Biology subjects

Safina, A.

Publications and source records attributed to Safina, A..

4 recordsLinked to original sources

bioRxiv2026

Oncogenic transformation proceeds through a transient state of cellular plasticity constrained by lineage-specific barriers.

Normal tissues frequently harbor oncogenic mutations without progressing to cancer, but the cellular basis of this resistance remains poorly defined. We asked whether transformation requires selection of a rare, permissive state within normal-like cell populations. Dermal fibroblasts and mammary epithelial cells responded uniformly to combined HRAS-G12V expression and p53 disruption. Cellular barcoding revealed no loss or enrichment of clones during morphological transformation, arguing against clonal selection as the primary driver of neoplastic reprogramming. Instead, all transduced cells underwent an early, shared transcriptional transition characterized by loss of differentiation markers, induction of RAS-associated and inflammatory programs, activation of alternative-lineage signatures, increased single-cell entropy, and chromatin decondensation. These changes were transient: entropy and chromatin accessibility subsequently declined, and some cells moved toward the control transcriptional state, whereas others stabilized in altered states. The two lineages followed distinct trajectories. Fibroblasts showed greater initial transcriptional plasticity but subsequently reverted more strongly toward the normal state, whereas epithelial cells changed more gradually and continued to diverge from it, suggesting a stronger barrier to transformation in the mesenchymal lineage. Thus, oncogenic perturbation initiated reprogramming throughout the population but did not uniformly produce a stable transformed state. Together, these findings support a model in which normal-like cells tolerate oncogenic mutations not because most cells fail to respond, but because a p53-independent, cell-intrinsic barrier limits the stabilization of malignant transformation following a transient period of heightened plasticity. This framework may facilitate the identification of mechanisms that constrain tumor initiation.. Significance StatementLoss of TP53 and activation of oncogenic RAS are common drivers of human cancer and frequently coexist in the same tumor. Nevertheless, these alterations often fail to induce malignant transformation. To investigate why, we introduced both alterations into fibroblasts and epithelial cells and tracked their responses using clonal barcoding, single-cell transcriptomics, and phenotypic assays. Initially, cells uniformly reprogrammed their transcriptional and chromatin states without detectable clonal selection. They then diverged: some reacquired transcriptional profiles resembling those of the original normal cells, whereas others became transformed. Thus, normal cells resist transformation through an intrinsic barrier that operates despite p53 disruption. Because this transition is transient and reversible, it provides a tractable window for studying the earliest stages of cancer development.

cancer biology↗

bioRxiv2023

Comparison of cell response to chromatin and DNA damage

DNA-targeting drugs may damage DNA or chromatin. Many anti-cancer drugs damage both, making it difficult to understand their mechanisms of action. Using molecules causing DNA breaks without altering nucleosome structure (bleomycin) or destabilizing nucleosomes without damaging DNA (curaxin), we investigated the consequences of DNA or chromatin damage in normal and tumor cells. As expected, DNA damage caused p53-dependent growth arrest followed by senescence. Chromatin damage caused higher p53 accumulation than DNA damage; however, growth arrest was p53-independent and did not result in senescence. Chromatin damage activated the transcription of multiple genes, including classical p53 targets, in a p53-independent manner. Although these genes were not highly expressed in basal conditions, they had chromatin organization around the transcription start sites (TSS) characteristic of most highly expressed genes and the highest level of paused RNA polymerase. We hypothesized that nucleosomes around the TSS of these genes were the most sensitive to chromatin damage. Therefore, nucleosome loss upon curaxin treatment would enable transcription without the assistance of sequence-specific transcription factors. We confirmed this hypothesis by showing greater nucleosome loss around the TSS of these genes upon curaxin treatment and activation of a p53-specific reporter in p53-null cells by chromatin-damaging agents but not DNA-damaging agents.

molecular biology↗

bioRxiv2018

Prevention of chromatin destabilization by FACT is crucial for malignant transformation

Expression of histone chaperone FACT is increased in tumors and associated with poor prognosis. We investigated why aggressive tumor cells need FACT using a model where FACT could be turned off and confirmed that while FACT is not essential for non-tumor cells, cells become dependent on FACT following oncogene-induced transformation. We compared the phenotypic and transcriptional changes induced by FACT loss and excluded a direct role for FACT in the transcription of genes essential for the viability of transformed cells. Moreover, we established that in immortalized and transformed cells, FACT has a weak negative effect on gene expression. At the same time, we observed a positive correlation between FACT enrichment and the rate of transcription, which was consistent with previous reports. To explain these puzzling observations, we hypothesized that FACT does not facilitate transcription elongation in transformed cells, but prevents nucleosome loss associated with transcription. Indeed, we observed destabilization of chromatin in immortalized and transformed cells upon FACT loss. Furthermore, transformed cells had less stable chromatin than non-transformed cells, which made them vulnerable to FACT loss. However, the mechanisms of cell death upon chromatin destabilization needs to be established. Our data suggest that malignant transformation is accompanied by general chromatin destabilization, and FACT prevents irredeemable chromatin loss.

cell biology↗

bioRxiv2017

TRAIN in response to treatment with anti-cancer small molecule destabilizing chromatin

The anticancer activity of genotoxic agents has been intensively studied, while the mechanisms of action of drugs destabilizing the epigenome are far less understood. We previously found that DNA hypomethylation in the absence of p53 leads to transcriptional desilencing of repetitive DNA elements, such as pericentromeric repeats and endogenous retroelements, which is associated with an interferon type I response, a phenomenon we named TRAIN (Transcription of Repeats Activates INterferon). Here, we report that curaxin, a small molecule anticancer drug candidate, which destabilizes nucleosomes via disruption of histone/DNA interactions, can induce TRAIN independently of the p53 status of a cell. Furthermore, curaxin inhibits oncogene-induced transformation in an interferon-dependent manner, suggesting that cancer prevention by curaxin, previously attributed to its p53-activating and NF-kappaB-inhibiting activities, may also involve the induction of the interferon response to epigenetic derepression of the cellular \"repeatome.\" Moreover, we observed that another type of drugs decondensing chromatin, histone deacetylase inhibitor, also induces TRAIN. Thus, we proposed that TRAIN may be one of the mechanisms ensuring epigenetic integrity of cells via elimination of cells with desilenced chromatin.

molecular biology↗