SEARCH · Search PubMed

Results for “Somatic mutation”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,207 records · Page 67Linked to original sources

PubMedDate not supplied

Rare somatic p53 mutation identified in breast cancer: a case report.

Most p53 mutations occur in the central part of the p53 gene that codes for the DNA-binding domain. Missense mutations are prevalent. However, 10-25% of all mutations occur outside exons 5-8 and include a prevalence of frameshift, nonsense and splice site mutations. Functional analysis of p53 transactivation ability in yeast (FASAY) was used to screen for p53 mutations in tumors and a mutant p53 protein retaining partial activity was identified. We characterized this somatic p53 mutation in codon 337: transition C-->T, changing codon CGC to TGC and causing substitution of arginine for cysteine in exon 10, which codes for the tetramerization domain of p53. We detected high accumulation of this mutant p53 protein within the tumor tissue and found that it cannot be immunoprecipitated by either a wild-type p53-specific antibody (PAb1620) or by a mutant p53-specific antibody (PAb240). We confirmed the somatic origin of the mutation by analysis of p53 status in peripheral leukocytes.

Alleles↗

PubMed2002

Mutations of the immunoglobulin heavy chain variable region gene in CD99-deficient BJAB cell line.

Hodgkin's disease (HD) is a lymphoid neoplasm characterized by a low frequency of malignant giant tumor cells, known as Hodgkin's and Reed-Sternberg (HRS) cells. Sequence analysis of the immunoglobulin heavy chain hypervariable region (IgH V) genes of HRS cells revealed multiple nucleotide substitutions, indicating somatic mutations, and suggested that HRS cells originate from germinal center B cells or their progeny. We previously reported that CD99-antisense transfected B cell lines led to the generation of cells with a HRS phenotype. Because it is considered that HRS cells in HD carry somatic mutations of the IgH genes, we assume that somatic mutation may take place in the IgH genes of HRS-like cells which do not express CD99. Here we report that CD99 downregulated BJAB cell line has several mutations in IgH V genes. The frequency of mutation was 5.2 x 10(-4) mut.bp(-1) out of total sequenced cell clones. On the contrary, control vector transfected BJAB cell line or CD99 downregulated IM9 cell line did not show any mutations on single strand conformational polymorphism (SSCP) and sequence analysis. We expect that the analysis of the mutation pattern of the CD99-deficient BJAB cell line might be the basis for the understanding of the molecular and cellular mechanism that regulate somatic mutation and B cell selection.

12E7 Antigen↗

PubMed1996

Structural elements controlling anti-DNA antibody affinity and their relationship to anti-phosphorylcholine activity.

The heavy chains of the anti-DNA autoantibody D42, derived from an autoimmune NZB/NZW F1 mouse, and the anti-phosphorylcholine (PC) Ab 6G6, obtained from an immunized CBA/J mouse, are both encoded by the same VH11 (S107) germ-line gene. We have combined VH CDR3 exchange, site-directed mutagenesis, transfection of mutant hybridoma cells, and equilibrium affinity measurements of the expressed Abs to analyze the contribution of germ line-encoded genetic elements and somatic mutations to DNA binding affinity as well as to test the possibility that an anti-PC Ab can be converted to an anti-DNA Ab by somatic mutation. Our results indicate that the major contribution to DNA binding affinity is provided by the nonmutated rearranged configuration of the autoantibody and depends on the particular H/L chain pairing and the structure of the VH CDR3 gene segment. Two heavy chain somatic mutations increased the DNA binding affinity of the D42 anti-DNA Ab by about 10-fold. One of these mutations abolished PC binding of the 6G6 Ab, but did not convert it to an anti-DNA. These results suggest that activation of autoreactive B cells bearing germ-line-encoded Ag receptors may be required to initiate the affinity maturation of an anti-DNA response, and that B cells responding by somatic mutation to external Ags, such as PC, may be unable to contribute significantly to the high affinity immune response that is typical of disease-related anti-DNA autoantibodies.

Amino Acid Sequence↗

PubMed2003

In vivo somatic microsatellite mutations identified in non-malignant human tissue.

Microsatellite instability (MSI) has been described in cancer cells and in vitro cell lines, and meiotic changes in repeat length have also been documented. We report the novel observation of somatic microsatellite mutation (SMM) in normal human somatic cells in vivo, detected while genotyping 5767 prenatal samples (4640 amniotic fluid samples and 1127 chorionic villus biopsies) as a diagnostic test for exclusion of trisomy 13, 18 or 21. Quantitative fluorescence-PCR using a multiplex of 12 primer pairs, for four loci on each of the three chromosomes, was followed by fragment analysis on a capillary-based genetic analyser. Forty-seven (4.2%) chorionic villus samples and six (0.1%) amniotic fluid samples showed allelic mosaicism, interpreted as SMM. In four cases, analysis of parental blood samples confirmed the presence of a de novo allele. SMM was detected at all but two of the 12 loci tested, and the incidence of mutation increased with repeat length. Detection of SMM in chorionic villus samples may imply less rigorous correction of replication errors in these extra-embryonic tissues, and is likely to have been facilitated by clonal expansion in the small samples of tissue tested. The presence of the same phenomenon in six amniotic fluid samples would imply that in these pregnancies, the instability event had occurred early in embryogenesis. The results suggest that defective proof reading during DNA replication may be more common in non-malignant human somatic tissue than previously recognised.

Alleles↗

PubMedDate not supplied

Expression of activation-induced cytidine deaminase decreases throughout the life.

Activation-induced cytidine deaminase (AID) is an RNA editing enzyme, which contributes to generation of new functional genes from a restricted number of genes of plant and animal genome. This enzyme was involved in the process of somatic mutation and class switching in vertebrate. Since the rate of somatic mutations is variable throughout ontogeny, we have studied the transcription of AID in 3 to 24 month-old Balb/c mice. Our results demonstrate a significant decrease of the transcription of the AID gene with aging. The decreased AID activity is not related to variation of phenotypic and functional properties of B cells throughout the life. This observation can explain the low rate of somatic mutation in aged animals.

Aging↗

PubMed1991

Chemical induction of somatic gene mutations and chromosomal aberrations in lung fibroblasts of rats.

Rats can be used to detect both somatic gene mutations and chromosomal aberrations induced in vivo. The technique adapted from Chinese hamsters for the isolation and analysis of lung fibroblasts confirm the surprising results obtained in hamsters; namely, methyl methanesulphonate induces many micronuclei but no significant increase in gene mutations. In contrast ethylnitrosourea induces both micronuclei and gene mutations.

Animals↗

PubMed1999

The first dose of a Haemophilus influenzae type b conjugate vaccine reactivates memory B cells: evidence for extensive clonal selection, intraclonal affinity maturation, and multiple isotype switches to IgA2.

The Ab response of a healthy adult to the first dose of a Haemophilus influenzae type b capsular polysaccharide (HibCP) conjugate vaccine was studied at the level of Ig gene usage by circulating Ab-secreting cells. Forty-one IgA and 17 IgG mRNA sequences were obtained. The major part of the response was confined to IgA Ab-secreting cells, and 72% of the IgA sequences were derived from the progeny of a single rearranged B cell. These sequences could be arranged in a genealogical tree showing multiple somatic mutations and at least two intraclonal isotype switches to IgA2. Fourteen somatic mutations were shared by this clonal progeny, indicating that extreme clonal selection had occurred early in the clonal development. Taking into account the frequency of somatic mutations and the clone size, it was evident that the responding cell population must have originated from a mutated, highly selected, and expanded population of cells existing before vaccination, i.e., memory B cells. The dominating heavy and light chains of the response were combined in a Fab that bound HibCP. It was shown that the shared heavy and light chain mutations increased the affinity for HibCP considerably, indicating that the clonal selection had been driven by affinity. Pre-existing memory cells in unvaccinated adults may explain several features of Ab responses to polysaccharide vaccines and may play a role in acquiring the ability to respond to pure polysaccharides during infancy.

Adult↗

PubMed2003

The newly detected mutations in the RET proto-oncogene in exon 16 as a cause of sporadic medullary thyroid carcinoma.

Medullary thyroid carcinoma (MTC) occurs as a sporadic form or, less frequently, as an autosomal dominant inherited familial disorder. Germline mutations in the RET proto-oncogene in exons 10, 11, 13, 14, 15, and 16 are found in most of the familial cases (nearly 95%). Somatic mutations in sporadic MTC are detected in 23-69% of patients. The most frequent somatic mutation is located in exon 16 at codon 918, and only a small percentage of mutations are found in exons 10, 11, 13, and 15. We have searched for somatic mutations in Czech MTC patients using direct sequencing. We report here two new somatic missense mutations in exon 16 of the RET proto-oncogene associated with the sporadic MTC detected in two Czech men. A homozygous mutation at codon 922 TCC(Ser)-->CCC(Pro) as a result of loss of heterozygosity was revealed in the first patient. In the second one a heterozygous mutation at codon 930 ACG(Thr)-->ATG(Met) was found.

Carcinoma, Medullary↗

PubMed1996

Why do stem cells exist?

Self-renewing tissues have a differentiation hierarchy such that the stem cells are the only permanent residents of the tissue, and it is in these cells that most cancerous mutations arise. The progeny of the stem cells either remain stem cells or enter a transient proliferating cell population that differentiates to produce the functional cells of the tissue. The reason that this differentiation hierarchy exists has not been established. We show here that alternative hierarchies, in which there would be no stem cells, are feasible and biologically plausible. We show that current evidence from somatic mutation frequencies at both transgenic and endogenous loci implicates cell division in the origin of most somatic mutations. We suggest, therefore, that the existence of stem cells is an evolutionary consequence of a selective pressure to avoid cancer by reducing the number of somatic mutations. The stem cell hierarchy reduces the number of cell divisions of those cells that reside permanently in the tissue, which reduces the number of somatic mutations and thus minimizes the cancer rate. In the small intestine, the existence of stem cells reduces the mutant frequency in the stem cells by about one order of magnitude. Since two or more mutations are required to transform a cell, the protective effect may be 100-fold or more. Similar factors may be expected in other tissues.

Age Factors↗

PubMed1996

Distinction between sporadic and hereditary medullary thyroid carcinoma (MTC) by mutation analysis of the RET proto-oncogene. "Study Group Multiple Endocrine Neoplasia Austria (SMENA)".

Germline and somatic mutations of the RET proto-oncogene are important pathogenetic factors in hereditary and sporadic forms of medullary thyroid carcinoma (MTC). We have therefore analysed exons 10, 11, 13, 14 and 16 of this gene in 85 individuals from 16 Austrian families who, according to clinical criteria, were at risk of suffering from hereditary forms of MTC. We found mutations (codons 620,634 and 804) in the germline of 3 families with familial medullary thyroid carcinoma (FMTC), of 5 with multiple endocrine neoplasia type 2A (MEN 2A; codon 634) and of 2 with multiple endocrine neoplasia type 2B (MEN 2B; codon 918). The codon 804 mutation in one FMTC family led to the substitution of Val (GTG) for Met (ATG) and has not been reported previously. Within these 10 families, 32 carriers and 32 non-carriers were identified. Somatic mutations in the tumors of 3 other families suggested a sporadic origin of the neoplasms. In the remaining 3 families, no mutations were identified. Fifty-nine individuals with an apparently sporadic MTC lacked germline mutations in the RET gene, whereas 7 of 24 available tumors (29%) contained a somatic mutation in codon 918. Our findings provide further evidence that molecular genetic evaluation of hereditary and sporadic forms of MTC is a necessary prerequisite for counselling and management of patients and their families.

Adult↗

PubMed1997

Germinal center development.

Using a set of surface markers including IgD and CD38, human tonsillar B cells were classified into discrete subpopulations. Molecular and functional analysis allowed us to identify: i) two sets of naive B cells (Bm1 and Bm2); ii) germinal center founder cells (Bm2'); iii) an obscure population of germinal center B cells, displaying a high load of somatic mutations in IgV genes, C mu to C delta switch and preferential Ig lambda light chain usage: these cells may represent the precursors of normal and malignant IgD-secreting plasma cells; iv) the centroblasts (Bm3) in which somatic mutation machinery is activated; v) the centrocytes (Bm4) in which isotype switch occurs; vi) the memory B cells. The characterization of these subpopulations showed that: i) programmed cell death is set before somatic mutations, possibly providing an efficient way for affinity maturation; ii) only high affinity centrocytes are allowed to switch isotype; iii) CD40-ligation inhibits plasmacytic differentiation of mature B lymphocytes; iv) memory B cells preferentially differentiate into plasma cells; v) IgD isotype switch occurs in normal B cells; vi) receptor editing may be induced by somatic mutations in germinal centers. We also characterized two types of antigen-presenting cells in germinal centers: follicular dendritic cells that select high affinity B cells, and a new subset of germinal center dendritic cells that activate germinal center T cells.

Animals↗

PubMed1998

V(H) gene analysis of Burkitt's lymphoma in children from north-western Iran.

Cases of Burkitt's lymphoma (BL) from north-western Iran were investigated for the usage and somatic mutational pattern of their immunoglobulin variable region genes. Potentially functional V(H) genes were amplified from 6/12 of the tumour masses and all of these were derived from the V(H)3 family, with 4/6 being derived from the most commonly used V(H)3 family member, V3-23. All of the tumour sequences were mutated from their germline counterparts, to varying degrees, with a mean level of 5.8%, indicating that the cell of origin had encountered the germinal centre. Intraclonal sequence heterogeneity was also evident in 4/6 of the lymphomas, showing that the tumour cells had undergone further somatic mutation following neoplastic transformation. Analysis of the five potentially functional mutated V(H) sequences showed a significant clustering of replacement mutations in the complementarity-determining region 2, consistent with a role for antigen in selection of tumour cell sequences. The pattern of extensive somatic mutation, and intraclonal variation, in these mainly EBV+ve tumours, was similar to that previously reported in V(H) sequences of EBV+ve endemic BL (eBL) and EBV-ve sporadic BL (sBL), with the mean level of somatic mutation lying between those reported for eBL (7.7%) and sBL (4.0%). However, VH gene bias and the distribution of mutations in the Iranian cases showed features which differed from those reported for endemic or sporadic BL.

Amino Acid Sequence↗

PubMed1999

Characteristics of sequences around individual nucleotide substitutions in IgVH genes suggest different GC and AT mutators.

Somatic hypermutation affects Ig genes during T-dependent B cell responses and is characterized by a high frequency of single base substitutions. Hypermutation is not a completely random process; a study of mutations in different systems has revealed the presence of sequence motifs that target mutation. In a recent analysis of the sequences surrounding individual mutated bases in out-of-frame human IgVH genes, we found that the target motifs around mutated G's and C's are reverse complements of each other. This finding suggests that hypermutation acts on both strands of DNA, which contradicts evidence of a strand-dependent mechanism as suggested by an observed bias in A and T mutations and the involvement of transcriptional machinery. We have now extended our database of out-of-frame genes and determined the sequence motifs flanking mutated A and T nucleotides. In addition, we have analyzed the flanking sequences for different types of nucleotide substitutions separately. Our results confirm the relationship between the motifs for G and C mutations and show that the motifs surrounding mutated A's and T's are weaker and do not have the same relationship. Taken together with our observation of A/T strand bias in out-of-frame genes, this observation suggests that there is a semitargeted G/C mutator that is strand-independent and a separate A/T mutator that is strand-dependent and is less reliant on the local target sequence.

Adenine↗

PubMed1999

Differences in allelic distribution of two polymorphisms in the VHL-associated gene CUL2 in pheochromocytoma patients without somatic CUL2 mutations.

Although the two major familial forms of pheochromocytomas, multiple endocrine neoplasia type 2 and von-Hippel-Lindau disease (VHL), have been associated with mutations of the RET and VHL genes, respectively, the molecular pathogenesis of sporadic pheochromocytomas is largely unknown. Recently, a putative tumor suppressor gene has been identified, CUL2, whose product has been shown to interact with the VHL tumor suppressor. To examine whether CUL2 plays a role in pheochromocytoma pathogenesis, we analyzed a series of 26 distinct tumor samples for mutations in the whole coding region of this gene. There were no somatic pathogenic mutations in CUL2, except for 1 sporadic tumor that had a hemizygous gene deletion. We also found 3 novel polymorphisms in the gene. One of these variants, IVS5-6C/T, as well as another previously described one, c.2057G/A, were overrepresented among the pheochromocytoma patients compared to that in a control population (P < 0.005 and P < 0.01, respectively). Although our findings suggest that CUL2 does not play a major role in the pathogenesis of pheochromocytomas, it is still unknown whether epigenetic mechanisms are involved in its inactivation in VHL-associated tumors. Furthermore, the potential role for the overrepresented alleles in the pheochromocytoma group requires further investigation.

Adolescent↗

PubMed1987

Activation of memory and virgin B cell clones in hyperimmune animals.

To study the long-term memory response, BALB/c mice were allowed to rest for over a year after a secondary immunization with the hapten 2-phenyl-oxazol-5-one (phOx). For the tertiary immunization two different protocols were used. In one protocol mice were injected i.v. and 3 days later spleen cells were fused to a nonproducing hybridoma line. PhOx-specific hybridomas were established and the sequence of the heavy and light chain mRNA was determined. This tertiary response resembled the diversity pattern of the secondary response with a further increase both in somatic mutations and in the average dissociation constant. The high number of somatic mutations demonstrates the persistence of memory B cell clones over a long time period. In the second protocol mice were boosted with an i.p. injection of alumprecipitated antigen phOx and 7 or 14 days later spleen cells were fused. Sequence analysis of heavy and light chain mRNA showed that these tertiary response antibody molecules had surprisingly few somatic mutations, indicating an activation of virgin B cell clones in these hyperimmunized animals. The maturation of these newly stimulated B cell clones seems to follow somewhat similar rules to those found for the primary response. It appears therefore that the two immunization protocols reflect the response of memory and virgin B cells, respectively.

Amino Acid Sequence↗

PubMed1989

Patterns of mutations and selection in antibodies to the phosphocholine-specific determinant in Proteus morganii.

The contribution of somatic mutation to the generation of an antibody response was investigated by using the phosphocholine (PC) determinant in the bacterium Proteus morganii as the model Ag. The response to this determinant is restricted to a single VH/VL pair and apparently is derived from only one or two precursors per mouse. In this study we examined hybridoma antibodies from nine individual mice which produced representatives of 12 different clones. We found that all antibodies reactive with the PC Ag of P. morganii contained somatic mutations; the number ranged from 2 to 20. Two clusters of mutations were observed, one in complementarity-determining residue (CDR) 2 and the other in CDR 3 of VH. Examination of a three-dimensional model of M603, an antibody with the same V region composition as the anti-PC antibodies under study, showed that these clusters occupied an area of the binding site which presumably interacts with carrier elements of the PC epitope in P. morganii. A high incidence of recurring mutations were found in both clusters, and one of these was invariant, leading to an Asn for Asp substitution at 95. Ag binding studies with these antibodies and an additional one, which was unmutated except for the invariant substitution at 95, showed that: 1) antibodies having only the 95Asn mutation failed to bind the PC Ag of P. morganii, 2) addition of a second recurring mutation, at 52a (CDR 2), was sufficient to create strong binding to the P. morganii Ag, and 3) accumulation of mutations was directly correlated with increased binding activity for Ag. These results show that somatic mutations play a critical, if not essential, role in generating specificity for this PC Ag, and that Ag, and most likely a carrier element of the epitope, is a primary force in the continued selection and expansion of Ag-reactive B cells.

Amino Acid Sequence↗

PubMed1995

New type of t(14;18) in a non-Hodgkin's lymphoma provides insight in molecular events in early B-cell differentiation.

In this report a follicular non-Hodgkin's lymphoma (NHL) carrying an unusual t(14;18) is described. This translocation most likely occurred during the VH to D-JH rearrangement process of the IgH locus. From the data combined with data from the literature we conclude that the chance for development of a t(14;18) decreases during progression of the immunoglobulin rearrangement process in the pre-B-cell ontogeny. This is probably due to decreased accessibility of the bcl-2 locus by reduced transcription. We analysed the somatic mutation pattern of the productively rearranged IgH gene. Like other follicular lymphomas, somatic mutations were present in this gene and indicated positive selection, probably for an antigen. We found no evidence for ongoing induction of somatic mutations during lymphoma development. We conclude that bcl-2 gene deregulation, but not the precise moment at which this occurs during the pre-B-cell stage, influences the development of follicular NHL.

Adult↗

PubMed1999

Molecular analysis of single B cells from T-cell-rich B-cell lymphoma shows the derivation of the tumor cells from mutating germinal center B cells and exemplifies means by which immunoglobulin genes are modified in germinal center B cells.

T-cell-rich B-cell lymphoma (TCRBCL) belongs to the group of diffuse large cell lymphomas (DLL). It is characterized by a small number of tumor B cells among a major population of nonmalignant polyclonal T cells. To identify the developmental stage of the tumor progenitor cells, we micromanipulated the putative neoplastic large CD20(+) cells from TCRBCLs and amplified and sequenced immunoglobulin (Ig) V gene rearrangements from individual cells. In six cases, clonal Ig heavy, as well as light chain, gene rearrangements were amplified from the isolated B cells. All six cases harbored somatically mutated V gene rearrangements with an average mutation frequency of 15.5% for heavy (VH) and 5.9% for light (VL) chains and intraclonal diversity based on somatic mutation. These findings identify germinal center (GC) B cells as the precursors of the transformed B cells in TCRBCL. The study also exemplifies various means how Ig gene rearrangements can be modified by GC B cells or their malignant counterparts in TCRBCL: In one case, the tumor precursor may have switched from kappa to lambda light chain expression after acquiring a crippling mutation within the initially functional kappa light chain gene. In another case, the tumor cells harbor two in-frame VH gene rearrangements, one of which was rendered nonfunctional by somatic mutation. Either the tumor cell precursor entered the GC with two potentially functional in-frame rearrangements or the second VHDHJH rearrangement occurred in the GC after the initial in-frame rearrangement was inactivated by somatic mutation. Finally, in each of the six cases, at least one cell contained two (or more) copies of a clonal Ig gene rearrangement with sequence variations between these copies. The presence of sequence variants for V region genes within single B cells has so far not been observed in any other normal or transformed B lymphocyte. Fluorescence in situ hybridization (FISH) points to a generalized polyploidy of the tumor cells.

Adult↗