Germline Rearrangements Research Articles

Molecular Analysis of Immunoglobulin Variable Genes in HIV-Related Non-Hodgkin Lymphoma: Implications for Disease Pathogenesis and Histogenesis.

Molecular analysis of immunoglobulin variable region (IGV) genes can provide insights into the histogenesis and clonal history of B-cell NHL. We investigated 67 HIV-related NHL (HIV-NHL), including 30 HIV-diffuse large B cell lymphomas (DLBCL), 21 HIV-Burkitt lymphoma (BL), 6 HIV-primary effusion lymphomas (PEL) and 10 HIV-plasmablastic lymphomas (PBL) for usage, mutation frequency and intratumoral heterogeneity of clonal IGV rearrangements as well as mutation profile and CDR3 structure of IGHV, IGKV and IGLV genes. Results were compared to 200 IGV rearrangements from aggressive lymphomas of immunocompetent hosts and to the normal B-cell repertoire. We identified a total of 65 IGHV and 56 IGV light chain rearrangements in HIV-NHL. A functional IGHV rearrangement was found in 60/67 (90%) cases, a functional IGKV chain rearrangement in 17/38 (44.7%) cases and a functional IGLV rearrangement in 21/38 cases (55.3%). Fifty-three of 60 HIV-NHL (88.3%) showed somatic hypermutation in IGHV and/or IGV light chain genes. The average mutation frequency was 9.42% (median 7.50%, range 2.04%–23.3%) for IGHV genes and 5.42% (median 4.20%, range 2.01%–12.5%) for IGV light chain genes. IGV germline rearrangements selectively associated with HIV-PBL (p<0.001). Among mutated cases, average mutation frequencies did not differ among HIV-NHL groups. HIV-NHL showed a significant overrepresentation of the IGHV4 family (28/60; 46.6%) and a significant underrepresentation of IGHV3 family (18/60, 30.0%) compared to aggressive lymphomas of immunocompetent hosts (p<0.05) and to normal B-cells (p<0.05). IGHV4–34 was the IGHV gene most frequently rearranged (17/60; 28.3%) and was overrepresented in HIV-NHL versus aggressive lymphoma of immunocompetent hosts (17%; p<0.03) and normal B-cells (4%; p<0.001). IGHV4-34 expressing cells preferentially associated with lambda chain rearrangements (70%). The IGKV4-1 gene was the IGKV segment most frequently rearranged (6/17; 35.3%) and its usage was biased in HIV-NHL compared to normal B-cells (5.30; p<0.001). The single IGLV gene most frequently encountered was IGLV1-44 (6/17; 35,3%). Distribution of replacement and silent mutations in IGHV sequences showed tendency to conserve FR sequences and maintain antigen binding in 34/52 (65.4%) cases. A higher than expected number of CDR replacement mutations, suggesting selection for high affinity antigen binding, occurred in 17/52 (32.7%) cases. Analysis of intraclonal heterogeneity showed the presence of ongoing mutations in only 1 HIV-BL and 2 HIV-DLBCL. Implications of these data are multifold. First, most HIV-NHL derive from B-cells persistently subjected to GC reaction, suggesting a potential role for antigen stimulation in the pathogenesis of these lymphomas. This hypothesis is supported by the finding of antigen binding preservation in the majority of HIV-NHL and selection for high affinity antigen binding in a fraction of cases. Second, the preferential usage of IGHV4-34 and IGKV4-1 genes in a fraction of HIV-NHL may suggest a role for stimulation of pre-neoplastic B-cells with polyreactive and/or autoreactive antigens. Finally, at variance with NHL of immucompetent hosts, the presence of intraclonal heterogeneity is a rare finding in HIV-NHL, suggesting a derivation from B-cells that have concluded the GC-reaction.

Screening for germline rearrangements in BRCA1 and BRCA2in Norwegian families with breast or breast/ovarian cancer

Standard PCR-based mutation detection strategies performed on the BRCA1 and BRCA2 genes of breast and ovarian cancer families are mostly aimed at identifying changes in the coding sequences and in the donor-acceptor splice sites. Hence, mutations in the promoter and the untranslated regions, and large rearrangements, are not detected by these methods. To assess the importance of BRCA1 and BRCA2 alterations that are neglected by standard screening methods, we monitored germline rearrangements in these genes using 'multiplex ligation-dependent probe amplification' technology [1]. One hundred and seventy-nine Norwegian breast and ovarian cancer families were screened for rearrangements in BRCA1 while 97 families were tested for aberrations in BRCA2. Whereas no rearrangements were detected in BRCA2, four distinct deletions were found in BRCA1. Those deletions originating by Alu-mediated homologous recombination include: exons 1–13, exons 3–16, exons 8–13 and exon 23, respectively. The large 23.8 kb deletion excluding exons 8–13 in BRCA1 has been found both in the French and British breast cancer population [2-4]. The deletions of exons 1–13, exons 3–16 and exon 23 have not been previously reported.

Consensus JH Gene Probes with Conjugated 3′-Minor Groove Binder for Monitoring Minimal Residual Disease in Acute Lymphoblastic Leukemia

Several approaches for the detection of minimal residual disease (MRD) in childhood acute lymphoblastic leukemia (ALL) have shown the importance of determining the level of MRD precisely. In the present study, we tested a new real-time quantitative polymerase chain reaction (RQ-PCR) strategy with minor groove binder (MGB) technology for immunoglobulin heavy chain gene rearrangements by positioning a MGB probe at the germline JH segments and one of the primers at the downstream introns in combination with an allele-specific oligonucleotide (ASO) primer complementary to the VH-DH or DH-JH junctional region. A MGB probe forms extremely stable duplexes with single-stranded DNA targets, allowing the use of shorter probes for hybridization-based assays. Therefore, it shows positional flexibility. We have designed two novel consensus MGB JH germline probes for analyzing all of the germline rearrangements registered in the V BASE database, and demonstrated that the MRD was detectable with the probes in 17 cases of childhood ALL. The actual copy number for the targets and dynamic changes before and after treatment were almost identical between the JH MGB probe and conventional non-MGB probes in each patient. MGB technology will undoubtedly contribute to MRD-PCR studies of childhood ALL.

Mutational Mechanisms of Williams-Beuren Syndrome Deletions

Williams-Beuren syndrome (WBS) is a segmental aneusomy syndrome that results from a heterozygous deletion of contiguous genes at 7q11.23. Three large region-specific low-copy repeat elements (LCRs), composed of different blocks (A, B, and C), flank the WBS deletion interval and are thought to predispose to misalignment and unequal crossing-over, causing the deletions. In this study, we have determined the exact deletion size and LCR copy number in 74 patients with WBS, as well as precisely defined deletion breakpoints in 30 of them, using LCR-specific nucleotide differences. Most patients (95%) exhibit a 1.55-Mb deletion caused by recombination between centromeric and medial block B copies, which share approximately 99.6% sequence identity along 105-143 kb. In these cases, deletion breakpoints were mapped at several sites within the recombinant block B, with a cluster (>27%) occurring at a 12 kb region within the GTF2I/GTF2IP1 gene. Almost one-third (28%) of the transmitting progenitors were found to be heterozygous for an inversion between centromeric and telomeric LCRs. All deletion breakpoints in the patients with the inversion occurred in the distal 38-kb block B region only present in the telomeric and medial copies. Finally, only four patients (5%) displayed a larger deletion ( approximately 1.84 Mb) caused by recombination between centromeric and medial block A copies. We propose models for the specific pairing and precise aberrant recombination leading to each of the different germline rearrangements that occur in this region, including inversions and deletions associated with WBS. Chromosomal instability at 7q11.23 is directly related to the genomic structure of the region.

Screening for large rearrangements of the BRCA1 gene in German breast or ovarian cancer families using semi-quantitative multiplex PCR method.

Since the identification of the breast and ovarian cancer susceptibility genes BRCA1 and BRCA2, a large number of different germline mutations in both genes have been found by conventional PCR-based mutation detection methods. Complex germline rearrangements such as those reported in the BRCA1 gene are often not detectable by these standard diagnostic techniques. To detect large deletions or duplications encompassing one or more exons of the BRCA1 gene and in order to estimate the frequency of BRCA1 rearrangements in German breast or ovarian cancer families, a semi-quantitative multiplex PCR method was developed and applied to DNA samples of patients from families negatively tested for disease causing mutations in the BRCA1 and BRCA2 coding regions by direct sequencing. Out of 59 families analysed, one family was found to carry a rearrangement in the BRCA1 gene (duplication of exon 13). The results indicate that the semi-quantitative multiplex PCR method is useful for the detection of large rearrangements in the BRCA1 gene and therefore represents an additional valuable tool for mutation analysis of BRCA1 and BRCA2.

Screening for TP53 rearrangements in families with the Li-Fraumeni syndrome reveals a complete deletion of the TP53 gene.

The absence of detectable germline TP53 mutations in a fraction of families with Li-Fraumeni syndrome (LFS) has suggested the involvement of other genes, but this hypothesis remains controversial. The density of Alu repeats within the TP53 gene led us to search genomic rearrangements of TP53 in families without detectable TP53 mutation. To this aim, we adapted the quantitative multiplex PCR of short fluorescent fragments (QMPSF) method to the analysis of the 11 exons of TP53. We analysed 98 families, either fulfilling (six families) or partially meeting (92 families) the criteria for LFS, and in which classical methods had failed to reveal TP53 alterations. We identified, in a large family fulfilling the criteria for LFS, a complete heterozygous deletion of TP53. Additional QMPSF analyses indicated that this deletion, which partially removed the centromeric FLJ10385 locus, covered approximately 45 kb. This deletion was shown to result from a complex rearrangement involving two distinct Alu-mediated recombinations. We conclude that TP53 germline rearrangements occur as rare events, but must be considered in LFS families without detectable point TP53 mutation.

Multigenerational familial medullary thyroid cancer (FMTC): evidence for FMTC phenocopies and association with papillary thyroid cancer

Occurrence in a familial setting is well established for medullary thyroid carcinoma (MTC) and has been more recently reported for papillary thyroid cancer (PTC). Germline mutations or rearrangements of the RET proto-oncogene are the genetic background of the majority of hereditary MTCs and of about 25-40% of PTCs. A large multigenerational familial medullary thyroid cancer (FMTC) family, comprised of four generations and a total of 60 subjects, has been fully evaluated. Studies on germline RET mutations and polymorphisms, on somatic RET activation and on haplotyping with RET-linked markers, were performed. RET mutational analysis revealed a rare missense point mutation in exon 15 of RET (A891S), associated with FMTC. Haplotype analysis showed a co-segregation between the allelic variant 5 of D10S578 marker (which is tightly linked to the RET locus) and the RET mutation. Two patients, from different branches of the family, did not harbour the point mutation A891S despite histological confirmation of MTC. In these cases, haplotype analysis excluded the involvement of the RET gene itself in the pathogenesis of the MTC. In three patients, the coexistence, in different foci, of medullary and papillary thyroid cancer was documented. The genetic studies did not show ret/PTC rearrangements. The microsatellite analysis excluded co-segregation of RET locus with the MTC/PTC phenotype. We report a full clinical and molecular analysis of a large FMTC kindred with an uncommon RET mutation. In two family members, phenotype and genotype were not concordant, representing the first evidence of FMTC phenocopies. Furthermore, the association of familial forms of medullary and papillary thyroid cancers has been found in 30% of patients undergoing thyroidectomy for MTC. In these situations, genetic analyses excluded the possible germline involvement of RET. Though FMTC phenocopies are likely to represent an exceptional finding, such a possibility should be taken into account in the genetic counselling for MEN 2 syndromes.

NF1 microdeletion breakpoints are clustered at flanking repetitive sequences.

Neurofibromatosis type 1 patients with a submicroscopic deletion spanning the NF1 tumor suppressor gene are remarkable for an early age at onset of cutaneous neurofibromas, suggesting the deletion of an additional locus that potentiates neurofibromagenesis. Construction of a 3.5 Mb BAC/PAC/YAC contig at chromosome 17q11.2 and analysis of somatic cell hybrids from microdeletion patients showed that 14 of 17 cases had deletions of 1.5 Mb in length. The deletions encompassed the entire 350 kb NF1 gene, three additional genes, one pseudogene and 16 expressed sequence tags (ESTs). In these cases, both proximal and distal breakpoints mapped at chromosomal regions of high identity, termed NF1REPs. These REPs, or clusters of paralogous loci, are 15-100 kb and harbor at least four ESTs and an expressed SH3GL pseudogene. The remaining three patients had at least one breakpoint outside an NF1REP element; one had a smaller deletion thereby narrowing the critical region harboring the putative locus that exacerbates neurofibroma development to 1 Mb. These data show that the likely mechanism of NF1 microdeletion is homologous recombination between NF1REPs on sister chromatids. NF1 microdeletion is the first REP-mediated rearrangement identified that results in loss of a tumor suppressor gene. Therefore, in addition to the germline rearrangements reported here, NF1REP-mediated somatic recombination could be an important mechanism for the loss of heterozygosity at NF1 in tumors of NF1 patients.

Application of representational microarrays to genetic analysis of primary tumours

We have explored using DNA microarrays for measuring gene copy number in cancer biopsies. The high nucleotide complexity of the human genome makes hybridization analysis of the entire genome problematic. Therefore, we have used the approach of making complexity-reducing representations1. Accordingly, the printed probes themselves are derived from simplified representations of the human genome, and are hybridized to representations of tumour and normal DNA. Data from pilot experiments indicate that this method can be used to detect amplifications and deletions in cancer specimens. The theoretical resolving power of these microarrays is on the order of 100 kb with a 30,000-member array, but higher resolving power is not excluded. In contrast to expression array analysis, only minute amounts of starting material (5,000 nuclei) are sufficient for sample preparation. Also, the starting material for analysis is DNA not RNA, which is easier to obtain from surgical specimens. The two methods should work best in concert; that is, combining copy-number analysis with expression analysis for the same tumours, enabling the user to more readily identify the primary defects in cancer cells. Presently we have produced a 2,000-member array that contains fragments of known sequence and mapping location as well as fragments cloned randomly from a representation. The copy number of many of these probes is known in respect to several tumours we have characterized by more conventional methods. Representations from these tumour pairs have been hybridized to these arrays and analysed. By querying the hybridization results we have identified the fragments known to be effected in these tumours. We are now confirming the results of the hybridizations by more accepted techniques. Several obstacles remain to creating a high-density genomic chip, including the assembly of a collection of probes, mapping them and developing the software tools to seamlessly analyse the data. Genomic chips have uses beyond cancer, including detection of polymorphisms in individuals and de novo germline rearrangements.

Multiple sclerosis: a polygenic disease involving epistatic interactions, germline rearrangements and environmental effects.

Several regions of the human genome are associated with susceptibility to multiple sclerosis (MS). We review studies of linkage of MS to germline genes using microsatellites. A modest effect on susceptibility was seen with markers in the vicinity of 6p21 (HLA) and 17q22. The influence of epistatic interactions between these genes is considered. The impact of genetic rearrangements of certain germline genes on susceptibility to MS is described. Analysis of TCR gene rearrangements has established some of the target antigens of the immune response in MS. Environmental influences on MS are described with particular attention given to how microbes might trigger demyelinating disease.

Hippel-Lindau syndrome and sporadic renal cell carcinomas. Pathogenesis, morphologic spectrum and molecular genetics

von Hippel-Lindau (VHL) disease is an autosomal dominant heritable disease that often occurs in association with various benign and malignant tumours. Clinically the disease is classified as VHL 1 (without phaeochromocytoma) and VHL 2 (with phaeochromocytoma). Genetically, VHL is caused by germline mutations in the VHL tumour suppressor gene. More than 100 germline mutations and rearrangements have been identified, but the biological function of a hypothetical VHL protein is not yet known. Genotype-phenotype correlations should aid in the understanding of this biological role. All VHL manifestations subsequently develop to VHL mutations, but some mutations may act in a tissue-specific manner. Whereas missense mutations cause tumour suppression to fail in adrenal cells, more severe structural mutations are usually necessary for tumour development in renal cells. As predicted by the tumour suppressor theory, the VHL gene also plays a critical part in the pathogenesis of sporadic non-VHL-associated tumours. In a large number of sporadic renal clear cell carcinomas, mutations and hypermethylation cause inactivation of the VHL gene. Together with allelic 3p loss, these constitute rate-limiting events in renal tumourigenesis. Insights into the molecular basis of phenotypic variability in VHL disease and the confirmation of the tumour-suppressor criteria in VHL and non-VHL sporadic tumours indicate an important role of the VHL gene in the development of these tumours.

Expression and genomic configuration of GM-CSF, IL-3, M-CSF receptor (C-FMS), early growth response gene-1 (EGR-1) and M-CSF genes in primary myelodysplastic syndromes.

Peripheral blood mononuclear cells from seventeen patients with primary myelodysplastic syndromes (MDS) in advanced stage were enriched for blasts and tested for (1) karyotype, (2) genomic configuration and (3) expression of IL-3, GM-CSF, FMS and EGR-1 genes which are all located on the long arm of chromosome 5. The expression of the M-CSF gene, that has been recently reassigned to the short arm of chromosome 1 (lp), was also investigated. Aims of the study were to (1) assess the potential role of the expression of these genes in the maintenance and expansion of the neoplastic clones and (2) search for constitutional losses or rearrangements of one allele followed by a deletion of the second allele of the same genes in the leukemic cells. The latter issue was investigated by comparing, in 8 cases, constitutive DNA from skin fibroblasts with leukemic DNA. Eleven of the 17 patients had abnormal karyotypes. The M-CSF gene was expressed in 6 cases and the FMS and the EGR-1 genes were expressed in 2 of the latter cases. An autocrine mechanism of growth could be hypothesized only for the 2 patients whose cells expressed both the M-CSF and FMS genes. No germline changes or rearrangements were observed in any of the genes studied. Thus, deregulation of genes encoding for certain hemopoietic growth factors or receptors does not seem to represent a major mechanism of MDS progression.

Mapping the Von Hippel-Lindau disease tumour suppressor gene: identification of germline deletions by pulsed field gel electrophoresis.

Von Hippel-Lindau (VHL) disease is a dominantly inherited familial cancer syndrome in which affected individuals have a greatly increased predisposition to the development of haemangioblastomas of the central nervous system and retina, renal cell carcinoma and phaeochromocytoma. The VHL gene has been mapped to chromosome 3p25-p26 by genetic linkage studies and we have previously demonstrated that the VHL gene is tightly linked to the D3S601 locus (Zmax = 18.86 at theta = 0.0) suggesting that D3S601 maps close to the VHL disease gene. We have constructed a long range physical map around D3S601 and screened 91 VHL patients from 80 kindreds for germline rearrangements using pulsed field gel electrophoresis. Two patients showed abnormal fragments in Mlul digested DNA probed with D3S601. Further analysis was consistent with both patients having germline deletions (approximately 120 kb and 50 kb) telomeric to D3S601. These results have (i) established the position of the VHL disease gene with respect to D3S601, (ii) refined the localisation of the VHL disease gene to a small region (approximately 50 kb) of chromosome 3p25-p26 and (iii) excluded the plasma membrane Ca(+)+-transporting ATPase isoform 2 (PMCA-2) gene as a candidate gene for VHL disease.