Expression Of Recombination Activating Genes Research Articles

RORγt up-regulates RAG gene expression in DP thymocytes to expand the Tcra repertoire.

Recombination activating gene (RAG) expression increases as thymocytes transition from the CD4-CD8- double-negative (DN) to the CD4+CD8+ double-positive (DP) stage, but the physiological importance and mechanism of transcriptional up-regulation are unknown. Here, we show that a DP-specific component of the recombination activating genes antisilencer (DPASE) provokes elevated RAG expression in DP thymocytes. Mouse DP thymocytes lacking the DPASE display RAG expression equivalent to that in DN thymocytes, but this supports only a partial Tcra repertoire due to inefficient secondary Vα-Jα rearrangement. These data indicate that RAG up-regulation is required for a replete Tcra repertoire and that RAG expression is fine-tuned during lymphocyte development to meet the requirements of distinct antigen receptor loci. We further show that transcription factor RORγt directs RAG up-regulation in DP thymocytes by binding to the DPASE and that RORγt influences the Tcra repertoire by binding to the Tcra enhancer. These data, together with prior work showing RORγt to control Tcra rearrangement by regulating DP thymocyte proliferation and survival, reveal RORγt to orchestrate multiple pathways that support formation of the Tcra repertoire.

High Recombination Activating Gene (RAG) Expression and RAG Mediated Recombination Is Associated with Oncogenic Rearrangement Observed with Tyrosine Kinase Inhibitor Resistant CML

BackgroundPatients with chronic myeloid leukemia (CML) who develop blast crisis are resistant to TKI therapy. A key focus in CML research is the identification of genetic factors that promote blast crisis and TKI resistance. By using an integrative genomic approach we recently reported frequent structural variation in CML patients, particularly at lymphoid blast crisis (LBC) (Blood, 2018). Developing lymphocytes are uniquely equipped with a molecular toolkit capable of programmed DNA damage and structural variant formation; the V(D)J recombination pathway. Recombination activating genes (RAG1 and RAG2) are involved in cleavage and recombination of immunoglobulin genes to provide diversity in antibodies and T cell receptors. Off target RAG activity is reported to occur in lymphoid malignancies and cause oncogenic structural rearrangements. However, RAG expression and the extent of RAG mediated structural variation in CML are largely uncharacterized.AimTo elucidate the role of RAG mediated recombination as a source of oncogenic structural rearrangement in CML.MethodsIn a study of samples of 49 patients at chronic phase (CP) diagnosis (Dx), 20 at LBC and 19 at myeloid blast crisis (MBC), we performed whole exome sequencing and/or RNAseq. Bioinformatic analyses included fusion detection (Manta & STAR), gene expression analysis (EdgeR), and copy number variation analysis (in house developed tool). Unsupervised motif detection of sequences surrounding breakpoints was performed with MEME, and fusions were visualized with Jcircos. To identify off target RAG mediated mutation we interrogated the breakpoints of structural variants, excluding those associated with the Philadelphia translocation and those solely involving antigen receptor gene rearrangement.Results33 structural variants were identified in 22 patients with samples at Dx and/or blast crisis involving genes regularly mutated in hematologic malignancy such as MLL, MECOM, RUNX1 and IKZF1. Differential expression analysis between patients at Dx, MBC and LBC revealed >1000 genes that were differentially expressed, P<0.001. Amongst the most upregulated genes at LBC were RAG1, RAG2 and DNTT, reflected in the most enriched gene ontology: V(D)J recombination. V(D)J recombination genes were sufficient alone in stratifying LBC samples from CP Dx and MBC [Figure 1A]. Furthermore, RAG expression was detectably elevated at Dx in most patients who subsequently developed LBC [Figure 1B].To identify off target RAG mediated structural variation, we interrogated the sequence surrounding breakpoints of the 33 identified structural variants (66 breakpoints) that were separated into groups of high (n=40) and low (n=26) RAG expression. The canonical heptamer CACAGTG recombination signal sequence (RSS) was enriched only at breakpoints in the high RAG group with sequences from 31/40 breakpoints making up the motif [Figure 1C]. The comparable group of low RAG breakpoints were not enriched for the motif. Another indicator of RAG involvement is the addition of non-template nucleotides at the breakpoint, consistent with DNTT nucleotidyl-transferase activity. This was detected almost exclusively at breakpoints in patients with high RAG, 16/20 structural variants, compared to 1/13 with low RAG.There was an association between high RAG expression and structural variants bearing the RAG RSS motif at breakpoints with nucleotide additions. The most frequently observed of these were intragenic deletions of IKZF1 in 7 patients, including 3 at Dx with subsequent LBC, 3 at LBC and 1 at MBC. A number of novel structural variants also had the RAG recombination signature: IKZF1-IGK fusion, RUNX1 deletion and recurrent HBS1L-MYB intergenic locus deletion.RAG mediated structural variation was further investigated on a genomic level using putative low level fusions identified from RNAseq. By assessing the immunoglobulin/T cell receptor genes, as known sites of RAG activity, we found enrichment of interchromosomal fusions involving these genes in samples with high RAG, compared to Dx and MBC with low RAG [Figure 1D]. An agnostic motif enrichment search at sequences surrounding putative fusions showed enrichment of a motif resembling the recombination signal sequence.ConclusionOur results implicate RAG as a driver of structural variation and the formation of novel oncogenic rearrangements in CML. [Display omitted] DisclosuresHughes:Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees; Incyte: Honoraria, Membership on an entity's Board of Directors or advisory committees; BMS: Honoraria, Membership on an entity's Board of Directors or advisory committees. Branford:Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Qiagen: Honoraria, Membership on an entity's Board of Directors or advisory committees; BMS: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Cepheid: Honoraria.

The c-Myc/miR17-92/PTEN Axis Tunes PI3K Activity to Control Expression of Recombination Activating Genes in Early B Cell Development.

Appropriate PI3K signals generated by the antigen receptor are essential to promote B cell development. Regulation of recombination activating gene (RAG)-1 and RAG-2 expression is one key process that is mediated by PI3K to ensure developmental progression and selection. When PI3K signals are too high or too low, expression of RAGs does not turn off and B cell development is impaired or blocked. Yet, the mechanism which tunes PI3K activity to control RAG expression during B cell development in the bone marrow is unknown. Recently we showed that a c-Myc/miR17-92/PTEN axis regulates PI3K activity for positive and negative selection of immature B cells. Here, we show that the c-Myc/miR17-92/PTEN axis tunes PI3K activity to control the expression of RAGs in proB cells. Using different genetically engineered mouse models we show that impaired function of the c-Myc/miR17-92/PTEN axis alters the PI3K/Akt/Foxo1 pathway to result in dis-regulated expression of RAG and a block in B cell development. Studies using 38c-13 B lymphoma cells, where RAGs are constitutively expressed, suggest that this regulatory effect is mediated post-translationally through Foxo1.

Understanding V(D)J recombination initiator RAG1 gene using molecular phylogenetic and genetic variant analyses and upgrading missense and non-coding variants of clinical importance

The recombination-activating genes (RAGs) encode for V(D)J recombinases responsible for rearrangements of antigen-receptor genes during T and B cell development, and RAG expression is known to correlate strictly with the process of rearrangement. There have been several studies of RAG1 illustrating biochemical, physiological and immunological properties. Hitherto, there are limited studies on RAG1 focusing molecular phylogenetic analyses, evolutionary traits, and genetic variants in human populations. Hence, there is a need of a comprehensive study on this topic. In the current report, we have shed light into insights of evolutionary traits and genetic variants of human RAG1 gene using 1092 genomes from human populations. Syntenic analyses revealed that two RAG genes are physically linked and conserved on the same locus in head-to-head orientation from sea urchin to human for about 550 MY. Spliceosomal introns have been in invaded in fishes and sea urchin, whereas gene structures of RAG1 gene from tetrapods remained single exon architecture. We compiled 751 genetic variants in human RAG1 gene using 1092 human genomes; where major stockholders of variant classes are 79% single nucleotide polymorphisms (SNPs), 12.2% somatic single nucleotide variants (somatic SNVs) and 6.8% deletion. Out of 267 missense variants, 140 are deleterious mutations. We identified 284 non-coding variants with 94% regulatory in nature.

Versatility in NK cell memory

Versatility in NK cell memory

NWC, a new gene within RAG locus: could it keep GOD under control?

NWC, newly discovered, evolutionarily conserved gene within recombination activating gene (RAG) locus is constitutively expressed in all cells except lymphocytes, in which it is developmentally regulated by RAG1 promoter. In lymphocytes, NWC promoter, which is located within RAG2 intron and drives expression of NWC in non-lymphocytes, is inactive. Here, a hypothesis on the role of transcription of NWC in lymphocyte-specific regulation of RAG expression and their suppression in all other cells is presented. It is proposed that during development, inactivation of NWC promoter and the placement of NWC under the control of RAG1 promoter releases RAG genes from permanent suppression and allows their lymphocyte specific expression but at the same time subjects them to transcriptional feedback inhibition type of suppression which could permit for a stringent control over their threat to genome stability and oncogenic potential.

Expression of recombination-activating genes and T cell receptor gene recombination in the human T cell leukemia cell line

Recent studies have suggested that mature T cells can change their specificity through reexpression of recombination-activating genes (RAG) and RAG-mediated V(D)J recombination. This process is named receptor revision and has been observed in mature peripheral T cells from transgenic mice and human donors. However, whether thebreceptor revision in mature T cells is a random or orientated process remains poorly understood. Here we used the Jurkathuman T cell line, which represents a mature stage of T cell development, as a model to investigate the regulation of Tcell receptor (TCR) gene recombination. TCR Dbeta-Jbeta signal joint T cell receptor excision DNA circles (sjTRECs) were determined by nested and seminested PCR. Double-strand DNA breaks at recombination signal sequences (RSSs) in the TCRVbeta chain locus were detected by ligation-mediated-PCR. Further analysis of the complementarity-determining region 3 (CDR3) size of the TCRVbeta chain was examined by the TCR GeneScan technique. RAG1, RAG2, and three crucial components of the nonhomologous DNA end-joining (NHEJ) pathway were readily detected in Jurkat. Characteristics of junctional diversity of Dbeta2-Jbeta2 signal joints and ds RSS breaks associated with the Dbeta2 5' and Dbeta 2 3' sites were detected in DNA from Jurkat cells. CDR3 size and the gene sequences of the TCRVbeta chain did not change during cell proliferation. RAG1 and RAG2 and ongoing TCR gene recombination are coexpressed in Jurkat cells, but the ongoing recombination process may not play a role in modification of the TCR repertoire.However, the results suggest that Jurkat could be used as a model for studying the regulation of RAGs and V(D)J recombination and as a "special" model of the coexistence of TCR gene rearrangements and "negative" receptor revision.

Fetal thymocyte development: putting a zinc finger on it?

Lymphocyte development must be tightly regulated in utero to prevent rejection. New work shows that the zinc finger protein Zfp608 negatively regulates the expression of recombination-activating genes 1 and 2 and may suppress fetal T cell development.

Control of thymocyte development and recombination-activating gene expression by the zinc finger protein Zfp608

The products of recombination-activating gene 1 (Rag1) and Rag2 are required for T cell receptor gene assembly and thymocyte maturation, yet their transcriptional control mechanisms remain unclear. A congenic strain (called 'ZORI' here) with defects in Rag1 and Rag2 expression, thymocyte maturation and peripheral T cell homeostasis has been developed. Here, we mapped the mutation in this strain to a chromosome 18 locus containing a single known gene encoding the zinc finger protein Zfp608. This gene (Zfp608) was highly expressed in neonatal thymus but was extinguished thereafter. In contrast to wild-type mice, ZORI mice had sustained thymocyte expression of Zfp608 throughout life. The ZORI mutation produced a thymocyte-intrinsic developmental defect. Overexpression of Zfp608 in BALB/c thymocytes substantially impaired Rag1 and Rag2 expression, indicating the underlying mechanism for the defect in ZORI thymocyte development. Thus, the normal function of Zfp608 may be to prevent Rag1 and Rag2 expression in utero.

FOXtrot and RAGtime in B cells

Networks of transcription factors regulate cell fate 'decisions'. The forkhead protein Foxp1 is now identified as a key regulator of B cell development that influences the expression of recombination-activating genes.

Regulatory mechanisms of immunoglobulin E synthesis by human B cells

SummaryProduction of antigen‐specific IgE antibodies by B cells contributes to induction and maintenance of allergic inflammation. Antibody diversity is acquired through V (variable)–D (diversity)–J (joining) recombination, which is mediated by the products of recombination‐activating gene (RAG)‐1 and RAG‐2 during the early stages of B cell development. IgE isotype specificity is determined in mature B cells by IL‐4 and IL‐13 and acquired through class switch recombination (CSR), which is induced by three members of the TNF superfamily. CD40 ligand (CD40L) expressed by Th2 cells induces T cell‐dependent CSR, whereas B lymphocyte stimulator (BLyS) and a proliferation‐inducing ligand (APRIL) expressed by dendritic cells induce T cell‐independent CSR. CD40L, BLyS, and APRIL collaborate with IL‐4 and IL‐13 to induce expression of activation‐induced cytidine deaminase (AID), essential for CSR and somatic hypermutation (SHM), and to perform DNA excision and ligation required for IgE class switching. RAG‐1 and RAG‐2 expression is also inducible only in the presence of IL‐4 by CD40L, BLyS, and APRIL. Thus IL‐4, unlike IL‐13, is effective for inducing RAG expression despite many overlapping activities of these cytokines. RAG products expressed by mature B cells are involved in secondary V(D)J recombination, termed receptor revision. Given that receptor revision contributes to affinity maturation in a fashion different from SHM, it is suggested that IgE antibodies induced by IL‐4 may have higher affinity than those induced by IL‐13.

Identification of a third evolutionarily conserved gene within theRAG locus and itsRAG1-dependent and -independent regulation

Recombination-activating gene (RAG)1 and RAG2 encode T and B lymphocyte-specific endonucleases indispensable for rearrangements of antigen-receptor gene segments but also capable of causing deleterious chromosome rearrangements. The mechanisms regulating RAG expression and repression are not clear. Here we identify NWC, a third evolutionarily conserved gene within the RAG locus, and show that it is ubiquitously expressed, with the notable exception of RAG-nonexpressing immature and mature T and B lymphocytes because in lymphocytes it is regulated by the RAG1 promoter and transcribed as RAG1-NWC hybrid mRNA molecules. We also show that in all other cells NWC is controlled by the RAG2 intragenic promoter, which in immature and mature T and B lymphocytes is silent. The possible implications of these findings for understanding the activation and inactivation of RAG genes in lymphocytes and their repression in other cells are discussed.

Expression and Reexpression of Recombination Activating Genes: Relevance to the Development of Autoimmune States

Like all antibodies, autoreactive antibodies are generated in developing B cells in the bone marrow by variable (V), diversity (D), and joining (J) recombination under the regulation of recombination activating gene (RAG) 1 and RAG2 proteins. Deletion, anergy, and receptor edition prevent the emergence of autoreactive B cells. In the periphery, somatic hypermutation during the course of germinal center responses can lead to the emergence of autoreactive and low-affinity antibody-producing B cells. Deletion and receptor revision regulate autoreactive and inappropriate B cells. Defects in central or peripheral tolerance mechanisms associated with RAG expression could contribute to the appearance of autoreactive B cells. We demonstrate the presence of RAG(+) B cells in CD5-expressing cells outside germinal centers. Our data suggest that receptor revision in the periphery also may occur in unusual sites when B cells are induced to express CD5. This revision may correspond to a novel regulation checkpoint in which impaired control of RAG expression could generate autoreactive B cells and lead to autoimmune states.

Identification and characterisation of a homolog of an activation gene for the recombination activating gene 1 (RAG 1) in amphioxus

Expression of recombination activating genes (RAG) involved in the V (D) J recombination is regulated by the RAG1 gene activator (RGA) in mammals. The sequence of a cDNA clone from an amphioxus cDNA library was found to be homologous to that of RGA from mouse stromal cells with 45% identity. The full-length cDNA sequence comprises 1119 bp and encodes a putative protein of 210 amino acid residues. Characterisation of the amino acid sequence revealed that two MtN3 domains and seven transmembrane spans are present in this protein, indicating a potential role as a plasma membrane protein. This gene is expressed in many tissues and at differential developmental stages. A high expression level of RGA is detected in gonad tissues, and gastrula embryo and adult stages. The presence of the RGA gene in amphioxus suggests that the signal pathway required for the expression of RAG could exist in this primitive protochordate. It also implies that in the related molecules, primitive adaptive immunity may have existed in cephalochordate although the complete machinery of VDJ rearrangement may not be formed.

Recombination activating genes (RAG) induce secondary Ig gene rearrangement in and subsequent apoptosis of human peripheral blood circulating B lymphocytes.

Recombination activating gene (RAG) re-expression and secondary Ig gene rearrangement in mature B lymphocytes have been reported. Here, we have studied RAG expression of peripheral blood B lymphocytes in humans. Normal B cells did not express RAG1 and RAG2 spontaneously. More than a half of circulating B cells expressed RAG proteins, when activated with Staphylococcus aureus Cowan I (SAC) + IL-2. DNA binding activity of the RAG complex has been verified by a gel shift assay employing the recombination signal sequence (RSS). Secondary Ig light chain rearrangement in the RAG-expressing B cells was confirmed by linker-mediated (LM)-PCR. Highly purified surface kappa+ B cells activated by SAC + IL-2 became RAG+, and thereafter they started to express lambda chain mRNA. 2 colour immunofluorescence analysis disclosed that a part of the RAG+ cells derived from the purified kappa+ B cells activated by SAC + IL-2 turned to lambda+ phenotype in vitro. Similarly, apoptosis induction was observed in a part of the RAG+ B cells. Our study suggests that a majority of peripheral blood B cells re-expresses RAG and the RAG+ B lymphocytes could be eliminated from the B cell repertoire either by changing Ag receptor specificity due to secondary rearrangement or by apoptosis induction. Thus, RAG expression of mature B cells in peripheral blood would contribute to not only receptor revision for further diversification of B cell repertoire but in some cases (or in some B cell subsets) to prevention or induction of autoAb responses at this differentiation stage in humans.

Rare detection of phenotypically immature lymphocytes in Hashimoto thyroiditis and rheumatoid arthritis

It has been suggested that recombination activating gene (RAG)-dependent revision of the immunoglobulin genes in germinal centres may contribute to local production of autoantibodies in Hashimoto thyroiditis (HT) and rheumatoid arthritis (RA). To test this hypothesis we examined HT and RA tissues for expression of RAG and terminal deoxynucleotidyl transferase (TdT) in situ. Paraffin-embedded tissues from 19 HT patients and from 20 RA patients were subjected to immunohistochemistry using TdT-specific antibodies. Expression of the RAGs was studied by in situ hybridisation. Tonsil sections were used as a control. Expression of TdT and RAGs was detected in extrafollicular lymphocytes in control tonsil sections. By contrast, only rare TdT-expressing cells were identified in 11 of 19 HT and in 2 of 20 RA samples. Germinal centre B-cells were consistently TdT- and RAG-negative. These results suggest that local RAG-dependent receptor revision in germinal centres is unlikely to contribute to production of autoantibodies in HT and RA. The presence of TdT-positive extrafollicular cells may represent an influx of immature cells in the context of chronic immune stimulation.

Rare detection of phenotypically immature lymphocytes in Hashimoto thyroiditis and rheumatoid arthritis

It has been suggested that recombination activating gene (RAG)-dependent revision of the immunoglobulin genes in germinal centres may contribute to local production of autoantibodies in Hashimoto thyroiditis (HT) and rheumatoid arthritis (RA). To test this hypothesis we examined HT and RA tissues for expression of RAG and terminal deoxynucleotidyl transferase (TdT) in situ. Paraffin-embedded tissues from 19 HT patients and from 20 RA patients were subjected to immunohistochemistry using TdT-specific antibodies. Expression of the RAGs was studied by in situ hybridisation. Tonsil sections were used as a control. Expression of TdT and RAGs was detected in extrafollicular lymphocytes in control tonsil sections. By contrast, only rare TdT-expressing cells were identified in 11 of 19 HT and in 2 of 20 RA samples. Germinal centre B-cells were consistently TdT- and RAG-negative. These results suggest that local RAG-dependent receptor revision in germinal centres is unlikely to contribute to production of autoantibodies in HT and RA. The presence of TdT-positive extrafollicular cells may represent an influx of immature cells in the context of chronic immune stimulation.

Expression of recombination-activating gene in mature peripheral T cells in Peyer's patch.

Recombination-activating gene (RAG) 1 and 2 are essential for the gene rearrangement of antigen receptors of both T and B cells. To investigate RAG gene expression in peripheral lymphoid organs other than the thymus and bone marrow, we established mice in which a green fluorescent protein (GFP) gene is knocked-in the RAG2 gene locus (RAG2-GFP mice). In the thymus and bone marrow of heterozygous RAG2-GFP mice, as expected, GFP expression was detected in the appropriate stages of developing T and B cells. Interestingly, only a fraction of Thy-1.2(+) cells in the Peyer's patch were found to be GFP(+) amongst the peripheral lymphoid organs. The GFP(+) cells expressed high levels of surface TCRbeta and CD3, suggesting mature T cells with rearranged TCRalphabeta. However, they showed activated/memory phenotypes, i.e. CD45RB(low), CD69(high), CD44(high) and CD62L(low), and belonged to a CD4(+)CD8(+) population expressing c-kit, IL-7R and pTalpha characteristic of immature developing lymphocytes. Moreover, RAG(+) Peyer's patch T cells seem to be of thymic origin as judged by their expression of CD8alphabeta. These results show that there exists a fraction of mature T cells expressing RAG genes in the Peyer's patch, implying a potential for a secondary rearrangement of TCR in extrathymic tissues.

Expression of IgVH mRNAs in plasma cells derived from rheumatoid arthritis synovium detected by single-cell RT-PCR

The synovial membrane in rheumatoid arthritis (RA) contains large lymphocytic infiltrates, sometimes organized in germinal-like centres. The presence of plasma cells within the synovium and the production of clonally related immunoglobulin transcripts have been observed. The exact nature of clonal expansion and its role in generation of specific, mutated antibodies in RA is not known. Somatic mutations and isotype switching in synovial B lymphocytes might suggest the antigen-driven process. This would be supported by the expression of recombination-activating genes 1 and 2 (Rag1 and Rag2).

Differential expression of IgVH mRNAs in human RA synovium detected by single-cell RT-PCR

In rheumatoid arthritis (RA), the synovial membranes contain lymphocytic infiltrates sometimes resembling germinal centres. The production of clonally related immunoglobulin (Ig) transcripts, the presence of plasma cells within RA synovial tissue, somatic mutations and isotype switching in RF-specific synovial B lymphocytes have been observed. In addition, the expression of recombination-activating genes 1 and 2 (Rag1 and 2) has been detected in RA synovial B cells.