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PubMed2001

Epitope clusters in the major outer membrane protein of Chlamydia trachomatis.

Immunopathology that is caused by re-infection with Chlamydia trachomatis is very common in humans despite regular responses to multiple, often conserved, antibody and T cell epitopes. Recurrent mutations that disrupt T cell epitopes in the major outer membrane protein in clinical isolates and the reduced transcription of HLA genes by infected cells may be evidence for pathogen evasion of protective immune responses. Subunit vaccines containing recently discovered clusters of T cell epitopes in the major outer membrane protein that are presented with diverse HLA allotypes may allow widespread protective immunization while avoiding the suppression of lasting immunity that occurs by unknown mechanisms associated with infection.

Amino Acid Sequence↗
PubMed2002

Using cancer genetics to guide the selection of anticancer drug targets.

The genetic alterations that cause cancer are coming into view. Genes that are recurrently mutated in a particular form of human cancer flag the proteins (or molecular pathways) that are critical for the evolution of that malignancy. The first generation of anticancer agents prospectively guided by these principles, for which imatinib mesylate is a prototype, inhibit the biochemical activities that result from gain-of-function oncogenic mutations. Advances in somatic cell genetics and chemical biology should facilitate the development of a second generation of agents that will inhibit proteins that are selectively required for survival in the context of specific cancer-causing mutations, whether loss-of-function or gain-of-function.

Animals↗
PubMed2005

Shared promiscuous activities and evolutionary features in various members of the amidohydrolase superfamily.

The amidohydrolase superfamily comprises hundreds of hydrolytic enzymes of the (beta/alpha)8 barrel fold with mono- or binuclear active-site metal centers, and a diverse spectrum of substrates and reactions. Promiscuous activities, or cross-reactivities, between different members of the same superfamily may provide important hints regarding evolutionary and mechanistic relationships. We examined three members: dihydroorotase (DHO), phosphotriesterase (PTE), and PTE-homology protein (PHP). Of particular interest are PTE, which is thought to have evolved within the last several decades, and PHP, an amidohydrolase superfamily member of unknown function, and the closest known homologue of PTE. We found a diverse and partially overlapping pattern of promiscuous activities in these enzymes, including a significant lactonase activity in PTE, esterase activities in both PTE and PHP, and a weak PTE activity in DHO. Directed evolution was applied to improve the promiscuous esterase activities of PTE and PHP. Remarkably, the most recurrent mutation increasing esterase activity in PTE, or PHP, maps to the same location in their superposed 3D structures. The evolved variants also exhibit newly acquired promiscuous activities that were not selected for, including very weak, yet measurable, paraoxonase activity in PHP. Our results illustrate the mechanistic, structural, and evolutionary links between these enzymes, and highlight the importance of studying laboratory evolution intermediates that might resemble node intermediates along the evolutionary pathways leading to the divergence of enzyme superfamilies.

Amidohydrolases↗
PubMed1988

MHC polymorphism pre-dating speciation.

Two features distinguish the polymorphism of the major histocompatibility complex (MHC) loci from that of other loci: its high diversity and the large genetic distance between MHC alleles. More than 100 alleles exist in natural populations in the mouse at each of the functional class I and class II alleles, all alleles occurring at frequencies that cannot be explained by recurrent mutations. Some of the alleles differ by approximately 70 nucleotides in the coding region alone and some of the products of the allelic genes differ by more than 50 amino acids. It has generally been assumed that these differences accumulated after species inception. Here, we present evidence for an alternative explanation of the origin of MHC polymorphism: a large part of the MHC polymorphism pre-dates speciation and is passed on from species to species. We describe allelic differences that must have arisen before the separation of mice and rats from a common ancestor more than 10 million years ago.

Alleles↗
PubMed2026

Histone variant H2A.J is an epigenetic regulator of metastasis in lung adenocarcinoma.

Metastasis is a major contributor to poor patient survival in lung adenocarcinoma (LUAD); however, the underlying mechanisms remain incompletely understood. Unlike tumorigenesis-associated mutations, recurrent genetic alterations specifically linked to metastasis have not been identified, suggesting that epigenetic mechanisms may play a key role. In this study, we report that histone H2A variant H2A.J expression is significantly down-regulated in LUAD, and that low H2A.J levels are associated with unfavorable survival outcomes. Functional assays revealed that H2A.J overexpression suppresses cancer cell invasion and metastatic potential by modulating the expression of metastasis-associated genes, including TMEM158. Mechanistically, H2A.J is deposited in the promoter region of TMEM158, where it alters the local chromatin status to suppress transcriptional activity. Taken together, our findings suggest that H2A.J functions as an epigenetic suppressor of metastasis in LUAD and highlights its potential as both a prognostic biomarker and a therapeutic target to metastatic progression.

Humans↗
PubMed2025

Compensatory evolution to DNA replication stress is robust to nutrient availability.

Evolutionary repair refers to the compensatory evolution that follows perturbations in cellular processes. While evolutionary trajectories are often reproducible, other studies suggest they are shaped by genotype-by-environment (GxE) interactions. Here, we test the predictability of evolutionary repair in response to DNA replication stress-a severe perturbation impairing the conserved mechanisms of DNA synthesis, resulting in genetic instability. We conducted high-throughput experimental evolution on Saccharomyces cerevisiae experiencing constitutive replication stress, grown under different glucose availability. We found that glucose levels impact the physiology and adaptation rate of replication stress mutants. However, the genetics of adaptation show remarkable robustness across environments. Recurrent mutations collectively recapitulated the fitness of evolved lines and are advantageous across macronutrient availability. We also identified a novel role of the mediator complex of RNA polymerase II in adaptation to replicative stress. Our results highlight the robustness and predictability of evolutionary repair mechanisms to DNA replication stress and provide new insights into the evolutionary aspects of genome stability, with potential implications for understanding cancer development.

DNA Replication↗
PubMed1998

Rapid genotypic diagnosis of type 2A von Willebrand's disease by heteroduplex analysis.

We have previously reported a rapid heteroduplex-based technique which is able to identify at least 10 recurrent mutations associated with type 2A von Willebrand's disease. Thirteen patients with this disorder were genotyped by this method and a specific mutation was identified in nine cases. This simple DNA based approach can provide useful information to support data derived from phenotype tests in the initial assessment of such patients.

DNA↗
PubMed2001

Junctional epidermolysis bullosa gravis (Herlitz): diagnostic and genetic aspects.

We report on a boy suffering from lethal junctional epidermolysis bullosa gravis (JEBH) (Herlitz-type) (OMIM 226700). Screening for mutations of LAMB3 gene with polymerase chain reaction (PCR) amplification of all exons from genomic DNA and subsequent heteroduplex analysis and dideoxynucleotide sequencing of heteroduplex forming PCR products disclosed two mutations: the recurrent maternal mutation R635X and the novel paternal mutation 1629insG, both in exon 14 of LAMB3. Both mutations lead to a premature termination code, non-sense mediated mRNA decay and to absence of the synthesis of the beta3 chain of laminin 5. During the mutation screening of the index patient a second pregnancy was ascertained. After amniocentesis (14 + 1 week of pregnancy), prenatal diagnosis from fetal cells was performed and compound heterozygosity for both mutations was evident. The consultants decided to have a termination of pregnancy shortly after the diagnosis. Remarkable skin fragility of the fetus was evident by clinical examination. Complete absence of laminin 5 could be demonstrated by immunofluorescence staining. By the third pregnancy of this couple so far screened for mutations by chorionic villus sampling for prenatal molecular diagnosis a healthy but heterozygous child is expected.

Epidermolysis Bullosa, Junctional↗
PubMed1997

Genetic diversity among Leishmania (Viannia) parasites.

The mode of reproduction in, and population structure of Leishmania (Viannia) parasites were deduced from the nature and extent of genetic variation in the parasites. Forty-seven zymodemes belonging to the Viannia subgenus were analysed by enzyme electrophoresis and the profiles compared with those of two zymodemes belonging to the Leishmania subgenus. The results revealed extensive genetic variation in Viannia. The widespread occurrence of certain zymodemes, the level of heterozygosity and the great similarity observed among the samples are indicative of a clonal population structure. However, the large number of recurrent mutations needed to explain the variation observed and the presence of hybrid parasites indicate that occasional bouts of genetic exchange may occur.

Animals↗
PubMed1987

Homogenization of tandemly repeated nucleotide sequences by distance-dependent nucleotide sequence conversion.

Previous work revealed that recurrent mutations (= mutation occurring more than once) in the tandemly repeated arrays present in nontranscribed spacers (NTS) of ribosomal RNA genes (rDNA) are clustered, i.e., they most frequently occur in repeats with adjacent or alternate distribution. A possible explanation is that the likelihood of heteroduplex formation, a prerequisite of gene conversion, decreases with the distance between repeats. To test this possibility, evolution of an array of 11 initially homogeneous repeats was computer simulated using three models, two assuming that the likelihood of heteroduplex formation decreases with increasing distance between the repeats and one assuming that it is constant. Patterns of mutation distribution obtained in computer simulations were compared with the distribution of mutations found in the repeated arrays in the NTS of seven rDNA clones. The patterns of mutations generated by the models assuming that the likelihood of heteroduplex formation decreases as distance between the repeats increases agreed with the patterns observed in rDNA; the patterns generated by the model assuming that the likelihood is independent of distance between repeats disagreed with the patterns observed in the rDNA clones. The topology of the heteroduplex formed between DNA in adjacent repeats predicts that the most frequently occurring conversions in the NTS repeated arrays will be shorter than the length of the repeat. The topology of the heteroduplex also predicts that if the heteroduplex leads to crossing over a circular repeat is excised. It is speculated that the circle can transpose or can be amplified via rolling circle replication and subsequently transpose. It is also shown that homogenization of the NTS repeated arrays proceeds at different rates in different species.

Animals↗
PubMed1992

Mitochondrial DNA length variation and heteroplasmy in populations of white sturgeon (Acipenser transmontanus).

Southern blot analysis was used to quantify the extent of mtDNA D-loop length variation in two populations of white sturgeon, Acipenser transmontanus. Over 42% of individuals were heteroplasmic for up to six different mtDNA length variants attributable to varying copy numbers of an 82-bp repeat sequence. Chi-square analyses revealed that the frequencies of length genotypes and the incidence of heteroplasmy were significantly different between Fraser and Columbia River sturgeon populations but not between restriction site haplotypes. Heteroplasmic fish have, on average, higher copy number than homoplasmic fish. Forty-five of 101 homoplasmic individuals carry only a single copy of the repeat, while none of the 73 heteroplasmic fish has the single repeat as the predominant variant. On the basis of differences in frequency distributions of copy number within and between fish, we suggest that (1) heteroplasmy is maintained by high recurrent mutation of multiple copy genomes, favoring increased copy number and (2) the mutation pressure toward higher copy number heteroplasmy is partially offset by selection to reduced genome size and segregation to the homoplasmic condition.

Animals↗
PubMed1995

The pattern of neutral molecular variation under the background selection model.

Stochastic simulations of the infinite sites model were used to study the behavior of genetic diversity at a neutral locus in a genomic region without recombination, but subject to selection against deleterious alleles maintained by recurrent mutation (background selection). In large populations, the effect of background selection on the number of segregating sites approaches the effect on nucleotide site diversity, i.e., the reduction in genetic variability caused by background selection resembles that caused by a simple reduction in effective population size. We examined, by coalescence-based methods, the power of several tests for the departure from neutral expectation of the frequency spectra of alleles in samples from randomly mating populations (Tajima's, Fu and Li's, and Watterson's tests). All of the tests have low power unless the selection against mutant alleles is extremely weak. In Drosophila, significant Tajima's tests are usually not obtained with empirical data sets from loci in genomic regions with restricted recombination frequencies and that exhibit low genetic diversity. This is consistent with the operation of background selection as opposed to selective sweeps. It remains to be decided whether background selection is sufficient to explain the observed extent of reduction in diversity in regions of restricted recombination.

Animals↗
PubMed1996

Length variation, heteroplasmy and sequence divergence in the mitochondrial DNA of four species of sturgeon (Acipenser).

The extent of mtDNA length variation and heteroplasmy as well as DNA sequences of the control region and two tRNA genes were determined for four North American sturgeon species: Acipenser transmontanus, A. medirostris, A. fulvescens and A. oxyrhnychus. Across the Continental Divide, a division in the occurrence of length variation and heteroplasmy was observed that was concordant with species biogeography as well as with phylogenies inferred from restriction fragment length polymorphisms (RFLP) of whole mtDNA and pairwise comparisons of unique sequences of the control region. In all species, mtDNA length variation was due to repeated arrays of 78-82-bp sequences each containing a D-loop strand synthesis termination associated sequence (TAS). Individual repeats showed greater sequence conservation within individuals and species rather than between species, which is suggestive of concerted evolution. Differences in the frequencies of multiple copy genomes and heteroplasmy among the four species may be ascribed to differences in the rates of recurrent mutation. A mechanism that may offset the high rate of mutation for increased copy number is suggested on the basis that an increase in the number of functional TAS motifs might reduce the frequency of successfully initiated H-strand replications.

Animals↗
PubMed2000

Cladistic structure within the human Lipoprotein lipase gene and its implications for phenotypic association studies.

Haplotype variation in 9.7 kb of genomic DNA sequence from the human lipoprotein lipase (LPL) gene was scored in three populations: African-Americans from Jackson, Mississippi (24 individuals), Finns from North Karelia, Finland (24), and non-Hispanic whites from Rochester, Minnesota (23). Earlier analyses had indicated that recombination was common but concentrated into a hotspot and that recurrent mutations at multiple sites may have occurred. We show that much evolutionary structure exists in the haplotype variation on either side of the recombinational hotspot. By peeling off significant recombination events from a tree estimated under the null hypothesis of no recombination, we also reveal some cladistic structure not disrupted by recombination during the time to coalescence of this variation. Additional cladistic structure is estimated to have emerged after recombination. Many apparent multiple mutational events at sites still remain after removing the effects of the detected recombination/gene conversion events. These apparent multiple events are found primarily at sites identified as highly mutable by previous studies, strengthening the conclusion that they are true multiple events. This analysis portrays the complexity of the interplay among many recombinational and mutational events that would be needed to explain the patterns of haplotype diversity in this gene. The cladistic structure in this region is used to identify four to six single-nucleotide polymorphisms (SNPs) that would provide disequilibrium coverage over much of this region. These sites may be useful in identifying phenotypic associations with variable sites in this gene. Evolutionary considerations also imply that the SNPs in the 3' region should have general utility in most human populations, but the 5' SNPs may be more population specific. Choosing SNPs at random would generally not provide adequate disequilibrium coverage of the sequenced region.

Black or African American↗
PubMed2001

Estimating the total number of alleles using a sample coverage method.

Previously reported methods for estimating the number of different alleles at a single locus in a population have not described a useful general result. Using the number of alleles observed in a sample gives an underestimate for the true number of alleles. The similar problem of estimating the number of species in a population was first investigated in 1943. In this article we use the sample coverage method proposed by Chao and Lee in 1992 to estimate the number of alleles in a population when there are unequal allele frequencies. Simulation studies under the recurrent mutation model show that, for reasonable sample sizes, a significantly better estimate of the true number can be obtained than that using only the observed alleles. Results under the stepwise mutation model and infinite-allele model are presented. Possible applications include improving the characterization of the prior distribution for the allele frequencies, adjusting the estimates of genetic diversity, and estimating the range of microsatellite alleles.

Alleles↗
PubMed2021

Functional impact of cancer-associated cohesin variants on gene expression and cellular identity.

Cohesin is a ring-shaped protein complex that controls dynamic chromosome structure. Cohesin activity is important for a variety of biological processes, including formation of DNA loops that regulate gene expression. The precise mechanisms by which cohesin shapes local chromosome structure and gene expression are not fully understood. Recurrent mutations in cohesin complex members have been reported in various cancers, though it is not clear whether many cohesin sequence variants have phenotypes and contribute to disease. Here, we utilized CRISPR/Cas9 genome editing to introduce a variety of cohesin sequence variants into murine embryonic stem cells and investigate their molecular and cellular consequences. Some of the cohesin variants tested caused changes to transcription, including altered expression of gene encoding lineage-specifying developmental regulators. Altered gene expression was also observed at insulated neighborhoods, where cohesin-mediated DNA loops constrain potential interactions between genes and enhancers. Furthermore, some cohesin variants altered the proliferation rate and differentiation potential of murine embryonic stem cells. This study provides a functional comparison of cohesin variants found in cancer within an isogenic system, revealing the relative roles of various cohesin perturbations on gene expression and maintenance of cellular identity.

Animals↗
PubMed1997

Abnormal FGFR 3 expression in cartilage of thanatophoric dysplasia fetuses.

Thanatophoric dysplasia (TD), the commonest lethal skeletal dysplasia in humans, is accounted for by recurrent mutations in the fibroblast growth factor receptor 3 gene (FGFR 3), causing its constitutive activation in vitro. Taking advantage of medical abortion of 18 TD fetuses, cartilage sections were studied for FGFR 3 gene expression by in situ hybridization and immunohistochemistry. Specific antibodies revealed high amounts of FGFR 3 in cartilage of TD fetuses with no increased level of the corresponding mRNA. The specific signal was mainly detected in the nucleus of proliferative and hypertrophic chondrocytes. Based on this observation and the abnormal expression of collagen type X in hypertrophic TD chondrocytes, we suggest that constitutive activation of the receptor through formation of a stable dimer increases its stability and promotes its translocation into the nucleus, where it might interfere with terminal chondrocyte differentiation.

Cartilage↗
PubMed1998

Molecular analysis of the PDS gene in Pendred syndrome.

Pendred syndrome is an autosomal recessive disorder characterized by the association between sensorineural hearing loss and thyroid swelling or goitre and is likely to be the most common form of syndromic deafness. Within the thyroid gland of affected individuals, iodide is incompletely organified with variable effects upon thyroid hormone biosynthesis, whilst the molecular basis of the hearing loss is unknown. The PDS gene has been identified by positional cloning of chromosome 7q31, within the Pendred syndrome critical linkage interval and encodes for a putative ion transporter called pendrin. We have investigated a cohort of 56 kindreds, all with features suggestive of a diagnosis of Pendred syndrome. Molecular analysis of the PDS gene identified 47 of the 60 (78%) mutant alleles in 31 families (includes three homozygous consanguineous kindreds and one extended family segregating three mutant alleles). Moreover, four recurrent mutations accounted for 35 (74%) of PDS disease chromosomes detected and haplotype analysis would favour common founders rather than mutational hotspots within the PDS gene. Whilst these findings demonstrate molecular heterogeneity for PDS mutations associated with Pendred syndrome, this study would support the use of molecular analysis of the PDS gene in the assessment of families with congenital hearing loss.

DNA Mutational Analysis↗