bims-ectoca Biomed News
on Epigenetic control of tolerance in cancer
Issue of 2021‒09‒26
fifteen papers selected by
Ankita Daiya, Birla Institute of Technology and Science



  1. Oncotarget. 2021 Sep 14. 12(19): 1962-1965
      The question of whether cancer recurrence is mediated by a process that is exclusively Darwinian or that involves both Darwinian and Lamarckian processes is long standing and far from answered. The major open question is the origin of variation, whether it relays exclusively on stable, mostly genetic, mechanisms or whether it can also involve dynamic processes. Recent evidence with single-cell epigenomic and transcriptomic profiling and measurement of phenotypes in colonies indicate that several phenotypes quickly change with a few cell divisions. Most importantly, cell fitness under basal as well as in the presence of chemotherapeutic agents changes considerably over short periods of time and this dynamic is reduced by epigenetic modulators. These studies contribute to establish the dynamic nature of fitness and are key for the interplay between cancer cell dynamics and stable genetic and epigenetic alterations in the survival of a few cancer cells after therapy.
    Keywords:  dynamic phenotype; fitness; single cell; tumor evolution; tumor resistance
    DOI:  https://doi.org/10.18632/oncotarget.28006
  2. Front Oncol. 2021 ;11 741746
      Accurate orchestration of gene expression is critical for the process of normal hematopoiesis, and dysregulation is closely associated with leukemogenesis. Epigenetic aberration is one of the major causes contributing to acute myeloid leukemia (AML), where chromosomal rearrangements are frequently found. Increasing evidences have shown the pivotal roles of histone deacetylases (HDACs) in chromatin remodeling, which are involved in stemness maintenance, cell fate determination, proliferation and differentiation, via mastering the transcriptional switch of key genes. In abnormal, these functions can be bloomed to elicit carcinogenesis. Presently, HDAC family members are appealing targets for drug exploration, many of which have been deployed to the AML treatment. As the majority of AML events are associated with chromosomal translocation resulting in oncogenic fusion proteins, it is valuable to comprehensively understand the mutual interactions between HDACs and oncogenic proteins. Therefore, we reviewed the process of leukemogenesis and roles of HDAC members acting in this progress, providing an insight for the target anchoring, investigation of hyperacetylated-agents, and how the current knowledge could be applied in AML treatment.
    Keywords:  AML; HDACs; chromosomal translocation; epigenetic modification; leukemogenesis; oncogenic fusion protein
    DOI:  https://doi.org/10.3389/fonc.2021.741746
  3. Front Cell Dev Biol. 2021 ;9 689962
      Angiogenesis is a multi-stage process of new blood vessel development from pre-existing vessels toward an angiogenic stimulus. The process is essential for tissue maintenance and homeostasis during embryonic development and adult life as well as tumor growth. Under normal conditions, angiogenesis is involved in physiological processes, such as wound healing, cyclic regeneration of the endometrium, placental development and repairing certain cardiac damage, in pathological conditions, it is frequently associated with cancer development and metastasis. The control mechanisms of angiogenesis in carcinogenesis are tightly regulated at the genetic and epigenetic level. While genetic alterations are the critical part of gene silencing in cancer cells, epigenetic dysregulation can lead to repression of tumor suppressor genes or oncogene activation, becoming an important event in early development and the late stages of tumor development, as well. The global alteration of the epigenetic spectrum, which includes DNA methylation, histone modification, chromatin remodeling, microRNAs, and other chromatin components, is considered one of the hallmarks of cancer, and the efforts are concentrated on the discovery of molecular epigenetic markers that identify cancerous precursor lesions or early stage cancer. This review aims to highlight recent findings on the genetic and epigenetic changes that can occur in physiological and pathological angiogenesis and analyze current knowledge on how deregulation of epigenetic modifiers contributes to tumorigenesis and tumor maintenance. Also, we will evaluate the clinical relevance of epigenetic markers of angiogenesis and the potential use of "epi-drugs" in modulating the responsiveness of cancer cells to anticancer therapy through chemotherapy, radiotherapy, immunotherapy and hormone therapy as anti-angiogenic strategies in cancer.
    Keywords:  angiogenesis; cancer treatment; development; epigenetic regulation; tumors progression
    DOI:  https://doi.org/10.3389/fcell.2021.689962
  4. Acc Chem Res. 2021 Sep 23.
      ConspectusThe hereditary blueprint of a eukaryotic cell is encoded in its genomic DNA that is tightly compacted into chromatin together with histone proteins. The basic repeating units of chromatin fibers are nucleosomes, in which approximately 1.7 turns of DNA wrap around a proteinaceous octamer consisting of two copies of histones H2A, H2B, H3, and H4. Histones are extensively decorated by a variety of posttranslational modifications (PTMs, e.g., methylation, acetylation, ubiquitylation, phosphorylation, etc.), serving as one of the cellular mechanisms that regulates DNA-templated processes, including but not limited to gene transcription, DNA replication, and DNA damage repair. Most of the histone PTMs exist in dynamic fluctuations, and their on and off states are exquisitely regulated by enzymes known as "writers" and "erasers", respectively. When installed at certain sites, histone PTMs can change the local physicochemical environment and thereby directly influence the nucleosome and chromatin structures. Alternatively, histone PTMs can recruit effectors (or "readers") to signal the downstream events. A "histone code" hypothesis has been proposed in which the combinatory actions of different histone PTMs orchestrate the epigenetic landscape of cells, modulating the activity of the underlying DNA and maintaining the genome stability between generations. Accumulating evidence also suggests that malfunctions of histone PTMs are associated with the pathogenesis of human diseases, such as cancer. It is therefore important to fully decipher the histone code, namely, to dissect the regulatory mechanisms and biological functions of histone PTMs.Owing to the advances in state-of-the-art mass spectrometry, dozens of novel histone modifications have been archived during the past decade. However, most of these newly identified histone PTMs remain poorly explored. To unravel the roles played by these PTMs in histone code, key questions that have driven our study are (i) how to detect the novel histone PTMs; (ii) how to identify the enzymes that catalyze the addition (writers) and removal (erasers) of the histone PTMs along with the regulating mechanisms; (iii) what is the biological significance of the histone PTMs and how do they function, by affecting the nucleosome and chromatin dynamics or by recruiting readers; and (iv) how to develop chemical probes to interrogate the histone PTMs or even serve as potential leads for the drug discovery campaigns to treat diseases caused by abnormalities in the regulation of histone PTMs.This Account focuses on our efforts in developing and applying chemical tools and methods to answer the above questions. Specifically, we review the detection of negatively charged histone acylations by developing and applying chemical reporters; preparing homogeneous nucleosomes carrying negatively charged acylations by protein chemistry approaches and the in vitro biophysical analyses of the effects of the acylations on nucleosome structures; investigating the negatively charged acylations' influence on chromatin dynamics in vivo using yeast genetic approaches; identifying and characterizing protein-protein interactions (PPIs) mediated by histone PTMs in different biological contexts (i.e., to identify the readers and erasers) by establishing a chemical proteomics platform that is enabled by photo-cross-linking chemistry and quantitative proteomics strategies; and manipulating PTM-mediated PPIs by the structure-guided design of inhibitors. We also discuss possible future directions in our journey to fully decipher the histone code.
    DOI:  https://doi.org/10.1021/acs.accounts.1c00463
  5. Methods Mol Biol. 2022 ;2364 299-318
      Cancer cells from cell lines and tumor biopsy tissue undergo aggregation and aggregate coalescence when dispersed in a 3D Matrigel™ matrix. Coalescence is a dynamic process mediated by a subset of cells within the population of cancer cells. In contrast, non-tumorigenic cells from normal cell lines and normal tissues do not aggregate or coalesce, nor do they possess the motile cell types that orchestrate coalescence of cancer cells. Therefore, coalescence is a cancer cell-specific phenotype that may drive tumor growth in vivo, especially in cases of field cancerization. Here, we describe a simple 3D tumorigenesis model that takes advantage of the coalescence capabilities of cancer cells and uses this feature as the basis for a screen for treatments that inhibit tumorigenesis. The screen is especially useful in testing monoclonal antibodies that target cell-cell interactions, cell-matrix interactions, cell adhesion molecules, cell surface receptors, and general cell surface markers. The model can also be used for 2D imaging in a 96-well plate for rapid screening and is adaptable for 3D high-resolution assessment. In the latter case, we show how the 3D model can be optically sectioned with differential interference contrast (DIC) optics, then reconstructed in 4D and quantitatively analyzed by computer-assisted methods, or, alternatively, imaged with confocal microscopy for 4D quantitative analysis of cancer cell interactions with normal cells within the tumor microenvironment. We demonstrate reconstructions and quantitative analyses using the advanced image analysis software J3D-DIAS 4.2, in order to illustrate the types of detailed phenotypic characterizations that have proven useful. Other software packages may be able to perform similar types of analyses.
    Keywords:  3D model; Cancer therapy drug screen; Cell migration; Coalescence; Monoclonal antibody; Tumorigenesis
    DOI:  https://doi.org/10.1007/978-1-0716-1661-1_14
  6. Pharmacol Res. 2021 Sep 18. pii: S1043-6618(21)00485-0. [Epub ahead of print] 105901
      Despite the intense research on developing new therapies for neuropathic pain states, available treatments have limited efficacy and unfavorable safety profiles. Epigenetic alterations have a great influence on the development of cancer and neurological diseases, as well as neuropathic pain. Histone acetylation has prevailed as one of the well investigated epigenetic modifications in these diseases. Altered spinal activity of histone deacetylase (HDAC) and Bromo and Extra terminal domain (BET) have been described in neuropathic pain models and restoration of these aberrant epigenetic modifications showed pain-relieving activity. Over the last decades HDACs and BETs have been the focus of drug discovery studies, leading to the development of numerous small-molecule inhibitors. Clinical trials to evaluate their anticancer activity showed good efficacy but raised toxicity concerns that limited translation to the clinic. To maximize activity and minimize toxicity, these compounds can be applied in combination of sub-maximal doses to produce additive or synergistic interactions (combination therapy). Recently, of particular interest, dual BET/HDAC inhibitors (multi-target drugs) have been developed to assure simultaneous modulation of BET and HDAC activity by a single molecule. This review will summarize the most recent advances with these strategies, describing advantages and limitations of single drug treatment vs combination regimens. This review will also provide a focus on dual BET/HDAC drug discovery investigations as future therapeutic opportunity for human therapy of neuropathic pain.
    Keywords:  Bromo and Extra terminal domain inhibitor; combination therapy; dual BET/HDAC inhibitor; epigenetics; histone deacetylase inhibitor; neuropathic pain
    DOI:  https://doi.org/10.1016/j.phrs.2021.105901
  7. Nanomedicine (Lond). 2021 Sep 23.
      Histone deacetylase inhibitors (HDACi) are cancer therapeutics that operate at the epigenetic level and which have recently gained wide attention. However, the applications of HDACi are generally hindered by their poor physicochemical characteristics and unfavorable pharmacokinetic profile. Inspired by the approved nanomedicine-based drugs in the market, nanocarriers could provide a resort to circumvent the limitations imposed by HDACi. Enhanced tumor targeting, improved cellular uptake and reduced toxicity are major advantages offered by HDACi-loaded nanoparticles. More importantly, site-specific drug delivery can be achieved via engineered stimuli-responsive nanosystems. In this review we elucidate the anticancer mechanisms of HDACi and their structure-activity relationships, with a special focus on their nanomedicine-based delivery, different drug loading concepts and their implications.
    Keywords:  HDAC inhibitors; cancer drug resistance; drug delivery; epigenetics; nanoparticles
    DOI:  https://doi.org/10.2217/nnm-2021-0196
  8. BMC Biol. 2021 Sep 21. 19(1): 207
      BACKGROUND: Intra-tumor heterogeneity (ITH) encompasses cellular differences in tumors and is related to clinical outcomes such as drug resistance. However, little is known about the dynamics of ITH, owing to the lack of time-series analysis at the single-cell level. Mouse models that recapitulate cancer development are useful for controlled serial time sampling.RESULTS: We performed single-cell exome and transcriptome sequencing of 200 cells to investigate how ITH is generated in a mouse colorectal cancer model. In the model, a single normal intestinal cell is grown into organoids that mimic the intestinal crypt structure. Upon RNAi-mediated downregulation of a tumor suppressor gene APC, the transduced organoids were serially transplanted into mice to allow exposure to in vivo microenvironments, which play relevant roles in cancer development. The ITH of the transcriptome increased after the transplantation, while that of the exome decreased. Mutations generated during organoid culture did not greatly change at the bulk-cell level upon the transplantation. The RNA ITH increase was due to the emergence of new transcriptional subpopulations. In contrast to the initial cells expressing mesenchymal-marker genes, new subpopulations repressed these genes after the transplantation. Analyses of colorectal cancer data from The Cancer Genome Atlas revealed a high proportion of metastatic cases in human subjects with expression patterns similar to the new cell subpopulations in mouse. These results suggest that the birth of transcriptional subpopulations may be a key for adaptation to drastic micro-environmental changes when cancer cells have sufficient genetic alterations at later tumor stages.
    CONCLUSIONS: This study revealed an evolutionary dynamics of single-cell RNA and DNA heterogeneity in tumor progression, giving insights into the mesenchymal-epithelial transformation of tumor cells at metastasis in colorectal cancer.
    Keywords:  Cancer genomics; Colorectal cancer; Intra-tumor heterogeneity; Single-cell sequencing; Tumorigenesis
    DOI:  https://doi.org/10.1186/s12915-021-01147-5
  9. J Cell Mol Med. 2021 Sep 21.
      Osteosarcoma (OS) is a type of malignant primary bone cancer, which is highly aggressive and occurs more commonly in children and adolescents. Thus, novel potential drugs and therapeutic methods are urgently needed. In the present study, we aimed to elucidate the effects and mechanism of melatonin on OS cells to provide a potential treatment strategy for OS. The cell survival rate, cell viability, proliferation, migration, invasion and metastasis were examined by trypan blue assay, MTT, colony formation, wound healing, transwell invasion and attachment/detachment assay, respectively. The expression of relevant lncRNAs in OS cells was determined by real-time qPCR analysis. The functional roles of lncRNA JPX in OS cells were further examined by gain and loss of function assays. The protein expression was measured by western blot assay. Melatonin inhibited the cell viability, proliferation, migration, invasion and metastasis of OS cells (Saos-2, MG63 and U2OS) in a dose-dependent manner. Melatonin treatment significantly downregulated the expression of lncRNA JPX in Saos-2, MG63 and U2OS cells. Overexpression of lncRNA JPX into OS cell lines elevated the cell viability and proliferation, which was accompanied by the increased metastasis. We also found that melatonin inhibited the OS progression by suppressing the expression of lncRNA JPX via regulating the Wnt/β-catenin pathway. Our results suggested that melatonin inhibited the biological functions of OS cells by repressing the expression of lncRNA JPX through regulating the Wnt/β-catenin signalling pathway, which indicated that melatonin might be applied as a potentially useful and effective natural agent in the treatment of OS.
    Keywords:  LncRNAs; Wnt/β-catenin pathway; melatonin; osteosarcoma; therapeutic methods
    DOI:  https://doi.org/10.1111/jcmm.16894
  10. BMC Res Notes. 2021 Sep 20. 14(1): 366
      OBJECTIVE: Among the different methods to profile the genome-wide patterns of transcription factor binding and histone modifications in cells and tissues, CUT&RUN has emerged as a more efficient approach that allows for a higher signal-to-noise ratio using fewer number of cells compared to ChIP-seq. The results from CUT&RUN and other related sequence enrichment assays requires comprehensive quality control (QC) and comparative analysis of data quality across replicates. While several computational tools currently exist for read mapping and analysis, a systematic reporting of data quality is lacking. Our aims were to (1) compare methods for using frozen versus fresh cells for CUT&RUN and (2) to develop an easy-to-use pipeline for assessing data quality.RESULTS: We compared a workflow for CUT&RUN with fresh and frozen samples, and present an R package called ssvQC for quality control and comparison of data quality derived from CUT&RUN and other enrichment-based sequence data. Using ssvQC, we evaluate results from different CUT&RUN protocols for transcription factors and histone modifications from fresh and frozen tissue samples. Overall, this process facilitates evaluation of data quality across datasets and permits inspection of peak calling analysis, replicate analysis of different data types. The package ssvQC is readily available at https://github.com/FrietzeLabUVM/ssvQC .
    Keywords:  CUT&RUN; ChIP-seq; Data quality control; Data visualization
    DOI:  https://doi.org/10.1186/s13104-021-05781-8
  11. Nat Commun. 2021 Sep 24. 12(1): 5636
      Single-cell transcriptomic studies that require intracellular protein staining, rare cell sorting, or inactivation of infectious pathogens are severely limited. This is because current high-throughput single-cell RNA sequencing methods are either incompatible with or necessitate laborious sample preprocessing for paraformaldehyde treatment, a common tissue and cell fixation and preservation technique. Here we present FD-seq (Fixed Droplet RNA sequencing), a high-throughput method for droplet-based RNA sequencing of paraformaldehyde-fixed, permeabilized and sorted single cells. We show that FD-seq preserves the RNA integrity and relative gene expression levels after fixation and permeabilization. Furthermore, FD-seq can detect a higher number of genes and transcripts than methanol fixation. We first apply FD-seq to analyze a rare subpopulation of cells supporting lytic reactivation of the human tumor virus KSHV, and identify TMEM119 as a potential host factor that mediates viral reactivation. Second, we find that infection with the human betacoronavirus OC43 leads to upregulation of pro-inflammatory pathways in cells that are exposed to the virus but fail to express high levels of viral genes. FD-seq thus enables integrating phenotypic with transcriptomic information in rare cell subpopulations, and preserving and inactivating pathogenic samples.
    DOI:  https://doi.org/10.1038/s41467-021-25871-2
  12. Apoptosis. 2021 Sep 25.
      Cancer cell death is the utmost aim in cancer therapy. Anti-cancer agents can induce apoptosis, mitotic catastrophe, senescence, or autophagy through the production of free radicals and induction of DNA damage. However, cancer cells can acquire some new properties to adapt to anti-cancer agents. An increase in the incidence of apoptosis, mitotic catastrophe, senescence, and necrosis is in favor of overcoming tumor resistance to therapy. Although an increase in the autophagy process may help the survival of cancer cells, some studies indicated that stimulation of autophagy cell death may be useful for cancer therapy. Using some low toxic agents to amplify cancer cell death is interesting for the eradication of clonogenic cancer cells. Resveratrol (a polyphenol agent) may affect various signaling pathways related to cell death. It can induce death signals and also downregulate the expression of anti-apoptotic genes. Resveratrol has also been shown to modulate autophagy and induce mitotic catastrophe and senescence in some cancer cells. This review focuses on the important targets and mechanisms for the modulation of cancer cell death by resveratrol.
    Keywords:  Apoptosis; Autophagy; Cancer cell death; Cancer resistance; Mitotic catastrophe; Resveratrol
    DOI:  https://doi.org/10.1007/s10495-021-01689-7
  13. Trends Biochem Sci. 2021 Sep 21. pii: S0968-0004(21)00190-0. [Epub ahead of print]
      Protein aggregation propensity is a pervasive and seemingly inescapable property of proteomes. Strikingly, a significant fraction of the proteome is supersaturated, meaning that, for these proteins, their native conformation is less stable than the aggregated state. Maintaining the integrity of a proteome under such conditions is precarious and requires energy-consuming proteostatic regulation. Why then is aggregation propensity maintained at such high levels over long evolutionary timescales? Here, we argue that the conformational stability of the native and aggregated states are correlated thermodynamically and that codon usage strengthens this correlation. As a result, the folding of stable proteins requires kinetic control to avoid aggregation, provided by aggregation gatekeepers. These unique residues are evolutionarily selected to kinetically favor native folding, either on their own or by coopting chaperones.
    Keywords:  amyloid; kinetic partitioning; protein aggregation; protein stability; protein structure; proteostasis
    DOI:  https://doi.org/10.1016/j.tibs.2021.08.010
  14. Sci Rep. 2021 Sep 23. 11(1): 18882
      Identification of post-translational modifications (PTM) is significant in the study of computational proteomics, cell biology, pathogenesis, and drug development due to its role in many bio-molecular mechanisms. Though there are several computational tools to identify individual PTMs, only three predictors have been established to predict multiple PTMs at the same lysine residue. Furthermore, detailed analysis and assessment on dataset balancing and the significance of different feature encoding techniques for a suitable multi-PTM prediction model are still lacking. This study introduces a computational method named 'iMul-kSite' for predicting acetylation, crotonylation, methylation, succinylation, and glutarylation, from an unrecognized peptide sample with one, multiple, or no modifications. After successfully eliminating the redundant data samples from the majority class by analyzing the hardness of the sequence-coupling information, feature representation has been optimized by adopting the combination of ANOVA F-Test and incremental feature selection approach. The proposed predictor predicts multi-label PTM sites with 92.83% accuracy using the top 100 features. It has also achieved a 93.36% aiming rate and 96.23% coverage rate, which are much better than the existing state-of-the-art predictors on the validation test. This performance indicates that 'iMul-kSite' can be used as a supportive tool for further K-PTM study. For the convenience of the experimental scientists, 'iMul-kSite' has been deployed as a user-friendly web-server at http://103.99.176.239/iMul-kSite .
    DOI:  https://doi.org/10.1038/s41598-021-98458-y
  15. Tissue Eng Part B Rev. 2021 Sep 24.
      The mechanical behaviour of soft tissue extracellular matrix is time dependent. Moreover, it evolves over time due to physiological processes as well as aging and disease. Measuring and quantifying the time-dependent mechanical behaviour of soft tissues and materials poses a challenge, partly because of their labile and hydrated nature but also because of the lack of a common definition of terms and understanding of models for characterising viscoelasticity. Here we review the most important measurement techniques and models used to determine the viscoelastic properties of soft hydrated materials - or hydrogels - underlining the difference between viscoelastic behaviour and the properties and descriptors used to quantify viscoelasticity. We then discuss the principal factors which determine tissue viscoelasticity in vivo and summarise what we currently know about cell response to time-dependent materials, outlining fundamental factors that have to be considered when interpreting results. Particular attention is given to the relationship between the different time scales involved (mechanical, cellular and observation time scales), as well as scaling principles, all of which must be considered when designing viscoelastic materials and performing experiments for biomechanics or mechanobiology applications. From this overview, key considerations and directions for furthering insights and applications in the emergent field of cell viscoelastic mechanotransduction are provided.
    DOI:  https://doi.org/10.1089/ten.TEB.2021.0151