bims-ectoca Biomed News
on Epigenetic control of tolerance in cancer
Issue of 2021–11–28
fourteen papers selected by
Ankita Daiya, Birla Institute of Technology and Science
  1. Metabolism, HDACs, and HDAC Inhibitors: A Systems Biology Perspective.
  2. The role of chromatin at transcription-replication conflicts as a genome safeguard.
  3. A Class of Protein-Coding RNAs Binds to Polycomb Repressive Complex 2 and Alters Histone Methylation.
  4. A Portrait of Intratumoral Genomic and Transcriptomic Heterogeneity at Single-Cell Level in Colorectal Cancer.
  5. Identification of Enhancers and Promoters in the Genome by Multidimensional Scaling.
  6. Control of Chromatin Organization and Chromosome Behavior during the Cell Cycle through Phase Separation.
  7. Tumor-Progressive Mechanisms Mediating miRNA-Protein Interaction.
  8. New Insight to Overcome Tumor Resistance: An Overview from Cellular to Clinical Therapies.
  9. Dissecting the Role of Circular RNAs in Sarcomas with Emphasis on Osteosarcomas.
  10. Microtubule-Based Mitochondrial Dynamics as a Valuable Therapeutic Target in Cancer.
  11. EZH2 presents a therapeutic target for neuroendocrine tumors of the small intestine.
  12. The role of protein acetylation in regulating mitochondrial fusion and fission.
  13. Bioinformatic reanalysis of public proteomics data reveals that nuclear proteins are recurrent in cancer secretomes.
  14. A tumor-penetrable drug nanococktail made from human histones for interventional nucleus-targeted chemophotothermal therapy of drug-resistant tumors.
  1. Metabolites. 2021 Nov 20. pii: 792. [Epub ahead of print]11(11):
    Metabolism, HDACs, and HDAC Inhibitors: A Systems Biology Perspective.
    Jacob King, Maya Patel, Sriram Chandrasekaran.
      Histone deacetylases (HDACs) are epigenetic enzymes that play a central role in gene regulation and are sensitive to the metabolic state of the cell. The cross talk between metabolism and histone acetylation impacts numerous biological processes including development and immune function. HDAC inhibitors are being explored for treating cancers, viral infections, inflammation, neurodegenerative diseases, and metabolic disorders. However, how HDAC inhibitors impact cellular metabolism and how metabolism influences their potency is unclear. Discussed herein are recent applications and future potential of systems biology methods such as high throughput drug screens, cancer cell line profiling, single cell sequencing, proteomics, metabolomics, and computational modeling to uncover the interplay between metabolism, HDACs, and HDAC inhibitors. The synthesis of new systems technologies can ultimately help identify epigenomic and metabolic biomarkers for patient stratification and the design of effective therapeutics.
    Keywords:  epigenome; gene regulation; histone acetylation; histone deacetylases; metabolomics; proteomics; transcriptomics
    DOI:  https://doi.org/10.3390/metabo11110792
  2. Biochem Soc Trans. 2021 Nov 25. pii: BST20210691. [Epub ahead of print]
    The role of chromatin at transcription-replication conflicts as a genome safeguard.
    Aleix Bayona-Feliu, Andrés Aguilera.
      DNA replication ensures the correct copying of the genome and the faithful transfer of the genetic information to the offspring. However, obstacles to replication fork (RF) progression cause RF stalling and compromise efficient genome duplication. Since replication uses the same DNA template as transcription, both transcription and replication must be coordinated to prevent Transcription-Replication Conflicts (TRCs) that could stall RF progression. Several factors contribute to limit the occurrence of such conflicts and their harmful impact on genome integrity. Increasing evidence indicates that chromatin homeostasis plays a key role in the cellular response to TRCs as well as in the preservation of genome integrity. Indeed, chromatin regulating enzymes are frequently mutated in cancer cells, a common characteristic of which is genome instability. Therefore, understanding the role of chromatin in TRC occurrence and resolution may help identify the molecular mechanism by which chromatin protects genome integrity, and the causes and physiological relevance of the high mutation rates of chromatin regulating factors in cancer. Here we review the current knowledge in the field, as well as the perspectives and future applications.
    Keywords:  DNA breaks; R-loops; cancer; chromatin; genome instability; transcription-replication conflicts
    DOI:  https://doi.org/10.1042/BST20210691
  3. Front Oncol. 2021 ;11 739830
    A Class of Protein-Coding RNAs Binds to Polycomb Repressive Complex 2 and Alters Histone Methylation.
    Meijian Liao, Xiaolin Sun, Shoucui Gao, Yaou Zhang.
      Polycomb repressive complex 2 (PRC2) is a multi-subunit protein complex mediating the methylation of lysine 27 on histone H3 and playing an important role in transcriptional repression during tumorigenesis and development. Previous studies revealed that both protein-coding and non-coding RNAs could bind to PRC2 complex. However, the functions of protein-coding RNAs that bind to PRC2 complex in tumor are still unknown. Through data mining and RNA immunoprecipitation (RIP) assay, our study found that there were a class of protein-coding RNAs bound to PRC2 complex and H3 with tri-methylation on lysine 27. The Bayesian gene regulatory network analysis pointed out that these RNAs regulated the expression of PRC2-regulated genes in cancer. In addition, gene set enrichment analysis (GSEA), gene ontology (GO) analysis, and weighted gene co-expression network analysis (WGCNA) also confirmed that these RNAs were associated with histone modification in cancer. We also confirmed that MYO1C, a PRC2-bound transcript, inhibited the modification level of H3K27me3. Further detailed study showed that TMEM117 regulated TSLP expression through EZH2-mediated H3K27me3 modification. Interestingly, the RNA recognition motif of PRC2 complex might help these RNAs bind to the PRC2 complex more easily. The same regulatory pattern was found in mice as well.
    Keywords:  H3K27me3 modification; LncRNA; PRC2 complex; TMEM117; protein-coding RNA
    DOI:  https://doi.org/10.3389/fonc.2021.739830
  4. Medicina (Kaunas). 2021 Nov 17. pii: 1257. [Epub ahead of print]57(11):
    A Portrait of Intratumoral Genomic and Transcriptomic Heterogeneity at Single-Cell Level in Colorectal Cancer.
    Andrea Angius, Antonio Mario Scanu, Caterina Arru, Maria Rosaria Muroni, Ciriaco Carru, Alberto Porcu, Paolo Cossu-Rocca, Maria Rosaria De Miglio.
      In the study of cancer, omics technologies are supporting the transition from traditional clinical approaches to precision medicine. Intra-tumoral heterogeneity (ITH) is detectable within a single tumor in which cancer cell subpopulations with different genome features coexist in a patient in different tumor areas or may evolve/differ over time. Colorectal carcinoma (CRC) is characterized by heterogeneous features involving genomic, epigenomic, and transcriptomic alterations. The study of ITH is a promising new frontier to lay the foundation towards successful CRC diagnosis and treatment. Genome and transcriptome sequencing together with editing technologies are revolutionizing biomedical research, representing the most promising tools for overcoming unmet clinical and research challenges. Rapid advances in both bulk and single-cell next-generation sequencing (NGS) are identifying primary and metastatic intratumoral genomic and transcriptional heterogeneity. They provide critical insight in the origin and spatiotemporal evolution of genomic clones responsible for early and late therapeutic resistance and relapse. Single-cell technologies can be used to define subpopulations within a known cell type by searching for differential gene expression within the cell population of interest and/or effectively isolating signal from rare cell populations that would not be detectable by other methods. Each single-cell sequencing analysis is driven by clustering of cells based on their differentially expressed genes. Genes that drive clustering can be used as unique markers for a specific cell population. In this review we analyzed, starting from published data, the possible achievement of a transition from clinical CRC research to precision medicine with an emphasis on new single-cell based techniques; at the same time, we focused on all approaches and issues related to this promising technology. This transition might enable noninvasive screening for early diagnosis, individualized prediction of therapeutic response, and discovery of additional novel drug targets.
    Keywords:  colorectal carcinoma; intratumor heterogeneity; precision medicine; single-cell next-generation sequencing
    DOI:  https://doi.org/10.3390/medicina57111257
  5. Genes (Basel). 2021 Oct 23. pii: 1671. [Epub ahead of print]12(11):
    Identification of Enhancers and Promoters in the Genome by Multidimensional Scaling.
    Ryo Ishibashi, Y-H Taguchi.
      The positions of enhancers and promoters on genomic DNA remain poorly understood. Chromosomes cannot be observed during the cell division cycle because the genome forms a chromatin structure and spreads within the nucleus. However, high-throughput chromosome conformation capture (Hi-C) measures the physical interactions of genomes. In previous studies, DNA extrusion loops were directly derived from Hi-C heat maps. Multidimensional Scaling (MDS) is used in this assessment to more precisely locate enhancers and promoters. MDS is a multivariate analysis method that reproduces the original coordinates from the distance matrix between elements. We used Hi-C data of cultured osteosarcoma cells and applied MDS as the distance matrix of the genome. In addition, we selected columns 2 and 3 of the orthogonal matrix U as the desired structure. Overall, the DNA loops from the reconstructed genome structure contained bioprocesses involved in transcription, such as the pre-transcriptional initiation complex and RNA polymerase II initiation complex, and transcription factors involved in cancer, such as Foxm1 and CREB3. Therefore, our results are consistent with the biological findings. Our method is suitable for identifying enhancers and promoters in the genome.
    Keywords:  enhancer; high-throughput chromosome conformation capture; multidimensional scaling; promoter
    DOI:  https://doi.org/10.3390/genes12111671
  6. Int J Mol Sci. 2021 Nov 12. pii: 12271. [Epub ahead of print]22(22):
    Control of Chromatin Organization and Chromosome Behavior during the Cell Cycle through Phase Separation.
    Jiaxiang Li, Jinmin Gao, Ruoxi Wang.
      Phase-separated condensates participate in various biological activities. Liquid-liquid phase separation (LLPS) can be driven by collective interactions between multivalent and intrinsically disordered proteins. The manner in which chromatin-with various morphologies and activities-is organized in a complex and small nucleus still remains to be fully determined. Recent findings support the claim that phase separation is involved in the regulation of chromatin organization and chromosome behavior. Moreover, phase separation also influences key events during mitosis and meiosis. This review elaborately dissects how phase separation regulates chromatin and chromosome organization and controls mitotic and meiotic chromosome behavior.
    Keywords:  chromosome organization; liquid-liquid phase separation (LLPS); meiosis; mitosis
    DOI:  https://doi.org/10.3390/ijms222212271
  7. Int J Mol Sci. 2021 Nov 14. pii: 12303. [Epub ahead of print]22(22):
    Tumor-Progressive Mechanisms Mediating miRNA-Protein Interaction.
    Hiroaki Konishi, Hiroki Sato, Kenji Takahashi, Mikihiro Fujiya.
      MicroRNAs (miRNAs) are single-stranded short-chain RNAs that are endogenously expressed in vertebrates; they are considered the fine-tuners of cellular protein expression that act by modifying mRNA translation. miRNAs control tissue development and differentiation, cell growth, and apoptosis in cancer and non-cancer cells. Aberrant regulation of miRNAs is involved in the pathogenesis of various diseases including cancer. Numerous investigations have shown that the changes in cellular miRNA expression in cancerous tissues and extracellular miRNAs enclosed in exosomes are correlated with cancer prognosis. Therefore, miRNAs can be used as cancer biomarkers and therapeutic targets for cancer in clinical applications. In the previous decade, miRNAs have been shown to regulate cellular functions by directly binding to proteins and mRNAs, thereby controlling cancer progression. This regulatory system implies that cancer-associated miRNAs can be applied as molecular-targeted therapy. This review discusses the roles of miRNA-protein systems in cancer progression and its future applications in cancer treatment.
    Keywords:  RNA-binding protein; cancer therapy; microRNA
    DOI:  https://doi.org/10.3390/ijms222212303
  8. Life (Basel). 2021 Oct 24. pii: 1131. [Epub ahead of print]11(11):
    New Insight to Overcome Tumor Resistance: An Overview from Cellular to Clinical Therapies.
    Giulia Mitola, Paolo Falvo, Francesco Bertolini.
      Disease relapse caused by drug resistance still represents a major clinical hurdle in cancer treatments. Tumor cells may take advantage of different intracellular and genetic systems attenuating the drug effects. Resistant cells or minimal residual disease (MRD) cells have strong clinical relevance, as they might give rise to secondary tumors when the therapy is concluded. Thus, MRDs are crucial therapeutic targets in order to prevent tumor relapse. Therefore, several groups aim at understanding how MRDs are orginated, characterizing their molecular features, and eradicating them. In this review, we will describe MRD from a genetic, evolutionary, and molecular point of view. Moreover, we will focus on the new in vitro, in vivo, preclinical, and clinical studies that aim at eradicating tumor resistance.
    Keywords:  in vitro and in vivo studies; preclinical studies; tumor resistance
    DOI:  https://doi.org/10.3390/life11111131
  9. Biomedicines. 2021 Nov 08. pii: 1642. [Epub ahead of print]9(11):
    Dissecting the Role of Circular RNAs in Sarcomas with Emphasis on Osteosarcomas.
    Eleftheria Lakiotaki, Dimitrios S Kanakoglou, Andromachi Pampalou, Eleni A Karatrasoglou, Christina Piperi, Penelope Korkolopoulou.
      Circular RNAs (circRNAs) are single-stranded RNAs generated from exons back-splicing from a single pre-mRNA, forming covalently closed loop structures which lack 5'-3'-polarity or polyadenylated tail. Ongoing research depicts that circRNAs play a pivotal role in tumorigenesis, tumor progression, metastatic potential and chemoresistance by regulating transcription, microRNA (miRNA) sponging, RNA-binding protein interactions, alternative splicing and to a lesser degree, protein coding. Sarcomas are rare malignant tumors stemming from mesenchymal cells. Due to their clinically insidious onset, they often present at advanced stage and their treatment may require aggressive chemotherapeutic or surgical options. This review is mainly focused on the regulatory functions of circRNAs on osteosarcoma progression and their potential role as biomarkers, an area which has prompted lately extensive research. The attributed oncogenic role of circRNAs on other mesenchymal tumors such as Kaposi Sarcoma (KS), Rhabdomyosarcoma (RMS) or Gastrointestinal Stromal Tumors (GISTs) is also described. The involvement of circRNAs on sarcoma oncogenesis and relevant emerging diagnostic, prognostic and therapeutic applications are expected to gain more research interest in the future.
    Keywords:  Kaposi sarcoma; circular RNAs; diagnosis; gastrointestinal stromal tumors; osteosarcoma; rhabdomyosarcoma; therapy
    DOI:  https://doi.org/10.3390/biomedicines9111642
  10. Cancers (Basel). 2021 Nov 19. pii: 5812. [Epub ahead of print]13(22):
    Microtubule-Based Mitochondrial Dynamics as a Valuable Therapeutic Target in Cancer.
    Rosa Vona, Anna Maria Mileo, Paola Matarrese.
      Mitochondria constitute an ever-reorganizing dynamic network that plays a key role in several fundamental cellular functions, including the regulation of metabolism, energy production, calcium homeostasis, production of reactive oxygen species, and programmed cell death. Each of these activities can be found to be impaired in cancer cells. It has been reported that mitochondrial dynamics are actively involved in both tumorigenesis and metabolic plasticity, allowing cancer cells to adapt to unfavorable environmental conditions and, thus, contributing to tumor progression. The mitochondrial dynamics include fusion, fragmentation, intracellular trafficking responsible for redistributing the organelle within the cell, biogenesis, and mitophagy. Although the mitochondrial dynamics are driven by the cytoskeleton-particularly by the microtubules and the microtubule-associated motor proteins dynein and kinesin-the molecular mechanisms regulating these complex processes are not yet fully understood. More recently, an exchange of mitochondria between stromal and cancer cells has also been described. The advantage of mitochondrial transfer in tumor cells results in benefits to cell survival, proliferation, and spreading. Therefore, understanding the molecular mechanisms that regulate mitochondrial trafficking can potentially be important for identifying new molecular targets in cancer therapy to interfere specifically with tumor dissemination processes.
    Keywords:  cancer bioenergetics; microtubules; mitochondria dynamics; mitophagy; tunneling nanotubes
    DOI:  https://doi.org/10.3390/cancers13225812
  11. Sci Rep. 2021 Nov 23. 11(1): 22733
    EZH2 presents a therapeutic target for neuroendocrine tumors of the small intestine.
    Elham Barazeghi, Per Hellman, Olov Norlén, Gunnar Westin, Peter Stålberg.
      Small intestinal neuroendocrine tumors (SI-NETs) are slow-growing tumors that seem genetically quite stable without highly recurrent mutations, but are epigenetically dysregulated. In contrast to the undetectable expression of the enhancer of zeste homolog 2 (EZH2) histone methyltransferase in the enterochromaffin cells of the small intestine, we found high and differential expression of EZH2 in primary SI-NETs and corresponding metastases. Silencing EZH2 in the SI-NET cell line CNDT2.5 reduced cell proliferation and induced apoptosis. Furthermore, EZH2 knockout inhibited tumor progression in a CNDT2.5 SI-NET xenograft mouse model, and treatment of SI-NET cell lines CNDT2.5 and GOT1 with the EZH2-specific inhibitor CPI-1205 decreased cell viability and promoted apoptosis. Moreover, CPI-1205 treatment reduced migration capacity of CNDT2.5 cells. The EZH2 inhibitor GSK126 also repressed proliferation of CNDT2.5 cells. Recently, metformin has received wide attention as a therapeutic option in diverse cancers. In CNDT2.5 and GOT1 cells, metformin suppressed EZH2 expression, and inhibited cell proliferation. Exposure of GOT1 three-dimensional cell spheroids to CPI-1205 or metformin arrested cell proliferation and decreased spheroid size. These novel findings support a possible role of EZH2 as a candidate oncogene in SI-NETs, and suggest that CPI-1205 and metformin should be further evaluated as therapeutic options for patients with SI-NETs.
    DOI:  https://doi.org/10.1038/s41598-021-02181-7
  12. Biochem Soc Trans. 2021 Nov 23. pii: BST20210798. [Epub ahead of print]
    The role of protein acetylation in regulating mitochondrial fusion and fission.
    Golam M Uddin, Rafa Abbas, Timothy E Shutt.
      The dynamic processes of mitochondrial fusion and fission determine the shape of mitochondria, which can range from individual fragments to a hyperfused network, and influence mitochondrial function. Changes in mitochondrial shape can occur rapidly, allowing mitochondria to adapt to specific cues and changing cellular demands. Here, we will review what is known about how key proteins required for mitochondrial fusion and fission are regulated by their acetylation status, with acetylation promoting fission and deacetylation enhancing fusion. In particular, we will examine the roles of NAD+ dependant sirtuin deacetylases, which mediate mitochondrial acetylation, and how this post-translational modification provides an exquisite regulatory mechanism to co-ordinate mitochondrial function with metabolic demands of the cell.
    Keywords:  acetylation/deacetylation; fission; fusion; mitochondria; sirtuins
    DOI:  https://doi.org/10.1042/BST20210798
  13. Traffic. 2021 Nov 22.
    Bioinformatic reanalysis of public proteomics data reveals that nuclear proteins are recurrent in cancer secretomes.
    Juliana A De Morais, André Zelanis.
      Proteins secreted by tumoral cells (cancer secretomes) have been continuously associated with cancer development and progression processes. In this context, secreted proteins contribute to the signaling mechanisms related to tumor growth and spreading and studies on tumor secretomes provide valuable clues on putative tumor biomarkers. Although the in vitro identification of intracellular proteins in cancer secretome studies has usually been associated with contamination derived from cell lysis or fetal bovine serum, accumulated evidence reports on intracellular proteins with moonlighting functions in the extracellular environment. In this study, we performed a systematic reanalysis of public proteomics data regarding different cancer secretomes, aiming to identify intracellular proteins potentially secreted by tumor cells via unconventional secretion pathways. We found a similar repertoire of unconventionally secreted proteins, including the recurrent identification of nuclear proteins secreted by different cancer cells. In addition, in some cancer types, immunohistochemical data were in line with proteomics identifications and suggested that nuclear proteins might relocate from the nucleus to the cytoplasm. Both the presence of nuclear proteins and the likely unconventional secretion of such proteins may comprise biological signatures of malignant transformation in distinct cancer types and may be targeted for further analysis aiming at the prognostic/therapeutic value of such features.
    Keywords:  Bioinformatics; Cancer; Proteomics; Secretome; Unconventional protein secretion pathways
    DOI:  https://doi.org/10.1111/tra.12827
  14. Bioact Mater. 2022 Mar;9 554-565
    A tumor-penetrable drug nanococktail made from human histones for interventional nucleus-targeted chemophotothermal therapy of drug-resistant tumors.
    Jianquan Guo, Dongsheng Tan, Chenmei Lou, Shiying Guo, Xing Jin, Haijing Qu, Lijia Jing, Sijin Li.
      Nanoparticle-based chemophotothermal therapy (CPT) is a promising treatment for multidrug resistant tumors. In this study, a drug nanococktail of DIR825@histone was developed by employing doxorubicin (DOX), NIR dye IR825 and human histones for interventional nucleus-targeted CPT of multidrug resistant tumors with an interventional laser. After localized intervention, DIR825@histone penetrated tumor tissues by transcytosis, efficiently entered tumor cells and targeted the cell nuclei. DIR825@histone also exhibited good photothermal performance and thermal-triggered drug release. Efficient multidrug resistant tumor inhibition was achieved by enhanced CPT sensitization and MDR reversion via nuclear targeting. Moreover, an interventional laser assisted DIR825@histone in inhibiting multidrug resistant tumors by promoting the sufficient delivery of laser energy inside the tumor while reducing skin injury. Therefore, DIR825@histone together with this interventional nucleus-targeted CPT strategy holds great promise for treating multidrug resistant tumors.
    Keywords:  Chemotherapy; Drug resistant tumor; Human histones; Localized intervention; Nuclear targeting; Photothermal therapy
    DOI:  https://doi.org/10.1016/j.bioactmat.2021.07.018
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