Estimation of mutation rates in cultured mammalian cells

Improved sequence variant analysis strategy by automated false positive removal

Sequence variant analysis (SVA) is critical in therapeutic protein development because it ensures the absence of genetic mutations of a production clone or high-level misincorporations during cell culture. While software for searching sequence variants from mass spectrometry data are available, effectively distinguishing true positives from a large number of false positives in the reported hits or identifications found in the error tolerant search mode is a challenge. This verification process must be done manually and can take several days or even weeks to accomplish. We report here the use of a Perl-based script to evaluate every identified hit to remove the false positives from the search results of PepFinder™ (also known as MassAnalyzer) based on orthogonal criteria. Our data show that the false positives from PepFinder™ output were reduced ∼4-fold without loss of accuracy in the detection of true identifications, representing a more than 70% reduction in time compared with the manual data verification process.

Adaptation prevents the extinction of Chlamydomonas reinhardtii under toxic beryllium

The current biodiversity crisis represents a historic challenge for natural communities: the environmental rate of change exceeds the population’s adaptation capability. Integrating both ecological and evolutionary responses is necessary to make reliable predictions regarding the loss of biodiversity. The race against extinction from an eco-evolutionary perspective is gaining importance in ecological risk assessment. Here, we performed a classical study of population dynamics—a fluctuation analysis—and evaluated the results from an adaption perspective. Fluctuation analysis, widely used with microorganisms, is an effective empirical procedure to study adaptation under strong selective pressure because it incorporates the factors that influence demographic, genetic and environmental changes. The adaptation of phytoplankton to beryllium (Be) is of interest because human activities are increasing the concentration of Be in freshwater reserves; therefore, predicting the effects of human-induced pollutants is necessary for proper risk assessment. The fluctuation analysis was performed with phytoplankton, specifically, the freshwater microalgae Chlamydomonas reinhardtii, under acute Be exposure. High doses of Be led to massive microalgae death; however, by conducting a fluctuation analysis experiment, we found that C. reinhardtii was able to adapt to 33 mg/l of Be due to pre-existing genetic variability. The rescuing adapting genotype presented a mutation rate of 9.61 × 10⁻⁶ and a frequency of 10.42 resistant cells per million wild-type cells. The genetic adaptation pathway that was experimentally obtained agreed with the theoretical models of evolutionary rescue (ER). Furthermore, the rescuing genotype presented phenotypic and physiologic differences from the wild-type genotype, was 25% smaller than the Be-resistant genotype and presented a lower fitness and quantum yield performance. The abrupt distinctions between the wild-type and the Be-resistant genotype suggest a pleiotropic effect mediated by an advantageous mutation; however, no sequencing confirmation was performed.

Mutation of cancer driver MLL2 results in transcription stress and genome instability

Genome instability is a recurring feature of tumorigenesis. Mutation in MLL2, encoding a histone methyltransferase, is a driver in numerous different cancer types, but the mechanism is unclear. Here, we present evidence that MLL2 mutation results in genome instability. Mouse cells in which MLL2 gene deletion can be induced display elevated levels of sister chromatid exchange, gross chromosomal aberrations, 53BP1 foci, and micronuclei. Human MLL2 knockout cells are characterized by genome instability as well. Interestingly, MLL2 interacts with RNA polymerase II (RNAPII) and RECQL5, and, although MLL2 mutated cells have normal overall H3K4me levels in genes, nucleosomes in the immediate vicinity of RNAPII are hypomethylated. Importantly, MLL2 mutated cells display signs of substantial transcription stress, and the most affected genes overlap with early replicating fragile sites, show elevated levels of γH2AX, and suffer frequent mutation. The requirement for MLL2 in the maintenance of genome stability in genes helps explain its widespread role in cancer and points to transcription stress as a strong driver in tumorigenesis.

A stochastic model for estimation of mutation rates in multiple-replication proliferation processes

In this paper we propose a stochastic model based on the branching process for estimation and comparison of the mutation rates in proliferation processes of cells or microbes. We assume in this model that cells or microbes (the elements of a population) are reproduced by generations and thus the model is more suitably applicable to situations in which the new elements in a population are produced by older elements from the previous generation rather than by newly created elements from the same current generation. Cells and bacteria proliferate by binary replication, whereas the RNA viruses proliferate by multiple replication. The model is in terms of multiple replications, which includes the special case of binary replication. We propose statistical procedures for estimation and comparison of the mutation rates from data of multiple cultures with divergent culture sizes. The mutation rate is defined as the probability of mutation per replication per genome and thus can be assumed constant in the entire proliferation process. We derive the number of cultures for planning experiments to achieve desired accuracy for estimation or desired statistical power for comparing the mutation rates of two strains of microbes. We establish the efficiency of the proposed method by demonstrating how the estimation of mutation rates would be affected when the culture sizes were assumed similar but actually diverge.

Occurrence of copper resistant mutants in the toxic cyanobacteria Microcystis aeruginosa: characterisation and future implications in the use of copper sulphate as algaecide

Freshwater toxic cyanobacteria are an increasing problem to human and animal health. Control of cyanobacteria in water supply reservoirs involves the use of algaecides, such as copper sulphate, usually in a repetitive way. Repercussions of recurrent algaecide treatments on cyanobacteria population dynamics remain still unknown. We studied the adaptation of cyanobacteria to lethal doses of copper sulphate by using Microcystis aeruginosa as an experimental model. A fluctuation analysis demonstrated that copper-resistant cells arise by spontaneous mutations that occur randomly prior to exposition to copper sulphate. The rate of spontaneous mutation from copper sensitivity to resistance was 1.76 x 10(-6) mutants per cell division. Resistant mutants exhibited a diminished fitness in the absence of copper sulphate, but only these variants were able to grow at Cu(2+) concentrations higher than 5.8 microM. In addition, copper-resistant cells were significantly smaller than wild-type ones. Warnings on the long-term consequences of repetitive algaecide treatments in water supplies are suggested.

Induction of genomic instability in TK6 human lymphoblasts exposed to 137Cs gamma radiation: comparison to the induction by exposure to accelerated 56Fe particles

The induction of genomic instability in TK6 human lymphoblasts by exposure to (137)Cs gamma radiation was investigated by measuring the frequency and characteristics of unstable clones isolated approximately 36 generations after exposure. Clones surviving irradiation and control clones were analyzed for 17 characteristics including chromosomal aberrations, growth defects, alterations in response to a second irradiation, and mutant frequencies at the thymidine kinase and Na(+)/K(+) ATPase loci. Putative unstable clones were defined as those that exhibited a significant alteration in one or more characteristics compared to the controls. The frequency and characteristics of the unstable clones were compared in clones exposed to (137)Cs gamma rays or (56)Fe particles. The majority of the unstable clones isolated after exposure to either gamma rays or (56)Fe particles exhibited chromosomal instability. Alterations in growth characteristics, radiation response and mutant frequencies occurred much less often than cytogenetic alterations in these unstable clones. The frequency and complexity of the unstable clones were greater after exposure to (56)Fe particles than to gamma rays. Unstable clones that survived 36 generations after exposure to gamma rays exhibited increases in the incidence of dicentric chromosomes but not of chromatid breaks, whereas unstable clones that survived 36 generations after exposure to (56)Fe particles exhibited increases in both chromatid and chromosome aberrations.

Characteristics of genomic instability in clones of TK6 human lymphoblasts surviving exposure to 56Fe ions

Genomic instability in the human lymphoblast cell line TK6 was studied in clones surviving 36 generations after exposure to accelerated 56Fe ions. Clones were assayed for 20 characteristics, including chromosome aberrations, plating efficiency, apoptosis, cell cycle distribution, response to a second irradiation, and mutant frequency at two loci. The primary effect of the 56Fe-ion exposure on the surviving clones was a significant increase in the frequency of unstable chromosome aberrations compared to the very low spontaneous frequency, along with an increase in the phenotypic complexity of the unstable clones. The radiation-induced increase in the frequency of unstable chromosome aberrations was much greater than that observed previously in clones of the related cell line, WTK1, which in comparison to the TK6 cell line expresses an increased radiation resistance, a mutant TP53 protein, and an increased frequency of spontaneous unstable chromosome aberrations. The characteristics of the unstable clones of the two cell lines also differed. Most of the TK6 clones surviving exposure to 56Fe ions showed unstable cytogenetic abnormalities, while the phenotype of the WTK1 clones was more diverse. The results underscore the importance of genotype in the characteristics of instability after radiation exposure.

Diverse delayed effects in human lymphoblastoid cells surviving exposure to high-LET (56)Fe particles or low-LET (137)Cs gamma radiation

To obtain information on the origin of radiation-induced genomic instability, we characterized a total of 166 clones that survived exposure to (56)Fe particles or (137)Cs gamma radiation, isolated approximately 36 generations after exposure, along with their respective control clones. Cytogenetic aberrations, growth alterations, responses to a second irradiation, and mutant frequencies at the Na(+)/K(+) ATPase and thymidine kinase loci were determined. A greater percentage of clones that survived exposure to (56)Fe particles exhibited instability (defined as clones showing one or more outlying characteristics) than in the case of those that survived gamma irradiation. The phenotypes of the unstable clones that survived exposure to (56)Fe particles were also qualitatively different from those of the clones that survived gamma irradiation. A greater percentage (20%) of the unstable clones that survived gamma irradiation than those that survived exposure to (56)Fe particles (4%) showed an altered response to the second irradiation, while an increase in the percentage of clones that had an outlying frequency of ouabain-resistant and thymidine kinase mutants was more evident in the clones exposed to (56)Fe particles than in those exposed to gamma rays. Growth alterations and increases in dicentric chromosomes were found only in clones with more than one alteration. These results underscore the complex nature of genomic instability and the likelihood that radiation-induced genomic instability arises from different original events.

Loss of Werner syndrome protein function promotes aberrant mitotic recombination

The chromosome 8p11-12 Werner syndrome (WRN ) locus encodes a RecQ helicase protein of unknown function that possesses both 3' --> 5' helicase and 3' --> 5' exonuclease activities. We show that WRN cell lines display a marked reduction in cell proliferation following mitotic recombination, and generate few viable gene conversion-type recombinants. These findings indicate that WRN plays a role in mitotic recombination, and that a loss of WRN function may promote genetic instability and disease via recombination-initiated mitotic arrest, cell death, or gene rearrangement.

A note on efficient estimation of mutation rates using Luria-Delbrück fluctuation analysis

The maximum likelihood and Luria-Delbrück P0 methods for the estimation of spontaneous mutation rates are compared. The maximum likelihood method is fully efficient, utilizing all available information in a fluctuation experiment, but can be numerically cumbersome. Under certain conditions, there is little loss of efficiency using the P0 method, which is readily implemented numerically. Design considerations should aid investigators in minimizing statistical errors associated with the statistical analysis of fluctuation experiments.

Differences in the rates of gene amplification in nontumorigenic and tumorigenic cell lines as measured by Luria-Delbrück fluctuation analysis

It has been hypothesized that genomic fluidity is an important component of tumorigenesis. Previous studies described the relationship between tumorigenicity and one marker for genomic fluidity, gene amplification. In this report, these studies are extended with the rat liver epithelial cell lines to show that: (i) the amplification in these cells arises in a spontaneous fashion in the population (i.e., the variants detected are not preexisting in the population), and (ii) the rate of spontaneous amplification (mutation), as measured by Luria-Delbrück fluctuation analysis, is significantly lower in the nontumorigenic cells than in the tumorigenic cells. The rate was estimated by using the Po method and the method of means. The rate of spontaneous amplification of the gene encoding the multifunctional protein CAD (containing the enzymatic activities carbamoyl-phosphate synthase, aspartate transcarbamylase, and dihydroorotase) in the highly tumorigenic cells was significantly greater than that for the nontumorigenic cells, reaching almost 1 x 10(-4) events per cell per generation. The rate of this mutagenic event is high compared to the rate of point mutations usually reported in mammalian cells, and its potential contribution to the tumorigenic process will be discussed.

Lack of correlation between deoxyribonucleotide pool sizes, spontaneous mutation rates and malignant potential in Chinese hamster ovary cells

To examine the relationship between altered spontaneous mutation rates and malignant characteristics of cells, two hydroxyurea-resistant Chinese hamster ovary cell lines, with alterations in ribonucleotide reductase, were examined for their rates of spontaneous mutation to 6-thioguanine and ouabain resistance, tumor growth rates and their ability to form experimental lung metastases. The most resistant cell line, HR-R2T, showed no changes in the rate of spontaneous mutation to 6-thioguanine or ouabain resistance compared to the parental wild-type cell line; however, the mutant line formed lung metastases in experimental metastasis assays with BALB/c nu/nu mice, and exhibited metastatic abilities significantly different from the wild-type population. Furthermore, the HR-R2T population did not show imbalances in any of the deoxyribonucleoside triphosphate pool sizes, which are frequently observed in cells altered in ribonucleotide reductase activity. The second hydroxyurea-resistant line, HNR-AT, had gross alterations in dCTP and dGTP pools and although the rate of spontaneous mutation to 6-thioguanione resistance was unaltered, it showed a moderate decrease in the rate of spontaneous mutation to ouabain resistance when compared to the parental wild-type population. Interestingly, the HNR-AT cell line did not form any lung metastases in the experimental metastasis assay. Both mutant cell lines, HR-R2T, and HNR-AT, had increased tumor growth rates in C57 BALB/c "beige" nude (nu/nu) mice as compared to the parental wild-type population. In total, the results obtained with the two mutant cell lines question the association of altered mutation rates with increased metastatic potential. Although several explanations are possible for the altered malignant properties exhibited by HR-R2T and HNR-AT cells, it is interesting to note that the results are consistent with earlier suggestions that changes in ribonucleotide reductase may accompany modifications in the malignant characteristics of cells.

Functional immunoglobulin light chain genes are replaced by ongoing rearrangements of germline V kappa genes to downstream J kappa segment in a murine B cell line

A murine B cell lymphoma (38C13) was subjected to immunoselection with mAbs directed against the idiotypic determinants of its cell surface Ig. Variants emerged with altered Ig receptors containing identical heavy chains but different light chains. The functional light chain genes in these variants were composed of V kappa segments drawn from the V kappa Ox-1 family, which had replaced the V kappa gene expressed by the parental tumor by rearranging to downstream J kappa segments. Rearrangement at the kappa locus continued to occur spontaneously, giving rise to secondary and tertiary variants at a rate of 1.9 x 10(-4) per cell per generation. Variants were isolated that had ceased production of surface Ig but went on to rearrange again and to become surface Ig+. The Ig- state may be an intermediate step providing a stimulus for continued rearrangement. This process provides an additional mechanism for generating diversity within B cell clones and expands the use of the available repertoire of Ig genes.

Evaluation of methods for the estimation of mutation rates in cultured mammalian cell populations

A systematic comparison of 5 different statistical methods for the estimation of mutation rate (mu) in cultured Chinese hamster V79 cells is presented. Fluctuation tests were performed with several large batches of parallel cell cultures each allowed to grow for a different length of time in order to reach different population size (Nt). Based on Lea and Coulson's theoretical distribution, a comparison has been made between the experimental data and the expected distribution of the number of ouabain-resistant mutants per culture in these hamster cell populations. The sum of squared deviation between the observed and expected values, or SSD, was used as a means of the adequacy of the estimation method; the method which gives the smallest SSD is regarded as the best one for the estimation of mu. Our results show that when Nt is small, the occurrence of mutation is infrequent, and SSDs from different methods are similar. However, when Nt is large, there is a great discrepancy of the SSD values, suggesting a preference of using the maximum likelihood method, the Po method, the median method, the upper quartile method and the mean method, in that order, for the estimation of mu. The order of preference is correlated with estimation efficiencies. Depending on the size of Nt and the method used, the estimated mu may vary up to more than 3-fold. At a large Nt, the mu obtained from the maximum likelihood method is very precise. This suggests the importance of choosing an appropriate Nt as well as method for the estimation of mu.

Multipotent mutator strain of mouse teratocarcinoma cells

A mutator strain [AraCr (1.5)4], isolated from mutagenized cultures of multipotent mouse teratocarcinoma cells (embryonal carcinoma stem cells), exhibited a dNTP pool imbalance, with more than a 10-fold relative increase in the intracellular concentration of dCTP. The increase in the spontaneous rate of mutation for 6-thioguanine resistance was 3.6-fold and for ouabain resistance, 7.9-fold. Normalization of the dCTP/dTTP ratio by addition of thymidine and deoxycytidine to the media was associated with normalization of the mutation rates. AraCr (1.5)4 cell retained its multipotency (including chimerization potential) when injected into blastocysts. Moreover, its differentiated progeny expressed the dNTP pool imbalance and mutator phenotype in vitro. The preliminary finding of an increased frequency of morphologically abnormal embryos derived from a series of transplanted blastocysts injected with AraC2 (1.5)4 stem cells is consistent with significant phenotypic effects in vivo.

Pleiotropic mutants of Chinese hamster cells with altered cytidine 5'-triphosphate synthetase

Following chemical mutagenesis and multiple-step indirect selection, four clones of Chinese hamster V79 cells were isolated which exhibited auxotrophy for thymidine, deoxycytidine, or deoxyuridine but not for cytidine or uridine. All were resistant to uridine, 3-deazauridine, 5-fluorouridine, thymidine, and cytosine arabinoside at concentrations that were toxic to wild-type V79 cells. The cytidine 5'-triphosphate (CTP) and deoxycytidine 5'-triphosphate (dCTP) pools in the mutants were expanded, but the uridine 5'-triphosphate (UTP) pool either decreased or remained unchanged relative to the wild-type level. Furthermore, since the parental cells appear to be deficient in dCMP deaminase activity and CTP (or one of its metabolites) has been shown to inhibit uridine 5'-diphosphate (UDP) reduction, an elevated CTP level should lead to the observed thymidine auxotrophy. It also explains the joint resistance of mutant clones to thymidine and cytosine arabinoside. The change in the ratio of intracellular dCTP to thymidine 5'-triphosphate (dTTP) may be responsible for the elevation in the rates of spontaneous mutations in these mutants.