• gene regulation in immune cells
• t cells
• central tolerance
• immune cell death

• Animals
• Nuclear Receptor Subfamily 4, Group A, Member 1/genetics
• Nuclear Receptor Subfamily 4, Group A, Member 1/metabolism
• Thymocytes/immunology
• Thymocytes/metabolism
• Mice
• Clonal Deletion
• Transcriptome
• Receptors, Thyroid Hormone/metabolism
• Receptors, Thyroid Hormone/genetics
• Clonal Anergy
• Mice, Inbred C57BL
• Mice, Knockout
• Receptors, Steroid/metabolism
• Receptors, Steroid/genetics
• Thymus Gland/immunology
• Thymus Gland/cytology
• DNA-Binding Proteins/metabolism
• DNA-Binding Proteins/genetics
• T-Lymphocytes, Regulatory/immunology
• T-Lymphocytes, Regulatory/metabolism
• Immune Tolerance
• Receptors, Antigen, T-Cell/metabolism
• Bcl-2-Like Protein 11/metabolism
• Bcl-2-Like Protein 11/genetics
• Male
• Female
• Nerve Tissue Proteins

• R01 AI165706 NIAID NIH HHS
• K12 GM081266 NIGMS NIH HHS
• R01AI165706 U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)
• R01 AI114575 NIAID NIH HHS
• T32 AR079068 NIAMS NIH HHS
• R01 AI148487 NIAID NIH HHS
• U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)

• Foxp3
• T cell development
• autoimmunity
• diabetes
• immune tolerance
• pTreg
• scurfy
• tTreg

• Mice
• Humans
• Animals
• Aged
• T-Lymphocytes, Regulatory
• Mice, Inbred NOD
• Mice, Inbred C57BL
• Thymus Gland
• Transcription Factors/metabolism
• Diabetes Mellitus, Type 1/metabolism
• Forkhead Transcription Factors/metabolism

• CTLA4
• PD-1
• T cell development
• checkpoint
• thymus

• T cell selection
• TCR signaling
• Zeb1
• development
• transcription

• Animals
• Cell Differentiation
• Cell Proliferation
• Mice
• Mice, Inbred C57BL
• Mice, Transgenic
• Receptors, Antigen, T-Cell, alpha-beta/genetics
• Signal Transduction/genetics
• T-Lymphocyte Subsets
• Thymus Gland

• Agence Nationale de la Recherche (French National Research Agency)
• China Scholarship Council (CSC)

• cell death regulation
• diabetes mellitus
• diabetic complications
• tripartite motif-containing (TRIM) family proteins
• ubiquitin-proteasome system

• Cell cycle
• Double negative T cells
• Transgenic mice
• Type 1 diabetes

• Epigenetic modifications
• Glutathione
• Intermediary metabolism
• Methylation
• Oncogenes
• Protein complexes
• R2TP/prefoldin complex
• Redox stress
• S-adenosylmethionine synthesis
• p53 and DNA damage-regulated gene 1

• B cells
• LMP2A
• autoimmune diseases
• germinal center
• plasma cell differentiation

Deregulation of c-myc by translocation onto immunoglobulin (Ig) loci can promote B cell malignant proliferations with phenotypes as diverse as acute lymphoid leukemia, Burkitt lymphoma, diffuse large B cell lymphoma, myeloma… The B cell receptor (BCR) normally providing tonic signals for cell survival and mitogenic responses to antigens, can also contribute to lymphomagenesis upon sustained ligand binding or activating mutations. BCR signaling varies among cell compartments and BCR classes. For unknown reasons, some malignancies associate with expression of either IgM or class-switched Ig. We explored whether an IgA BCR, with strong tonic signaling, would affect lymphomagenesis in c-myc IgH 3′RR transgenic mice prone to lymphoproliferations. Breeding c-myc transgenics in a background where IgM expression was replaced with IgA delayed lymphomagenesis. By comparison to single c-myc transgenics, lymphomas from double mutant animals were more differentiated and less aggressive, with an altered transcriptional program. Larger tumor cells more often expressed CD43 and CD138, which culminated in a plasma cell phenotype in 10% of cases. BCR class-specific signals thus appear to modulate lymphomagenesis and may partly explain the observed association of specific Ig classes with human B cell malignancies of differential phenotype, progression and prognosis.

• CD4 T-cells
• Genome-wide gene expression profiling
• Molecular pathway analysis
• NOD mice
• Preinsulitis
• Type 1 diabetes susceptibility regions

αβT cell differentiation from thymic precursors is a complex process, explored here with the breadth of ImmGen expression datasets, analyzing how differentiation of thymic precursors gives rise to transcriptomes. After surprisingly gradual changes though early T commitment, transit through the CD4⁺CD8⁺ stage involves a shutdown or rare breadth, and correlating tightly with MYC. MHC-driven selection promotes a large-scale transcriptional reactivation. We identify distinct signatures that mark cells destined for positive selection versus apoptotic deletion. Differential expression of surprisingly few genes accompany CD4 or CD8 commitment, a similarity that carries through to peripheral T cells and their activation, revealed by mass cytometry phosphoproteomics. The novel transcripts identified as candidate mediators of key transitions help define the “known unknown” of thymocyte differentiation.

Expression of the transcription factor Helios identifies thymocyte divergence during positive and negative selection.

Acquisition of self-tolerance in the thymus requires T cells to discriminate strong versus weak T cell receptor binding by self-peptide–MHC complexes. We find this discrimination is reported by expression of the transcription factor Helios, which is induced during negative selection but decreases during positive selection. Helios and the proapoptotic protein Bim were coinduced in 55% of nascent CCR7⁻ CD4⁺ CD69⁺ thymocytes. These were short-lived cells that up-regulated PD-1 and down-regulated CD4 and CD8 during Bim-dependent apoptosis. Helios and Bim were also coinduced at the subsequent CCR7⁺ CD4⁺ CD69⁺ CD8⁻ stage, and this second wave of Bim-dependent negative selection involved 20% of nascent cells. Unlike CCR7⁻ counterparts, Helios⁺ CCR7⁺ CD4⁺ cells mount a concurrent Card11- and c-Rel–dependent activation response that opposes Bim-mediated apoptosis. This “hollow” activation response consists of many NF-κB target genes but lacks key growth mediators like IL-2 and Myc, and the thymocytes were not induced to proliferate. These findings identify Helios as the first marker known to diverge during positive and negative selection of thymocytes and reveal the extent, stage, and molecular nature of two distinct waves of clonal deletion in the normal thymus.

Islet leukocytic infiltration (insulitis) is first obvious at around 4 weeks of age in the NOD mouse – a model for human type 1 diabetes (T1D). The molecular events that lead to insulitis and initiate autoimmune diabetes are poorly understood. Since TID is caused by numerous genes, we hypothesized that multiple molecular pathways are altered and interact to initiate this disease. We evaluated the molecular phenotype (mRNA and protein expression) and molecular networks of ex vivo unfractionated spleen leukocytes from 2 and 4 week-old NOD mice in comparison to two control strains. Analysis of the global gene expression profiles and hierarchical clustering revealed that the majority (∼90%) of the differentially expressed genes in NOD mice were repressed. Furthermore, analysis using a modern suite of multiple bioinformatics approaches identified abnormal molecular pathways that can be divided broadly into 2 categories: metabolic pathways, which were predominant at 2 weeks, and immune response pathways, which were predominant at 4 weeks. Network analysis by Ingenuity pathway analysis identified key genes/molecules that may play a role in regulating these pathways. These included five that were common to both ages (TNF, HNF4A, IL15, Progesterone, and YWHAZ), and others that were unique to 2 weeks (e.g. MYC/MYCN, TGFB1, and IL2) and to 4 weeks (e.g. IFNG, beta-estradiol, p53, NFKB, AKT, PRKCA, IL12, and HLA-C). Based on the literature, genes that may play a role in regulating metabolic pathways at 2 weeks include Myc and HNF4A, and at 4 weeks, beta-estradiol, p53, Akt, HNF4A and AR. Our data suggest that abnormalities in regulation of metabolic pathways in the immune cells of young NOD mice lead to abnormalities in the immune response pathways and as such may play a role in the initiation of autoimmune diabetes. Thus, targeting metabolism may provide novel approaches to preventing and/or treating autoimmune diabetes.

• Animals
• Antigens/immunology
• Antigens, CD/metabolism
• Immunologic Techniques
• Lectins, C-Type/metabolism
• Minor Histocompatibility Antigens
• Receptors, Cell Surface/metabolism
• T-Lymphocytes, Regulatory/immunology
• Transforming Growth Factor beta/metabolism
• Tretinoin/metabolism

• AI-53102 NIAID NIH HHS

• apoptotic cell death
• autophagic cell death
• necrosis
• animal development
• developmental control mechanisms

• Animals
• Apoptosis
• Autophagy
• Caenorhabditis elegans
• Drosophila melanogaster
• Gene Expression Regulation, Developmental
• Mice

• R01 GM069950-06A1 NIGMS NIH HHS
• R01 GM069950-05 NIGMS NIH HHS
• R01 GM076651-02 NIGMS NIH HHS
• R01 GM069950-02 NIGMS NIH HHS
• R01 GM069950-04 NIGMS NIH HHS
• R01 GM076651-01A2 NIGMS NIH HHS
• R01 GM069950-03 NIGMS NIH HHS
• R01 GM069950 NIGMS NIH HHS
• R01 GM076651 NIGMS NIH HHS
• R01 GM069950-01 NIGMS NIH HHS

• Animals
• Blotting, Western
• Clonal Deletion/genetics
• Female
• Flow Cytometry
• Gene Expression/immunology
• Gene Expression Profiling
• Male
• Mice
• Mice, Inbred C57BL
• Mice, Transgenic
• Oligonucleotide Array Sequence Analysis
• Receptors, Antigen, T-Cell/genetics
• Reverse Transcriptase Polymerase Chain Reaction
• Transcription, Genetic

• AI-50105 NIAID NIH HHS