Cancer therapies that target epigenetic repressors can mediate their effects by activating retroelements within the human genome. Retroelement transcripts can form double-stranded RNA (dsRNA) that ...activates the MDA5 pattern recognition receptor
. This state of viral mimicry leads to loss of cancer cell fitness and stimulates innate and adaptive immune responses
. However, the clinical efficacy of epigenetic therapies has been limited. To find targets that would synergize with the viral mimicry response, we sought to identify the immunogenic retroelements that are activated by epigenetic therapies. Here we show that intronic and intergenic SINE elements, specifically inverted-repeat Alus, are the major source of drug-induced immunogenic dsRNA. These inverted-repeat Alus are frequently located downstream of 'orphan' CpG islands
. In mammals, the ADAR1 enzyme targets and destabilizes inverted-repeat Alu dsRNA
, which prevents activation of the MDA5 receptor
. We found that ADAR1 establishes a negative-feedback loop, restricting the viral mimicry response to epigenetic therapy. Depletion of ADAR1 in patient-derived cancer cells potentiates the efficacy of epigenetic therapy, restraining tumour growth and reducing cancer initiation. Therefore, epigenetic therapies trigger viral mimicry by inducing a subset of inverted-repeats Alus, leading to an ADAR1 dependency. Our findings suggest that combining epigenetic therapies with ADAR1 inhibitors represents a promising strategy for cancer treatment.
Mammalian physiology exhibits 24-hour cyclicity due to circadian rhythms of gene expression controlled by transcription factors that constitute molecular clocks. Core clock transcription factors bind ...to the genome at enhancer sequences to regulate circadian gene expression, but not all binding sites are equally functional. We found that in mice, circadian gene expression in the liver is controlled by rhythmic chromatin interactions between enhancers and promoters. Rev-erbα, a core repressive transcription factor of the clock, opposes functional loop formation between Rev-erbα-regulated enhancers and circadian target gene promoters by recruitment of the NCoR-HDAC3 co-repressor complex, histone deacetylation, and eviction of the elongation factor BRD4 and the looping factor MED1. Thus, a repressive arm of the molecular clock operates by rhythmically modulating chromatin loops to control circadian gene transcription.
We demonstrate that DNA hypomethylating agent (HMA) treatment can directly modulate the anti-tumor response and effector function of CD8+ T cells. In vivo HMA treatment promotes CD8+ T cell tumor ...infiltration and suppresses tumor growth via CD8+ T cell-dependent activity. Ex vivo, HMAs enhance primary human CD8+ T cell activation markers, effector cytokine production, and anti-tumor cytolytic activity. Epigenomic and transcriptomic profiling shows that HMAs vastly regulate T cell activation-related transcriptional networks, culminating with over-activation of NFATc1 short isoforms. Mechanistically, demethylation of an intragenic CpG island immediately downstream to the 3′ UTR of the short isoform was associated with antisense transcription and alternative polyadenylation of NFATc1 short isoforms. High-dimensional single-cell mass cytometry analyses reveal a selective effect of HMAs on a subset of human CD8+ T cell subpopulations, increasing both the number and abundance of a granzyme Bhigh, perforinhigh effector subpopulation. Overall, our findings support the use of HMAs as a therapeutic strategy to boost anti-tumor immune response.
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•DNA hypomethylating agents (HMAs) suppress tumor growth via CD8+ T cell activity•HMAs promote CD8+ T cell activation, effector function, and cytolytic potential•HMAs drive transcriptomic changes toward a heightened CD8+ T cell activation state•HMAs select for a granzyme Bhigh, perforinhigh effector CD8+ T cell subpopulation
DNA hypomethylating agents (HMAs) induce endogenous dsRNA-mediated viral mimicry in cancer cells. Yet the direct effects of HMAs in immune cells remains less clear. Here, Loo Yau et al. demonstrate that HMA treatments promote CD8+ T cell activation and effector function, selecting for a granzyme Bhigh, perforinhigh effector subpopulation.
Triple-negative breast cancer (TNBC) is the most aggressive breast cancer subtype with the worst prognosis and few effective therapies. Here we identified MS023, an inhibitor of type I protein ...arginine methyltransferases (PRMTs), which has antitumor growth activity in TNBC. Pathway analysis of TNBC cell lines indicates that the activation of interferon responses before and after MS023 treatment is a functional biomarker and determinant of response, and these observations extend to a panel of human-derived organoids. Inhibition of type I PRMT triggers an interferon response through the antiviral defense pathway with the induction of double-stranded RNA, which is derived, at least in part, from inverted repeat Alu elements. Together, our results represent a shift in understanding the antitumor mechanism of type I PRMT inhibitors and provide a rationale and biomarker approach for the clinical development of type I PRMT inhibitors.
Hematopoietic stem cell (HSC) dormancy is understood as supportive of HSC function and its long-term integrity. Although regulation of stress responses incurred as a result of HSC activation is ...recognized as important in maintaining stem cell function, little is understood of the preventive machinery present in human HSCs that may serve to resist their activation and promote HSC self-renewal. We demonstrate that the transcription factor PLAG1 is essential for long-term HSC function and, when overexpressed, endows a 15.6-fold enhancement in the frequency of functional HSCs in stimulatory conditions. Genome-wide measures of chromatin occupancy and PLAG1-directed gene expression changes combined with functional measures reveal that PLAG1 dampens protein synthesis, restrains cell growth and division, and enhances survival, with the primitive cell advantages it imparts being attenuated by addition of the potent translation activator, c-MYC. We find PLAG1 capitalizes on multiple regulatory factors to ensure protective diminished protein synthesis including 4EBP1 and translation-targeting miR-127 and does so independently of stress response signaling. Overall, our study identifies PLAG1 as an enforcer of human HSC dormancy and self-renewal through its highly context-specific regulation of protein biosynthesis and classifies PLAG1 among a rare set of bona fide regulators of messenger RNA translation in these cells. Our findings showcase the importance of regulated translation control underlying human HSC physiology, its dysregulation under activating demands, and the potential if its targeting for therapeutic benefit.
•The PLAG1 transcription factor promotes human HSC self-renewal and dormancy.•PLAG1 enforces stemness by dampening expression of translation machinery activated in HSC-stimulatory conditions.
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Children with Down syndrome have a 150-fold increased risk of developing myeloid leukemia, but the mechanism of predisposition is unclear. Because Down syndrome leukemogenesis initiates during fetal ...development, we characterized the cellular and developmental context of preleukemic initiation and leukemic progression using gene editing in human disomic and trisomic fetal hematopoietic cells and xenotransplantation. GATA binding protein 1 (
) mutations caused transient preleukemia when introduced into trisomy 21 long-term hematopoietic stem cells, where a subset of chromosome 21 microRNAs affected predisposition to preleukemia. By contrast, progression to leukemia was independent of trisomy 21 and originated in various stem and progenitor cells through additional mutations in cohesin genes. CD117
/KIT proto-oncogene (KIT) cells mediated the propagation of preleukemia and leukemia, and KIT inhibition targeted preleukemic stem cells.
The identification of regions of DNA sequences that code for proteins is one of the most fundamental applications in bioinformatics. These protein-coding regions are in contrast to other DNA regions ...that encode functional RNA molecules, provide structural stability of chromosomes, serve as genetic raw materials, represent molecular fossils, or have no known purpose (sometimes called "junk DNA"). A number of approaches have been suggested for differentiating between the protein-coding and non-protein-coding regions of DNA. A selection of these approaches is based on digital signal processing (DSP) techniques. These DSP techniques rely on the phenomenon that protein-coding regions have a prominent power spectrum peak at frequency f=⅓ arising from the length of codons (three nucleic acids). This article partitions the identification of protein-coding regions into four discrete steps. Based on this partitioning, DSP techniques can be easily described and compared based on their unique implementations of the processing steps. We compare the approaches, and discuss strengths and weaknesses of each in the context of different applications. Our work provides an accessible introduction and comparative review of DSP methods for the identification of protein-coding regions. Additionally, by breaking down the approaches into four steps, we suggest new combinations that may be worthy of future study.
Prediction of protein coding regions is an important topic in the field of genomic sequence analysis. Several spectrum-based techniques for the prediction of protein coding regions have been ...proposed. However, the outstanding issue in most of the proposed techniques is that these techniques depend on an experimentally-selected, predefined value of the window length. In this paper, we propose a new Wide-Range Wavelet Window (WRWW) method for the prediction of protein coding regions. The analysis of the proposed wavelet window shows that its frequency response can adapt its width to accommodate the change in the window length so that it can allow or prevent frequencies other than the basic frequency in the analysis of DNA sequences. This feature makes the proposed window capable of analyzing DNA sequences with a wide range of the window lengths without degradation in the performance. The experimental analysis of applying the WRWW method and other spectrum-based methods to five benchmark datasets has shown that the proposed method outperforms other methods along a wide range of the window lengths. In addition, the experimental analysis has shown that the proposed method is dominant in the prediction of both short and long exons.
Through a clustered regularly insterspaced short palindromic repeats (CRISPR) screen to identify mitochondrial genes necessary for the growth of acute myeloid leukemia (AML) cells, we identified the ...mitochondrial outer membrane protein mitochondrial carrier homolog 2 (MTCH2). In AML, knockdown of MTCH2 decreased growth, reduced engraftment potential of stem cells, and induced differentiation. Inhibiting MTCH2 in AML cells increased nuclear pyruvate and pyruvate dehydrogenase (PDH), which induced histone acetylation and subsequently promoted the differentiation of AML cells. Thus, we have defined a new mechanism by which mitochondria and metabolism regulate AML stem cells and gene expression.
•Inhibiting MTCH2 increased levels of pyruvate and PDH in nucleus leading to differentiation and loss of engraftment potential in AML.•Defined a new mechanism by which mitochondrial pathways control epigenetics and differentiation in AML.
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Progression to aggressive secondary acute myeloid leukaemia (sAML) poses a significant challenge in the management of myeloproliferative neoplasms (MPNs). Since the physiopathology of MPN is closely ...linked to the activation of interferon (IFN) signalling and that AML initiation and aggressiveness is driven by leukaemia stem cells (LSCs), we investigated these pathways in MPN to sAML progression. We found that high IFN signalling correlated with low LSC signalling in MPN and AML samples, while MPN progression and AML transformation were characterized by decreased IFN signalling and increased LSC signature. A high LSC to IFN expression ratio in MPN patients was associated with adverse clinical prognosis and higher colony forming potential. Moreover, treatment with hypomethylating agents (HMAs) activates the IFN signalling pathway in MPN cells by inducing a viral mimicry response. This response is characterized by double-stranded RNA (dsRNA) formation and MDA5/RIG-I activation. The HMA-induced IFN response leads to a reduction in LSC signature, resulting in decreased stemness. These findings reveal the frequent evasion of viral mimicry during MPN-to-sAML progression, establish the LSC-to-IFN expression ratio as a progression biomarker, and suggests that HMAs treatment can lead to haematological response in murine models by re-activating dsRNA-associated IFN signalling.
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