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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.

Glioblastoma (GBM) remains an aggressive brain tumor with a high rate of mortality. Immune checkpoint (IC) molecules are expressed on tumor infiltrating lymphocytes (TILs) and promote T cell exhaustion upon binding to IC ligands expressed by the tumor cells. Interfering with IC pathways with immunotherapy has promoted reactivation of anti-tumor immunity and led to success in several malignancies. However, IC inhibitors have achieved limited success in GBM patients, suggesting that other checkpoint molecules may be involved with suppressing TIL responses. Numerous IC pathways have been described, with current testing of inhibitors underway in multiple clinical trials. Identification of the most promising checkpoint pathways may be useful to guide the future trials for GBM. Here, we analyzed the The Cancer Genome Atlas (TCGA) transcriptomic database and identified PD1 and TIGIT as top putative targets for GBM immunotherapy. Additionally, dual blockade of PD1 and TIGIT improved survival and augmented CD8 + TIL accumulation and functions in a murine GBM model compared with either single agent alone. Furthermore, we demonstrated that this combination immunotherapy affected granulocytic/polymorphonuclear (PMN) myeloid derived suppressor cells (MDSCs) but not monocytic (Mo) MDSCs in in our murine gliomas. Importantly, we showed that suppressive myeloid cells express PD1, PD-L1, and TIGIT-ligands in human GBM tissue, and demonstrated that antigen specific T cell proliferation that is inhibited by immunosuppressive myeloid cells can be restored by TIGIT/PD1 blockade. Our data provide new insights into mechanisms of GBM αPD1/αTIGIT immunotherapy.

PurposeA history of atopy or allergy has been shown to be protective against the development of glioma, however the effect of atopy on patient outcomes, especially in conjunction with the survival benefit associated with IDH mutation, has not yet been investigated, and is the focus of the study we present here.MethodsLow grade glioma (LGG) data from the TCGA was downloaded, along with IDH, TERT, 1p/19q and ATRX mutational status and genetic alterations. History of asthma, eczema, hay fever, animal, or food allergies, as documented in TCGA, was used to determine patient atopy status. Patients with missing variables were excluded from the study.Results374 LGG studies were included. Patients with a history of atopy demonstrated longer overall survival (OS) compared to those without (145.3 vs. 81.5 months, p = 00.0195). IDH mutant patients with atopy had longer OS compared those without atopy (158.8 vs. 85 months, p = 0.035). Multivariate cox regression analysis demonstrated that the effects of atopy on survival were independent of IDH and histological grade, (p = 0.002, HR 0.257, 95% 0.109–0.604), (p =  < 0.001, HR 0.217, 95% 0.107–0.444), and (p = 0.004, HR 2.72, 95% 1.373–5.397), respectively. In terms of treatment outcomes, patients with atopy did not differ in treatment response compared to their counterpart. Pathway analysis demonstrated an upstream activation of the BDNF pathway (p = 0.00027).ConclusionA history of atopy confers a survival benefit in patients with diffuse low-grade glioma. Activation of the BDNF pathway may drive the observed differences.

FAcilitates Chromatin Transcription (FACT) is a complex of SSRP1 and SPT16 that is involved in chromatin remodeling during transcription, replication, and DNA repair. FACT has been mostly studied in cell-free or single cell model systems because general FACT knockout (KO) is embryonically lethal (E3.5). FACT levels are limited to the early stages of development and stem cell niches of adult tissues. FACT is upregulated in poorly differentiated aggressive tumors. Importantly, FACT inhibition (RNAi) is lethal for tumors but not normal cells, making FACT a lucrative target for anticancer therapy. To develop a better understanding of FACT function in the context of the mammalian organism under normal physiological conditions and in disease, we aimed to generate a conditional FACT KO mouse model. Because SPT16 stability is dependent on the SSRP1-SPT16 association and the presence of SSRP1 mRNA, we targeted the Ssrp1 gene using a CreERT2- LoxP approach to generate the FACT KO model. Here, we highlight the limitations of the CreERT2-LoxP (Rosa26) system that we encountered during the generation of this model. In vitro studies showed an inefficient excision rate of ectopically expressed CreERT2 (retroviral CreERT2) in fibroblasts with homozygous floxed Ssrp1. In vitro and in vivo studies showed that the excision efficiency could only be increased with germline expression of two alleles of Rosa26CreERT2. The expression of one germline Rosa26CreERT2 allele led to the incomplete excision of Ssrp1. The limited efficiency of the CreERT2-LoxP system may be sufficient for studies involving the deletion of genes that interfere with cell growth or viability due to the positive selection of the phenotype. However, it may not be sufficient for studies that involve the deletion of genes supporting growth, or those crucial for development. Although CreERT2-LoxP is broadly used, it has limitations that have not been widely discussed. This paper aims to encourage such discussions.

FAcilitates Chromatin Transcription (FACT) is a complex of SSRP1 and SPT16 that is involved in chromatin remodeling during transcription, replication, and DNA repair. FACT has been mostly studied in cell-free or single cell model systems because general FACT knockout (KO) is embryonically lethal (E3.5). FACT levels are limited to the early stages of development and stem cell niches of adult tissues. FACT is upregulated in poorly differentiated aggressive tumors. Importantly, FACT inhibition (RNAi) is lethal for tumors but not normal cells, making FACT a lucrative target for anticancer therapy. To develop a better understanding of FACT function in the context of the mammalian organism under normal physiological conditions and in disease, we aimed to generate a conditional FACT KO mouse model. Because SPT16 stability is dependent on the SSRP1-SPT16 association and the presence of SSRP1 mRNA, we targeted the Ssrp1 gene using a CreER.sup.T2 - LoxP approach to generate the FACT KO model. Here, we highlight the limitations of the CreER.sup.T2 -LoxP (Rosa26) system that we encountered during the generation of this model. In vitro studies showed an inefficient excision rate of ectopically expressed CreER.sup.T2 (retroviral CreER.sup.T2) in fibroblasts with homozygous floxed Ssrp1. In vitro and in vivo studies showed that the excision efficiency could only be increased with germline expression of two alleles of Rosa26CreER.sup.T2 . The expression of one germline Rosa26CreER.sup.T2 allele led to the incomplete excision of Ssrp1. The limited efficiency of the CreER.sup.T2 -LoxP system may be sufficient for studies involving the deletion of genes that interfere with cell growth or viability due to the positive selection of the phenotype. However, it may not be sufficient for studies that involve the deletion of genes supporting growth, or those crucial for development. Although CreER.sup.T2 -LoxP is broadly used, it has limitations that have not been widely discussed. This paper aims to encourage such discussions.

FAcilitates Chromatin Transcription (FACT) is a heterodimeric complex of subunits SSRP1 and Spt16 that is involved in chromatin remodeling during transcription, replication, and DNA repair. Due to early embryonic lethality of FACT knockout (KO)[1] FACT’s function in normal cells of mammalian organisms was not possible to observe. Therefore, it was mostly studied in single cell organisms and in tumor cell lines in vitro, where it was considered to be ubiquitously expressed and have housekeeping-like functions. Conversely, our lab has shown FACT expression to be selectively limited to early stages of development and stem cell niches in adult. Also, FACT was found to be expressed in multiple types of undifferentiated aggressive human tumors with poor prognosis. These tumors could not tolerate FACT inhibition (chemical: Curaxin and RNAi mediated), unlike normal cells. Furthermore, our lab has shown a peculiar mechanism of regulation of FACT; stability and functionality of FACT depends on dimerization of the two subunits: SPT16 and SSRP1 and the stability of both subunits is also interdependent. Here, we aimed to develop a better understanding of FACT’s function in the context of mammalian organism in normal physiological conditions and in disease e.g. cancer, and propose that inhibition of FACT may be safe and effective approach to eradicate cancer. We generated a conditional KO of Ssrp1 mice model, using CreERT2-LoxP system, and assessed FACT’s function in the context of the whole organism, with temporal and spatial control. In our efforts to generate a conditional KO of Ssrp1 mice model we found inefficient excision rate of CreERT2 when expressed ectopically (retroviral CreERT2 plasmid) potentially due to its mosaic expression in cells, and hence incomplete excision of the gene occurs. Additionally, inefficient excision of Ssrp1 in these cells may also be because of loss of activity of CreERT2, as it may not be stable in absence of its ligand. Furthermore, in vitro and in vivo studies show excision efficiency of Ssrp1 by single allele of CreERT2 expressed through germline is also poor. However, germline expression of two alleles of CreERT2 resulted in homozygous excision of Ssrp1 and hence, completes FACT inactivation. Using this model, we show that FACT is upregulated during in vitro transformation and demonstrate differential dependence of cells on FACT at different stages of in vitro transformation. FACT inactivation is tolerable by normal cells however, not by tumor and transformed cells. Furthermore, its inactivation strongly affected malignant properties of transformed cells in vitro and in vivo. Gene expression analysis upon FACT inactivation, in these cell types, did not affect the rate of global transcription, however did affect transcriptions of few specific genes. More importantly, there were even fewer changes in gene expression which were common to all three cell types involved in maintenance of differentiation status and cell death. Based on this study, we propose that the differential dependence on FACT of cell types, of same origin, may be due to the differences in the rate of replication, the presence of replication stress, differences in chromatin organization, or other factors involved in maintaining genome integrity, which further needs to be explored. Nevertheless, this selective dependence on FACT of tumor and transformed cells, but not of normal cells, suggests FACT inactivation as an antitumor therapeutic approach to be safe and efficacious.

Diffuse gliomas are epigenetically dysregulated, immunologically cold, and fatal tumors characterized by mutations in isocitrate dehydrogenase (IDH). Although IDH mutations yield a uniquely immunosuppressive tumor microenvironment, the regulatory mechanisms that drive the immune landscape of IDH mutant (IDHm) gliomas remain unknown. Here, we reveal that transcriptional repression of retinoic acid (RA) pathway signaling impairs both innate and adaptive immune surveillance in IDHm glioma through epigenetic silencing of retinol binding protein 1 (RBP1) and induces a profound anti-inflammatory landscape marked by loss of inflammatory cell states and infiltration of suppressive myeloid phenotypes. Restorative retinoic acid therapy in murine glioma models promotes clonal CD4 + T cell expansion and induces tumor regression in IDHm, but not IDH wildtype (IDHwt), gliomas. Our findings provide a mechanistic rationale for RA immunotherapy in IDHm glioma and is the basis for an ongoing investigator-initiated, single-center clinical trial investigating all-trans retinoic acid (ATRA) in recurrent IDHm human subjects.Diffuse gliomas are epigenetically dysregulated, immunologically cold, and fatal tumors characterized by mutations in isocitrate dehydrogenase (IDH). Although IDH mutations yield a uniquely immunosuppressive tumor microenvironment, the regulatory mechanisms that drive the immune landscape of IDH mutant (IDHm) gliomas remain unknown. Here, we reveal that transcriptional repression of retinoic acid (RA) pathway signaling impairs both innate and adaptive immune surveillance in IDHm glioma through epigenetic silencing of retinol binding protein 1 (RBP1) and induces a profound anti-inflammatory landscape marked by loss of inflammatory cell states and infiltration of suppressive myeloid phenotypes. Restorative retinoic acid therapy in murine glioma models promotes clonal CD4 + T cell expansion and induces tumor regression in IDHm, but not IDH wildtype (IDHwt), gliomas. Our findings provide a mechanistic rationale for RA immunotherapy in IDHm glioma and is the basis for an ongoing investigator-initiated, single-center clinical trial investigating all-trans retinoic acid (ATRA) in recurrent IDHm human subjects.

Replication and transcription machineries access DNA through unwrapping it from histone core. Preservation of nucleosome structure during replication is a focus of intensive research, while maintenance of nucleosomes during transcription is less studied. Histone chaperone FACT is involved in transcription elongation, although whether it opens nucleosomes for polymerase or protects core histones from loss during passage of polymerase is still unclear. We used conditional knockout model of Ssrp1, subunit of FACT complex, to deplete FACT in mice and monitored consequences of FACT loss to establish the functional relevance of FACT in mammals. FACT loss was lethal for mice at all ages due to failure of hematopoietic and intestinal tissues. In these tissues, only the progenitors completely vanished upon FACT loss, while number of some other cell types were changed up and down. Using isolated stem cells of several tissues we showed that FACT loss was toxic only for stem cells, but not for cells which were differentiated in vitro. Chromatin accessibility in stem cells was increased genome wide upon FACT depletion in transcription dependent manner. The most prominent response to the loss of chromatin integrity upon FACT depletion in cells was activation of interferon signaling, followed by accumulation of immune cells in sensitive organs. Thus, in undifferentiated mammalian cells FACT keeps chromatin stable during transcription elongation and this function of FACT is essential for viability of stem cells. Competing Interest Statement The authors have declared no competing interest.

Preservation of nucleosomes during replication has been extensively studied, while the maintenance of nucleosomes during transcription has gotten less attention. The histone chaperone FACT is involved in transcription elongation, although whether it disassembles or assembles nucleosomes during this process is still unclear. We deleted the FACT subunit in adult mice to clarify the function of FACT in mammals. FACT loss was lethal due to the loss of the earliest progenitors in bone marrow and intestine, while mor differentiated cells were not affected. Using cells isolated from several tissues, we showed that FACT loss was lethal only for stem cells but not cells differentiated in vitro. FACT depletion led to increased chromatin accessibility in a transcription-dependent manner, suggesting that nucleosomes are lost during transcription in the absence of FACT. The most prominent response to the loss of nucleosomes was the activation of interferon signaling and the accumulation of immunocytes in sensitive organs. FACT maintained chromatin integrity during transcription in mammalian adult stem cells, suggesting that chromatin transcription in these cells is different from more differentiated cells.

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.