bims-ectoca Biomed News
on Epigenetic control of tolerance in cancer
Issue of 2022‒07‒17
eight papers selected by
Ankita Daiya
BITS Pilani
  1. YAP induces an oncogenic transcriptional program through TET1-mediated epigenetic remodeling in liver growth and tumorigenesis.
  2. Single cell cancer epigenetics.
  3. A role for nuclear stretching and NPCs changes in the cytoplasmic-nuclear trafficking of YAP: An experimental and numerical modelling approach.
  4. Persister cells that survive chemotherapy are pinpointed.
  5. EZH2 promotes the progression of osteosarcoma through the activation of the AKT/GSK3β pathway.
  6. Generating specificity in genome regulation through transcription factor sensitivity to chromatin.
  7. Drug Repurposing by Tumor Tissue Editing.
  8. H3K27me3 shapes DNA methylome by inhibiting UHRF1-mediated H3 ubiquitination.
  1. Nat Genet. 2022 Jul 14.
    YAP induces an oncogenic transcriptional program through TET1-mediated epigenetic remodeling in liver growth and tumorigenesis.
    Bo-Kuan Wu, Szu-Chieh Mei, Elizabeth H Chen, Yonggang Zheng, Duojia Pan.
      Epigenetic remodeling is essential for oncogene-induced cellular transformation and malignancy. In contrast to histone post-translational modifications, how DNA methylation is remodeled by oncogenic signaling remains poorly understood. The oncoprotein YAP, a coactivator of the TEAD transcription factors mediating Hippo signaling, is widely activated in human cancers. Here, we identify the 5-methylcytosine dioxygenase TET1 as a direct YAP target and a master regulator that coordinates the genome-wide epigenetic and transcriptional reprogramming of YAP target genes in the liver. YAP activation induces the expression of TET1, which physically interacts with TEAD to cause regional DNA demethylation, histone H3K27 acetylation and chromatin opening in YAP target genes to facilitate transcriptional activation. Loss of TET1 not only reverses YAP-induced epigenetic and transcriptional changes but also suppresses YAP-induced hepatomegaly and tumorigenesis. These findings exemplify how oncogenic signaling regulates the site specificity of DNA demethylation to promote tumorigenesis and implicate TET1 as a potential target for modulating YAP signaling in physiology and disease.
    DOI:  https://doi.org/10.1038/s41588-022-01119-7
  2. Trends Cancer. 2022 Jul 09. pii: S2405-8033(22)00133-9. [Epub ahead of print]
    Single cell cancer epigenetics.
    Marta Casado-Pelaez, Alberto Bueno-Costa, Manel Esteller.
      Bulk sequencing methodologies have allowed us to make great progress in cancer research. Unfortunately, these techniques lack the resolution to fully unravel the epigenetic mechanisms that govern tumor heterogeneity. Consequently, many novel single cell-sequencing methodologies have been developed over the past decade, allowing us to explore the epigenetic components that regulate different aspects of cancer heterogeneity, namely: clonal heterogeneity, tumor microenvironment (TME), spatial organization, intratumoral differentiation programs, metastasis, and resistance mechanisms. In this review, we explore the different sequencing techniques that enable researchers to study different aspects of epigenetics (DNA methylation, chromatin accessibility, histone modifications, DNA-protein interactions, and chromatin 3D architecture) at the single cell level, their potential applications in cancer, and their current technical limitations.
    Keywords:  cancer; epigenetics; heterogeneity; omics; sequencing; single cell
    DOI:  https://doi.org/10.1016/j.trecan.2022.06.005
  3. Mater Today Bio. 2022 Jun;15 100335
    A role for nuclear stretching and NPCs changes in the cytoplasmic-nuclear trafficking of YAP: An experimental and numerical modelling approach.
    Stefania Saporito, Carlo F Natale, Costantino Menna, Paolo Antonio Netti, Maurizio Ventre.
      Mechanical forces, acting on eukaryotic cells, are responsible for cell shape, cell proliferation, cell polarity, and cell differentiation thanks to two cells abilities known as mechanosensing and mechanotransduction. Mechanosensing consists of the ability of a cell to sense mechanical cues, while mechanotransduction is the capacity of a cell to respond to these signals by translating mechanical stimuli into biochemical ones. These signals propagate from the extracellular matrix to the nucleus with different well known physical connections, but how the mechanical signals are transduced into biochemical ones remains an open challenge. Recent findings showed that the cell-generated forces affect the translocation of transcription factors (TFs) from the cytoplasm to the nucleus. This mechanism is affected by the features of nuclear pore complexes. Owing to the complex patterns of strains and stresses of the nuclear envelope caused by cytoskeletal forces, it is likely that the morphology of NPC changes as cytoskeleton assemblies' change. This may ultimately affect molecular transport through the nucleus, hence altering cell functions. Among the various TFs, Yes-associated protein (YAP), which is typically involved in cell proliferation, survival, and differentiation, is able to activate specific pathways when entrapped into the cell nucleus. Here, starting from experimental results, we develop a multiscale finite element (FE) model aimed to simulate the macroscopic cell spreading and consequent changes in the cell mechanical behaviour to be related to the NPCs changes and YAP nuclear transport.
    Keywords:  Finite element models; Mechanobiology; Micropatterning; Nuclear pores; Stem cells
    DOI:  https://doi.org/10.1016/j.mtbio.2022.100335
  4. Nature. 2022 Jul 12.
    Persister cells that survive chemotherapy are pinpointed.
    Sumaiyah K Rehman, Catherine A O'Brien.
      
    Keywords:  Cancer; Medical research
    DOI:  https://doi.org/10.1038/d41586-022-01866-x
  5. Clin Exp Pharmacol Physiol. 2022 Jul 11.
    EZH2 promotes the progression of osteosarcoma through the activation of the AKT/GSK3β pathway.
    Dongdong Wan, Xiuxin Han, Chao Zhang, Yan Zhang, Yulin Ma, Guowen Wang.
      Enhancer of zeste homolog 2 (EZH2) is a clarified promoter in a list of tumors, including osteosarcoma (OS). Our research was projected to define the mechanism involved in EZH2-mediated OS progression through the protein kinase B (AKT)/glycogen synthase kinase 3β (GSK3β) pathway. EZH2 expression was tested in 66 OS tissues and 5 osteosarcoma cell lines (143B, SJSA-1, HOS, MG63, and U2OS). In HOS and U2OS cells, cellular malignant characteristics, and the markers of the AKT/GSK3β signaling pathway were measured when EZH2 was silenced or overexpressed. Meanwhile, rescue assays were implemented to observe whether the AKT/GSK3β signaling pathway inhibitor (MK-2206) could affect the role of overexpressed EZH2 in OS cells. EZH2 was up-regulated in tumor tissues of OS patients. OS cell lines (HOS and U2OS) showed impairments of proliferative, migratory, invasive and anti-apoptotic properties when EZH2 was silenced. Downregulated EZH2 inhibited the activation of the AKT/GSK3 signaling pathway. However, the situation in HOS and U2OS cells over-expressing EZH2 was opposite. MK-2206 erased EZH2 up-regulation-induced promotion of OS cell growth. It is demonstrated that EZH2 promotes the progression of OS via inducing the activation of the AKT/GSK3β pathway, offering a therapeutic direction for OS treatment.
    Keywords:  AKT/GSK3β pathway; Enhancer of zeste homolog 2; Invasion; Migration; Osteosarcoma; Proliferation
    DOI:  https://doi.org/10.1111/1440-1681.13701
  6. Nat Rev Genet. 2022 Jul 12.
    Generating specificity in genome regulation through transcription factor sensitivity to chromatin.
    Luke Isbel, Ralph S Grand, Dirk Schübeler.
      Cell type-specific gene expression relies on transcription factors (TFs) binding DNA sequence motifs embedded in chromatin. Understanding how motifs are accessed in chromatin is crucial to comprehend differential transcriptional responses and the phenotypic impact of sequence variation. Chromatin obstacles to TF binding range from DNA methylation to restriction of DNA access by nucleosomes depending on their position, composition and modification. In vivo and in vitro approaches now enable the study of TF binding in chromatin at unprecedented resolution. Emerging insights suggest that TFs vary in their ability to navigate chromatin states. However, it remains challenging to link binding and transcriptional outcomes to molecular characteristics of TFs or the local chromatin substrate. Here, we discuss our current understanding of how TFs access DNA in chromatin and novel techniques and directions towards a better understanding of this critical step in genome regulation.
    DOI:  https://doi.org/10.1038/s41576-022-00512-6
  7. Front Oncol. 2022 ;12 900985
    Drug Repurposing by Tumor Tissue Editing.
    Florian Lüke, Dennis Christoph Harrer, Pan Pantziarka, Tobias Pukrop, Lina Ghibelli, Christopher Gerner, Albrecht Reichle, Daniel Heudobler.
      The combinatory use of drugs for systemic cancer therapy commonly aims at the direct elimination of tumor cells through induction of apoptosis. An alternative approach becomes the focus of attention if biological changes in tumor tissues following combinatory administration of regulatorily active drugs are considered as a therapeutic aim, e.g., differentiation, transdifferentiation induction, reconstitution of immunosurveillance, the use of alternative cell death mechanisms. Editing of the tumor tissue establishes new biological 'hallmarks' as a 'pressure point' to attenuate tumor growth. This may be achieved with repurposed, regulatorily active drug combinations, often simultaneously targeting different cell compartments of the tumor tissue. Moreover, tissue editing is paralleled by decisive functional changes in tumor tissues providing novel patterns of target sites for approved drugs. Thus, agents with poor activity in non-edited tissue may reveal new clinically meaningful outcomes. For tissue editing and targeting edited tissue novel requirements concerning drug selection and administration can be summarized according to available clinical and pre-clinical data. Monoactivity is no pre-requisite, but combinatory bio-regulatory activity. The regulatorily active dose may be far below the maximum tolerable dose, and besides inhibitory active drugs stimulatory drug activities may be integrated. Metronomic scheduling often seems to be of advantage. Novel preclinical approaches like functional assays testing drug combinations in tumor tissue are needed to select potential drugs for repurposing. The two-step drug repurposing procedure, namely establishing novel functional systems states in tumor tissues and consecutively providing novel target sites for approved drugs, facilitates the systematic identification of drug activities outside the scope of any original clinical drug approvals.
    Keywords:  PPAR γ; anakoinosis; biomodulation; mTOR; metronomic chemotherapy; molecular diagnostics; pioglitazone; umbrella trial
    DOI:  https://doi.org/10.3389/fonc.2022.900985
  8. Sci China Life Sci. 2022 Jul 11.
    H3K27me3 shapes DNA methylome by inhibiting UHRF1-mediated H3 ubiquitination.
    Honglian Zhang, Ying Liu, Yali Xie, Yunji Zhu, Jingwen Liu, Falong Lu.
      DNA methylation and histone lysine tri-methylation at H3K27 (H3K27me3) are two chromatin modifications for transcriptional gene silencing, which play important roles in diverse biological processes, including cell fate determination and cell lineage commitment. These two marks are largely mutually exclusive and target distinct sets of genes in the mammalian genome. However, how H3K27me3 shapes the DNA methylome remains elusive. Here, we report that the loss of H3K27me3 modification leads to increased DNA methylation at previously marked H3K27me3 sites, indicating that H3K27me3 negatively regulates DNA methylation. Genome-wide analysis of H3 ubiquitination, essential for recruitment and activation of DNA methyltransferase DNMT1, reveals the absence of H3 ubiquitination at H3K27me3 marked nucleosomes. Moreover, loss of H3K27me3 modification induces an increase in H3K18 ubiquitination at the corresponding hyper-methylated loci. Importantly, we show that H3K27me3 directly inhibits UHRF1-mediated H3 ubiquitination toward nucleosomes in a defined biochemical assay. Taken together, our findings reveal a general mechanism for H3K27me3-mediated shaping of the mammalian DNA methylome via modulation of H3 ubiquitination.
    Keywords:  DNA methylation; H3 ubiquitination; H3K27me3; Polycomb; UHRF1
    DOI:  https://doi.org/10.1007/s11427-022-2155-0
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