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PubMed1986

The combined effect of DBE and X-rays on the induction of somatic mutations in Tradescantia.

The induction of somatic mutations in the stamen hair cells of Tradescantia KU 9 has been used to investigate the effects of combined exposure to 1,2-dibromoethane (DBE) and X-rays. At low radiation doses a synergistic interaction has been found between the two agents for both DBE exposure followed by acute X-rays and chronic simultaneous exposures. The synergism is discussed in terms of an interaction of single strand lesions in the DNA. It is concluded that although this type of interaction should not be too important for radiological protection, it could be of significance in evaluating the effects of chemicals at low exposure rates.

Dose-Response Relationship, Drug↗
PubMed1999

Human B cells accumulate immunoglobulin V gene somatic mutations in a cell contact-dependent manner in cultures supported by activated T cells but not in cultures supported by CD40 ligand.

The acquisition of somatic mutations in the rearranged immunoglobulin V regions in B cells occurs within the tightly regulated microenvironment of a germinal centre. The precise mechanism responsible for turning on the mutational process is unknown. To dissect the role of different components of the germinal centre in this mechanism, we have used in vitro cultures of normal human IgD+ peripheral blood B lymphocytes co-cultured with activated CD4+ T cells, or with resting CD4+ T cells, or with CD40 ligand and IL-4. We observed that if the cultures included activated CD4+ T cells, then up to 100% of VH transcripts on day 14 were somatically mutated. Transcripts were found to carry from one to 36 substitutions (median five). In contrast, in the absence of activated T cells, transcripts contained only background levels of somatic mutation irrespective of the presence of resting T cells or CD40 ligand and IL-4. Cell-cell contact was required for mutation because mutations were not detected when B cells were separated from activated T cells by a membrane.

Animals↗
PubMed2006

Mitochondrial DNA D-loop in pancreatic cancer: somatic mutations are epiphenomena while the germline 16519 T variant worsens metabolism and outcome.

We ascertained the frequency of mitochondrial DNA (mtDNA) D-loop region somatic mutations in pancreatic cancer (PC) and verified whether polymorphisms were linked to diagnosis, prognosis, and PC-associated diabetes mellitus (DM) in 99 PC cases, 42 chronic pancreatitis (CP) cases, 18 pancreatobiliary tract tumors, and 87 healthy control subjects (CSs). Tissue samples were obtained from 19 patients with PC and 5 with CP. The D-loop region was sequenced from all tissue samples and from blood DNA of the same patients and 12 CSs. D-loop somatic mutations were found in 3 PC tissue samples (16%). Four single nucleotide polymorphisms (SNPs; T152C, T16189C, T16519C, A73G), more frequently found in PC than in CS, were analyzed by denaturing high-performance liquid chromatography-restriction fragment length polymorphism using blood DNA as the starting template in all cases. The T allele of 16519 SNP correlated with DM. The survival of patients with PC correlated with tumor stage and grade and with DM at diagnosis. When survival analysis was performed considering only patients with locally advanced disease, the T allele of mtDNA 16519 SNP correlated with shorter life expectancy. mtDNA D-loop somatic mutations, rarely found in PC, cannot be considered causative events for this tumor type and probably are epiphenomena; the mtDNA D-loop 16519 variant, which worsens PC prognosis, seems to be a predisposing genetic factor for DM.

Adenocarcinoma↗
PubMed1996

Somatic mutations of the APC gene in sporadic hepatoblastomas.

Hepatoblastoma is a rare hepatic malignancy that occurs in children with an average age of 2 or 3 years and is known to be one of the extracolonic manifestations of familial adenomatous polyposis. Only a single hepatoblastoma with a germ-line mutation of the adenomatous polyposis coli (APC) gene has been reported thus far. To elucidate the possible roles of APC gene alterations in sporadic hepatoblastomas, we examined loss of heterozygosity (LOH) at the APC and MCC loci and performed a sequencing analysis of a part of the APC gene, including the mutation cluster region, in 13 hepatoblastomas of non-familial adenomatous polyposis patients. LOH at the APC and/or MCC loci was observed in four of seven (57%) informative cases. Of the 13 cases, somatic mutations were detected in 8 (61.5%), with 9 (69%) cases showing genetic alterations in the APC gene as LOH or somatic mutations. Two cases demonstrated double mutations. Furthermore, the nature of the somatic mutations observed in the present study was unusual because 9 of the 10 mutations were missense, with only 1 case featuring a frame-shift mutation due to an insertion. Previous reports have described almost all (>90%) mutations of the APC gene in colorectal tumors to result in a truncated APC protein due to either frame-shift or nonsense mutations. These findings suggest that a mutation of the APC gene may play an important role in the genesis of sporadic hepatoblastomas, and the mechanisms of APC gene alteration may be different from those reported previously for colorectal tumors.

Base Sequence↗
PubMed2006

[Somatic mutations of mitochondrial DNA in thyroid papillary carcinoma].

OBJECTIVE: To analyze the somatic mutations in the D-loop of mtDNA and further evaluate the possibility of mitochondrial genetic instability in thyroid papillary carcinoma. METHODS: Hypervariable regions ( HVR-I and HVR-II) in the D-loop of mtDNA from the specimen of 35 thyroid papillary cancers and matched lymphocytes were amplified by PCR, and then were sequenced. RESULTS: Comparing the sequences of tumors to those of matched lymphocytes and normal thyroid tissues, 5 somatic mutations in 2 patients (5.7%) were found. Two mutations were insertions of C in a poly-cytidine (nt303) microsatellite, and 3 at positions 73, 152 and 194 in HVR-II. In addition, of the 294 genetic variants detected, 292 were previously recorded polymorphisms, whereas 2 were new polymorphisms (nt324:C-->G, nt16092:T-->A). CONCLUSIONS: Mutations in the D-loop of mtDNA were found in thyroid papillary cancers, this mutation rate was lower than the reported rate of alteration in tumors of epithelial origin, and further work is required to elucidate the relationship between this mutations and the development of thyroid papillary carcinoma.

Adenocarcinoma, Papillary↗
PubMed1998

Somatic mutation in autoantibody-associated VH genes of circulating IgM+IgD+ B cells.

Naive B cells expressing IgM and IgD on their surface have no or little somatic mutations in V genes. We have demonstrated that the human IgM+IgD+B cell clone (0-81), which expresses nephritogenic idiotypes, produces IgM anti-DNA antibodies which show monospecificity to DNA. Using a DNA probe which specifically links to the VH gene of antibody 0-81, we identified the counterpart germ-line V gene of 0-81, V3-7, which appears to be used by pathogenic autoantibodies in humans. Clone 0-81, which may belong to naive B cells in terms of cell phenotype, uses a somatically mutated V3-7 gene. We further studied DNA sequences of V3-7 genes in circulating IgM+IgD+B cells from normal subjects and patients with systemic lupus erythematosus (SLE). The results revealed that rearranged V3-7 genes in IgM+IgD+B cells from patients with SLE contained somatically mutated sequences at significantly increased frequencies. These data indicate an abnormal maturation of B cells in autoimmune states that may be associated with an escape of self-reactive B cells from the elimination process in the germinal center.

Amino Acid Sequence↗
PubMed2000

Somatic mutation theory of carcinogenesis: why it should be dropped and replaced.

The somatic mutation theory of carcinogenesis has been the dominant force driving cancer research during the 20th century. In brief, it proposes that successive DNA mutations in a single cell cause cancer (monoclonality). This theory places carcinogenesis at the cellular and subcellular hierarchical levels of biological complexity. Its basic premises are that (1) cancer is a defect of the control of cell proliferation and (2) the default state of metazoan cells is quiescence. These two premises have recently been contradicted by evidence. Supporters of the theory have dealt with these lacks of fit by incorporating ad hoc explanations similar to the use of epicycles in pre-Copernican astronomy. We propose the adoption of an alternative theory, the tissue organization field theory of carcinogenesis and neoplasia. Its basic premises are that (1) proliferation is the default state of all cells and (2) carcinogenesis and neoplasia are defects of tissue architecture. Carcinogens would act initially by disrupting the normal interactions that take place among cells in the parenchyma and stroma of an organ (the equivalent of the "morphogenetic fields" of developing organisms). Stroma appears as the primary target of carcinogens. Carcinogenesis and neoplasia occur entirely through emergent (supracellular) phenomena. Neoplastic cells may be reprogrammed to behave like "normal" cells within normal tissues. We argue that it is necessary to abandon the somatic mutation theory. Researchers will then become free to adopt alternative reliable premises to build a theory that explains carcinogenesis as another outcome, aberrant as it may be, of biological organization.

Animals↗
PubMed2005

Somatic mutations of mitochondrial DNA in digestive tract cancers.

BACKGROUND: Somatic mutations of mitochondrial DNA (mtDNA) have been reported to play an important role in the carcinogenesis of several human cancers. However, there are few reports on mtDNA mutations in digestive tract cancers, including esophageal, gastric and colorectal cancers. The present study examined somatic mtDNA mutations in these cancers. METHODS: Samples of 82 esophageal cancers, 96 gastric cancers and 138 colorectal cancers were collected. Mutations in the D310 mononucleotide repeat of mtDNA were examined by microsatellite assay. RESULTS: Frequencies of mtDNA mutations were similar in each digestive tract cancer: 14% (7/51) in esophageal cancers, 15% (14/94) in gastric cancers and 8% (11/133) in colorectal cancers. There were no significant relationships between mtDNA mutations and clinicopathological features, such as patient age or sex, tumor location, depth of tumor invasion and lymph node metastasis in each digestive tract cancer. CONCLUSIONS: The results suggest that mtDNA mutations play a role in the development but not progression in each digestive tract cancer, and that the role of mtDNA mutations might be similar among the digestive tract cancers.

Aged↗
PubMed1993

Peripheral human CD5+ and CD5- B cells may express somatically mutated VH5- and VH6-encoded IgM receptors.

Previous studies have indicated that a sizable fraction of adult human peripheral blood B cells may express IgM receptors encoded by somatically mutated V regions. From these studies it was uniquely associated with the peripheral blood B cell compartment, was uniquely associated with the peripheral blood B cell compartment, associated with particular VH gene segments and/or B cell subpopulations. We have addressed these issues by analyzing > 80 VH5 and VH6-encoded mu transcripts from unseparated peripheral blood, tonsil, and spleen B cells, as well as from B cells separated on the basis of CD5 Ag expression. The results demonstrate that somatically mutated VH5 and VH6 regions are ubiquitously expressed in IgM-bearing B cells in all peripheral adult human lymphoid organs, and that the occurrence of somatic mutations does not segregate with either CD5+ or CD5- B cell populations. The distribution and nature of mutations, as well as the occurrence of clonally related but divergent transcripts suggests that at least some of the mutations were selected by Ag.

Adult↗
PubMed2002

Accumulation of somatic mutation in mitochondrial DNA extracted from peripheral blood cells in diabetic patients.

AIMS/HYPOTHESIS: A point mutation of mitochondrial DNA at nucleotide number 3243 A to G is responsible for both the major genetic aetiologies of the MELAS (mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes) and mitochondrial diabetes. Otherwise, this mutation is also reported to occur as an acquired somatic mutation, possibly due to oxidative stress. Since diabetes can cause severe oxidative stress, we hypothesize that the accumulation of the somatic 3243 A to G mutation in mitochondrial DNA can be accelerated by diabetes. METHODS: DNA was extracted from blood samples of 290 non-diabetic healthy subjects (age 20-60) including 98 newborn infants and from 383 patients with Type II (non-insulin-dependent) diabetes mellitus (age 18-80). The extent of somatic 3243 A to G mutation to total mitochondrial DNA was detected by real-time PCR using the TaqMan Probe. RESULTS: Whereas the level of the 3243 A to G mutation was negligible in the newborn group, it was increased in healthy subjects who were 20 to 29 and 41 to 60 years of age, suggesting that this mutation was somatic. In the diabetic patients the mutation rate increased along with age and the duration of diabetes. In the middle-aged group (age 41-60), the 3243 A to G mutation accumulates fourfold higher in the diabetic patients than the healthy subjects. Moreover, multiple regression analysis showed that the most critical factor associated with this mutation in diabetic patients was the duration of diabetes. CONCLUSION/INTERPRETATION: Diabetes accelerates the accumulation of the somatic 3243 A to G mutation in mitochondrial DNA, which can accelerate the ageing process. This somatic mutation could possibly be a new marker for estimating the duration of diabetes.

Adenine↗
PubMed1982

An in vivo method for the detection of somatic mutations at the cellular level in mice.

This new method for detection of somatic mutations is based on the fact that recessive mutations at the dilute (d) and leaden (ln) loci change the shape of pigment-cells in the hair follicles from their normal highly dendritic appearance (nucleofugal) to a rounded-up almost non-dendritic form (nucleopetal). Gene action is autonomous and individual mutant melanocytes can be recognised in whole mounts of dorsal skin made after the post-natal onset of melanogenesis. Foetal heterozygotes for d and ln were treated with X-rays (0-200 rad) or procarbazine (0-300 mg/kg body mass by maternal i.p. injection) 17 days after detection of a vaginal plug; whole mounts of dorsal skin (fixed 3 days after birth) were microscopically scanned for mutant melanocytes in the hair follicles.About half a million follicular melanocytes were present in the 2 mounts made per mouse. Mutant cells were mainly in the form of small intrafollicular clones; the few mount containing large interfollicular clones were excluded from the analysis. For both treatments, dose-response relationships showed good fits to both a quadratic and a power-law curve. Equations for the latter were: For X-rays, y = 3.2 x 10(-5) + 3.12 x 10(-9) D2.07; for procarbazine, y = 3.6 x 10(-5) + 0.4 x 10(-10) D2.60. However, neither of these differed significantly from a square-law relationship. The estimated mutation rate at the 100 rad X-ray level of 4.7 x 10(-7)/rad/locus was in good agreement with that obtained by Russell and Major's (1957) pioneer studies of somatic mutation in mice, by looking for mutant patches in the coat ("spot test"). Possible ways in which the present method might be improved and extended are discussed.

Animals↗
PubMed2025

Methylation-based droplet digital polymerase chain reaction shows high concordance with chronic lymphocytic leukemia IGHV somatic mutation status.

OBJECTIVE: Somatic hypermutation at immunoglobulin heavy chain variable (IGHV) genes, an established prognostic and predictive biomarker for chronic lymphocytic leukemia (CLL), is assessed by gene sequencing. We developed a single methylation-specific droplet digital polymerase chain reaction (methyl-ddPCR) to predict IGHV status in patients with CLL. METHODS: The CLL methylation array and IGHV data from the International Cancer Genome Consortium (ICGC) were used for biomarker discovery. Top-ranked candidate regions were manually screened for PCR primer and probe binding sites. A single methyl-ddPCR was evaluated on an internal cohort of CLLs with mutated (M), unmutated (U), and inconclusive IGHV results originally determined by next-generation sequencing (NGS). RESULTS: Analysis of ICGC data identified array probe cg23844018 as a candidate for the PCR. The corresponding CpG site showed high methylation levels in U-CLL and lower levels in M-CLL. On the internal cohort, a single optimal cutoff correctly classified 104 of 115 U- and M-CLLs (90.4%; area under the curve = 0.96). The PCR data correlated with some prognostic fluorescence in situ hybridization and CLL subset groupings. Limited analysis suggests that the PCR may be able to stratify some patients with CLL who have inconclusive results on IGHV NGS testing. CONCLUSIONS: The methyl-ddPCR showed high concordance with CLL IGHV status in an internal cohort.

Humans↗
PubMed2021

Somatic Mutations in UBA1 Define a Distinct Subset of Relapsing Polychondritis Patients With VEXAS.

OBJECTIVE: Somatic mutations in UBA1 cause a newly defined syndrome known as VEXAS (vacuoles, E1 enzyme, X-linked, autoinflammatory, somatic syndrome). More than 50% of patients currently identified as having VEXAS met diagnostic criteria for relapsing polychondritis (RP), but clinical features that characterize VEXAS within a cohort of patients with RP have not been defined. We undertook this study to define the prevalence of somatic mutations in UBA1 in patients with RP and to create an algorithm to identify patients with genetically confirmed VEXAS among those with RP. METHODS: Exome and targeted sequencing of UBA1 was performed in a prospective observational cohort of patients with RP. Clinical and immunologic characteristics of patients with RP were compared based on the presence or absence of UBA1 mutations. The random forest method was used to derive a clinical algorithm to identify patients with UBA1 mutations. RESULTS: Seven of 92 patients with RP (7.6%) had UBA1 mutations (referred to here as VEXAS-RP). Patients with VEXAS-RP were all male, were on average &#x2265;45 years of age at disease onset, and commonly had fever, ear chondritis, skin involvement, deep vein thrombosis, and pulmonary infiltrates. No patient with VEXAS-RP had chondritis of the airways or costochondritis. Mortality was greater in VEXAS-RP than in RP (23% versus 4%; P = 0.029). Elevated acute-phase reactants and hematologic abnormalities (e.g., macrocytic anemia, thrombocytopenia, lymphopenia, multiple myeloma, myelodysplastic syndrome) were prevalent in VEXAS-RP. A decision tree algorithm based on male sex, a mean corpuscular volume >100 fl, and a platelet count <200 &#xd7;103 /&#x3bc;l differentiated VEXAS-RP from RP with 100% sensitivity and 96% specificity. CONCLUSION: Mutations in UBA1 were causal for disease in a subset of patients with RP. This subset of patients was defined by disease onset in the fifth decade of life or later, male sex, ear/nose chondritis, and hematologic abnormalities. Early identification is important in VEXAS given the associated high mortality rate.

Aged↗
PubMed1996

Monitoring exposure to atomic bomb radiation by somatic mutation.

Atomic bomb survivors are a population suitable for studying the relationship between somatic mutation and cancer risk because their exposure doses are relatively well known and their dose responses in terms of cancer risk have also been thoroughly studied. An analysis has been made of erythrocyte glycophorin A (GPA) gene mutations in 1,226 atomic bomb survivors in Hiroshima and Nagasaki. The GPA mutation frequency (Mf) increased slightly but significantly with age at the time of measurement and with the number of cigarettes smoked. After adjustment for the effect of smoking, the Mf was significantly higher in males than in females and higher in Hiroshima than in Nagasaki. All of these characteristics of the background GPA Mf were in accord with those of solid tumor incidence obtained from an earlier epidemiological study of A-bomb survivors. Analysis of the dose effect on Mf revealed the doubling dose to be about 1.20 Sv and the minimum dose for detection of a significant increase to be about 0.24 Sv. No significant dose effect for difference in sex, city, or age at the time of bombing was observed. Interestingly, the doubling dose for the GPA Mf approximated that for solid cancer incidence (1.59 Sv). And the minimum dose for detection was not inconsistent with the data for solid cancer incidence. The dose effect was significantly higher in those diagnosed with cancer before or after measurement than in those without a history of cancer. These findings are consistent with the hypothesis that somatic mutations are the main cause of excess cancer risk from radiation exposure.

Adult↗
PubMedDate not supplied

Immunoglobulin gene joints compensate for reduced on-rates imposed by somatic mutations in a V(H) gene.

Affinity maturation in the B lymphocyte response to a protein epitope appears to be largely due to a decrease in the off-rate constant of the antibodies (Ab) resulting from somatic mutation without a significant increase in the on-rate constant. Here, we show by site-directed mutagenesis of a germline encoded single-chain Fv that somatic mutations frequently selected in the Ab response to mouse cytochrome c (CYT) at heavy (H) chain positions 31 and 58 actually cause a two and three-fold decrease, respectively, in the on-rate constant as well as a two and five-fold decrease, respectively, in the off-rate constant and together cause nearly an eight-fold decrease in the off-rate. However, additional selection for a tyrosine residue at position 96 in the V(kappa)-J(kappa) joint compensates for the decreased on-rate imposed by the somatic mutations. This allows for an increase in the affinity of Ab during the secondary response. Certain sequences at the V(H)-D-J(H) joint were also shown to maintain a normal on-rate constant in the context of the common H chain mutations and, in addition, to reduce the off-rate, thus increasing the affinity. The results support the idea that both faster on-rates and slower off-rates for B lymphocyte antigen-specific receptors are favored during the maturation of the Ab response to mouse CYT.

Animals↗
PubMed2003

Acquired somatic mutations in the molecular pathogenesis of COPD.

Chronic obstructive pulmonary disease (COPD) is caused mostly by cigarette smoking but its specific molecular mechanisms are obscure. Current theories suggest that the inflammation and oxidative stress induced by smoking lead to proteolytic imbalance and progressive lung structural derangement, with disease susceptibility being controlled by inherited variations in protective or inflammatory genes. However, cigarette smoke is directly mutagenic. Acquired somatic mutations, rather than inherited polymorphisms, might therefore be major determinants of COPD. Somatic mutations in oncogenes such as p53, Ras, EGFR and PTEN abound in the epithelium of smokers. These mutations are persistent, explaining the paradox that smoking cessation does not resolve inflammation. Moreover, the recognition that these somatic mutations converge on key inflammation, host defense and steroid response pathways might help to explain the clinical defects in these processes in COPD and guide discovery of future therapies.

Animals↗
PubMed1989

Clonal diversity, somatic mutation, and immune memory to phosphocholine-keyhole limpet hemocyanin.

Group II antibodies to phosphocholine (PC)-keyhole limpet hemocyanin in BALB/c mice are genetically diverse and of a defined binding phenotype which recognizes the hapten, phenyl-PC, and PC coupled to protein but not free PC. We sequenced the V regions of 14 kappa and lambda-bearing group II antibodies. Both types show extensive somatic mutations. The pattern of the mutations differs between kappa and lambda antibodies. The nature of the somatic mutation in lambda chains suggests strong Ag selection on the L chain but not the H chain of the lambda-bearing antibodies. The reverse pattern of selection was observed among kappa-containing antibodies wherein the accumulation of replacement mutations in the CDR of the H chain appears to result from selection while changes in the L chain appear unselected. From these findings it appears that somatic mutation plays a major role in anti-PC-keyhole limpet hemocyanin memory development because all 14 antibodies displayed changes from germ-line sequences.

Amino Acid Sequence↗