Abnormalities in DNA rearrangements of immunoglobulin gene loci in precursor B cells derived from X-linked agammaglobulinemia patient and a severe combined immunodeficiency patient

A mathematical model predicting the frequency of aberrant rearrangements in the T-cell receptor gene

The T-cell receptor (TCR) genetic loci undergo an orderly process of recombination in ontogeny in order to generate a diverse array of antigen receptors. Normally occurring, out-of-frame and incomplete rearrangements produce non-productive TCR transcripts. Abnormalities in the rearrangement process occur at very low frequencies but may predominate in inborn errors of recombination. Detecting these abnormalities in surviving pools of lymphocytes is difficult and typically focuses on identification of abnormally rearranged alleles or on detecting abnormalities in recombinase proteins. Thus, there currently exists no rapid screening method to identify aberrant V(D)J recombination. To address this issue, a mathematical model was developed to predict the error rate from the measured proportions of different non-productive TCR alleles. Since the proportions of different non-productive rearrangements vary in a characteristic fashion in response to abnormalities in the recombination process, the mathematical model presented here provides a tool to indirectly assess the error rate of TCR recombination. The model was applied to a group of patients with Omenn's syndrome, most of whom had an unknown primary defect. The results indicate that these patients had a > 90% rate of aberrant TCR recombination.

The gene loci for immunoglobulin heavy chains in precursor B cell lines from a patient with severe combined immunodeficiency appear able to participate in DNA rearrangement but have a germ-line configuration

In a previous study (Immunogenetics 1988. 27:330) with Epstein-Barr virus, we established lines of precursor B cells from bone marrow cells of a patient with severe combined immunodeficiency in whom the numbers of B cells and T cells were markedly reduced. Although based on their surface markers these cell lines appeared to be at an early stage of B cell differentiation, the gene loci for immunoglobulin heavy chains (IgH) retained the germ-line configuration on both chromosomes in almost all the transformants. In this study, we found that the enhancer sequence, located between the JH and mu genes, was hypomethylated and an abundance of the germ-line Cmu transcript was detected in these cell lines by Northern hybridization. These results suggest that the chromatin structure of the IgH gene locus in these cell lines is accessible to VDJ recombinase and is able to participate fully in DNA rearrangement. By contrast, we did not detect transcripts of the RAG-1 and RAG-2 genes, which are required for V(D)J recombination at gene loci for immunoglobulin and T cell receptors. Thus, it seems likely that these cell lines fail to initiate the V(D)J recombination process because of some deficiency in the formation of VDJ recombinase, which includes the inability to express RAG genes.

Sequence and chromosome assignment to 11p13-p12 of human RAG genes

The recombination-activating genes RAG-1 and RAG-2 are required for V(D)J DNA rearrangements at loci for immunoglobulin and T cell receptor genes. We isolated the human RAG-2 gene and determined its nucleotide sequence. Mapping analysis of RAG-1 and RAG-2 genes on human chromosomes by fluorescence in situ hybridization indicated that the genes are located on chromosome 11p13-p12. RAG-1 and RAG-2 do not seem to be linked to any of the primary immunodeficiencies for which defective genes have already been mapped.

Evidence for failure of V(D)J recombination in bone marrow pre-B cells from X-linked agammaglobulinemia

X-linked agammaglobulinemia (XLA) results from a failure of B lymphoid development. We have previously examined pre-B cell hybrids from three patients with XLA and found them to be limited to production of a novel germ line transcript of the Ig H chain locus composed of a leader sequence (LS) spliced to the constant region of mu chain (C mu) as mRNA and polypeptide. These transcripts result from transcriptional activation of the germ line heavy chain locus from an LS exon upstream of the embryonic JH locus. Germ line LS-C mu transcripts are produced by pre-B cells from normal bone marrow and fetal liver, indicating that they are products of normal pre-B cell development, as part of the process of transcriptional activation to provide access for the recombinase. Bone marrow from three patients with XLA has been examined directly by polymerase chain reaction amplification to determine whether the exclusive production of LS-C mu by XLA pre-B cell hybrids is representative of XLA pre-B cells. I report that LS-C mu is the predominant Ig molecule produced by XLA pre-B cells, with limited production of the D mu product of DJH intermediate stage of V(D)J recombination. Mature VHDJH recombinations were not detected with a variety of primers that amplify VH sequences. I conclude that XLA is associated with a limitation in V(D)J recombination that may cause the failure of pre-B cell development.

Severe combined immunodeficiency (SCID) in man: B cell-negative (B-) SCID patients exhibit an irregular recombination pattern at the JH locus

Human severe combined immunodeficiency (SCID) patients were analyzed by a polymerase chain reaction assay for their recombination capability at the DHQ52-JH region of the immunoglobulin heavy chain locus. Five patients with B cells (B+ SCID) exhibited a recombination pattern also observed in healthy persons. In contrast, six patients lacking B cells (B- SCID) showed a grossly altered rearrangement pattern characterized by the (partial) absence of regular DHQ52-JH recombinations and the presence of abnormal rearrangements. These events were caused by deletions surpassing the boundaries of immunoglobulin coding elements and thus resemble the pattern of deletional recombinations previously described in SCID mice.

Severe combined immunodeficiency in man with an absence of immunoglobulin gene rearrangements but normal T cell receptor assembly

An autosomal recessive type of severe combined immunodeficiency disease (SCID) was characterized by an absence of immunoglobulins (Ig) in the serum and of Ig+ lymphocytes in bone barrow (BM) and peripheral blood. In the BM CD10+/terminal deoxynucleotidyl transferase-positive lymphocytes were identified. Epstein-Barr virus-transformed B lymphoblastoid cell lines (BLCL) obtained from BM and peripheral blood did not synthesize Ig. The Ig heavy and light chain gene complexes in the BLCL had retained the germ-line configuration. Mature T cells were present but their numbers in peripheral blood were decreased. T lymphoblastoid cells derived from peripheral blood expressed normal T cell receptor (TcR) CD3 complexes and manifested various genomic TcR rearrangements. It was concluded that this type of SCID entailed a complete arrest of B lymphocyte differentiation in an early stage prior to Ig rearrangements and a quantitative defect of T lymphocytes which nevertheless allowed development of mature T cells. Repeated failures of BM transplantation and the striking absence of Ig assembly suggested that this SCID defect resides in the BM microenvironment.

Presence of immunoglobulin (Ig) M and IgG double isotype-bearing cells and defect of switch recombination in hyper IgM immunodeficiency

We established a transformed B cell line expressing both IgM and IgG on the cell surface from a patient with hyper IgM immunodeficiency using Epstein-Barr viruses. DNA and RNA of the cells were analyzed. DNA rearrangements of Ig JH gene loci were observed on both chromosomes. Cloning and DNA sequence analyses showed that one has a VHDHJH structure while the other has a DHJH structure. Southern hybridization with 5'-S mu and S gamma region-containing probes indicated germline configuration in the switch regions of mu and gamma genes on both chromosomes. To test expression of mu and gamma chains in the transformed cells at the mRNA-level, we used the polymerase chain reaction with three kinds of synthetic oligonucleotides as primers, one of which was part of the VH gene, while the other two were complementary to parts of C mu and C gamma genes. Sequence analysis of the amplified products showed that the same VHDHJH sequence is directly connected with either the C mu or the C gamma sequence in the mRNAs. This is direct evidence showing that in double isotype-bearing cells one VHDHJH exon in the transcript is alternatively spliced to C mu or C gamma without DNA rearrangement. The defect in this disease could be at the S-S recombination stage.

Early human IgH gene assembly in Epstein-Barr virus-transformed fetal B cell lines. Preferential utilization of the most JH-proximal D segment (DQ52) and two unusual VH-related rearrangements

We have analyzed the phenotypic characteristics and IgH gene rearrangements in a panel of EBV-transformed B lineage cell lines from human fetal liver and bone marrow. Some lines contained only populations of immature, Ig- Be cells, while others contained mixed populations of mature and immature B cells. The majority of identifiable IgH rearrangements involved joining of the most JH-proximal D segment, DQ52, to various JH segments, implying that DQ52 is a preferred target for initial DJH rearrangements. Three other rearrangements involving VH-related sequences were also characterized. Two involved VHDJH joining using VH3 genes, although one of these had a very unusual DJH structure. The third consisted of inverted 3' signal sequences and flanking regions of a VH4 gene appended to a JH. The mechanisms by which the later rearrangement could have occurred and its potential physiological significance are discussed.