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PubMed1997

Percolation on the fitness hypercube and the evolution of reproductive isolation.

We study the structure and properties of adaptive landscapes arising from the assumption that genotype fitness can only be 0 (inviable genotype) or 1 (viable genotype). An appropriate image of resulting ("holey") fitness landscapes is a (multidimensional) flat surface with many holes. We have demonstrated that in the genotype space there are clusters of viable genotypes whose members can evolve from any member by single substitutions and that there are "species" defined according to the biological species concept. Assuming that the number of genes, n, is very large while the proportion of viable genotypes among all possible genotypes, p, is very small, we have deduced many qualitative and quantitative properties of holey adaptive landscapes which may be related to the patterns of speciation. Relationship between p and n determines two qualitatively different regimes: subcritical and supercritical. The subcritical regime takes place if p is extremely small. In this case, the largest clusters of viable genotypes in the genotype space have size of order n and there are many of such size; typical members of a cluster are connected by a single ("evolutionary") path; the number of different (biological) species in the cluster has order n; the expected number of different species in the cluster within k viable substitutions from any its member is of order k. The supercritical regime takes place if p is small but not extremely small. In this case, there exists a cluster of viable genotypes (a "giant" component) that has size of order 2n/n; the giant component comes "near" every point of the genotype space; typical members of the giant component are connected by many evolutionary paths; the number of different (biological) species on the "giant" component has at least order n2; the expected number of different species on the "giant" component within k viable substitution from any its member is at least of order kn. At the boundary of two regimes all properties of adaptive landscapes undergo dramatic changes, a physical analogy of which is a phase transition. We have considered the most probable (within the present framework) scenario of biological evolution on holey landscapes assuming that it starts on a genotype from the largest connected component and proceeds along it by mutation and genetic drift. In this scenario, there is no need to cross any "adaptive valleys"; reproductive isolation between populations evolves as a side effect of accumulating different mutations. The rate of divergence is very fast: a few substitutions are sufficient to result in a new biological species. We argue that macroevolution and speciation on "rugged" fitness landscapes proceed according to the properties of the corresponding holey landscapes.

Animals↗
PubMed1996

TP53 alterations in atypical ductal hyperplasia and ductal carcinoma in situ of the breast.

Abnormalities in the TP53 tumour suppressor gene in 75 atypical ductal hyperplasias and 62 ductalcarcinomas in situ (DCIS) of the breast were studied using immunohistochemistry and mutation analysis. Accumulation of p53 protein was detected in 10 out of 62 (16%) DCIS, whereas no cases of positive staining was observed in the atypical lesions. TP53 mutations were identified in four out of 30 (13%) DCIS by constant denaturant gel electrophoresis (CDGE). Two of these cases were positive and two negative for p53 protein. A total of 12 out of 62 DCIS (19%) carried TP53 mutation and/or p53 protein over-expression. The present results suggest that TP53 alterations may be important in the development of a subset of DCIS.

Breast↗
PubMed2005

Putting the brakes on snake venom evolution: the unique molecular evolutionary patterns of Aipysurus eydouxii (Marbled sea snake) phospholipase A2 toxins.

Accelerated evolution of toxins is a unique feature of venoms, with the toxins evolving via the birth-and-death mode of molecular evolution. The venoms of sea snakes, however, are remarkably simple in comparison to those of land snakes, which contain highly complex venoms. Aipysurus eydouxii (Marbled sea snake) is a particularly unique sea snake, feeding exclusively upon fish eggs. Secondary to this ecological change, the fangs have been lost and the venom glands greatly atrophied. We recently showed that the only neurotoxin (a three-finger toxin) gene found in the sea snake A. eydouxii has a dinucleotide deletion, resulting in the loss of neurotoxic activity. During these studies, we isolated and identified a number of cDNA clones encoding isozymes of phospholipase A(2) (PLA(2)) toxins from its venom gland. Sixteen unique PLA(2) clones were sequenced from the cDNA library and TA cloning of reverse transcription-polymerase chain reaction products. Phylogenetic analysis of these clones revealed that less diversification of the PLA(2) toxins has occurred in the A. eydouxii venom gland in comparison to equivalent terrestrial and other marine snakes. As there is no longer a positive selection pressure acting upon the venom, mutations have accumulated in the toxin-coding regions that would have otherwise had a deleterious effect upon the ability to use the venom for prey capture. Such mutations include substitutions of highly conserved residues; in one clone, the active site His(48) is replaced by Arg, and in two other clones, highly conserved cysteine residues are replaced. These mutations significantly affect the functional and structural properties of these PLA(2) enzymes, respectively. Thus, in A. eydouxii, the loss of the main neurotoxin is accompanied by a much slower rate of molecular evolution of the PLA(2) toxins as a consequence of the snake's shift in ecological niche. This is the first case of decelerated evolution of toxins in snake venom.

Amino Acid Sequence↗
PubMed2002

Hepatitis C virus nonstructural 5A protein and interferon resistance: a new model for testing the reliability of mutational analyses.

Presumably due to the capability of the hepatitis C virus (HCV) to evade the antiviral effects of alpha interferon, treatment is ineffective in more than half of chronically genotype HCV type 1 (HCV-1)-infected patients. Previous approaches to correlate the number of amino acid mutations within regions of HCV nonstructural (NS)-5A protein with virologic treatment response provided conflicting results. In the present study, we developed a new mathematical model to investigate NS5A sequences of HCV-1-infected patients. The mean number of all mutations within the complete NS5A protein was significantly higher in virologic responders compared to nonresponders (P = 0.008 and P = 0.0001 for amino acid residues predicted on the surface of the NS5A protein). Differences did not achieve statistical significance for NS5A regions that are currently assumed to be functionally relevant (e.g., the interferon sensitivity-determining region, the RNA-activated protein kinase-binding domain, etc.). Analyses of smoothed mutational frequencies showed that the number of mutations in other NS5A regions correlated with virologic response. Such a correlation was observed for both genuine and randomly generated NS5A sequences. The existence of local accumulations of mutations within genuine NS5A isolates that truly correlated with treatment response was defined by a refined test procedure. Upon considering the predicted residue accessibility, we identified the main focus of mutations correlating with treatment response to be the sequence from amino acids 2350 to 2370. Thus, evaluation of NS5A mutations in correlation with treatment response is improved by consideration of functional and predicted conformational amino acid properties. As shown by simulations with randomly generated sequences, multiple analyses of simple counts of local NS5A amino acid mutations and correlation with treatment response are insufficient. For improvement of mutational analysis, a refined specific functional data test procedure is proposed.

Adult↗
PubMed1998

p53-based immunotherapy of cancer.

Immunotherapy targeting p53 missense mutations, which occur in nearly half of all human tumors, is limited by several factors, including the constraints of antigen processing and presentation. Due to the accumulation of mutated p53 molecules in tumors expressing p53 mutations, an alternative approach would be to target wild-type sequence, CTL-defined p53 epitopes. Obviously, the possibility of an autoimmune response is a major potential drawback to this therapy. Immunization of BALB/c mice with bone marrow-derived dendritic cells (DC) generated in the presence of GM-CSF/IL-4 and prepulsed with the H-2Kd-binding wild-type p53(232-240) peptide has been shown to induce anti-peptide CTL. These effectors were cross-reactive against sarcomas expressing p53 missense mutations outside of the p53(232-240) epitope, but not within it. Mitogen-activated splenocytes, which express elevated levels of p53, were not sensitive to these CTL. The p53 peptide-pulsed DC-based vaccine was shown to be effective in inducing tumor rejection in immunization and therapy models in the absence of any observable deleterious effect on naive mice. The murine model has now been extended to include the use of genetically modified DC-based vaccines as well.

Animals↗
PubMed2000

The effect of mismatch repair deficiency on tumourigenesis; microsatellite instability affecting genes containing short repeated sequences.

We have investigated microsatellite instability (MSI) in colorectal, gastric, endometrial and ovarian cancer as a result of mismatch repair (MMR) deficiency. We detected frameshift mutations in several genes that carry short repeated sequences and are important in cell fidelity and growth control; hMSH3, hMSH6, BAX, IGFIIR, TGFbetaIIR, E2F4 and BRCA2. Accumulation of mutations was heterogeneous and mainly restricted to tumours showing MSI at several loci (MSI-H). Both insertions and deletions were evident and occasional intratumour heterogeneity was evident with more than one different additional allele in the tumour. Most MSI-H tumours had acquired mutations in more than one gene and longer repeated sequences were more frequently targets for mutations. The TGFbetaIIR gene was mutated in 62%, the hMSH3 gene in 43%, the E2F4 gene in 35%, the hMSH6 in 32%, the BAX gene in 32%, the IGFIIR gene in 26%, and the BRCA2 gene in 2% of the MSI-H tumours. Homozygous mutations or mutation of both alleles were evident in all genes except BRCA2, in total 23/105 mutated cases, varying from 7% for BAX to 50% for E2F4. E2F4 mutations were exclusively found in colon tumours and E2F4 polymorphisms was found in 8% of cases. No difference in mutation prevalence was noted between cancer types apart from TGFbetaIIR mutations, which were frequently found in colon and gastric tumours but not in endometrial tumours, suggesting that endometrial tumours progress by a different route where TGFbetaIIR mutations are less favourable.

Aged↗
PubMed2002

Insertions in the reverse transcriptase increase both drug resistance and viral fitness in a human immunodeficiency virus type 1 isolate harboring the multi-nucleoside reverse transcriptase inhibitor resistance 69 insertion complex mutation.

Recent studies have shown that the accumulation of multiple mutations associated with nucleoside reverse transcriptase inhibitor (NRTI) resistance may be grouped as multi-NRTI resistance (MNR) complexes. In this study, we have examined the viral fitness of recombinant viruses carrying the reverse transcriptase (RT) of a human immunodeficiency virus type 1 (HIV-1) primary isolate harboring mutations comprising the MNR 69 insertion complex. Different RT mutants were prepared in the sequence context of either the wild-type RT sequence of the HIV-1(BH10) isolate or the sequence found in a clinical HIV-1 isolate with the MNR 69 insertion mutation. As expected, in the presence of zidovudine, recombinant viruses harboring the MNR RT from the patient were more fit than wild-type viruses. However, in the absence of drug, the virus with the RT from the original clinical isolate (SS) was more fit than (i) the wild-type virus with an engineered serine insertion between residues 69 and 70 (T69SSS) and (ii) the recombinant virus with the MNR RT where the insertion was removed (2S0S). These results suggest that RT insertions, in the right sequence context (i.e., additional mutations contained in the MNR 69 insertion complex), enhance NRTI resistance and may improve viral fitness. Thus, comparing complex mutation patterns with viral fitness may help to elucidate the role of uncharacterized drug resistance mutations in antiretroviral treatment failure.

Adult↗
PubMed1999

Analysis of p53 mutation and cyclin D1 expression in breast tumors.

P53 and cyclin D1 are interacting regulatory genes and both are frequently altered in breast cancer. We analysed p53 mutation by SSCP and sequencing methods as well as p53 protein accumulation immunohistochemically in 34 consecutively operated breast tumors. None of 4 fibroadenomas revealed p53 mutation or p53 protein accumulation. Mutation of p53 was present in 7 carcinomas. Immunohistochemistry revealed accumulation of p53 protein in 6 carcinomas and there was a significant correlation between p53 mutation and protein accumulation. Overexpression of cyclin D1 protein was observed in 11 carcinomas by immunohistochemistry and no correlation was observed between cyclin D1 overexpression and p53 mutation or accumulation. Our data support the concept that the p53-cyclin D1 signal pathway and the cyclin D1 cascade are disregulated in breast cancer.

Breast Neoplasms↗
PubMed1986

Protein sorting in yeast: mutants defective in vacuole biogenesis mislocalize vacuolar proteins into the late secretory pathway.

We have devised a genetic selection for mutant yeast cells that fail to properly deliver the vacuolar glycoprotein CPY to the lysosome-like vacuole. This has allowed us to identify mutations in eight VPL complementation groups that result in aberrant secretion of up to approximately 90% of the immunoreactive CPY. Other soluble vacuolar proteins are also affected by each vpl mutation, demonstrating that a sorting system for multiple vacuolar proteins exists in yeast. Mislocalized CPY apparently traverses late stages of the secretory pathway, since a vesicle-accumulating sec1 mutation prevents secretion of this protein. Despite the presence of abnormal membrane-enclosed organelles in some of the vpl mutants, maturation and secretion of invertase are not substantially perturbed. Thus vpl mutations define a new class of genes that encode products required for sorting of newly synthesized vacuolar proteins from secretory proteins during their transit through the yeast secretory pathway.

Aspartic Acid Endopeptidases↗
PubMed1993

Effect of dietary restriction on in vivo somatic mutation in mice.

Dietary restriction is the one experimental variable which has been shown reproducibly to retard ageing. The effect of dietary restriction on in vivo mutation was studied in mice by feeding experimental mice 60% of the amount eaten by control mice and measuring mutations in lymphocytes at the hypoxanthine phosphoribosyl transferase locus at 4 weeks, 6 months and 12 months of age. Dietary restriction markedly decreased the age-associated accumulation of mutations observed in control mice, which suggests that somatic mutation is involved in the ageing process and that the majority of in vivo mutations result from dietary factors.

Aging↗
PubMed2004

Decreased Fas expression in advanced-stage bladder cancer is not related to p53 status.

OBJECTIVES: The Fas-Fas ligand system is an important regulator of apoptosis and is involved in tumor development. Invasive cancers downregulate Fas expression to evade antitumor immune responses. Fas is a transcriptional target of p53, which is often mutated in bladder cancers. Therefore, Fas expression and its relation to p53 mutation was investigated. METHODS: Expression of Fas protein and p53 status was studied by immunohistochemistry in 83 bladder cancer specimens. In addition, mRNA levels for soluble (decoy) and membrane-bound forms of Fas were compared between 10 bladder cancer cell lines and primary uroepithelial cells by quantitative TaqMan polymerase chain reaction. Mutational analysis of the death domain of the Fas gene was performed in all cell lines. RESULTS: Organ-confined tumors maintained specific Fas staining at the cell membrane and often also in the cytoplasm. In higher stage carcinomas, Fas expression became restricted to a smaller fraction of cells or was lacking entirely. The correlation of Fas staining with tumor stage was highly significant but no correlation to tumor grade or survival was found. Furthermore, no statistically significant relationship was observed with either the presence or lack of mutated p53 accumulation. Membrane-bound Fas mRNA was decreased in most, and soluble Fas was increased in all transitional cell carcinoma lines compared with primary uroepithelial cells. No mutations in the death domain were detected. CONCLUSIONS: Fas downregulation occurring in advanced bladder cancer is unrelated to p53 mutations. The results of immunohistochemistry and mRNA studies of soluble and membrane-bound Fas in transitional cell carcinoma lines support the hypothesis of immune evasion in advanced bladder cancer.

Carcinoma, Papillary↗
PubMed2007

Theory of lethal mutagenesis for viruses.

Mutation is the basis of adaptation. Yet, most mutations are detrimental, and elevating mutation rates will impair a population's fitness in the short term. The latter realization has led to the concept of lethal mutagenesis for curing viral infections, and work with drugs such as ribavirin has supported this perspective. As yet, there is no formal theory of lethal mutagenesis, although reference is commonly made to Eigen's error catastrophe theory. Here, we propose a theory of lethal mutagenesis. With an obvious parallel to the epidemiological threshold for eradication of a disease, a sufficient condition for lethal mutagenesis is that each viral genotype produces, on average, less than one progeny virus that goes on to infect a new cell. The extinction threshold involves an evolutionary component based on the mutation rate, but it also includes an ecological component, so the threshold cannot be calculated from the mutation rate alone. The genetic evolution of a large population undergoing mutagenesis is independent of whether the population is declining or stable, so there is no runaway accumulation of mutations or genetic signature for lethal mutagenesis that distinguishes it from a level of mutagenesis under which the population is maintained. To detect lethal mutagenesis, accurate measurements of the genome-wide mutation rate and the number of progeny per infected cell that go on to infect new cells are needed. We discuss three methods for estimating the former. Estimating the latter is more challenging, but broad limits to this estimate may be feasible.

Antiviral Agents↗
PubMed2003

The nature of diversity and diversification at the ABO locus.

In this study we analyzed the complete genomic sequences, except intron 1, and 2 regulatory regions of 6 common (ABO*A101, ABO*A201, ABO*B101, ABO*O01, ABO*O02, and ABO*O03) and 18 rare ABO alleles, 3 of which were new. This was done by phylogenetic analysis and correlating sequence data with the ABO phenotypes. The study revealed multiple polymorphisms in noncoding regions. The intron-based phylogenetic analysis revealed 5 main lineages: ABO*A, ABO*B, ABO*O01, ABO*O02, and ABO*O03. The genomic sequences of most rare ABO alleles differed slightly from those of the common alleles. Singular mutations or hybrid alleles were most common, but a few exhibited mosaic sequence pattern containing multiple exon and/or intron motifs from other ABO lineages. Thus, both an accumulation of mutations as well as an assortment of the mutations by recombination seems to be responsible for the ABO gene diversity. The prevalence of replacement mutations indicates positive selection for allelic diversity. Phenotype-genotype correlation showed that sequence variations within the complete coding sequence can affect A- and B-antigen expression. All variant ABO*A/B alleles and one new ABO*O03-like allele were associated with weak ABO phenotypes. These findings are suggestive of the requirement of a comprehensive coding sequence database for sequence-based phenotype prediction.

ABO Blood-Group System↗
PubMed2003

K65R with and without S68: a new resistance profile in vivo detected in most patients failing abacavir, didanosine and stavudine.

Antiretroviral treatment with three nucleoside reverse transcriptase inhibitors (NRTIs) is widely used, but the combination of abacavir, didanosine and stavudine has never been investigated. We describe the surprising and consistent genotypic and phenotypic outcome in patients failing this combination. As part of a Danish multicentre study, 60 antiretroviral-naive patients were randomized to treatment with abacavir, didanosine and stavudine. Failure was defined as one HIV-1 RNA >400 copies/ml. Genotyping was performed using TrueGene HIV-1 assay (Visible Genetics, London, UK). Phenotypic susceptibilities were determined with the Virco Antivirogram assay. Eight patients failed treatment with a median viral load of 2.980 copies/ml (range 478-5.950). At baseline, five patients were wild-type. Three patients harboured nucleoside excision mutations (NEMs), but phenotypic susceptibilities were within normal range. All five patients with wild-type virus developed K65R and four of these patients also acquired the S68G mutation. Phenotypic susceptibility decreased towards abacavir (median 8.9-fold) and didanosine (median 3.2-fold), while susceptibility towards stavudine was unchanged (median 0.8-fold). Susceptibility towards lamivudine and tenofovir decreased median 14.2- and 4.0-fold, respectively. In two patients with baseline resistance mutations, further accumulation of NEMs and V75T or L74V was observed. One patient developed Q151M. Failure of a triple NRTI regimen is possible and frequent with only the K65R mutation. Under adequate selection pressure K65R can easily emerge in vivo and may compromise several future treatment options including newer NRTIs. The unexpected high incidence of S68G suggests a functional role of this mutation in viruses harbouring K65R.

Anti-HIV Agents↗
PubMed2006

Muller's ratchet in symbiont populations.

Muller's ratchet, the inevitable accumulation of deleterious mutations in asexual populations, has been proposed as a major factor in genome degradation of obligate symbiont organisms. Essentially, if left unchecked the ratchet will with certainty cause extinction due to the ever increasing mutational load. This paper examines the evolutionary fate of insect symbionts, using mathematical modelling to simulate the accumulation of deleterious mutations. We investigate the effects of a hierarchical two level population structure. Since each host contains its own subpopulation of symbionts, there will be a large number of small symbiont populations linked indirectly via selection on the host level. We show that although the separate subpopulations will accumulate deleterious mutations quickly, the symbiont population as a whole will be protected from extinction by selection acting on the hosts. As a consequence, the extent of genome degradation observed in present day symbionts is more likely to represent loss of functions that were (near-) neutral to the host, rather than a snap shot of a decline towards complete genetic collapse.

Animals↗
PubMed1994

Control of autoantibody affinity by selection against amino acid replacements in the complementarity-determining regions.

Rheumatoid factor (RF) autoantibodies can be produced in healthy individuals after infections or immunizations and thus escape normal tolerization mechanisms. It has not been clear whether such autoantibodies can undergo somatic hypermutation and affinity maturation similar to antibodies to exogenous antigens. We have investigated how these autoantibodies are regulated in normal individuals by analyzing the sequences of monoclonal IgM RFs obtained as hybridomas from donors after immunization. The variable regions undergo extensive hypermutation, but in contrast to antibodies against exogenous antigens, there is a strong selection against mutations that result in replacement of amino acids in the hypervariable, or complementarity-determining, regions. Furthermore, we found no increase in affinity of these RFs with the accumulation of mutations. This suggests that high-affinity variants are tolerized during the hypermutation process and there is a peripheral mechanism operating on certain autoreactive B cells that, while not deleting or anergizing all autoreactive cells, prevents the generation of high-affinity autoantibodies. Comparison of RFs by using the VH1 DP-10 heavy chain variable region segment from both normal individuals and rheumatoid arthritis (RA) patients suggests that RF from RA patients may not be subject to such a controlling mechanism.

Antibody Affinity↗
PubMed1995

Molecular mechanisms of multiple drug resistance in clinical isolates of Mycobacterium tuberculosis.

The molecular mechanisms of resistance to streptomycin, rifampin, and isoniazid in 53 Mycobacterium tuberculosis clinical isolates were examined. Twenty-five of 44 streptomycin-resistant strains had mutations in the rpsL gene and 5 of these had rrs gene perturbations. The region of the rpoB gene that is associated with resistance to rifampin was altered in 28 of 29 rifampin-resistant strains. Mutations in known genetic markers of isoniazid resistance were detected in 25 of 42 isoniazid-resistant isolates: 20 strains had katG gene alterations and 5 had perturbations in the inhA operon. Of the 20 multiply resistant strains with reduced sensitivity to streptomycin, rifampin, and isoniazid, 11 had mutations in genetic markers associated with resistance to each of these three drugs. These studies suggest that the primary mechanism of multiple drug resistance in tuberculosis is the accumulation of mutations in individual drug target genes.

Antitubercular Agents↗
PubMed1999

A model for radiation-related cancer suggested by atomic bomb survivor data.

The age-time patterns of excess cancer risk among A-bomb survivors followed up by the Radiation Effects Research Foundation inevitably carry implications regarding the mechanisms of radiation-related cancer. It has recently been found, quite surprisingly and in contrast to impressions given by the relative risks, that for most solid cancers the excess incidence rates themselves depend very little on age at exposure or time since exposure, but mainly on attained age. This paper investigates a mechanistic model that conforms to these age-time patterns. The essence of the model, which is highly idealized, is that: (a) a cancer is caused by mutations that accumulate in a stem cell throughout life, essentially the Armitage-Doll multistage model, and (b) radiation is a general mutagen that can cause virtually any of these mutations. Although postulate (b) departs from previous modeling considerations, the extent to which it explains various aspects of the data in substantial detail is remarkable. A strength of the model is that, similarly to the Armitage-Doll multistage model but differently from many others, it predicts characteristic age-time patterns of excess rates rather independently of its parameter values. The consequence of (a) is that, in Armitage-Doll fashion, background rates increase throughout life as a power of age. The consequence of (b) is that excess absolute rates do not depend on age at exposure and increase with age to a power one less than that of the background rates. Thus the excess relative risk, which is the ratio of these rates, decreases throughout life as 1/age with no dependence on age at exposure. Although this age pattern of relative risks corresponds closely to the RERF data for solid cancer, the interpretation of such a description is quite different from the usual one in which age at exposure plays a primary role.

Adult↗