bims-ectoca Biomed News
on Epigenetic control of tolerance in cancer
Issue of 2023‒06‒18
fourteen papers selected by
Ankita Daiya, Birla Institute of Technology and Science



  1. Oncol Res. 2021 ;29(6): 377-391
      The Yes-associated protein (YAP) is a downstream effector of the Hippo pathway and acts as a key transcription co-factor to regulate cell migration, proliferation, and survival. The Hippo pathway is evolutionarily conserved and controls tissue growth and organ size. Dysregulation and heterogeneity of this pathway are found in cancers, including oral squamous cell carcinoma (OSCC), leading to overexpression of YAP and its regulated proliferation machinery. The activity of YAP is associated with its nuclear expression and is negatively regulated by the Hippo kinase-mediated phosphorylation resulting in an induction of its cytoplasmic translocation. This review focuses on the role of YAP in OSCC in the context of cancer metastatic potential and highlights the latest findings about the heterogeneity of YAP expression and its nuclear transcription activity in oral cancer cell lines. The review also discusses the potential target of YAP in oral cancer therapy and the recent finding of the unprecedented role of the desmosomal cadherin desmoglein-3 (DSG3) in regulating Hippo-YAP signaling.
    Keywords:  Desmoglein-3; Hippo pathway; OSCC; Oral cancer cell migration; Phospho-YAP; Review; TAZ; YAP; desmosomes
    DOI:  https://doi.org/10.32604/or.2022.026085
  2. Int J Mol Sci. 2023 May 31. pii: 9543. [Epub ahead of print]24(11):
      Globally, viral infections substantially contribute to cancer development. Oncogenic viruses are taxonomically heterogeneous and drive cancers using diverse strategies, including epigenomic dysregulation. Here, we discuss how oncogenic viruses disrupt epigenetic homeostasis to drive cancer and focus on how virally mediated dysregulation of host and viral epigenomes impacts the hallmarks of cancer. To illustrate the relationship between epigenetics and viral life cycles, we describe how epigenetic changes facilitate the human papillomavirus (HPV) life cycle and how changes to this process can spur malignancy. We also highlight the clinical impact of virally mediated epigenetic changes on cancer diagnosis, prognosis, and treatment.
    Keywords:  DNA methylation; epigenome dysregulation; histone deacetylase inhibitors; histone post-translational modifications; non-coding RNAs; oncogenic viruses; viral oncoproteins
    DOI:  https://doi.org/10.3390/ijms24119543
  3. Cancer Metastasis Rev. 2023 Jun 15.
      Pancreatic cancer is a paradigm for adaptation to extreme stress. That is because genetic drivers are selected during tissue injury with epigenetic imprints encoding wound healing responses. Ironically, epigenetic memories of trauma that facilitate neoplasia can also recreate past stresses to restrain malignant progression through symbiotic tumor:stroma crosstalk. This is best exemplified by positive feedback between neoplastic chromatin outputs and fibroinflammatory stromal cues that encase malignant glands within a nutrient-deprived desmoplastic stroma. Because epigenetic imprints are chemically encoded by nutrient-derived metabolites bonded to chromatin, primary tumor metabolism adapts to preserve malignant epigenetic fidelity during starvation. Despite these adaptations, stromal stresses inevitably awaken primordial drives to seek more hospitable climates. The invasive migrations that ensue facilitate entry into the metastatic cascade. Metastatic routes present nutrient-replete reservoirs that accelerate malignant progression through adaptive metaboloepigenetics. This is best exemplified by positive feedback between biosynthetic enzymes and nutrient transporters that saturate malignant chromatin with pro-metastatic metabolite byproducts. Here we present a contemporary view of pancreatic cancer epigenetics: selection of neoplastic chromatin under fibroinflammatory pressures, preservation of malignant chromatin during starvation stresses, and saturation of metastatic chromatin by nutritional excesses that fuel lethal metastasis.
    Keywords:  Cancer; Epigenetics; Metabolism; Metastasis; Pancreatic
    DOI:  https://doi.org/10.1007/s10555-023-10116-z
  4. Cancer Sci. 2023 Jun 14.
      Osteosarcoma (OS), which is a common and aggressive primary bone malignancy, occurs mainly in children and adolescent. Long noncoding RNAs (lncRNAs) are reported to play a pivotal role in various cancers. Here, we found that the lncRNA HOTAIRM1 is upregulated in OS cells and tissues. A set of functional experiments suggested that HOTAIRM1 knockdown attenuated the proliferation and stimulated the apoptosis of OS cells. A subsequent mechanistic study revealed that HOTAIRM1 functions as a competing endogenous RNA to elevate ras homologue enriched in brain (Rheb) expression by sponging miR-664b-3p. Immediately afterward, upregulated Rheb facilitates proliferation and suppresses apoptosis by promoting the mTOR pathway-mediated Warburg effect in OS. In summary, our findings demonstrated that HOTAIRM1 promotes the proliferation and suppresses the apoptosis of OS cells by enhancing the Warburg effect via the miR-664b-3p/Rheb/mTOR axis. Understanding the underlying mechanisms and targeting the HOTAIRM1/miR-664b-3p/Rheb/mTOR axis are essential for OS clinical treatment.
    Keywords:  HOTAIRM1; Rheb; mTOR; miR-664b-3p; osteosarcoma
    DOI:  https://doi.org/10.1111/cas.15881
  5. Front Oncol. 2023 ;13 1074268
      Gastric cancer is one of the most serious malignant tumor and threatens the health of people worldwide. Its heterogeneity leaves many clinical problems unsolved. To treat it effectively, we need to explore its heterogeneity. Single-cell transcriptome sequencing, or single-cell RNA sequencing (scRNA-seq), reveals the complex biological composition and molecular characteristics of gastric cancer at the level of individual cells, which provides a new perspective for understanding the heterogeneity of gastric cancer. In this review, we first introduce the current procedure of scRNA-seq, and discuss the advantages and limitations of scRNA-seq. We then elaborate on the research carried out with scRNA-seq in gastric cancer in recent years, and describe how it reveals cell heterogeneity, the tumor microenvironment, oncogenesis and metastasis, as well as drug response in to gastric cancer, to facilitate early diagnosis, individualized therapy, and prognosis evaluation.
    Keywords:  gastric cancer; individualized therapy; oncogenesis; single-cell RNA sequencing; tumor heterogeneity
    DOI:  https://doi.org/10.3389/fonc.2023.1074268
  6. Chem Biol Interact. 2023 Jun 09. pii: S0009-2797(23)00269-7. [Epub ahead of print]382 110602
      Osteosarcoma (OS) is the most common primary bone malignancy in children and adolescents with extremely poor prognosis. Gambogenic acid (GNA), one of the major bioactive ingredients isolated from Gamboge, has been shown to possess a multipotent antitumor effect, its activity on OS remains unclear yet. In this study, we found that GNA could trigger multiple cell death modalities, including ferroptosis and apoptosis in human OS cells, reduce the cell viability, inhibit the proliferation and invasiveness. Furthermore, GNA provoked oxidative stress leading to GSH depletion-inducing ROS generation and lipid peroxidation, altered iron metabolism represented by the induction of labile iron, mitochondrial membrane potential decreased, mitochondrial morphological changed, decreased the cell viability. In addition, ferroptosis inhibitors (Fer-1) and apoptosis inhibitors (NAC) can partially reversed GNA' s effects on OS cells. Further investigation showed that GNA augmented the expression of P53, bax, caspase 3 and caspase 9 and decreased the expression of Bcl-2, SLC7A11 and glutathione peroxidase-4 (GPX4). In vivo, GNA was showed to delay tumor growth significantly in axenograft osteosarcoma mouse model. In conclusion, this study reveals that GNA simultaneously triggers ferroptosis and apoptosis in human OS cells by inducing oxidative stress via the P53/SLC7A11/GPX4 axis.
    Keywords:  Apoptosis; Ferroptosis; GPX4; Gambogenic acid; Osteosarcoma; P53
    DOI:  https://doi.org/10.1016/j.cbi.2023.110602
  7. Sci Adv. 2023 Jun 16. 9(24): eade1122
      How chromatin dynamics relate to transcriptional activity remains poorly understood. Using single-molecule tracking, coupled with machine learning, we show that histone H2B and multiple chromatin-bound transcriptional regulators display two distinct low-mobility states. Ligand activation results in a marked increase in the propensity of steroid receptors to bind in the lowest-mobility state. Mutational analysis revealed that interactions with chromatin in the lowest-mobility state require an intact DNA binding domain and oligomerization domains. These states are not spatially separated as previously believed, but individual H2B and bound-TF molecules can dynamically switch between them on time scales of seconds. Single bound-TF molecules with different mobilities exhibit different dwell time distributions, suggesting that the mobility of TFs is intimately coupled with their binding dynamics. Together, our results identify two unique and distinct low-mobility states that appear to represent common pathways for transcription activation in mammalian cells.
    DOI:  https://doi.org/10.1126/sciadv.ade1122
  8. EMBO J. 2023 Jun 12. e113349
      NRF2 is a transcription factor responsible for antioxidant stress responses that is usually regulated in a redox-dependent manner. p62 bodies formed by liquid-liquid phase separation contain Ser349-phosphorylated p62, which participates in the redox-independent activation of NRF2. However, the regulatory mechanism and physiological significance of p62 phosphorylation remain unclear. Here, we identify ULK1 as a kinase responsible for the phosphorylation of p62. ULK1 colocalizes with p62 bodies, directly interacting with p62. ULK1-dependent phosphorylation of p62 allows KEAP1 to be retained within p62 bodies, thus activating NRF2. p62S351E/+ mice are phosphomimetic knock-in mice in which Ser351, corresponding to human Ser349, is replaced by Glu. These mice, but not their phosphodefective p62S351A/S351A counterparts, exhibit NRF2 hyperactivation and growth retardation. This retardation is caused by malnutrition and dehydration due to obstruction of the esophagus and forestomach secondary to hyperkeratosis, a phenotype also observed in systemic Keap1-knockout mice. Our results expand our understanding of the physiological importance of the redox-independent NRF2 activation pathway and provide new insights into the role of phase separation in this process.
    Keywords:  KEAP1; NRF2/NFE2L2; ULK1; liquid-liquid phase separation; p62/SQSTM1
    DOI:  https://doi.org/10.15252/embj.2022113349
  9. Geroscience. 2023 Jun 14.
      Following prolonged cell division, mesenchymal stem cells enter replicative senescence, a state of permanent cell cycle arrest that constrains the use of this cell type in regenerative medicine applications and that in vivo substantially contributes to organismal ageing. Multiple cellular processes such as telomere dysfunction, DNA damage and oncogene activation are implicated in promoting replicative senescence, but whether mesenchymal stem cells enter different pre-senescent and senescent states has remained unclear. To address this knowledge gap, we subjected serially passaged human ESC-derived mesenchymal stem cells (esMSCs) to single cell profiling and single cell RNA-sequencing during their progressive entry into replicative senescence. We found that esMSC transitioned through newly identified pre-senescent cell states before entering into three different senescent cell states. By deconstructing this heterogeneity and temporally ordering these pre-senescent and senescent esMSC subpopulations into developmental trajectories, we identified markers and predicted drivers of these cell states. Regulatory networks that capture connections between genes at each timepoint demonstrated a loss of connectivity, and specific genes altered their gene expression distributions as cells entered senescence. Collectively, this data reconciles previous observations that identified different senescence programs within an individual cell type and should enable the design of novel senotherapeutic regimes that can overcome in vitro MSC expansion constraints or that can perhaps slow organismal ageing.
    Keywords:  Cellular senescence; ESC-derived mesenchymal stem cells; Gene expression heterogeneity; Single cell RNA-seq data
    DOI:  https://doi.org/10.1007/s11357-023-00829-y
  10. Cell Commun Signal. 2023 Jun 14. 21(1): 136
      The dimerization of RAF kinases represents a key event in their activation cycle and in RAS/ERK pathway activation. Genetic, biochemical and structural approaches provided key insights into this process defining RAF signaling output and the clinical efficacy of RAF inhibitors (RAFi). However, methods reporting the dynamics of RAF dimerization in living cells and in real time are still in their infancy. Recently, split luciferase systems have been developed for the detection of protein-protein-interactions (PPIs), incl. proof-of-concept studies demonstrating the heterodimerization of the BRAF and RAF1 isoforms. Due to their small size, the Nanoluc luciferase moieties LgBiT and SmBiT, which reconstitute a light emitting holoenzyme upon fusion partner promoted interaction, appear as well-suited to study RAF dimerization. Here, we provide an extensive analysis of the suitability of the Nanoluc system to study the homo- and heterodimerization of BRAF, RAF1 and the related KSR1 pseudokinase. We show that KRASG12V promotes the homo- and heterodimerization of BRAF, while considerable KSR1 homo- and KSR1/BRAF heterodimerization already occurs in the absence of this active GTPase and requires a salt bridge between the CC-SAM domain of KSR1 and the BRAF-specific region. We demonstrate that loss-of-function mutations impairing key steps of the RAF activation cycle can be used as calibrators to gauge the dynamics of heterodimerization. This approach identified the RAS-binding domains and the C-terminal 14-3-3 binding motifs as particularly critical for the reconstitution of RAF mediated LgBiT/SmBiT reconstitution, while the dimer interface was less important for dimerization but essential for downstream signaling. We show for the first time that BRAFV600E, the most common BRAF oncoprotein whose dimerization status is controversially portrayed in the literature, forms homodimers in living cells more efficiently than its wildtype counterpart. Of note, Nanoluc activity reconstituted by BRAFV600E homodimers is highly sensitive to the paradox-breaking RAFi PLX8394, indicating a dynamic and specific PPI. We report the effects of eleven ERK pathway inhibitors on RAF dimerization, incl. third-generation compounds that are less-defined in terms of their dimer promoting abilities. We identify Naporafenib as a potent and long-lasting dimerizer and show that the split Nanoluc approach discriminates between type I, I1/2 and II RAFi. Video Abstract.
    Keywords:  BRAF; Belvarafenib; KRAS; KSR1; LgBiT; MAPK pathway; NanoBit Oplophorus luciferase; RAF1; SmBiT; Sorafenib
    DOI:  https://doi.org/10.1186/s12964-023-01146-9
  11. Methods Mol Biol. 2023 ;2679 25-39
      Rapid and accurate cancer drug screening is of great importance in precision medicine. However, the limited amount of tumor biopsy samples has hindered the application of traditional drug screening methods with microwell plates for individual patients. A microfluidic system provides an ideal platform for handling trace amounts of samples. This emerging platform has a good role in nucleic acid-related and cell related assays. Nevertheless, convenient drug dispensing remains a challenge for clinical on-chip cancer drug screening. Similar sized droplets are merged to add drugs for a desired screened concentration which significantly complicated the on-chip drug dispensing protocols. Here, we introduce a novel digital microfluidic system with a specially structured electrode (a drug dispenser) to dispense drugs by droplet electro-ejection under a high-voltage actuation signal, which can be conveniently adjusted by external electric controls. With this system, the screened drug concentrations span up to four orders of magnitude with small sample consumption. Various amounts of drugs can be delivered to the cell sample with desired amount in a flexible electric control. Moreover, single drug or combinatorial multidrug on-chip screening can be readily achieved. The drug response of normal MCF-10A breast cells and MDA-MB-231 breast tumor cells to two chemotherapeutic substances, cisplatin (Cis) and epirubicin (EP), was tested individually and in combination for proof-of-principle verification. The comparable on-chip and off-chip results confirmed the feasibility of our innovative DMF system for cancer drug screening.
    Keywords:  Cancer drug screening; Cisplatin; Digital microfluidics; Drug dispenser; Epirubicin; MCF-10A cell; MDA-MB-231 cell
    DOI:  https://doi.org/10.1007/978-1-0716-3271-0_3
  12. Front Mol Biosci. 2023 ;10 1170026
      Melanoma is the most lethal skin cancer with increasing incidence worldwide. Despite a great improvement of diagnostics and treatment of melanoma patients, this disease is still a serious clinical problem. Therefore, novel druggable targets are in focus of research. EZH2 is a component of the PRC2 protein complex that mediates epigenetic silencing of target genes. Several mutations activating EZH2 have been identified in melanoma, which contributes to aberrant gene silencing during tumor progression. Emerging evidence indicates that long non-coding RNAs (lncRNAs) are molecular "address codes" for EZH2 silencing specificity, and targeting lncRNAs-EZH2 interaction may slow down the progression of many solid cancers, including melanoma. This review summarizes current knowledge regarding the involvement of lncRNAs in EZH2-mediated gene silencing in melanoma. The possibility of blocking lncRNAs-EZH2 interaction in melanoma as a novel therapeutic option and plausible controversies and drawbacks of this approach are also briefly discussed.
    Keywords:  EZH2; PRC2; epigenetics; immunotherapy; lncRNAs; melanoma; targeted therapy
    DOI:  https://doi.org/10.3389/fmolb.2023.1170026
  13. Adv Ther. 2023 Jun 14.
      This article has been co-authored by a patient with right-sided BRAFV600E metastatic colorectal cancer (mCRC), his caregiver, and an oncologist. Here the patient and caregiver discuss their personal experiences struggling with cancer, including their fears, expectations, and attitudes as the disease progresses. The oncologist describes how patients with BRAFV600E mCRC are treated and how the management strategy can be balanced to mitigate any side effects. Improved diagnostic techniques and the availability of numerous treatment options, including various chemotherapy schemes and molecular-targeted drugs, can aid rapid implementation of treatment algorithms. The pivotal roles of patients' associations in the general support of patients and those close to them, and in facilitating the link with healthcare professionals, are highlighted in this perspective piece.
    Keywords:  BRAF V600E metastatic colorectal cancer; Caregiver; Metastatic; Oncology; Patient perspective
    DOI:  https://doi.org/10.1007/s12325-023-02552-8