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2 results on '"Irf8 Gene"'

1. De novo characterization of the spleen transcriptome of the large yellow croaker (Pseudosciaena crocea) and analysis of the immune relevant genes and pathways involved in the antiviral response

Author

Mu, Yinnan, Li, Mingyu, Ding, Feng, Ding, Yang, Ao, Jingqun, Hu, Songnian, Chen, Xinhua, Mu, Yinnan, Li, Mingyu, Ding, Feng, Ding, Yang, Ao, Jingqun, Hu, Songnian, and Chen, Xinhua

Abstract

The large yellow croaker (Pseudosciaena crocea) is an economically important marine fish in China. To understand the molecular basis for antiviral defense in this species, we used Illumia paired-end sequencing to characterize the spleen transcriptome of polyriboinosinic:polyribocytidylic acid [poly(I:C)]-induced large yellow croakers. The library produced 56,355,728 reads and assembled into 108,237 contigs. As a result, 15,192 unigenes were found from this transcriptome. Gene ontology analysis showed that 4,759 genes were involved in three major functional categories: biological process, cellular component, and molecular function. We further ascertained that numerous consensus sequences were homologous to known immune-relevant genes. Kyoto Encyclopedia of Genes and Genomes orthology mapping annotated 5,389 unigenes and identified numerous immune-relevant pathways. These immune-relevant genes and pathways revealed major antiviral immunity effectors, including but not limited to: pattern recognition receptors, adaptors and signal transducers, the interferons and interferon-stimulated genes, inflammatory cytokines and receptors, complement components, and B-cell and T-cell antigen activation molecules. Moreover, the partial genes of Toll-like receptor signaling pathway, RIG-I-like receptors signaling pathway, Janus kinase-Signal Transducer and Activator of Transcription (JAK-STAT) signaling pathway, and T-cell receptor (TCR) signaling pathway were found to be changed after poly(I:C) induction by real-time polymerase chain reaction (PCR) analysis, suggesting that these signaling pathways may be regulated by poly(I:C), a viral mimic. Overall, the antivirus-related genes and signaling pathways that were identified in response to poly(I:C) challenge provide valuable leads for further investigation of the antiviral defense mechanism in the large yellow croaker. © 2014 Mu et al.

Published
2014

2. Identification of IRF8, TMEM39A, and IKZF3-ZPBP2 as susceptibility loci for systemic lupus erythematosus in a large-scale multiracial replication study

Author

Lessard, Christopher J., Adrianto, Indra, Ice, John A., Wiley, Graham B., Kelly, Jennifer A., Glenn, Stuart B., Adler, Adam J., Li, He, Rasmussen, Astrid, Williams, Adrienne H., Ziegler, Julie, Comeau, Mary, Marion, Miranda, Wakeland, Benjamin E., Liang, Chaoying, Ramos, Paula S., Grundahl, Kiely M., Gallant, Caroline J., Alarcón-Riquelme, Marta E., Alarcón, Graciela S., Anaya, Juan-Manuel, Bae, Sang-Cheol, Boackle, Susan, Brown, Elizabeth E., Chang, Deh-Ming, Cho, Soo-Kyung, Criswel, Lindsey A., Edberg, Jeffrey C., Freedman, Barry I., Gilkeson, Gary S., Jacob, Chaim O., James, Judith A., Kamen, Diane L., Kimberly, Robert P., Kim, Jae-Hoon, Martin, Javier, Merrill, Joan T., Niewold, Timothy B., Park, So-Yeon, Petri, Michelle A., Pons-Estel, Bernardo A., Ramsey-Goldman, Rosalind, Reveille, John D., Scofield, Robert H., Song, Yeong Wook, Stevens, Anne M., Tsao, Betty P., Vila, Luis M., Vyse, Timothy J., Yu, Chack-Yung, Guthridge, Joel M., Kaufman, Kenneth M., Harley, John B., Wakeland, Edward K., Langefeld, Carl D., Gaffney, Patrick M., Montgomery, Courtney G., and Moser, Kathy L.

Subjects
Male, Chromosome 17Q, Hispanic, Ikzf3 Gene, Genetic Susceptibility, Gene, Genetic Risk, Or8D4 Gene, Indians, Lpp Gene, Ethnicity, Haplotype, African American, European American, Membrane Protein, Immune Response, Irf8 Gene, African Continental Ancestry Group, Transmembrane Protein 39A, Cadm2 Gene, C1Orf64 Gene, Chromosome Mapping, Fam19A2 Gene, Patología, Single Nucleotide, Slu7 Gene, Tmem39A Gene, Genetic Predisposition To Disease, High Risk Population, Interferon Consensus Sequence Binding Protein, Gene Locus, Zpbp2 Gene, Genetic Variability, American Indian, Interferon Regulatory Factors, Priority Journal, Interferon, Female, Hispanic Americans, Sequence Analysis, Genetic Association, North American, Human, Asian Continental Ancestry Group, Gene Sequence, Genotype, Major Clinical Study, European Continental Ancestry Group, Protein Ikzf3, Il12A Gene, Loc6392 Gene, Systemic Lupus Erythematosus, Article, Heritability, Ikaros Transcription Factor, Unclassified Drug, Autoantigen, Lupus eritematoso sistémico, Humans, Zona Pellucida Binding Protein 2, Controlled Study, Gene Identification, Polymorphism, Cfhr1 Gene, Asian, Environmental Factor, Lupus Erythematosus, Gene Mapping, Egg Proteins, Systemic, Immunoregulation, Membrane Proteins, Dna, Genome Analysis, Genética, Haplotypes, Stxbp6 Gene, Single Nucleotide Polymorphism, Adamtsl1 Gene, Immunological Tolerance
Abstract

Systemic lupus erythematosus (SLE) is a chronic heterogeneous autoimmune disorder characterized by the loss of tolerance to self-antigens and dysregulated interferon responses. The etiology of SLE is complex, involving both heritable and environmental factors. Candidate-gene studies and genome-wide association (GWA) scans have been successful in identifying new loci that contribute to disease susceptibility; however, much of the heritable risk has yet to be identified. In this study, we sought to replicate 1,580 variants showing suggestive association with SLE in a previously published GWA scan of European Americans; we tested a multiethnic population consisting of 7,998 SLE cases and 7,492 controls of European, African American, Asian, Hispanic, Gullah, and Amerindian ancestry to find association with the disease. Several genes relevant to immunological pathways showed association with SLE. Three loci exceeded the genome-wide significance threshold: interferon regulatory factor 8 (IRF8; rs11644034; p meta-Euro = 2.08 × 10 -10), transmembrane protein 39A (TMEM39A; rs1132200; p meta-all = 8.62 × 10 -9), and 17q21 (rs1453560; p meta-all = 3.48 × 10 -10) between IKAROS family of zinc finger 3 (AIOLOS; IKZF3) and zona pellucida binding protein 2 (ZPBP2). Fine mapping, resequencing, imputation, and haplotype analysis of IRF8 indicated that three independent effects tagged by rs8046526, rs450443, and rs4843869, respectively, were required for risk in individuals of European ancestry. Eleven additional replicated effects (5 × 10 -8 < p meta-Euro < 9.99 × 10 -5) were observed with CFHR1, CADM2, LOC730109/IL12A, LPP, LOC63920, SLU7, ADAMTSL1, C10orf64, OR8D4, FAM19A2, and STXBP6. The results of this study increase the number of confirmed SLE risk loci and identify others warranting further investigation. © 2012 The American Society of Human Genetics.

Published
2012

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