A5049686869- Extracellular vesicles in disease
- Viral-associated cancers and disorders
- RNA Research and Splicing
- Cytomegalovirus and herpesvirus research
- Cancer-related molecular mechanisms research
- RNA modifications and cancer
- T-cell and Retrovirus Studies
- scientometrics and bibliometrics research
- Animal Disease Management and Epidemiology
- Immune Cell Function and Interaction
- MicroRNA in disease regulation
- Lymphoma Diagnosis and Treatment
- Academic Writing and Publishing
- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Atherosclerosis and Cardiovascular Diseases
- Phagocytosis and Immune Regulation
- Histone Deacetylase Inhibitors Research
- Health and Medical Research Impacts
- Sarcoma Diagnosis and Treatment
- Big Data and Business Intelligence
- Polyomavirus and related diseases
- Plant and Fungal Interactions Research
- Health Sciences Research and Education
- Nursing education and management
Tulane University
2013-2024
University of Liège
2011-2022
Louisiana Cancer Research Center
2013-2015
Icahn School of Medicine at Mount Sinai
2011-2012
Stony Brook University
2012
University of New Orleans
2008
Annotation of herpesvirus genomes has traditionally been undertaken through the detection open reading frames and other genomic motifs, supplemented with sequencing individual cDNAs. Second generation high-density microarray studies have revealed vastly greater transcriptome complexity than is captured by existing annotation. The pervasive nature overlapping transcription throughout genomes, however, poses substantial problems in resolving transcript structures using these methods alone. We...
Abstract Background Extracellular vesicles (EVs) are released by nearly every cell type and have attracted much attention for their ability to transfer protein diverse RNA species from donor recipient cells. Much has been given so far the features of EV short RNAs such as miRNAs. However, while presence mRNA long noncoding (lncRNA) transcripts in EVs also reported multiple different groups, properties function these longer less thoroughly explored than miRNA. Additionally, impact export on...
Abstract Tumour‐derived extracellular vesicles (EVs) participate in tumour progression by deregulating various physiological processes including angiogenesis and inflammation. Here we report that EVs released endothelial cells a mammary environment the recruitment of macrophages within tumour, leading to an immunomodulatory phenotype permissive for growth. Using RNA‐Seq approaches, identified several microRNAs (miRNAs) found sharing common targets involved regulation immune system. To...
ABSTRACT Using high-throughput RNA sequencing data from 50 common lymphoma cell culture models the Cancer Cell Line Encyclopedia project, we performed an unbiased global interrogation for presence of a panel 740 viruses and strains known to infect human other mammalian cells. This led findings previously identified infections by Epstein-Barr virus (EBV), Kaposi's sarcoma herpesvirus (KSHV), T-lymphotropic type 1 (HTLV-1). In addition, also found unreported infection one line (DEL) with...
ABSTRACT Epstein-Barr virus (EBV) reactivation involves the ordered induction of approximately 90 viral genes that participate in generation infectious virions. Using strand-specific RNA-seq to assess EBV transcriptome during reactivation, we found extensive bidirectional transcription extending across nearly entire genome. In contrast, only 4% genome is currently bidirectionally annotated. Most newly identified transcribed regions show little evidence coding potential, supporting noncoding...
We have previously shown that the Epstein-Barr virus (EBV) likely encodes hundreds of viral long noncoding RNAs (vlncRNAs) are expressed during reactivation. Here we show EBV latency origin replication (oriP) is transcribed bi-directionally reactivation and both leftward (oriPtLs) rightward (oriPtRs) transcripts largely localized in nucleus. While oriPtLs most noncoding, at least some oriPtRs contain BCRF1/vIL10 open reading frame. Nonetheless, oriPtR with 5' untranslated regions may...
As a fundamental aspect of normal cell signaling and disease states, there is great interest in determining alternative splicing (AS) changes physiologic, pathologic, pharmacologic settings. High throughput RNA sequencing specialized software to detect AS has greatly enhanced our ability determine transcriptome-wide changes. Despite the richness this data, deriving meaning from sometimes thousands events substantial bottleneck for most investigators. We present SpliceTools, suite data...
Abstract Kaposi's sarcoma-associated herpesvirus is the etiologic agent of sarcoma and two B-cell malignancies. Recent advancements in sequencing technologies have led to high resolution transcriptomes for several human herpesviruses that densely encode genes on both strands. However, KSHV progress remained limited due overall low percentage transcripts, even during lytic replication. To address this challenge, we developed a target enrichment method increase KSHV-specific reads short-...
Abstract Summary: AnnTools is a versatile bioinformatics application designed for comprehensive annotation of full spectrum human genome variation: novel and known single-nucleotide substitutions (SNP/SNV), short insertions/deletions (INDEL) structural variants/copy number variation (SV/CNV). The variants are interpreted by interrogating data compiled from 15 constantly updated sources. In addition to detailed functional characterization the coding variants, searches overlaps with regulatory...
ABSTRACT Comprehensive virome analysis of RNA sequence (RNA-seq) data sets from 118 non-Hodgkin's B-cell lymphomas revealed a small subset that is positive for Epstein-Barr virus (EBV) or human herpesvirus 6B (HHV-6B), with one coinfection. EBV transcriptome expression the latency genes RPMS1, LMP1, and LMP2, sample additionally showing high level early lytic another EBNA2 expression. HHV-6B majority were transcribed.
The gammaherpesviruses, including Epstein-Barr virus (EBV), Kaposi's sarcoma-associated herpesvirus (KSHV), and murine gammaherpesvirus 68 (MHV68, MuHV-4, γHV68), are etiologic agents of a wide range lymphomas non-hematological malignancies. These viruses possess large highly dense dsDNA genomes that feature >80 bidirectionally positioned open reading frames (ORFs). abundance overlapping transcripts extensive splicing throughout these have until now prohibited high throughput-based...
Viral infections are known to hijack the transcription and translation of host cell. However, extent which viral proteins coordinate these perturbations remains unclear. Here we used a model system, human T-cell leukemia virus type 1 (HTLV-1), systematically analyzed transcriptome interactome key effectors oncoviral Tax HBZ. We showed that HBZ target distinct but also common factors. Unexpectedly, uncovered large set interactions with RNA-binding proteins, including U2 auxiliary factor...
Abstract Viruses are master remodelers of the host cell environment in support infection and virus production. For example, viruses typically regulate gene expression through modulating canonical promoter activity. Here, we show that Epstein Barr (EBV) replication causes ‘de novo’ transcription initiation at 29674 new start sites throughout genome. De novo is facilitated part by unique properties viral pre-initiation complex (vPIC) binds a TATT[T/A]AA, TATA box-like sequence activates with...
ERG family proteins (ERG, FLI1 and FEV) are a subfamily of ETS transcription factors with key roles in physiology development. In Ewing sarcoma, the oncogenic fusion protein EWS-FLI1 regulates both alternative splicing pre-messenger RNAs. However, whether wild-type might regulate is unknown. Here, we show that associate spliceosomal components, found on nascent RNAs, induce when recruited onto reporter minigene. Transcriptomic analysis revealed large numbers spliced exons (ASEs) enriched...
Abstract The U6 snRNA, the core catalytic component of spliceosome, is extensively modified post-transcriptionally, with 2’-O-methylation being most common. However, how regulated remains largely unknown. Here we report that TFIP11, human homolog yeast spliceosome disassembly factor Ntr1, localizes to nucleoli and Cajal Bodies essential for U6. Mechanistically, demonstrate TFIP11 knockdown reduces association snRNA fibrillarin associated snoRNAs, therefore altering 2′-O-methylation. We show...
Abstract Desmoplastic small round cell tumor (DSRCT) is an aggressive pediatric cancer caused by the EWSR1-WT1 fusion oncoprotein. The refractory to treatment with a 5-year survival rate of only 15–25%, necessitating development novel therapeutics, especially those able target chemoresistant subpopulations. Novel in vitro stem cell-like (CSC-like) culture conditions increase expression stemness markers (SOX2, NANOG) and reduce DSRCT line susceptibility chemotherapy while maintaining ability...
Gammaherpesviruses, including the human pathogens Epstein⁻Barr virus (EBV) and Kaposi's sarcoma-associated herpesvirus (KSHV) are oncogenic viruses that establish lifelong infections in hosts associated with development of lymphoproliferative diseases lymphomas. Recent studies have shown majority mammalian genome is transcribed gives rise to numerous long non-coding RNAs (lncRNAs). Likewise, large double-stranded DNA genomes herpesviruses undergo pervasive transcription, expression many as...
Genotoxic agents, that are used in cancer therapy, elicit the reprogramming of transcriptome cells. These changes reflect cellular response to stress and underlie some mechanisms leading drug resistance. Here, we profiled genome-wide pre-mRNA splicing induced by cisplatin breast Among set cisplatin-induced alternative events focused on COASY, a gene encoding mitochondrial enzyme involved coenzyme A biosynthesis. Treatment with induces production short isoform COASY lacking exons 4 5, whose...
Muscle formation is controlled by a number of key myogenic transcriptional regulators that govern stage-specific gene expression programs and act as terminal effectors intracellular signaling pathways. To date, the role phosphatases in cascades instructing muscle development remains poorly understood. Here, we show specific PP2A-B55δ holoenzyme necessary for skeletal myogenesis. The primary to dephosphorylate histone deacetylase 4 (HDAC4) following myocyte differentiation ensure repression...
Postdoctoral scholars are highly productive researchers employed by academic institutions, nonprofits, government, and private industry in a variety of fields, particularly the sciences. Because research-focused nature their positions, they have strong needs for information, search skills, publication support, other library resources services. Librarians should consider postdocs institutions endeavor to match resources, services, policies this possibly underserved group.
Introduction B cell activation and differentiation is central to the adaptive immune response. Changes in exon usage can have major impacts on cellular signaling but not been systematically explored differentiating cells. Methods We analyzed intron retention RNA-Seq data from subsets of human cells at various stages differentiation, an vitro laboratory model (Epstein Barr virus infection). Results Blood naïve were found unusual splicing profile, with unannotated events over 30% expressed...
<title>Abstract</title> Virus genomes harbor highly compacted repertoires of genes and regulatory elements. Here, we report the most comprehensive Epstein Barr virus (EBV) transcriptome analysis to date, significantly expanding number known transcript isoforms 1453 resolving major isoform all but one lytic open reading frame. We also categorize each according their dependence on viral DNA replication, classifying transcripts as “early”, “leaky late”, or “late”. show that late gene...