Genetic profiling of chromosome 1 in breast cancer: mapping of regions of gains and losses and identification of candidate genes on 1q.

Chromosome 1 is involved in quantitative anomalies in 50-60% of breast tumours. However, the structure of these anomalies and the identity of the affected genes remain to be determined. To characterise these anomalies and define their consequences on gene expression, we undertook a study combining array-CGH analysis and expression profiling using specialised arrays. Array-CGH data showed that 1p was predominantly involved in losses and 1q almost exclusively in gains. Noticeably, high magnitude amplification was infrequent. In an attempt to fine map regions of copy number changes, we defined 19 shortest regions of overlap (SROs) for gains (one at 1p and 18 at 1q) and of 20 SROs for losses (all at 1p). These SROs, whose sizes ranged from 170 kb to 3.2 Mb, represented the smallest genomic intervals possible based on the resolution of our array. The elevated incidence of gains at 1q, added to the well-established concordance between DNA copy increase and augmented RNA expression, made us focus on gene expression changes at this chromosomal arm. To identify candidate oncogenes, we studied the RNA expression profiles of 307 genes located at 1q using a home-made built cDNA array. We identified 30 candidate genes showing significant overexpression correlated to copy number increase. In order to substantiate their involvement, RNA expression levels of these candidate genes were measured by quantitative (Q)-RT-PCR in a panel of 25 breast cancer cell lines previously typed by array-CGH. Q-PCR showed that 11 genes were significantly overexpressed in the presence of a genomic gain in these cell lines, and 20 overexpressed when compared to normal breast.

Structure and chromosomal assignment to 22q12 and 17qter of the ras-related Rac2 and Rac3 human genes.

Members of the Rho/Rac/Cdc42Hs family of GTPases have been shown to participate in many aspects of the signaling of cell growth and differentiation. Although the biochemical properties of these GTPases have been extensively studied, very little is known about the structure of the corresponding genes. To gain insight on the evolution of the Rho family, we were interested in studying the genomic structure of several members. We report here the structure and the localization to 22q12 of the human Rac2 gene, as well as the localization to 17qter of Rac3, a new member closely related to Rac1 and Rac2. Unlike the structure of its closest relative ARH-G gene, which contains a single intron, Rac2 is made of at least 7 exons, spanning over 18 kb of DNA. Comparison of gene structure and exonic borders suggests that the emergence of the whole superfamily took place early during evolution.

Haplotypes of the human immunoglobulin lambda IGLV7S1 and IGLV1S1 genes defined by restriction-site polymorphism and insertion/deletion of a 6-kb DNA fragment.

Haplotypes were defined in the human immunoglobulin lambda locus by using three probes--V lambda VII, V lambda A, and V lambda I--hybridized to BamHI, KpnI, EcoRI, and HindIII digests. Four KpnI alleles were described. Two of them, 13 kb and 16 kb, detected with both the V lambda VII and V lambda A probes, were correlated with 4.6-kb and 10.5-kb KpnI fragments, respectively, which hybridize to the V lambda I probe. The two others (17 kb and 24 kb) were detected with the three probes V lambda VII, V lambda A, and V lambda I. Moreover, we show that two of those haplotypes may reflect an insertion of 6 kb between V lambda A and V lambda 1S1. Familial studies were performed to demonstrate the Mendelian inheritance. Our results demonstrate the absence of association between the C lambda alleles and V lambda haplotypes.

[Polymerase chain reaction: general methodology]. / Réactions de polymérisation en chaîne: méthodologie générale.

The polymerase chain reaction method (PCR) is extremely sensitive and needs a precise control of the different steps and analytes of the reaction. In this article, we described the principle of the method and the characteristics of the main enzyme, the Taq polymerase. The concentration range of the analytes is reviewed to optimize the amplification of the nucleic acid sequence.

Reciprocal hybrid joints demonstrate successive V-J rearrangements on the same chromosome in the human TCR gamma locus.

Novel variable (V)--joining (J) gene rearrangements are described in the human T cell receptor gamma locus, in which, on the one hand, the V3 variable gene is joined to the heptamer--nonamer recombination signals of the J1 segment and, on the other hand, the J1 segment is joined to the V3 recombination signals through head-to-head fusion. These recombination products, or hybrid joints, have been originated through an inversion of 47 kb DNA. Interestingly the inverted DNA stretch contains a normal V9-J9 rearrangement. These findings are the first direct demonstration that successive rearrangements occur, on the same chromosome, in the human T cell receptor gamma locus, and suggest that the chronology of the joining events plays a role in the ontogeny of T cells and their differentiation in gamma/delta + and alpha/beta + lineages.

Genotypic analysis in large cell lymphomas expressing a restricted set of differentiation antigens.

Immunophenotyping and immunogenotyping were performed in a series of 8 large cell lymphomas exhibiting anaplastic or "histiocytic" morphology and displaying an uncertain phenotype due to a restricted number of differentiation antigens. 6 cases expressed the Ki-1 antigen. 4 cases expressed one or two B-cell markers and contained rearrangements of the immunoglobulin genes. One of them also exhibited a T-cell receptor (TCR) beta gene rearrangement. 3 cases expressed a single T-cell differentiation antigen. Among them, only 1 displayed both gamma and beta TCR gene rearrangement; 1 only contained a gamma TCR gene rearrangement and 1 completely lacked clonal rearrangements. The eight cases expressed an inconclusive immunophenotype due to an abundant population of reactive cells but showed an immunoglobulin gene rearrangement. In conclusion, 5 out of the 8 unusual lymphomas studied here could be characterized by immunogenotyping. This approach was, however, inconclusive in the 3 remaining cases, whose lineage and differentiation stage remain poorly defined.

Definition of the human immunoglobulin variable lambda (IGLV) gene subgroups.

Comparison of 60 human immunoglobulin variable lambda (IGLV) sequences allowed us to define seven subgroups designated V lambda I to V lambda VII. We demonstrate that all lambda proteins sequenced so far fall into the subgroups I, II, III and VI, and that the lambda regions previously assigned to subgroups IV and V belong, in fact, to subgroups III and II, respectively. Four sequences not belonging to any of the subgroups I, II, III and VI define the new subgroups IV, V and VII. Interestingly, these subgroups show a higher homology to rabbit or mouse V lambda genes than to the other human V lambda subgroups. By comparison of the proteins either with the sequences deduced from the germ-line genes or with the consensus sequences, the rate of amino acid changes due to somatic mutations or allelic variations was evaluated in several lambda proteins. Framework and complementarity-determining regions of the human IGLV genes and proteins were delineated. Alignment of the lambda sequences shows that functional V-J rearrangement occurs, with or without deletion of nucleotides encoding one or two amino acids at the 3' end of the V gene. Diversity of the third complementarity-determining region is due to somatic mutations and to flexible V-J junction, but there is no evidence of N-diversity in the human lambda locus.

Coordinated V gamma and V delta gene segment rearrangements in human T cell receptor gamma/delta+ lymphocytes.

Monoclonal antibodies (mAb) were used to characterize a panel (n = 46) of T cell receptor (TcR) gamma/delta+ T cell clones. Three of these antibodies have been described to react with specific variable region-encoded protein products and can therefore be used to detect functional gene rearrangements. The majority of peripheral blood-derived clones (43 out of 45) expressed the epitopes recognized by mAb BB3, encoded by the V delta 2 gene segment and mAb Ti gamma A, encoded by the V gamma 9 gene segment. These clones lacked the antigenic determinant recognized by mAb delta-TCS-1, encoded by the V delta 1 gene segment. The other two peripheral blood-derived clones and an ascites-derived clone were Ti gamma A-, BB3- and delta-TCS-1+. Biochemical analysis revealed that all Ti gamma A+, BB3+ T cell clones expressed the disulfide-linked form of the receptor. The two peripheral blood-derived delta-TCS-1+ T cell clones expressed the nondisulfide-linked form whereas the ascites-derived delta-TCS-1+ clone, AK119 expressed the disulfide-linked form of the TcR gamma/delta heterodimer. This indicates that V delta 1-encoded delta chains can be associated either with a C gamma 1- or a C gamma 2-encoded gamma chain. The preferential use of certain V gamma and V delta gene segments suggests the existence of a limited combinatorial diversity in TcR gamma/delta heterodimers, i.e. Ti gamma A+ (V gamma 9), BB3+ (V delta 2) and delta-TCS-1- disulfide-linked heterodimers and Ti gamma A-, BB3- and delta-TCS-1+ (V delta 1) disulfide- or non disulfide-linked forms.

Molecular mapping of the human T cell receptor gamma (TRG) genes and linkage of the variable and constant regions.

In the human T cell receptor gamma (TRG) locus, fourteen variable (TRGV) genes belonging to four subgroups have been identified upstream of two constant region (TRGC) genes. Three joining segments, JP1, JP and J1, have been localized upstream of TRGC1, and two others, JP2 and J2, upstream of TRGC2. In this report, we demonstrate that a unique Xho I fragment of 120 kilobases (kb) contains the fourteen TRGV genes and that the hybridization of that fragment in pulsed-field gel electrophoresis (PFGE) allows linkage of the variable region to the constant region locus. We also show that the variable and the constant regions are remarkably close to each other since the distance between V11, the most 3' V gamma gene, and JP1, the most 5' J gamma segment, is only 16 kb. With its 14 V gamma genes, spanning 100 kb, the two C gamma genes and 5 joining segments covering less than 40 kb and only 16 kb separating the most 3' V gene from the most 5' J segment, the human TRG locus spans 160 kb of genomic DNA and represents a particularly condensed locus compared to the other rearranging gene loci.