bims-dresag Biomed News
on DNA damage and repair, cellular senescence and aging, gene therapy
Issue of 2021–08–01
eleven papers selected by
Pengyi Yan, Shanghai Jiao Tong University
  1. The Cancer SENESCopedia: A delineation of cancer cell senescence.
  2. PCR-mediated One-day Synthesis of Guide RNA for the CRISPR/Cas9 System.
  3. Cellular senescence or stemness: hypoxia flips the coin.
  4. Targeting viruses in their phase.
  5. Cracking genetic codes of longevity.
  6. Dissecting primary and secondary senescence to enable new senotherapeutic strategies.
  7. Cell cycle on the crossroad of tumorigenesis and cancer therapy.
  8. Loss of Cyclin C or CDK8 provides ATR inhibitor resistance by suppressing transcription-associated replication stress.
  9. The p53 transcriptional response across tumor types reveals core and senescence-specific signatures modulated by long noncoding RNAs.
  10. Defining R-loop classes and their contributions to genome instability.
  11. Understanding the DNA double-strand break repair and its therapeutic implications.
  1. Cell Rep. 2021 Jul 27. pii: S2211-1247(21)00858-5. [Epub ahead of print]36(4): 109441
    The Cancer SENESCopedia: A delineation of cancer cell senescence.
    Fleur Jochems, Bram Thijssen, Giulia De Conti, Robin Jansen, Ziva Pogacar, Kelvin Groot, Liqin Wang, Arnout Schepers, Cun Wang, Haojie Jin, Roderick L Beijersbergen, Rodrigo Leite de Oliveira, Lodewyk F A Wessels, René Bernards.
      Cellular senescence is characterized as a stable proliferation arrest that can be triggered by multiple stresses. Most knowledge about senescent cells is obtained from studies in primary cells. However, senescence features may be different in cancer cells, since the pathways that are involved in senescence induction are often deregulated in cancer. We report here a comprehensive analysis of the transcriptome and senolytic responses in a panel of 13 cancer cell lines rendered senescent by two distinct compounds. We show that in cancer cells, the response to senolytic agents and the composition of the senescence-associated secretory phenotype are more influenced by the cell of origin than by the senescence trigger. Using machine learning, we establish the SENCAN gene expression classifier for the detection of senescence in cancer cell samples. The expression profiles and senescence classifier are available as an interactive online Cancer SENESCopedia.
    Keywords:  ABT-263; SASP; SENCAN; SENESCopedia; cancer; cell cycle; gene expression classifier; senescence; senolytics; transcriptome profiling
    DOI:  https://doi.org/10.1016/j.celrep.2021.109441
  2. Bio Protoc. 2021 Jul 05. 11(13): e4082
    PCR-mediated One-day Synthesis of Guide RNA for the CRISPR/Cas9 System.
    Naim Hassan, Farhana Easmin, Keisuke Ekino, Satoshi Harashima.
      Nowadays, CRISPR (clustered regularly interspaced short palindromic repeats) and the CRISPR-associated protein (Cas9) system play a major role in genome editing. To target the desired sequence of the genome successfully, guide RNA (gRNA) is indispensable for the CRISPR/Cas9 system. To express gRNA, a plasmid expressing the gRNA sequence is typically constructed; however, construction of plasmids involves much time and labor. In this study, we propose a novel procedure to express gRNA via a much simpler method that we call gRNA-TES (gRNA-transient expression system). This method employs only PCR, and all the steps including PCR and yeast transformation can be completed within 1 day. In comparison with the plasmid-based gRNA delivery system, the performance of gRNA-TES is more effective, and its total time and cost are significantly reduced.
    Keywords:  CRISPR/Cas9; Genome editing; Guide RNA; PCR-based; Yeast
    DOI:  https://doi.org/10.21769/BioProtoc.4082
  3. J Exp Clin Cancer Res. 2021 Jul 29. 40(1): 243
    Cellular senescence or stemness: hypoxia flips the coin.
    Daniel Otero-Albiol, Amancio Carnero.
      Cellular senescence is a complex physiological state whose main feature is proliferative arrest. Cellular senescence can be considered the reverse of cell immortalization and continuous tumor growth. However, cellular senescence has many physiological functions beyond being a putative tumor suppressive trait. It remains unknown whether low levels of oxygen or hypoxia, which is a feature of every tissue in the organism, modulate cellular senescence, altering its capacity to suppress the limitation of proliferation. It has been observed that the lifespan of mammalian primary cells is increased under low oxygen conditions. Additionally, hypoxia promotes self-renewal and pluripotency maintenance in adult and embryonic stem cells (ESCs), induced pluripotent stem cells (iPSCs) and cancer stem cells (CSCs). In this study, we discuss the role of hypoxia facilitating senescence bypass during malignant transformation and acquisition of stemness properties, which all contribute to tumor development and cancer disease aggressiveness.
    Keywords:  cancer; cellular senescence; dedifferentiation; hypoxia; immortalization; oxygen; stemness
    DOI:  https://doi.org/10.1186/s13046-021-02035-0
  4. Nat Rev Drug Discov. 2021 Jul 27.
    Targeting viruses in their phase.
    Paulina Strzyz.
      
    DOI:  https://doi.org/10.1038/d41573-021-00129-0
  5. Nat Rev Mol Cell Biol. 2021 Jul 26.
    Cracking genetic codes of longevity.
    Meng C Wang.
      
    DOI:  https://doi.org/10.1038/s41580-021-00403-4
  6. Ageing Res Rev. 2021 Jul 21. pii: S1568-1637(21)00159-8. [Epub ahead of print]70 101412
    Dissecting primary and secondary senescence to enable new senotherapeutic strategies.
    Tesfahun Dessale Admasu, Michael Rae, Alexandra Stolzing.
      Cellular senescence is a state of stable cell cycle arrest that is known to be elicited in response to different stresses or forms of damage. Senescence limits the replication of old, damaged, and precancerous cells in the short-term but is implicated in diseases and debilities of aging due to loss of regenerative reserve and secretion of a complex combination of factors called the senescence-associated secretory phenotype (SASP). More recently, investigators have discovered that senescent cells induced by these methods (what we term "primary senescent cells") are also capable of inducing other non-senescent cells to undergo senescence - a phenomenon we call "secondary senescence." Secondary senescence has been demonstrated to occur via two broad types of mechanisms. First, factors in the SASP have been shown to be involved in spreading senescence; we call this phenomenon "paracrine senescence." Second, primary senescent cells can induce senescence via an additional group of mechanisms involving cell-to-cell contacts of different types; we term this phenomenon "juxtacrine senescence." "Secondary senescence" in our definition is thus the overarching term for both paracrine and juxtacrine senescence together. By allowing cells that are inherently small in number and incapable of replication to increase in number and possibly spread to anatomically distant locations, secondary senescence allows an initially small number of senescent cells to contribute further to age-related pathologies. We propose that understanding how primary and secondary senescent cells differ from each other and the mechanisms of their spread will enable the development of new rejuvenation therapies to target different senescent cell populations and interrupt their spread, extending human health- and potentially lifespan.
    Keywords:  Aging; Bystander; Juxtacrine; Paracrine; SASP; Secondary senescence; Senescence
    DOI:  https://doi.org/10.1016/j.arr.2021.101412
  7. Trends Cell Biol. 2021 Jul 22. pii: S0962-8924(21)00140-9. [Epub ahead of print]
    Cell cycle on the crossroad of tumorigenesis and cancer therapy.
    Jing Liu, Yunhua Peng, Wenyi Wei.
      Aberrancy in cell cycle progression is one of the fundamental mechanisms underlying tumorigenesis, making regulators of the cell cycle machinery rational anticancer therapeutic targets. A growing body of evidence indicates that the cell cycle regulatory pathway integrates into other hallmarks of cancer, including metabolism remodeling and immune escape. Thus, therapies against cell cycle machinery components can not only repress the division of cancer cells, but also reverse cancer metabolism and restore cancer immune surveillance. Besides the ongoing effects on the development of small molecule inhibitors (SMIs) of the cell cycle machinery, proteolysis targeting chimeras (PROTACs) have recently been used to target these oncogenic proteins related to cell cycle progression. Here, we discuss the rationale of cell cycle targeting therapies, particularly PROTACs, to more efficiently retard tumorigenesis.
    Keywords:  PROTAC; cancer; cancer immune; cell cycle; degradation; metabolism
    DOI:  https://doi.org/10.1016/j.tcb.2021.07.001
  8. Nucleic Acids Res. 2021 Jul 30. pii: gkab628. [Epub ahead of print]
    Loss of Cyclin C or CDK8 provides ATR inhibitor resistance by suppressing transcription-associated replication stress.
    Rebecca L Lloyd, Vaclav Urban, Francisco Muñoz-Martínez, Iñigo Ayestaran, John C Thomas, Christelle de Renty, Mark J O'Connor, Josep V Forment, Yaron Galanty, Stephen P Jackson.
      The protein kinase ATR plays pivotal roles in DNA repair, cell cycle checkpoint engagement and DNA replication. Consequently, ATR inhibitors (ATRi) are in clinical development for the treatment of cancers, including tumours harbouring mutations in the related kinase ATM. However, it still remains unclear which functions and pathways dominate long-term ATRi efficacy, and how these vary between clinically relevant genetic backgrounds. Elucidating common and genetic-background specific mechanisms of ATRi efficacy could therefore assist in patient stratification and pre-empting drug resistance. Here, we use CRISPR-Cas9 genome-wide screening in ATM-deficient and proficient mouse embryonic stem cells to interrogate cell fitness following treatment with the ATRi, ceralasertib. We identify factors that enhance or suppress ATRi efficacy, with a subset of these requiring intact ATM signalling. Strikingly, two of the strongest resistance-gene hits in both ATM-proficient and ATM-deficient cells encode Cyclin C and CDK8: members of the CDK8 kinase module for the RNA polymerase II mediator complex. We show that Cyclin C/CDK8 loss reduces S-phase DNA:RNA hybrid formation, transcription-replication stress, and ultimately micronuclei formation induced by ATRi. Overall, our work identifies novel biomarkers of ATRi efficacy in ATM-proficient and ATM-deficient cells, and highlights transcription-associated replication stress as a predominant driver of ATRi-induced cell death.
    DOI:  https://doi.org/10.1093/nar/gkab628
  9. Proc Natl Acad Sci U S A. 2021 Aug 03. pii: e2025539118. [Epub ahead of print]118(31):
    The p53 transcriptional response across tumor types reveals core and senescence-specific signatures modulated by long noncoding RNAs.
    Ephrath Tesfaye, Elena Martinez-Terroba, Jordan Bendor, Lauren Winkler, Christiane Olivero, Kevin Chen, David M Feldser, Jesse R Zamudio, Nadya Dimitrova.
      The p53 pathway is a universal tumor suppressor mechanism that limits tumor progression by triggering apoptosis or permanent cell cycle arrest, called senescence. In recent years, efforts to reactivate p53 function in cancer have proven to be a successful therapeutic strategy in murine models and have gained traction with the development of a range of small molecules targeting mutant p53. However, knowledge of the downstream mediators of p53 reactivation in different oncogenic contexts has been limited. Here, we utilized a panel of murine cancer cell lines from three distinct tumor types susceptible to alternative outcomes following p53 restoration to define unique and shared p53 transcriptional signatures. While we found that the majority of p53-bound sites and p53-responsive transcripts are tumor-type specific, analysis of shared targets identified a core signature of genes activated by p53 across all contexts. Furthermore, we identified repression of E2F and Myc target genes as a key feature of senescence. Characterization of p53-induced transcripts revealed core and senescence-specific long noncoding RNAs (lncRNAs) that are predominantly chromatin associated and whose production is coupled to cis-regulatory activities. Functional investigation of the contributions of p53-induced lncRNAs to p53-dependent outcomes highlighted Pvt1b, the p53-dependent isoform of Pvt1, as a mediator of p53-dependent senescence via Myc repression. Inhibition of Pvt1b led to decreased activation of senescence markers and increased levels of markers of proliferation. These findings shed light on the core and outcome-specific p53 restoration signatures across different oncogenic contexts and underscore the key role of the p53-Pvt1b-Myc regulatory axis in mediating proliferative arrest.
    Keywords:  lncRNA; p53; senescence; transcription; tumor suppression
    DOI:  https://doi.org/10.1073/pnas.2025539118
  10. DNA Repair (Amst). 2021 Jul 17. pii: S1568-7864(21)00138-5. [Epub ahead of print]106 103182
    Defining R-loop classes and their contributions to genome instability.
    Daisy Castillo-Guzman, Frédéric Chédin.
      R-loops are non-B DNA structures that form during transcription when the nascent RNA anneals to the template DNA strand forming a RNA:DNA hybrid. Understanding the genomic distribution and function of R-loops is an important goal, since R-loops have been implicated in a number of adaptive and maladaptive processes under physiological and pathological conditions. Based on R-loop mapping datasets, we propose the existence of two main classes of R-loops, each associated with unique characteristics. Promoter-paused R-loops (Class I) are short R-loops that form at high frequency during promoter-proximal pausing by RNA polymerase II. Elongation-associated R-loops (Class II) are long structures that occur throughout gene bodies at modest frequencies. We further discuss the relationships between each R-loop class with instances of genome instability and suggest that increased class I R-loops, resulting from enhanced promoter-proximal pausing, represent the main culprits for R-loop mediated genome instability under pathological conditions.
    Keywords:  DNA damage; Elongation; Genome instability; Promoter-pausing; R-loops; Transcription
    DOI:  https://doi.org/10.1016/j.dnarep.2021.103182
  11. DNA Repair (Amst). 2021 Jul 09. pii: S1568-7864(21)00133-6. [Epub ahead of print]106 103177
    Understanding the DNA double-strand break repair and its therapeutic implications.
    Ujjayinee Ray, Sathees C Raghavan.
      Repair of DNA double-strand breaks (DSBs) and its regulation are tightly integrated inside cells. Homologous recombination, nonhomologous end joining and microhomology mediated end joining are three major DSB repair pathways in mammalian cells. Targeting proteins associated with these repair pathways using small molecule inhibitors can prove effective in tumors, especially those with deregulated repair. Sensitization of cancer to current age therapy including radio and chemotherapy, using small molecule inhibitors is promising and warrant further development. Although several are under clinical trial, till date no repair inhibitor is approved for commercial use in cancer patients, with the exception of PARP inhibitors targeting single-strand break repair. Based on molecular profiling of repair proteins, better prognostic and therapeutic output can be achieved in patients. In the present review, we highlight the different mechanisms of DSB repair, chromatin dynamics to provide repair accessibility and modulation of inhibitors in association with molecular profiling and current gold standard treatment modalities for cancer.
    Keywords:  Cancer therapy; Chromatin accessibility; DSB repair; Double-strand break; Genomic instability; Homologous recombination; MMEJ; Microhomology mediated end joining; NHEJ; Nonhomologous DNA end joining
    DOI:  https://doi.org/10.1016/j.dnarep.2021.103177
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