bims-numges 2020-05-24 papers

bims-numges

Biomed News

on Nucleotide metabolism and genome stability

Issue of 2020–05–24
37 papers selected by
Sean Rudd, Karolinska Institutet

HLTF Promotes Fork Reversal, Limiting Replication Stress Resistance and Preventing Multiple Mechanisms of Unrestrained DNA Synthesis.
UAP56/DDX39B is a major cotranscriptional RNA-DNA helicase that unwinds harmful R loops genome-wide.
Homologous recombination and Mus81 promote replication completion in response to replication fork blockage.
Combined PARP and ATR inhibition potentiates genome instability and cell death in ATM-deficient cancer cells.
The 6-4 photoproduct is the trigger of UV-induced replication blockage and ATR activation.
Hypoxia Drives the Assembly of the Multi-Enzyme Purinosome Complex.
PAICS, a De Novo Purine Biosynthetic Enzyme, Is Overexpressed in Pancreatic Cancer and Is Involved in Its Progression.
Mammalian Nudix proteins cleave nucleotide metabolite caps on RNAs.
Physiological levels of folic acid reveal purine alterations in Lesch-Nyhan disease.
Enhancing the Antiviral Efficacy of RNA-Dependent RNA Polymerase Inhibition by Combination with Modulators of Pyrimidine Metabolism.
Molecular mechanisms and cellular functions of cGAS-STING signalling.
Emerging functions of Fanconi Anemia genes in replication fork protection pathways.
The dark side of RNA:DNA hybrids.
Replication Fork Remodeling and Therapy Escape in DNA Damage Response-Deficient Cancers.
New insights into abasic site repair and tolerance.
Chromatin as a key consumer in the metabolite economy.
RecQ Family Helicases in Replication Fork Remodeling and Repair: Opening New Avenues Towards Identification of Potential Targets for Cancer Chemotherapy.
Hypermutation in single-stranded DNA.
Mdm4 supports DNA replication in a p53-independent fashion.
HDAC1 modulates OGG1-initiated oxidative DNA damage repair in the aging brain and Alzheimer's disease.
Interaction between RECQL4 and OGG1 promotes repair of oxidative base lesion 8-oxoG and is regulated by SIRT1 deacetylase.
Persistent DNA damage-induced NLRP12 improves hematopoietic stem cell function.
Germline Mutation in MUS81 Resulting in Impaired Protein Stability is Associated with Familial Breast and Thyroid Cancer.
Parallel CRISPR-Cas9 screens clarify impacts of p53 on screen performance.
Activation-induced cytidine deaminase can target multiple topologies of double-stranded DNA in a transcription-independent manner.
Histone H2A variants alpha1-extension helix directs RNF168-mediated ubiquitination.
Interaction with single-stranded DNA-binding protein localizes ribonuclease HI to DNA replication forks and facilitates R-loop removal.
Tau affects P53 function and cell fate during the DNA damage response.
Preliminary study on the function of the POLD1 (CDC2) EXON2 c.56G>A mutation.
Disassembly of the Shieldin Complex by TRIP13.
RIF1 controls replication initiation and homologous recombination repair in a radiation dose-dependent manner.
RNF8 has both KU-dependent and independent roles in chromosomal break repair.
Opposing p53 and mTOR/AKT promote an in vivo switch from apoptosis to senescence upon telomere shortening in zebrafish.
Dietary serine-microbiota interaction enhances chemotherapeutic toxicity without altering drug conversion.
Metabolic Adaptation during nab-Paclitaxel Resistance in Pancreatic Cancer Cell Lines.
Enzyme-mediated depletion of serum l-Met abrogates prostate cancer growth via multiple mechanisms without evidence of systemic toxicity.
Reprogramming of serine, glycine and one-carbon metabolism in cancer.

Mol Cell. 2020 May 19. pii: S1097-2765(20)30273-2. [Epub ahead of print]

HLTF Promotes Fork Reversal, Limiting Replication Stress Resistance and Preventing Multiple Mechanisms of Unrestrained DNA Synthesis.

Gongshi Bai, Chames Kermi, Henriette Stoy, Carl J Schiltz, Julien Bacal, Angela M Zaino, M Kyle Hadden, Brandt F Eichman, Massimo Lopes, Karlene A Cimprich.

  DNA replication stress can stall replication forks, leading to genome instability. DNA damage tolerance pathways assist fork progression, promoting replication fork reversal, translesion DNA synthesis (TLS), and repriming. In the absence of the fork remodeler HLTF, forks fail to slow following replication stress, but underlying mechanisms and cellular consequences remain elusive. Here, we demonstrate that HLTF-deficient cells fail to undergo fork reversal in vivo and rely on the primase-polymerase PRIMPOL for repriming, unrestrained replication, and S phase progression upon limiting nucleotide levels. By contrast, in an HLTF-HIRAN mutant, unrestrained replication relies on the TLS protein REV1. Importantly, HLTF-deficient cells also exhibit reduced double-strand break (DSB) formation and increased survival upon replication stress. Our findings suggest that HLTF promotes fork remodeling, preventing other mechanisms of replication stress tolerance in cancer cells. This remarkable plasticity of the replication fork may determine the outcome of replication stress in terms of genome integrity, tumorigenesis, and response to chemotherapy.

Keywords:  DNA replication, replication stress response, fork reversal, HLTF, PRIMPOL, REV1, DNA damage tolerance, translesion synthesis, ATR inhibition, replication catastrophe

DOI:  https://doi.org/10.1016/j.molcel.2020.04.031
Genes Dev. 2020 May 21.

UAP56/DDX39B is a major cotranscriptional RNA-DNA helicase that unwinds harmful R loops genome-wide.

Carmen Pérez-Calero, Aleix Bayona-Feliu, Xiaoyu Xue, Sonia I Barroso, Sergio Muñoz, Víctor M González-Basallote, Patrick Sung, Andrés Aguilera.

  Nonscheduled R loops represent a major source of DNA damage and replication stress. Cells have different ways to prevent R-loop accumulation. One mechanism relies on the conserved THO complex in association with cotranscriptional RNA processing factors including the RNA-dependent ATPase UAP56/DDX39B and histone modifiers such as the SIN3 deacetylase in humans. We investigated the function of UAP56/DDX39B in R-loop removal. We show that UAP56 depletion causes R-loop accumulation, R-loop-mediated genome instability, and replication fork stalling. We demonstrate an RNA-DNA helicase activity in UAP56 and show that its overexpression suppresses R loops and genome instability induced by depleting five different unrelated factors. UAP56/DDX39B localizes to active chromatin and prevents the accumulation of RNA-DNA hybrids over the entire genome. We propose that, in addition to its RNA processing role, UAP56/DDX39B is a key helicase required to eliminate harmful cotranscriptional RNA structures that otherwise would block transcription and replication.

Keywords:  R loops; RNA–DNA helicase; RNA–DNA hybrids; UAP56/DDX39B; double-strand breaks; genome instability; replication fork stalling

DOI:  https://doi.org/10.1101/gad.336024.119
EMBO Rep. 2020 May 17. e49367

Homologous recombination and Mus81 promote replication completion in response to replication fork blockage.

Benjamin Pardo, María Moriel-Carretero, Thibaud Vicat, Andrés Aguilera, Philippe Pasero.

  Impediments to DNA replication threaten genome stability. The homologous recombination (HR) pathway has been involved in the restart of blocked replication forks. Here, we used a method to increase yeast cell permeability in order to study at the molecular level the fate of replication forks blocked by DNA topoisomerase I poisoning by camptothecin (CPT). Our results indicate that Rad52 and Rad51 HR factors are required to complete DNA replication in response to CPT. Recombination events occurring during S phase do not generally lead to the restart of DNA synthesis but rather protect blocked forks until they merge with convergent forks. This fusion generates structures requiring their resolution by the Mus81 endonuclease in G2 /M. At the global genome level, the multiplicity of replication origins in eukaryotic genomes and the fork protection mechanism provided by HR appear therefore to be essential to complete DNA replication in response to fork blockage.

Keywords:  BIR; Mus81; fork restart; recombination; replication

DOI:  https://doi.org/10.15252/embr.201949367
Oncogene. 2020 May 23.

Combined PARP and ATR inhibition potentiates genome instability and cell death in ATM-deficient cancer cells.

Rebecca L Lloyd, Paul W G Wijnhoven, Antonio Ramos-Montoya, Zena Wilson, Giuditta Illuzzi, Katarzyna Falenta, Gemma N Jones, Neil James, Christophe D Chabbert, Jonathan Stott, Emma Dean, Alan Lau, Lucy A Young.

The poly (ADP-ribose) polymerase (PARP) inhibitor olaparib is FDA approved for the treatment of BRCA-mutated breast, ovarian and pancreatic cancers. Olaparib inhibits PARP1/2 enzymatic activity and traps PARP1 on DNA at single-strand breaks, leading to replication-induced DNA damage that requires BRCA1/2-dependent homologous recombination repair. Moreover, DNA damage response pathways mediated by the ataxia-telangiectasia mutated (ATM) and ataxia-telangiectasia mutated and Rad3-related (ATR) kinases are hypothesised to be important survival pathways in response to PARP-inhibitor treatment. Here, we show that olaparib combines synergistically with the ATR-inhibitor AZD6738 (ceralasertib), in vitro, leading to selective cell death in ATM-deficient cells. We observe that 24 h olaparib treatment causes cells to accumulate in G2-M of the cell cycle, however, co-administration with AZD6738 releases the olaparib-treated cells from G2 arrest. Selectively in ATM-knockout cells, we show that combined olaparib/AZD6738 treatment induces more chromosomal aberrations and achieves this at lower concentrations and earlier treatment time-points than either monotherapy. Furthermore, single-agent olaparib efficacy in vitro requires PARP inhibition throughout multiple rounds of replication. Here, we demonstrate in several ATM-deficient cell lines that the olaparib and AZD6738 combination induces cell death within 1-2 cell divisions, suggesting that combined treatment could circumvent the need for prolonged drug exposure. Finally, we demonstrate in vivo combination activity of olaparib and AZD6738 in xenograft and PDX mouse models with complete ATM loss. Collectively, these data provide a mechanistic understanding of combined PARP and ATR inhibition in ATM-deficient models, and support the clinical development of AZD6738 in combination with olaparib.

DOI: https://doi.org/10.1038/s41388-020-1328-y
Proc Natl Acad Sci U S A. 2020 May 22. pii: 201917196. [Epub ahead of print]

The 6-4 photoproduct is the trigger of UV-induced replication blockage and ATR activation.

Kai-Feng Hung, Julia M Sidorova, Paul Nghiem, Masaoki Kawasumi.

  The most prevalent human carcinogen is sunlight-associated ultraviolet (UV), a physiologic dose of which generates thousands of DNA lesions per cell, mostly of two types: cyclobutane pyrimidine dimers (CPDs) and 6-4 photoproducts (6-4PPs). It has not been possible, in living cells, to precisely characterize the respective contributions of these two lesion types to the signals that regulate cell cycle progression, DNA replication, and cell survival. Here we coupled multiparameter flow cytometry with lesion-specific photolyases that eliminate either CPDs or 6-4PPs and determined their respective contributions to DNA damage responses. Strikingly, only 6-4PP lesions activated the ATR-Chk1 DNA damage response pathway. Mechanistically, 6-4PPs, but not CPDs, impeded DNA replication across the genome as revealed by microfluidic-assisted replication track analysis. Furthermore, single-stranded DNA accumulated preferentially at 6-4PPs during DNA replication, indicating selective and prolonged replication blockage at 6-4PPs. These findings suggest that 6-4PPs, although eightfold fewer in number than CPDs, are the trigger for UV-induced DNA damage responses.

Keywords:  6-4PP; CPD; Chk1; DNA damage response; DNA replication

DOI:  https://doi.org/10.1073/pnas.1917196117
J Biol Chem. 2020 May 21. pii: jbc.RA119.012175. [Epub ahead of print]

Hypoxia Drives the Assembly of the Multi-Enzyme Purinosome Complex.

Cyrielle Doigneaux, Anthony M Pedley, Ishna N Mistry, Monika Papayova, Stephen J Benkovic, Ali Tavassoli.

  The purinosome is a dynamic metabolic complex composed of enzymes responsible for de novo purine biosynthesis, whose formation has been associated with elevated purine demand. However, the physiological conditions that govern purinosome formation in cells remain unknown. Here, we report that purinosome formation is up-regulated in cells in response to a low-oxygen microenvironment (hypoxia). We demonstrate that increased purinosome assembly in hypoxic human cells requires the activation of hypoxia inducible factor 1 (HIF-1) and not HIF-2. Hypoxia-driven purinosome assembly was inhibited in cells lacking 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase (ATIC), a single enzyme in de novo purine biosynthesis, and in cells treated with a small molecule inhibitor of ATIC homodimerization. However, despite the increase in purinosome assembly in hypoxia, we observed no associated increase in de novo purine biosynthesis was observed in cells. Our results indicate that this was likely due to a reduction in mitochondrial one-carbon metabolism, resulting in reduced mitochondrion-derived one-carbon units needed for de novo purine biosynthesis. The findings of our study further clarify and deepen our understanding of purinosome formation by revealing that this process does not solely depend on cellular purine demand.

Keywords:  5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase (ATIC); cell metabolism; de novo purine biosynthesis; hypoxia; hypoxia-inducible factor (HIF); metabolism; metabolon; purine; purinosome

DOI:  https://doi.org/10.1074/jbc.RA119.012175
Transl Oncol. 2020 May 14. pii: S1936-5233(20)30104-2. [Epub ahead of print]13(7): 100776

PAICS, a De Novo Purine Biosynthetic Enzyme, Is Overexpressed in Pancreatic Cancer and Is Involved in Its Progression.

Sumit Agarwal, Balabhadrapatruni V S K Chakravarthi, Hyung-Gyoon Kim, Nirzari Gupta, Kevin Hale, Sai Akshaya Hodigere Balasubramanya, Patsy G Oliver, Dafydd G Thomas, Isam-Eldin A Eltoum, Donald J Buchsbaum, Upender Manne, Sooryanarayana Varambally.

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer with an extremely poor prognosis. There is an urgent need to identify new therapeutic targets and also understand the mechanism of PDAC progression that leads to aggressiveness of the disease. To find therapeutic targets, we analyzed data related to PDAC transcriptome sequencing and found overexpression of the de novo purine metabolic enzyme phosphoribosylaminoimidazole succinocarboxamide synthetase (PAICS). Immunohistochemical analysis of PDAC tissues showed high expression of the PAICS protein. To assess the biological roles of PAICS, we used RNA interference and knock down of its expression in PDAC cell lines that caused a reduction in PDAC cell proliferation and invasion. Furthermore, results of chorioallantoic membrane assays and pancreatic cancer xenografts demonstrated that PAICS regulated pancreatic tumor growth. Our data also showed that, in PDAC cells, microRNA-128 regulates and targets PAICS. PAICS depletion in PDAC cells caused upregulation in E-cadherin, a marker of the epithelial-mesenchymal transition. In PDAC cells, a BET inhibitor, JQ1, reduced PAICS expression. Thus, our investigations show that PAICS is a therapeutic target for PDAC and, as an enzyme, is amenable to targeting by small molecules.

DOI: https://doi.org/10.1016/j.tranon.2020.100776
Nucleic Acids Res. 2020 May 20. pii: gkaa402. [Epub ahead of print]

Mammalian Nudix proteins cleave nucleotide metabolite caps on RNAs.

Sunny Sharma, Ewa Grudzien-Nogalska, Keith Hamilton, Xinfu Jiao, Jun Yang, Liang Tong, Megerditch Kiledjian.

We recently reported the presence of nicotinamide adenine dinucleotide (NAD)-capped RNAs in mammalian cells and a role for DXO and the Nudix hydrolase Nudt12 in decapping NAD-capped RNAs (deNADding) in cells. Analysis of 5'caps has revealed that in addition to NAD, mammalian RNAs also contain other metabolite caps including flavin adenine dinucleotide (FAD) and dephosphoCoA (dpCoA). In the present study we systematically screened all mammalian Nudix proteins for their potential deNADing, FAD cap decapping (deFADding) and dpCoA cap decapping (deCoAping) activity. We demonstrate that Nudt16 is a novel deNADding enzyme in mammalian cells. Additionally, we identified seven Nudix proteins-Nudt2, Nudt7, Nudt8, Nudt12, Nudt15, Nudt16 and Nudt19, to possess deCoAping activity in vitro. Moreover, our screening revealed that both mammalian Nudt2 and Nudt16 hydrolyze FAD-capped RNAs in vitro with Nudt16 regulating levels of FAD-capped RNAs in cells. All decapping activities identified hydrolyze the metabolite cap substrate within the diphosphate linkage. Crystal structure of human Nudt16 in complex with FAD at 2.7 Å resolution provide molecular insights into the binding and metal-coordinated hydrolysis of FAD by Nudt16. In summary, our study identifies novel cellular deNADding and deFADding enzymes and establishes a foundation for the selective functionality of the Nudix decapping enzymes on non-canonical metabolite caps.

DOI: https://doi.org/10.1093/nar/gkaa402
Proc Natl Acad Sci U S A. 2020 May 19. pii: 202003475. [Epub ahead of print]

Physiological levels of folic acid reveal purine alterations in Lesch-Nyhan disease.

José M López, Esther L Outtrim, Rong Fu, Diane J Sutcliffe, Rosa J Torres, H A Jinnah.

  Lesch-Nyhan disease (LND), caused by a deficient salvage purine pathway, is characterized by severe neurological manifestations and uric acid overproduction. However, uric acid is not responsible for brain dysfunction, and it has been suggested that purine nucleotide depletion, or accumulation of other toxic purine intermediates, could be more relevant. Here we show that purine alterations in LND fibroblasts depend on the level of folic acid in the culture media. Thus, physiological levels of folic acid induce accumulation of 5-aminoimidazole-4-carboxamide riboside 5'-monophosphate (ZMP), an intermediary of de novo purine biosynthetic pathway, and depletion of ATP. Additionally, Z-nucleotide derivatives (AICAr, AICA) are detected at high levels in the urine of patients with LND and its variants (hypoxanthine-guanine phosphoribosyltransferase [HGprt]-related neurological dysfunction and HGprt-related hyperuricemia), and the ratio of AICAr/AICA is significantly increased in patients with neurological problems (LND and HGprt-related neurological dysfunction). Moreover, AICAr is present in the cerebrospinal fluid of patients with LND, but not in control individuals. We hypothesize that purine alterations detected in LND fibroblasts may also occur in the brain of patients with LND.

Keywords:  AICAr; Lesch-Nyhan disease; ZMP; folic acid; purines

DOI:  https://doi.org/10.1073/pnas.2003475117
Cell Chem Biol. 2020 May 19. pii: S2451-9456(20)30148-3. [Epub ahead of print]

Enhancing the Antiviral Efficacy of RNA-Dependent RNA Polymerase Inhibition by Combination with Modulators of Pyrimidine Metabolism.

Qi Liu, Amita Gupta, Ayse Okesli-Armlovich, Wenjie Qiao, Curt R Fischer, Mark Smith, Jan E Carette, Michael C Bassik, Chaitan Khosla.

  Genome-wide analysis of the mode of action of GSK983, a potent antiviral agent, led to the identification of dihydroorotate dehydrogenase as its target along with the discovery that genetic knockdown of pyrimidine salvage sensitized cells to GSK983. Because GSK983 is an ineffective antiviral in the presence of physiological uridine concentrations, we explored combining GSK983 with pyrimidine salvage inhibitors. We synthesized and evaluated analogs of cyclopentenyl uracil (CPU), an inhibitor of uridine salvage. We found that CPU was converted into its triphosphate in cells. When combined with GSK983, CPU resulted in large drops in cellular UTP and CTP pools. Consequently, CPU-GSK983 suppressed dengue virus replication in the presence of physiological concentrations of uridine. In addition, the CPU-GSK983 combination markedly enhanced the effect of RNA-dependent RNA polymerase (RdRp) inhibition on viral infection. Our findings highlight a new host-targeting strategy for potentiating the antiviral activity of RdRp inhibitors.

Keywords:  RNA-dependent RNA polymerase; antiviral therapy; combination; cytidine monophosphate kinase; dengue; dihydroorotate dehydrogenase; pyrimidine metabolism; uridine-cytidine kinase

DOI:  https://doi.org/10.1016/j.chembiol.2020.05.002
Nat Rev Mol Cell Biol. 2020 May 18.

Molecular mechanisms and cellular functions of cGAS-STING signalling.

Karl-Peter Hopfner, Veit Hornung.

The cGAS-STING signalling axis, comprising the synthase for the second messenger cyclic GMP-AMP (cGAS) and the cyclic GMP-AMP receptor stimulator of interferon genes (STING), detects pathogenic DNA to trigger an innate immune reaction involving a strong type I interferon response against microbial infections. Notably however, besides sensing microbial DNA, the DNA sensor cGAS can also be activated by endogenous DNA, including extranuclear chromatin resulting from genotoxic stress and DNA released from mitochondria, placing cGAS-STING as an important axis in autoimmunity, sterile inflammatory responses and cellular senescence. Initial models assumed that co-localization of cGAS and DNA in the cytosol defines the specificity of the pathway for non-self, but recent work revealed that cGAS is also present in the nucleus and at the plasma membrane, and such subcellular compartmentalization was linked to signalling specificity of cGAS. Further confounding the simple view of cGAS-STING signalling as a response mechanism to infectious agents, both cGAS and STING were shown to have additional functions, independent of interferon response. These involve non-catalytic roles of cGAS in regulating DNA repair and signalling via STING to NF-κB and MAPK as well as STING-mediated induction of autophagy and lysosome-dependent cell death. We have also learnt that cGAS dimers can multimerize and undergo liquid-liquid phase separation to form biomolecular condensates that could importantly regulate cGAS activation. Here, we review the molecular mechanisms and cellular functions underlying cGAS-STING activation and signalling, particularly highlighting the newly emerging diversity of this signalling pathway and discussing how the specificity towards normal, damage-induced and infection-associated DNA could be achieved.

DOI: https://doi.org/10.1038/s41580-020-0244-x
Hum Mol Genet. 2020 May 18. pii: ddaa087. [Epub ahead of print]

Emerging functions of Fanconi Anemia genes in replication fork protection pathways.

Arun Mouli Kolinjivadi, Wayne Crismani, Joanne Ngeow.

Germline mutations in Fanconi Anemia (FA) genes predispose to chromosomes instability syndromes, such as FA and cancers. FA gene products have traditionally been studied for their role in inter-strand cross link (ICL) repair. A fraction of FA gene products are classical Homologous Recombination (HR) factors that are involved in repairing DNA Double Strand Breaks (DSB's) in an error-free manner. Emerging evidence suggests that, independent of ICL and HR repair, FA genes protect DNA replication forks in the presence of replication stress. Therefore, understanding the precise function of FA genes and their role in promoting genome stability in response to DNA replication stress is crucial for diagnosing FA and FA-associated cancers. Moreover, molecular understanding of the FA pathway will greatly help to establish proper functional assays for Variants of Unknown Significance (VUS), often encountered in clinics. In this short review, we discuss the recently uncovered molecular details of FA genes in replication fork protection pathways. Finally, we examine how novel FA variants predispose to FA and cancer, due to defective replication fork protection activity.

DOI: https://doi.org/10.1093/hmg/ddaa087
Mutat Res. 2020 Apr - Jun;784:pii: S1383-5742(19)30094-8. [Epub ahead of print]784 108300

The dark side of RNA:DNA hybrids.

Alessandra Brambati, Luca Zardoni, Eleonora Nardini, Achille Pellicioli, Giordano Liberi.

  RNA:DNA hybrids form when nascent transcripts anneal to the DNA template strand or any homologous DNA region. Co-transcriptional RNA:DNA hybrids, organized in R-loop structures together with the displaced non-transcribed strand, assist gene expression, DNA repair and other physiological cellular functions. A dark side of the matter is that RNA:DNA hybrids are also a cause of DNA damage and human diseases. In this review, we summarize recent advances in the understanding of the mechanisms by which the impairment of hybrid turnover promotes DNA damage and genome instability via the interference with DNA replication and DNA double-strand break repair. We also discuss how hybrids could contribute to cancer, neurodegeneration and susceptibility to viral infections, focusing on dysfunctions associated with the anti-R-loop helicase Senataxin.

Keywords:  DNA damage; DSB repair; R-loops; RNA:DNA hybrids; Replication-transcription collisions; Senataxin

DOI:  https://doi.org/10.1016/j.mrrev.2020.108300
Front Oncol. 2020 ;10 670

Replication Fork Remodeling and Therapy Escape in DNA Damage Response-Deficient Cancers.

Martin Liptay, Joana S Barbosa, Sven Rottenberg.

  Most cancers have lost a critical DNA damage response (DDR) pathway during tumor evolution. These alterations provide a useful explanation for the initial sensitivity of tumors to DNA-targeting chemotherapy. A striking example is dysfunctional homology-directed repair (HDR), e.g., due to inactivating mutations in BRCA1 and BRCA2 genes. Extensive efforts are being made to develop novel targeted therapies exploiting such an HDR defect. Inhibitors of poly(ADP-ribose) polymerase (PARP) are an instructive example of this approach. Despite the success of PARP inhibitors, the presence of primary or acquired therapy resistance remains a major challenge in clinical oncology. To move the field of precision medicine forward, we need to understand the precise mechanisms causing therapy resistance. Using preclinical models, various mechanisms underlying chemotherapy resistance have been identified. Restoration of HDR seems to be a prevalent mechanism but this does not explain resistance in all cases. Interestingly, some factors involved in DNA damage response (DDR) have independent functions in replication fork (RF) biology and their loss causes RF instability and therapy sensitivity. However, in BRCA-deficient tumors, loss of these factors leads to restored stability of RFs and acquired drug resistance. In this review we discuss the recent advances in the field of RF biology and its potential implications for chemotherapy response in DDR-defective cancers. Additionally, we review the role of DNA damage tolerance (DDT) pathways in maintenance of genome integrity and their alterations in cancer. Furthermore, we refer to novel tools that, combined with a better understanding of drug resistance mechanisms, may constitute a great advance in personalized diagnosis and therapeutic strategies for patients with HDR-deficient tumors.

Keywords:  BRCA1/2; DNA damage response; DNA damage tolerance; DNA replication; PARP inhibitors; chemotherapy; drug resistance; replication fork

DOI:  https://doi.org/10.3389/fonc.2020.00670
DNA Repair (Amst). 2020 Apr 30. pii: S1568-7864(20)30114-2. [Epub ahead of print]90 102866

New insights into abasic site repair and tolerance.

Petria S Thompson, David Cortez.

  Thousands of apurinic/apyrimidinic (AP or abasic) sites form in each cell, each day. This simple DNA lesion can have profound consequences to cellular function, genome stability, and disease. As potent blocks to polymerases, they interfere with the reading and copying of the genome. Since they provide no coding information, they are potent sources of mutation. Due to their reactive chemistry, they are intermediates in the formation of lesions that are more challenging to repair including double-strand breaks, interstrand crosslinks, and DNA protein crosslinks. Given their prevalence and deleterious consequences, cells have multiple mechanisms of repairing and tolerating these lesions. While base excision repair of abasic sites in double-strand DNA has been studied for decades, new interest in abasic site processing has come from more recent insights into how they are processed in single-strand DNA. In this review, we discuss the source of abasic sites, their biological consequences, tolerance mechanisms, and how they are repaired in double and single-stranded DNA.

Keywords:  Abasic site; Base excision repair; DNA-protein crosslinks; Genome stability; HMCES

DOI:  https://doi.org/10.1016/j.dnarep.2020.102866
Nat Chem Biol. 2020 Jun;16(6): 620-629

Chromatin as a key consumer in the metabolite economy.

Katharine L Diehl, Tom W Muir.

In eukaryotes, chromatin remodeling and post-translational modifications (PTMs) shape the local chromatin landscape to establish permissive and repressive regions within the genome, orchestrating transcription, replication, and DNA repair in concert with other epigenetic mechanisms. Though cellular nutrient signaling encompasses a huge number of pathways, recent attention has turned to the hypothesis that the metabolic state of the cell is communicated to the genome through the type and concentration of metabolites in the nucleus that are cofactors for chromatin-modifying enzymes. Importantly, both epigenetic and metabolic dysregulation are hallmarks of a range of diseases, and this metabolism-chromatin axis may yield a well of new therapeutic targets. In this Perspective, we highlight emerging themes in the inter-regulation of the genome and metabolism via chromatin, including nonenzymatic histone modifications arising from chemically reactive metabolites, the expansion of PTM diversity from cofactor-promiscuous chromatin-modifying enzymes, and evidence for the existence and importance of subnucleocytoplasmic metabolite pools.

DOI: https://doi.org/10.1038/s41589-020-0517-x
Anticancer Agents Med Chem. 2020 May 17.

RecQ Family Helicases in Replication Fork Remodeling and Repair: Opening New Avenues Towards Identification of Potential Targets for Cancer Chemotherapy.

Chetan Kumar Jain, Swagata Mukhopadhyay, Agneyo Ganguly.

  Replication fork reversal and restart has gained immense interest as a central response mechanism to replication stress following DNA damage. Although the exact mechanism of fork reversal has not been elucidated precisely, involvement of diverse pathways and different factors has been demonstrated that are central to this phenomenon. RecQ helicases known for their vital role in DNA repair and maintaining genome stability has recently been implicated in restart of regressed replication forks. Through interaction with vital proteins like Poly (ADP) ribose polymerase 1 (PARP1) these helicases participate in the replication fork reversal and restart phenomenon. Most therapeutic agents used for cancer chemotherapy act by causing DNA damage in replicating cells and subsequent cell death. These DNA damages can be repaired by mechanisms involving fork reversal as the key phenomenon eventually reducing the efficacy of the therapeutic agent. Hence the factors contributing to this repair process can be good selective targets for developing more efficient chemotherapeutic agents. In this review we have discussed in details the role of various proteins in replication fork reversal and restart with special emphasis on RecQ helicases. Involvement of other proteins like PARP1, recombinase rad51, SWI/SNF complex has also been discussed. Since RecQ helicases play a central role in the DNA damage response following chemotherapeutic treatment, we propose that targeting these helicases can emerge as an alternate to available intervention strategies. We have also summarized the current research status of available RecQ inhibitors and siRNA based therapeutic approaches that targetsRecQ helicases. In summary, our review gives an overview of the DNA damage responses involving replication fork reversal and provides new directions for development of more efficient and sustainable chemotherapeutic approaches.

Keywords:  DNA repair; PARP1.; RecQ helicases; Replication fork reversal; chemotherapy; replication fork restart

DOI:  https://doi.org/10.2174/1871520620666200518082433
DNA Repair (Amst). 2020 May 18. pii: S1568-7864(20)30116-6. [Epub ahead of print]91-92 102868

Hypermutation in single-stranded DNA.

Natalie Saini, Dmitry A Gordenin.

  Regions of genomic DNA can become single-stranded in the course of normal replication and transcription as well as during DNA repair. Abnormal repair and replication intermediates can contain large stretches of persistent single-stranded DNA, which is extremely vulnerable to DNA damaging agents and hypermutation. Since such single-stranded DNA spans only a fraction of the genome at a given instance, hypermutation in these regions leads to tightly-spaced mutation clusters. This phenomenon of hypermutation in single-stranded DNA has been documented in several experimental models as well as in cancer genomes. Recently, hypermutated single-stranded RNA viral genomes also have been documented. Moreover, indications of hypermutation in single-stranded DNA may also be found in the human germline. This review will summarize key current knowledge and the recent developments in understanding the diverse mechanisms and sources of ssDNA hypermutation.

Keywords:  Cancer; Hypermutation; Mutation clusters; Single-stranded DNA

DOI:  https://doi.org/10.1016/j.dnarep.2020.102868
Oncogene. 2020 May 19.

Mdm4 supports DNA replication in a p53-independent fashion.

Kai Wohlberedt, Ina Klusmann, Polina K Derevyanko, Kester Henningsen, Josephine Ann Mun Yee Choo, Valentina Manzini, Anna Magerhans, Celeste Giansanti, Christine M Eischen, Aart G Jochemsen, Matthias Dobbelstein.

The Mdm4 (alias MdmX) oncoprotein, like its paralogue and interaction partner Mdm2, antagonizes the tumor suppressor p53. p53-independent roles of the Mdm proteins are emerging, and we have reported the ability of Mdm2 to modify chromatin and to support DNA replication by suppressing the formation of R-loops (DNA/RNA-hybrids). We show here that the depletion of Mdm4 in p53-deficient cells compromises DNA replication fork progression as well. Among various deletion mutants, only full-length Mdm4 was able to support DNA replication fork progression. Co-depletion of Mdm4 and Mdm2 further impaired DNA replication, and the overexpression of each partially compensated for the other's loss. Despite impairing replication, Mdm4 depletion only marginally hindered cell proliferation, likely due to compensation through increased firing of replication origins. However, depleting Mdm4 sensitized p53-/- cells to the nucleoside analog gemcitabine, raising the future perspective of using Mdm4 inhibitors as chemosensitizers. Mechanistically, Mdm4 interacts with members of the Polycomb Repressor Complexes and supports the ubiquitination of H2A, thereby preventing the accumulation of DNA/RNA-hybrids. Thus, in analogy to previously reported activities of Mdm2, Mdm4 enables unperturbed DNA replication through the avoidance of R-loops.

DOI: https://doi.org/10.1038/s41388-020-1325-1
Nat Commun. 2020 May 18. 11(1): 2484

HDAC1 modulates OGG1-initiated oxidative DNA damage repair in the aging brain and Alzheimer's disease.

Ping-Chieh Pao, Debasis Patnaik, L Ashley Watson, Fan Gao, Ling Pan, Jun Wang, Chinnakkaruppan Adaikkan, Jay Penney, Hugh P Cam, Wen-Chin Huang, Lorena Pantano, Audrey Lee, Alexi Nott, Trongha X Phan, Elizabeta Gjoneska, Sara Elmsaouri, Stephen J Haggarty, Li-Huei Tsai.

DNA damage contributes to brain aging and neurodegenerative diseases. However, the factors stimulating DNA repair to stave off functional decline remain obscure. We show that HDAC1 modulates OGG1-initated 8-oxoguanine (8-oxoG) repair in the brain. HDAC1-deficient mice display age-associated DNA damage accumulation and cognitive impairment. HDAC1 stimulates OGG1, a DNA glycosylase known to remove 8-oxoG lesions that are associated with transcriptional repression. HDAC1 deficiency causes impaired OGG1 activity, 8-oxoG accumulation at the promoters of genes critical for brain function, and transcriptional repression. Moreover, we observe elevated 8-oxoG along with reduced HDAC1 activity and downregulation of a similar gene set in the 5XFAD mouse model of Alzheimer's disease. Notably, pharmacological activation of HDAC1 alleviates the deleterious effects of 8-oxoG in aged wild-type and 5XFAD mice. Our work uncovers important roles for HDAC1 in 8-oxoG repair and highlights the therapeutic potential of HDAC1 activation to counter functional decline in brain aging and neurodegeneration.

DOI: https://doi.org/10.1038/s41467-020-16361-y
Nucleic Acids Res. 2020 May 20. pii: gkaa392. [Epub ahead of print]

Interaction between RECQL4 and OGG1 promotes repair of oxidative base lesion 8-oxoG and is regulated by SIRT1 deacetylase.

Shunlei Duan, Xuerui Han, Mansour Akbari, Deborah L Croteau, Lene Juel Rasmussen, Vilhelm A Bohr.

OGG1 initiated base excision repair (BER) is the major pathway for repair of oxidative DNA base damage 8-oxoguanine (8-oxoG). Here, we report that RECQL4 DNA helicase, deficient in the cancer-prone and premature aging Rothmund-Thomson syndrome, physically and functionally interacts with OGG1. RECQL4 promotes catalytic activity of OGG1 and RECQL4 deficiency results in defective 8-oxoG repair and increased genomic 8-oxoG. Furthermore, we show that acute oxidative stress leads to increased RECQL4 acetylation and its interaction with OGG1. The NAD+-dependent protein SIRT1 deacetylates RECQL4 in vitro and in cells thereby controlling the interaction between OGG1 and RECQL4 after DNA repair and maintaining RECQL4 in a low acetylated state. Collectively, we find that RECQL4 is involved in 8-oxoG repair through interaction with OGG1, and that SIRT1 indirectly modulates BER of 8-oxoG by controlling RECQL4-OGG1 interaction.

DOI: https://doi.org/10.1093/nar/gkaa392
JCI Insight. 2020 May 21. pii: 133365. [Epub ahead of print]5(10):

Persistent DNA damage-induced NLRP12 improves hematopoietic stem cell function.

Qiqi Lin, Limei Wu, Zhilin Ma, Fabliha Ahmed Chowdhury, Habibul Hasan Mazumder, Wei Du.

  NOD-like receptor 12 (NLRP12) is a member of the nucleotide-binding domain and leucine-rich repeat containing receptor inflammasome family that plays a central role in innate immunity. We previously showed that DNA damage upregulated NLRP12 in hematopoietic stem cells (HSCs) of mice deficient in the DNA repair gene Fanca. However, the role of NLRP12 in HSC maintenance is not known. Here, we show that persistent DNA damage-induced NLRP12 improves HSC function in both mouse and human models of DNA repair deficiency and aging. Specifically, treatment of Fanca-/- mice with the DNA cross-linker mitomycin C or ionizing radiation induces NLRP12 upregulation in phenotypic HSCs. NLRP12 expression is specifically induced by persistent DNA damage. Functionally, knockdown of NLRP12 exacerbates the repopulation defect of Fanca-/- HSCs. Persistent DNA damage-induced NLRP12 was also observed in the HSCs from aged mice, and depletion of NLRP12 in these aged HSCs compromised their self-renewal and hematopoietic recovery. Consistently, overexpression of NLRP12 substantially improved the long-term repopulating function of Fanca-/- and aged HSCs. Finally, persistent DNA damage-induced NLRP12 maintains the function of HSCs from patients with FA or aged donors. These results reveal a potentially novel role of NLRP12 in HSC maintenance and suggest that NLRP12 targeting has therapeutic potential in DNA repair disorders and aging.

Keywords:  Aging; DNA repair; Hematology; Hematopoietic stem cells

DOI:  https://doi.org/10.1172/jci.insight.133365
Cancers (Basel). 2020 May 20. pii: E1289. [Epub ahead of print]12(5):

Germline Mutation in MUS81 Resulting in Impaired Protein Stability is Associated with Familial Breast and Thyroid Cancer.

Maisa Pinheiro, Fernanda Cristina Sulla Lupinacci, Karina Miranda Santiago, Sandra Aparecida Drigo, Fabio Albuquerque Marchi, Carlos Eduardo Fonseca-Alves, Sonia Cristina da Silva Andrade, Mads Malik Aagaard, Tatiane Ramos Basso, Mariana Bisarro Dos Reis, Rolando André Rios Villacis, Martin Roffé, Glaucia Noeli Maroso Hajj, Igor Jurisica, Luiz Paulo Kowalski, Maria Isabel Achatz, Silvia Regina Rogatto.

  Multiple primary thyroid cancer (TC) and breast cancer (BC) are commonly diagnosed, and the lifetime risk for these cancers is increased in patients with a positive family history of both TC and BC. Although this phenotype is partially explained by TP53 or PTEN mutations, a significant number of patients are negative for these alterations. We judiciously recruited patients diagnosed with BC and/or TC having a family history of these tumors and assessed their whole-exome sequencing. After variant prioritization, we selected MUS81 c.1292G>A (p.R431H) for further investigation. This variant was genotyped in a healthy population and sporadic BC/TC tissues and investigated at the protein level and cellular models. MUS81 c.1292G>A was the most frequent variant (25%) and the strongest candidate due to its function of double-strand break repair. This variant was confirmed in four relatives from two families. MUS81 p.R431H protein exhibited lower expression levels in tumors from patients positive for the germline variant, compared with wild-type BC, and normal breast and thyroid tissues. Using cell line models, we showed that c.1292G>A induced protein instability and affected DNA damage response. We suggest that MUS81 is a novel candidate involved in familial BC/TC based on its low frequency in healthy individuals and proven effect in protein stability.

Keywords:  MUS81; breast cancer; exome sequencing; familial cancer; functional analysis; thyroid cancer

DOI:  https://doi.org/10.3390/cancers12051289
Elife. 2020 May 22. pii: e55325. [Epub ahead of print]9

Parallel CRISPR-Cas9 screens clarify impacts of p53 on screen performance.

Anne Ramsay Bowden, David A Morales-Juarez, Matylda Sczaniecka-Clift, Maria Martin Agudo, Natalia Lukashchuk, John Christopher Thomas, Stephen P Jackson.

  CRISPR-Cas9 genome engineering has revolutionised high-throughput functional genomic screens. However, recent work has raised concerns regarding the performance of CRISPR-Cas9 screens using TP53 wild-type human cells due to a p53-mediated DNA damage response (DDR) limiting the efficiency of generating viable edited cells. To directly assess the impact of cellular p53 status on CRISPR-Cas9 screen performance, we carried out parallel CRISPR-Cas9 screens in wild-type and TP53 knockout human retinal pigment epithelial cells using a focused dual guide RNA library targeting 852 DDR-associated genes. Our work demonstrates that although functional p53 status negatively affects identification of significantly depleted genes, optimal screen design can nevertheless enable robust screen performance. Through analysis of our own and published screen data, we highlight key factors for successful screens in both wild-type and p53-deficient cells.

Keywords:  CRISPR screening; DNA damage response; TP53; genetics; genomics; human

DOI:  https://doi.org/10.7554/eLife.55325
FASEB J. 2020 May 21.

Activation-induced cytidine deaminase can target multiple topologies of double-stranded DNA in a transcription-independent manner.

Sarah A Branton, Atefeh Ghorbani, Brittany N Bolt, Heather Fifield, Lesley M Berghuis, Mani Larijani.

  Activation-induced cytidine deaminase (AID) mutates immunoglobulin genes and acts genome-wide. AID targets robustly transcribed genes, and purified AID acts on single-stranded (ss) but not double-stranded (ds) DNA oligonucleotides. Thus, it is believed that transcription is the generator of ssDNA for AID. Previous cell-free studies examining the relationship between transcription and AID targeting have employed a bacterial colony count assay wherein AID reverts an antibiotic resistance stop codon in plasmid substrates, leading to colony formation. Here, we established a novel assay where kb-long dsDNA of varying topologies is incubated with AID, with or without transcription, followed by direct sequencing. This assay allows for an unselected and in-depth comparison of mutation frequency and pattern of AID targeting in the absence of transcription or across a range of transcription dynamics. We found that without transcription, AID targets breathing ssDNA in supercoiled and, to a lesser extent, in relaxed dsDNA. The most optimal transcription only modestly enhanced AID action on supercoiled dsDNA in a manner dependent on RNA polymerase speed. These data suggest that the correlation between transcription and AID targeting may reflect transcription leading to AID-accessible breathing ssDNA patches naturally occurring in de-chromatinized dsDNA, as much as being due to transcription directly generating ssDNA.

Keywords:  RNA polymerase; breathing DNA structures; cytidine deamination; genome mutagenesis

DOI:  https://doi.org/10.1096/fj.201903036RR
Nat Commun. 2020 May 18. 11(1): 2462

Histone H2A variants alpha1-extension helix directs RNF168-mediated ubiquitination.

Jessica L Kelliher, Kirk L West, Qingguo Gong, Justin W C Leung.

Histone ubiquitination plays an important role in the DNA damage response (DDR) pathway. RNF168 catalyzes H2A and H2AX ubiquitination on lysine 13/15 (K13/K15) upon DNA damage and promotes the accrual of downstream repair factors at damaged chromatin. Here, we report that RNF168 ubiquitinates the non-canonical H2A variants H2AZ and macroH2A1/2 at the divergent N-terminal tail lysine residue. In addition to their evolutionarily conserved nucleosome acidic patch, we identify the positively charged alpha1-extension helix as essential for RNF168-mediated ubiquitination of H2A variants. Moreover, mutation of the RNF168 UMI (UIM- and MIU-related UBD) hydrophilic acidic residues abolishes RNF168-mediated ubiquitination as well as 53BP1 and BRCA1 ionizing radiation-induced foci formation. Our results reveal a juxtaposed bipartite electrostatic interaction utilized by the nucleosome to direct RNF168 orientation towards the target lysine residues in proximity to the H2A alpha1-extension helix, which plays an important role in the DDR pathway.

DOI: https://doi.org/10.1038/s41467-020-16307-4
Mol Microbiol. 2020 May 19.

Interaction with single-stranded DNA-binding protein localizes ribonuclease HI to DNA replication forks and facilitates R-loop removal.

Christine Wolak, Hui Jun Ma, Nicolas Soubry, Steven J Sandler, Rodrigo Reyes-Lamothe, James L Keck.

DNA replication complexes (replisomes) routinely encounter proteins and unusual nucleic acid structures that can impede their progress. Barriers can include transcription complexes and R-loops that form when RNA hybridizes with complementary DNA templates behind RNA polymerases. Cells encode several RNA polymerase and R-loop clearance mechanisms to limit replisome exposure to these potential obstructions. One such mechanism is hydrolysis of R-loops by ribonuclease HI (RNase HI). Here, we examine the cellular role of the interaction between Escherichia coli RNase HI and the single-stranded DNA-binding protein (SSB) in this process. Interaction with SSB localizes RNase HI foci to DNA replication sites. Mutation of rnhA to encode an RNase HI variant that cannot interact with SSB but that maintains enzymatic activity (rnhAK60E) eliminates RNase HI foci. The mutation also produces a media-dependent slow-growth phenotype and an activated DNA damage response in cells lacking Rep helicase, which is an enzyme that disrupts stalled transcription complexes. RNA polymerase variants that are thought to increase or decrease R-loop accumulation enhance or suppress, respectively, the growth phenotype of rnhAK60E rep::kan strains. These results identify a cellular role for the RNase HI/SSB interaction in helping to clear R-loops that block DNA replication.

DOI: https://doi.org/10.1111/mmi.14529
Commun Biol. 2020 May 19. 3(1): 245

Tau affects P53 function and cell fate during the DNA damage response.

Martina Sola, Claudia Magrin, Giona Pedrioli, Sandra Pinton, Agnese Salvadè, Stéphanie Papin, Paolo Paganetti.

Cells are constantly exposed to DNA damaging insults. To protect the organism, cells developed a complex molecular response coordinated by P53, the master regulator of DNA repair, cell division and cell fate. DNA damage accumulation and abnormal cell fate decision may represent a pathomechanism shared by aging-associated disorders such as cancer and neurodegeneration. Here, we examined this hypothesis in the context of tauopathies, a neurodegenerative disorder group characterized by Tau protein deposition. For this, the response to an acute DNA damage was studied in neuroblastoma cells with depleted Tau, as a model of loss-of-function. Under these conditions, altered P53 stability and activity result in reduced cell death and increased cell senescence. This newly discovered function of Tau involves abnormal modification of P53 and its E3 ubiquitin ligase MDM2. Considering the medical need with vast social implications caused by neurodegeneration and cancer, our study may reform our approach to disease-modifying therapies.

DOI: https://doi.org/10.1038/s42003-020-0975-4
Mol Genet Genomic Med. 2020 May 20. e1280

Preliminary study on the function of the POLD1 (CDC2) EXON2 c.56G>A mutation.

Jing Liu, Yu Liu, Jingxuan Fu, Chengeng Liu, Tingting Yang, Xiaomin Zhang, Min Cao, Peichang Wang.

   BACKGROUND: Fanconi anemia (FA) is a rare recessive disease characterized by DNA damage repair deficiency, and DNA polymerase δ (whose catalytic subunit is encoded by POLD1, also known as CDC2) is closely related to DNA damage repair. Our previous study identified a novel POLD1 missense mutation c.56G>A (p. Arg19>His) in FA family members. However, the function of the POLD1 missense mutation is currently unknown. This study aimed to uncover the biological function of the POLD1 missense mutation.
METHODS: Stable cell lines overexpressing wild-type POLD1 or mutant POLD1 (c.56G>A, p.Arg19His) were constructed by lentivirus infection. Cell growth curve analysis, cell cycle analysis, and a comet assay were used to analyze the function of the POLD1 mutation.
RESULTS: The growth and proliferative ability of the cells with POLD1 mutation was decreased significantly compared with those of the wild-type cells (Student's t test, p < .05). The percentage of cells in the G0/G1 phase increased, and the percentage of cells in the S phase decreased significantly when POLD1 was mutated (Student's t test, p < .05). Moreover, the Olive tail moment value of the cells with the POLD1 mutation was significantly higher than that of the cells with wild-type POLD1 after H2 O2 treatment.
CONCLUSIONS: The POLD1 mutation inhibited cell proliferation, slowed cell cycle progression, and reduced DNA damage repair.

Keywords:  DNA polymerase δ; Fanconi anemia; POLD1 mutation

DOI:  https://doi.org/10.1002/mgg3.1280
Cell Cycle. 2020 May 18. 1-11

Disassembly of the Shieldin Complex by TRIP13.

Prabha Sarangi, Connor S Clairmont, Alan D D'Andrea.

  In the past decade, the study of the major DNA double strand break (DSB) repair pathways, homologous recombination (HR) and classical non-homologous end joining (C-NHEJ), has revealed a vast and intricate network of regulation. The choice between HR and C-NHEJ is largely controlled at the step of DNA end-resection. A pro-C-NHEJ cascade commencing with 53BP1 and culminating in the newly discovered REV7-Shieldin complex impedes end resection and therefore HR. Importantly, loss of any component of this pathway confers PARP inhibitor resistance in BRCA1-deficient cells; hence, their study is of great clinical importance. The newest entrant on the scene of end resection regulation is the ATPase TRIP13 that disables the pro-C-NHEJ cascade by promoting a novel conformational change of the HORMA protein REV7. Here, we tie these new findings and factors with previous research on the regulation of DSB repair and HORMA proteins, and suggest testable hypotheses for how TRIP13 could specifically inactivate REV7-Shieldin to promote HR. We also discuss these biological questions in the context of clinical therapeutics.

Keywords:  HORMA protein; Keywords REV7; PARP inhibitor; Shieldin; TRIP13DNA repair; fanconi anemia; homologous recombination

DOI:  https://doi.org/10.1080/15384101.2020.1758435
J Cell Sci. 2020 May 20. pii: jcs.240036. [Epub ahead of print]

RIF1 controls replication initiation and homologous recombination repair in a radiation dose-dependent manner.

Yuichiro Saito, Junya Kobayashi, Masato T Kanemaki, Kenshi Komatsu.

  RIF1 controls both the DNA replication timing and DNA double-strand break (DSB) repair pathways to maintain genome integrity. However, it remains unclear how RIF1 links these two processes when exposed to ionizing radiation (IR). Here, we show that homologous-recombination repair (HRR) inhibition by RIF1 occurs in a dose-dependent manner and is controlled via DNA replication. RIF1 inhibits both DNA end resection and RAD51 accumulation after exposure to high doses of IR. Contrastingly, HRR inhibition by RIF1 is antagonized by BRCA1 at a low-dose IR exposure. At high IR doses, RIF1 suppresses replication initiation by dephosphorylating MCM helicase. Notably, the dephosphorylation of MCM helicase inhibits both DNA end resection and HRR even without RIF1. Thus, our data show the importance of active DNA replication for HRR and suggest a common suppression mechanism for DNA replication and HRR at high IR doses, both of which are controlled by RIF1.

Keywords:  DNA repair; Homologous recombination; RIF1; Radiation biology

DOI:  https://doi.org/10.1242/jcs.240036
Nucleic Acids Res. 2020 May 19. pii: gkaa380. [Epub ahead of print]

RNF8 has both KU-dependent and independent roles in chromosomal break repair.

Linda Jillianne Tsai, Felicia Wednesday Lopezcolorado, Ragini Bhargava, Carlos Mendez-Dorantes, Eva Jahanshir, Jeremy M Stark.

Chromosomal double strand breaks (DSBs) can initiate several signaling events, such as ubiquitination, however the precise influence of such signaling on DSB repair outcomes remains poorly understood. With an RNA interference screen, we found that the E3 ubiquitin ligase RNF8 suppresses a deletion rearrangement mediated by canonical non-homologous end joining (C-NHEJ). We also found that RNF8 suppresses EJ without insertion/deletion mutations, which is a hallmark of C-NHEJ. Conversely, RNF8 promotes alternative EJ (ALT-EJ) events involving microhomology that is embedded from the edge of the DSB. These ALT-EJ events likely require limited end resection, whereas RNF8 is not required for single-strand annealing repair involving extensive end resection. Thus, RNF8 appears to specifically facilitate repair events requiring limited end resection, which we find is dependent on the DSB end protection factor KU. However, we also find that RNF8 is important for homology-directed repair (HDR) independently of KU, which appears linked to promoting PALB2 function. Finally, the influence of RNF8 on EJ is distinct from 53BP1 and the ALT-EJ factor, POLQ. We suggest that RNF8 mediates both ALT-EJ and HDR, but via distinct mechanisms, since only the former is dependent on KU.

DOI: https://doi.org/10.1093/nar/gkaa380
Elife. 2020 May 19. pii: e54935. [Epub ahead of print]9

Opposing p53 and mTOR/AKT promote an in vivo switch from apoptosis to senescence upon telomere shortening in zebrafish.

Mounir El Maï, Marta Marzullo, Inês Pimenta de Castro, Miguel Godinho Ferreira.

  Progressive telomere shortening during lifespan is associated with restriction of cell proliferation, genome instability and aging. Apoptosis and senescence are the two major outcomes upon irreversible cellular damage. Here, we show a transition of these two cell fates during aging of telomerase deficient zebrafish. In young telomerase mutants, proliferative tissues exhibit DNA damage and p53-dependent apoptosis, but no senescence. However, these tissues in older animals display loss of cellularity and senescence becomes predominant. Tissue alterations are accompanied by a pro-proliferative stimulus mediated by AKT signaling. Upon AKT activation, FoxO transcription factors are phosphorylated and translocated out of the nucleus. This results in reduced SOD2 expression causing an increase of ROS and mitochondrial dysfunction. These alterations induce p15/16 growth arrest and senescence. We propose that, upon telomere shortening, early apoptosis leads to cell depletion and insufficient compensatory proliferation. Following tissue damage, the mTOR/AKT is activated causing mitochondrial dysfunction and p15/16-dependent senescence.

Keywords:  AKT; aging; apoptosis; cell biology; p53; regenerative medicine; senescence; stem cells; telomeres; zebrafish

DOI:  https://doi.org/10.7554/eLife.54935
Nat Commun. 2020 May 22. 11(1): 2587

Dietary serine-microbiota interaction enhances chemotherapeutic toxicity without altering drug conversion.

Wenfan Ke, James A Saba, Cong-Hui Yao, Michael A Hilzendeger, Anna Drangowska-Way, Chintan Joshi, Vinod K Mony, Shawna B Benjamin, Sisi Zhang, Jason Locasale, Gary J Patti, Nathan Lewis, Eyleen J O'Rourke.

The gut microbiota metabolizes drugs and alters their efficacy and toxicity. Diet alters drugs, the metabolism of the microbiota, and the host. However, whether diet-triggered metabolic changes in the microbiota can alter drug responses in the host has been largely unexplored. Here we show that dietary thymidine and serine enhance 5-fluoro 2'deoxyuridine (FUdR) toxicity in C. elegans through different microbial mechanisms. Thymidine promotes microbial conversion of the prodrug FUdR into toxic 5-fluorouridine-5'-monophosphate (FUMP), leading to enhanced host death associated with mitochondrial RNA and DNA depletion, and lethal activation of autophagy. By contrast, serine does not alter FUdR metabolism. Instead, serine alters E. coli's 1C-metabolism, reduces the provision of nucleotides to the host, and exacerbates DNA toxicity and host death without mitochondrial RNA or DNA depletion; moreover, autophagy promotes survival in this condition. This work implies that diet-microbe interactions can alter the host response to drugs without altering the drug or the host.

DOI: https://doi.org/10.1038/s41467-020-16220-w
Cells. 2020 May 19. pii: E1251. [Epub ahead of print]9(5):

Metabolic Adaptation during nab-Paclitaxel Resistance in Pancreatic Cancer Cell Lines.

Lukas M Braun, Simon Lagies, Jessica Guenzle, Stefan Fichtner-Feigl, Uwe A Wittel, Bernd Kammerer.

  Pancreatic ductal adenocarcinoma (PDAC) correlates with high mortality and is about to become one of the major reasons for cancer-related mortality in the next decades. One reason for that high mortality is the limited availability of effective chemotherapy as well as the intrinsic or acquired resistance against it. Here, we report the impact of nab-paclitaxel on the cellular metabolome of PDAC cell lines. After establishment of nab-paclitaxel resistant cell lines, comparison of parental and resistant PDAC cell lines by metabolomics and biochemical assessments revealed altered metabolism, enhanced viability and reduced apoptosis. The results unveiled that acute nab-paclitaxel treatment affected primary metabolism to a minor extent. However, acquisition of resistance led to altered metabolites in both cell lines tested. Specifically, aspartic acid and carbamoyl-aspartic acid were differentially abundant, which might indicate an increased de novo pyrimidine synthesis. This pathway has already shown a similar behavior in other cancerous entities and thus might serve in the future as vulnerable target fighting resistance acquisition occurring in common malignancies.

Keywords:  GC/MS; PDAC; chemotherapy resistance; metabolic reprogramming; metabolomics; nab-Paclitaxel; pancreatic cancer; pancreatic ductal adenocarcinoma

DOI:  https://doi.org/10.3390/cells9051251
Proc Natl Acad Sci U S A. 2020 May 20. pii: 201917362. [Epub ahead of print]

Enzyme-mediated depletion of serum l-Met abrogates prostate cancer growth via multiple mechanisms without evidence of systemic toxicity.

Wei-Cheng Lu, Achinto Saha, Wupeng Yan, Kendra Garrison, Candice Lamb, Renu Pandey, Seema Irani, Alessia Lodi, Xiyuan Lu, Stefano Tiziani, Yan Jessie Zhang, George Georgiou, John DiGiovanni, Everett Stone.

  Extensive studies in prostate cancer and other malignancies have revealed that l-methionine (l-Met) and its metabolites play a critical role in tumorigenesis. Preclinical and clinical studies have demonstrated that systemic restriction of serum l-Met, either via partial dietary restriction or with bacterial l-Met-degrading enzymes exerts potent antitumor effects. However, administration of bacterial l-Met-degrading enzymes has not proven practical for human therapy because of problems with immunogenicity. As the human genome does not encode l-Met-degrading enzymes, we engineered the human cystathionine-γ-lyase (hMGL-4.0) to catalyze the selective degradation of l-Met. At therapeutically relevant dosing, hMGL-4.0 reduces serum l-Met levels to >75% for >72 h and significantly inhibits the growth of multiple prostate cancer allografts/xenografts without weight loss or toxicity. We demonstrate that in vitro, hMGL-4.0 causes tumor cell death, associated with increased reactive oxygen species, S-adenosyl-methionine depletion, global hypomethylation, induction of autophagy, and robust poly(ADP-ribose) polymerase (PARP) cleavage indicative of DNA damage and apoptosis.

Keywords:  hMGL; l-methionine depletion; prostate cancer

DOI:  https://doi.org/10.1073/pnas.1917362117
Biochim Biophys Acta Mol Basis Dis. 2020 May 18. pii: S0925-4439(20)30188-5. [Epub ahead of print] 165841

Reprogramming of serine, glycine and one-carbon metabolism in cancer.

Albert M Li, Jiangbin Ye.

  Metabolic pathways leading to the synthesis, uptake, and usage of the nonessential amino acid serine are frequently amplified in cancer. Serine encounters diverse fates in cancer cells, including being charged onto tRNAs for protein synthesis, providing head groups for sphingolipid and phospholipid synthesis, and serving as a precursor for cellular glycine and one-carbon units, which are necessary for nucleotide synthesis and methionine cycle reloading. This review will focus on the participation of serine and glycine in the mitochondrial one-carbon (SGOC) pathway during cancer progression, with an emphasis on the genetic and epigenetic determinants that drive SGOC gene expression. We will discuss recently elucidated roles for SGOC metabolism in nucleotide synthesis, redox balance, mitochondrial function, and epigenetic modifications. Finally, therapeutic considerations for targeting SGOC metabolism in the clinic will be discussed.

Keywords:  Cancer; Glycine; Metabolism; Mitochondria; One-carbon; Serine

DOI:  https://doi.org/10.1016/j.bbadis.2020.165841