bims-numges 2020-10-04 papers

bims-numges

Biomed News

on Nucleotide metabolism and genome stability

Issue of 2020–10–04
33 papers selected by
Sean Rudd, Karolinska Institutet

Repeat expansions confer WRN dependence in microsatellite-unstable cancers.
Visualizing Rev1 catalyze protein-template DNA synthesis.
Targeting the PI3K/mTOR pathway augments CHK1 inhibitor-induced replication stress and antitumor activity in high-grade serous ovarian cance.
An ordered assembly of MYH glycosylase, SIRT6 protein deacetylase, and Rad9-Rad1-Hus1 checkpoint clamp at oxidatively damaged telomeres.
Envisioning how the prototypic molecular machine TFIIH functions in transcription initiation and DNA repair.
First-in-Human Trial of the Oral Ataxia Telangiectasia and Rad3-Related Inhibitor BAY 1895344 in Patients with Advanced Solid Tumors.
TDP-43 dysfunction results in R-loop accumulation and DNA replication defects.
Poly(ADP-Ribose) Glycohydrolase (PARG) vs. Poly(ADP-Ribose) Polymerase (PARP) - Function in Genome Maintenance and Relevance of Inhibitors for Anti-cancer Therapy.
STAT3 imparts BRCAness by impairing homologous recombination repair in Epstein-Barr virus-transformed B lymphocytes.
Under-Replicated DNA: The Byproduct of Large Genomes?
Analysis of mutational signatures in C. elegans: Implications for cancer genome analysis.
Modulation of the Apurinic/Apyrimidinic Endonuclease Activity of Human APE1 and of Its Natural Polymorphic Variants by Base Excision Repair Proteins.
Bacterial Chromosome Replication and DNA Repair During the Stringent Response.
Reality CHEK: Understanding the biology and clinical potential of CHK1.
A hand-off of DNA between archaeal polymerases allows high-fidelity replication to resume at a discrete intermediate three bases past 8-oxoguanine.
Role of POT1 in Human Cancer.
Radio-Resistance and DNA Repair in Pediatric Diffuse Midline Gliomas.
Exploiting DNA repair defects in triple negative breast cancer to improve cell killing.
A human cancer cell line initiates DNA replication normally in the absence of ORC5 and ORC2 proteins.
Ubiquitin and TFIIH-stimulated DDB2 dissociation drives DNA damage handover in nucleotide excision repair.
Structural basis of DNA replication origin recognition by human Orc6 protein binding with DNA.
Loss of mitochondrial localization of human FANCG causes defective FANCJ helicase.
PP2A Regulates Phosphorylation-Dependent Isomerization of Cytoplasmic and Mitochondrial-Associated ATR by Pin1 in DNA Damage Responses.
Ewing sarcoma protein promotes dissociation of poly(ADP-ribose) polymerase 1 from chromatin.
The bromodomain and extra-terminal domain inhibitor JQ1 synergistically sensitizes human colorectal cancer cells to topoisomerase I inhibitors through repression of Mre11-mediated DNA repair pathway.
Single-nucleotide polymorphism of the DNA cytosine deaminase APOBEC3H haplotype I leads to enzyme destabilization and correlates with lung cancer.
Nanoscale insight into chromatin remodeling and DNA repair complex in HeLa cells after ionizing radiation.
CtIP-mediated DNA resection is dispensable for IgH class switch recombination by alternative end-joining.
Proteomics-Based Identification of DUB Substrates Using Selective Inhibitors.
Investigating the amino acid sequences of membrane bound dihydroorotate:quinone oxidoreductases (DHOQOs): structural and functional implications.
Specific mechanisms of chromosomal instability indicate therapeutic sensitivities in high-grade serous ovarian carcinoma.
Tenofovir alafenamide does not inhibit mitochondrial function and cholesterol biosynthesis in human T lymphoblastoid cell line.
Comparative evaluation of purine dysmetabolism in gastric and pulmonary adenocarcinomas.

Nature. 2020 Sep 30.

Repeat expansions confer WRN dependence in microsatellite-unstable cancers.

Niek van Wietmarschen, Sriram Sridharan, William J Nathan, Anthony Tubbs, Edmond M Chan, Elsa Callen, Wei Wu, Frida Belinky, Veenu Tripathi, Nancy Wong, Kyla Foster, Javad Noorbakhsh, Kiran Garimella, Abimael Cruz-Migoni, Joshua A Sommers, Yongqing Huang, Ashir A Borah, Jonathan T Smith, Jeremie Kalfon, Nikolas Kesten, Kasper Fugger, Robert L Walker, Egor Dolzhenko, Michael A Eberle, Bruce E Hayward, Karen Usdin, Catherine H Freudenreich, Robert M Brosh, Stephen C West, Peter J McHugh, Paul S Meltzer, Adam J Bass, André Nussenzweig.

The RecQ DNA helicase WRN is a synthetic lethal target for cancer cells with microsatellite instability (MSI), a form of genetic hypermutability that arises from impaired mismatch repair1-4. Depletion of WRN induces widespread DNA double-strand breaks in MSI cells, leading to cell cycle arrest and/or apoptosis. However, the mechanism by which WRN protects MSI-associated cancers from double-strand breaks remains unclear. Here we show that TA-dinucleotide repeats are highly unstable in MSI cells and undergo large-scale expansions, distinct from previously described insertion or deletion mutations of a few nucleotides5. Expanded TA repeats form non-B DNA secondary structures that stall replication forks, activate the ATR checkpoint kinase, and require unwinding by the WRN helicase. In the absence of WRN, the expanded TA-dinucleotide repeats are susceptible to cleavage by the MUS81 nuclease, leading to massive chromosome shattering. These findings identify a distinct biomarker that underlies the synthetic lethal dependence on WRN, and support the development of therapeutic agents that target WRN for MSI-associated cancers.

DOI: https://doi.org/10.1038/s41586-020-2769-8
Proc Natl Acad Sci U S A. 2020 Sep 30. pii: 202010484. [Epub ahead of print]

Visualizing Rev1 catalyze protein-template DNA synthesis.

Tyler M Weaver, Luis M Cortez, Thu H Khoang, M Todd Washington, Pratul K Agarwal, Bret D Freudenthal.

  During DNA replication, replicative DNA polymerases may encounter DNA lesions, which can stall replication forks. One way to prevent replication fork stalling is through the recruitment of specialized translesion synthesis (TLS) polymerases that have evolved to incorporate nucleotides opposite DNA lesions. Rev1 is a specialized TLS polymerase that bypasses abasic sites, as well as minor-groove and exocyclic guanine adducts. Lesion bypass is accomplished using a unique protein-template mechanism in which the templating base is evicted from the DNA helix and the incoming dCTP hydrogen bonds with an arginine side chain of Rev1. To understand the protein-template mechanism at an atomic level, we employed a combination of time-lapse X-ray crystallography, molecular dynamics simulations, and DNA enzymology on the Saccharomyces cerevisiae Rev1 protein. We find that Rev1 evicts the templating base from the DNA helix prior to binding the incoming nucleotide. Binding the incoming nucleotide changes the conformation of the DNA substrate to orient it for nucleotidyl transfer, although this is not coupled to large structural changes in Rev1 like those observed with other DNA polymerases. Moreover, we found that following nucleotide incorporation, Rev1 converts the pyrophosphate product to two monophosphates, which drives the reaction in the forward direction and prevents pyrophosphorolysis. Following nucleotide incorporation, the hydrogen bonds between the incorporated nucleotide and the arginine side chain are broken, but the templating base remains extrahelical. These postcatalytic changes prevent potentially mutagenic processive synthesis by Rev1 and facilitate dissociation of the DNA product from the enzyme.

Keywords:  DNA polymerase; DNA repair; translesion synthesis

DOI:  https://doi.org/10.1073/pnas.2010484117
Cancer Res. 2020 Sep 30. pii: canres.1439.2020. [Epub ahead of print]

Targeting the PI3K/mTOR pathway augments CHK1 inhibitor-induced replication stress and antitumor activity in high-grade serous ovarian cance.

Tzu-Ting Huang, Ethan Brill, Jayakumar R Nair, Xiaohu Zhang, Kelli M Wilson, Lu Chen, Craig J Thomas, Jung-Min Lee.

High-grade serous ovarian carcinoma (HGSOC) is the most lethal gynecologic malignancy in industrialized countries and has limited treatment options. Targeting ATR/CHK1-mediated S and G2/M cell cycle checkpoints has been a promising therapeutic strategy in HGSOC. To improve the efficacy of CHK1 inhibitors (CHK1i), we conducted a high-throughput drug combination screening in HGSOC cells. PI3K/mTOR pathway inhibitors (PI3K/mTORi) showed supra-additive cytotoxicity with CHK1i. Combined treatment with CHK1i and PI3K/mTORi significantly attenuated cell viability and increased DNA damage, chromosomal breaks and mitotic catastrophe compared to monotherapy. PI3K/mTORi decelerated fork speed by promoting new origin firing via increased CDC45, thus potentiating CHK1i-induced replication stress. PI3K/mTORi also augmented CHK1i-induced DNA damage by attenuating DNA homologous recombination repair activity and RAD51 foci formation. High expression of replication stress markers was associated with poor prognosis in patients with HGSOC. Our findings indicate that combined PI3K/mTORi and CHK1i induces greater cell death in HGSOC cells and in vivo models by causing lethal replication stress and DNA damage. This insight can be translated therapeutically by further developing combinations of PI3K and cell cycle pathway inhibitors in HGSOC.

DOI: https://doi.org/10.1158/0008-5472.CAN-20-1439
Aging (Albany NY). 2020 Sep 29. 12

An ordered assembly of MYH glycosylase, SIRT6 protein deacetylase, and Rad9-Rad1-Hus1 checkpoint clamp at oxidatively damaged telomeres.

Jun Tan, Xiangyu Wang, Bor-Jang Hwang, Rex Gonzales, Olivia Konen, Li Lan, A-Lien Lu.

  In the base excision repair pathway, MYH/MUTYH DNA glycosylase prevents mutations by removing adenine mispaired with 8-oxoG, a frequent oxidative lesion. MYH glycosylase activity is enhanced by Rad9-Rad1-Hus1 (9-1-1) checkpoint clamp and SIRT6 histone/protein deacetylase. Here, we show that MYH, SIRT6, and 9-1-1 are recruited to confined oxidatively damaged regions on telomeres in mammalian cells. Using different knockout cells, we show that SIRT6 responds to damaged telomeres very early, and then recruits MYH and Hus1 following oxidative stress. However, the recruitment of Hus1 to damaged telomeres is partially dependent on SIRT6. The catalytic activities of SIRT6 are not important for SIRT6 response but are essential for MYH recruitment to damaged telomeres. Compared to wild-type MYH, the recruitment of hMYHV315A mutant (defective in both SIRT6 and Hus1 interactions), but not hMYHQ324H mutant (defective in Hus1 interaction only), to damaged telomeres is severely reduced. The formation of MYH/SIRT6/9-1-1 complex is of biological significance as interrupting their interactions can increase cell's sensitivity to H2O2 and/or elevate cellular 8-oxoG levels after H2O2 treatment. Our results establish that SIRT6 acts as an early sensor of BER enzymes and both SIRT6 and 9-1-1 serve critical roles in DNA repair to maintain telomere integrity.

Keywords:  DNA damage response; MutY homolog (MYH or MUTYH); SIRT6; checkpoint clamp Rad9/Rad1/Hus1 (9-1-1); telomeres

DOI:  https://doi.org/10.18632/aging.103934
DNA Repair (Amst). 2020 Sep 17. pii: S1568-7864(20)30221-4. [Epub ahead of print]96 102972

Envisioning how the prototypic molecular machine TFIIH functions in transcription initiation and DNA repair.

Susan E Tsutakawa, Chi-Lin Tsai, Chunli Yan, Amer Bralić, Walter J Chazin, Samir M Hamdan, Orlando D Schärer, Ivaylo Ivanov, John A Tainer.

  Critical for transcription initiation and bulky lesion DNA repair, TFIIH provides an exemplary system to connect molecular mechanisms to biological outcomes due to its strong genetic links to different specific human diseases. Recent advances in structural and computational biology provide a unique opportunity to re-examine biologically relevant molecular structures and develop possible mechanistic insights for the large dynamic TFIIH complex. TFIIH presents many puzzles involving how its two SF2 helicase family enzymes, XPB and XPD, function in transcription initiation and repair: how do they initiate transcription, detect and verify DNA damage, select the damaged strand for incision, coordinate repair with transcription and cell cycle through Cdk-activating-kinase (CAK) signaling, and result in very different specific human diseases associated with cancer, aging, and development from single missense mutations? By joining analyses of breakthrough cryo-electron microscopy (cryo-EM) structures and advanced computation with data from biochemistry and human genetics, we develop unified concepts and molecular level understanding for TFIIH functions with a focus on structural mechanisms. We provocatively consider that TFIIH may have first evolved from evolutionary pressure for TCR to resolve arrested transcription blocks to DNA replication and later added its key roles in transcription initiation and global DNA repair. We anticipate that this level of mechanistic information will have significant impact on thinking about TFIIH, laying a robust foundation suitable to develop new paradigms for DNA transcription initiation and repair along with insights into disease prevention, susceptibility, diagnosis and interventions.

Keywords:  DNA damage; DNA repair; Helicase; Nucleotide excision repair; TFIIH; Transcription initiation; Transcription-coupled repair; Translocase; XPB; XPD

DOI:  https://doi.org/10.1016/j.dnarep.2020.102972
Cancer Discov. 2020 Sep 28. pii: CD-20-0868. [Epub ahead of print]

First-in-Human Trial of the Oral Ataxia Telangiectasia and Rad3-Related Inhibitor BAY 1895344 in Patients with Advanced Solid Tumors.

Timothy A Yap, David Sp Tan, Angelika Terbuch, Reece Caldwell, Christina Guo, Boon Cher Goh, Valerie Heong, Noor R Md Haris, Saira Bashir, Yvette Drew, David S Hong, Funda Meric-Bernstam, Gary Wilkinson, Joseph Hreiki, Antje M Wengner, Friedhelm Bladt, Andreas Schlicker, Matthias Ludwig, Yinghui Zhou, Li Liu, Sonal Bordia, Ruth Plummer, Eleni Lagkadinou, Johann S de Bono.

Targeting the ataxia telangiectasia and Rad3-related (ATR) enzyme represents a promising anticancer strategy for tumors with DNA damage response (DDR) defects and replication stress, including inactivation of ataxia telangiectasia mutated (ATM) signaling. We report the dose-escalation portion of the phase I first-in-human trial of oral ATR inhibitor BAY 1895344 intermittently dosed 5-80 mg twice daily (BID) in 21 patients with advanced solid tumors. The maximum tolerated dose was 40 mg BID 3 days on/4 days off. Commonest adverse events were manageable and reversible hematological toxicities. Partial responses were achieved in 4 patients and stable disease in 8 patients. Median duration of response was 315.5 days. Responders had ATM protein loss and/or deleterious ATM mutations and received doses greater than or equal to 40 mg BID. Overall, BAY 1895344 is well tolerated with antitumor activity against cancers with certain DDR defects, including ATM loss. An expansion phase continues in patients with DDR deficiency.

DOI: https://doi.org/10.1158/2159-8290.CD-20-0868
J Cell Sci. 2020 Sep 28. pii: jcs.244129. [Epub ahead of print]

TDP-43 dysfunction results in R-loop accumulation and DNA replication defects.

Matthew Wood, Annabel Quinet, Yea-Lih Lin, Albert A Davis, Philippe Pasero, Yuna M Ayala, Alessandro Vindigni.

  TDP-43 is an RNA binding protein whose aggregation is a hallmark of the neurodegenerative disorders amyotrophic lateral sclerosis (ALS) and frontotemporal dementia. TDP-43 loss increases DNA damage and compromises cell viability, but the actual function of TDP-43 in preventing genome instability remains unclear. Here, we show that loss of TDP-43 increases R-loop formation in a transcription-dependent manner and results in DNA replication stress. TDP-43 nucleic-acid binding and self-assembly activities are important in inhibiting R-loop accumulation and preserving normal DNA replication. We also find that TDP-43 cytoplasmic aggregation impairs TDP-43 function in R-loop regulation. Furthermore, increased R-loop accumulation and DNA damage is observed in neurons upon loss of TDP-43. Together, our findings indicate that TDP-43 function and normal protein homeostasis are critical in maintaining genomic stability through a co-transcriptional process that prevents aberrant R-loop accumulation. We propose that the increased R-loop formation and genomic instability associated with TDP-43 loss are linked to the pathogenesis of TDP-43 proteinopathies.

Keywords:  DNA Replication; R-loops; RNA:DNA hybrids; TDP-43; Tardbp

DOI:  https://doi.org/10.1242/jcs.244129
Front Mol Biosci. 2020 ;7 191

Poly(ADP-Ribose) Glycohydrolase (PARG) vs. Poly(ADP-Ribose) Polymerase (PARP) - Function in Genome Maintenance and Relevance of Inhibitors for Anti-cancer Therapy.

Daniel Harrision, Polly Gravells, Ruth Thompson, Helen E Bryant.

  Poly(ADP-ribose) polymerases (PARPs) are a family of enzymes that catalyze the addition of poly(ADP-ribose) (PAR) subunits onto themselves and other acceptor proteins. PARPs are known to function in a large range of cellular processes including DNA repair, DNA replication, transcription and modulation of chromatin structure. Inhibition of PARP holds great potential for therapy, especially in cancer. Several PARP1/2/3 inhibitors (PARPi) have had success in treating ovarian, breast and prostate tumors harboring defects in the homologous recombination (HR) DNA repair pathway, especially BRCA1/2 mutated tumors. However, treatment is limited to specific sub-groups of patients and resistance can occur, limiting the use of PARPi. Poly(ADP-ribose) glycohydrolase (PARG) reverses the action of PARP enzymes, hydrolysing the ribose-ribose bonds present in poly(ADP-ribose). Like PARPs, PARG is involved in DNA replication and repair and PARG depleted/inhibited cells show increased sensitivity to DNA damaging agents. They also display an accumulation of perturbed replication intermediates which can lead to synthetic lethality in certain contexts. In addition, PARG is thought to play an important role in preventing the accumulation of cytoplasmic PAR and therefore parthanatos, a caspase-independent PAR-mediated type of cell death. In contrast to PARP, the therapeutic potential of PARG has been largely ignored. However, several recent papers have demonstrated the exciting possibilities that inhibitors of this enzyme may have for cancer treatment, both as single agents and in combination with cytotoxic drugs and radiotherapy. This article discusses what is known about the functions of PARP and PARG and the potential future implications of pharmacological inhibition in anti-cancer therapy.

Keywords:  cancer; chemosensitization; poly(ADP-ribose)glycohydrolase (PARG); poly(ADP-ribose)polymerase (PARP); radiosensitization; synthetic lethality

DOI:  https://doi.org/10.3389/fmolb.2020.00191
PLoS Pathog. 2020 Oct;16(10): e1008849

STAT3 imparts BRCAness by impairing homologous recombination repair in Epstein-Barr virus-transformed B lymphocytes.

Michael T McIntosh, Siva Koganti, J Lucas Boatwright, Xiaofan Li, Salvatore V Spadaro, Alexis C Brantly, Jasmine B Ayers, Ramon D Perez, Eric M Burton, Sandeepta Burgula, Thomas MacCarthy, Sumita Bhaduri-McIntosh.

Epstein-Barr virus (EBV) causes lymphomas and epithelial cell cancers. Though generally silent in B lymphocytes, this widely prevalent virus can cause endemic Burkitt lymphoma and post-transplant lymphoproliferative disorders/lymphomas in immunocompromised hosts. By learning how EBV breaches barriers to cell proliferation, we hope to undermine those strategies to treat EBV lymphomas and potentially other cancers. We had previously found that EBV, through activation of cellular STAT3 prevents phosphorylation of Chk1, and thereby, suppresses activation of the intra-S phase cell-cycle checkpoint, a potent barrier to oncogene-driven proliferation. This observation prompted us to examine the consequences on DNA repair since homologous recombination repair, the most error-free form, requires phosphoChk1. We now report that the defect in Chk1 phosphorylation also curtails RAD51 nucleation, and thereby, homologous recombination repair of DNA double strand breaks. The resulting reliance on error-prone microhomology-mediated end-joining (MMEJ) repair makes EBV-transformed cells susceptible to PARP inhibition and simultaneous accrual of genome-wide deletions and insertions resulting from synthesis-dependent MMEJ. Analysis of transcriptomic and drug susceptibility data from hundreds of cancer lines reveals a STAT3-dependent gene-set predictive of susceptibility of cancers to synthetic lethal PARP inhibition. These findings i) demonstrate how the tumor virus EBV re-shapes cellular DNA repair, ii) provide the first genome-wide evidence for insertions resulting from MMEJ in human cells, and iii) expand the range of cancers (EBV-related and -unrelated) that are likely to respond to synthetic lethal inhibitors given the high prevalence of cancers with constitutively active STAT3.

DOI: https://doi.org/10.1371/journal.ppat.1008849
Cancers (Basel). 2020 Sep 25. pii: E2764. [Epub ahead of print]12(10):

Under-Replicated DNA: The Byproduct of Large Genomes?

Agustina P Bertolin, Jean-Sébastien Hoffmann, Vanesa Gottifredi.

  In this review, we provide an overview of how proliferating eukaryotic cells overcome one of the main threats to genome stability: incomplete genomic DNA replication during S phase. We discuss why it is currently accepted that double fork stalling (DFS) events are unavoidable events in higher eukaryotes with large genomes and which responses have evolved to cope with its main consequence: the presence of under-replicated DNA (UR-DNA) outside S phase. Particular emphasis is placed on the processes that constrain the detrimental effects of UR-DNA. We discuss how mitotic DNA synthesis (MiDAS), mitotic end joining events and 53BP1 nuclear bodies (53BP1-NBs) deal with such specific S phase DNA replication remnants during the subsequent phases of the cell cycle.

Keywords:  53BP1; DNA replication stress; RAD52; break-induced repair (BIR); common fragile sites (CFS); double fork stalling (DFS); genomic instability; mitotic DNA synthesis (MiDAS); under-replicated DNA (UR-DNA)

DOI:  https://doi.org/10.3390/cancers12102764
DNA Repair (Amst). 2020 Aug 28. pii: S1568-7864(20)30206-8. [Epub ahead of print]95 102957

Analysis of mutational signatures in C. elegans: Implications for cancer genome analysis.

Bettina Meier, Nadezda V Volkova, Moritz Gerstung, Anton Gartner.

  Genome integrity is constantly challenged by exogenous and endogenous insults, and mutations are associated with inherited disease and cancer. Here we summarize recent studies that utilized C. elegans whole genome next generation sequencing to experimentally determine mutational signatures associated with mutagen exposure, DNA repair deficiency or a combination of both and discuss the implications of these results for the understanding of cancer genome evolution. The experimental analysis of wild-type and DNA repair deficient nematodes propagated under unchallenged conditions over many generations revealed increased mutagenesis in approximately half of all DNA repair deficient strains, its rate, except for DNA mismatch repair, only being moderately increased. The exposure of wild-type and DNA repair defective strains to selected genotoxins, including UV-B and ionizing radiation, alkylating compounds, aristolochic acid, aflatoxin-B1, and cisplatin enabled the systematic analysis of the relative contributions of redundant repair modalities that mend DNA damage. Combining genotoxin exposure with DNA repair deficiency can manifest as altered mutation rates and/or as a change in mutational profiles, and reveals how different DNA alterations induced by one genotoxin are repaired by separate DNA repair pathways, often in a highly redundant way. Cancer genomes provide a snapshot of all mutational events that happened prior to cancer detection and sequencing, necessitating computational models to deduce mutational signatures using mathematical best fit approaches. While computationally deducing signatures from cancer genomes has been tremendously successful in associating some signatures to known mutagenic causes, many inferred signatures lack a clear link to a known mutagenic process. Moreover, analytical signatures might not reflect any distinct mutagenic processes. Nonetheless, combined effects of mutagen exposure and DNA damage-repair deficiency are also present in cancer genomes, but cannot be as easily detected owing to the unknown histories of genotoxic exposures and because biallelic in contrast to monoallelic DNA repair deficiency is rare. The impact of damage-repair interactions also manifests through selective pressure for DNA repair gene inactivation during cancer evolution. Using these considerations, we discuss a theoretical framework that explains why minute mutagenic changes, possibly too small to manifest as change in a signature, can have major effects in oncogenesis. Overall, the experimental analysis of mutational processes underscores that the interpretation of mutational signatures requires considering both the primary DNA lesion and repair status and imply that mutational signatures derived from cancer genomes may be more variable than currently anticipated.

Keywords:  C. elegans; DNA repair; Mutational signatures

DOI:  https://doi.org/10.1016/j.dnarep.2020.102957
Int J Mol Sci. 2020 Sep 28. pii: E7147. [Epub ahead of print]21(19):

Modulation of the Apurinic/Apyrimidinic Endonuclease Activity of Human APE1 and of Its Natural Polymorphic Variants by Base Excision Repair Proteins.

Olga A Kladova, Irina V Alekseeva, Murat Saparbaev, Olga S Fedorova, Nikita A Kuznetsov.

  Human apurinic/apyrimidinic endonuclease 1 (APE1) is known to be a critical player of the base excision repair (BER) pathway. In general, BER involves consecutive actions of DNA glycosylases, AP endonucleases, DNA polymerases, and DNA ligases. It is known that these proteins interact with APE1 either at upstream or downstream steps of BER. Therefore, we may propose that even a minor disturbance of protein-protein interactions on the DNA template reduces coordination and repair efficiency. Here, the ability of various human DNA repair enzymes (such as DNA glycosylases OGG1, UNG2, and AAG; DNA polymerase Polβ; or accessory proteins XRCC1 and PCNA) to influence the activity of wild-type (WT) APE1 and its seven natural polymorphic variants (R221C, N222H, R237A, G241R, M270T, R274Q, and P311S) was tested. Förster resonance energy transfer-based kinetic analysis of abasic site cleavage in a model DNA substrate was conducted to detect the effects of interacting proteins on the activity of WT APE1 and its single-nucleotide polymorphism (SNP) variants. The results revealed that WT APE1 activity was stimulated by almost all tested DNA repair proteins. For the SNP variants, the matters were more complicated. Analysis of two SNP variants, R237A and G241R, suggested that a positive charge in this area of the APE1 surface impairs the protein-protein interactions. In contrast, variant R221C (where the affected residue is located near the DNA-binding site) showed permanently lower activation relative to WT APE1, whereas neighboring SNP N222H did not cause a noticeable difference as compared to WT APE1. Buried substitution P311S had an inconsistent effect, whereas each substitution at the DNA-binding site, M270T and R274Q, resulted in the lowest stimulation by BER proteins. Protein-protein molecular docking was performed between repair proteins to identify amino acid residues involved in their interactions. The data uncovered differences in the effects of BER proteins on APE1, indicating an important role of protein-protein interactions in the coordination of the repair pathway.

Keywords:  AP endonuclease; DNA repair; coordination of DNA repair process; protein–protein interaction; single-nucleotide polymorphism

DOI:  https://doi.org/10.3390/ijms21197147
Front Microbiol. 2020 ;11 582113

Bacterial Chromosome Replication and DNA Repair During the Stringent Response.

Anurag Kumar Sinha, Anders Løbner-Olesen, Leise Riber.

  The stringent response regulates bacterial growth rate and is important for cell survival under changing environmental conditions. The effect of the stringent response is pleiotropic, affecting almost all biological processes in the cell including transcriptional downregulation of genes involved in stable RNA synthesis, DNA replication, and metabolic pathways, as well as the upregulation of stress-related genes. In this Review, we discuss how the stringent response affects chromosome replication and DNA repair activities in bacteria. Importantly, we address how accumulation of (p)ppGpp during the stringent response shuts down chromosome replication using highly different strategies in the evolutionary distant Gram-negative Escherichia coli and Gram-positive Bacillus subtilis. Interestingly, (p)ppGpp-mediated replication inhibition occurs downstream of the origin in B. subtilis, whereas replication inhibition in E. coli takes place at the initiation level, suggesting that stringent cell cycle arrest acts at different phases of the replication cycle between E. coli and B. subtilis. Furthermore, we address the role of (p)ppGpp in facilitating DNA repair activities and cell survival during exposure to UV and other DNA damaging agents. In particular, (p)ppGpp seems to stimulate the efficiency of nucleotide excision repair (NER)-dependent repair of DNA lesions. Finally, we discuss whether (p)ppGpp-mediated cell survival during DNA damage is related to the ability of (p)ppGpp accumulation to inhibit chromosome replication.

Keywords:  (p)ppGpp; Bacillus subtilis; DNA repair; DNA replication; Escherichia coli; genome stability; stringent response

DOI:  https://doi.org/10.3389/fmicb.2020.582113
Cancer Lett. 2020 Sep 26. pii: S0304-3835(20)30485-7. [Epub ahead of print]

Reality CHEK: Understanding the biology and clinical potential of CHK1.

Fiifi Neizer-Ashun, Resham Bhattacharya.

  The DNA damage response enables cells to cope with various stresses that threaten genomic integrity. A critical component of this response is the serine/threonine kinase CHK1 which is encoded by the CHEK1 gene. Originally identified as a regulator of the G2/M checkpoint, CHK1 has since been shown to play important roles in DNA replication, mitotic progression, DNA repair, and overall cell cycle regulation. However, the potential of CHK1 as a cancer therapy has not been realized clinically. Herein we expound our current understanding of the principal roles of CHK1 and highlight different avenues for CHK1 targeting in cancer therapy.

Keywords:  CHK1; Cell cycle; DNA Damage response

DOI:  https://doi.org/10.1016/j.canlet.2020.09.016
Nucleic Acids Res. 2020 Sep 30. pii: gkaa803. [Epub ahead of print]

A hand-off of DNA between archaeal polymerases allows high-fidelity replication to resume at a discrete intermediate three bases past 8-oxoguanine.

Matthew T Cranford, Joseph D Kaszubowski, Michael A Trakselis.

During DNA replication, the presence of 8-oxoguanine (8-oxoG) lesions in the template strand cause the high-fidelity (HiFi) DNA polymerase (Pol) to stall. An early response to 8-oxoG lesions involves 'on-the-fly' translesion synthesis (TLS), in which a specialized TLS Pol is recruited and replaces the stalled HiFi Pol for lesion bypass. The length of TLS must be long enough for effective bypass, but it must also be regulated to minimize replication errors by the TLS Pol. The exact position where the TLS Pol ends and the HiFi Pol resumes (i.e. the length of the TLS patch) has not been described. We use steady-state and pre-steady-state kinetic assays to characterize lesion bypass intermediates formed by different archaeal polymerase holoenzyme complexes that include PCNA123 and RFC. After bypass of 8-oxoG by TLS PolY, products accumulate at the template position three base pairs beyond the lesion. PolY is catalytically poor for subsequent extension from this +3 position beyond 8-oxoG, but this inefficiency is overcome by rapid extension of HiFi PolB1. The reciprocation of Pol activities at this intermediate indicates a defined position where TLS Pol extension is limited and where the DNA substrate is handed back to the HiFi Pol after bypass of 8-oxoG.

DOI: https://doi.org/10.1093/nar/gkaa803
Cancers (Basel). 2020 Sep 24. pii: E2739. [Epub ahead of print]12(10):

Role of POT1 in Human Cancer.

Yangxiu Wu, Rebecca C Poulos, Roger R Reddel.

  Telomere abnormalities facilitate cancer development by contributing to genomic instability and cellular immortalization. The Protection of Telomeres 1 (POT1) protein is an essential subunit of the shelterin telomere binding complex. It directly binds to single-stranded telomeric DNA, protecting chromosomal ends from an inappropriate DNA damage response, and plays a role in telomere length regulation. Alterations of POT1 have been detected in a range of cancers. Here, we review the biological functions of POT1, the prevalence of POT1 germline and somatic mutations across cancer predisposition syndromes and tumor types, and the dysregulation of POT1 expression in cancers. We propose a framework for understanding how POT1 abnormalities may contribute to oncogenesis in different cell types. Finally, we summarize the clinical implications of POT1 alterations in the germline and in cancer, and possible approaches for the development of targeted cancer therapies.

Keywords:  POT1; alternative lengthening of telomeres; cancer; genomic instability; mutation; shelterin; telomerase; telomere; telomere length

DOI:  https://doi.org/10.3390/cancers12102739
Cancers (Basel). 2020 Sep 30. pii: E2813. [Epub ahead of print]12(10):

Radio-Resistance and DNA Repair in Pediatric Diffuse Midline Gliomas.

Henriette Pedersen, Kjeld Schmiegelow, Petra Hamerlik.

  Malignant gliomas (MG) are among the most prevalent and lethal primary intrinsic brain tumors. Although radiotherapy (RT) is the most effective nonsurgical therapy, recurrence is universal. Dysregulated DNA damage response pathway (DDR) signaling, rampant genomic instability, and radio-resistance are among the hallmarks of MGs, with current therapies only offering palliation. A subgroup of pediatric high-grade gliomas (pHGG) is characterized by H3K27M mutation, which drives global loss of di- and trimethylation of histone H3K27. Here, we review the most recent literature and discuss the key studies dissecting the molecular biology of H3K27M-mutated gliomas in children. We speculate that the aberrant activation and/or deactivation of some of the key components of DDR may be synthetically lethal to H3K27M mutation and thus can open novel avenues for effective therapeutic interventions for patients suffering from this deadly disease.

Keywords:  DNA damage response; H3K27M mutation; pediatric high-grade gliomas; radio-resistance

DOI:  https://doi.org/10.3390/cancers12102813
Ther Adv Med Oncol. 2020 ;12 1758835920958354

Exploiting DNA repair defects in triple negative breast cancer to improve cell killing.

Kevin J Lee, Elise Mann, Griffin Wright, Cortt G Piett, Zachary D Nagel, Natalie R Gassman.

   Background: The lack of molecular targets for triple negative breast cancer (TNBC) has limited treatment options and reduced survivorship. Identifying new molecular targets may help improve patient survival and decrease recurrence and metastasis. As DNA repair defects are prevalent in breast cancer, we evaluated the expression and repair capacities of DNA repair proteins in preclinical models.
Methods: DNA repair capacity was analyzed in four TNBC cell lines, MDA-MB-157 (MDA-157), MDA-MB-231 (MDA-231), MDA-MB-468 (MDA-468), and HCC1806, using fluorescence multiplex host cell reactivation (FM-HCR) assays. Expression of DNA repair genes was analyzed with RNA-seq, and protein expression was evaluated with immunoblot. Responses to the combination of DNA damage response inhibitors and primary chemotherapy drugs doxorubicin or carboplatin were evaluated in the cell lines.
Results: Defects in base excision and nucleotide excision repair were observed in preclinical TNBC models. Gene expression analysis showed a limited correlation between these defects. Loss in protein expression was a better indicator of these DNA repair defects. Over-expression of PARP1, XRCC1, RPA, DDB1, and ERCC1 was observed in TNBC preclinical models, and likely contributed to altered sensitivity to chemotherapy and DNA damage response (DDR) inhibitors. Improved cell killing was achieved when primary therapy was combined with DDR inhibitors for ATM, ATR, or CHK1.
Conclusion: Base excision and nucleotide excision repair pathways may offer new molecular targets for TNBC. The functional status of DNA repair pathways should be considered when evaluating new therapies and may improve the targeting for primary and combination therapies with DDR inhibitors.

Keywords:  DNA damage; chemotherapy; homologous recombination; nonhomologous end joining; nucleotide excision repair; small molecule inhibitor

DOI:  https://doi.org/10.1177/1758835920958354
J Biol Chem. 2020 Sep 28. pii: jbc.RA120.015450. [Epub ahead of print]

A human cancer cell line initiates DNA replication normally in the absence of ORC5 and ORC2 proteins.

Etsuko Shibata, Anindya Dutta.

  The Origin Recognition Complex (ORC), composed of six subunits, ORC1-6, binds to origins of replication as a ring-shaped heterohexameric ATPase that is believed to be essential to recruit and load MCM2-7, the minichromosome maintenance protein complex, around DNA and initiate DNA replication. We previously reported the creation of viable cancer cell lines that lacked detectable ORC1 or ORC2 protein without a reduction in the number of origins firing. Here, using CRISPR-Cas9 mediated mutations, we report that human HCT116 colon cancer cells also survive when ORC5 protein expression is abolished via a mutation in the initiator ATG of the ORC5 gene. Even if an internal methionine is used to produce an undetectable, N terminally deleted ORC5, the protein would lack 80% of the AAA+ ATPase domain, including the Walker A motif. The ORC5-depleted cells show normal chromatin binding of MCM2-7 and initiate replication from similar number of origins as wild type cells. In addition, we introduced a second mutation in ORC2 in the ORC5 mutant cells rendering both ORC5 and ORC2 proteins undetectable in the same cells, and destabilizing the ORC1, ORC3 and ORC4 proteins. Yet the double mutant cells grow, recruit MCM2-7 normally to chromatin and initiate DNA replication with normal number of origins. Thus, in these selected cancer cells, either a crippled ORC lacking ORC2 and ORC5 and present at minimal levels on the chromatin can recruit and load enough MCM2-7 to initiate DNA replication, or human cell-lines can sometimes recruit MCM2-7 to origins independent of ORC.

Keywords:  DNA replication; cancer; cell proliferation; chromatin; gene knockout

DOI:  https://doi.org/10.1074/jbc.RA120.015450
Nat Commun. 2020 09 28. 11(1): 4868

Ubiquitin and TFIIH-stimulated DDB2 dissociation drives DNA damage handover in nucleotide excision repair.

Cristina Ribeiro-Silva, Mariangela Sabatella, Angela Helfricht, Jurgen A Marteijn, Arjan F Theil, Wim Vermeulen, Hannes Lans.

DNA damage sensors DDB2 and XPC initiate global genome nucleotide excision repair (NER) to protect DNA from mutagenesis caused by helix-distorting lesions. XPC recognizes helical distortions by binding to unpaired ssDNA opposite DNA lesions. DDB2 binds to UV-induced lesions directly and facilitates efficient recognition by XPC. We show that not only lesion-binding but also timely DDB2 dissociation is required for DNA damage handover to XPC and swift progression of the multistep repair reaction. DNA-binding-induced DDB2 ubiquitylation and ensuing degradation regulate its homeostasis to prevent excessive lesion (re)binding. Additionally, damage handover from DDB2 to XPC coincides with the arrival of the TFIIH complex, which further promotes DDB2 dissociation and formation of a stable XPC-TFIIH damage verification complex. Our results reveal a reciprocal coordination between DNA damage recognition and verification within NER and illustrate that timely repair factor dissociation is vital for correct spatiotemporal control of a multistep repair process.

DOI: https://doi.org/10.1038/s41467-020-18705-0
Nucleic Acids Res. 2020 Sep 28. pii: gkaa751. [Epub ahead of print]

Structural basis of DNA replication origin recognition by human Orc6 protein binding with DNA.

Naining Xu, Yingying You, Changdong Liu, Maxim Balasov, Lee Tung Lun, Yanyan Geng, Chun Po Fung, Haitao Miao, Honglei Tian, To To Choy, Xiao Shi, Zhuming Fan, Bo Zhou, Katarina Akhmetova, Rahman Ud Din, Hongyu Yang, Quan Hao, Peiyuan Qian, Igor Chesnokov, Guang Zhu.

The six-subunit origin recognition complex (ORC), a DNA replication initiator, defines the localization of the origins of replication in eukaryotes. The Orc6 subunit is the smallest and the least conserved among ORC subunits. It is required for DNA replication and essential for viability in all species. Orc6 in metazoans carries a structural homology with transcription factor TFIIB and can bind DNA on its own. Here, we report a solution structure of the full-length human Orc6 (HsOrc6) alone and in a complex with DNA. We further showed that human Orc6 is composed of three independent domains: N-terminal, middle and C-terminal (HsOrc6-N, HsOrc6-M and HsOrc6-C). We also identified a distinct DNA-binding domain of human Orc6, named as HsOrc6-DBD. The detailed analysis of the structure revealed novel amino acid clusters important for the interaction with DNA. Alterations of these amino acids abolish DNA-binding ability of Orc6 and result in reduced levels of DNA replication. We propose that Orc6 is a DNA-binding subunit of human/metazoan ORC and may play roles in targeting, positioning and assembling the functional ORC at the origins.

DOI: https://doi.org/10.1093/nar/gkaa751
Mol Cell Biol. 2020 Sep 28. pii: MCB.00306-20. [Epub ahead of print]

Loss of mitochondrial localization of human FANCG causes defective FANCJ helicase.

Jagadeesh Chandra Bose K, Bishwajit Singh Kapoor, Kamal Mondal, Shubhrima Ghosh, Raveendra B Mokhamatam, Sunil K Manna, Sudit S Mukhopadhyay.

Fanconi anemia (FA) is a unique DNA damage repair pathway. To date, twenty-two genes have been identified which are associated with the FA pathway. Defect in any of those genes causes genomic instability, and the patients bear the mutation become susceptible to cancer. In our earlier work, we have identified that Fanconi anemia protein G (FANCG) protects the mitochondria from oxidative stress. In this report, we have identified eight patients having mutation (C.65G>C; p.Arg22Pro) in the N-terminal of FANCG. The mutant protein hFANCGR22P is able to repair the DNA and able to retain the monoubiquitination of FANCD2 in FANCGR22P/FGR22P cell. However, it lost mitochondrial localization and failed to protect mitochondria from oxidative stress. Mitochondrial instability in the FANCGR22P cell causes the transcriptional down-regulation of mitochondrial iron-sulfur cluster biogenesis protein Frataxin (FXN) and resulting iron deficiency of FA protein FANCJ, an iron-sulfur containing helicase involved in DNA repair.

DOI: https://doi.org/10.1128/MCB.00306-20
Front Cell Dev Biol. 2020 ;8 813

PP2A Regulates Phosphorylation-Dependent Isomerization of Cytoplasmic and Mitochondrial-Associated ATR by Pin1 in DNA Damage Responses.

Yetunde Makinwa, Brian M Cartwright, Phillip R Musich, Zhengke Li, Himadri Biswas, Yue Zou.

  Ataxia telangiectasia and Rad3-related protein (ATR) is a serine/threonine-protein kinase of the PI3K family and is well known for its key role in regulating DNA damage responses in the nucleus. In addition to its nuclear functions, ATR also was found to be a substrate of the prolyl isomerase Pin1 in the cytoplasm where Pin1 isomerizes cis ATR at the Ser428-Pro429 motif, leading to formation of trans ATR. Cis ATR is an antiapoptotic protein at mitochondria upon UV damage. Here we report that Pin1's activity on cis ATR requires the phosphorylation of the S428 residue of ATR and describe the molecular mechanism by which Pin1-mediated ATR isomerization in the cytoplasm is regulated. We identified protein phosphatase 2A (PP2A) as the phosphatase that dephosphorylates Ser428 following DNA damage. The dephosphorylation led to an increased level of the antiapoptotic cis ATR (ATR-H) in the cytoplasm and, thus, its accumulation at mitochondria via binding with tBid. Inhibition or depletion of PP2A promoted the isomerization by Pin1, resulting in a reduction of cis ATR with an increased level of trans ATR. We conclude that PP2A plays an important role in regulating ATR's anti-apoptotic activity at mitochondria in response to DNA damage. Our results also imply a potential strategy in enhancing cancer therapies via selective moderation of cis ATR levels.

Keywords:  ATR; ATR antiapoptotic activity at mitochondria; BID; DNA damage response; PP2A; Pin1; UV irradiation

DOI:  https://doi.org/10.3389/fcell.2020.00813
EMBO Rep. 2020 Oct 01. e48676

Ewing sarcoma protein promotes dissociation of poly(ADP-ribose) polymerase 1 from chromatin.

Seon-Gyeong Lee, Namwoo Kim, Su-Min Kim, In Bae Park, Hyejin Kim, Shinseog Kim, Byung-Gyu Kim, Jung Me Hwang, In-Joon Baek, Anton Gartner, Jun Hong Park, Kyungjae Myung.

  Poly(ADP-ribose) polymerase 1 (PARP1) facilitates DNA damage response (DDR). While the Ewing's sarcoma breakpoint region 1 (EWS) protein fused to FLI1 triggers sarcoma formation, the physiological function of EWS is largely unknown. Here, we investigate the physiological role of EWS in regulating PARP1. We show that EWS is required for PARP1 dissociation from damaged DNA. Abnormal PARP1 accumulation caused by EWS inactivation leads to excessive Poly(ADP-Ribosy)lation (PARylation) and triggers cell death in both in vitro and in vivo models. Consistent with previous work, the arginine-glycine-glycine (RGG) domain of EWS is essential for PAR chain interaction and PARP1 dissociation from damaged DNA. Ews and Parp1 double mutant mice do not show improved survival, but supplementation with nicotinamide mononucleotides extends Ews-mutant pups' survival, which might be due to compensatory activation of other PARP proteins. Consistently, PARP1 accumulates on chromatin in Ewing's sarcoma cells expressing an EWS fusion protein that cannot interact with PARP1, and tissues derived from Ewing's sarcoma patients show increased PARylation. Taken together, our data reveal that EWS is important for removing PARP1 from damaged chromatin.

Keywords:   EWS ; PAR ; DNA damage response; PARP-1; PARylation

DOI:  https://doi.org/10.15252/embr.201948676
Invest New Drugs. 2020 Sep 26.

The bromodomain and extra-terminal domain inhibitor JQ1 synergistically sensitizes human colorectal cancer cells to topoisomerase I inhibitors through repression of Mre11-mediated DNA repair pathway.

Linping Lei, Xuqin Xie, Long He, Keling Chen, Zhaoying Lv, Bin Zhou, Yuan Li, Wenjun Hu, Zongguang Zhou.

  Camptothecin (CPT) and its derivatives, irinotecan and topotecan are specific topoisomerase I (Top1) inhibitors and potent anticancer drugs. Mechanistically, they induce DNA double-strand breaks (DSBs). Although CPT is an effective chemotherapeutic agent used in the management of advanced colorectal cancer, there exist associated side effects. Herein, we aimed to establish novel drug combinations that can effectively aid in managing the CPT-related side effects. Besides, bromodomain and extra-terminal domain (BET) inhibitors have proved as promising drugs that target epigenetic mechanisms in various cancers, they alter DNA repair processes, hence are a potential candidate for CPT synthetic lethality. A novel BET inhibitor JQ1 synergized with CPT, exerted antiproliferative effects. Through cell cycle analyses and apoptosis assays, we revealed that a combination of CPT and JQ1 induces subG1-phase arrest and enhances cell apoptosis. This combination increased the intensity of γ-H2AX staining, a specific marker of DSBs. Moreover, colorectal cancer cells highly expressing Top1 showed greater sensitivity to JQ1, which was lowered through the lentiviral shRNA-mediated knockdown of Top1. JQ1, combined with CPT, impeded the recruitment of the Mre11-mediated MRN complex. Finally, JQ1 enhanced the in vivo sensitivity of tumors to CPT without inducing toxicity. These results demonstrate that a combination of BET inhibitor with Top1 inhibitor is safe and exerts positive chemotherapeutic effects in colorectal cancer.

Keywords:  BET inhibitor; Colorectal cancer; Combination therapy; DNA repair; Topoisomerase I inhibitor

DOI:  https://doi.org/10.1007/s10637-020-01014-0
NAR Cancer. 2020 Sep;2(3): zcaa023

Single-nucleotide polymorphism of the DNA cytosine deaminase APOBEC3H haplotype I leads to enzyme destabilization and correlates with lung cancer.

Mark A Hix, Lai Wong, Ben Flath, Linda Chelico, G Andrés Cisneros.

A number of APOBEC family DNA cytosine deaminases can induce mutations in tumor cells. APOBEC3H haplotype I is one of the deaminases that has been proposed to cause mutations in lung cancer. Here, we confirmed that APOBEC3H haplotype I can cause uracil-induced DNA damage in lung cancer cells that results in γH2AX foci. Interestingly, the database of cancer biomarkers in DNA repair genes (DNArCdb) identified a single-nucleotide polymorphism (rs139298) of APOBEC3H haplotype I that is involved in lung cancer. While we thought this may increase the activity of APOBEC3H haplotype I, instead we found through computational modeling and cell-based experiments that this single-nucleotide polymorphism causes the destabilization of APOBEC3H Haplotype I. Computational analysis suggests that the resulting K121E change affects the structure of APOBEC3H leading to active site disruption and destabilization of the RNA-mediated dimer interface. A K117E mutation in a K121E background stabilized the APOBEC3H haplotype I, thus enabling biochemical study. Subsequent analysis showed that K121E affected catalytic activity, single-stranded DNA binding and oligomerization on single-stranded DNA. The destabilization of a DNA mutator associated with lung cancer supports the model that too much APOBEC3-induced mutation could result in immune recognition or death of tumor cells.

DOI: https://doi.org/10.1093/narcan/zcaa023
DNA Repair (Amst). 2020 Sep 19. pii: S1568-7864(20)30223-8. [Epub ahead of print]96 102974

Nanoscale insight into chromatin remodeling and DNA repair complex in HeLa cells after ionizing radiation.

Ruqun Wu, Wenjing Liu, Yujie Sun, Cheng Shen, Jinlong Guo, Jing Zhao, Guangbo Mao, Yaning Li, Guanghua Du.

  The dynamic structure of nuclear chromatin and its regulation in the formation of repair complex is essential in DNA damage response and repair. Using single molecule localization microscopy STORM this work discovered that the nuclear chromatin organization was relaxed from 200 to 400 nm thick irregular frame and remodeled to dispersed sub-100 nm structure in HeLa cells after X-ray irradiation. The DSB repair factors (γ-H2AX, MDC1, 53BP1) showed distribution as microscale-colocalized and nanoscale interlaced substructure in the DSB repair complex. The dual-color nanoscopic imaging of γ-H2AX and chromatin at the DSB sites suggest that DNA damage response and repair cascade are chromatin structure-dependent and also partly dependent on the distance to the DSB sites. The sub-100 nm structure of fibers and nanoclusters of the relaxed nuclear chromatin and the DSB repair factors highly resembled the cross-section view of chromatin organization. These data demonstrated the polymorphic and dynamic behavior of the chromatin organization in vivo, and provided nanoscale insight into the interplay between chromatin remodeling and DNA damage response and DNA repair.

Keywords:  Chromatin remodeling; DNA double-strand break; DNA repair; Ionizing radiation; Single molecule localization microscopy

DOI:  https://doi.org/10.1016/j.dnarep.2020.102974
Proc Natl Acad Sci U S A. 2020 Sep 28. pii: 202010972. [Epub ahead of print]

CtIP-mediated DNA resection is dispensable for IgH class switch recombination by alternative end-joining.

Xiaobin S Wang, Junfei Zhao, Foon Wu-Baer, Zhengping Shao, Brian J Lee, Olivia M Cupo, Raul Rabadan, Jean Gautier, Richard Baer, Shan Zha.

  To generate antibodies with different effector functions, B cells undergo Immunoglobulin Heavy Chain (IgH) class switch recombination (CSR). The ligation step of CSR is usually mediated by the classical nonhomologous end-joining (cNHEJ) pathway. In cNHEJ-deficient cells, a remarkable ∼25% of CSR can be achieved by the alternative end-joining (Alt-EJ) pathway that preferentially uses microhomology (MH) at the junctions. While A-EJ-mediated repair of endonuclease-generated breaks requires DNA end resection, we show that CtIP-mediated DNA end resection is dispensable for A-EJ-mediated CSR using cNHEJ-deficient B cells. High-throughput sequencing analyses revealed that loss of ATM/ATR phosphorylation of CtIP at T855 or ATM kinase inhibition suppresses resection without altering the MH pattern of the A-EJ-mediated switch junctions. Moreover, we found that ATM kinase promotes Alt-EJ-mediated CSR by suppressing interchromosomal translocations independent of end resection. Finally, temporal analyses reveal that MHs are enriched in early internal deletions even in cNHEJ-proficient B cells. Thus, we propose that repetitive IgH switch regions represent favored substrates for MH-mediated end-joining contributing to the robustness and resection independence of A-EJ-mediated CSR.

Keywords:  CtIP; alternative end-joining; class switch recombination

DOI:  https://doi.org/10.1073/pnas.2010972117
Cell Chem Biol. 2020 Sep 23. pii: S2451-9456(20)30377-9. [Epub ahead of print]

Proteomics-Based Identification of DUB Substrates Using Selective Inhibitors.

Jonathan W Bushman, Katherine A Donovan, Nathan J Schauer, Xiaoxi Liu, Wanyi Hu, Anthony C Varca, Sara J Buhrlage, Eric S Fischer.

  Deubiquitinating enzymes (DUBs) catalyze the removal of ubiquitin, thereby reversing the activity of E3 ubiquitin ligases and are central to the control of protein abundance and function. Despite the growing interest in DUBs as therapeutic targets, cellular functions for DUBs remain largely unknown and technical challenges often preclude the identification of DUB substrates in a comprehensive manner. Here, we demonstrate that treatment with potent DUB inhibitors coupled to mass spectrometry-based proteomics can identify DUB substrates at a proteome-wide scale. We applied this approach to USP7, a DUB widely investigated as a therapeutic target and identified many known substrates and additional targets. We demonstrate that USP7 substrates are enriched for DNA repair enzymes and E3 ubiquitin ligases. This work provides not only a comprehensive annotation of USP7 substrates, but a general protocol widely applicable to other DUBs, which is critical for translational development of DUB targeted agents.

Keywords:  DUBs; chemical probe; deubiquitinating enzymes; drug discovery; proteomics

DOI:  https://doi.org/10.1016/j.chembiol.2020.09.005
Biochim Biophys Acta Bioenerg. 2020 Sep 26. pii: S0005-2728(20)30171-7. [Epub ahead of print] 148321

Investigating the amino acid sequences of membrane bound dihydroorotate:quinone oxidoreductases (DHOQOs): structural and functional implications.

Filipe M Sousa, Patricia N Refojo, Manuela M Pereira.

  Dihydroorotate:quinone oxidoreductases (DHOQOs) are membrane bound enzymes responsible for oxidizing dihydroorotate (DHO) to orotate with concomitant reduction of quinone to quinol. They have FMN as prosthetic group and are part of the monotopic quinone reductase superfamily. These enzymes are also members of the dihydroorotate dehydrogenases (DHODHs) family, which besides membrane bound DHOQOs, class 2, includes soluble enzymes which reduce either NAD+ or fumarate, class 1. As key enzymes in both the de novo pyrimidine biosynthetic pathway as well as in the energetic metabolism, inhibitors of DHOQOs have been investigated as leads for therapeutics in cancer, immunological disorders and bacterial/viral infections. This work is a thorough bioinformatic approach on the structural conservation and taxonomic distribution of DHOQOs. We explored previously established structural/functional hallmarks of these enzymes, while searching for uncharacterized common elements. We also discuss the cellular role of DHOQOs and organize the identified protein sequences within six sub-classes 2A to 2F, according to their taxonomic origin and sequence traits. We concluded that DHOQOs are present in Archaea, Eukarya and Bacteria, including the first recognition in Gram-positive organisms. DHOQOs can be the single dihydroorotate dehydrogenase encoded in the genome of a species, or they can coexist with other DHODHs, as the NAD+ or fumarate reducing enzymes. Furthermore, we show that the type of catalytic base present in the active site is not an absolute criterium to distinguish between class 1 and class 2 enzymes. We propose the existence of a quinone binding motif ("ExAH") adjacent to a hydrophobic cavity present in the membrane interacting N-terminal domain.

Keywords:  flavoproteins; monotopic quinone reductases; nucleotide metabolism; respiratory chain; taxonomic profile

DOI:  https://doi.org/10.1016/j.bbabio.2020.148321
Cancer Res. 2020 Sep 30. pii: canres.0852.2019. [Epub ahead of print]

Specific mechanisms of chromosomal instability indicate therapeutic sensitivities in high-grade serous ovarian carcinoma.

Naoka Tamura, Nadeem Shaikh, Daniel Muliaditan, Tanya N Soliman, Jennifer R McGuinness, Eleni Maniati, Daniela Moralli, Mary-Anne Durin, Catherine M Green, Frances R Balkwill, Jun Wang, Kit Curtius, Sarah E McClelland.

Chromosomal instability (CIN) comprises continual gain and loss of chromosomes or parts of chromosomes and occurs in the majority of cancers, often conferring poor prognosis. Due to a scarcity of functional studies and poor understanding of how genetic or gene expression landscapes connect to specific CIN mechanisms, causes of CIN in most cancer types remain unknown. High-grade serous ovarian carcinoma (HGSC), the most common subtype of ovarian cancer, is the major cause of death due to gynaecological malignancy in the Western world, with chemotherapy resistance developing in almost all patients. HGSC exhibits high rates of chromosomal aberrations and knowledge of causative mechanisms would represent an important step towards combating this disease. Here we perform the first in-depth functional characterization of mechanisms driving CIN in HGSC in seven cell lines that accurately recapitulate HGSC genetics. Multiple mechanisms co-existed to drive CIN in HGSC, including elevated microtubule dynamics and DNA replication stress that can be partially rescued to reduce CIN by low doses of paclitaxel and nucleoside supplementation, respectively. Distinct CIN mechanisms indicated relationships with HGSC-relevant therapy including Poly (ADP-Ribose) Polymerase (PARP) inhibition and microtubule-targeting agents. Comprehensive genomic and transcriptomic profiling revealed deregulation of various genes involved in genome stability but were not directly predictive of specific CIN mechanisms, underscoring the importance of functional characterization to identify causes of CIN. Overall, we show that HGSC CIN is complex and suggest that specific CIN mechanisms could be used as functional biomarkers to indicate appropriate therapy.

DOI: https://doi.org/10.1158/0008-5472.CAN-19-0852
Antiviral Res. 2020 Sep 24. pii: S0166-3542(20)30362-4. [Epub ahead of print] 104948

Tenofovir alafenamide does not inhibit mitochondrial function and cholesterol biosynthesis in human T lymphoblastoid cell line.

Min Li, Lei Zhou, Harold G Dorsey, Charles Musoff, Dereck Amakye Jnr, Natalie Schoen, Kweku Djan, Elijah Paintsil.

  In clinical trials, the concentration of tenofovir diphosphate (TFV-DP) in peripheral mononuclear cells was 4 to 5-fold higher in individuals treated with tenofovir alafenamide (TAF) compared to individuals treated with tenofovir disoproxil fumarate (TDF). We hypothesized that the higher intracellular accumulation of TFV-DP could cause mitochondrial toxicity from either polymerase gamma (Pol-γ)-dependent or Pol-γ-independent mechanism(s). To test this hypothesis, we cultured human T lymphoblastoid cell line (CEM cells) for up to 12 days with TAF or TDF (multiplicities of Cmax) to investigate the effects on mitochondrial function and respiration, and cholesterol biosynthesis. Both TAF and TDF treatments had no significant effect on cell growth, mitochondrial potential (ΔΨ), production of reactive oxygen species (ROS), and mitochondrial respiratory parameters. TAF had no statistically significant effect on expression of Pol-γ mRNA, mitochondria DNA (mtDNA) content, expression of proteins of the electron transport chain (ETC), and key genes of cholesterol biosynthesis. TDF had significant reduction in mtDNA content at 8xCmax, and statistically significant reduction in mRNA expression of squalene epoxidase (SQLE). Our findings do not support our hypothesis that the higher intracellular accumulation of TFV-DP in cells treated with TAF could cause mitochondrial dysfunction. In conclusion, our findings add to the emerging data that TAF may have a low potential for causing mitochondrial toxicity in HIV-infected individuals on TAF-containing regimens.

Keywords:  Antiretroviral toxicity; Cholesterol biosynthesis; Mitochondria function; Nucleoside reverse transcriptase inhibitors; Tenofovir alafenamide

DOI:  https://doi.org/10.1016/j.antiviral.2020.104948
Exp Oncol. 2020 09;42(3): 220-223

Comparative evaluation of purine dysmetabolism in gastric and pulmonary adenocarcinomas.

Y V Dumanskiy, O Y Stoliarova, O V Syniachenko, R F Aliev, М V Iermolaeva, О P Sokrut.

AIM: To study the state of purine metabolism in gastric (GAC) and pulmonary (PAC) adenocarcinomas and to assess its clinical and pathogenetic significance.
PATIENTS AND METHODS: One hundred and six male patients were examined, among whom were 63 subjects aged 34 to 79 suffering from GAC, and 43 subjects aged 24 to 76 suffering from PAC. In GAC, the ratio of the pyloric, corporeal and antral localization of the tumor and variant of overall gastric lesion accounted to 24:5:1:1; and that of the central and peripheral PAC was 2:1. Serum levels of purine metabolism products (uric acid, oxypurinol, adenine, guanine, xanthine, hypoxanthine) were measured and activities of xanthine oxidase, xanthine deaminase, adenosine deaminase and 5-nucleotidase were analyzed.
RESULTS: Purine metabolism disorders are observed in all GAC and 91% of PAC patients; among other things, hyperuricemia is observed in ¾ and ½ of cases, respectively; moreover, the nature of changes is more pronounced in gastric cancer and, in both groups of patients, these indices reflect the disease course severity, are associated with the neoplastic process localization, have a predictive value, trigger the development of metastases.
CONCLUSION: Сhanges in purine metabolism are involved in the pathogenetic patterns of GAC and PAC, reflect the course of the tumor process, are associated with tumor localization and have prognostic significance.