Genomic analysis of Canadian children with food allergies points to the immunoglobulin heavy chain gene locus

bcl-2/IgH fusion is considered a genetic error which occurs at the diversity (D) to joining (J(H)) stage of the gene rearrangement process in the immunoglobulin heavy chain (IgH) gene locus. Translocations of the bcl-2 protooncogene to the IgH locus at ontogenetically later IgH gene rearrangements are thought to represent exceptions. In the present study we analysed the junctional nucleotide sequence of 18 bcl-2/IgH fusion genes identifiable by polymerase chain reaction performed on DNA extracted from diagnostic lymph node tissue of 14 follicular lymphoma patients. In all clones studied, segments of variable length were found interposed between bcl-2 and J(H) gene sequences. Nucleotide sequence data analysis and comparisons performed with the corresponding germline sequences using the GenBank/EMBL database revealed the presence of D segments in most of the bcl-2/IgH fusion genes under study (13/18). By the same kind of computer-aided analysis, previously unrecognized D segments were identified in many published junctional sequences. These results suggest that bcl-2/IgH fusion events are very prevalent in rather more differentiated stages in B-cell ontogeny than previously recognized.

RAGs’ eye view of the immunoglobulin heavy chain gene locus

Chromatin Interactions in the Control of Immunoglobulin Heavy Chain Gene Assembly.

Immunoglobulin heavy chain (IGH) gene locus is expressed monoallelically in human B cells. Aim. To study the role of nuclear organization in regulation of the IGH expression during B-cell differentiation. Methods. Immunofluorescence in situ hybridization on 3D-preserved nuclei (3D immuno-FISH). Results. Active RNA polymerase II (Pol II) molecules and the IGH locus were detected in the periphery of the nucleoli at some stages of B-cell differentiation. Conclusions. We observed significant changes in the pattern of distribution of RNA polymerase II in the nucleus during B-cell differentiation, but no preferential co-localization of the productive IGH allele with the transcription factories in the vicinity of the nucleolus and in the nucleoplasm was observed. © 2016 A. Pichugin et al.

Arid3a/Bright/Dril1 is a B cell-specific transactivator that regulates immunoglobulin heavy chain (IgH) gene transcription by binding promoter and enhancer-associated matrix attachment regions (MARs) within the IgH gene locus. Promoter MAR-mediated Arid3a transactivation is antagonized by direct competition of MAR binding by Cux1/CDP—a ubiquitously expressed repressor originally termed NF-μNR. We report that the NF-μNR complex includes Arid3a in B cells but not in non-B cells through mobility shift assays. The binding activity of NF-μNR and Arid3a in B cells is reciprocally altered during the cell division cycle and by the B cell mitogen lipopolysaccharide LPS. LPS treatment had no effect on Arid3a localization but increased its total abundance within the nucleus and cytoplasm. We show that this increased level of Arid3a is capable of displacing Cux from the MARs to facilitate IgH gene transcription. Finally, we showed that the MARs (termed Bf150 and Tx125) associated with the VH1 rearranged variable region expressed in the S107 murine plasmacytoma, can repress reporter gene transcription in non-B cells and that they can relieve the repression mediated by Eμ enhancer in B cells. These results have significant implications for early human development and demonstrate that MARs in IgH locus, NF-µNR and Arid3a regulate IgH gene expression in a concerted fashion. This paves the way for future studies examining the misregulation of this pathway in pediatric disease.

The genomes of classical inbred mouse strains include genes derived from all three major subspecies of the house mouse, Mus musculus. We recently posited that genetic diversity in the immunoglobulin heavy chain (IGH) gene loci of C57BL/6 and BALB/c mice reflects differences in subspecies origin. To investigate this hypothesis, we conducted high-throughput sequencing of IGH gene rearrangements to document IGH variable (IGHV), joining (IGHJ) and diversity (IGHD) genes in four inbred wild-derived mouse strains (CAST/EiJ, LEWES/EiJ, MSM/MsJ and PWD/PhJ) and a single disease model strain (NOD/ShiLtJ), collectively representing genetic backgrounds of several major mouse subspecies. A total of 341 germline IGHV sequences were inferred in the wild-derived strains, including 247 not curated in the international ImMunoGeneTics information system. By contrast, 83/84 inferred NOD IGHV genes had previously been observed in C57BL/6 mice. Variability among the strains examined was observed for only a single IGHJ gene, involving a description of a novel allele. By contrast, unexpected variation was found in the IGHD gene loci, with four previously unreported IGHD gene sequences being documented. Very few IGHV sequences of C57BL/6 and BALB/c mice were shared with strains representing major subspecies, suggesting that their IGH loci may be complex mosaics of genes of disparate origins. This suggests a similar level of diversity is likely present in the IGH loci of other classical inbred strains. This must now be documented if we are to properly understand interstrain variation in models of antibody-mediated disease.

Precisely regulated rearrangements that yield imprecise recombination junctions are hallmarks of antigen receptor gene assembly. At the immunoglobulin heavy chain (IgH) gene locus this is initiated by rearrangement of a D (H) gene segment to a J (H) gene segment to generate DJ(H) junctions, followed by rearrangement of a V (H) gene segment to the DJ(H) junction to generate fully recombined VDJ alleles. In this review we discuss the regulatory features of each step of IgH gene assembly and the role of epigenetic mechanisms in achieving regulatory precision.

Opposite Effects of Bruton Tyrosine Kinase (BTK) Inhibitor Therapy with Ibrutinib and FCR Chemo-Immunotherapy on the Normal B Lymphocyte Repertoire in Patients with Chronic Lymphocytic Leukemia

B-cell lymphomas, mainly follicular lymphomas, carrying a t(14;18) chromosomal translocation associated with rearrangement of the BCL2 gene and the immunoglobulin heavy chain (IGH) gene, share many similarities with germinal center B cells in the secondary lymphoid follicle. In the germinal center, antigen-stimulated B cells proliferate and differentiate while undergoing isotype class switching of their immunoglobulin heavy chains. To examine whether BCL2-positive lymphoma cells show class switch recombination similar to that in the germinal center B cells, we studied the genomic configurations of the IGH gene loci in 38 patients with B-cell lymphomas. Sixteen (80%) out of 20 patients with BCL2-positive lymphomas showed class switch recombination on translocated and/or productive IGH gene loci. Lymphoma cells from 7 of the 16 patients expressed the gamma-heavy chain on their surfaces, indicating functional class switching to the gamma-constant gene on the productive allele. By contrast, 6 (33%) of the 18 patients lacking the BCL2 rearrangements exhibited class switch recombination. Statistical analysis revealed that the BCL2-positive lymphomas underwent switch recombination on either allele at a significantly higher frequency than the BCL2-negative lymphomas (P = 0.0099). This indicates that follicular lymphoma, not only morphologically but also functionally, recapitulates the germinal center. We propose that the up-regulated BCL2 expression itself is capable of playing an important role in immunoglobulin class switching.

MUM1 (multiple myeloma oncogene 1)/IRF4 (interferon regulatory factor 4) gene has been identified as an oncogene transcriptionally activated by t(6;14)(p25;q32) chromosomal translocation in multiple myeloma (MM). The significance of this alteration in MM remains unknown, as it is not detectable by means of conventional cytogenetic analysis. To address this issue, we established diagnostic procedures based on pulsed-field gel electrophoresis (PFGE) analysis and double color fluorescence in situ hybridization (DCFISH) using DNA probes derived from the MUM1 and the immunoglobulin heavy chain (IgH) gene loci. Among a panel of 17 MM cell lines, three (17.6%) showed fusions between these two loci, which resulted in the juxtaposition of the MUM1 to the IgH 3' alpha-enhancer region by virtue of t(6;14) or insertion of the IgH sequences into the vicinity of the MUM1 gene and in the concomitant overexpression of the MUM1 mRNA. With similar results, fusions between MUM1 and IgH loci were observed by means of interphase DCFISH in eight (21.1%) out of the 38 MM cases, although no definite relationships between MUM1 status and specific clinical findings could be established.

Chromosome translocations involving the immunoglobulin heavy chain (IGH) gene locus at chromosome region 14q32 are often observed in B-cell lymphoid neoplasms. Of these, t(14;18)(q32;q21) results in juxtaposition of the IGH gene on chromosome 14 and the BCL2 gene on chromosome 18, leading to the overexpression of BCL2 anti-apoptotic protein, which plays a critical role in the development of follicular lymphoma (FL). However, BCL2 overexpression is not observed in approximately 10% of FL, and the molecular pathogenesis of BCL2-negative FL has not been elucidated. Here, we identify the SRY-related high-morbidity-group (HMG) box 5 (SOX5) gene on chromosome 12p12 as a novel IGH-involved translocation partner in the case of BCL2-negative follicular lymphoma (FL) with a complex karyotype including t(12;14)(p12.2;q32) by long-distance inverse PCR. As a result of this translocation, the SOX5 gene is juxtaposed to the enhancer of the IGH gene; SOX5 overexpression in neoplastic cells was demonstrated by immunohistochemistry. The results of the present study suggest a role for SOX5 in the molecular pathogenesis of FL.

Characterization of a 14q +marker chromosome in Philadelphia chromosome positive acute lymphoblastic leukemia by DNA analysis and fluorescence in situ hybridization

Author SummaryDNA methylation at CpG dinucleotides is implicated in the regulation of gene expression in mammals. However, the regulation of DNA methylation itself is less clear despite recent advances in identifying enzymes that add or remove methyl groups. We have investigated the dynamics of DNA methylation during genome rearrangements that assemble antigen receptor genes in developing B lymphocytes to determine whether methylation status correlates with rearrangement potential. Two recombination events generate immunoglobulin heavy chain (IgH) genes. The first step brings together diversity (DH) and joining (JH) gene segments to produce DJH junctions. We show that both gene segments are methylated prior to rearrangement, whereas the DJH product is demethylated. DJH junctional demethylation is tissue-specific and requires an enhancer, Eμ, located within the IgH locus. The latter observations indicate that localized demethylation of the DJH junction occurs after the first recombination step and thus does not guide this first step of IgH gene assembly. Our working hypothesis is that recombination induces demethylation of recombinant product and may mark the junction for the second step of IgH rearrangement, juxtaposition of variable (VH) gene segments to rearranged DJH products to produce fully recombined V(D)J alleles.

Erroneous class switching and false VDJ recombination: Molecular dissection of t(8;14)/MYC-IGH translocations in Burkitt-type lymphoblastic leukemia/B-cell lymphoma

The pathogenesis and clinical heterogeneity of gastric diffuse large B-cell lymphoma (DLBCL) are poorly understood. We have comprehensively investigated the incidence and clinical significance of lymphoma-associated chromosomal translocations, particularly those involving the immunoglobulin heavy chain (IGH) gene locus, in a large series of gastric DLBCL. One hundred forty-one cases of primary gastric DLBCL [58 with mucosa-associated lymphoid tissue (MALT) lymphoma and 83 without MALT lymphoma] were enrolled. Translocations involving BCL6, c-MYC, FOXP1, MALT1, and IGH were investigated using interphase fluorescence in situ hybridization. In positive cases, additional fluorescence in situ hybridization was done with appropriate probes for potential partner genes. Cases were classified into germinal center B-cell-like (GCB) or non-GCB subgroups by immunophenotyping with CD10, BCL6, and MUM1. Translocations involving IGH were detected in 36 (32%) of 111 cases; their partner genes included BCL6 (n = 10), c-MYC (n = 5), and FOXP1 (n = 3) but remained unknown in the remaining 18 cases. t(14;18)/IGH-BCL2, t(14;18)/IGH-MALT1, and t(1;14)/BCL10-IGH were not detected in any case. t(11;18)/API2-MALT1 was detected in none of the cases, except for one case of DLBCL with MALT lymphoma, which showed positive signals only in MALT lymphoma cells. IGH-involved translocation was associated with younger age but not with any other clinicopathologic factors including GCB or non-GCB immunophenotypes. Cox multivariate analysis revealed that IGH-involved translocation, in addition to younger age and early stage, was an independent prognostic factor for better overall and EFSs. IGH-involved translocations are frequent in gastric DLBCL and seem to identify cases with favorable prognosis.