T cell receptor alpha chain genes are located on chromosome 14 at 14q11-14q12 in humans

TRAC variants associate with IgA nephropathy

The T cell receptor alpha constant gene (TRAC) encodes the constant region of the alpha chain for the T cell receptor, and the association of its gene variants with IgA nephropathy remains controversial. The authors resequenced the gene in 100 patients with IgA nephropathy and 100 controls, tested its linkage disequilibrium pattern, constructed haplotypes, and performed association and functional studies. First, the association between TRAC variants and IgA nephropathy was tested in 704 patients and 704 controls. Next, these 704 patients were divided into two independent datasets--310 with family member(s) and 394 single patients--to test the association separately. Results showed that the gene is located in a recombination hot spot, with nine linkage disequilibrium blocks within a 6.9-kb region. There is a hypervariable region with six single-nucleotide polymorphisms (SNPs) in an 85-bp stretch in intron 1. We identified multiple SNPs and two haplotypes that associate with IgA nephropathy (P = 0.0000013-0.0096 by logistic regression for SNPs; P = 0.0003 and P = 0.0398 for haplotype associations). The family-based study replicated both haplotype findings, and the 394 single-patient case-control study replicated the association with haplotype 1 (P = 0.0033). The overtransmitted/observed haplotypes demonstrated reduced transcription activity compared with the undertransmitted/observed haplotypes. In conclusion, this study suggests an association between TRAC variants and susceptibility to IgA nephropathy.

Analysis of T cell receptor variable regions and complementarity determining region 3 of infiltrating T lymphocytes in the liver of patients with chronic type B hepatitis

OBJECTIVES

T cell receptor (TCR) variable regions and complementarity determining regions 3 (CDR3) of infiltrating T cells in the livers of patients with chronic hepatitis B were examined in detail.

METHODS

TCR usage was examined by the inverse polymerase chain reaction in 2 hepatitis B e antigen-positive patients, one at an early stage and the other at an advanced stage.

RESULTS

In 61 productively rearranged clones bearing TCRalpha genes in the liver of the patient with early stage chronic hepatitis B, the Valpha 7.2 gene segment was most frequently used (16.4%), while the other Valpha gene segments were used less frequently. All but one of the clones with the Valpha7.2 gene were joined with the Jalpha33 gene, and the CDR3 regions of these clones were the same length and similar in amino acid sequence. In contrast, in 68 productively rearranged clones from the liver of the patient with advanced stage disease, all Valpha gene segments were used less frequently, and combinations of the Valpha and Jalpha gene segments varied.

CONCLUSIONS

Our data suggest a relatively restricted usage of TCR in the liver in early stage chronic hepatitis B.

Association of a T-cell receptor constant alpha chain gene polymorphism with progression of IgA nephropathy in Japanese patients

Immunogenetic studies have suggested the role of the T-cell receptor (TCR) in the development of immune-mediated diseases. We investigated whether a genetic polymorphism in the TCR constant alpha (Calpha) chain region might modify the susceptibility or progression of immunoglobulin A (IgA) nephropathy. The TCR Calpha chain genotype was studied in 213 Japanese patients with IgA nephropathy and 73 individuals from the general population. A polymerase chain reaction-based TaqI restriction fragment length polymorphism assay (TaqI RFLP) was applied on the 5' flanking region of the TCR Calpha first exon. The TaqI-undigested (t) and TaqI-digested (T) alleles showed similar genotype distributions between the patients with IgA nephropathy and controls (tt:Tt:TT = 16.9%:46.5%:36.6% in IgA nephropathy v 9.6%:58.9%:31.5% in controls; chi(2) = 1.9; P = not significant). To further investigate the role of TCR Calpha chain gene polymorphism in renal prognosis, we analyzed those patients with IgA nephropathy in whom renal status had been monitored for a period of more than 3 years (n = 182). According to outcome, two groups were formed. The stable (S) group included 98 patients with renal function that remained unchanged during an average follow-up of 10.7 +/- 0.4 (SE) years. The progressive (P) group (n = 84) included patients with progressively declining renal function, with an average follow-up of 11.9 +/- 0.5 years. The genotype distributions of the TCR Calpha chain gene polymorphisms between these two groups differed significantly (tt:Tt:TT = 25.5%:40.8%:33.7% in S v 10.7%:44.1%:45.2% in P; chi(2) = 7.0; P < 0.05). The frequency of the T allele was greater in the P group (67.3% in P v 54.1% in S; chi(2) = 6.6; P = 0.01). The TT or Tt genotypes were more commonly observed in patients from the P group (89.3% of T allele carriers in P v 74.5% in S; chi(2) = 6.5; P = 0.01). It appeared the T allele might foreshadow a poor renal prognosis, conferring a potential risk for developing renal failure with time (odds ratio, 2.7; confidence interval, 1.2 to 6.0; P < 0.05). In summary, TCR Calpha chain genetic variability was associated with loss of renal function over time in patients with IgA nephropathy. In conclusion, the TCR Calpha chain polymorphism might prove helpful to predict progression to chronic renal failure in Japanese patients with IgA nephropathy.

Association of IgA nephropathy with T-cell receptor constant alpha chain gene polymorphism

T-cell receptor (TCR) proteins recognize a complex of an antigen-derived peptide bound to the cell surface products of the major histocompatibility complex (MHC) that could be of importance in the immunopathogenesis of IgA nephropathy (IgAN). Previous studies found no difference on TCR constant beta chain gene frequencies in IgAN compared with control. Yet no study on the TCR alpha gene in IgAN was reported. We studied the TCR C alpha gene polymorphisms by restriction fragment length polymorphism (RFLP) in 53 patients with IgAN and in comparison with 67 healthy controls. The patients were also classified into different histopathological grading (I, II, and III with increasing histological severity) and renal functions. The extracted DNA were digested with Taq I enzymes and probed with a full-length TCR-alpha cDNA clone p1.2alpha probe. A 7-kb C-alpha Taq 1 fragment is found in 32 of 53 patients (60.3%) compared with 26 of 67 controls (38.8%) (P < 0.05). There was no association of any polymorphic fragment, including the 7-kb fragment, with either the histological grading or renal function. It is concluded that the TCR C-alpha gene is associated with IgAN but not with the prognosis of the disease.

TCR gene polymorphisms and autoimmune disease

Autoimmunity may result from abnormal regulation within the immune system. As the T cell is the principal regulator of the immune system and its normal function depends on immune recognition or self/non-self discrimination, abnormalities of the idiotypic T-cell receptor (TCR) may be one cause of autoimmune disease. The TCR is a clonally distributed, cell-surface heterodimer which binds peptide antigen when complexed with HLA molecules. In order to recognize the variety of antigens it may possibly encounter, the TCR, by necessity, is a diverse structure. As with immunoglobulin, it is the variable domain of the TCR which interacts with antigen and exhibits the greatest amount of amino acid variability. The underlying genetic basis for this structural diversity is similar to that described for immunoglobulin, with TCR diversity relying on the somatic recombination, in a randomly imprecise manner, of smaller gene segments to form a functional gene. There are a large number of gene segments to choose from (particularly the TCRAV, TCRAJ and TCRBV gene segments) and some of these also exhibit allelic variation. Finally, polymorphisms in non-coding regions of TCR genes, leading to biased recombination or expression, are also beginning to be recognized. All these factors contribute to the polymorphic nature of the TCR, in terms of both structure and repertoire formation. It follows that inherited abnormalities in either coding or regulatory regions of TCR genes may predispose to aberrant T-cell function and autoimmune disease. This review will outline the genomic organization of the TCR genes, the genetic mechanisms responsible for the generation of diversity, and the results of investigations into the association between germline polymorphisms and autoimmune disease.

Human T-cell receptor variable gene segment families

Multiple DNA and protein sequence alignments have been constructed for the human T-cell receptor alpha/delta, beta, and gamma (TCRA/D, B, and G) variable (V) gene segments. The traditional classification into subfamilies was confirmed using a much larger pool of sequences. For each sequence, a name was derived which complies with the standard nomenclature. The traditional numbering of V gene segments in the order of their discovery was continued and changed when in conflict with names of other segments. By discriminating between alleles at the same locus versus genes from different loci, we were able to reduce the number of more than 150 different TCRBV sequences in the database to a repertoire of only 47 functional TCRBV gene segments. An extension of this analysis to the over 100 TCRAV sequences results in a predicted repertoire of 42 functional TCRAV gene segments. Our alignment revealed two residues that distinguish between the highly homologous V delta and V alpha, one at a site that in VH contacts the constant region, the other at the interface between immunoglobulin VH and VL. This site may be responsible for restricted pairing between certain V delta and V gamma chains. On the other hand, V beta and V gamma appear to be related by the fact that their CDR2 length is increased by four residues as compared with that of V alpha/delta peptides.

Gene rearrangements and chromosomal translocations in T cell lymphoma--diagnostic applications and their limits

The diversity of the T cell receptor (TCR) repertoire is established for individual T lymphocytes by developmentally regulated gene rearrangements and shaped by predominantly intrathymic selection procedures. TCR gene probes in Southern blot experiments and TCR primers for the polymerase chain reaction (PCR) help to distinguish polyclonal from abnormal clonal T cell proliferations and to monitor clonal disease after treatment. Rearrangement studies can identify the lineage and developmental stage of a lymphocyte clone. Cross-lineage rearrangements, false positive or negative results are rarely misleading when morphology and immunophenotypical findings are considered. Rearrangement studies, however, have not contributed significantly to the comprehension of lymphomagenesis. Analyses of characteristic chromosomal translocations in T cell leukaemias and lymphomas may provide further insight into the mechanisms of malignant transformation. Transcription factors are often involved and sometimes abnormally transcribed, which may alter the physiological intracellular signalling in T cells. Interphase cytogenetic analysis by chromosomal fluorescence in situ hybridization (FISH) has become a new tool in the search for transformed T cells carrying specific translocations. Archival biopsy material is now accessible for PCR rearrangement studies and FISH cytogenetics. This adds another dimension to the diagnosis, disease monitoring and biological understanding of malignant T cell lymphomas and leukaemias.

Repertoire of Vα and Vβ regions of T cell antigen receptors on CD4+ and CD8+ peripheral blood T cells in a novel X-linked combined immunodeficiency disease

The repertoire of V regions of alpha/beta+ T cell receptor (TcR) on CD4+ and CD8+ T cells from the peripheral blood of six patients with a novel X-linked combined immunodeficiency was investigated by flow cytometry. The relative frequencies of V region subfamilies V alpha 2a on CD4+ T lymphocytes and V beta 5b and V beta 12a on CD8+ T lymphocytes from the peripheral blood from the affected males were decreased significantly. Also, the relative frequencies of certain other V region subfamilies on CD4+ or CD8+ T cells from the peripheral blood of some patients were either considerably below or above the ranges found in normal subjects. Although there may be other explanations including an extrathymic event, we suggest that the abnormalities in the TcR repertoire of peripheral blood T cells are consistent with a dysregulation of the intrathymic maturation/selection of T cells that leads to deficiencies in T cell populations in the peripheral blood of males with this disease.

Establishment and characterization of a human T-cell lymphoblastic lymphoma cell line (HT-1) carrying an inversion of chromosome 14

A new human lymphoblastic lymphoma cell line was established (designated HT-1) from the pleural fluid lymphoma cells of a patient with lymphoblastic lymphoma of T-cell type. The HT-1 cells expressed CD1, CD2, CD3, CD4, CD5, CD7, CD8, CD57, and terminal deoxynucleotidyl transferase (TdT) but lacked B-cell-associated antigens and myeloid-associated antigens. In addition, HT-1 cells had rearranged T-cell receptor (TCR) beta-chain gene and gamma-chain gene but retained germlines of immunoglobulin (Ig) heavy chain gene. These findings indicate that HT-1 cell line represents a common thymocyte in the T-cell lineage. Cytogenetic studies revealed that HT-1 cells carry an inversion (inv) of the long arm of chromosome 14. This cell line is the second T-cell line carrying inv(14) chromosome and may be useful for the molecular investigation of the cytogenetic break points of inv(14).

CD8 gamma delta cells: presence in the adult rat thymus and generation in vitro from CD4-/CD8- thymocytes in the presence of interleukin 2

Three to fifteen percent of peripheral T cells in adults express the recently described gamma delta T-cell antigen receptor (TcR) heterodimer. A small subpopulation of gamma delta cells express the CD8 accessory molecule. In this study, we analyzed the potential of highly purified CD4-/CD8-, double negative (DN) rat precursor thymocytes to give rise to gamma delta cells. We observed that in the presence of interleukin 2 (IL-2) and concanavalin A (ConA), both DN and CD8 cells expressing the gamma delta TcR were generated in vitro. We then examined the rat thymus for these cells and confirmed the presence of a previously undescribed CD8 TcR-alpha beta- subset in the rat thymus, expressing high levels of TcR-gamma and delta messages with no detectable TcR-alpha transcripts, similar to the cells generated in vitro in the presence of IL-2 and ConA.

Genotypic and cytogenetic study of acute myelocytic leukemia and chronic myelocytic leukemia in blast crisis: specific delta rearrangement pattern does not involve J delta gene locus

We have analysed the configuration of immunoassociated genes and the karyotypes of 30 patients with acute myelocytic leukemia (AML) and 10 with chronic myelocytic leukemia in blast crisis (CML-BC). In AML, the frequencies of T-cell receptor (TcR) beta, gamma, and delta chain and immunoglobulin heavy and light chain gene rearrangements were 4.2%, 19%, 8%, 10.7% and 10.5%, respectively. In CML-BC, they were 10%, 20%, 40%, 50% and 0%, respectively. Nine patients had abnormalities in chromosome 2, 7 or 14, upon which immunoassociated genes are located. There seems to be no apparent relationship between these chromosome abnormalities and gene rearrangements. In all patients but one (5/6), the delta rearrangement was accompanied by other immunoassociated gene rearrangements. Molecular size analysis revealed specific delta rearranged band(s) (19.5 kb-BamHI and/or 6.9 kb-EcoRI), as commonly detected in B-acute lymphocytic leukemia (ALL). All the patients with the delta rearranged band, however, had a germline configuration of J delta gene loci, suggesting a DD or V(D)D (probably V delta 2(D)D) pattern. This study also indicates that the delta rearrangement is specific in AML or CML-BC and distinct from that in early T leukemia/lymphoma.

Characterization of a novel, human cytotoxic lymphocyte-specific serine protease cDNA clone (CSP-C)

A human cDNA clone encoding a novel serine protease, cytotoxic serine protease-C(CSP-C), has been isolated from a cDNA library prepared from recombinant interleukin-2 (IL-2)-activated lymphocytes of a patient with a large granular lymphoproliferative disorder. The clone has a 741-base pair open reading frame encoding a putative 246-amino acid protein. The protein sequence contains the catalytic charge relay system characteristic of a serine protease and the conserved N-terminal amino acid sequence of the mature cytotoxic lymphocyte serine proteases found in both mouse and human. The amino acid sequence of CSP-C has 71% identity with the previously reported cytotoxic serine protease-B(CSP-B)/human lymphocyte protease (HLP)/SECT and 57% identity with the granulocyte-specific serine protease cathepsin G. The homology with another lymphocyte-specific serine protease, human Hanukah factor (HF)/Granzyme A was 41%. The transcript is expressed in lymphocytes stimulated with IL-2 or IL-2 plus phytohemagglutinin (PHA). CSP-C is not expressed in B-lymphoblastoid cell lines or in the T-leukemia cell line MOLT4. The cDNA sequence suggests that the protein is expressed as a prepropeptide, as has been found in the other murine and human serine proteases of lymphocyte origin. It has recently been reported that human chromosome 14q11, in addition to containing the genes encoding cytotoxic serine protease B (CSP-B), cathepsin G, and the T-cell receptor alpha and delta genes, also includes an additional genomic DNA clone which cross-hybridized with CSP-B and cathepsin G, cathepsin-like gene-2 (CGL-2). It is likely that the CSP-C cDNA clone reported in this study corresponds to CGL-2.

Two distinct mechanisms for the SCL gene activation in the t(1;14) translocation of T-cell leukemias

Molecular study of a t(1;14)(p32;q11) translocation found in an acute T-cell leukemia (Kd cells) with a relatively mature phenotype is reported. Complex DNA rearrangements were characterized in the TCR alpha/delta locus. Besides a productive V alpha/J alpha assembly found on the normal allele, two deletions within the J alpha cluster were identified in the translocated allele. The translocation breakpoints involved the TCR delta gene on chromosome 14 and the SCL locus on chromosome band Ip32 that was recently shown to be activated by the t(1;14) translocation of the DU 528 leukemic cell line. Significantly, both Kd and DU 528 translocation breakpoints were located at the boundaries of D delta or J delta segments and were clustered in a 10 kb genomic fragment of the SCL gene. The presence of recombination signal motifs (heptamer-12/23 bp spacer-nonamer) on both normal chromosome partners, and N nucleotide addition on both derivative chromosomes involved the recombinase system in the translocation event. The SCL locus was highly expressed as a 5 kb transcript in Kd cells and, as already reported, as a 2 kb transcript in DU 528 cells. Importantly, a 5 kb SCL transcript was also detected in immature nonlymphoid hematopoietic cells but not in normal mature T cells, suggesting that it might correspond to the normal SCL transcript. Taken together, our data support the notion that the involvement of the SCL gene in the leukemogenic process may occur through overexpression of an apparently normal transcript (Kd cells) or expression of a truncated RNA (DU 528 cells).

T-cell receptor gene rearrangements and the diagnosis of human T-cell neoplasms

The rearranging antigen receptor genes of lymphoid cells serve as unique clonal markers of lymphoid neoplasms. Gene rearrangement analysis is a highly sensitive and reproducible tool which is useful in the diagnosis and classification of malignant lymphoma/leukemia. Although clonality can often be determined among B cell neoplasms by virtue of immunoglobulin isotype analysis, no such phenotypic marker of clonality exists for T cells. Therefore, clonality of T lymphoproliferative processes is most readily determined by rearrangement analysis of the T cell antigen receptor genes. The alpha, beta, gamma, and delta genes of the T cell receptor gene family encode heterodimeric surface antigen receptors and undergo rearrangement early in T cell differentiation. Identification of rearrangement of T cell antigen receptor genes provides valuable diagnostic information concerning cellular lineage, clonality and classification of T cell neoplasms. This molecular approach is applicable to the diagnosis of occult disease, relapse, and resolution of diagnostic dilemmas in any type of tissue sample including fluids and needle aspirations.

An (8;14)(q24;q11) translocation involving the T-cell receptor alpha-chain gene and the MYC oncogene 3' region in a B-cell lymphoma

We describe a t(8;14)(q24;q11) involving the T-cell receptor alpha-chain gene (TCRA) and the 3' region of the MYC protooncogene in a B-cell lymphoma. The B-cell origin of this tumor was determined by its histological architecture, by immunophenotypic analysis, and by Southern analysis of immunoglobulin gene rearrangements. An identical fragment encompassing the translocation breakpoint junction was detected through Southern analysis using both a TCRAJ and a MYC probe. The other alleles at the TCRAJ and MYC loci were in the germline configuration. Restriction enzyme and nucleotide sequencing analyses revealed that the breakpoint junction on chromosome 8 lies approximately 700 base pairs (bp) downstream of the 3' end of the third MYC exon; on chromosome 14, the break is located 12.6 kilobases (kb) downstream of the 3' end of the C delta fourth exon. A heptamer-like consensus sequence on chromosome 14 adjacent to the translocation breakpoint implies the involvement of recombinase activity. However, no consensus sequences were found on chromosome 8 within 140 bp in either direction from the breakpoint. It is possible that this translocation involving MYC occurred during an attempt at an inappropriate rearrangement of the TCRA locus in a cell of B-cell lineage.

Chromosomal translocation in a human leukemic stem-cell line disrupts the T-cell antigen receptor delta-chain diversity region and results in a previously unreported fusion transcript

We have studied a leukemic stem-cell line, DU.528, that is able to differentiate into myeloid and lymphoid cells. The leukemic cells have a translocation between chromosomes 1 and 14, t(1;14)(p33;q11), which we have molecularly cloned and sequenced. Initial screening used joining (J)-segment probes from the T-cell receptor (TCR) alpha- and delta-chain loci. In apparent concert with the translocation, a deletion has occurred between delta-chain diversity (D)-region genes D delta 1 and D delta 2. D delta 2 was observed on derivative chromosome 1 [der(1)] and D delta 1 on der(14) with a deletion of the intervening 10 kilobases of germ-line DNA. The nature of the D delta 1-D delta 2 deletional event implicates a lymphoid recombinase in the mechanism of the translocation. As a consequence of the translocation, an unusual fusion transcript was generated. Probes from chromosome 1 detected a previously unreported transcript in RNA from both the cell line and the patient. A chromosome 14 probe identified the same transcript, thus confirming a fusion transcript derived from both chromosomes 1 and 14. This translocation may identify a gene for which we propose the name SCL (stem-cell leukemia) that is important for hemopoietic development and oncogenesis and that has been disrupted or altered in this stem-cell line.

Molecular genetic markers in lymphoproliferative disorders

The elucidation of the genetic mechanisms involved in the generation of antibody diversity is little more than a decade old, but the impact has already been felt in many areas of biology and medicine. In order for a B or T cell to become a functional antigen recognizing cell it must produce a unique protein to act as a membrane receptor. In the case of the B cell this is an immunoglobulin molecule while in the T cell it is an analogous dimeric protein, the T cell receptor. Diversity in these proteins is generated by a shuffling of the genes responsible for these respective proteins and is unique to each cell. Using Southern blot hybridization to exploit this, it is possible to determine whether a group of lymphocytes is derived from a single progenitor cell, i.e., clonal, and also whether they are of B or T cell origin. Oncogene activity and chromosomal translocations are believed to be responsible for a variety of lymphomas and leukemias. The association of established oncogenes, such as c-myc, with translocations to regions near immunoglobulin enhancers in some lymphomas has prompted successful searches for novel proto-oncogenes in other forms of lymphomas that also have characteristic, but different, translocations.

Proximity of the CTLA-1 serine esterase and Tcr alpha loci in mouse and man

The serine esterase CTLA-1 gene was shown by in situ hybridization to map to the D segment of mouse chromosome 14, the same localization as a member of the immunoglobulin superfamily, Tcr alpha. To further demonstrate the proximity of CTLA-1 and Tcr alpha, genetic linkage was tested in mouse using restriction fragment length polymorphisms and a backcross progeny, and no recombination was observed in the 100 backcross products studied. Recombination events between Tcr alpha/CTLA-1 and the markers Gdh-X and NP-1 show that the most probable order of these loci in the mouse 14D region is NP-1-Tcr alpha/Ctla-1-Gdh-X. In man, the human homologue of CTLA-1 was shown by in situ hybridization to map on chromosome 14, at 14q11-q12, where Tcr alpha also maps. Using the human cell line SUP-T1, bearing the inversion inv(14) (q11;q32), we further demonstrated the loci order in man to be centromere-NP-1-Tcr alpha-CTLA-1. To complement the cytogenetic and genetic mapping data, we tried to determine the physical distance between the two genes by pulsed field gel electrophoresis (PFGE). DNA prepared from various cell types, both mouse and human, were digested with a panel of rare cutter enzymes and hybridized first with CTLA-1, then with Tcr alpha probes. None of the bands identified hybridized with both Tcr alpha and CTLA-1 probes for either mouse or human cells. Although the physical mapping by PFGE is inconclusive, the cytogenetic and genetic data support close linkage of the Tcr alpha and CTLA-1 genes in both mouse and man, suggesting homology between the D region of mouse chromosome 14 and the q11-q12 region of human chromosome 14, encompassing the Tcr alpha and CTLA-1 loci. These findings also provide another example of proximity of genes coding for a member of the Ig super-family and a serine esterase.

Breakage of the T cell receptor alpha chain locus in non malignant clones from patients with ataxia telangiectasia

Patients with ataxia telangiectasia (A-T) develop specific chromosome translocations, which may confer a proliferative advantage, resulting in the appearance of large clones in the peripheral blood lymphocytes. These lymphocytes are not malignant. Using in situ hybridisation techniques we have investigated a consistent 14q11 translocation breakpoint observed in a t(X;14)(q28;q11) translocation clone from each of two different patients and a t(14;14)(q11;q32) clone from a third patient. In all cases the chromosome translocation involved breakage within the alpha chain locus of the T cell receptor (TCR alpha), between the variable and constant regions, at 14q11. Chromosome rearrangement involving breakage within TCR alpha can therefore precede the development of malignancy. Further chromosomal rearrangement may be required in these patients, for progression to the leukaemic state.

The human T cell receptor alpha-delta locus: a physical map of the variable, joining and constant region genes

In this study a physical macro-restriction map of the entire human alpha locus that spans about 1000 kilobase pairs and includes the V alpha, J alpha and C alpha genes is presented. Evidence is provided that gene duplications were involved in the increase of genomic diversity of V alpha genes. In addition, we show a detailed map of a 40-kb region located approximately 100 kg upstream of the human C alpha gene. Direct evidence is provided to support that the human alpha chain locus, like the murine, also contains another T cell constant region gene in the alpha chain locus, the human delta chain gene. In addition, two J segments and one D segment have been identified. Using these genomic probes, we show that several T cell lines, including those known to express the surface gamma/delta heterodimer, have rearranged this region. The design of two separate centers of rearrangement within one locus that are involved in rearrangement events at different times, and the presence of high number of J segments in this region, may render the locus highly vulnerable to chromosomal translocation during T cell development.

T cell receptor alpha-, beta-, and gamma-genes in T cell and pre-B cell acute lymphoblastic leukemia

We examined alpha-, beta-, and gamma-T cell receptor (TCR) gene activation within acute lymphoblastic leukemias (ALLs) that represent early stages of B and T cell development. We wished to determine if TCR rearrangement and expression was lineage restricted, showed any developmental hierarchy, or could identify new subsets of T cells. Rearrangement of gamma and beta TCR genes occurred early in development but in no set order, and most T-ALLs (22/26) were of sufficient maturity to have rearranged both genes. T-ALLs preferentially rearranged C gamma 2 versus the C gamma 1 complex; no preference within the beta locus was apparent. Once rearranged, the beta TCR continued to be expressed (11/13), whereas the gamma TCR was rarely expressed (3/14). The alpha TCR was expressed only in more mature T-ALLs (8/14) that usually displayed T3. The 3A-1 T cell associated antigen appeared earliest in development followed by T11 and T3. Within pre-B cell ALL a higher incidence of lineage spillover was noted for gamma TCR rearrangements (8/17) than for beta rearrangements (3/17). This also contrasts with the only occasional rearrangement of immunoglobulin (Ig) heavy chains (3/25) in T-ALL. However, in pre-B ALL the pattern of gamma TCR usage was distinct from that of T cells, with the C gamma 1 complex utilized more frequently. Almost all ALLs could be classified as pre-B or T cell in type by combining Ig and TCR genes with monoclonal antibodies recognizing surface antigens, although examples of lineage duality were noted. Unique subpopulations of cells were discovered including two genetically uncommitted ALLs that failed to rearrange either Ig or TCR loci. Moreover, two T lymphoblasts were identified that possessed the T3 molecule but failed to express alpha plus beta TCR genes. These T-ALLs may represent a fortuitous transformation of T cell subsets with alternative T3-Ti complexes.

The mechanism of chromosome 14 inversion in a human T cell lymphoma

The chromosome 14 inversion produces cytogenetic breakpoints at either end of the long arm of this chromosome. Previous studies have shown that a hybrid gene (designated IgT) consisting of an immunoglobulin VH gene segment and T cell receptor J alpha C alpha segments encompasses the telomeric breakpoint in SUP-T1, a cell line derived from a human T cell lymphoma. Here, we report that the centromeric breakpoint in SUP-T1 constitutes the reciprocal of a VH-J alpha join but involves gene segments different from those at the telomeric breakpoint. Therefore, chromosome inversion and IgT formation were mediated by two sequential VH-J alpha joining events. Moreover, sequences adjacent to the centromeric breakpoint detect a T-cell-specific RNA, encoded within the immunoglobulin VH locus, whose transcriptional activity may have facilitated the illegitimate VH-J alpha rearrangements.

Monoclonality in human T-cell disorders

The genes coding for the T-cell antigen receptor have recently been cloned. They have proven to be invaluable tools for the study of the molecular mechanisms governing T-cell recognition of foreign antigens associated with histocompatibility antigens. In addition, they have also provided sensitive means of detecting clonal cell populations and determining cell lineage. In this review we describe the general organisation of these genes, the results of their utilization in the analysis of hematological pathologies, and discuss the possible implications of the involvement of these genes in translocations observed in certain T-cell malignancies.

Fragile sites limited to lymphocytes: molecular recombination and malignancy

Fragile sites on chromosomes are points at which rearrangements tend to occur nonrandomly. Because translocations between chromosomes #7 and #14 occur nonrandomly in normal cultured lymphocytes, we analyzed chromosomes #7 and #14 in 53,580 cultured lymphocytes and 109,300 other human cells. We found one rearrangement per 1,218 lymphocytes. These rearrangements were not restricted to translocations but included inversions and hitherto undetected duplications and deletions. In lymphocytes cultured for only 48 hours, rearrangements were seen indicating their presence in vivo. The breakpoints were exclusively in chromosome bands 7p13, 7q35, 14q11, and 14q32. The predisposition to form these rearrangements appeared nonrandom and inherited. These four bands act as if they contain fragile sites limited to lymphocytes. Fragility was not observed in these bands in cells from amniotic fluid, bone marrow, skin, or chorionic villi. Bands 7p13, 7q35, and 14q11 contain T-cell receptor (TCR) genes, whereas, band 14q32 contains the immunoglobulin heavy (IgH) chain locus. Rearrangements of these bands may result from molecular recombination between TCR or between TCR and IgH genes forming TCR/TCR and TCR/IgH chimeric genes important to understanding lymphocyte development and neoplasia. TCR/IgH chimeric genes have been found in T- and B-cell malignancy.

The arrangement of immunoglobulin and T cell receptor genes in human lymphoproliferative disorders

Immunoglobulin and T cell antigen receptor genes in their germ-line form are organized as discontinuous DNA elements that are joined by recombinations during lymphocyte development. The analysis of immunoglobulin gene structure and arrangement has been of great value in the study of human lymphoid neoplasms. The analysis of rearranged immunoglobulin and T cell receptor genes has been of value in defining the lineage (T or B cell) of neoplasms that were of controversial origin previously, determining the clonality of abnormal lymphocyte proliferations, diagnosing and monitoring the therapy of lymphoid malignancies, determining the state of maturation and the causes for failure of maturation of cells of the B cell series, and providing major insights into the cause of malignant transformation of B and T lymphoid cells. Thus, the application of this molecular genetic approach has great potential for complementing conventional marker analysis, cytogenetics, and histopathology, thus broadening the scientific basis for the classification, diagnosis, and monitoring of the therapy of lymphoid neoplasia.

A comprehensive list of cloned human DNA sequences

A list of DNA sequences cloned from the human genome is presented. Intended as a guide to clone availability, this list includes published reports of cDNA, genomic and synthetic clones comprising gene and pseudogene sequences, uncharacterized DNA segments and repetitive DNA elements.

T-cell receptor alpha-chain gene is split in a human T-cell leukemia cell line with a t(11;14)(p15;q11)

Chromosomal rearrangements in malignant T-cell disease frequently involve the chromosome bands containing the T-cell receptor genes. The RPMI 8402 cell line, which was established from the leukemia cells of a patient with T-cell acute lymphoblastic leukemia, is characterized by a translocation involving chromosome 14 (band q11) and chromosome 11 (band p15) [t(11;14)(p15;q11)]. By using in situ chromosomal hybridization and Southern blot analysis to examine RPMI 8402 cells, we determined that the break at 14q11 occurs within the variable region sequences of the T-cell receptor alpha-chain gene (TCRA); the break at 11p15 occurs between the HRAS1 gene and the genes for insulin and the insulin-like growth factor 2. These results suggest that the TCRA sequences activate a cellular gene located at 11p15 in malignant T-cell disorders.

Molecular cloning of the breakpoint junction of a human chromosomal 8;14 translocation involving the T-cell receptor alpha-chain gene and sequences on the 3' side of MYC

The MOLT-16 cell line, which was established from the malignant cells of a patient with T-cell acute lymphoblastic leukemia, is characterized by a translocation involving chromosome 8 (band q24) and chromosome 14 (band q11) [t(8;14)(q24;q11)]. To determine the position of the gene encoding the alpha chain of the T-cell receptor and of the protooncogene MYC (formerly c-myc) in relation to the breakpoint junction and to evaluate their possible role in the pathogenesis of T-cell neoplasia, we applied the techniques of in situ chromosomal hybridization, Southern blot analysis, and molecular cloning to MOLT-16 cells. Our results indicate that the breakpoint on chromosome 14 at band q11 occurs close to a joining sequence of the gene encoding the alpha chain of the T-cell receptor. The constant region and part of the joining region of this gene are translocated to the 3' side of the MYC exons. The breakpoints on chromosomes 8 and 14 are close to, but distinct from, those found in SKW-3, another T-cell leukemia cell line, which has a t(8;14). The identification of a breakpoint to the 3' side of MYC suggests that this recurring translocation is analogous to the variant t(2;8) and t(8;22) translocations observed in the B-cell malignancies.

Sequences and repertoire of human T cell receptor alpha chain variable region genes in mature T lymphocytes

24 human T cell receptor alpha chain messages have been examined by cDNA sequence analysis and Southern blot. The data indicate that there are approximately 40 alpha chain T cell receptor variable gene segments, which can be divided into 12 families. Comparison of the J gene segments from the cDNAs to previously determined germline J alpha sequences places the number of J alpha gene segments over 21, and indicates their number to be approximately 55. Identical nucleotide sequences in independent isolates of V alpha and J alpha gene segments indicate that hypermutation may not be a common mechanism for the expansion of diversity in these genes, and suggest that the major source of diversity within the alpha chain repertoire is a result of recombinational joinings between germline V alpha and J alpha sequences, combined with imprecise junctional joining. Analysis of the V regions of these alpha chain messages reveals the presence of three domains of hypervariability roughly analogous to the CDR1, CDR2, and CDR3 regions of immunoglobulin.

Gene encoding the alpha chain of the T-cell receptor is moved immediately downstream of c-myc in a chromosomal 8;14 translocation in a cell line from a human T-cell leukemia

The SKW-3 cell line, which was established from the malignant cells of a patient with T-cell chronic lymphocytic leukemia, is characterized by a translocation involving chromosome 8 (band q24) and chromosome 14 (band q11) [t(8;14)(q24;q11)]. To determine the position of the gene encoding the alpha chain of the T-cell receptor and of the human protooncogene myc (c-myc) in relation to the breakpoint junctions and to evaluate their possible role in the pathogenesis of T-cell neoplasia, we applied the techniques of in situ chromosomal hybridization and Southern blot analysis to SKW-3 cells. Our results indicate that the breakpoint on chromosome 14 at band q11 occurs close to a joining sequence of the gene encoding the alpha chain of the T-cell receptor. Additional rearrangements within the alpha-chain locus appear to split the variable region cluster. As a result of the rearrangements, the constant region of this gene, as well as some variable region segments, are translocated to chromosome 8, to the 3' side of the c-myc-coding exons. The identification of a breakpoint to the 3' side of c-myc suggests that this translocation is analogous to the variant (2;8) and t(8;22) translocations observed in the B-cell malignancies.

A chromosome 14 inversion in a T-cell lymphoma is caused by site-specific recombination between immunoglobulin and T-cell receptor loci

Specific chromosomal aberrations are associated with specific types of cancer (for review see ref. 1). The distinctiveness of each association has led to the belief that these chromosomal aberrations are clues to oncogenic events or to the state of differentiation in the malignant cell type. Malignancies of T lymphocytes demonstrate such an association characterized most frequently by structural translocations or inversions of chromosomes 7 and 14 (refs 7-9). Analyses of these chromosomally marked tumours at the molecular level may therefore provide insight into the aetiology of the cancers as well as the mechanisms by which chromosomes break and rejoin. Here we report such an analysis of the tumour cell line SUP-T1 derived from a patient with childhood T-cell lymphoma carrying an inversion of one chromosome 14 between bands q11.2 and q32.3, that is, inv(14) (q11.2; q32.2). These are the same chromosomal bands to which the T-cell receptor alpha-chain (14q11.2) and the immunoglobulin heavy-chain locus (14q32.3) have been assigned. Our analysis reveals that this morphological inversion of chromosome 14 was mediated by a site-specific recombination event between an immunoglobulin heavy-chain variable region (Ig VH) and a T-cell receptor (TCR) alpha-chain joining segment (TCR J alpha). S1 nuclease analysis shows that this hybrid gene is transcribed into poly(A)+ RNA.

Regional location of alpha 1-antichymotrypsin and alpha 1-antitrypsin genes on human chromosome 14

The human protease inhibitor genes alpha 1 antitrypsin (alpha 1-PI) and alpha 1-antichymotrypsin (alpha 1-ACT) are acute-phase proteins which are induced in response to inflammation. These inhibitors function to limit the activity of serine proteases in vivo. alpha 1-PI acts as an inhibitor of neutrophil elastase to protect the elastin fibers of the lung. Genetic deficiencies of alpha 1-PI result in development of chronic pulmonary emphysema. The physiologic role of alpha 1-ACT has not been clearly defined, but it also appears to function in the maintenance of protease-protease inhibitor equilibrium in the lung. Nucleic acid and protein sequence homologies detected between alpha 1-PI and alpha 1-ACT suggested an evolutionary relationship. Gene mapping experiments were performed to determine if these protease inhibitor genes reside at the same chromosomal locus in man. In situ hybridization data demonstrate that both alpha 1-PI and alpha 1-ACT map to the same region, q31-q32.3, on chromosome 14.

Organization and sequences of the diversity, joining, and constant region genes of the human T-cell receptor beta chain

The organization and sequences of the human beta-chain T-cell receptor diversity, joining, and constant region segments are described. The beta chain of the human T-cell receptor, analogous to the mouse counterpart, consists of two distinct constant region genes approximately equal to 10 kilobases apart. The two constant region genes, C beta 1 and C beta 2, are very similar not only in sequence but also in genomic organization. The coding sequences of each of these C beta constant region genes are divided into four exons. The first two exons encode most of the extracellular constant domain. The third exon encodes a major part of the presumed transmembrane portion, and the last exon contains the cytoplasmic coding sequence as well as 3' untranslated sequences. Except for a stretch of approximately equal to 95 highly conserved nucleotides extending 3' of the first exon of the C region genes, little homology can be found between the intron sequences of C beta 1 and C beta 2. A small cluster of joining region (J beta) gene segments is located approximately equal to 5 kilobases upstream of each of these two constant regions. The first cluster, J beta 1, contains six functional J gene segments while the second, J beta 2, contains seven functional J gene segments. In addition, diversity region (D beta) gene segments are located approximately equal to 600 base pairs upstream of each J beta. Recombinational signals containing highly conserved heptamer and nonamer sequences separated by 12 or 23 bases are found adjacent to all of these D beta and J beta gene segments. These signal sequences are thought to be involved in the somatic recombination processes. These results indicate that what appears to be a gene duplication event giving rise to these two distinct regions must have arisen a long time ago in the evolution of this gene locus.

Fusion of an immunoglobulin variable gene and a T cell receptor constant gene in the chromosome 14 inversion associated with T cell tumors

An inversion of chromosome 14, inv(14)(q11,q32), is frequently observed in human T cell tumors; the cytogenetic breakpoints are of interest because the T cell receptor alpha-chain and immunoglobulin heavy chain genes reside on chromosome bands 14q11 and 14q32, respectively. We have investigated the structure of the alpha-chain genes in a T cell line harboring the chromosome 14 inversion. On the normal chromosome 14, a V alpha segment has rearranged nonproductively with a J alpha segment. In contrast, the inverted chromosome features an unprecedented rearrangement in which an immunoglobulin heavy chain variable gene segment (VH) on chromosome band 14q32 has joined with a J alpha segment from band 14q11. The VH-J alpha C alpha rearrangement is productive at the genomic level and therefore may encode a hybrid immunoglobulin/T cell receptor polypeptide.

Breakpoints in the human T-cell antigen receptor alpha-chain locus in two T-cell leukaemia patients with chromosomal translocations

Specific chromosomal translocations have been observed in several human and animal tumours and are believed to be important in tumorigenesis. In many of these translocations the breakpoints lie near cellular homologues of transforming genes, suggesting that tumour development is partly due to the activation of these genes. The best-characterized example of such a translocation occurs in mouse plasmacytoma and human B-cell lymphoma, where c-myc, the cellular homologue of the viral oncogene myc, is brought into close proximity with either the light- or heavy-chain genes of the immunoglobulin loci, resulting in a change in the regulation of the myc gene. T-cell malignancies also have characteristic chromosomal abnormalities, many of which seem to involve the 14q11-14q13 region. This region has recently been found to contain the alpha-chain genes of the human T-cell antigen receptor. Here we determine more precisely the chromosome breakpoints in two patients whose leukaemic T cells contain reciprocal translocations between 11p13 and 14q13. Segregation analysis of somatic cell hybrids demonstrates that in both patients the breakpoints occur between the variable (V) and constant (C) region genes of the T-cell receptor alpha-chain locus, resulting in the translocation of the C-region gene from chromosome 14 to chromosome 11. As the 11p13 locus has been implicated in the development of Wilms' tumour, it is possible that either the Wilms' tumour gene or a yet unidentified gene in this region is involved in tumorigenesis and is altered as a result of its translocation into the T-cell receptor alpha-chain locus.

Translocations that highlight chromosomal regions of differentiated activity

The frequent translocation of the c-myc oncogene into the immunoglobulin loci in tumors of B lymphocytes prompted us to ask whether or not disease-associated chromosomal translocations specific for other disorders in different cell types would also involve regions of the genome encoding important differentiation-specific products made by these cells. We have studied the karyotypes of two patients with erythroleukemia and an established erythroleukemia cell line, K562 (late passages), and find translocations within the chromosomal regions to which the genes that encode alpha and beta globin have been assigned. Additionally, we have analyzed the karyotype of cloned B-lymphocytes, including both kappa and lambda producing cells, from a patient with ataxia telangiectasia (AT) and find a translocation between the regions encoding immunoglobulin (Ig) light and heavy chain genes whereas a different translocation not involving these regions is seen in T-lymphocytes from the same patient. These examples provide insight into the mechanism of chromosomal translocation in both cancerous and noncancerous conditions and lead to the speculation that genomic activity is a necessary factor in the generation of some chromosomal translocations.

Organization and sequences of the variable, joining and constant region genes of the human T-cell receptor alpha-chain

An essential property of the immune system is its ability to generate great diversity in antibody and T-cell immune responses. The genetic and molecular mechanisms responsible for the generation of antibody diversity have been investigated during the past several years. The gene for the variable (V) region, which determines antigen specificity, is assembled when one member of each of the dispersed clusters of V gene segments, diversity (D) elements (for heavy chains only) and joining (J) segments are fused by DNA rearrangement. The cloning of the beta-chain of the T-cell antigen receptor revealed that the organization of the beta-chain locus, which is similar to that of immunoglobulin genes, is also composed of noncontiguous segments of V, D, J and constant (C) region genes. The structure of the alpha-chain seems to consist of a V and a C domain connected by a J segment. We report here that the human T-cell receptor alpha-chain gene consists of a number of noncontiguous V and J gene segments and a C region gene. The V region gene segment is interrupted by a single intron, whereas the C region contains four exons. The J segments, situated 5' of the C region gene, are dispersed over a distance of at least 35 kilobases (kb). Signal sequences, which are presumably involved in DNA recombination, are found next to the V and J gene segments.