Long Noncoding RNA Expression during Human B-Cell Development. 2015

Andreas Petri, and Karen Dybkær, and Martin Bøgsted, and Charlotte Albæk Thrue, and Peter H Hagedorn, and Alexander Schmitz, and Julie Støve Bødker, and Hans Erik Johnsen, and Sakari Kauppinen
Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark; Department of Haematology, Aalborg University Hospital, Aalborg, Denmark.

Long noncoding RNAs (lncRNAs) have emerged as important regulators of diverse cellular processes, but their roles in the developing immune system are poorly understood. In this study, we analysed lncRNA expression during human B-cell development by array-based expression profiling of eleven distinct flow-sorted B-cell subsets, comprising pre-B1, pre-B2, immature, naive, memory, and plasma cells from bone marrow biopsies (n = 7), and naive, centroblast, centrocyte, memory, and plasmablast cells from tonsil tissue samples (n = 6), respectively. A remapping strategy was used to assign the array probes to 37630 gene-level probe sets, reflecting recent updates in genomic and transcriptomic databases, which enabled expression profiling of 19579 long noncoding RNAs, comprising 3947 antisense RNAs, 5277 lincRNAs, 7625 pseudogenes, and 2730 additional lncRNAs. As a first step towards inferring the functions of the identified lncRNAs in developing B-cells, we analysed their co-expression with well-characterized protein-coding genes, a method known as "guilt by association". By using weighted gene co-expression network analysis, we identified 272 lincRNAs, 471 antisense RNAs, 376 pseudogene RNAs, and 64 lncRNAs within seven sub-networks associated with distinct stages of B-cell development, such as early B-cell development, B-cell proliferation, affinity maturation of antibody, and terminal differentiation. These data provide an important resource for future studies on the functions of lncRNAs in development of the adaptive immune response, and the pathogenesis of B-cell malignancies that originate from distinct B-cell subpopulations.

UI MeSH Term Description Entries
D008957 Models, Genetic Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment. Genetic Models,Genetic Model,Model, Genetic
D001854 Bone Marrow Cells Cells contained in the bone marrow including fat cells (see ADIPOCYTES); STROMAL CELLS; MEGAKARYOCYTES; and the immediate precursors of most blood cells. Bone Marrow Cell,Cell, Bone Marrow,Cells, Bone Marrow,Marrow Cell, Bone,Marrow Cells, Bone
D002454 Cell Differentiation Progressive restriction of the developmental potential and increasing specialization of function that leads to the formation of specialized cells, tissues, and organs. Differentiation, Cell,Cell Differentiations,Differentiations, Cell
D006801 Humans Members of the species Homo sapiens. Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D001402 B-Lymphocytes Lymphoid cells concerned with humoral immunity. They are short-lived cells resembling bursa-derived lymphocytes of birds in their production of immunoglobulin upon appropriate stimulation. B-Cells, Lymphocyte,B-Lymphocyte,Bursa-Dependent Lymphocytes,B Cells, Lymphocyte,B Lymphocyte,B Lymphocytes,B-Cell, Lymphocyte,Bursa Dependent Lymphocytes,Bursa-Dependent Lymphocyte,Lymphocyte B-Cell,Lymphocyte B-Cells,Lymphocyte, Bursa-Dependent,Lymphocytes, Bursa-Dependent
D014066 Palatine Tonsil A round-to-oval mass of lymphoid tissue embedded in the lateral wall of the PHARYNX. There is one on each side of the oropharynx in the fauces between the anterior and posterior pillars of the SOFT PALATE. Tonsil,Tonsil, Palatine,Palatine Tonsils,Tonsils,Tonsils, Palatine
D016000 Cluster Analysis A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both. Clustering,Analyses, Cluster,Analysis, Cluster,Cluster Analyses,Clusterings
D016175 B-Lymphocyte Subsets A classification of B-lymphocytes based on structurally or functionally different populations of cells. B-Cell Subsets,Tumor-Infiltrating B Cells,Tumor-Infiltrating B Lymphocytes,B Effector 1 Cells,B Effector 2 Cells,B-1 Cells,B-1 Lymphocytes,B-2 Lymphocytes,B-Lymphocytes, Effector,B1 Lymphocytes,B2 Lymphocytes,Be1 Cells,Be2 Cells,Effector B Cells,B 1 Cells,B 1 Lymphocytes,B 2 Lymphocytes,B Cell Subsets,B Cell, Tumor-Infiltrating,B Lymphocyte Subsets,B Lymphocyte, Tumor-Infiltrating,B-1 Cell,B-1 Lymphocyte,B-2 Lymphocyte,B-Cell Subset,B-Lymphocyte Subset,B-Lymphocyte, Effector,B1 Lymphocyte,B2 Lymphocyte,Be1 Cell,Be2 Cell,Cell, B-1,Cell, Be1,Cell, Be2,Effector B Cell,Effector B-Lymphocyte,Effector B-Lymphocytes,Lymphocyte, B-1,Lymphocyte, B-2,Lymphocyte, B1,Lymphocyte, B2,Tumor Infiltrating B Cells,Tumor Infiltrating B Lymphocytes,Tumor-Infiltrating B Cell,Tumor-Infiltrating B Lymphocyte
D053263 Gene Regulatory Networks Interacting DNA-encoded regulatory subsystems in the GENOME that coordinate input from activator and repressor TRANSCRIPTION FACTORS during development, cell differentiation, or in response to environmental cues. The networks function to ultimately specify expression of particular sets of GENES for specific conditions, times, or locations. Gene Circuits,Gene Modules,Gene Networks,Transcriptional Networks,Gene Module,Circuit, Gene,Circuits, Gene,Gene Circuit,Gene Network,Gene Regulatory Network,Module, Gene,Modules, Gene,Network, Gene,Network, Gene Regulatory,Network, Transcriptional,Networks, Gene,Networks, Gene Regulatory,Networks, Transcriptional,Regulatory Network, Gene,Regulatory Networks, Gene,Transcriptional Network
D054448 Precursor Cells, B-Lymphoid Lymphocyte progenitor cells that are restricted in their differentiation potential to the B lymphocyte lineage. The pro-B cell stage of B lymphocyte development precedes the pre-B cell stage. B-Lymphoid Precursor Cell,Immature B Cell,Immature B-Cell,Immature B-Lymphocyte,Immature B-Lymphocytes,Pre-B Cell,Pre-B Lymphocyte,Pre-B Lymphocytes,Pre-B-Cell,Precursor B-Cell,Precursor B-Lymphocyte,Precursor B-Lymphocytes,Pro-B Cell,Pro-B Lymphocyte,Pro-B-Cell,Progenitor B-Cell,Progenitor B-Lymphocyte,Progenitor B-Lymphocytes,Transitional B-Cell,Transitional B-Lymphocyte,Transitional B-Lymphocytes,B-Lymphoid Precursor Cells,Immature B-Cells,Pre-B Cells,Pre-B-Cells,Precursor B-Cells,Pro-B Cells,Pro-B Lymphocytes,Pro-B-Cells,Progenitor B-Cells,Transitional B-Cells,B Cell, Immature,B Cells, Immature,B Lymphoid Precursor Cell,B Lymphoid Precursor Cells,B-Cell, Immature,B-Cell, Precursor,B-Cell, Progenitor,B-Cell, Transitional,B-Cells, Immature,B-Cells, Precursor,B-Cells, Progenitor,B-Cells, Transitional,B-Lymphocyte, Immature,B-Lymphocyte, Precursor,B-Lymphocyte, Progenitor,B-Lymphocyte, Transitional,B-Lymphocytes, Immature,B-Lymphocytes, Precursor,B-Lymphocytes, Progenitor,B-Lymphocytes, Transitional,Cell, B-Lymphoid Precursor,Cell, Immature B,Cell, Pre-B,Cell, Pro-B,Cells, B-Lymphoid Precursor,Cells, Immature B,Cells, Pre-B,Cells, Pro-B,Immature B Cells,Immature B Lymphocyte,Immature B Lymphocytes,Lymphocyte, Pre-B,Lymphocyte, Pro-B,Lymphocytes, Pre-B,Lymphocytes, Pro-B,Pre B Cell,Pre B Cells,Pre B Lymphocyte,Pre B Lymphocytes,Precursor B Cell,Precursor B Cells,Precursor B Lymphocyte,Precursor B Lymphocytes,Precursor Cell, B-Lymphoid,Precursor Cells, B Lymphoid,Pro B Cell,Pro B Cells,Pro B Lymphocyte,Pro B Lymphocytes,Progenitor B Cell,Progenitor B Cells,Progenitor B Lymphocyte,Progenitor B Lymphocytes,Transitional B Cell,Transitional B Cells,Transitional B Lymphocyte,Transitional B Lymphocytes

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