bims-numges 2020-07-05 papers

bims-numges

Biomed News

on Nucleotide metabolism and genome stability

Issue of 2020–07–05
37 papers selected by
Sean Rudd, Karolinska Institutet

The plasticity of DNA replication forks in response to clinically relevant genotoxic stress.
Poly(ADP-ribose) glycohydrolase inhibition sequesters NAD+ to potentiate the metabolic lethality of alkylating chemotherapy in IDH mutant tumor cells.
Telomere Stress Potentiates STING-Dependent Anti-tumor Immunity.
Interferon-stimulated gene 15 accelerates replication fork progression inducing chromosomal breakage.
Folate stress induces SLX1- and RAD51-dependent mitotic DNA synthesis at the fragile X locus in human cells.
METTL3 and N6-Methyladenosine Promote Homologous Recombination-Mediated Repair of DSBs by Modulating DNA-RNA Hybrid Accumulation.
Screen identifies DYRK1B network as mediator of transcription repression on damaged chromatin.
Conditional knockout of RAD51-related genes in Leishmania major reveals a critical role for homologous recombination during genome replication.
Persistent telomere cohesion protects aged cells from premature senescence.
Jack of all trades? The versatility of RNA in DNA double-strand break repair.
RADX condenses single-stranded DNA to antagonize RAD51 loading.
ATR-CHK1 pathway as a therapeutic target for acute and chronic leukemias.
Modulation of DNA Damage Response by Sphingolipid Signaling: An Interplay that Shapes Cell Fate.
TREX1 - Apex predator of cytosolic DNA metabolism.
DNA Repair and Ovarian Carcinogenesis: Impact on Risk, Prognosis and Therapy Outcome.
The Intermediate Filament Synemin Regulates Non-Homologous End Joining in an ATM-Dependent Manner.
Role of DNA repair defects in predicting immunotherapy response.
JMJD6 participates in the maintenance of ribosomal DNA integrity in response to DNA damage.
The role of PARP inhibitors in germline BRCA-associated pancreatic ductal adenocarcinoma.
DNA-PK in human malignant disorders: Mechanisms and implications for pharmacological interventions.
Synergistic therapy with tangeretin and 5-fluorouracil accelerates the ROS/JNK mediated apoptotic pathway in human colorectal cancer cell.
Twenty years of t-loops: A case study for the importance of collaboration in molecular biology.
Dendrogenin A synergizes with Cytarabine to Kill Acute Myeloid Leukemia Cells In Vitro and In Vivo.
Targeting DNA Damage Repair Pathways in Pancreatic Adenocarcinoma.
A genome-wide and cotranscriptional suppressor of R loops.
Chromatin Architectural Factors as Safeguards against Excessive Supercoiling during DNA Replication.
Expression of a germline variant in the N-terminal domain of the human DNA glycosylase NTHL1 induces cellular transformation without impairing enzymatic function or substrate specificity.
Not Black or White but Shades of Gray: Homologous Recombination Deficiency as a Continuous Variable Modulated by RNF168.
DSS1 and ssDNA regulate oligomerization of BRCA2.
Immunofluorescence Imaging of DNA Damage and Repair Foci in Human Colon Cancer Cells.
Inhibition of O-GlcNAc transferase renders prostate cancer cells dependent on CDK9.
Recognition and Unfolding of c-MYC and Telomeric G-Quadruplex DNAs by the RecQ C-Terminal Domain of Human Bloom Syndrome Helicase.
A comprehensive population-based study comparing the phenotype and genotype in a pretherapeutic screen of dihydropyrimidine dehydrogenase deficiency.
The transcription factors aryl hydrocarbon receptor and MYC cooperate in the regulation of cellular metabolism.
A novel stop-gain mutation in DPYS gene causing Dihidropyrimidinase deficiency, a case report.
Pharmacokinetics of Gemcitabine and its Amino Acid Ester Prodrug following Intravenous and Oral Administrations in Mice.
Impact of DPYD, DPYS and UPB1 gene variations on severe drug-related toxicity in cancer patients.

Nat Rev Mol Cell Biol. 2020 Jul 01.

The plasticity of DNA replication forks in response to clinically relevant genotoxic stress.

Matteo Berti, David Cortez, Massimo Lopes.

Complete and accurate DNA replication requires the progression of replication forks through DNA damage, actively transcribed regions, structured DNA and compact chromatin. Recent studies have revealed a remarkable plasticity of the replication process in dealing with these obstacles, which includes modulation of replication origin firing, of the architecture of replication forks, and of the functional organization of the replication machinery in response to replication stress. However, these specialized mechanisms also expose cells to potentially dangerous transactions while replicating DNA. In this Review, we discuss how replication forks are actively stalled, remodelled, processed, protected and restarted in response to specific types of stress. We also discuss adaptations of the replication machinery and the role of chromatin modifications during these transactions. Finally, we discuss interesting recent data on the relevance of replication fork plasticity to human health, covering its role in tumorigenesis, its crosstalk with innate immunity responses and its potential as an effective cancer therapy target.

DOI: https://doi.org/10.1038/s41580-020-0257-5
Cancer Discov. 2020 Jun 30. pii: CD-20-0226. [Epub ahead of print]

Poly(ADP-ribose) glycohydrolase inhibition sequesters NAD+ to potentiate the metabolic lethality of alkylating chemotherapy in IDH mutant tumor cells.

Hiroaki Nagashima, Christine K Lee, Kensuke Tateishi, Fumi Higuchi, Megha Subramanian, Seamus Rafferty, Lisa Melamed, Julie J Miller, Hiroaki Wakimoto, Daniel P Cahill.

Nicotinamide adenine dinucleotide (NAD+) is an essential cofactor metabolite and is the currency of metabolic transactions critical for cell survival. Depending on tissue context and genotype, cancer cells have unique dependencies on NAD+ metabolic pathways. Poly(ADP-ribose) polymerases (PARPs) catalyze oligomerization of NAD+ monomers into poly(ADP-ribose) (PAR) chains during cellular response to alkylating chemotherapeutics, including procarbazine or temozolomide. Here, we find that, in endogenous IDH1 mutant tumor models, alkylator-induced cytotoxicity is markedly augmented by pharmacologic inhibition or genetic knockout of the PAR breakdown enzyme poly(ADP-ribose) glycohydrolase (PARG). Both in vitro and in vivo, we observe that concurrent alkylator and PARG inhibition depletes freely available NAD+ by preventing PAR breakdown, resulting in NAD+ sequestration and collapse of metabolic homeostasis. This effect reversed with NAD+ rescue supplementation, confirming the mechanistic basis of cytotoxicity. Thus, alkylating chemotherapy exposes a genotype-specific metabolic weakness in tumor cells that can be exploited by PARG inactivation.

DOI: https://doi.org/10.1158/2159-8290.CD-20-0226
Cancer Cell. 2020 Jun 10. pii: S1535-6108(20)30270-1. [Epub ahead of print]

Telomere Stress Potentiates STING-Dependent Anti-tumor Immunity.

Ilgen Mender, Anli Zhang, Zhenhua Ren, Chuanhui Han, Yafang Deng, Silvia Siteni, Huiyu Li, Jiankun Zhu, Aishwarya Vemula, Jerry W Shay, Yang-Xin Fu.

  Telomerase is an attractive target for anti-tumor therapy as it is almost universally expressed in cancer cells. Here, we show that treatment with a telomere-targeting drug, 6-thio-2'-deoxyguanosine (6-thio-dG), leads to tumor regression through innate and adaptive immune-dependent responses in syngeneic and humanized mouse models of telomerase-expressing cancers. 6-thio-dG treatment causes telomere-associated DNA damages that are sensed by dendritic cells (DCs) and activates the host cytosolic DNA sensing STING/interferon I pathway, resulting in enhanced cross-priming capacity of DCs and tumor-specific CD8+ T cell activation. Moreover, 6-thio-dG overcomes resistance to checkpoint blockade in advanced cancer models. Our results unveil how telomere stress increases innate sensing and adaptive anti-tumor immunity and provide strong rationales for combining telomere-targeting therapy with immunotherapy.

Keywords:  6-thio-dG; DNA damage; PD-1/PD-L1; STING; anti-tumor immunity; checkpoint blockade; immunotherapy; innate sensing; telomerase; telomere-targeting therapy

DOI:  https://doi.org/10.1016/j.ccell.2020.05.020
J Cell Biol. 2020 Aug 03. pii: e202002175. [Epub ahead of print]219(8):

Interferon-stimulated gene 15 accelerates replication fork progression inducing chromosomal breakage.

Maria Chiara Raso, Nikola Djoric, Franziska Walser, Sandra Hess, Fabian Marc Schmid, Sibylle Burger, Klaus-Peter Knobeloch, Lorenza Penengo.

DNA replication is highly regulated by the ubiquitin system, which plays key roles upon stress. The ubiquitin-like modifier ISG15 (interferon-stimulated gene 15) is induced by interferons, bacterial and viral infection, and DNA damage, but it is also constitutively expressed in many types of cancer, although its role in tumorigenesis is still largely elusive. Here, we show that ISG15 localizes at the replication forks, in complex with PCNA and the nascent DNA, where it regulates DNA synthesis. Indeed, high levels of ISG15, intrinsic or induced by interferon-β, accelerate DNA replication fork progression, resulting in extensive DNA damage and chromosomal aberrations. This effect is largely independent of ISG15 conjugation and relies on ISG15 functional interaction with the DNA helicase RECQ1, which promotes restart of stalled replication forks. Additionally, elevated ISG15 levels sensitize cells to cancer chemotherapeutic treatments. We propose that ISG15 up-regulation exposes cells to replication stress, impacting genome stability and response to genotoxic drugs.

DOI: https://doi.org/10.1083/jcb.202002175
Proc Natl Acad Sci U S A. 2020 Jun 29. pii: 201921219. [Epub ahead of print]

Folate stress induces SLX1- and RAD51-dependent mitotic DNA synthesis at the fragile X locus in human cells.

Lorenza Garribba, Victoria A Bjerregaard, Marisa M Gonçalves Dinis, Özgün Özer, Wei Wu, Despoina Sakellariou, Javier Pena-Diaz, Ian D Hickson, Ying Liu.

  Folate deprivation drives the instability of a group of rare fragile sites (RFSs) characterized by CGG trinucleotide repeat (TNR) sequences. Pathological expansion of the TNR within the FRAXA locus perturbs DNA replication and is the major causative factor for fragile X syndrome, a sex-linked disorder associated with cognitive impairment. Although folate-sensitive RFSs share many features with common fragile sites (CFSs; which are found in all individuals), they are induced by different stresses and share no sequence similarity. It is known that a pathway (termed MiDAS) is employed to complete the replication of CFSs in early mitosis. This process requires RAD52 and is implicated in generating translocations and copy number changes at CFSs in cancers. However, it is unclear whether RFSs also utilize MiDAS and to what extent the fragility of CFSs and RFSs arises by shared or distinct mechanisms. Here, we demonstrate that MiDAS does occur at FRAXA following folate deprivation but proceeds via a pathway that shows some mechanistic differences from that at CFSs, being dependent on RAD51, SLX1, and POLD3. A failure to complete MiDAS at FRAXA leads to severe locus instability and missegregation in mitosis. We propose that break-induced DNA replication is required for the replication of FRAXA under folate stress and define a cellular function for human SLX1. These findings provide insights into how folate deprivation drives instability in the human genome.

Keywords:  MiDAS; break-induced DNA replication (BIR); chromosome fragile sites; homologous recombination; structure-specific endonucleases

DOI:  https://doi.org/10.1073/pnas.1921219117
Mol Cell. 2020 Jun 26. pii: S1097-2765(20)30402-0. [Epub ahead of print]

METTL3 and N6-Methyladenosine Promote Homologous Recombination-Mediated Repair of DSBs by Modulating DNA-RNA Hybrid Accumulation.

Canfeng Zhang, Liping Chen, Di Peng, Ao Jiang, Yunru He, Yanru Zeng, Chen Xie, Haoxian Zhou, Xiaotong Luo, Haiying Liu, Liang Chen, Jian Ren, Wengong Wang, Yong Zhao.

  Double-strand breaks (DSBs) are the most deleterious DNA lesions, which, if left unrepaired, may lead to genome instability or cell death. Here, we report that, in response to DSBs, the RNA methyltransferase METTL3 is activated by ATM-mediated phosphorylation at S43. Phosphorylated METTL3 is then localized to DNA damage sites, where it methylates the N6 position of adenosine (m6A) in DNA damage-associated RNAs, which recruits the m6A reader protein YTHDC1 for protection. In this way, the METTL3-m6A-YTHDC1 axis modulates accumulation of DNA-RNA hybrids at DSBs sites, which then recruit RAD51 and BRCA1 for homologous recombination (HR)-mediated repair. METTL3-deficient cells display defective HR, accumulation of unrepaired DSBs, and genome instability. Accordingly, depletion of METTL3 significantly enhances the sensitivity of cancer cells and murine xenografts to DNA damage-based therapy. These findings uncover the function of METTL3 and YTHDC1 in HR-mediated DSB repair, which may have implications for cancer therapy.

Keywords:  ATM; DDR; DNA-RNA hybrids; DSB; METTL3; YTHDC1; cancer therapy; genome stability; homologous recombination; m6A

DOI:  https://doi.org/10.1016/j.molcel.2020.06.017
Proc Natl Acad Sci U S A. 2020 Jul 01. pii: 202002193. [Epub ahead of print]

Screen identifies DYRK1B network as mediator of transcription repression on damaged chromatin.

Chao Dong, Kirk L West, Xin Yi Tan, Junshi Li, Toyotaka Ishibashi, Cheng-Han Yu, Shirley M H Sy, Justin W C Leung, Michael S Y Huen.

  DNA double-strand breaks (DSBs) trigger transient pausing of nearby transcription, an emerging ATM-dependent response that suppresses chromosomal instability. We screened a chemical library designed to target the human kinome for new activities that mediate gene silencing on DSB-flanking chromatin, and have uncovered the DYRK1B kinase as an early respondent to DNA damage. We showed that DYRK1B is swiftly and transiently recruited to laser-microirradiated sites, and that genetic inactivation of DYRK1B or its kinase activity attenuated DSB-induced gene silencing and led to compromised DNA repair. Notably, global transcription shutdown alleviated DNA repair defects associated with DYRK1B loss, suggesting that DYRK1B is strictly required for DSB repair on active chromatin. We also found that DYRK1B mediates transcription silencing in part via phosphorylating and enforcing DSB accumulation of the histone methyltransferase EHMT2. Together, our findings unveil the DYRK1B signaling network as a key branch of mammalian DNA damage response circuitries, and establish the DYRK1B-EHMT2 axis as an effector that coordinates DSB repair on transcribed chromatin.

Keywords:  DNA damage; DNA double-strand breaks; DNA repair; DYRK1B; transcription

DOI:  https://doi.org/10.1073/pnas.2002193117
PLoS Genet. 2020 Jul 01. 16(7): e1008828

Conditional knockout of RAD51-related genes in Leishmania major reveals a critical role for homologous recombination during genome replication.

Jeziel D Damasceno, João Reis-Cunha, Kathryn Crouch, Dario Beraldi, Craig Lapsley, Luiz R O Tosi, Daniella Bartholomeu, Richard McCulloch.

Homologous recombination (HR) has an intimate relationship with genome replication, both during repair of DNA lesions that might prevent DNA synthesis and in tackling stalls to the replication fork. Recent studies led us to ask if HR might have a more central role in replicating the genome of Leishmania, a eukaryotic parasite. Conflicting evidence has emerged regarding whether or not HR genes are essential, and genome-wide mapping has provided evidence for an unorthodox organisation of DNA replication initiation sites, termed origins. To answer this question, we have employed a combined CRISPR/Cas9 and DiCre approach to rapidly generate and assess the effect of conditional ablation of RAD51 and three RAD51-related proteins in Leishmania major. Using this approach, we demonstrate that loss of any of these HR factors is not immediately lethal but in each case growth slows with time and leads to DNA damage and accumulation of cells with aberrant DNA content. Despite these similarities, we show that only loss of RAD51 or RAD51-3 impairs DNA synthesis and causes elevated levels of genome-wide mutation. Furthermore, we show that these two HR factors act in distinct ways, since ablation of RAD51, but not RAD51-3, has a profound effect on DNA replication, causing loss of initiation at the major origins and increased DNA synthesis at subtelomeres. Our work clarifies questions regarding the importance of HR to survival of Leishmania and reveals an unanticipated, central role for RAD51 in the programme of genome replication in a microbial eukaryote.

DOI: https://doi.org/10.1371/journal.pgen.1008828
Nat Commun. 2020 Jul 03. 11(1): 3321

Persistent telomere cohesion protects aged cells from premature senescence.

Kameron Azarm, Amit Bhardwaj, Eugenie Kim, Susan Smith.

Human telomeres are bound by the telomere repeat binding proteins TRF1 and TRF2. Telomere shortening in human cells leads to a DNA damage response that signals replicative senescence. While insufficient loading of TRF2 at shortened telomeres contributes to the DNA damage response in senescence, the contribution of TRF1 to senescence induction has not been determined. Here we show that counter to TRF2 deficiency-mediated induction of DNA damage, TRF1 deficiency serves a protective role to limit induction of DNA damage induced by subtelomere recombination. Shortened telomeres recruit insufficient TRF1 and as a consequence inadequate tankyrase 1 to resolve sister telomere cohesion. Our findings suggest that the persistent cohesion protects short telomeres from inappropriate recombination. Ultimately, in the final division, telomeres are no longer able to maintain cohesion and subtelomere copying ensues. Thus, the gradual loss of TRF1 and concomitant persistent cohesion that occurs with telomere shortening ensures a measured approach to replicative senescence.

DOI: https://doi.org/10.1038/s41467-020-17133-4
Essays Biochem. 2020 Jul 03. pii: EBC20200008. [Epub ahead of print]

Jack of all trades? The versatility of RNA in DNA double-strand break repair.

Ruth F Ketley, Monika Gullerova.

  The mechanisms by which RNA acts in the DNA damage response (DDR), specifically in the repair of DNA double-strand breaks (DSBs), are emerging as multifaceted and complex. Different RNA species, including but not limited to; microRNA (miRNA), long non-coding RNA (lncRNA), RNA:DNA hybrid structures, the recently identified damage-induced lncRNA (dilncRNA), damage-responsive transcripts (DARTs), and DNA damage-dependent small RNAs (DDRNAs), have been shown to play integral roles in the DSB response. The diverse properties of these RNAs, such as sequence, structure, and binding partners, enable them to fulfil a variety of functions in different cellular contexts. Additionally, RNA can be modified post-transcriptionally, a process which is regulated in response to cellular stressors such as DNA damage. Many of these mechanisms are not yet understood and the literature contradictory, reflecting the complexity and expansive nature of the roles of RNA in the DDR. However, it is clear that RNA is pivotal in ensuring the maintenance of genome integrity. In this review, we will discuss and summarise recent evidence which highlights the roles of these various RNAs in preserving genomic integrity, with a particular focus on the emerging role of RNA in the DSB repair response.

Keywords:  DNA damage; RNA; RNA modifications; lncRNA; miRNA

DOI:  https://doi.org/10.1042/EBC20200008
Nucleic Acids Res. 2020 Jul 04. pii: gkaa559. [Epub ahead of print]

RADX condenses single-stranded DNA to antagonize RAD51 loading.

Hongshan Zhang, Jeffrey M Schaub, Ilya J Finkelstein.

RADX is a mammalian single-stranded DNA-binding protein that stabilizes telomeres and stalled replication forks. Cellular biology studies have shown that the balance between RADX and Replication Protein A (RPA) is critical for DNA replication integrity. RADX is also a negative regulator of RAD51-mediated homologous recombination at stalled forks. However, the mechanism of RADX acting on DNA and its interactions with RPA and RAD51 are enigmatic. Using single-molecule imaging of the key proteins in vitro, we reveal that RADX condenses ssDNA filaments, even when the ssDNA is coated with RPA at physiological protein ratios. RADX compacts RPA-coated ssDNA filaments via higher-order assemblies that can capture ssDNA in trans. Furthermore, RADX blocks RPA displacement by RAD51 and prevents RAD51 loading on ssDNA. Our results indicate that RADX is an ssDNA condensation protein that inhibits RAD51 filament formation and may antagonize other ssDNA-binding proteins on RPA-coated ssDNA.

DOI: https://doi.org/10.1093/nar/gkaa559
Cancer Treat Rev. 2020 May 16. pii: S0305-7372(20)30064-5. [Epub ahead of print]88 102026

ATR-CHK1 pathway as a therapeutic target for acute and chronic leukemias.

Miroslav Boudny, Martin Trbusek.

  Progress in cancer therapy changed the outcome of many patients and moved therapy from chemotherapy agents to targeted drugs. Targeted drugs already changed the clinical practice in treatment of leukemias, such as imatinib (BCR/ABL inhibitor) in chronic myeloid leukemia (CML) and acute lymphoblastic leukemia (ALL), ibrutinib (Bruton's tyrosine kinase inhibitor) in chronic lymphocytic leukemia (CLL), venetoclax (BCL2 inhibitor) in CLL and acute myeloid leukemia (AML) or midostaurin (FLT3 inhibitor) in AML. In this review, we focused on DNA damage response (DDR) inhibition, specifically on inhibition of ATR-CHK1 pathway. Cancer cells harbor often defects in different DDR pathways, which render them vulnerable to DDR inhibition. Some DDR inhibitors showed interesting single-agent activity even in the absence of cytotoxic drug especially in cancers with underlying defects in DDR or DNA replication. Almost no mutations were found in ATR and CHEK1 genes in leukemia patients. Together with the fact that ATR-CHK1 pathway is essential for cell development and survival of leukemia cells, it represents a promising therapeutic target for treatment of leukemia. ATR-CHK1 inhibition showed excellent results in preclinical testing in acute and chronic leukemias. However, results in clinical trials are so far insufficient. Therefore, the ongoing and future clinical trials will decide on the success of ATR/CHK1 inhibitors in clinical practice of leukemia treatment.

Keywords:  ATR; CHK1; DDR; Inhibition; Leukemia

DOI:  https://doi.org/10.1016/j.ctrv.2020.102026
Int J Mol Sci. 2020 Jun 24. pii: E4481. [Epub ahead of print]21(12):

Modulation of DNA Damage Response by Sphingolipid Signaling: An Interplay that Shapes Cell Fate.

Marina Francis, Alaa Abou Daher, Patrick Azzam, Manal Mroueh, Youssef H Zeidan.

  Although once considered as structural components of eukaryotic biological membranes, research in the past few decades hints at a major role of bioactive sphingolipids in mediating an array of physiological processes including cell survival, proliferation, inflammation, senescence, and death. A large body of evidence points to a fundamental role for the sphingolipid metabolic pathway in modulating the DNA damage response (DDR). The interplay between these two elements of cell signaling determines cell fate when cells are exposed to metabolic stress or ionizing radiation among other genotoxic agents. In this review, we aim to dissect the mediators of the DDR and how these interact with the different sphingolipid metabolites to mount various cellular responses.

Keywords:  ATM; DNA damage response; double strand breaks; ionizing radiation; metabolic stress; nuclear sphingolipids; oxidative stress; p53; sphingolipids

DOI:  https://doi.org/10.3390/ijms21124481
DNA Repair (Amst). 2020 Jun 12. pii: S1568-7864(20)30142-7. [Epub ahead of print]94 102894

TREX1 - Apex predator of cytosolic DNA metabolism.

Sean R Simpson, Wayne O Hemphill, Teesha Hudson, Fred W Perrino.

  The cytosolic Three prime Repair EXonuclease 1 (TREX1) is a powerful DNA-degrading enzyme required for clearing cytosolic DNA to prevent aberrant inflammation and autoimmunity. In the absence of TREX1 activity, cytosolic DNA pattern recognition receptors of the innate immune system are constitutively activated by undegraded TREX1 substrates. This triggers a chronic inflammatory response in humans expressing mutant TREX1 alleles, eliciting a spectrum of rare autoimmune diseases dependent on the nature of the mutation. The precise origins of cytosolic DNA targeted by TREX1 continue to emerge, but DNA emerging from the nucleus or taken up by the cell could represent potential sources. In this Review, we explore the biochemical and immunological data supporting the role of TREX1 in suppressing cytosolic DNA sensing, and discuss the possibility that TREX1 may contribute to maintenance of genome integrity.

Keywords:  Autoimmunity; Cytosolic DNA metabolism; DNA sensing; Genome stability; TREX1

DOI:  https://doi.org/10.1016/j.dnarep.2020.102894
Cancers (Basel). 2020 Jun 28. pii: E1713. [Epub ahead of print]12(7):

DNA Repair and Ovarian Carcinogenesis: Impact on Risk, Prognosis and Therapy Outcome.

Kristyna Tomasova, Andrea Cumova, Karolina Seborova, Josef Horak, Kamila Koucka, Ludmila Vodickova, Radka Vaclavikova, Pavel Vodicka.

  There is ample evidence for the essential involvement of DNA repair and DNA damage response in the onset of solid malignancies, including ovarian cancer. Indeed, highpenetrance germline mutations in DNA repair genes are important players in familial cancers: BRCA1, BRCA2 mutations or mismatch repair, and polymerase deficiency in colorectal, breast, and ovarian cancers. Recently, some molecular hallmarks (e.g., TP53, KRAS, BRAF, RAD51C/D or PTEN mutations) of ovarian carcinomas were identified. The manuscript overviews the role of DNA repair machinery in ovarian cancer, its risk, prognosis, and therapy outcome. We have attempted to expose molecular hallmarks of ovarian cancer with a focus on DNA repair system and scrutinized genetic, epigenetic, functional, and protein alterations in individual DNA repair pathways (homologous recombination, non-homologous end-joining, DNA mismatch repair, base- and nucleotide-excision repair, and direct repair). We suggest that lack of knowledge particularly in non-homologous end joining repair pathway and the interplay between DNA repair pathways needs to be confronted. The most important genes of the DNA repair system are emphasized and their targeting in ovarian cancer will deserve further attention. The function of those genes, as well as the functional status of the entire DNA repair pathways, should be investigated in detail in the near future.

Keywords:  DNA repair; carcinogenesis; ovarian cancer; prognosis; therapy response

DOI:  https://doi.org/10.3390/cancers12071713
Cancers (Basel). 2020 Jun 28. pii: E1717. [Epub ahead of print]12(7):

The Intermediate Filament Synemin Regulates Non-Homologous End Joining in an ATM-Dependent Manner.

Sara Sofia Deville, Anne Vehlow, Sarah Förster, Ellen Dickreuter, Kerstin Borgmann, Nils Cordes.

  The treatment resistance of cancer cells is a multifaceted process in which DNA repair emerged as a potential therapeutic target. DNA repair is predominantly conducted by nuclear events; yet, how extra-nuclear cues impact the DNA damage response is largely unknown. Here, using a high-throughput RNAi-based screen in three-dimensionally-grown cell cultures of head and neck squamous cell carcinoma (HNSCC), we identified novel focal adhesion proteins controlling DNA repair, including the intermediate filament protein, synemin. We demonstrate that synemin critically regulates the DNA damage response by non-homologous end joining repair. Mechanistically, synemin forms a protein complex with DNA-PKcs through its C-terminal tail domain for determining DNA repair processes upstream of this enzyme in an ATM-dependent manner. Our study discovers a critical function of the intermediate filament protein, synemin in the DNA damage response, fundamentally supporting the concept of cytoarchitectural elements as co-regulators of nuclear events.

Keywords:  ATM; DNA repair; DNA-PKcs; HNSCC; NHEJ; radiosensitivity; synemin

DOI:  https://doi.org/10.3390/cancers12071717
Biomark Res. 2020 ;8 23

Role of DNA repair defects in predicting immunotherapy response.

Jing Zhang, David J H Shih, Shiaw-Yih Lin.

  Defect in DNA damage response (DDR) is a common feature of cancer cells, which regulates tumor growth and therapeutic response. Recently, the approval of immune checkpoint blockade (ICB) for tumors with defective mismatch repair has paved the way for investigating the role of other DDR defects in sensitizing cancer to ICB therapy. Despite great progress in understanding DDR pathways, the mechanisms that link DDR defects and ICB response remain incompletely understood. Further, the clinical activity of ICB in patients with DDR defective tumors has not been well described. Here, we discuss recent studies demonstrating that biomarkers in DDR pathways may serve as potential predictors to guide the selection of patients for ICB therapy. A better understanding of the relationship between deficiency in DDR and response to ICB would facilitate efforts in optimizing the efficacy of immunotherapy.

Keywords:  Biomarkers; DNA damage response; Immune checkpoint blockade; Immunotherapy

DOI:  https://doi.org/10.1186/s40364-020-00202-7
PLoS Genet. 2020 Jun 29. 16(6): e1008511

JMJD6 participates in the maintenance of ribosomal DNA integrity in response to DNA damage.

Jérémie Fages, Catherine Chailleux, Jonathan Humbert, Suk-Min Jang, Jérémy Loehr, Jean-Philippe Lambert, Jacques Côté, Didier Trouche, Yvan Canitrot.

Ribosomal DNA (rDNA) is the most transcribed genomic region and contains hundreds of tandem repeats. Maintaining these rDNA repeats as well as the level of rDNA transcription is essential for cellular homeostasis. DNA damages generated in rDNA need to be efficiently and accurately repaired and rDNA repeats instability has been reported in cancer, aging and neurological diseases. Here, we describe that the histone demethylase JMJD6 is rapidly recruited to nucleolar DNA damage and is crucial for the relocalisation of rDNA in nucleolar caps. Yet, JMJD6 is dispensable for rDNA transcription inhibition. Mass spectrometry analysis revealed that JMJD6 interacts with the nucleolar protein Treacle and modulates its interaction with NBS1. Moreover, cells deficient for JMJD6 show increased sensitivity to nucleolar DNA damage as well as loss and rearrangements of rDNA repeats upon irradiation. Altogether our data reveal that rDNA transcription inhibition is uncoupled from rDNA relocalisation into nucleolar caps and that JMJD6 is required for rDNA stability through its role in nucleolar caps formation.

DOI: https://doi.org/10.1371/journal.pgen.1008511
Clin Adv Hematol Oncol. 2020 Mar;18(3): 168-179

The role of PARP inhibitors in germline BRCA-associated pancreatic ductal adenocarcinoma.

Gordon T Moffat, Eileen M O'Reilly.

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy that remains a challenge to treat. In pursuit of personalized medicine, researchers continue active exploration of the genetic and molecular framework of PDAC to apply novel therapeutics and enhance outcomes. In patients who have PDAC, germline mutations-such as those in the BRCA1/2 and PALB2 genes-are predominantly associated with the DNA damage response and repair pathway. On the basis of studies completed in patients with BRCA-mutated advanced breast and ovarian cancer, the poly(ADP-ribose) polymerase (PARP) inhibitors have been evaluated for safety, tolerability, and efficacy in patients with advanced PDAC who are carrying germline BRCA gene mutations. Results have demonstrated meaningful activity and identified BRCA as a predictive and targetable biomarker in PDAC, and have also identified the role of olaparib as a maintenance therapy in PDAC. On the basis of the principle of synthetic lethality, and to avert resistance to PARP inhibitors, clinical trials of combination therapy with PARP inhibitors and platinum-based chemotherapy have been conducted with an early signal. As we continue to explore the role of PARP inhibitors in the management of PDAC, recent clinical trials are studying the effectiveness of PARP inhibitors in combination with immunotherapy, targeted inhibitors, and angiogenesis inhibitors. The next steps are to understand the role of PARP inhibitors beyond germline BRCA in other homologous recombination repair gene mutations and in other subgroups of patients with PDAC.
Pharmacol Ther. 2020 Jun 28. pii: S0163-7258(20)30147-9. [Epub ahead of print] 107617

DNA-PK in human malignant disorders: Mechanisms and implications for pharmacological interventions.

Michaela Medová, Matúš Medo, Lusine Hovhannisyan, Carmen Muñoz Maldonado, Daniel M Aebersold, Yitzhak Zimmer.

  The DNA-PK holoenzyme is a fundamental element of the DNA damage response machinery (DDR), which is responsible for cellular genomic stability. Consequently, and predictably, over the last decades since its identification and characterization, numerous pre-clinical and clinical studies reported observations correlating aberrant DNA-PK status and activity with cancer onset, progression and responses to therapeutic modalities. Notably, various studies have established in recent years the role of DNA-PK outside the DDR network, corroborating its role as a pleiotropic complex involved in transcriptional programs that operate biologic processes as epithelial to mesenchymal transition (EMT), hypoxia, metabolism, nuclear receptors signaling and inflammatory responses. In particular tumor entities as prostate cancer, immense research efforts assisted mapping and describing the overall signaling networks regulated by DNA-PK that control metastasis and tumor progression. Correspondingly, DNA-PK emerges as an obvious therapeutic target in cancer and data pertaining to various pharmacological approaches have been published, largely in context of combination with DNA-damaging agents (DDAs) that act by inflicting DNA double strand breaks (DSBs). Currently, new generation inhibitors are tested in clinical trials. Several excellent reviews have been published in recent years covering the biology of DNA-PK and its role in cancer. In the current article we are aiming to systematically describe the main findings on DNA-PK signaling in major cancer types, focusing on both preclinical and clinical reports and present a detailed current status of the DNA-PK inhibitors repertoire.

Keywords:  Cancer; Clinical trials; DNA-PK; Non-homologous end-joining; Targeting

DOI:  https://doi.org/10.1016/j.pharmthera.2020.107617
Food Chem Toxicol. 2020 Jun 30. pii: S0278-6915(20)30419-1. [Epub ahead of print] 111529

Synergistic therapy with tangeretin and 5-fluorouracil accelerates the ROS/JNK mediated apoptotic pathway in human colorectal cancer cell.

Debasish Kumar Dey, Sukkum Ngullie Chang, Yellamandayya Vadlamudi, Jae Gyu Park, Sun Chul Kang.

  Synergistic therapy is emerging as a promising strategy for improving the chemotherapeutic efficacy of anticancer drugs. Addition of adjuvants with standard anticancer drugs has shown successful reduction of adverse side effects. The synthetic drug 5-Fluorouracil (5-FU) shows several side effects upon prolonged chemotherapy, thereby restricting its long-term clinical application. Several studies have reported anticancer potential and anti-inflammatory activity of tangeretin (TAN) towards mammalian cells. Therefore, we investigate whether the combination of TAN with 5-FU increases their anticancer potential against colorectal cancer. In this study, we examined the synergistic activity of TAN and 5-FU on the viability of several human cancer and normal cells. Several possible mechanistic pathways were screened, and found that co-exposure of TAN and 5-FU accelerates oxidative-stress and increases endogenous-ROS generation, which sequentially triggers the DNA damage response and activates the apoptotic pathway, by down-regulating autophagy and DNA repair system in HCT-116 cells. TAN and 5-FU co-treatment also remarkably reduces the mitochondrial membrane potential, and sequentially decreases ATPase activity. Collectively, results indicate that combination of TAN and 5-FU significantly accelerates apoptosis via JNK mediated pathway. To our knowledge gained from literature, this study is the first to describe synergistic activity of TAN and 5-FU against colorectal cancer cells.

Keywords:  Apoptosis; Colon cancer; DNA damage; Mitochondria; Oxidative stress

DOI:  https://doi.org/10.1016/j.fct.2020.111529
DNA Repair (Amst). 2020 Jun 26. pii: S1568-7864(20)30149-X. [Epub ahead of print] 102901

Twenty years of t-loops: A case study for the importance of collaboration in molecular biology.

Ľubomír Tomáška, Anthony J Cesare, Taghreed M AlTurki, Jack D Griffith.

  Collaborative studies open doors to breakthroughs otherwise unattainable by any one laboratory alone. Here we describe the initial collaboration between the Griffith and de Lange laboratories that led to thinking about the telomere as a DNA template for homologous recombination, the proposal of telomere looping, and the first electron micrographs of t-loops. This was followed by collaborations that revealed t-loops across eukaryotic phyla. The Griffith and Tomáška/Nosek collaboration revealed circular telomeric DNA (t-circles) derived from the linear mitochondrial chromosomes of nonconventional yeast, which spurred discovery of t-circles in ALT-positive human cells. Collaborative work between the Griffith and McEachern labs demonstrated t-loops and t-circles in a series of yeast species. The de Lange and Zhuang laboratories then applied super-resolution light microscopy to demonstrate a genetic role for TRF2 in loop formation. Recent work from the Griffith laboratory linked telomere transcription with t-loop formation, providing a new model of the t-loop junction. A recent collaboration between the Cesare and Gaus laboratories utilized super-resolution light microscopy to provide details about t-loops as protective elements, followed by the Boulton and Cesare laboratories showing how cell cycle regulation of TRF2 and RTEL enables t-loop opening and reformation to promote telomere replication. Twenty years after the discovery of t-loops, we reflect on the collective history of their research as a case study in collaborative molecular biology.

Keywords:  DNA repair; Double strand breaks; R-loop; Super resolution microscopy; T-circle; T-loop; Telomeres

DOI:  https://doi.org/10.1016/j.dnarep.2020.102901
Cancers (Basel). 2020 Jun 29. pii: E1725. [Epub ahead of print]12(7):

Dendrogenin A synergizes with Cytarabine to Kill Acute Myeloid Leukemia Cells In Vitro and In Vivo.

Nizar Serhan, Pierre-Luc Mouchel, Philippe de Medina, Gregory Segala, Aurélie Mougel, Estelle Saland, Arnaud Rives, Antonin Lamaziere, Gaëtan Despres, Jean-Emmanuel Sarry, Clément Larrue, François Vergez, Laetitia Largeaud, Michel Record, Christian Récher, Sandrine Silvente-Poirot, Marc Poirot.

  Dendrogenin A (DDA) is a mammalian cholesterol metabolite that displays potent antitumor properties on acute myeloid leukemia (AML). DDA triggers lethal autophagy in cancer cells through a biased activation of the oxysterol receptor LXRβ, and the inhibition of a sterol isomerase. We hypothesize that DDA could potentiate the activity of an anticancer drug acting through a different molecular mechanism, and conducted in vitro and in vivo combination tests on AML cell lines and patient primary tumors. We report here results from tests combining DDA with antimetabolite cytarabine (Ara-C), one of the main drugs used for AML treatment worldwide. We demonstrated that DDA potentiated and sensitized AML cells, including primary patient samples, to Ara-C in vitro and in vivo. Mechanistic studies revealed that this sensitization was LXRβ-dependent and was due to the activation of lethal autophagy. This study demonstrates a positive in vitro and in vivo interaction between DDA and Ara-C, and supports the clinical evaluation of DDA in combination with Ara-C for the treatment of AML.

Keywords:  Acute myeloid leukemia; Dendrogenin A; cholesterol metabolism; primary cancer cells; synergy; tumor suppressor

DOI:  https://doi.org/10.3390/cancers12071725
Curr Treat Options Oncol. 2020 Jun 29. 21(8): 62

Targeting DNA Damage Repair Pathways in Pancreatic Adenocarcinoma.

Satya Das, Dana Cardin.

   OPINION STATEMENT: Metastatic (and locally advanced) pancreatic adenocarcinoma (mPDA) represents a major challenge for the oncology community given the rising mortality burden from the disease and the preponderance of patients diagnosed with unresectable disease. Although systemic therapies have become more potent with the development of fluorouracil, irinotecan, and oxaliplatin (FOLFIRINOX) and gemcitabine plus nab-paclitaxel as first-line treatments, the median overall survival for patients treated with either of these regimens remains just above 1 year. A significant need exists to build upon the effectiveness of first-line regimens, incorporate tolerable maintenance treatments, and add effective later-line options for patients with this disease. We believe every newly diagnosed mPDA patient should undergo next-generation sequencing (NGS) testing, preferably from tumor tissue, to assess for the presence of DNA damage repair (DDR) defects, microsatellite instability, and other possible actionable molecular alterations (such as neurotrophic tropomysin receptor kinase (NTRK) fusions, anaplastic lymphoma kinase (ALK) rearrangements, or human epidermal growth factor receptor 2 (HER2) amplification). Existing clinical data suggests that patients, whose tumors harbor DDR defects, benefit from treatment with platinum-based chemotherapy and poly (ADP-ribose) polymerase (PARP) inhibitors. Preclinically, inhibitors of other critical players in DDR such as ataxia-telangiectasia and Rad3 related (ATR), ataxia-telangiectasia mutated (ATM), DNA-dependent protein kinase (DNA-PK), and WEE1 have demonstrated promising anti-tumor activity in PDA cell lines and xenografts. How to move forward the preclinical promise of these newer DDR-targeting therapies into rational clinical trial combinations and sequence PARP inhibitors in relation to platinum chemotherapy remain areas of tremendous clinical research interest. We believe clinical trials should be considered early for mPDA patients, in all treatment lines, so that novel therapies may be added to the treatment armamentarium for patients with this disease. Beyond NGS testing from tumor tissue, we believe it is important to consider germline genetic testing for all patients diagnosed with PDA given recent data suggesting a much stronger hereditary component of the disease than previously understood, and the potential screening implications for family members.

Keywords:  DNA damage repair defects; Homologous recombination defects; Pancreatic adenocarcinoma; Platinum sensitivity; Poly (ADP-ribose) polymerase inhibitors

DOI:  https://doi.org/10.1007/s11864-020-00763-7
Genes Dev. 2020 Jul 01. 34(13-14): 863-864

A genome-wide and cotranscriptional suppressor of R loops.

Jacob P Matson, Lee Zou.

  R loops arise from hybridization of RNA transcripts with template DNA during transcription. Unrepaired R loops lead to transcription-replication collisions, causing DNA damage and genomic instability. In this issue of Genes & Development, Pérez-Calero and colleagues (pp. 898-912) identify UAP56 as a cotranscriptional RNA-DNA helicase that unwinds R loops. They found that UAP56 helicase activity is required to remove R loops formed from different sources and prevent R-loop accumulation genome-wide at actively transcribed genes.

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.339861.120
Int J Mol Sci. 2020 Jun 24. pii: E4504. [Epub ahead of print]21(12):

Chromatin Architectural Factors as Safeguards against Excessive Supercoiling during DNA Replication.

Syed Moiz Ahmed, Peter Dröge.

  Key DNA transactions, such as genome replication and transcription, rely on the speedy translocation of specialized protein complexes along a double-stranded, right-handed helical template. Physical tethering of these molecular machines during translocation, in conjunction with their internal architectural features, generates DNA topological strain in the form of template supercoiling. It is known that the build-up of transient excessive supercoiling poses severe threats to genome function and stability and that highly specialized enzymes-the topoisomerases (TOP)-have evolved to mitigate these threats. Furthermore, due to their intracellular abundance and fast supercoil relaxation rates, it is generally assumed that these enzymes are sufficient in coping with genome-wide bursts of excessive supercoiling. However, the recent discoveries of chromatin architectural factors that play important accessory functions have cast reasonable doubts on this concept. Here, we reviewed the background of these new findings and described emerging models of how these accessory factors contribute to supercoil homeostasis. We focused on DNA replication and the generation of positive (+) supercoiling in front of replisomes, where two accessory factors-GapR and HMGA2-from pro- and eukaryotic cells, respectively, appear to play important roles as sinks for excessive (+) supercoiling by employing a combination of supercoil constrainment and activation of topoisomerases. Looking forward, we expect that additional factors will be identified in the future as part of an expanding cellular repertoire to cope with bursts of topological strain. Furthermore, identifying antagonists that target these accessory factors and work synergistically with clinically relevant topoisomerase inhibitors could become an interesting novel strategy, leading to improved treatment outcomes.

Keywords:  DNA topological strain; DNA/chromatin supercoiling; GapR; HMGA2; chromatin architectural factors; replication stress; topoisomerases

DOI:  https://doi.org/10.3390/ijms21124504
Oncotarget. 2020 Jun 16. 11(24): 2262-2272

Expression of a germline variant in the N-terminal domain of the human DNA glycosylase NTHL1 induces cellular transformation without impairing enzymatic function or substrate specificity.

Carolyn G Marsden, Pawel Jaruga, Erdem Coskun, Robyn L Maher, David S Pederson, Miral Dizdaroglu, Joann B Sweasy.

  Oxidatively-induced DNA damage, widely accepted as a key player in the onset of cancer, is predominantly repaired by base excision repair (BER). BER is initiated by DNA glycosylases, which locate and remove damaged bases from DNA. NTHL1 is a bifunctional DNA glycosylase in mammalian cells that predominantly removes oxidized pyrimidines. In this study, we investigated a germline variant in the N-terminal domain of NTHL1, R33K. Expression of NTHL1 R33K in human MCF10A cells resulted in increased proliferation and anchorage-independent growth compared to NTHL1 WT-expressing cells. However, wt-NTHL1 and R33K-NTHL1 exhibited similar substrate specificity, excision kinetics, and enzyme turnover in vitro and in vivo. The results of this study indicate an important function of R33 in BER that is disrupted by the R33K mutation. Furthermore, the cellular transformation induced by R33K-NTHL1 expression suggests that humans harboring this germline variant may be at increased risk for cancer incidence.

Keywords:  NTHL1; base excision repair; cellular transformation; germline variant

DOI:  https://doi.org/10.18632/oncotarget.27548
Cancer Res. 2020 Jul 01. 80(13): 2720-2721

Not Black or White but Shades of Gray: Homologous Recombination Deficiency as a Continuous Variable Modulated by RNF168.

Lin Wang, Gerburg M Wulf.

In this issue of Cancer Research, the study by Krais and colleagues underscores that DNA damage repair by homologous recombination (HR) is not an all-or-nothing phenomenon, but that HR competency comes on a spectrum, ranging from complete deficiency to proficiency. Residual low-level HR in BRCA1-mutant cancer cells turns out to be critically important for their survival and is afforded by low levels of Histone 2A (H2A) ubiquitination resulting from lowered RNF168 levels. The findings raise the possibility that, if ubiquitination of H2A could be enforced by inhibition of deubiquitinases, residual HR in BRCA1mt cells might be extinguished. Extinction of residual HR might improve the therapeutic efficacy of the emerging inhibitors of DNA damage repair. The development of methods to measure HR directly and quantitatively is crucial to develop this field.See related article by Krais et al., p. 2848.

DOI: https://doi.org/10.1158/0008-5472.CAN-20-1248
Nucleic Acids Res. 2020 Jul 01. pii: gkaa555. [Epub ahead of print]

DSS1 and ssDNA regulate oligomerization of BRCA2.

Hang Phuong Le, Xiaoyan Ma, Jorge Vaquero, Megan Brinkmeyer, Fei Guo, Wolf-Dietrich Heyer, Jie Liu.

The tumor suppressor BRCA2 plays a key role in initiating homologous recombination by facilitating RAD51 filament formation on single-stranded DNA. The small acidic protein DSS1 is a crucial partner to BRCA2 in this process. In vitro and in cells (1,2), BRCA2 associates into oligomeric complexes besides also existing as monomers. A dimeric structure was further characterized by electron microscopic analysis (3), but the functional significance of the different BRCA2 assemblies remains to be determined. Here, we used biochemistry and electron microscopic imaging to demonstrate that the multimerization of BRCA2 is counteracted by DSS1 and ssDNA. When validating the findings, we identified three self-interacting regions and two types of self-association, the N-to-C terminal and the N-to-N terminal interactions. The N-to-C terminal self-interaction of BRCA2 is sensitive to DSS1 and ssDNA. The N-to-N terminal self-interaction is modulated by ssDNA. Our results define a novel role of DSS1 to regulate BRCA2 in an RPA-independent fashion. Since DSS1 is required for BRCA2 function in recombination, we speculate that the monomeric and oligomeric forms of BRCA2 might be active for different cellular events in recombinational DNA repair and replication fork stabilization.

DOI: https://doi.org/10.1093/nar/gkaa555
J Vis Exp. 2020 Jun 09.

Immunofluorescence Imaging of DNA Damage and Repair Foci in Human Colon Cancer Cells.

Kamila Maliszewska-Olejniczak, Agnieszka Dróżdż, Martyna Waluś, Michał Dorosz, Michał A Gryziński.

The purpose of the manuscript is to provide a step-by-step protocol for performing immunofluorescence microscopy to study the radiation-induced DNA damage response induced by neutron-gamma mixed-beam used in boron neutron capture therapy (BNCT). Specifically, the proposed methodology is applied for the detection of repair proteins activation which can be visualized as foci using antibodies specific to DNA double-strand breaks (DNA-DSBs). DNA repair foci were assessed by immunofluorescence in colon cancer cells (HCT-116) after irradiation with the neutron-mixed beam. DNA-DSBs are the most genotoxic lesions and are repaired in mammalian cells by two major pathways: non-homologous end-joining pathway (NHEJ) and homologous recombination repair (HRR). The frequencies of foci, immunochemically stained, for commonly used markers in radiobiology like γ-H2AX, 53BP1 are associated with DNA-DSB number and are considered as efficient and sensitive markers for monitoring the induction and repair of DNA-DSBs. It was established that γ-H2AX foci attract repair proteins, leading to a higher concentration of repair factors near a DSB. To monitor DNA damage at the cellular level, immunofluorescence analysis for the presence of DNA-PKcs representative repair protein foci from the NHEJ pathway and Rad52 from the HRR pathway was planned. We have developed and introduced a reliable immunofluorescence staining protocol for the detection of radiation-induced DNA damage response with antibodies specific for repair factors from NHEJ and HRR pathways and observed radiation-induced foci (RIF). The proposed methodology can be used for investigating repair protein that is highly activated in the case of neutron-mixed beam radiation, thereby indicating the dominance of the repair pathway.

DOI: https://doi.org/10.3791/61399
Mol Cancer Res. 2020 Jul 01. pii: molcanres.0339.2020. [Epub ahead of print]

Inhibition of O-GlcNAc transferase renders prostate cancer cells dependent on CDK9.

Harri M Itkonen, Ninu Poulose, Rebecca E Steele, Sara E S Martin, Zebulon G Levine, Damien Y Duveau, Ryan Carelli, Reema Singh, Alfonso Urbanucci, Massimo Loda, Craig J Thomas, Ian G Mills, Suzanne Walker.

O-GlcNAc transferase (OGT) is a nutrient-sensitive glycosyltransferase that is overexpressed in prostate cancer, the most common cancer in males. We recently developed specific and potent inhibitor targeting this enzyme, and here we report a synthetic lethality screen using this compound. Our screen identified pan-cyclin-dependent kinase (CDK) inhibitor AT7519 as lethal in combination with OGT inhibition. Follow-up chemical and genetic approaches identified CDK9 as the major target for synthetic lethality with OGT inhibition in prostate cancer cells. OGT expression is regulated through retention of the fourth intron in the gene and CDK9 inhibition blunted this regulatory mechanism. CDK9 phosphorylates carboxy-terminal domain (CTD) of RNA Polymerase II (RNA Pol II) to promote transcription elongation. We show that OGT inhibition augments effects of CDK9 inhibitors on CTD phosphorylation and general transcription. Finally, the combined inhibition of both OGT and CDK9 blocked growth of organoids derived from metastatic prostate cancer patients but had minimal effects on normal prostate spheroids. We report a novel synthetic lethal interaction between inhibitors of OGT and CDK9 that specifically kills prostate cancer cells but not normal cells. Our study highlights the potential of combining OGT inhibitors with other treatments to exploit cancer specific vulnerabilities. Implications: The primary contribution of OGT to cell proliferation is unknown, and in this study we use a compound screen to indicate that OGT and CDK9 collaborate to sustain a cancer cell specific pro-proliferative program. A better understanding of how OGT and CDK9 cross-talk will refine our understanding of this novel synthetic lethal interaction.

DOI: https://doi.org/10.1158/1541-7786.MCR-20-0339
ACS Omega. 2020 Jun 23. 5(24): 14513-14522

Recognition and Unfolding of c-MYC and Telomeric G-Quadruplex DNAs by the RecQ C-Terminal Domain of Human Bloom Syndrome Helicase.

Sungjin Lee, Jinwoo Kim, Suyeong Han, Chin-Ju Park.

G-quadruplex (G4) is a noncanonical DNA secondary structure formed by Hoogsteen base pairing. It is recognized by various DNA helicases involved in DNA metabolism processes such as replication and transcription. Human Bloom syndrome protein (BLM), one of five human RecQ helicases, is a G4 helicase. While several studies revealed the mechanism of G4 binding and unfolding by the conserved RecQ C-terminal (RQC) domain of BLM, how RQC recognizes different G4 topologies is still unclear. Here, we investigated the interaction of Myc-22(14/23T) G4 from the c-Myc promoter and hTelo G4 from the telomeric sequence with RQC. Myc-22(14/23T) and hTelo form parallel and (3+1) hybrid topologies, respectively. Our circular dichroism (CD) spectroscopy data indicate that RQC can partially unfold the parallel G4, even with a short 3' overhang, while it can only partially unfold the (3+1) hybrid G4 with a 3' overhang of 6 nucleotides or longer. We found that the intrinsic thermal stability of G4 does not determine RQC-induced G4 unfolding by comparing T m of G4s. We also showed that both parallel and (3+1) hybrid G4s bind to the β-wing region of RQC. Thermodynamic analysis using isothermal titration calorimetry (ITC) showed that all interactions were endothermic and entropically driven. We suggest that RQC partially unfolds the parallel G4 more efficiently than the (3+1) hybrid G4 and binds to various G4 structures using its β-wing region. By this information, our research provides new insights into the influence of G4 structure on DNA metabolic processes involving BLM.

DOI: https://doi.org/10.1021/acsomega.0c01176
Br J Cancer. 2020 Jun 29.

A comprehensive population-based study comparing the phenotype and genotype in a pretherapeutic screen of dihydropyrimidine dehydrogenase deficiency.

Nicolas Pallet, Salma Hamdane, Simon Garinet, Hélène Blons, Aziz Zaanan, Elena Paillaud, Julien Taieb, Olivier Laprevote, Marie-Anne Loriot, Céline Narjoz.

BACKGROUND: Pretherapeutic screening for dihydropyrimidine dehydrogenase (DPD) deficiency is recommended or required prior to the administration of fluoropyrimidine-based chemotherapy. However, the best strategy to identify DPD-deficient patients remains elusive.
METHODS: Among a nationwide cohort of 5886 phenotyped patients with cancer who were screened for DPD deficiency over a 3 years period, we assessed the characteristics of both DPD phenotypes and DPYD genotypes in a subgroup of 3680 patients who had completed the two tests. The extent to which defective allelic variants of DPYD predict DPD activity as estimated by the plasma concentrations of uracil [U] and its product dihydrouracil [UH2] was evaluated.
RESULTS: When [U] was used to monitor DPD activity, 6.8% of the patients were classified as having DPD deficiency ([U] > 16 ng/ml), while the [UH2]:[U] ratio identified 11.5% of the patients as having DPD deficiency (UH2]:[U] < 10). [U] classified two patients (0.05%) with complete DPD deficiency (> 150 ng/ml), and [UH2]:[U] < 1 identified three patients (0.08%) with a complete DPD deficiency. A defective DPYD variant was present in 4.5% of the patients, and two patients (0.05%) carrying 2 defective variants of DPYD were predicted to have low metabolism. The mutation status of DPYD displayed a very low positive predictive value in identifying individuals with DPD deficiency, although a higher predictive value was observed when [UH2]:[U] was used to measure DPD activity. Whole exon sequencing of the DPYD gene in 111 patients with DPD deficiency and a "wild-type" genotype (based on the four most common variants) identified seven heterozygous carriers of a defective allelic variant.
CONCLUSIONS: Frequent genetic DPYD variants have low performances in predicting partial DPD deficiency when evaluated by [U] alone, and [UH2]:[U] might better reflect the impact of genetic variants on DPD activity. A clinical trial comparing toxicity rates after dose adjustment according to the results of genotyping or phenotyping testing to detect DPD deficiency will provide critical information on the best strategy to identify DPD deficiency.

DOI: https://doi.org/10.1038/s41416-020-0962-z
J Biol Chem. 2020 Jul 01. pii: jbc.AC120.014189. [Epub ahead of print]

The transcription factors aryl hydrocarbon receptor and MYC cooperate in the regulation of cellular metabolism.

M Carmen Lafita-Navarro, Lizbeth Perez-Castro, Lauren G Zacharias, Spencer Barnes, Ralph J DeBerardinis, Maralice Conacci-Sorrell.

  The transcription factor aryl hydrocarbon receptor (AHR) drives the expression of genes involved in detoxification pathways in cells exposed to pollutants and other small molecules. Moreover, AHR supports transcriptional programs that promote ribosome biogenesis and protein synthesis in cells stimulated to proliferate by the oncoprotein MYC. Thus, AHR is necessary for the proliferation of MYC-overexpressing cells. To define metabolic pathways in which AHR cooperates with MYC in supporting cell growth, here we used LC-MS-based metabolomics to examine the metabolome of MYC-expressing cells uponAHR knockdown. We found that AHR knockdown reduced lactate, S-lactoyl-glutathione,N-acetyl-L-alanine, 2-hydroxyglutarate, and uridine-5-monophosphate (UMP) levels. Using our previously obtained RNA-seq data, we found that AHR mediates the expression of the UMP-generating enzymes dihydroorotate dehydrogenase (quinone) (DHODH) and uridine monophosphate synthetase (UMPS), as well as lactate dehydrogenase A (LDHA), establishing a mechanism by which AHR regulates lactate and UMP production in MYC-overexpressing cells. AHR knockdown in glioblastoma cells also reduced the expression of LDHA (and lactate), DHODH,and UMPS, but did not affect UMP levels, likely due to compensatory mechanisms in these cells. Our results indicate that AHR contributes to the regulation of metabolic pathways necessary for the proliferation of transformed cells.

Keywords:  Myc (c-Myc); aryl hydrocarbon receptor (AhR) (AHR); cancer; gene regulation; glioblastoma; glycolysis; metabolism; metabolomics; oncogene; pyrimidine

DOI:  https://doi.org/10.1074/jbc.AC120.014189
BMC Med Genet. 2020 Jun 29. 21(1): 138

A novel stop-gain mutation in DPYS gene causing Dihidropyrimidinase deficiency, a case report.

Malihe Mirzaei, Arghavan Kavosi, Mahboobeh Sharifzadeh, Ghazale Mahjoub, Mohammad Ali Faghihi, Parham Habibzadeh, Majid Yavarian.

   BACKGROUND: Dihidropyrimidinase (DHP) deficiency is an inherited inborn error of pyrimidine metabolism with a variable clinical presentation and even asymptomatic subjects. Dihydropyrimidinase is encoded by the DPYS gene, thus pathogenic mutations in this gene can cause DHP deficiency. To date, several variations in the DPYS gene have been reported but only 23 of them have been confirmed to be pathogenic. Therefore, the biochemical, clinical and genetic aspects of this disease are still unclear.
CASE PRESENTATION: Here, we report a 22-year-old woman with DHP deficiency. To identify the genetic cause of DHP deficiency in this patient, Whole Exome Sequencing (WES) was performed, which revealed a novel homozygote stop gain mutation (NM_001385: Exon 9, c.1501 A > T, p.K501X) in the DPYS gene. Sanger sequencing was carried out on proband and other family members in order to confirm the identified mutation. According to the homozygote genotype of the patient and heterozygote genotype of her parents, the autosomal recessive pattern of inheritance was confirmed. In addition, bioinformatics analysis of the identified variant using Mutation Taster and T-Coffee Multiple Sequence Alignment showed the pathogenicity of mutation. Moreover, mRNA expression level of DPYS gene in the proband's liver biopsy showed about 6-fold reduction compared to control, which strongly suggested the pathogenicity of the identified mutation.
CONCLUSIONS: This study identified a novel pathogenic stop gain mutation in DPYS gene in a DHP deficient patient. Our findings can improve the knowledge about the genetic basis of the disease and also provide information for accurate genetic counseling for the families at risk of these types of disorders.

Keywords:  Case report; DPYS; Dihidropyrimidnase deficiency (DHP deficiency); Novel stop gain mutation

DOI:  https://doi.org/10.1186/s12881-020-01070-6
Biochem Pharmacol. 2020 Jun 27. pii: S0006-2952(20)30363-4. [Epub ahead of print] 114127

Pharmacokinetics of Gemcitabine and its Amino Acid Ester Prodrug following Intravenous and Oral Administrations in Mice.

Brian R Thompson, Jian Shi, Hao-Jie Zhu, David E Smith.

  Gemcitabine is an intravenously administered anti-cancer nucleoside analogue. Systemic exposure following oral administration of gemcitabine is limited by extensive first-pass metabolism via cytidine deaminase (CDA) and potentially by saturation of nucleoside transporter-mediated intestinal uptake. An amino acid ester prodrug of gemcitabine, 5'-l-valyl-gemcitabine (V-Gem), was previously shown to be a substrate of the intestinally expressed peptide transporter 1 (PEPT1) and stable against CDA-mediated metabolism. However, preliminary studies did not evaluate the in vivo oral performance of V-Gem as compared to parent drug. In the present study, we evaluated the pharmacokinetics and in vivo oral absorption of gemcitabine and V-Gem following intravenous and oral administrations in mice. These studies revealed that V-Gem undergoes rapid systemic elimination (half-life < 1 min) and has a low oral bioavailability (< 1%). Most importantly, the systemic exposure of gemcitabine was not different following oral administration of equimolar doses of gemcitabine (gemcitabine bioavailability of 18.3%) and V-Gem (gemcitabine bioavailability of 16.7%). Single-pass intestinal perfusions with portal blood sampling in mice revealed that V-Gem undergoes extensive activation in intestinal epithelial cells and that gemcitabine undergoes first-pass metabolism in intestinal epithelial cells. Thus, formulation of gemcitabine as the prodrug V-Gem does not increase systemic gemcitabine exposure following oral dosing, due, in part, to the instability of V-Gem in intestinal epithelial cells.

Keywords:  Bioavailability; Gemcitabine; PEPT1; Prodrug

DOI:  https://doi.org/10.1016/j.bcp.2020.114127
Cancer Sci. 2020 Jul 03.

Impact of DPYD, DPYS and UPB1 gene variations on severe drug-related toxicity in cancer patients.

Katsuyuki Yokoi, Yoko Nakajima, Hiroshi Matsuoka, Yasuko Shinkai, Takuma Ishihara, Yasuhiro Maeda, Takema Kato, Hidetoshi Katsuno, Koji Masumori, Kenji Kawada, Tetsushi Yoshikawa, Tetsuya Ito, Hiroki Kurahashi.

  Cancer treatment with a fluoropyrimidine (FP) is often accompanied by severe toxicity that may be dependent on the activity of catalytic enzymes encoded by the DPYD, DPYS and UPB1 genes. Genotype-guided dose individualization of FP therapy has been proposed in Western countries, but our knowledge of the relevant genetic variants in East Asian populations is presently limited. To investigate the association between these genetic variations and FP-related high toxicity in a Japanese population, we obtained blood samples from 301 patients who received this chemotherapy and sequenced the coding exons and flanking intronic regions of their DPYD, DPYS and UPB1 genes. In total, 24 single nucleotide variants (15 in DPYD, 7 in DPYS and 2 in UPB1) were identified including 3 novel variants in DPYD and 1 novel variant in DPYS. We did not find a significant association between FP-related high toxicity and each of these individual variants, although a certain trend toward significance was observed for p.Arg181Trp and p.Gln334Arg in DPYS (p=0.0813 and 0.087). When we focused on 7 DPYD rare variants (p.Ser199Asn, p.IIe245Phe, p.Thr305Lys, p.Glu386Ter, p.Ser556Arg, p.Ala571Asp, p.Trp621Cys) which have an allele frequency of less than 0.01% in the Japanese population and are predicted to be loss-of-function mutations by in silico analysis, the group of patients who were heterozygous carriers of at least one these rare variants showed a strong association with FP-related high toxicity (p= 0.003). Although the availability of screening of these rare loss-of-function variants is still unknown, our data provide useful information that may help to alleviate FP-related toxicity in Japanese cancer patients.

Keywords:   DPYD ; DPYS ; UPB1 ; 5-fluorouracil; Fluoropyrimidine

DOI:  https://doi.org/10.1111/cas.14553