Somatic Mutation Hypothesis Research Articles

Coherent somatic mutation in autoimmune disease.

BackgroundMany aspects of autoimmune disease are not well understood, including the specificities of autoimmune targets, and patterns of co-morbidity and cross-heritability across diseases. Prior work has provided evidence that somatic mutation caused by gene conversion and deletion at segmentally duplicated loci is relevant to several diseases. Simple tandem repeat (STR) sequence is highly mutable, both somatically and in the germ-line, and somatic STR mutations are observed under inflammation.ResultsProtein-coding genes spanning STRs having markers of mutability, including germ-line variability, high total length, repeat count and/or repeat similarity, are evaluated in the context of autoimmunity. For the initiation of autoimmune disease, antigens whose autoantibodies are the first observed in a disease, termed primary autoantigens, are informative. Three primary autoantigens, thyroid peroxidase (TPO), phogrin (PTPRN2) and filaggrin (FLG), include STRs that are among the eleven longest STRs spanned by protein-coding genes. This association of primary autoantigens with long STR sequence is highly significant (). Long STRs occur within twenty genes that are associated with sixteen common autoimmune diseases and atherosclerosis. The repeat within the TTC34 gene is an outlier in terms of length and a link with systemic lupus erythematosus is proposed.ConclusionsThe results support the hypothesis that many autoimmune diseases are triggered by immune responses to proteins whose DNA sequence mutates somatically in a coherent, consistent fashion. Other autoimmune diseases may be caused by coherent somatic mutations in immune cells. The coherent somatic mutation hypothesis has the potential to be a comprehensive explanation for the initiation of many autoimmune diseases.

Somatic alpha‐synuclein mutations in Parkinson's disease: Hypothesis and preliminary data

Alpha-synuclein (SNCA) is crucial in the pathogenesis of Parkinson's disease (PD), yet mutations in the SNCA gene are rare. Evidence for somatic genetic variation in normal humans, also involving the brain, is increasing, but its role in disease is unknown. Somatic SNCA mutations, arising in early development and leading to mosaicism, could contribute to PD pathogenesis and yet be absent or undetectable in DNA derived from peripheral lymphocytes. Such mutations could underlie the widespread pathology in PD, with the precise clinical outcome dependent on their type and the timing and location of their occurrence. We recently reported a novel SNCA mutation (c.150T>G, p.H50Q) in PD brain-derived DNA. To determine if there was mosaicism for this, a PCR and cloning strategy was used to take advantage of a nearby heterozygous intronic polymorphism. No evidence of mosaicism was found. High-resolution melting curve analysis of SNCA coding exons, which was shown to be sensitive enough to detect low proportions of 2 known mutations, did not reveal any further mutations in DNA from 28 PD brain-derived samples. We outline the grounds that make the somatic SNCA mutation hypothesis consistent with genetic, embryological, and pathological data. Further studies of brain-derived DNA are warranted and should include DNA from multiple regions and methods for detecting other types of genomic variation. © 2013 Movement Disorder Society

Unresolved Inflammation and Cancer: Loss of Natural Immune Surveillance as the Correct ‘Target’ for Therapy! Seeing the ‘Elephant’ in the Light of Logic

To begin this commentary, it is appropriate to remember the 1959 statement made by Peyton Rous (Nobel Laureate in Physiology or Medicine 1966) that ‘‘A hypothesis is best known by its fruits. What have been those of the somatic mutation hypothesis? It has resulted in no good thing as concerns the cancer problem, but in much that is bad... Most serious of all the results of the somatic mutation hypothesis has been its effect on research workers. It acts as a tranquilizer on those who believe in it.’’ This statement was made over 50 years ago and well before the genetic study of cancer was put on steroids!

REV1 Is Implicated in the Development of Carcinogen-Induced Lung Cancer

The somatic mutation hypothesis of cancer predicts that reducing the frequency of mutations induced by carcinogens will reduce the incidence of cancer. To examine this, we developed an antimutator strategy based on the manipulation of the level of a protein required for mutagenic bypass of DNA damage induced by the ubiquitous carcinogen benzo[a]pyrene. The expression of this protein, REV1, was reduced in mouse cells using a vector encoding a gene-specific targeting ribozyme. In the latter cells, mutagenesis induced by the activated form of benzo[a]pyrene was reduced by >90%. To examine if REV1 transcripts could be lowered in vivo, the plasmid was complexed with polyethyleneimine, a nonviral cationic polymer, and delivered to the lung via aerosol. The endogenous REV1 transcript in the bronchial epithelium as determined by quantitative real-time PCR in laser capture microdissected cells was reduced by 60%. There was a significant decrease in the multiplicity of carcinogen-induced lung tumors from 6.4 to 3.7 tumors per mouse. Additionally, REV1 inhibition completely abolished tumor formation in 27% of the carcinogen-exposed mice. These data support the central role of the translesion synthesis pathway in the development of lung cancer. Further, the selective modulation of members of this pathway presents novel potential targets for cancer prevention. The somatic mutation hypothesis of cancer predicts that the frequency of cancers will also be reduced.

Advances in chemical carcinogenesis: a historical review and prospective.

The American Association for Cancer Research has been the citadel for communicating research on chemical carcinogens for over a century. It therefore seems appropriate that a review of chemical carcinogenesis inaugurates a series of articles highlighting advances in understanding, treating, and

An integrated theory of aging as the result of mitochondrial-DNA mutation in differentiated cells

We maintain that aging of humans and animals derives from a mutation or inactivation (probably followed by endonuclease digestion) of the mitochondrial genome of differentiated cells. This extranuclear somatic mutation hypothesis of aging is based on the finding that mitochondrial DNA (mtDNA) synthesis takes place at the inner mitochondrial membrane near the sites of formation of highly reactive oxygen species and their products, such as lipoperoxides and malonaldehyde. The mtDNA may be unable to counteract the damage inflicted by those by-products of respiration because, in contrast to the nuclear genome, it lacks histone protection and scission repair. Since the mitochondrial genome controls the synthesis of several hydrophobic proteins of the inner mitochondrial membrane, the postulated mutation, inactivation or loss of mtDNA will prevent the replication of the organelles. Thus deprived of the ability to regenerate their mitochondrial populations, the cells will sustain an irreversible decline in their bioenergetic ability, with concomitant senescent loss of physiological performance and eventual death. The above hypothesis is integrated with the concepts of Minot, Pearl and others in order to offer a more comprehensive view of aging.

History and present status of human chromosome studies.

Until the second half of the century most advances in cytogenetics were limited to plant and invertebrate systems. Although there was great interest in mammalian and human cytogenetics, the technical difficulties encountered in making preparations prevented consistent progress. In addition to the desire to determine normal chromosome number and morphology in man and mammals, there was great interest in chromosome changes in malignancy. As early as the late 1800s pathologists observed unequal chromatin distribution in daughter tumor cells. In the early 1900s Boveri (8) developed a somatic mutation hypothesis of the origin of cancer based not on observations in cancer cells, but on his studies on sea urchin eggs. In these materials he observed unequal chromosome distributions resulting in aneuploidy and reasoned that changes such as these could play a vital role in the alteration of the cell from the normal to the malignant state. The desire to obtain the normal human karyotype that could then be compared to tumor cells was one of the main goals in studying human chromosomes. Reports from the 1700s that related soot to the scrotal cancers of chimney sweeps and the observations that had been made on induced chromosome abnormalities produced by phenols in allium meristems added to this interest (33,34). As with most discoveries the developments that permitted the determination of the human chromosome number and karyotype was not the result of a single event or breakthrough but of building on knowledge accumulated over the years by several investigators. The case of determining the human chromosome number (60) was made possible by combining four techniques. The first of these was the use of cell culture. This technique yields a higher mitotic index than most in vivo methodologies, but more important it made it possible to obtain single cell suspensions that make cells from organized tissues equivalent to cells from ascites tumors. With cells in suspension, even distribution of chemicals and solutions to all cells and manipulations of various kinds that improve the quality of the preparations are possible. The second technique was the use of colchicine to pretreat the cells. The effects of colchicine on plant chromosomes had been reported by Blakeslee and Avery (7) and also by Levan (31). By interrupting the spindle, colchicine collects mitotic figures and increases the contraction of individual chromosomes. At the time the

Fibroblasts from patients with hereditary cutaneous malignant melanoma are abnormally sensitive to the mutagenic effect of simulated sunlight and 4-nitroquinoline 1-oxide.

Because of a possible etiologic link between mutations and carcinogenesis, we compared fibroblasts derived from skin biopsies of several patients with hereditary cutaneous malignant melanoma and the dysplastic nevus syndrome for sensitivity to the mutagenic and/or cytotoxic effect of broad-spectrum simulated sunlight and of a UV mimetic carcinogen, 4-nitroquinoline 1-oxide (4NQO). The genetic marker was resistance to 6-thioguanine; loss of colony-forming ability was the assay for cytotoxicity. All five strains tested were more sensitive than normal to the killing effect of 4NQO (slopes of survival curves were 2- to 3-fold steeper), but only one strain was hypersensitive to killing by Sun Lamp radiation. Two strains were tested for mutagenicity. The response of each to the mutagenic action of these agents corresponded to its response to cell killing. Both strains were hypermutable after exposure to 4NQO, but only one showed a higher than normal frequency of mutants induced by simulated sunlight. The finding that nonmalignant fibroblasts from patients with a hereditary variant of malignant melanoma are abnormally susceptible to carcinogen-induced mutations suggests that hypersensitivity to mutagens contributes to risk of melanoma in patients. It also supports the somatic cell mutation hypothesis for the origin of cancer.

Immunologic memory to phosphorylcholine III. IgM includes a fine specificity population distinct from TEPC 15.

Group I and group II variable regions expressed in the PC-KLH memory response may originate from distinct germ-line genes or group II may arise by somatic mutation of group I (TEPC 15) germ-line genes. A current version of the somatic mutation hypothesis proposes that somatic mutation is activated by the class switch from IgM to IgG or IgA. If group II results from somatic mutation during class switching, group II IgM antibodies would not exist. This prediction was tested in the present experiments. Group I and group II antibodies were separated from whole serum by affinity chromatography on PC-Sepharose. An ELISA was used to characterize the fine specificity and idiotype of the isolated antibody populations. Group I antibodies were inhibited by both PC and NPPC haptens and were T15 idiotype-positive. Group II antibodies were inhibited appreciably only by NPPC and were negative for the T15 idiotype. The purified group II antibodies contained a significant IgM component, and high levels of group II IgM were detected during the early secondary response to PC-KLH. These observations are inconsistent with the hypothesis that group II originates by somatic mutation activated by the class switch. These results strongly suggest that one or more of the germ-line genes (V, D, or J) of groups I and II are different. Alternatively, if group II antibodies arise from group I by somatic mutation, this mutation must occur before class switching.

Amino acid diversity of immunoglobulins as a product of molecular evolution

Based on population genetics theory of the evolution of multigene families, the sequence variability of the variable regions of immunoglobulins compiled by Kabat et al. (1976) has been analysed. An amino acid identity coefficient either within or between species is calculated separately for both the hypervariable and the framework regions. Under the somatic mutation hypothesis, the somatic component of amino acid diversity is in addition to the germ line component and should contribute an amount of change between the hypervariable and framework regions that is independent of the time since the divergence of any two immunoglobulin gene families. The relationship between the identity coefficient of the hypervariable region and that of the framework region is shown to be not in accord with such prediction. The result indicates that the rate of evolutionary accumulation of amino acid replacements in the hypervariable region is roughly three times more rapid than in the framework region and the hypervariability within a species is a necessary consequence of the high evolutionary rate.

Mutagenicity of melanin from human red hair.

The Salmonella typhimurium histidine reversion test of Ames et al. was used to demonstrate the pheomelanin, the red-brown polymeric pigment produced in human skin and hair, becomes mutagenic after exposure to long wave-length UV-light; a finding consistent with the UV-induced somatic mutation hypothesis for the origin of freckles and the high susceptibility of redheads and blonds to sunlight-induced skin cancers.

Mechanisms of metal carcinogenesis

Experimental observations that pertain to mechanisms of metal carcinogenesis are summarized, with emphasis upon (a) interactions of metals with nucleic acids in vitro; (b) impairment by metals of the fidelity of DNA replication by DNA polymerase in vitro; (c) mutagenicity of metals in microorganisms; (d) cytogenetic aberrations induced by metals in tissue culture cells; (e) induction by metals of neoplastic transformation of tissue culture cells; and (f) nuclear uptake of metals in vivo and concomitant inhibitory effects of metals on synthesis of nucleic acids. Considered in toto, the experimental data support the somatic mutation hypothesis of chemical carcinogenesis. Sufficient experimental evidence is available regarding four carcinogenic metals (As, Be, Cr, and Ni) to permit speculations about the molecular reactions whereby these metals may induce somatic mutations.

Evidence for multispecificity of antibody molecules.

ONE of the salient questions in immunology concerns the means by which the immune system is capable of recognising an apparently limitless variety of antigenic determinants, including many that presumably did not exist during its evolution. Three major hypotheses have been put forward to explain the diversity of the immune response: a stringent germ line hypothesis, a recombinational germ line hypothesis and a somatic mutation hypothesis (see ref. 1 for discussion). If the assumption is made that an antibody-combining site has a single antigenic specificity, the first of the above hypotheses postulates about 1,000 variable genes and 1,000 constant genes to code for about 106 antigenic determinants. The second and, especially, the third hypotheses require the presence of many fewer genes in the germ line. Even fewer genes would be required if antibody-combining sites were multispecific. Evidence has been put forward to support the concept of multispecificity2. Moreover, the ability of single myeloma globulins to bind structurally diverse molecules3 and the multispecific character of a Bence-Jones4 dimer can be taken as additional supportive evidence. In an earlier paper5, we attempted to investigate the question of multispecificity by studying the binding specificities of a population of antibodies of limited heterogeneity generated by immunisation with a conjugate of adenosine-5′-phosphate and gramicidin S: (AMP)2–gramicidin S (ref. 6). Immunised rabbits produced predominantly three or four globulin proteins specific for AMP. Binding studies on the sera of one of the rabbits, in which there were three major AMP-specific globulins, yielded data that could be interpreted as evidence for multispecificity of antibody-combining sites. We have now succeeded in isolating three homogeneous anti-AMP antibodies from one of the rabbits immunised with (AMP)2–gramicidin S and have studied the ability of each globulin to bind AMP and other ligands. The isoelectric pattern of the specifically purified7 population of antibodies obtained from the serum of rabbit 449 (ref. 5) showed three major bands. The three bands were separated and isolated by preparative isoelectric focusing in polyacrylamide by an adaption of the procedure of Wrigley8, and were shown to be homogeneous by analytical isoelectric focusing. They were designated fractions A, B and C.

Age incidence curves for cancer.

Age incidence curves for carcinomas tend to be linear on doubly logarithmic graphs. This fact has been used to support the somatic mutation hypothesis. It is shown that this should also be expected on the epigenetic hypothesis when the reversible cellular changes are programmed to occur randomly. Such changes could be programmed differently to obtain the age incidence curves observed for other cancers, e.g., leukemias and sarcomas.

Frequency of ultraviolet light-induced mutations is higher in xeroderma pigmentosum variant cells than in normal human cells.

PATIENTS with the inherited disease, xeroderma pigmentosum (XP), are subject to multiple carcinomas of the skin on areas exposed to sunlight1. Fibroblasts from the skin of the majority of these patients (classical XP) have been shown to be deficient in excision repair of lesions induced in DNA by ultraviolet radiation1–3. One group of patients, however, has been designated ‘XP variants’ because, although they suffer the clinical manifestations of the disease, they carry on normal excision repair of such ultraviolet-light damage to DNA4–6. Lehmann et al.6 reported that cells from such XP variants are abnormally slow in converting initially low molecular weight DNA, synthesised after ultraviolet irradiation, into high molecular weight DNA similar in size to that produced in unirradiated cells. Although these authors suggest that such abnormal DNA replication might explain why such patients are susceptible to cancer of the skin, they do not propose any mechanism. If the somatic cell mutation hypothesis on the origin of cancer, first suggested by Boveri7, is correct one would expect the frequency of mutations induced by ultraviolet light to be higher in cells derived from skin biopsies from both classical and variant XP patients than in cells from normal persons. To test this hypothesis, we have carried out a series of quantitative investigations comparing the frequency of ultraviolet-light induced mutations to azaguanine resistance in normal human skin fibroblasts with that found in various strains derived from classical and variant XPs. We have found that cells derived from both kinds of XP patients indeed show much higher frequencies than normal cells. The data comparing two classical XP strains with normal cells have been published8,9. Here, we present data obtained with variant strain, XP4BE.

Immunoglobulin Genes: A Test of Somatic Vs. Germ Line Hypothesis by RNA/DNA Hybridization

Sequence analysis of immunoglobulin heavy (H) and light (L) chains has revealed a characteristic pattern: the N-terminal 110–120 amino acid residues vary in some positions from one peptide chain to another, whereas the remaining C-terminal part of the sequenee is common to peptide chains belonging to the same subclass (reviewed by Edelman and Gall, 1969). These two portions of immunoglobulin chains have been designated as the variable (V) and constant (C) regions, respectively. There is considerable genetic evidence that each C region is coded for by a single structural gene (reviewed by Baglioni, 1970). By contrast, it has not yet been established whether each V region is coded for by a different structural gene (germ line hypothesis) or a restricted number of V regions are encoded by structural genes, which undergo mutation during somatic differentiation (somatic mutation hypothesis).

The somatic mutation hypothesis of cancer genesis.

The somatic mutation hypothesis of cancer genesis.

Regarding the somatic mutation hypothesis of cancer

Regarding the somatic mutation hypothesis of cancer

Regarding the Somatic Mutation Hypothesis of Cancer

Regarding the Somatic Mutation Hypothesis of Cancer

Volume of Injection and Concentration of the Carcinogenic Chemical as Factors in the Initiation of the Malignant Process and Their Bearing on the Somatic Mutation Hypothesis

In a previous report (1) it was demonstrated that in animals injected in a varying number of foci with equal volumes of a single concentration of benzpyrene the average time at which the malignant change occurred and the probability of its occurrence were determined by the number of foci or the dose of the chemical. The percentage of induced tumors increased and the average time from injection to observation of the tumors decreased in relation to the number of uniform foci per animal. In both rats and mice of dissimilar genetic constitution the induced tumors showed a random distribution in the injected foci. The histogenesis of the induced tumors indicated that the potency for malignant change is a universal cell character since each morphological type was represented by a number consistent with the expectation that the change of a normal to a cancer cell is the result of the chance action of the irritant. In these experiments the amount of the carcinogenic chemical and the surface area of the tissue exposed were varied coincidently. The purpose of the experiment now to be described was to separate these two factors and determine their relative effectiveness. The carcinogenic agent used was 3:4-benzpyrene injected in warm paraffin wax (melting point 48° C), as previously described by Haagensen and Krehbiel (2). A glass tuberculin syringe and 20-gage needle were used for the injections, the syringe and beaker containing the material to be injected being maintained at a temperature of about 80° C. in a water bath.