New York, USA, November 2-5, 2011. ...
journal_title:Genome biology
pub_type:
doi:10.1186/gb-2011-12-12-310
更新日期:2011-12-28 00:00:00
abstract:BACKGROUND:Mutations in genes encoding ribosomal proteins (RPs) have been shown to cause an array of cellular and developmental defects in a variety of organisms. In Drosophila melanogaster, disruption of RP genes can result in the 'Minute' syndrome of dominant, haploinsufficient phenotypes, which include prolonged dev...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2007-8-10-r216
更新日期:2007-01-01 00:00:00
abstract:BACKGROUND:The human lung tissue microbiota remains largely uncharacterized, although a number of studies based on airway samples suggest the existence of a viable human lung microbiota. Here we characterized the taxonomic and derived functional profiles of lung microbiota in 165 non-malignant lung tissue samples from ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-016-1021-1
更新日期:2016-07-28 00:00:00
abstract::Identification of causal mutations in barley and wheat is hampered by their large genomes and suppressed recombination. To overcome these obstacles, we have developed MutChromSeq, a complexity reduction approach based on flow sorting and sequencing of mutant chromosomes, to identify induced mutations by comparison to ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-016-1082-1
更新日期:2016-10-31 00:00:00
abstract:BACKGROUND:Diet is a major contributor to metabolic disease risk, but there is controversy as to whether increased incidences of diseases such as non-alcoholic fatty liver disease arise from consumption of saturated fats or free sugars. Here, we investigate whether a sub-set of triacylglycerols (TAGs) were associated w...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-018-1439-8
更新日期:2018-06-20 00:00:00
abstract:BACKGROUND:Symbiotic bacteria known as rhizobia interact with the roots of legumes and induce the formation of nitrogen-fixing nodules. In rhizobia, essential genes for symbiosis are compartmentalized either in symbiotic plasmids or in chromosomal symbiotic islands. To understand the structure and evolution of the symb...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2003-4-6-r36
更新日期:2003-01-01 00:00:00
abstract:BACKGROUND:MicroRNAs (miRNAs) are oligoribonucleotides with an important role in regulation of gene expression at the level of translation. Despite imperfect target complementarity, they can also significantly reduce mRNA levels. The validity of miRNA target gene predictions is difficult to assess at the protein level....
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2008-9-5-r82
更新日期:2008-01-01 00:00:00
abstract::A novel in vivo screening approach has identified KLF17 as a key metastasis suppressor gene that acts through regulation of Id1 transcription factor-dependent induction of the epithelial-to-mesenchymal transition. ...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2009-10-11-244
更新日期:2009-01-01 00:00:00
abstract::A report of the fifth annual Personal Genomes and Medical Genomics meeting, held at Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA, November 14-17, 2012. ...
journal_title:Genome biology
pub_type:
doi:10.1186/gb-2012-13-12-324
更新日期:2012-12-19 00:00:00
abstract:BACKGROUND:Gene dosage change is a mild perturbation that is a valuable tool for pathway reconstruction in Drosophila. While it is often assumed that reducing gene dose by half leads to two-fold less expression, there is partial autosomal dosage compensation in Drosophila, which may be mediated by feedback or buffering...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2012-13-4-r28
更新日期:2012-04-24 00:00:00
abstract::A report of the First Golden Helix Symposium 'Copy Number Variation (CNV) and Genomic Alterations in Health and Disease', Athens, Greece, 28-29 November 2008. ...
journal_title:Genome biology
pub_type:
doi:10.1186/gb-2009-10-1-301
更新日期:2009-01-01 00:00:00
abstract:BACKGROUND:The embryo sac contains the haploid maternal cell types necessary for double fertilization and subsequent seed development in plants. Large-scale identification of genes expressed in the embryo sac remains cumbersome because of its inherent microscopic and inaccessible nature. We used genetic subtraction and...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2007-8-10-r204
更新日期:2007-01-01 00:00:00
abstract:BACKGROUND:Many genome-wide collections of candidate cis-regulatory elements (cCREs) have been defined using genomic and epigenomic data, but it remains a major challenge to connect these elements to their target genes. RESULTS:To facilitate the development of computational methods for predicting target genes, we deve...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1924-8
更新日期:2020-01-22 00:00:00
abstract::Chromosome conformation capture data, particularly from high-throughput approaches such as Hi-C, are typically very complex to analyse. Existing analysis tools are often single-purpose, or limited in compatibility to a small number of data formats, frequently making Hi-C analyses tedious and time-consuming. Here, we p...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02215-9
更新日期:2020-12-17 00:00:00
abstract:BACKGROUND:Previous methods employed for the identification of synergistic transcription factors (TFs) are based on either TF enrichment from co-regulated genes or phylogenetic footprinting. Despite the success of these methods, both have limitations. RESULTS:We propose a new strategy to identify synergistic TFs by fu...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2007-8-12-r257
更新日期:2007-01-01 00:00:00
abstract::The ability to accurately quantify all the microRNAs (miRNAs) in a sample is important for understanding miRNA biology and for development of new biomarkers and therapeutic targets. We develop a new method for preparing miRNA sequencing libraries, RealSeq®-AC, that involves ligating the miRNAs with a single adapter an...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-018-1488-z
更新日期:2018-09-03 00:00:00
abstract::The honey bee Apis mellifera displays the most complex behavior of any insect. This, and its utility to humans, makes it a fascinating object of study for biologists. Such studies are now further enabled by the release of the honey-bee genome sequence. ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2006-7-10-239
更新日期:2006-01-01 00:00:00
abstract:BACKGROUND:Polyploidy is ubiquitous in eukaryotic plant and fungal lineages, and it leads to the co-existence of several copies of similar or related genomes in one nucleus. In plants, polyploidy is considered a major factor in successful domestication. However, polyploidy challenges chromosome folding architecture in ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-01998-1
更新日期:2020-04-29 00:00:00