Mutation frequency analysis of mononucleotide and dinucleotide repeats after oxidative stress

Tracing brain genotoxic stress in Parkinson's disease with a novel single-cell genetic sensor

To develop an in vivo tool to probe brain genotoxic stress, we designed a viral proxy as a single-cell genetic sensor termed PRISM that harnesses the instability of recombinant adeno-associated virus genome processing and a hypermutable repeat sequence-dependent reporter. PRISM exploits the virus-host interaction to probe persistent neuronal DNA damage and overactive DNA damage response. A Parkinson's disease (PD)-associated environmental toxicant, paraquat (PQ), inflicted neuronal genotoxic stress sensitively detected by PRISM. The most affected cell type in PD, dopaminergic (DA) neurons in substantia nigra, was distinguished by a high level of genotoxic stress following PQ exposure. Human alpha-synuclein proteotoxicity and propagation also triggered genotoxic stress in nigral DA neurons in a transgenic mouse model. Genotoxic stress is a prominent feature in PD patient brains. Our results reveal that PD-associated etiological factors precipitated brain genotoxic stress and detail a useful tool for probing the pathogenic significance in aging and neurodegenerative disorders.

Methods to determine DNA structural alterations and genetic instability

Chromosomal DNA is a dynamic structure that can adopt a variety of non-canonical (i.e., non-B) conformations. In this regard, at least 10 different forms of non-B DNA conformations have been identified; many of them have been found to be mutagenic, and associated with human disease development. Despite the importance of non-B DNA structures in genetic instability and DNA metabolic processes, mechanisms by which instability occurs remain largely undefined. The purpose of this review is to summarize current methodologies that are used to address questions in the field of non-B DNA structure-induced genetic instability. Advantages and disadvantages of each method will be discussed. A focused effort to further elucidate the mechanisms of non-B DNA-induced genetic instability will lead to a better understanding of how these structure-forming sequences contribute to the development of human disease.

Models for chromosomal replication-independent non-B DNA structure-induced genetic instability

Regions of genomic DNA containing repetitive nucleotide sequences can adopt a number of different structures in addition to the canonical B-DNA form: many of these non-B DNA structures are causative factors in genetic instability and human disease. Although chromosomal DNA replication through such repetitive sequences has been considered a major cause of non-B form DNA structure-induced genetic instability, it is also observed in non-proliferative tissues. In this review, we discuss putative mechanisms responsible for the mutagenesis induced by non-B DNA structures in the absence of chromosomal DNA replication.

A genome-wide view of the spectrum of spontaneous mutations in yeast

The mutation process ultimately defines the genetic features of all populations and, hence, has a bearing on a wide range of issues involving evolutionary genetics, inheritance, and genetic disorders, including the predisposition to cancer. Nevertheless, formidable technical barriers have constrained our understanding of the rate at which mutations arise and the molecular spectrum of their effects. Here, we report on the use of complete-genome sequencing in the characterization of spontaneously arising mutations in the yeast Saccharomyces cerevisiae. Our results confirm some findings previously obtained by indirect methods but also yield numerous unexpected findings, in particular a very high rate of point mutation and skewed distribution of base-substitution types in the mitochondrion, a very high rate of segmental duplication and deletion in the nuclear genome, and substantial deviations in the mutational profile among various model organisms.

Flow cytometric detection of tandem repeat mutations induced by various chemical classes

To facilitate detection of genotoxicity from environmental mutagen exposure, we generated an in vitro enhanced green fluorescence protein (EGFP) reactivation assay that quickly and effectively detects frameshift mutations in tandem repeat sequences (TRS). Two murine cell lines, C3H10T1/2 and mismatch repair deficient MC2a, were stably transfected with EGFP reporter plasmids in which the EGFP constructs contain TRS that put the EGFP sequence out of frame. These included several 2, 3, 4, 5 and 6 bp repeat sequences, a control non-repetitive sequence and a human gene sequence containing a 4 bp repeat motif. Transfected cultures were exposed to five model mutagens and carcinogens: hydrogen peroxide (H(2)O(2)), 12-O-tetradecanoyl-phorbol-13-acetate (TPA), benzo-a-pyrene-diol-epoxide (BPDE), ethyl nitrosourea (ENU), 9-aminoacridine (9AA) and two controls: acetone and ethanol. Frameshift mutations resulted in green fluorescent revertants, as determined by flow cytometry, and were confirmed, for 9AA treatments, by sequencing. All five treatments with model agents induced statistically significant sequence- and exposure-dependent responses in MC2a cells and a negative response with the two negative control treatments, acetone and ethanol. Similar responses were seen in a smaller panel of treatments and plasmids in C3H10T1/2 cells. The mutation frequencies were higher in cells transfected with the plasmids containing TRS than those harbouring the control construct lacking repeats. The highest mutation frequencies were observed with H(2)O(2) and 9AA treatments, yielding up to a 50-fold difference between vehicle and highest concentration treatment. ENU, BPDE, and to a lesser extent TPA treatments, also showed a statistically significant exposure response. Results from these experiments reveal that the assay responds robustly to various classes of mutagenic substances, as well as to rodent carcinogens that are inactive in conventional mutation assays, and that responses are not linked to cytotoxicity. This assay is a promising approach for detecting chemically induced frameshifts within certain DNA sequences of interest, but further characterization and validation are required prior to general use in genotoxicity screening.

Molecular mechanisms of human carcinogenesis

Intensive research efforts during the last several decades have increased our understanding of carcinogenesis, and have identified a genetic basis for the multi-step process of cancer development. Tumors grow through a process of clonal expansion driven by mutation. Several forms of molecular alteration have been described in human cancers, and these can be generally classified as chromosomal abnormalities and nucleotide sequence abnormalities. Most cancer cells display a phenotype characterized by genomic hypermutability, suggesting that genomic instability may precede the acquisition of transforming mutations in critical target genes. Reduced to its essence, cancer is a disease of abnormal gene expression, and these genetic abnormalities contribute to cancer pathogenesis through inactivation of negative mediators of cell proliferation (including tumor suppressor genes) and activation of positive mediators of cell proliferation (including proto-oncogenes). In several human tumor systems, specific genetic alterations have been shown to correlate with well-defined histopathological stages of tumor development and progression. Although the significance of mutations to the etiological mechanisms of tumor development has been debated, a causal role for such genetic lesions is now commonly accepted for most human cancers. Thus, genetic lesions represent an integral part of the processes of neoplastic transformation, tumorigenesis, and tumor progression, and as such represent potentially valuable markers for cancer detection and staging.

Molecular dissection of mouse soluble guanylyl cyclase alpha1 promoter

Soluble guanylyl cyclase (sGC) is the only known receptor for nitric oxide (NO) and is downregulated in aging and hypertension. Little is known about sGC gene transcriptional regulation. In order to characterize the sGC transcriptional system, we cloned and sequenced the 5(') flanking region of mouse sGC alpha(1) gene (AY116663). Structurally, it is a non-canonical TATA-less promoter that we mapped to chromosome 3 with many putative regulation sites for Sp-1, NF-kappaB, and AP-1 transcription factors amongst others, and two (TG:CA)(n) dinucleotide microsatellites near the transcriptional start point. The cloned upstream sequence produced a 5-fold increase in luciferase activity in Cos7, HeLa, NIH3T3, and 293 cells as well as in mouse VSMC-like kidney mesangial cells. In the latter cell type, we showed that sGC alpha(1) promoter activity was dependent on the presence of its 5(') unstranslated region (5(')UTR).