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

Mutation frequency dynamics in HPRT locus in culture-adapted human embryonic stem cells and induced pluripotent stem cells correspond to their differentiated counterparts

The genomic destabilization associated with the adaptation of human embryonic stem cells (hESCs) to culture conditions or the reprogramming of induced pluripotent stem cells (iPSCs) increases the risk of tumorigenesis upon the clinical use of these cells and decreases their value as a model for cell biology studies. Base excision repair (BER), a major genomic integrity maintenance mechanism, has been shown to fail during hESC adaptation. Here, we show that the increase in the mutation frequency (MF) caused by the inhibition of BER was similar to that caused by the hESC adaptation process. The increase in MF reflected the failure of DNA maintenance mechanisms and the subsequent increase in MF rather than being due solely to the accumulation of mutants over a prolonged period, as was previously suggested. The increase in the ionizing-radiation-induced MF in adapted hESCs exceeded the induced MF in nonadapted hESCs and differentiated cells. Unlike hESCs, the overall DNA maintenance in iPSCs, which was reflected by the MF, was similar to that in differentiated cells regardless of the time spent in culture and despite the upregulation of several genes responsible for genome maintenance during the reprogramming process. Taken together, our results suggest that the changes in BER activity during the long-term cultivation of hESCs increase the mutagenic burden, whereas neither reprogramming nor long-term propagation in culture changes the MF in iPSCs.

Mutation rates: estimating phase variation rates when fitness differences are present and their impact on population structure

Phase variation is a mechanism of ON-OFF switching that is widely utilized by bacterial pathogens. There is currently no standardization to how the rate of phase variation is determined experimentally, and traditional methods of mutation rate estimation may not be appropriate to this process. Here, the history of mutation rate estimation is reviewed, describing the existing methods available. A new mathematical model that can be applied to this problem is also presented. This model specifically includes the confounding factors of back-mutation and the influence of fitness differences between the alternate phenotypes. These are central features of phase variation but are rarely addressed, with the result that some previously estimated phase variation rates may have been significantly overestimated. It is shown that, conversely, the model can also be used to investigate fitness differences if mutation rates are approximately known. In addition, stochastic simulations of the model are used to explore the impact of 'jackpot cultures' on the mutation rate estimation. Using the model, the impact of realistic rates and selection on population structure is investigated. In the absence of fitness differences it is predicted that there will be phenotypic stability over many generations. The rate of phenotypic change within a population is likely, therefore, to be principally determined by selection. A greater insight into the population dynamics of mutation rate processes can be gained if populations are monitored over successive time points.

Embryonic stem cells and somatic cells differ in mutation frequency and type

Pluripotent embryonic stem (ES) cells have been used to produce genetically modified mice as experimental models of human genetic diseases. Increasingly, human ES cells are being considered for their potential in the treatment of injury and disease. Here we have shown that mutation in murine ES cells, heterozygous at the selectable Aprt locus, differs from that in embryonic somatic cells. The mutation frequency in ES cells is significantly lower than that in mouse embryonic fibroblasts, which is similar to that in adult cells in vivo. The distribution of spontaneous mutagenic events is remarkably different between the two cell types. Although loss of the functional allele is the predominant mutation type in both cases, representing about 80% of all events, mitotic recombination accounted for all loss of heterozygosity events detected in somatic cells. In contrast, mitotic recombination in ES cells appeared to be suppressed and chromosome loss/reduplication, leading to uniparental disomy (UPD), represented more than half of the loss of heterozygosity events. Extended culture of ES cells led to accumulation of cells with adenine phosphoribosyltransferase deficiency and UPD. Because UPD leads to reduction to homozygosity at multiple recessive disease loci, including tumor suppressor loci, in the affected chromosome, the increased risk of tumor formation after stem cell therapy should be viewed with concern.

Chromosomal mutations and chromosome loss measured in a new human-hamster hybrid cell line, ALC: studies with colcemid, ultraviolet irradiation, and 137Cs gamma-rays

Small mutations, megabase deletions, and aneuploidy are involved in carcinogenesis and genetic defects, so it is important to be able to quantify these mutations and understand mechanisms of their creation. We have previously quantified a spectrum of mutations, including megabase deletions, in human chromosome 11, the sole human chromosome in a hamster-human hybrid cell line AL. S1- mutants have lost expression of a human cell surface antigen, S1, which is encoded by the M1C1 gene at 11p13 so that mutants can be detected via a complement-mediated cytotoxicity assay in which S1+ cells are killed and S1- cells survive. But loss of genes located on the tip of the short arm of 11 (11p15.5) is lethal to the AL hybrid, so that mutants that have lost the entire chromosome 11 die and escape detection. To circumvent this, we fused AL with Chinese hamster ovary (CHO) cells to produce a new hybrid, ALC, in which the requirement for maintaining 11p15.5 is relieved, allowing us to detect mutations events involving loss of 11p15.5. We evaluated the usefulness of this hybrid by conducting mutagenesis studies with colcemid, 137Cs gamma-radiation and UV 254 nm light. Colcemid induced 1000 more S1- mutants per unit dose in ALC than in AL; the increase for UV 254 nm light was only two-fold; and the increase for 137Cs gamma-rays was 12-fold. The increase in S1- mutant fraction in ALC cells treated with colcemid and 137Cs gamma-rays were largely due to chromosome loss and 11p deletions often containing a breakpoint within the centromeric region.

Rates of spontaneous mutation in an archaeon from geothermal environments

To estimate the efficacy of mechanisms which may prevent or repair thermal damage to DNA in thermophilic archaea, a quantitative assay of forward mutation at extremely high temperature was developed for Sulfolobus acidocaldarius, based on the selection of pyrimidine-requiring mutants resistant to 5-fluoro-orotic acid. Maximum-likelihood analysis of spontaneous mutant distributions in wild-type cultures yielded maximal estimates of (2.8 +/- 0.7) x 10(-7) and (1.5 +/- 0.6) x 10(-7) mutational events per cell per division cycle for the pyrE and pyrF loci, respectively. To our knowledge, these results provide the first accurate measurement of the genetic fidelity maintained by archaea that populate geothermal environments. The measured rates of forward mutation at the pyrE and pyrF loci in S. acidocaldarius are close to corresponding rates reported for protein-encoding genes of Escherichia coli. The normal rate of spontaneous mutation in E. coli at 37 degrees C is known to require the functioning of several enzyme systems that repair spontaneous damage in DNA. Our results provide indirect evidence that S. acidocaldarius has cellular mechanisms, as yet unidentified, which effectively compensate for the higher chemical instability of DNA at the temperatures and pHs that prevail within growing Sulfolobus cells.

Modeling and measurement of the spontaneous mutation rate in mammalian cells

The study of spontaneous mutation rates in mammalian cells has been hampered by the lack of an alternative to the cumbersome Luria and Delbrück fluctuation test. A brief review of mathematical treatments of spontaneous mutagenesis, along with some of the limitations of the fluctuation test, is presented. A new experimental method and a simple mathematical model for deriving the spontaneous mutation rate are described. Data from the transgenic Chinese hamster G12 cell line growing at two different rates is analyzed according to this model. The results support the concept that, at least for growing cells, the spontaneous mutation rate is independent of the growth rate, and the mutant fraction increases in a linear fashion with the number of generations.

An algorithm accounting for plating efficiency in estimating spontaneous mutation rates

An algorithm is described for calculating the probability distribution of the number of mutant colonies arising in a Luria-Delbrück fluctuation experiment subject to a plating efficiency of less than 100%. A table is constructed to facilitate the estimation of spontaneous mutation rates taking into account the plating efficiency.

An improved estimator of spontaneous mutation rates in Luria-Delbrück fluctuation experiments

In estimating the spontaneous mutation rate, mu, in cultured mammalian cells, the number of mutant cells in several parallel cultures, each a clone from a single cell, is determined. Luria and Delbrück (1943), and subsequently Lea and Coulson (1949), proposed several estimators of mu using data from such experiments. These methods of analysis were originally proposed to apply to mutants arising in microbial cultures, and some of the limitations in applying them to mammalian cell cultures have been outlined by Featherstone et al. (1987), and by Kendal and Frost (1988). For a given value of mu, the number of mutants, r, found in a culture is exceedingly variable, so that r contains very little information concerning mu. It is important, therefore, that an estimator of mu be efficient; that it not waste the limited information available in the experimental data. To this end, a new estimator is proposed which compounds the information previously utilized by the so-called P0 and median estimators. Using a spreadsheet program such as that available with MINITAB, the algorithm can be programmed in as few as 26 instructions. Tested against simulated data across a range of values of mu, the proposed compound estimator is more efficient than the currently used estimators.

Accounting for plating efficiency when estimating spontaneous mutation rates

When the spontaneous mutation rate mu in mammalian cell cultures is estimated using Luria-Delbrück fluctuation analysis, many factors contribute to the unreliability of the estimate. Some of these have been documented by Featherstone et al. (1987) and by Kendal and Frost (1988). In particular, the plating efficiencies for mammalian cells are often much less than 100%, and this can be taken into account. A derivation of a generalized P0 estimator, mg, based on the classical P0 estimator of Luria and Delbrück (1943) is offered. In an experiment involving C cultures, of which z exhibit no mutant colonies, and in which the plating efficiency is p, (0 < p < 1), the estimated mean number of mutations per culture is given by [formula: see text] The classical P0 estimator is shown to be the limiting case of mg as plating efficiency tends to 100%.

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.