We present a highly sensitive and selective chemical labeling and capture approach for genome-wide profiling of 5-hydroxylmethylcytosine (5hmC) using DNA isolated from ∼1,000 cells (nano-hmC-Seal). ...Using this technology, we assessed 5hmC occupancy and dynamics across different stages of hematopoietic differentiation. Nano-hmC-Seal profiling of purified Tet2-mutant acute myeloid leukemia (AML) murine stem cells allowed us to identify leukemia-specific, differentially hydroxymethylated regions that harbor known and candidate disease-specific target genes with differential 5hmC peaks compared to normal stem cells. The change of 5hmC patterns in AML strongly correlates with differential gene expression, demonstrating the importance of dynamic alterations of 5hmC in regulating transcription in AML. Together, covalent 5hmC labeling offers an effective approach to study and detect DNA methylation dynamics in in vivo disease models and in limited clinical samples.
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•Chemical labeling enables highly sensitive profiling of 5hmC using limited input DNA•Genome-wide 5hmC distributions obtained for hematopoietic stem cell differentiation•5hmC changes correlate with differential gene expression in an AML model•Redistributions of 5hmC in the Tet2-deficient leukemia stem cells
Han et al. developed a highly sensitive and robust 5hmC sequencing approach using genomic DNA isolated from ∼1,000 cells. Using their approach, 5hmC maps across different stages of mouse hematopoietic differentiation were obtained and insights into roles of 5hmC in tumor-initiating cells in an AML mouse model were gained.
The ever-increasing understanding of the complexity of factors and regulatory layers that contribute to immune evasion facilitates the development of immunotherapies. However, the diversity of ...malignant tumors limits many known mechanisms in specific genetic and epigenetic contexts, manifesting the need to discover general driver genes. Here, we have identified the m
A demethylase FTO as an essential epitranscriptomic regulator utilized by tumors to escape immune surveillance through regulation of glycolytic metabolism. We show that FTO-mediated m
A demethylation in tumor cells elevates the transcription factors c-Jun, JunB, and C/EBPβ, which allows the rewiring of glycolytic metabolism. Fto knockdown impairs the glycolytic activity of tumor cells, which restores the function of CD8
T cells, thereby inhibiting tumor growth. Furthermore, we developed a small-molecule compound, Dac51, that can inhibit the activity of FTO, block FTO-mediated immune evasion, and synergize with checkpoint blockade for better tumor control, suggesting reprogramming RNA epitranscriptome as a potential strategy for immunotherapy.
Hematopoietic stem cells (HSCs) build up the blood system throughout lifespan. N6-methyladenosine (m6A), the most prevalent RNA modification, modulates gene expression via the processes of "writing" ...and "reading". Recent studies showed that m6A "writer" genes (Mettl3 and Mettl14) play an essential role in HSCs. However, which reader deciphers the m6A modification to modulate HSCs remains unknown. In this study, we observed that dysfunction of Ythdf3 and Ccnd1 severely impaired the reconstitution capacity of HSCs, which phenocopies Mettl3 deficient HSCs. Dysfunction of Ythdf3 and Mettl3 results in the translational defect of Ccnd1. Ythdf3 and Mettl3 regulates HSCs by transmitting m6A RNA methylation on the 5'UTR of Ccnd1. Enforced Ccnd1 completely rescues the defect of Ythdf3-/- HSCs and partially rescues Mettl3-compromised HSCs. Taken together, this study for the first time identified that Ccnd1 is the target of METTL3 and YTHDF3 to transmit m6A RNA methylation signal to regulate HSCs reconstitution capacity.
Accumulating evidence indicates that the efficacy of tumor-targeted therapies relies on the host immune response, including targeted small-molecule and antibody approaches that were not previously ...thought to have an immune component. Here, we review the current understanding of how targeted therapies on tumor cells could have a major impact on the immune response, and how this relates to the therapeutic efficacy of these approaches. In this context, we evaluate different strategies that combine targeted therapies with immunotherapy approaches, and discuss past and ongoing clinical trials. We highlight gaps in knowledge, and argue that significant progress for combined therapies will require a better understanding of the complex interactions between immune cells, the tumor, and the tumor microenvironment (TME) in different cancer settings.
Characterization of RNA modifications has identified their distribution features and molecular functions. Dynamic changes in RNA modification on various forms of RNA are essential for the development ...and function of the immune system. In this review, we discuss the value of innovative RNA modification profiling technologies to uncover the function of these diverse, dynamic RNA modifications in various immune cells within healthy and diseased contexts. Further, we explore our current understanding of the mechanisms whereby aberrant RNA modifications modulate the immune milieu of the tumor microenvironment and point out outstanding research questions.
N6-methyladenosine (m6A) methyltransferase Mettl3 is involved in conventional T cell immunity; however, its role in innate immune cells remains largely unknown. Here, we show that Mettl3 ...intrinsically regulates invariant natural killer T (iNKT) cell development and function in an m6A-dependent manner. Conditional ablation of Mettl3 in CD4+CD8+ double-positive (DP) thymocytes impairs iNKT cell proliferation, differentiation, and cytokine secretion, which synergistically causes defects in B16F10 melanoma resistance. Transcriptomic and epi-transcriptomic analyses reveal that Mettl3 deficiency disturbs the expression of iNKT cell-related genes with altered m6A modification. Strikingly, Mettl3 modulates the stability of the Creb1 transcript, which in turn controls the protein and phosphorylation levels of Creb1. Furthermore, conditional targeting of Creb1 in DP thymocytes results in similar phenotypes of iNKT cells lacking Mettl3. Importantly, ectopic expression of Creb1 largely rectifies such developmental defects in Mettl3-deficient iNKT cells. These findings reveal that the Mettl3-m6A-Creb1 axis plays critical roles in regulating iNKT cells at the post-transcriptional layer.
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•Mettl3-dependent m6A methylation plays a key role in iNKT cell development•A comprehensive m6A landscape of low-input iNKT cells is established by m6A-LACE-seq•Mettl3 deficiency disrupts iNKT cell-related gene network in an m6A-dependent manner•The Mettl3-m6A-Creb1 axis is critical for sustaining iNKT cell differentiation and function
You et al. demonstrate that Mettl3 is essential for regulating iNKT cell proliferation, differentiation, and melanoma resistance. The study highlights the critical role of Mettl3-dependent m6A modification in controlling iNKT cell-related gene expression, particularly in maintaining the stability of Creb1 and c-Myc transcripts.
A new layer of transcriptional controlN6-methyladenosine (m6A) is the most abundant messenger RNA modification in almost all eukaryotes. Liu et al. now show that m6A is also cotranscriptionally added ...onto various chromosome-associated regulatory RNAs (carRNAs) in mammalian cells. Disruption of m6A modification of these RNAs increases their abundance and promotes gene transcription by increasing the chromatin accessibility. Thus, m6A serves as a switch to regulate carRNA levels by tuning nearby chromatin state and downstream transcription.Science, this issue p. 580N6-methyladenosine (m6A) regulates stability and translation of messenger RNA (mRNA) in various biological processes. In this work, we show that knockout of the m6A writer Mettl3 or the nuclear reader Ythdc1 in mouse embryonic stem cells increases chromatin accessibility and activates transcription in an m6A-dependent manner. We found that METTL3 deposits m6A modifications on chromosome-associated regulatory RNAs (carRNAs), including promoter-associated RNAs, enhancer RNAs, and repeat RNAs. YTHDC1 facilitates the decay of a subset of these m6A-modified RNAs, especially elements of the long interspersed element-1 family, through the nuclear exosome targeting–mediated nuclear degradation. Reducing m6A methylation by METTL3 depletion or site-specific m6A demethylation of selected carRNAs elevates the levels of carRNAs and promotes open chromatin state and downstream transcription. Collectively, our results reveal that m6A on carRNAs can globally tune chromatin state and transcription.
-methyladenosine (m
A) regulates stability and translation of messenger RNA (mRNA) in various biological processes. In this work, we show that knockout of the m
A writer
or the nuclear reader
in ...mouse embryonic stem cells increases chromatin accessibility and activates transcription in an m
A-dependent manner. We found that METTL3 deposits m
A modifications on chromosome-associated regulatory RNAs (carRNAs), including promoter-associated RNAs, enhancer RNAs, and repeat RNAs. YTHDC1 facilitates the decay of a subset of these m
A-modified RNAs, especially elements of the long interspersed element-1 family, through the nuclear exosome targeting-mediated nuclear degradation. Reducing m
A methylation by METTL3 depletion or site-specific m
A demethylation of selected carRNAs elevates the levels of carRNAs and promotes open chromatin state and downstream transcription. Collectively, our results reveal that m
A on carRNAs can globally tune chromatin state and transcription.
Macrophage phagocytosis of tumor cells mediated by CD47-specific blocking antibodies has been proposed to be the major effector mechanism in xenograft models. Here, using syngeneic immunocompetent ...mouse tumor models, we reveal that the therapeutic effects of CD47 blockade depend on dendritic cell but not macrophage cross-priming of T cell responses. The therapeutic effects of anti-CD47 antibody therapy were abrogated in T cell-deficient mice. In addition, the antitumor effects of CD47 blockade required expression of the cytosolic DNA sensor STING, but neither MyD88 nor TRIF, in CD11c+ cells, suggesting that cytosolic sensing of DNA from tumor cells is enhanced by anti-CD47 treatment, further bridging the innate and adaptive responses. Notably, the timing of administration of standard chemotherapy markedly impacted the induction of antitumor T cell responses by CD47 blockade. Together, our findings indicate that CD47 blockade drives T cell-mediated elimination of immunogenic tumors.
Celotno besedilo
Dostopno za:
DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SBMB, UILJ, UKNU, UL, UM, UPUK
Tumor-associated macrophages (TAMs) can dampen the antitumor activity of T cells, yet the underlying mechanism remains incompletely understood. Here, we show that C1q
TAMs are regulated by an RNA N
...-methyladenosine (m
A) program and modulate tumor-infiltrating CD8
T cells by expressing multiple immunomodulatory ligands. Macrophage-specific knockout of an m
A methyltransferase Mettl14 drives CD8
T cell differentiation along a dysfunctional trajectory, impairing CD8
T cells to eliminate tumors. Mettl14-deficient C1q
TAMs show a decreased m
A abundance on and a higher level of transcripts of Ebi3, a cytokine subunit. In addition, neutralization of EBI3 leads to reinvigoration of dysfunctional CD8
T cells and overcomes immunosuppressive impact in mice. We show that the METTL14-m
A levels are negatively correlated with dysfunctional T cell levels in patients with colorectal cancer, supporting the clinical relevance of this regulatory pathway. Thus, our study demonstrates how an m
A methyltransferase in TAMs promotes CD8
T cell dysfunction and tumor progression.
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