Showing papers by "Chris Sander published in 2005"
TL;DR: The characteristic features of the different primary cutaneous lymphomas and other hematologic neoplasms frequently presenting in the skin are described, and differences with the previous classification schemes are discussed.
3,530 citations
TL;DR: To identify other miRNA genes in pathogenic viruses, a new miRNA gene prediction method with small-RNA cloning from several virus-infected cell types was combined and predicted miRNAs in several large DNA viruses.
Abstract: Epstein-Barr virus (EBV or HHV4), a member of the human herpesvirus (HHV) family, has recently been shown to encode microRNAs (miRNAs). In contrast to most eukaryotic miRNAs, these viral miRNAs do not have close homologs in other viral genomes or in the genome of the human host. To identify other miRNA genes in pathogenic viruses, we combined a new miRNA gene prediction method with small-RNA cloning from several virus-infected cell types. We cloned ten miRNAs in the Kaposi sarcoma-associated virus (KSHV or HHV8), nine miRNAs in the mouse gammaherpesvirus 68 (MHV68) and nine miRNAs in the human cytomegalovirus (HCMV or HHV5). These miRNA genes are expressed individually or in clusters from either polymerase (pol) II or pol III promoters, and share no substantial sequence homology with one another or with the known human miRNAs. Generally, we predicted miRNAs in several large DNA viruses, and we could neither predict nor experimentally identify miRNAs in the genomes of small RNA viruses or retroviruses.
1,208 citations
TL;DR: Interestingly, the most pronounced similarities were observed among fully differentiated effector cells and precursors at comparable stages of differentiation, suggesting that in addition to regulating the process of commitment to particular cellular lineages, miRNAs might have an important general role in the mechanism of cell differentiation and maintenance of cell identity.
Abstract: MicroRNAs (miRNAs) are a class of recently discovered noncoding RNA genes that post-transcriptionally regulate gene expression. It is becoming clear that miRNAs play an important role in the regulation of gene expression during development. However, in mammals, expression data are principally based on whole tissue analysis and are still very incomplete. We used oligonucleotide arrays to analyze miRNA expression in the murine hematopoietic system. Complementary oligonucleotides capable of hybridizing to 181 miRNAs were immobilized on a membrane and probed with radiolabeled RNA derived from low molecular weight fractions of total RNA from several different hematopoietic and neuronal cells. This method allowed us to analyze cell type-specific patterns of miRNA expression and to identify miRNAs that might be important for cell lineage specification and/or cell effector functions. This is the first report of systematic miRNA gene profiling in cells of the hematopoietic system. As expected, miRNA expression patterns were very different between hematopoietic and non-hematopoietic cells, with further subtle differences observed within the hematopoietic group. Interestingly, the most pronounced similarities were observed among fully differentiated effector cells (Th1 and Th2 lymphocytes and mast cells) and precursors at comparable stages of differentiation (double negative thymocytes and pro-B cells), suggesting that in addition to regulating the process of commitment to particular cellular lineages, miRNAs might have an important general role in the mechanism of cell differentiation and maintenance of cell identity.
466 citations
TL;DR: It is revealed that the zygotes are essentially devoid of miRNAs and that their expression begins during the blastula period with a zebrafish-specific family of mi RNAs encoded by closely spaced multicopy genes.
Abstract: MicroRNAs (miRNAs) represent a family of small, regulatory, noncoding RNAs that are found in plants and animals. Here, we describe the miRNA profile of the zebrafish Danio rerio resolved in a developmental and cell-type-specific manner. The profiles were obtained from larger-scale sequencing of small RNA libraries prepared from developmentally staged zebrafish, and two adult fibroblast cell lines derived from the caudal fin (ZFL) and the liver epithelium (SJD). We identified a total of 154 distinct miRNAs expressed from 343 miRNA genes. Other experimental/computational sources support an additional 10 miRNAs encoded by 19 genes. The miRNAs can be classified into 87 distinct families. Cross-species comparison indicates that 81 families are conserved in mammals, 17 of which also have at least one member conserved in an invertebrate. Our analysis reveals that the zygotes are essentially devoid of miRNAs and that their expression begins during the blastula period with a zebrafish-specific family of miRNAs encoded by closely spaced multicopy genes. Computational predictions of zebrafish miRNA targets are provided that take into account the depth of evolutionary conservation. Besides miRNAs, we identified a prominent class of repeat-associated small interfering RNAs (rasiRNAs).
344 citations
University of Zurich1, Leiden University Medical Center2, National Institutes of Health3, University of Milan4, University of Graz5, Sapienza University of Rome6, Harvard University7, Charles University in Prague8, University of Vienna9, VU University Amsterdam10, University of Florence11, University of Copenhagen12, St Thomas' Hospital13, Humboldt University of Berlin14, University of Pittsburgh15
TL;DR: This article reviews the histological, phenotypical, and molecular genetic features of the various nosological entities included in the new WHO/EORTC classification of cutaneous lymphomas.
Abstract: The new WHO/EORTC classification for cutaneous lymphomas
comprises mature T-cell and natural killer (NK)-cell neoplasms,
mature B-cell neoplasms, and immature hematopoietic
malignancies. It reflects the unique features of
lymphoproliferative diseases of the skin, and at the same time
it is as compatible as possible with the concepts underlying
the WHO classification for nodal lymphomas and the EORTC
classification of cutaneous lymphomas. This article reviews the
histological, phenotypical, and molecular genetic features of
the various nosological entities included in this new
classification. These findings always have to be interpreted in
the context of the clinical features and biologic behavior
333 citations
TL;DR: It is demonstrated that injection of 2'O-methyl antisense oligoribonucleotides into early Drosophila embryos leads to specific and efficient depletion of microRNAs and thus permits systematic loss-of-function analysis in vivo.
325 citations
TL;DR: This work uses computational modeling to show that coupling of signaling with receptor trafficking results in a highly versatile signal-processing unit, able to sense by itself absolute levels of ligand, temporal changes in ligand concentration, and ratios of multiple ligands.
Abstract: The TGF-β pathway plays a central role in tissue homeostasis and morphogenesis. It transduces a variety of extracellular signals into intracellular transcriptional responses that control a plethora of cellular processes, including cell growth, apoptosis, and differentiation. We use computational modeling to show that coupling of signaling with receptor trafficking results in a highly versatile signal-processing unit, able to sense by itself absolute levels of ligand, temporal changes in ligand concentration, and ratios of multiple ligands. This coupling controls whether the response of the receptor module is transient or permanent and whether or not different signaling channels behave independently of each other. Our computational approach unifies seemingly disparate experimental observations and suggests specific changes in receptor trafficking patterns that can lead to phenotypes that favor tumor progression.
160 citations
TL;DR: Future pathway information systems for querying, visualization and analysis must support standard exchange formats to successfully integrate data on a large scale and greatly facilitate the constructive cycle of computational model building and experimental verification that lies at the heart of systems biology.
136 citations
TL;DR: The authors incorrectly named the products of two genes, gamma actin and betaAPP, as FMRP ligands because of a misreading of Table 1 from [1], which did not change the fact that betaAPP is a predicted microRNA target.
Abstract: In PLoS Biology, volume 2, issue 11: DOI: 10.1371/journal.pbio.0020363
We incorrectly named the products of two genes, gamma actin and betaAPP, as FMRP ligands because of a misreading of Table 1 from [1]. BetaAPP is incorrectly referred to as an FMRP ligand in Tables 2 and S9, gamma actin in Table S9 only. This does not change the use of FMRP binding as a way to support the target predictions, as the statistics remain virtually the same; the enrichment of FMRP targets within the predicted microRNA target set changes from 5.31 to 5.26 as a result of our misclassification. In addition, it does not change the fact that betaAPP is a predicted microRNA target. Our Web site at http://www.microrna.org/ contains the updated information with changes flagged. We thank Dr. Denman for pointing out this error to us.
97 citations
TL;DR: There are at least four times as many piRNAs in mouse testes than currently known and many of the piRNA clusters contain inverted repeats segments capable of forming double-strand RNA fold-back segments that may initiate piRNA processing analogous to transposon silencing.
Abstract: The recent discovery of a new class of 30-nucleotide long RNAs in mammalian testes, called PIWI-interacting RNA (piRNA), with similarities to microRNAs and repeat-associated small interfering RNAs (rasiRNAs), has raised puzzling questions regarding their biogenesis and function. We report a comparative analysis of currently available piRNA sequence data from the pachytene stage of mouse spermatogenesis that sheds light on their sequence diversity and mechanism of biogenesis. We conclude that (i) there are at least four times as many piRNAs in mouse testes than currently known; (ii) piRNAs, which originate from long precursor transcripts, are generated by quasi-random enzymatic processing that is guided by a weak sequence signature at the piRNA 5′ends resulting in a large number of distinct sequences; and (iii) many of the piRNA clusters contain inverted repeats segments capable of forming double-strand RNA fold-back segments that may initiate piRNA processing analogous to transposon silencing.
90 citations
01 Jan 2005
TL;DR: The scope of BioPAX is expanded to include representation of molecular binding interactions, protein post-translational modifications, basic experimental descriptions, and hierarchical pathways, which will increase access to and uniformity of pathway data from varied sources, thus increasing the efficiency of computational pathway research.
Abstract: At present, there are over 215 Internet-accessible databases that store biological pathway data. Biologists often need to use information from many of these to support their research, but since each has its own representation conventions and data access methods, integrating data from multiple databases is very difficult. A widely-adopted biological pathway data exchange format will help. BioPAX (Biological Pathway Exchange - http://www.biopax.org) enables the integration of diverse pathway resources by defining an open file format specification for the exchange of biological pathway data. By utilizing the BioPAX format, the problem of data integration reduces to a semantic mapping between the data models of each resource and the data model defined by BioPAX. Widespread adoption of BioPAX for data exchange will increase access to and uniformity of pathway data from varied sources, thus increasing the efficiency of computational pathway research. This document describes BioPAX Level 2, which expands the scope of BioPAX to include representation of molecular binding interactions, protein post-translational modifications, basic experimental descriptions, and hierarchical pathways. Adding coverage of these features will allow BioPAX to represent the bulk of the data in the PSI-MI Level 2 format (http://psidev.sourceforge.net/mi/rel2/doc/) and lays the groundwork for better support of signal transduction and molecular states.
TL;DR: The histologic grade of myxoid liposarcoma is determined by the extent of the round cell (RC) component, and for this study, MRLS was defined as having a round cell component.
Abstract: 9015 Background: Myxoid liposarcoma represents a morphologic continuum, with histologic grade determined by the extent of the round cell (RC) component. For this study, MRLS was defined as having a...