Cellular epigenetics: effects of passage history on competence of cells for "spontaneous" transformation

Interlaboratory evaluation of a digital holographic microscopy-based assay for label-free in vitro cytotoxicity testing of polymeric nanocarriers

State-of-the-art in vitro test systems for nanomaterial toxicity assessment are based on dyes and several staining steps which can be affected by nanomaterial interference. Digital holographic microscopy (DHM), an interferometry-based variant of quantitative phase imaging (QPI), facilitates reliable proliferation quantification of native cell populations and the extraction of morphological features in a fast and label- and interference-free manner by biophysical parameters. DHM therefore has been identified as versatile tool for cytotoxicity testing in biomedical nanotechnology. In a comparative study performed at two collaborating laboratories, we investigated the interlaboratory variability and performance of DHM in nanomaterial toxicity testing, utilizing complementary standard operating procedures (SOPs). Two identical custom-built off-axis DHM systems, developed for usage in biomedical laboratories, equipped with stage-top incubation chambers were applied at different locations in Europe. Temporal dry mass development, 12-h dry mass increments and morphology changes of A549 human lung epithelial cell populations upon incubation with two variants of poly(alkyl cyanoacrylate) (PACA) nanoparticles were observed in comparison to digitonin and cell culture medium controls. Digitonin as cytotoxicity control, as well as empty and cabazitaxel-loaded PACA nanocarriers, similarly impacted 12-h dry mass development and increments as well as morphology of A549 cells at both participating laboratories. The obtained DHM data reflected the cytotoxic potential of the tested nanomaterials and are in agreement with corresponding literature on biophysical and chemical assays. Our results confirm DHM as label-free cytotoxicity assay for polymeric nanocarriers as well as the repeatability and reproducibility of the technology. In summary, the evaluated DHM assay could be efficiently implemented at different locations and facilitates interlaboratory in vitro toxicity testing of nanoparticles with prospects for application in regulatory science.

Delineating the Effects of Passaging and Exposure in a Longitudinal Study of Arsenic-Induced Squamous Cell Carcinoma in a HaCaT Cell Line Model

Cutaneous squamous cell carcinoma (cSCC) is a major deleterious health effect of chronic arsenic (iAs) exposure. The molecular mechanism of arsenic-induced cSCC remains poorly understood. We recently demonstrated that chronic iAs exposure leads to temporally regulated genome-wide changes in profiles of differentially expressed mRNAs and miRNAs at each stage of carcinogenesis (7, 19 and 28 weeks) employing a well-established passage-matched HaCaT cell line model of arsenic-induced cSCC. Here, we performed longitudinal differential expression analysis (miRNA and mRNA) between the different time points (7 vs. 19 weeks and 19 vs. 28 weeks) within unexposed and exposed groups, coupled to expression pairing and pathway analyses to differentiate the relative effects of long-term passaging and chronic iAs exposure. Data showed that 66-105 miRNA [p < 0.05; log2(Fold Change)>I1I] and 2826-4079 mRNA [p < 0.001; log2(Fold Change)>I1I] molecules were differentially expressed depending on the longitudinal comparison. Several mRNA molecules differentially expressed as a function of time, independent of iAs exposure were being targeted by miRNA molecules which were also differentially expressed in a time dependent manner. Distinct pathways were predicted to be modulated as a function of time or iAs exposure. Some pathways were also modulated both by time and exposure. Thus, the HaCaT model can distinguish between the effects of passaging and chronic iAs exposure individually and corroborate our previously published data on effects of iAs exposure compared to unexposed passage matched HaCaT cells. In addition, this work provides a template for cell line based longitudinal chronic exposure studies to follow for optimal efficacy.

The impact of epigenomics on future drug design and new therapies

The future of drug design and the development of new therapeutics will rely on our ability to unravel the complexities of the epigenome in normal and disease states. Proper epigenetic regulation is essential for normal differentiation in embryogenesis and development. Conversely, abnormal epigenetic regulation is a feature of complex diseases, including cancer, diabetes, heart disease and other pathologies. Epigenetic therapies hold promise for a wide range of biological applications, from cancer treatment to the establishment of induced pluripotent stem cells. The creation of more specific and effective epigenetic therapies, however, requires a more complete understanding of epigenomic landscapes. Here, we give a historical overview of the epigenomics field and how epigenetic modifications can affect embryo development and disease etiology. We also discuss the impact of current and future epigenetic drugs.

Genome based cell population heterogeneity promotes tumorigenicity: the evolutionary mechanism of cancer

Cancer progression represents an evolutionary process where overall genome level changes reflect system instability and serve as a driving force for evolving new systems. To illustrate this principle it must be demonstrated that karyotypic heterogeneity (population diversity) directly contributes to tumorigenicity. Five well characterized in vitro tumor progression models representing various types of cancers were selected for such an analysis. The tumorigenicity of each model has been linked to different molecular pathways, and there is no common molecular mechanism shared among them. According to our hypothesis that genome level heterogeneity is a key to cancer evolution, we expect to reveal that the common link of tumorigenicity between these diverse models is elevated genome diversity. Spectral karyotyping (SKY) was used to compare the degree of karyotypic heterogeneity displayed in various sublines of these five models. The cell population diversity was determined by scoring type and frequencies of clonal and non-clonal chromosome aberrations (CCAs and NCCAs). The tumorigenicity of these models has been separately analyzed. As expected, the highest level of NCCAs was detected coupled with the strongest tumorigenicity among all models analyzed. The karyotypic heterogeneity of both benign hyperplastic lesions and premalignant dysplastic tissues were further analyzed to support this conclusion. This common link between elevated NCCAs and increased tumorigenicity suggests an evolutionary causative relationship between system instability, population diversity, and cancer evolution. This study reconciles the difference between evolutionary and molecular mechanisms of cancer and suggests that NCCAs can serve as a biomarker to monitor the probability of cancer progression.

The origin of phenotypic heterogeneity in a clonal cell population in vitro

Background

The spontaneous emergence of phenotypic heterogeneity in clonal populations of mammalian cells in vitro is a rule rather than an exception. We consider two simple, mutually non-exclusive models that explain the generation of diverse cell types in a homogeneous population. In the first model, the phenotypic switch is the consequence of extrinsic factors. Initially identical cells may become different because they encounter different local environments that induce adaptive responses. According to the second model, the phenotypic switch is intrinsic to the cells that may occur even in homogeneous environments.

Principal Findings

We have investigated the “extrinsic” and the “intrinsic” mechanisms using computer simulations and experimentation. First, we simulated in silico the emergence of two cell types in a clonal cell population using a multiagent model. Both mechanisms produced stable phenotypic heterogeneity, but the distribution of the cell types was different. The “intrinsic” model predicted an even distribution of the rare phenotype cells, while in the “extrinsic” model these cells formed small clusters. The key predictions of the two models were confronted with the results obtained experimentally using a myogenic cell line.

Conclusions

The observations emphasize the importance of the “ecological” context and suggest that, consistently with the “extrinsic” model, local stochastic interactions between phenotypically identical cells play a key role in the initiation of phenotypic switch. Nevertheless, the “intrinsic” model also shows some other aspects of reality: The phenotypic switch is not triggered exclusively by the local environmental variations, but also depends to some extent on the phenotypic intrinsic robustness of the cells.

Tumorigenesis: the adaptation of mammalian cells to sustained stress environment by epigenetic alterations and succeeding matched mutations

Recent studies indicate that during tumorigenic transformations, cells may generate mutations by themselves as a result of error-prone cell division with participation of error-prone polymerases and aberrant mitosis. These mechanisms may be activated in cells by continuing proliferative and survival signaling in a sustained stress environment (SSE). The paper hypothesizes that long-term exposure to this signaling epigenetically reprograms the genome of some cells and, in addition, leads to their senescence. The epigenetic reprogramming results in: (i) hypermethylation of tumor-suppressor genes involved in the onset of cell-cycle arrest, apoptosis and DNA repair; (ii) hypomethylation of proto-oncogenes associated with persistent proliferative activity; and (iii) the global demethylation of the genome and activation of DNA repeats. These epigenetic changes in the proliferating cells associate with their replicative senescence and allow the reprogrammed senescent cells to overcome the cell-cycle arrest and to activate error-prone replications. It is hypothesized that the generation of mutations in the error-prone replications of the epigenetically reprogrammed cells is not random. The mutations match epigenetic alterations in the cellular genome, namely gain of function mutations in the case of hypomethylation and loss of functions in the case of hypermethylation. In addition, continuing proliferation of the cells imposed by signaling in SSE speeds up the natural selection of the mutant cells favoring the survival of the cells with mutations that are beneficial in the environment. In this way, a stress-induced replication of the cells epigenetically reprograms their genome for quick adaptation to stressful environments providing an increased rate of mutations, epigenetic tags to beneficial mutations and quick selection process. In combination, these processes drive the origin of the transformed mammalian cells, cancer development and progression. Support from genomic, biochemical and medical studies for the proposed hypothesis, and its implementations are discussed.

Clonal dynamics of progressive neoplastic transformation

In a recent study, we found that newly isolated clones of NIH 3T3 mouse cells undergo neoplastic transformation more readily than uncloned cultures from which they were derived. After eleven low-density passages (LDPs), most of the 29 clones produced lightly stained early-stage transformed foci when grown to confluence in a primary assay for transformation, and one of them consistently produced a few tiny dense foci. In the present work, six of the clones were kept in LDPs for 56 passages and assayed for focus formation at confluence at six passage levels. The clone that produced tiny dense foci switched to light foci during the LDPs, four others produced light foci at different passage levels, and one progressed from light to dense foci after the last passage. By contrast, all the clones progressed to dense focus formation in five or fewer serial repetitions of the assay at confluence. Because all but one of the clones underwent about half as many total divisions at each LDP as they did when grown to the stationary state at confluence, the latter is more efficient in eliciting progression than the exponential growth of the LDPs. Extension of the period at confluence of uncloned cultures results in the appearance of dense foci within light foci. Because the latter are localized clonal populations, the intrafocal progression reinforces the conclusion that clonal expansion favors transformation. We discuss the significance of these results for the clonal origin of human cancer and the increased incidence of cancer with age.

The cellular ecology of progressive neoplastic transformation: a clonal analysis

A comparison was made of the competence for neoplastic transformation in three different sublines of NIH 3T3 cells and multiple clonal derivatives of each. Over 90% of the neoplastic foci produced by an uncloned transformed (t-SA') subline on a confluent background of nontransformed cells were of the dense, multilayered type, but about half of the t-SA' clones produced only light foci in assays without background. This asymmetry apparently arose from the failure of the light focus formers to register on a background of nontransformed cells. Comparison was made of the capacity for confluence-mediated transformation between uncloned parental cultures and their clonal derivatives by using two nontransformed sublines, one of which was highly sensitive and the other relatively refractory to confluence-mediated transformation. Transformation was more frequent in the clones than in the uncloned parental cultures for both sublines. This was dramatically so in the refractory subline, where the uncloned culture showed no overt sign of transformation in serially repeated assays but increasing numbers of its clones exhibited progressive transformation. The reason for the greater susceptibility of the pure clones is apparently the suppression of transformation among the diverse membership that makes up the uncloned parental culture. Progressive selection toward increasing degrees of transformation in confluent cultures plays a major role in the development of dense focus formers, but direct induction by the constraint of confluence may contribute by heritably damaging cells. In view of our finding of increased susceptibility to transformation in clonal versus uncloned populations, expansion of some clones at the expense of others during the aging process would contribute to the marked increase of cancer with age.

Sustained nontumorigenic phenotype correlates with a largely stable chromosome content during long-term culture of the human keratinocyte line HaCaT

Altered growth and differentiation and a highly abnormal karyotype are generally believed to be indicators for tumorigenic conversion of human cells. Inactivation of TP53 is supposedly one possible mechanism for accelerated genetic aberrations via reduced control of the genetic integrity. To examine the significance of this functional relationship, we investigated the long-term development of the spontaneously immortalized human skin keratinocyte line HaCaT, carrying UV-specific mutations in both alleles of the TP53 tumor suppressor gene. During > 300 passages, proliferation, clonogenicity, and serum-independent growth potential increased. In addition, HaCaT cells gained anchorage independence and at late passages showed reduced differentiation. Karyotypic analysis up to passage 225 revealed a high frequency of translocations and deletions, with a particular increase during passages 30 and 50. Nevertheless, the HaCaT cells remained nontumorigenic when injected subcutaneously, and noninvasive in surface transplants in nude mice. By comparative genomic hybridization, we confirmed the karyotypically identified phase of increased chromosomal aberrations between passages 30 and 50. However, before and thereafter, the CGH profiles of the individual chromosomes were largely unchanged, demonstrating that those translocations-also maintained in later passages-did not cause a gross chromosomal imbalance. Thus, our data suggest that multiple changes often correlated with a "transformed phenotype," including extensive karyotypic alterations and mutational inactivation of TP53, are well compatible with a nontumorigenic phenotype of the HaCaT cells, and that preserved chromosomal balance may be crucial for this stability during long-term propagation.

Immunobead filtration: a novel approach for the isolation and propagation of tumor cells

We have developed a method to facilitate the isolation and expansion of tumor cells from body fluids and tissue biopsies. Antibody-conjugated magnetic beads (immunobeads) were used to isolate tumor cells from blood, bone marrow, ascitic/pleural fluids, and enzyme-digested tissue biopsies. Filtration of the resulting cell suspension through a 20-micron nylon monofilament filter secured to the base of polystyrene 96-well strips purged the bead-rosetting cell fraction of contaminating normal cells and unbound beads. Tumor cells that bound the magnetic beads were retained on the membrane due to their increased size and concentrated into a small area (0.332 cm2), thus maintaining a high cell density. The filters provided a stable and uniform three-dimensional matrix for cell growth, with a total surface area of 1.42 cm2 available for cell attachment. The filters could be easily removed from the base of the 96-well strips to facilitate handling and transfer between culture vessels. Tumor cells grown on the filters could subsequently be harvested using trypsin/EDTA or left in situ for immunostaining with conventional immunohistochemical procedures. Filter-grown cells have shown extended passage in conventional cell culture in six cases. In two of five cases, the orthotopic implantation of confluent filters that contained approximately 10(4) cells/8 x 8 mm filter successfully produced tumors in nude mice after only 4 weeks. Our new approach may be of value in improving the success rate of generating long-term cultures from previously unproductive sources of tumor cells and thus may yield a greater variety of cell lines/strains for the study of malignant disease.

Neoplastic development: paradoxical relation between impaired cell growth at low population density and excessive growth at high density

The role of heritable, population-wide cell damage in neoplastic development was studied in the 28 L subline of NIH 3T3 cells. These cells differ from the 17(3c) subline used previously for such studies in their lower frequency of "spontaneous" transformation at high population density and their greater capacity to produce large, dense transformed foci. Three cultures of the 28 L subline of NIH 3T3 cells were held under the constraint of confluence for 5 wk (5 wk 1 degree assay) and then assayed twice in succession (2 degrees and 3 degrees assays) for transformed foci and saturation density. After the 2 degrees assay, the cells were also passaged at low density to determine their exponential growth rates and cloned to determine the size and morphological features of the colonies. Concurrent measurements were made in each case with control cells that had been kept only in frequent low-density passages and cells that had been kept at confluence for only 2 wk (2 wk 1 degree). Two of the three cultures transferred from the 2 degrees assay of the 5 wk 1 degree cultures produced light transformed foci, and the third produced dense foci. The light focus-forming cultures grew to twice the control saturation density in their 2 degrees assay and 6-8 times the control density in the 3 degrees assay; saturation densities for the dense focus formers were about 10 times the control values in both assays. All three of the cultures transferred from the 2 degrees assay of the 5 wk 1 degree cultures multiplied at lower rates than controls at low densities, but the dense focus formers multiplied faster than the light focus formers. The reduced rates of multiplication of the light focus formers persisted for > 50 generations of exponential multiplication at low densities. Isolated colonies formed from single cells of the light focus formers were of a lower population density than controls; colonies formed by the dense focus formers were slightly denser than the controls but occupied only half the area. A much higher proportion of the colonies from the 5 wk 1 degree cultures than the controls consisted of giant cells or mixtures of giant and normal-appearing cells. The results reinforce the previous conclusion that the early increases in saturation density and light focus formation are associated with, and perhaps caused by, heritable, population-wide damage to cells that is essentially epigenetic in nature. The more advanced transformation characterized by large increases in saturation density and dense focus formation could have originated from rare genetic changes, such as chromosome rearrangements, known to occur at an elevated frequency in cells destabilized by antecedent cellular damage.

A critical test of the role of population density in producing transformation

Cells of the NIH 3T3 line gain the capacity to produce neoplastically transformed foci when they are maintained at high density for more than 1 week and transferred in a standard assay for focus formation. This change in cell behavior has been variously attributed to an adaptive response to the constraint of the high population density or to a spontaneous genetic change that increases in probability for a culture with the increase in the total number of cell divisions. To distinguish between these alternatives, 200 cells of the 28H subline were seeded in many culture dishes of two size classes differing 6-fold in surface area and allowed to multiply for 1, 2, and 3 weeks. At each weekly interval, 18 dishes of each class were assayed for focus formation, and two of the original dishes were stained for focus formation. The cells in the small (S) and large (L) dishes multiplied to the same extent at 1 week and produced only a few small light foci in some of the assay dishes. At 2 weeks, cells in the S dishes had become confluent and had only one-third the number of cells as those in the nonconfluent L dishes. Upon assay, 14 of the 18 S cultures produced some foci whereas only 9 of the L cultures did so. In addition, 4 of the S cultures produced large dense foci while none of the L cultures did. By 3 weeks, the L cultures were confluent and had four times as many cells as the S cultures. When assayed at this time, both sets produced dense foci in many of the cultures and light foci in the remaining ones, indicating a narrowing of the differences between the S and L cultures between 2 and 3 weeks of incubation. There were differences in the morphology of the foci produced in parallel assays from different cultures. The results showed that transformation is a diverse graded response to the growth constraint of high population density and not a spontaneous event dependent on the number of cell divisions in a cell culture. Transformation thus is basically an epigenetic process since it represents a response to physiological restraint, but the final form of response may be modulated by genetic alterations.

Experimental control of neoplastic progression in cell populations: Foulds' rules revisited

Foulds introduced six rules of tumor progression based on his observations of spontaneous mammary cancer in mice and generalized them to all forms of neoplasia [Foulds, L. (1954) Cancer Res. 14, 327-339 and Foulds, L. (1969) Neoplastic Development (Academic, New York), Vol. 1, preface and pp. 72-74.] Rules III, IV, and V are considered controversial, and research in animals seems inadequate to resolve the controversies. A subline of NIH 3T3 cells undergoes progressive transformation to produce foci of increasing population density when repeatedly constrained by sequential rounds of growth to and maintenance at confluence. Analysis of the results provides a cellular basis for rules III, IV, and V. Rule III states that progression is independent of the growth of the tumor and occurs in tumors that are arrested. Cell culture shows that progression is actually favored by constraint of growth, a result inconsistent with a major role for point mutations in progression. Indeed, there is a suggestion that the transformation may arise from chromatin changes preceding apoptosis. Rule IV states that progression can be gradual or abrupt but the latter conclusion has been frequently criticized. Cell culture exhibits both forms of progression but, in particular, eliminates the doubt about the abrupt form. Rule V, which is in a sense an extension of rule IV, states that progression follows one of alternative paths of development. The results in culture indicate that every independent transforming event gives rise to foci of unique morphology. Thus, even for the single characteristic of transformed focus morphology, many alternative paths to neoplasia are available to cells. In addition to clarifying the rules of progression, a method is described for pinpointing the time of the occurrence of events that are only expressed as dense foci after a variable lag time. The results in culture reinforce Foulds' conclusion that neoplastic development is primarily an epigenetically driven process and identify some of the cellular interactions that underlie that process.

Selective nature of phorbol 12-myristate 13-acetate-induced neoplastic transformation in NIH 3T3 cells

The ability of phorbol 12-myristate 13-acetate (PMA) at 0.02 microgram/ml to induce neoplastic transformation in NIH 3T3 cells is highly dependent on the culture conditions. Optimal transformation, indicated by the saturation density and extent of focus formation in transferred cultures raised under standard conditions, was observed when the original cells were grown in 2% calf serum (CS) and exposed continually to PMA for at least 4 weeks before transfer into the assay. Transformation of stationary cultures in 10% CS occurred later and to a lesser degree than in 2% CS. The same cells subjected to thrice-weekly transfer in 2% or 10% CS at low cell density so that they were in a constant state of exponential growth exhibited no evidence of transformation in response to PMA. This strong condition-dependence of PMA-enhanced transformation is indicative of a selection process similar to that described for spontaneous transformation. In both cases, transformation is promoted by inhibiting multiplication and prevented by maximizing multiplication. Therefore, it has the earmarks of an epigenetic rather than a mutational process and requires phenotypic rather than genotypic variation to supply the states for selection. The concept of "progressive state selection," originally proposed to account for spontaneous transformation, can also account for PMA-enhanced transformation.

Cellular epigenetics: control of the size, shape, and spatial distribution of transformed foci by interactions between the transformed and nontransformed cells

NIH 3T3 cells that are passaged frequently at low density in high (10%) calf serum lose their original capacity to produce transformed foci on a monolayer of nontransformed cells. They can then be used to form a monolayered background for the assay of the number of focus-forming cells from a transformed population. Continuation of the low-density passages for many weeks gives rise to a population that can suppress the full development of foci by a transformed line. The suppression appears to occur only after the background cells have become confluent and contact inhibited. It can also cause the disappearance of light foci that had developed before suppression began. Another subline of cells that were passaged at cloning density only once a week lose their focus-forming capacity more slowly than those passaged thrice weekly. When used as a background for the assay of a transformed line, they permit continuous expansion of the foci, with no sign of suppression. Not only the number and size of foci but also their detailed morphology is influenced by the background on which they are formed. A suppressive background can also determine the spatial distribution of foci, presumably as a result of gradients in local cell density of the background. The permissiveness of a nontransformed cell population for focus formation by transformed cells appears to be related to the capacity of the nontransformed population itself to undergo transformation when exposed to the constraints used to induce transformation. These findings indicate there are many degrees of capacity to suppress focus formation and to overcome suppression. They have significance for tumor development and for the epigenetic interactions of normal development.

Cellular epigenetics: topochronology of progressive "spontaneous" transformation of cells under growth constraint

Early passages of NIH 3T3 cells yield about 10 transformed foci for every 10(5) cells seeded after the cells multiply to confluence in a standardized 2-week assay. The question arose whether more cells would give rise to foci if given more time for their development. This question could not be answered simply by extending the incubation period, since the original foci spread to cover much of the area of the culture dish. Transformed cells can also detach into the medium from the original foci to initiate new foci by reattaching at a distance. These problems were averted by growing cells in multiwell plates which in effect simulated partitioned culture dishes. All the wells in a given plate were assayed for focus formation at successive intervals up to 14 weeks. The results indicated the spatial pattern and sequence of transformation on different parts of the "partitioned" dish. The number of multiwells containing focus-forming cells increased steadily with time, indicating that all parts of a dish eventually undergo transformation. Also, most of the transformations were recorded long after confluence in the multiwells was reached. Hence such a transformation is much more likely to occur in the nondividing state rather than in the dividing state of the cells and is thus inconsistent with a mutational basis. The results suggest that "spontaneous" transformation is a population-wide, epigenetic phenomenon. This agrees with the results from clonal analysis and other studies and is well described by the concept of progressive state selection, in which "spontaneous" transformation represents a heterogeneous, adaptive response of competent cells to moderate constraints on cell growth.