The research is dealing with the analysis of chromosomal instability and phenotype of tumor cells of a glial and non-glial origin after exposure to cytotoxic stress factors. It was found that stable transfection of plasmid DNA, transgene CHI3L1 or long-term drug treatment (temozolomide, cisplatin, temsirolimus, and U0126) affected the phenotype of tumor cells by changing the level of genome instability and genetic heterogeneity. Chromosomal instability may be a universal mechanism of tumor cells adaptation to stresses of various nature. The stable transfection of plasmid DNA pcDNA3.1 caused an increase in the level of chromosomal instability (clonal and nonclonal chromosomal aberrations) in HEK293_pcDNA3.1 cells, which was associated with the decreased viability but increased colony formation efficiency (CFE) in soft agar. Changes in the genome and phenotype of tumor cells stably transfected with empty vector (without the target gene) raises a question about the adequacy of the cell models with stable transgene transfection for the investigation of oncogenic gene functions, since it is impossibile to distinguish, which phenotype changes are caused by the product of a (trans)gene and which are connected with the chromosome changes that accompany the stable transfection of the vector DNA, cytotoxic antibiotic treatment, and the transgene acute overproduction. The ectopic production of CHI3L1 increased the viability and CFE of HEK293_CHI3L1 cells compared to the control HEK293_pcDNA3.1 or parental HEK293 cells. On the contrary, despite ectopic production of CHI3L1 by HeLa_CHI3L1 clones, their viability and CFE were lower compared to the parental HeLa cells. Thus, we have observed the opposite changes in phenotype comparing HeLa_CHI3L1 clones and 293_CHI3L1 cells. We share the view that the effect and function of a (trans)gene can be opposite and versatile in cells with different genomes and are determined by genetic network, which is in turn defined by genome context. Thereby, caution in interpretation of molecular analysis data and the relationship between cause and effect in cells with unstable genome is needed. In contrast to 293 cells derivatives, karyotypes of HeLa_CHI3L1 clones were much more stable. We suppose that accuracy of chromosome integrity-controlling mechanisms determines the degree of genome destabilization after plasmid transfer (and other stresses). In any case, the possible indirect effects associated with the process of plasmid transfer itself and selection of antibiotic resistant clones should be verified and taken in consideration when interpreting results and making conclusions in transgene studies. EIther an increase or decrease in the genomic heterogeneity and aggressive malignant phenotype of tumor cells after long-term treatment with DNA-methylating clinical drug temozolomide were demonstrated depending on the cell lines. These findings pointed out that the clinical use of temozolomide might negatively influence the patient survival and recurrence treatment. The treatment of rat C6 glioma cells in vivo with drug cisplatin did not significantly affect the copy number of chromosome loci and growth pattern of resistant cells isolated from residual tumors. The fact that the treatment with cisplatin reduced the growth rate of C6 glioma and increased the survival of rats, but did not affect chromosomal stability and growth characteristics of the C6 cells in vitro, survived after treatment in vivo, can indicate a cytostatic effect rather than genotoxic effect of cisplatin on the C6 cells. The level of clonal and nonclonal chromosomal aberrations was increased in glial U251 and T98G cells after prolonged clinical treatment with targeted drug temsirolimus (TEM), an inhibitor of mTOR kinase. U251TEM cells had reduced proliferation, CFE and migration, whereas no difference between T98G and T98GTEM cells was observed. Long-term treatment of U251 cells, but not T98G, with targeted MEK kinase inhibitor U0126 increased their proliferation twice. Thus, long-term treatment of tumor cells with targeted agents induced cell-specific and inhibitor-specific adaptation effects. Finally, we showed that significance of over/underestimation of cell viability in the MTT assay depends on a cell line, a time point of viability measurement, inhibitor concentration, and other experimental parameters. To avoid a consistent proportion of false positive and false negatve results, two complementary techniques and several time points of the viability measurement are recommended. In conclusion, therapeutic promotion of tumor cell genomes to excessive instability is a double-edged sword: the primary positive objective response and reduced cell viability may be accompanied by increase in cell population genome heterogeneity and evolutionary potential of residual disease.
