bims-ectoca Biomed News
on Epigenetic control of tolerance in cancer
Issue of 2023‒09‒24
ten papers selected by
Ankita Daiya, BITS Pilani
  1. Epigenetic meets metabolism: novel vulnerabilities to fight cancer.
  2. Proteomics contributions to epigenetic drug discovery.
  3. Osteosarcoma's genetic landscape painted by genes' mutations.
  4. Histone mutations in cancer.
  5. Acetyl-methyllysine marks chromatin at active transcription start sites.
  6. Connections between metabolism and epigenetic modifications in cancer.
  7. TAZ facilitates breast tumor growth by promoting an immune-suppressive tumor microenvironment.
  8. The mitoepigenome responds to stress, suggesting novel mito-nuclear interactions in vertebrates.
  9. Engineered bone marrow as a clinically relevant ex vivo model for primary bone cancer research and drug screening.
  10. Chromatin meets the cytoskeleton: the importance of nuclear actin dynamics and associated motors for genome stability.
  1. Cell Commun Signal. 2023 Sep 21. 21(1): 249
    Epigenetic meets metabolism: novel vulnerabilities to fight cancer.
    Domenica Scumaci, Qingfei Zheng.
      Histones undergo a plethora of post-translational modifications (PTMs) that regulate nucleosome and chromatin dynamics and thus dictate cell fate. Several evidences suggest that the accumulation of epigenetic alterations is one of the key driving forces triggering aberrant cellular proliferation, invasion, metastasis and chemoresistance pathways. Recently a novel class of histone "non-enzymatic covalent modifications" (NECMs), correlating epigenome landscape and metabolic rewiring, have been described. These modifications are tightly related to cell metabolic fitness and are able to impair chromatin architecture. During metabolic reprogramming, the high metabolic flux induces the accumulation of metabolic intermediate and/or by-products able to react with histone tails altering epigenome homeostasis. The accumulation of histone NECMs is a damaging condition that cancer cells counteracts by overexpressing peculiar "eraser" enzymes capable of removing these modifications preserving histones architecture. In this review we explored the well-established NECMs, emphasizing the role of their corresponding eraser enzymes. Additionally, we provide a parterre of drugs aiming to target those eraser enzymes with the intent to propose novel routes of personalized medicine based on the identification of epi-biomarkers which might be selectively targeted for therapy. Video Abstract.
    Keywords:  Cancer onset and progression; Histone non-enzymatic covalent modification; Histone post-translational modification; Metabolic reprogramming
    DOI:  https://doi.org/10.1186/s12964-023-01253-7
  2. Proteomics. 2023 Sep 19. e2200435
    Proteomics contributions to epigenetic drug discovery.
    Roberta Noberini, Tiziana Bonaldi.
      The combined activity of epigenetic features, which include histone post-translational modifications, DNA methylation, and nucleosome positioning, regulates gene expression independently from changes in the DNA sequence, defining how the shared genetic information of an organism is used to generate different cell phenotypes. Alterations in epigenetic processes have been linked with a multitude of diseases, including cancer, fueling interest in the discovery of drugs targeting the proteins responsible for writing, erasing, or reading histone and DNA modifications. Mass spectrometry (MS)-based proteomics has emerged as a versatile tool that can assist drug discovery pipelines from target validation, through target deconvolution, to monitoring drug efficacy in vivo. Here, we provide an overview of the contributions of MS-based proteomics to epigenetic drug discovery, describing the main approaches that can be used to support different drug discovery pipelines and highlighting how they contributed to the development and characterization of epigenetic drugs.
    Keywords:  drug discovery; epigenetics; histone post-translational modification; mass spectrometry; proteomics; target deconvolution
    DOI:  https://doi.org/10.1002/pmic.202200435
  3. Acta Biochim Pol. 2023 Sep 17. 70(3): 671-678
    Osteosarcoma's genetic landscape painted by genes' mutations.
    Wiktoria Urban, Dagmara Krzystańska, Michał Piekarz, Jerzy Nazar, Anna Jankowska.
      PURPOSE: Osteosarcoma (OS) is one of the most common primary bone tumors. Direct pathogenesis remains unknown, however, genes' mutations are proven to participate in the process. This study aimed to examine the most frequently mutated genes in OS to appoint candidates for the cancer markers.METHODS: Using the COSMIC Catalogue twenty the most frequently mutated genes were selected leading to an up-to-date genetic OS landscape summary. The genes can be classified into four categories: suppressor genes (TP53, RB1, NCOR1, SMAD2, NF1, TSC2, KMT2C), proto-oncogenes (GNAS, BRAF, MLLT3), epigenetic and post-translational modification-related genes (SMARCA4, ARID1A, ATRX, BCOR, H3F3A) and cell growth and survival regulating genes (EGFR, CAMTA1, LRP1B, PDE4DIP, MED12).
    RESULTS AND CONCLUSIONS: Their role in cancerogenesis was confirmed by the analysis of available articles published previously. The results of the study indicate that examination of selected genes' mutations might help to identify patients' predisposition to OS development, as well as monitor the disease progression, and establish prognosis. However, to fully understand the pathogenesis of OS further studies are required.
    DOI:  https://doi.org/10.18388/abp.2020_6869
  4. Biochem Soc Trans. 2023 Sep 18. pii: BST20210567. [Epub ahead of print]
    Histone mutations in cancer.
    Kimberly N Espinoza Pereira, Jixiu Shan, Jonathan D Licht, Richard L Bennett.
      Genes encoding histone proteins are recurrently mutated in tumor samples, and these mutations may impact nucleosome stability, histone post-translational modification, or chromatin dynamics. The prevalence of histone mutations across diverse cancer types suggest that normal chromatin structure is a barrier to tumorigenesis. Oncohistone mutations disrupt chromatin structure and gene regulatory mechanisms, resulting in aberrant gene expression and the development of cancer phenotypes. Examples of oncohistones include the histone H3 K27M mutation found in pediatric brain cancers that blocks post-translational modification of the H3 N-terminal tail and the histone H2B E76K mutation found in some solid tumors that disrupts nucleosome stability. Oncohistones may comprise a limited fraction of the total histone pool yet cause global effects on chromatin structure and drive cancer phenotypes. Here, we survey histone mutations in cancer and review their function and role in tumorigenesis.
    Keywords:  cancer; chromatin; histones; point mutations
    DOI:  https://doi.org/10.1042/BST20210567
  5. Nature. 2023 Sep 20.
    Acetyl-methyllysine marks chromatin at active transcription start sites.
    William J Lu-Culligan, Leah J Connor, Yixuan Xie, Babatunde E Ekundayo, Brendan T Rose, Martin Machyna, Andreas P Pintado-Urbanc, Joshua T Zimmer, Isaac W Vock, Natarajan V Bhanu, Megan C King, Benjamin A Garcia, Franziska Bleichert, Matthew D Simon.
      Lysine residues in histones and other proteins can be modified by post-translational modifications that encode regulatory information1. Lysine acetylation and methylation are especially important for regulating chromatin and gene expression2-4. Pathways involving these post-translational modifications are targets for clinically approved therapeutics to treat human diseases. Lysine methylation and acetylation are generally assumed to be mutually exclusive at the same residue. Here we report cellular lysine residues that are both methylated and acetylated on the same side chain to form Nε-acetyl-Nε-methyllysine (Kacme). We show that Kacme is found on histone H4 (H4Kacme) across a range of species and across mammalian tissues. Kacme is associated with marks of active chromatin, increased transcriptional initiation and is regulated in response to biological signals. H4Kacme can be installed by enzymatic acetylation of monomethyllysine peptides and is resistant to deacetylation by some HDACs in vitro. Kacme can be bound by chromatin proteins that recognize modified lysine residues, as we demonstrate with the crystal structure of acetyllysine-binding protein BRD2 bound to a histone H4Kacme peptide. These results establish Kacme as a cellular post-translational modification with the potential to encode information distinct from methylation and acetylation alone and demonstrate that Kacme has all the hallmarks of a post-translational modification with fundamental importance to chromatin biology.
    DOI:  https://doi.org/10.1038/s41586-023-06565-9
  6. Med Rev (Berl). 2021 Dec;1(2): 199-221
    Connections between metabolism and epigenetic modifications in cancer.
    Guangchao Wang, Jingdong J Han.
      How cells sense and respond to environmental changes is still a key question. It has been identified that cellular metabolism is an important modifier of various epigenetic modifications, such as DNA methylation, histone methylation and acetylation and RNA N6-methyladenosine (m6A) methylation. This closely links the environmental nutrient availability to the maintenance of chromatin structure and gene expression, and is crucial to regulate cellular homeostasis, cell growth and differentiation. Cancer metabolic reprogramming and epigenetic alterations are widely observed, and facilitate cancer development and progression. In cancer cells, oncogenic signaling-driven metabolic reprogramming modifies the epigenetic landscape via changes in the key metabolite levels. In this review, we briefly summarized the current evidence that the abundance of key metabolites, such as S-adenosyl methionine (SAM), acetyl-CoA, α-ketoglutarate (α-KG), 2-hydroxyglutarate (2-HG), uridine diphospho-N-acetylglucosamine (UDP-GlcNAc) and lactate, affected by metabolic reprogramming plays an important role in dynamically regulating epigenetic modifications in cancer. An improved understanding of the roles of metabolic reprogramming in epigenetic regulation can contribute to uncover the underlying mechanisms of metabolic reprogramming in cancer development and identify the potential targets for cancer therapies.
    Keywords:  DNA methylation; RNA m6A; cancer metabolic reprogramming; epigenetic modifications; histone acetylation; histone methylation
    DOI:  https://doi.org/10.1515/mr-2021-0015
  7. Mol Oncol. 2023 Sep 16.
    TAZ facilitates breast tumor growth by promoting an immune-suppressive tumor microenvironment.
    Anat Gershoni, Ori Hassin, Nishanth Belugali Nataraj, Sivan Baruch, Adi Avioz-Seligman, Anna Chiara Pirona, Liat Fellus-Alyagor, Tomer Meir Salame, Saptaparna Mukherjee, Giuseppe Mallel, Yosef Yarden, Yael Aylon, Moshe Oren.
      The core Hippo pathway module consists of a tumor-suppressive kinase cascade that inhibits the transcriptional coactivators Yes-associated protein (YAP) and WW domain-containing transcription regulator protein 1 (WWTR1; also known as TAZ). When the Hippo pathway is downregulated, as often occurs in breast cancer, YAP/TAZ activity is induced. To elaborate the roles of TAZ in triple-negative breast cancer (TNBC), we depleted Taz in murine TNBC 4T1 cells, using either CRISPR/Cas9 or small hairpin RNA (shRNA). TAZ-depleted cells and their controls, harboring wild-type levels of TAZ, were orthotopically injected into the mammary fat pads of syngeneic BALB/c female mice, and mice were monitored for tumor growth. TAZ depletion resulted in smaller tumors compared to the tumors generated by control cells, in line with the notion that TAZ functions as an oncogene in breast cancer. Tumors, as well as their corresponding in vitro cultured cells, were then subjected to gene expression profiling by RNA sequencing (RNA-seq). Interestingly, pathway analysis of the RNA-seq data indicated a TAZ-dependent enrichment of 'Inflammatory Response', a pathway correlated with TAZ expression levels also in human breast cancer tumors. Specifically, the RNA-seq analysis predicted a significant depletion of regulatory T cells (Tregs) in TAZ-deficient tumors, which was experimentally validated by the staining of tumor sections and by quantitative cytometry by time of flight (CyTOF). Strikingly, the differences in tumor size were completely abolished in immune-deficient mice, demonstrating that the immune-modulatory capacity of TAZ is critical for its oncogenic activity in this setting. Cytokine array analysis of conditioned medium from cultured cells revealed that TAZ increased the abundance of a small group of cytokines, including plasminogen activator inhibitor 1 (Serpin E1; also known as PAI-1), CCN family member 4 (CCN4; also known as WISP-1) and interleukin-23 (IL-23), suggesting a potential mechanistic explanation for its in vivo immunomodulatory effect. Together, our results imply that TAZ functions in a non-cell-autonomous manner to modify the tumor immune microenvironment and dampen the anti-tumor immune response, thereby facilitating tumor growth.
    Keywords:  Breast cancer; Hippo pathway; TAZ; Tregs
    DOI:  https://doi.org/10.1002/1878-0261.13525
  8. BMC Genomics. 2023 Sep 22. 24(1): 561
    The mitoepigenome responds to stress, suggesting novel mito-nuclear interactions in vertebrates.
    John Lees, Fábio Pèrtille, Pia Løtvedt, Per Jensen, Carlos Guerrero Bosagna.
      The mitochondria are central in the cellular response to changing environmental conditions resulting from disease states, environmental exposures or normal physiological processes. Although the influences of environmental stressors upon the nuclear epigenome are well characterized, the existence and role of the mitochondrial epigenome remains contentious. Here, by quantifying the mitochondrial epigenomic response of pineal gland cells to circadian stress, we confirm the presence of extensive cytosine methylation within the mitochondrial genome. Furthermore, we identify distinct epigenetically plastic regions (mtDMRs) which vary in cytosinic methylation, primarily in a non CpG context, in response to stress and in a sex-specific manner. Motifs enriched in mtDMRs contain recognition sites for nuclear-derived DNA-binding factors (ATF4, HNF4A) important in the cellular metabolic stress response, which we found to be conserved across diverse vertebrate taxa. Together, these findings suggest a new layer of mito-nuclear interaction in which the nuclear metabolic stress response could alter mitochondrial transcriptional dynamics through the binding of nuclear-derived transcription factors in a methylation-dependent context.
    Keywords:  DNA-binding; Epigenome; Methylation; Mitochondrial genome; Pineal gland
    DOI:  https://doi.org/10.1186/s12864-023-09668-9
  9. Proc Natl Acad Sci U S A. 2023 Sep 26. 120(39): e2302101120
    Engineered bone marrow as a clinically relevant ex vivo model for primary bone cancer research and drug screening.
    Katherine H Griffin, Steven W Thorpe, Aimy Sebastian, Nicholas R Hum, Thomas P Coonan, Isabel S Sagheb, Gabriela G Loots, R Lor Randall, J Kent Leach.
      Osteosarcoma (OS) is the most common primary malignant bone cancer in children and adolescents. While numerous other cancers now have promising therapeutic advances, treatment options for OS have remained unchanged since the advent of standard chemotherapeutics and offer less than a 25% 5-y survival rate for those with metastatic disease. This dearth of clinical progress underscores a lack of understanding of OS progression and necessitates the study of this disease in an innovative system. Here, we adapt a previously described engineered bone marrow (eBM) construct for use as a three-dimensional platform to study how microenvironmental and immune factors affect OS tumor progression. We form eBM by implanting acellular bone-forming materials in mice and explanting the cellularized constructs after 8 wk for study. We interrogate the influence of the anatomical implantation site on eBM tissue quality, test ex vivo stability under normoxic (5% O2) and standard (21% O2) culture conditions, culture OS cells within these constructs, and compare them to human OS samples. We show that eBM stably recapitulates the composition of native bone marrow. OS cells exhibit differential behavior dependent on metastatic potential when cultured in eBM, thus mimicking in vivo conditions. Furthermore, we highlight the clinical applicability of eBM as a drug-screening platform through doxorubicin treatment and show that eBM confers a protective effect on OS cells that parallel clinical responses. Combined, this work presents eBM as a cellular construct that mimics the complex bone marrow environment that is useful for mechanistic bone cancer research and drug screening.
    Keywords:  bone marrow; cancer; model; osteosarcoma; tumorigenesis
    DOI:  https://doi.org/10.1073/pnas.2302101120
  10. DNA Repair (Amst). 2023 Sep 16. pii: S1568-7864(23)00125-8. [Epub ahead of print]131 103571
    Chromatin meets the cytoskeleton: the importance of nuclear actin dynamics and associated motors for genome stability.
    Hans-Peter Wollscheid, Helle D Ulrich.
      The actin cytoskeleton is of fundamental importance for numerous cellular processes, including intracellular transport, cell plasticity, and cell migration. However, functions of filamentous actin (F-actin) in the nucleus remain understudied due to the comparatively low abundance of nuclear actin and the resulting experimental limitations to its visualization. Owing to recent technological advances such as super-resolution microscopy and the development of nuclear-specific actin probes, essential roles of the actin cytoskeleton in the context of genome maintenance are now emerging. In addition to the contributions of monomeric actin as a component of multiple important nuclear protein complexes, nuclear actin has been found to undergo polymerization in response to DNA damage and DNA replication stress. Consequently, nuclear F-actin plays important roles in the regulation of intra-nuclear mobility of repair and replication foci as well as the maintenance of nuclear shape, two important aspects of efficient stress tolerance. Beyond actin itself, there is accumulating evidence for the participation of multiple actin-binding proteins (ABPs) in the surveillance of genome integrity, including nucleation factors and motor proteins of the myosin family. Here we summarize recent findings highlighting the importance of actin cytoskeletal factors within the nucleus in key genome maintenance pathways.
    Keywords:  Actin nucleation; Cytoskeleton; DNA repair; DNA replication stress; Genome stability; Myosin; Nuclear actin filaments
    DOI:  https://doi.org/10.1016/j.dnarep.2023.103571
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