Comparison of cell response to chromatin and DNA damage

DNA-targeting drugs are widely used for anti-cancer treatment. Many of these drugs cause different types of DNA damage, i.e. alterations in the chemical structure of DNA molecule. However, molecules binding to DNA may also interfere with DNA packing into chromatin. Interestingly, some molecules do not cause any changes in DNA chemical structure but interfere with DNA binding to histones and nucleosome wrapping. This results in histone loss from chromatin and destabilization of nucleosomes, a phenomenon that we call chromatin damage. Although the cellular response to DNA damage is well-studied, the consequences of chromatin damage are not. Moreover, many drugs used to study DNA damage also cause chromatin damage, therefore there is no clarity on which effects are caused by DNA or chromatin damage. In this study, we aimed to clarify this issue. We treated normal and tumor cells with bleomycin, nuclease mimicking drug which cut predominantly nucleosome-free DNA and therefore causes DNA damage in the form of DNA breaks, and CBL0137, which causes chromatin damage without direct DNA damage. We describe similarities and differences between the consequences of DNA and chromatin damage. Both agents were more toxic for tumor than normal cells, but while DNA damage causes senescence in both normal and tumor cells, chromatin damage does not. Both agents activated p53, but chromatin damage leads to the accumulation of higher levels of unmodified p53, which transcriptional activity was similar to or lower than that of p53 activated by DNA damage. Most importantly, we found that while transcriptional changes caused by DNA damage are limited by p53-dependent activation of a small number of p53 targets, chromatin damage activated many folds more genes in p53 independent manner.

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.

Abstract 4496: Induction of immunogenicity in tumor cells by small molecule drugs that destabilize nucleosomes

Curaxins are DNA binding small molecules that bind genomic DNA with high affinity and disrupt DNA-histone interactions, leading to dose-dependent nucleosome disassembly and chromatin decondensation in cells. Curaxins have anti-cancer activity against multiple mouse cancer models, and lead curaxin CBL0137 is currently being tested in several clinical trials. During preclinical testing, we observed that CBL0137 caused complete regression of spontaneous tumors in many transgenic mice but only inhibited tumor growth in xenograft models. One of the hypotheses to explain this difference is that the immune system, which is intact in transgenic mice but compromised in mice with xenograft tumors, may play an important role in the anti-cancer activity of curaxins. To test this hypothesis, we compared the growth of the same tumor cells (mouse 4T1 breast cancer cells) in syngeneic, immunocompetent BALB/c mice and immunocompromised SCID mice. CBL0137 had a much stronger inhibitory effect on tumor growth in BALB/c compared to SCID mice. There were also fewer suppressor cells and more active lymphocytes in tumors from BALB/c mice treated with CBL0137 compared to those treated with vehicle. Furthermore, CBL0137 substantially increased the abscopal effect of ionizing radiation. To understand the relationship between the immune system and CBL0137, we measured changes in gene expression in normal mouse organs and tumors upon treatment with CBL0137. The most prominent effect of CBL0137 observed was the induction of the type I interferon response (IFN-I). The same effect was also detected in PBMC from the blood of healthy volunteers treated ex vivo with CBL0137 and clinical trial cancer patients after a single IV injection of CBL0137. In this study, we aimed to establish how chromatin decondensation leads to IFN-I and increased immunogenicity of tumor cells. We identified several complementary mechanisms: (i) bi-directional expression of constitutive heterochromatin, leading to the accumulation of double-stranded RNA, known trigger of IFN-I; (ii) reactivation of facultative heterochromatin and expression of embryo-specific antigens, such as NY-ESO-I, recognized as a foreign antigen by T cells; (iii) increased expression of epigenetically silenced MHC-I proteins in tumor cells; (iv) departure of architectural chromatin proteins, such as HMGB1, from chromatin, which normally serve as a ligand-damage associated molecular pattern (DAMP) receptor. Thus, chromatin decondensation serves as a potent inducer of tumor cell immunogenicity. An immune response may significantly improve the anti-cancer activity of CBL0137, and the presence of an intact IFN-I could serve as a potential predictive marker of patient response to curaxin treatment.

Citation Format: Katerina Leonova, Alfiya Safina, Andrei V. Gudkov, Katerina V. Gurova. Induction of immunogenicity in tumor cells by small molecule drugs that destabilize nucleosomes [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4496.

Abstract 2866: Anticancer effect of a new cyclic peptide ALOS4 is associated with its systemic anti-inflammatory activity

The association of chronic inflammation with cancer development and progression has been well recognized. Here, we report a synthetic cyclic peptide, ALOS4, capable of suppressing tumor growth following systemic administration and possessing anti-inflammatory properties. Although ALOS4 was initially isolated by phage display for its ability to bind avb3 integrin and demonstrated tumor-suppressor activity in preclinical xenograft and syngeneic models of melanoma, it surprisingly showed no functional activity resembling RGD peptides in functional in vitro assays. Remarkably, ALOS4 displayed no signs of toxicity in treated animals, even at doses exceeding >100-fold beyond the efficacious dose. To identify the mechanisms underlying profound antitumor activity of this safe peptide, we used a large panel of cell-based repeater assays designed to detect modulators of a variety of signaling pathways including p53, NF-kB, and different types of stress responses including heat shock and hypoxia. We also tested the effects of ALOS4 on tumor cell growth, adhesion, clonogenicity, morphology and other in vitro properties. ALOS4 showed no detectable activity in any of these numerous assays with one exception: it suppressed the ability of treated cells to induce interferon type I signaling in response to mimics of double-stranded RNA (Poly I:C). Based on this observation, we hypothesized that the antitumor effect of ALOS4 is driven by a systemic anti-inflammatory effect rather than by a direct effect on tumor cells. Consistently, ALOS4 treatment dramatically altered both the abundance and content of the immunocyte population infiltrating subcutaneous melanomas in mice. These results suggest that ALOS4 may be an anticancer agent with a new mechanism of action that targets the tumor-supporting interferon-driven mechanism of tumor-host interaction.

Citation Format: Elimelech Nesher, Albert Pinhasov, Maria Becker, Michael Kirby, Raichel Cohen Harazi, Shiri Yakobovich, Oryan Agranyoni, Bar Shoval, Shany I. Elbaz, Olga Udartseva, Ilya Gitlin, Katerina Leonova, Katerina Gurova, Andrei Gudkov, Igor Koman. Anticancer effect of a new cyclic peptide ALOS4 is associated with its systemic anti-inflammatory activity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2866.

TRAIN (Transcription of Repeats Activates INterferon) in response to chromatin destabilization induced by small molecules in mammalian cells

Cellular responses to the loss of genomic stability are well-established, while how mammalian cells respond to chromatin destabilization is largely unknown. We previously found that DNA demethylation on p53-deficient background leads to transcription of repetitive heterochromatin elements, followed by an interferon response, a phenomenon we named TRAIN (Transcription of Repeats Activates INterferon). Here, we report that curaxin, an anticancer small molecule, destabilizing nucleosomes via disruption of histone/DNA interactions, also induces TRAIN. Furthermore, curaxin inhibits oncogene-induced transformation and tumor growth in mice in an interferon-dependent manner, suggesting that anticancer activity of curaxin, previously attributed to p53-activation and NF-kappaB-inhibition, may also involve induction of interferon response to epigenetic derepression of the cellular 'repeatome'. Moreover, we observed that another type of drugs decondensing chromatin, HDAC inhibitor, also induces TRAIN. Thus, we proposed that TRAIN may be one of the mechanisms ensuring epigenetic integrity of mammalian cells via elimination of cells with desilenced chromatin.

Aging of mice is associated with p16(Ink4a)- and β-galactosidase-positive macrophage accumulation that can be induced in young mice by senescent cells

Senescent cells (SCs) have been considered a source of age-related chronic sterile systemic inflammation and a target for anti-aging therapies. To understand mechanisms controlling the amount of SCs, we analyzed the phenomenon of rapid clearance of human senescent fibroblasts implanted into SCID mice, which can be overcome when SCs were embedded into alginate beads preventing them from immunocyte attack. To identify putative SC killers, we analyzed the content of cell populations in lavage and capsules formed around the SC-containing beads. One of the major cell types attracted by secretory factors of SCs was a subpopulation of macrophages characterized by p16(Ink4a) gene expression and β-galactosidase activity at pH6.0 (β-gal(pH6)), thus resembling SCs. Consistently, mice with p16(Ink4a) promoter-driven luciferase, developed bright luminescence of their peritoneal cavity within two weeks following implantation of SCs embedded in alginate beads. p16(Ink4a)/β-gal(pH6)-expressing cells had surface biomarkers of macrophages F4/80 and were sensitive to liposomal clodronate used for the selective killing of cells capable of phagocytosis. At the same time, clodronate failed to kill bona fide SCs generated in vitro by genotoxic stress. Old mice with elevated proportion of p16(Ink4a)/β-gal(pH6)-positive cells in their tissues demonstrated reduction of both following systemic clodronate treatment, indicating that a significant proportion of cells previously considered to be SCs are actually a subclass of macrophages. These observations point at a significant role of p16(Ink4a)/β-gal(pH6)-positive macrophages in aging, which previously was attributed solely to SCs. They require re-interpretation of the mechanisms underlying rejuvenating effects following eradication of p16(Ink4a)/β-gal(pH6)-positive cells and reconsideration of potential cellular target for anti-aging treatment.

Abstract PR02: “Guardians of repeats”: Novel and significant relationship of p53 and interferon

Large parts of mammalian genomes are transcriptionally inactive and enriched with various classes of interspersed and tandem repeats. Here we show that the tumor suppressor protein p53, along with DNA methylation, plays an essential role in maintaining silencing of a large portion of the mouse genome. In the absence of functional p53, hypomethylation of DNA results in massive transcription of major classes of short interspersed repeats (SINEs B1 and B2), both strands of near-centromeric satellite DNAs consisting of tandem repeats, and multiple species of non-coding RNAs. In p53-deficient mouse fibroblasts treated with the DNA demethylating agent 5-aza-2'-deoxycytidine, the abundance of these new transcripts exceeds the level of β-actin mRNA by more than 150-fold. Accumulation of these largely double-stranded transcripts, in the absence of p53, is accompanied with a strong endogenous type I interferon response that induces apoptotic cell death. Transcriptional activation of repeats and non-coding RNAs is observed in a significant proportion of spontaneous mouse tumors, presumably reflecting naturally occurring DNA hypomethylation and p53 inactivation. These observations suggest that p53 and IFN cooperate to prevent accumulation of cells with activated repeats. This model, which we have named TRAIN (Transcription of Repeats Activates INterferon), assigns a novel role to p53 as a guardian of repeats. TRAIN model provides plausible explanation for frequent deregulation of interferon pathway observed in a variety of tumors. Overall, this work highlights the cooperation between p53 and interferon as key players needed to maintain genetic stability, and even further outlines their significance in tumor progression and the evolution of the species.

Citation Format: Katerina Leonova, Andrei Gudkov. “Guardians of repeats”: Novel and significant relationship of p53 and interferon. [abstract]. In: Proceedings of the Third AACR International Conference on Frontiers in Basic Cancer Research; Sep 18-22, 2013; National Harbor, MD. Philadelphia (PA): AACR; Cancer Res 2013;73(19 Suppl):Abstract nr PR02.

Abstract 2959: p53 as a guardian of genomic junk: A novel role for p53 in epigenetic silencing of retroelements

Demethylating agents have been reported to be more toxic to p53-deficient cells than wild type (WT) cells in several models. To elucidate the mechanism underlying this phenomenon, we performed microarray-based global gene expression profiling of mouse embryo fibroblasts (MEFs) from p53-WT and p53-null mice with or without 5-aza-2′-deoxycytidine (5-aza-dC) treatment. This analysis revealed two major findings. First, all protein-coding transcripts induced by 5-aza-dC treatment in WT cells were highly expressed and irresponsive to the demethylating agent in untreated p53-deficient cells. This observation defines p53 as a major driver of DNA methylation-dependent gene silencing. Second, death of p53-null cells treated with 5-aza-dC is preceded by strong activation of transcription of interferon (IFN)-responsive genes driven by IFNα induction. Since no obvious candidates for the role of IFN-inducing factors were found among the genes represented on the microarray, we carried out high-throughput sequencing (HTS) of the entire transcriptome of p53-WT and p53-null MEFs, treated or untreated with 5-aza-dC. The HTS results revealed striking transcriptional upregulation of numerous genetic elements belonging to various classes of retrotransposons and non-coding RNAs in p53-null, but not in p53-WT cells, treated with 5-aza-dC. We named this phenomenon of massive induction of transcription of retroelements, which are normally repressed by p53, RETROSIS. Retrosis is likely to be the trigger of the observed IFN response and the mediator of toxicity in p53-null cells treated with 5-aza-dC. These findings define a novel role for p53, acting along with DNA methylation, in regulation of epigenetic silencing of the large proportion of the genome that consists of retroelements and suggest a new evolutionary role for this tumor suppressor. The impact of retrosis in tumor cells deficient in p53 and implications of this phenomenon for the tumor suppressor function of p53 will be discussed.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2959. doi:1538-7445.AM2012-2959

Abstract 4398: Liver is a major primary target for the Toll-like receptor-5 agonist CBLB502 providing radioprotective, antimicrobial and antitumor responses

We have previously shown that activation of Toll-like receptor 5 (TLR5) by bacterial flagellin and by pharmacologically optimized flagellin derivative CBLB502 protects mice and monkeys from lethal radiation injury to the hematopoietic and gastrointestinal systems. Here, we report that the liver is a major primary CBLB502 target organ in mice, with hepatocytes specifically showing rapid and strong NF-kB and STAT3 activation. Livers from CBLB502-treated mice showed up-regulation of numerous downstream genes encoding intracellular and secreted proteins with anti-apoptotic, anti-microbial and immunomodulatory activities. Unlike the TLR4 agonist LPS, the liver response to TLR5 agonists appears to be direct and does not involve high levels of proinflammatory cytokines. Thus, while LPS is toxic, TLR5 agonists have strong clinical potential. The importance of liver for CBLB502 radioprotective activity was confirmed by temporary occlusion of liver blood circulation which completely abrogated the protective effect of CBLB502 on hematopoietic precursor cells in irradiated mice. CBLB502 also protected liver tissue itself, increasing mouse resistance to lethal Salmonella tiphymurium liver infection and to hepatotoxic Fas agonistic antibodies. By testing CBLB502 in combination with radiation treatment of experimental mouse tumors in vivo, we demonstrated that its tissue protection properties are limited to normal tissues with no tumor protection detected in any of numerous mouse tumor models. Moreover, direct antitumor effects of CBLB502 treatment was observed in several tumor models. Comparison of the effect of CBLB502 on in vivo growth of isogenic pairs of tumor cell lines differing in their TLR5 status showed that the antitumor effect of the TLR5 agonist is TLR5 dependent and is associated with tumor infiltration by immunocytes, presumably attracted following activation of TLR5 signaling in the tumor cells. Remarkably, CBLB502 caused an immunotherapeutic effect in TLR5-negative tumors (CT26 colon adenocarcinoma and A20 lymphoma) growing as experimental liver metastases. Based on these results, we project clinical applications of CBLB502 as an anticancer immunotherapeutic drug against liver metastases independently on TLR5 status and TLR5-expressing tumors in other locations as well as supporting care drug to reduce adverse hepatotoxicity from radiation and chemotherapy.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4398. doi:1538-7445.AM2012-4398

Abstract A63: TLR5 agonist CBLB502 protects mice from Fas-mediated liver damage without protecting tumors

We have previously shown the strong radioprotective properties of the Toll-like receptor 5 (TLR5) agonist flagellin and its derivative CBLB502 in both mouse and non-human primate models (Burdelya et al., 2008, Science 320: 226–230). Because no protection has been observed in any in vitro cell model regardless of the TLR5 status of the cells, we hypothesized that the radioprotective effects of the TLR5 agonist are indirect and mediated by factors produced by primary cells responding to flagellin in the organism. Using a combination of tools, including NF-kB-responsive reporter mice and immunohistochemical determination of tissues responding to CBLB502 by NF-kB activation, we defined liver hepatocytes as the primary pharmacological targets of flagellin. Surgical exclusion of the liver from the blood circulation completely abolished radioprotection of the bone marrow hematopoietic progenitor cells by CBLB502 suggesting that the liver acts as a mediator of at least some of the effects of the TLR5 agonist. Since the induction of NF-kB is known to activate multiple pro-survival mechanisms, we further hypothesized that administration of the TLR5 agonist can result in liver resistance to otherwise toxic conditions. Mice treated with Fas agonistic antibodies were employed as a model of acute hepatotoxicity. Injection of CBLB502 showed a strong preventive effect against Fas-mediated injury rescuing all of the injected mice in contrast to complete lethality in the control groups. The ability of CBLB502 to protect the liver was also demonstrated via reduced levels of liver enzymes in the peripheral blood and caspase activation in liver extracts of mice treated with Fas agonistic antibodies. Using two syngeneic tumor models, colon adenocarcinoma CT26 and lymphoma A20, growing as liver metastases in mice, we found that CBLB502 injections not only prevented liver damage, but also suppressed tumor appearance and growth when injected with or without anti-Fas antibodies. Thus, TLR5 agonist has potential to become a new agent for liver protection and suppression of liver metastasis.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the Second AACR International Conference on Frontiers in Basic Cancer Research; 2011 Sep 14-18; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2011;71(18 Suppl):Abstract nr A63.