bims-numges Biomed News
on Nucleotide metabolism and genome stability
Issue of 2020‒11‒29
twenty papers selected by
Sean Rudd
Karolinska Institutet


  1. Mol Cell Oncol. 2020 Oct 27. 7(6): 1834902
    Zhou W, Wahl DR.
      Profound intratumoral genomic heterogeneity has limited the ability of targeted therapies to overcome therapy resistance in glioblastoma. We have defined purine metabolism as a key mediator of DNA repair and radiation resistance in glioblastoma. Because many glioblastoma oncogenic drivers activate purine metabolism, its inhibition may overcome therapy resistance despite intratumoral genomic heterogeneity.
    Keywords:  Glioblastoma; heterogeneity; metabolism; purine synthesis; radiation
    DOI:  https://doi.org/10.1080/23723556.2020.1834902
  2. Mol Cell Oncol. 2020 Sep 20. 7(6): 1804308
    Davenne T, Rehwinkel J.
      Purine nucleoside phosphorylase inhibitors (PNP-Is) were developed to ablate transformed lymphocytes. However, only some patients with leukemia benefit from PNP-Is. We provide a molecular explanation: the deoxyribonucleoside triphosphate (dNTP) hydrolase SAM and HD domain-containing protein 1 (SAMHD1) prevents the accumulation of toxic dNTP levels during purine nucleoside phosphorylase inhibition. We propose PNP-Is for targeted therapy of patients with acquired SAMHD1 mutations.
    Keywords:  CLL; PNP; SAMHD1; forodesine; leukemia
    DOI:  https://doi.org/10.1080/23723556.2020.1804308
  3. Curr Med Chem. 2020 Nov 25.
    Forey P, Cros-Perrial E, Dumontet C, Jordheim LP.
      The nucleotide metabolism has been targeted for many years and in various clinical settings, including cancer. The increased knowledge of certain enzymes involved in this metabolism and in associated cellular processes accumulated over the last few years, gives important information to the druggability of certain proteins and to the use of inhibitors for others. Here, we review recent data on such enzymes with major interest in drug development, i.e. SAMHD1 and the proteins of the NUDIX family. These include information on their roles in cancer progression, correlations with clinical outcome in cancer patients, and development and study of enzymatic inhibitors.
    Keywords:  MTH1; NUDIX; SAMHD1; cancer; inhibitors; treatment
    DOI:  https://doi.org/10.2174/0929867328666201125120422
  4. Front Oncol. 2020 ;10 554272
    Wolfe K, Kamata R, Coutinho K, Inoue T, Sasaki AT.
      Despite advances in targeted therapeutics and understanding in molecular mechanisms, metastasis remains a substantial obstacle for cancer treatment. Acquired genetic mutations and transcriptional changes can promote the spread of primary tumor cells to distant tissues. Additionally, recent studies have uncovered that metabolic reprogramming of cancer cells is tightly associated with cancer metastasis. However, whether intracellular metabolism is spatially and temporally regulated for cancer cell migration and invasion is understudied. In this review, we highlight the emergence of a concept, termed "membraneless metabolic compartmentalization," as one of the critical mechanisms that determines the metastatic capacity of cancer cells. In particular, we focus on the compartmentalization of purine nucleotide metabolism (e.g., ATP and GTP) at the leading edge of migrating cancer cells through the uniquely phase-separated microdomains where dynamic exchange of nucleotide metabolic enzymes takes place. We will discuss how future insights may usher in a novel class of therapeutics specifically targeting the metabolic compartmentalization that drives tumor metastasis.
    Keywords:  GTP-metabolism; cancer; leading edge; liquid-liquid phase separation; membraneless metabolic compartmentalization; metabolon; metastasis; purine biosynthesis
    DOI:  https://doi.org/10.3389/fonc.2020.554272
  5. Mol Cell Oncol. 2020 Oct 22. 7(6): 1827904
    Kharat SS, Sharan SK.
      Chemoresistance remains to be a common and significant hurdle with all chemotherapies. Tumors gain resistance by acquiring additional mutations. Some of the chemoresistance mechanisms are known and can be tackled. However, the majority of chemoresistance mechanisms are unknown. Our recent findings shed light on one such unknown mechanism. We identified a novel role for 5-hydroxymethycytosine (5hmC), an epigenetic mark on the DNA, in maintaining the integrity of stalled replication forks and its impact on genomic stability and chemoresistance.
    Keywords:  APE1; BRCA2; PARP inhibitors; TET2; chemoresistance; replication fork stability
    DOI:  https://doi.org/10.1080/23723556.2020.1827904
  6. Nucleic Acids Res. 2020 Nov 25. pii: gkaa1090. [Epub ahead of print]
    Yan Y, Xu Z, Huang J, Guo G, Gao M, Kim W, Zeng X, Kloeber JA, Zhu Q, Zhao F, Luo K, Lou Z.
      PrimPol has been recently identified as a DNA damage tolerant polymerase that plays an important role in replication stress response. However, the regulatory mechanisms of PrimPol are not well defined. In this study, we identify that the deubiquitinase USP36 interferes with degradation of PrimPol to regulate the replication stress response. Mechanistically, USP36 is deubiquitinated following DNA replication stress, which in turn facilitates its upregulation and interaction with PrimPol. USP36 deubiquitinates K29-linked polyubiquitination of PrimPol and increases its protein stability. Depletion of USP36 results in replication stress-related defects and elevates cell sensitivity to DNA-damage agents, such as cisplatin and olaparib. Moreover, USP36 expression positively correlates with the level of PrimPol protein and poor prognosis in patient samples. These findings indicate that the regulation of PrimPol K29-linked ubiquitination by USP36 plays a critical role in DNA replication stress and chemotherapy response.
    DOI:  https://doi.org/10.1093/nar/gkaa1090
  7. Front Oncol. 2020 ;10 581217
    Gachechiladze M, Skarda J, Bouchalova K, Soltermann A, Joerger M.
      Dysfunctional DNA repair with subsequent genome instability and high mutational burden represents a major hallmark of cancer. In established malignant tumors, increased DNA repair capacity mediates resistance to DNA-damaging therapeutics, including cytotoxic drugs, radiotherapy, and selected small molecules including inhibitors of poly (ADP-ribose) polymerase (PARP), Ataxia Telangiectasia Mutated (ATM), ataxia telangiectasia and Rad3-related protein (ATR), and Wee1 kinase (Wee1). In addition, DNA repair deficiency is not only associated with sensitivity to selected anticancer drugs, but also with increased mutagenicity and increased neoantigen load on tumor cells, resulting in increased immunogenicity and improved response to CTLA4- or PD-(L)1 targeting monoclonal antibodies. DNA damage response (DDR) is composed of complex signalling pathways, including the sensing of the DNA damage, signal transduction, cellular response pathways to DNA damage, and activation of DNA repair. DNA double strand breaks (DSBs) are the most dangerous form of DNA damage. Tumor cells are characterised by frequent accumulation of DSBs caused by either endogenous replication stress or the impact of cancer treatment, most prominently chemotherapy and radiotherapy. Therefore, response of cancer cells to DSBs represents a crucial mechanism for how tumors respond to systemic treatment or radiotherapy, and how resistance develops. Ample clinical evidence supports the importance of DDR associated kinases as predictive and prognostic biomarkers in cancer patients. The ATM-CHK2 and ATR-CHK1-WEE1 pathways initiate DNA DSB repair. In the current review, we focus on major DDR associated kinases including ATM, ATR, CHK1, CHK2, and WEE1, and discuss their potential prognostic and predictive value in solid malignancies.
    Keywords:  ATM; ATR; WEE1; inhibitor; prognostic
    DOI:  https://doi.org/10.3389/fonc.2020.581217
  8. Genes Chromosomes Cancer. 2020 Nov 27.
    Ali RMM, McIntosh SA, Savage KI.
      An underlying cause of breast cancers has been largely attributed to defects in the DNA damage response (DDR) pathway. In particular, the homologous recombination (HR) pathway repairs double-stranded breaks (DSBs) in DNA, ultimately protecting the cell from genomic instability and thus preventing the accumulation of transforming mutations. In line with this, mutations in a number of genes encoding HR proteins are a well-studied cause of HR deficiency (HRD), and, at the germline level, can confer risk to breast cancer but also occur somatically, contributing to sporadic breast cancer development, progression and response to therapy. Our understanding of the biological processes involved in HR and how these become compromised during breast cancer development has led to a better understanding of how HRD cells can be targeted with specific DNA damaging agents and/or with synthetic lethal targeting approaches such as PARP inhibition. Additionally, in vitro and preclinical modelling has supported the development of clinical trials to assess targeted therapies such as PARP inhibitors (PARPis), ultimately leading to development of therapies with greater clinical benefit. A number of challenges have been encountered, including resistance to therapy; however, addressing these challenges head-on and continually driving scientific research and clinical trials with innovative therapies will contribute to our ability to target HRD in breast cancers. Ongoing research efforts into HRD in breast cancer development are therefore essential, even in the era of targeted therapies, to provide innovative strategies for improved tumour responses. This article is protected by copyright. All rights reserved.
    Keywords:  DNA repair; PARP inhibitors; breast cancer; chemotherapy; homologous recombination
    DOI:  https://doi.org/10.1002/gcc.22921
  9. Mutat Res. 2020 Nov 02. pii: S0027-5107(20)30060-9. [Epub ahead of print]822 111727
    Tsukada K, Shimada M, Imamura R, Saikawa K, Ishiai M, Matsumoto Y.
      Polynucleotide kinase phosphatase (PNKP) has dual enzymatic activities as kinase and phosphatase for DNA ends, which are the prerequisite for the ligation, and thus is involved in base excision repair, single-strand break repair and non-homologous end joining for double-strand break (DSB) repair. In this study, we examined mechanisms for the recruitment of PNKP to DNA damage sites by laser micro-irradiation and live-cell imaging analysis using confocal microscope. We show that the forkhead-associated (FHA) domain of PNKP is essential for the recruitment of PNKP to DNA damage sites. Arg35 and Arg48 within the FHA domain are required for interactions with XRCC1 and XRCC4. PNKP R35A/R48A mutant failed to accumulate on the laser track and siRNA-mediated depletion of XRCC1 and/or XRCC4 reduced PNKP accumulation on the laser track, indicating that PNKP is recruited to DNA damage sites via the interactions between its FHA domain and XRCC1 or XRCC4. Furthermore, cells expressing PNKP R35A/R48A mutant exhibited increased sensitivity toward ionizing radiation in association with delayed SSB and DSB repair and genome instability, represented by micronuclei and chromosome bridges. Taken together, these findings revealed the importance of PNKP recruitment to DNA damage sites via its FHA domain for DNA repair and maintenance of genome stability.
    Keywords:  DNA repair; Genome stability; PNKP; The FHA domain
    DOI:  https://doi.org/10.1016/j.mrfmmm.2020.111727
  10. Curr Genet. 2020 Nov 25.
    Paeschke K, Burkovics P.
      The coordinated action of DNA polymerases and DNA helicases is essential at genomic sites that are hard to replicate. Among these are sites that harbour G-quadruplex DNA structures (G4). G4s are stable alternative DNA structures, which have been implicated to be involved in important cellular processes like the regulation of gene expression or telomere maintenance. G4 structures were shown to hinder replication fork progression and cause genomic deletions, mutations and recombination events. Many helicases unwind G4 structures and preserve genome stability, but a detailed understanding of G4 replication and the re-start of stalled replication forks around formed G4 structures is not clear, yet. In our recent study, we identified that Mgs1 preferentially binds to G4 DNA structures in vitro and is associated with putative G4-forming chromosomal regions in vivo. Mgs1 binding to G4 motifs in vivo is partially dependent on the helicase Pif1. Pif1 is the major G4-unwinding helicase in S. cerevisiae. In the absence of Mgs1, we determined elevated gross chromosomal rearrangement (GCR) rates in yeast, similar to Pif1 deletion. Here, we highlight the recent findings and set these into context with a new mechanistic model. We propose that Mgs1's functions support DNA replication at G4-forming regions.
    Keywords:  G-quadruplex; Genome stability; Mgs1; Replication
    DOI:  https://doi.org/10.1007/s00294-020-01128-1
  11. EMBO Mol Med. 2020 Nov 24. e12391
    Zhou Z, Huang F, Shrivastava I, Zhu R, Luo A, Hottiger M, Bahar I, Liu Z, Cristofanilli M, Wan Y.
      KLF4 plays a critical role in determining cell fate responding to various stresses or oncogenic signaling. Here, we demonstrated that KLF4 is tightly regulated by poly(ADP-ribosyl)ation (PARylation). We revealed the subcellular compartmentation for KLF4 is orchestrated by PARP1-mediated PARylation. We identified that PARylation of KLF4 is critical to govern KLF4 transcriptional activity through recruiting KLF4 from soluble nucleus to the chromatin. We mapped molecular motifs on KLF4 and PARP1 that facilitate their interaction and unveiled the pivotal role of the PBZ domain YYR motif (Y430, Y451 and R452) on KLF4 in enabling PARP1-mediated PARylation of KLF4. Disruption of KLF4 PARylation results in failure in DNA damage response. Depletion of KLF4 by RNA interference or interference with PARP1 function by KLF4YYR/AAA (a PARylation-deficient mutant) significantly sensitizes breast cancer cells to PARP inhibitors. We further demonstrated the role of KLF4 in modulating homologous recombination through regulating BRCA1 transcription. Our work points to the synergism between KLF4 and PARP1 in tumorigenesis and cancer therapy, which provides a potential new therapeutic strategy for killing BRCA1-proficient triple-negative breast cancer cells.
    Keywords:  DNA damage response; DNA repair; KLF4; PARP1; tumorigenesis and therapeutics
    DOI:  https://doi.org/10.15252/emmm.202012391
  12. Cancer Res. 2020 Nov 25. pii: canres.2626.2020. [Epub ahead of print]
    Prodhomme MK, Pommier RM, Franchet C, Fauvet F, Bergoglio V, Brousset P, Morel AP, Brunac AC, Devouassoux-Shisheboran M, Petrilli V, Moyret-Lalle C, Hoffmann JS, Puisieux A, Tissier A.
      A characteristic of cancer development is the acquisition of genomic instability, which results from the inaccurate repair of DNA damage. Among double-strand break repair mechanisms induced by oncogenic stress, the highly mutagenic theta-mediated end joining (TMEJ) pathway, which requires DNA polymerase theta (POLθ) encoded by the POLQ gene, has been shown to be overexpressed in several human cancers. However, little is known regarding the regulatory mechanisms of TMEJ and the consequence of its dysregulation. In this study, we combine a bioinformatics approach exploring both METABRIC and TCGA databases with CRISPR/Cas9-mediated depletion of the zinc finger E-box binding homeobox 1 (ZEB1) in claudin-low tumor cells or forced expression of ZEB1 in basal-like tumor cells, two triple-negative breast cancer (TNBC) subtypes, to demonstrate that ZEB1 represses POLQ expression. ZEB1, a master EMT inducing-transcription factor, interacted directly with the POLQ promoter. Moreover, downregulation of POLQ by ZEB1 fostered micronuclei formation in TNBC tumor cell lines. Consequently, ZEB1 expression prevented TMEJ activity, with a major impact on genome integrity. In conclusion, we showed that ZEB1 directly inhibits the expression of POLQ and therefore TMEJ activity, controlling both stability and integrity of breast cancer cell genomes.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-20-2626
  13. Mol Cell Oncol. 2020 ;7(6): 1801089
    Duan H, Pathania S.
      We recently identified E3 ligase RFWD3 as a modulator of stalled fork stability in BRCA2-deficient cells. We also show that BRCA1 might function upstream of BRCA2 during fork repair and that blocking fork degradation by depleting MRE11 does not guarantee fork repair. These findings provide new insights into the workings of BRCA1 and BRCA2 in the stalled fork repair pathway.
    Keywords:  BRCA1; BRCA2; MRE11; RFWD3; RPA ubiquitination; SMARCAL1; replication stress
    DOI:  https://doi.org/10.1080/23723556.2020.1801089
  14. Nucleic Acids Res. 2020 Nov 27. pii: gkaa1110. [Epub ahead of print]
    Chong SJF, Iskandar K, Lai JXH, Qu J, Raman D, Valentin R, Herbaux C, Collins M, Low ICC, Loh T, Davids M, Pervaiz S.
      Bcl-2 phosphorylation at serine-70 (S70pBcl2) confers resistance against drug-induced apoptosis. Nevertheless, its specific mechanism in driving drug-resistance remains unclear. We present evidence that S70pBcl2 promotes cancer cell survival by acting as a redox sensor and modulator to prevent oxidative stress-induced DNA damage and execution. Increased S70pBcl2 levels are inversely correlated with DNA damage in chronic lymphocytic leukemia (CLL) and lymphoma patient-derived primary cells as well as in reactive oxygen species (ROS)- or chemotherapeutic drug-treated cell lines. Bioinformatic analyses suggest that S70pBcl2 is associated with lower median overall survival in lymphoma patients. Empirically, sustained expression of the redox-sensitive S70pBcl2 prevents oxidative stress-induced DNA damage and cell death by suppressing mitochondrial ROS production. Using cell lines and lymphoma primary cells, we further demonstrate that S70pBcl2 reduces the interaction of Bcl-2 with the mitochondrial complex-IV subunit-5A, thereby reducing mitochondrial complex-IV activity, respiration and ROS production. Notably, targeting S70pBcl2 with the phosphatase activator, FTY720, is accompanied by an enhanced drug-induced DNA damage and cell death in CLL primary cells. Collectively, we provide a novel facet of the anti-apoptotic Bcl-2 by demonstrating that its phosphorylation at serine-70 functions as a redox sensor to prevent drug-induced oxidative stress-mediated DNA damage and execution with potential therapeutic implications.
    DOI:  https://doi.org/10.1093/nar/gkaa1110
  15. Biochemistry. 2020 Nov 27.
    Li M, Sengupta B, Benkovic SJ, Lee TH, Hedglin M.
      Translesion DNA synthesis (TLS) enables DNA replication through damaging modifications to template DNA and requires monoubiquitination of the proliferating cell nuclear antigen (PCNA) sliding clamp by the Rad6/Rad18 complex. This posttranslational modification is critical to cell survival following exposure to DNA-damaging agents and is tightly regulated to restrict TLS to damaged DNA. Replication protein A (RPA), the major single-strand DNA (ssDNA) binding protein complex, forms filaments on ssDNA exposed at TLS sites and plays critical yet undefined roles in regulating PCNA monoubiquitination. Here, we utilize kinetic assays and single-molecule FRET microscopy to monitor PCNA monoubiquitination and Rad6/Rad18 complex dynamics on RPA filaments, respectively. Results reveal that a Rad6/Rad18 complex is recruited to an RPA filament via Rad18·RPA interactions and randomly translocates along the filament. These translocations promote productive interactions between the Rad6/Rad18 complex and the resident PCNA, significantly enhancing monoubiquitination. These results illuminate critical roles of RPA in the specificity and efficiency of PCNA monoubiquitination and represent, to the best of our knowledge, the first example of ATP-independent translocation of a protein complex along a protein filament.
    DOI:  https://doi.org/10.1021/acs.biochem.0c00849
  16. Nature. 2020 Nov 25.
    Markiewicz-Potoczny M, Lobanova A, Loeb AM, Kirak O, Olbrich T, Ruiz S, Lazzerini Denchi E.
      In mammals, telomere protection is mediated by the essential protein TRF2, which binds chromosome ends and ensures genome integrity1,2. TRF2 depletion results in end-to-end chromosome fusions in all cell types that have been tested so far. Here we find that TRF2 is dispensable for the proliferation and survival of mouse embryonic stem (ES) cells. Trf2-/- (also known as Terf2) ES cells do not exhibit telomere fusions and can be expanded indefinitely. In response to the deletion of TRF2, ES cells exhibit a muted DNA damage response that is characterized by the recruitment of γH2AX-but not 53BP1-to telomeres. To define the mechanisms that control this unique DNA damage response in ES cells, we performed a CRISPR-Cas9-knockout screen. We found a strong dependency of TRF2-null ES cells on the telomere-associated protein POT1B and on the chromatin remodelling factor BRD2. Co-depletion of POT1B or BRD2 with TRF2 restores a canonical DNA damage response at telomeres, resulting in frequent telomere fusions. We found that TRF2 depletion in ES cells activates a totipotent-like two-cell-stage transcriptional program that includes high levels of ZSCAN4. We show that the upregulation of ZSCAN4 contributes to telomere protection in the absence of TRF2. Together, our results uncover a unique response to telomere deprotection during early development.
    DOI:  https://doi.org/10.1038/s41586-020-2959-4
  17. Cell Death Dis. 2020 Nov 26. 11(11): 1012
    Bouzidi A, Magnifico MC, Paiardini A, Macone A, Boumis G, Giardina G, Rinaldo S, Liberati FR, Lauro C, Limatola C, Lanzillotta C, Tramutola A, Perluigi M, Sgarbi G, Solaini G, Baracca A, Paone A, Cutruzzolà F.
      Nutrient utilization and reshaping of metabolism in cancer cells is a well-known driver of malignant transformation. Less clear is the influence of the local microenvironment on metastasis formation and choice of the final organ to invade. Here we show that the level of the amino acid serine in the cytosol affects the migratory properties of lung adenocarcinoma (LUAD) cells. Inhibition of serine or glycine uptake from the extracellular milieu, as well as knockdown of the cytosolic one-carbon metabolism enzyme serine hydroxymethyltransferase (SHMT1), abolishes migration. Using rescue experiments with a brain extracellular extract, and direct measurements, we demonstrate that cytosolic serine starvation controls cell movement by increasing reactive oxygen species formation and decreasing ATP levels, thereby promoting activation of the AMP sensor kinase (AMPK) by phosphorylation. Activation of AMPK induces remodeling of the cytoskeleton and finally controls cell motility. These results highlight that cytosolic serine metabolism plays a key role in controlling motility, suggesting that cells are able to dynamically exploit the compartmentalization of this metabolism to adapt their metabolic needs to different cell functions (movement vs. proliferation). We propose a model to explain the relevance of serine/glycine metabolism in the preferential colonization of the brain by LUAD cells and suggest that the inhibition of serine/glycine uptake and/or cytosolic SHMT1 might represent a successful strategy to limit the formation of brain metastasis from primary tumors, a major cause of death in these patients.
    DOI:  https://doi.org/10.1038/s41419-020-03215-0
  18. Mol Cell Oncol. 2020 Aug 31. 7(6): 1805256
    Xuan J, Pearson RB, Sanij E.
      Acquired drug resistance leads to poor clinical outcome in high grade serous ovarian cancer (HGSOC). We have demonstrated the efficacy of the novel drug CX-5461 in HGSOC is mediated through destabilization of DNA replication forks. The data highlights the potential of CX-5461 in overcoming a general mechanism of chemotherapeutic resistance.
    Keywords:  CX-5461; Ovarian cancer; PARPI; drug resistance
    DOI:  https://doi.org/10.1080/23723556.2020.1805256
  19. Chem Rev. 2020 Nov 24.
    Wright NJ, Lee SY.
      Nucleosides play central roles in all facets of life, from metabolism to cellular signaling. Because of their physiochemical properties, nucleosides are lipid bilayer impermeable and thus rely on dedicated transport systems to cross biological membranes. In humans, two unrelated protein families mediate nucleoside membrane transport: the concentrative and equilibrative nucleoside transporter families. The objective of this review is to provide a broad outlook on the current status of nucleoside transport research. We will discuss the role played by nucleoside transporters in human health and disease, with emphasis placed on recent structural advancements that have revealed detailed molecular principles of these important cellular transport systems and exploitable pharmacological features.
    DOI:  https://doi.org/10.1021/acs.chemrev.0c00644
  20. Leuk Lymphoma. 2020 Nov 22. 1-8
    Harrop S, Polliack A, Tam CS.
      The low grade chronic lymphoproliferative disorders include chronic lymphocytic leukemia, Waldenstroms macroglobulinemia, follicular lymphoma and hairy cell leukemia. Traditionally considered incurable, these disorders have been associated with a risk of haematological and solid organ malignancies secondary to both the underlying disease and the associated treatment. The introduction of purine analogues into treatment paradigms has seen increased rates of therapy related myelodysplasia reported and it remains unclear yet on the impact the targeted novel therapies play in the development of secondary cancers. We review the rates of secondary malignancy in the chronic lymphoproliferative disorders with a particular focus on the role of the purine analogues in the development of therapy related MDS.
    Keywords:  CLL; ; fludarabine; ; myelodysplastic syndrome
    DOI:  https://doi.org/10.1080/10428194.2020.1849682