bims-numges Biomed News
on Nucleotide metabolism and genome stability
Issue of 2021‒10‒31
33 papers selected by
Sean Rudd
Karolinska Institutet


  1. Nature. 2021 Oct 26.
      Replisome disassembly is the final step of eukaryotic DNA replication, and is triggered by ubiquitylation of the CMG (Cdc45-MCM-GINS) replicative helicase1-3. Despite being driven by evolutionarily diverse E3 ubiquitin ligases in different eukaryotes (SCFDia2 in budding yeast1, CUL2LRR1 in metazoa4-7), replisome disassembly is governed by a common regulatory principle, whereby CMG ubiquitylation is suppressed before replication termination, to prevent replication fork collapse. Recent evidence suggests this suppression is mediated by replication fork DNA8-10. However, how SCFDia2 and CUL2LRR1 discriminate terminated from elongating replisomes, to selectively ubiquitylate CMG only after termination, is unknown. Here, we used electron cryomicroscopy (cryo-EM) to solve high resolution structures of budding yeast and human replisome-E3 ligase assemblies. Our structures show that the leucine-rich repeat (LRR) domains of Dia2 and LRR1 are structurally distinct, but bind to a common site on CMG, including the MCM3 and MCM5 zinc finger domains. The LRR-MCM interaction is essential for replisome disassembly and, crucially, is occluded by the excluded DNA strand at replication forks, establishing the structural basis for the suppression of CMG ubiquitylation before termination. Our results elucidate a conserved mechanism for the regulation of replisome disassembly in eukaryotes, and reveal a previously unanticipated role for DNA in preserving replisome integrity.
    DOI:  https://doi.org/10.1038/s41586-021-04145-3
  2. EMBO J. 2021 Oct 25. e108819
      The human replisome is an elaborate arrangement of molecular machines responsible for accurate chromosome replication. At its heart is the CDC45-MCM-GINS (CMG) helicase, which, in addition to unwinding the parental DNA duplex, arranges many proteins including the leading-strand polymerase Pol ε, together with TIMELESS-TIPIN, CLASPIN and AND-1 that have key and varied roles in maintaining smooth replisome progression. How these proteins are coordinated in the human replisome is poorly understood. We have determined a 3.2 Å cryo-EM structure of a human replisome comprising CMG, Pol ε, TIMELESS-TIPIN, CLASPIN and AND-1 bound to replication fork DNA. The structure permits a detailed understanding of how AND-1, TIMELESS-TIPIN and Pol ε engage CMG, reveals how CLASPIN binds to multiple replisome components and identifies the position of the Pol ε catalytic domain. Furthermore, the intricate network of contacts contributed by MCM subunits and TIMELESS-TIPIN with replication fork DNA suggests a mechanism for strand separation.
    Keywords:  CMG helicase; DNA replication; cryo-EM; fork protection complex; replisome
    DOI:  https://doi.org/10.15252/embj.2021108819
  3. Clin Cancer Res. 2021 Oct 29. pii: clincanres.2863.2021. [Epub ahead of print]
      PURPOSE: In acute myeloid leukemia (AML), recurrent DNA methyltransferase 3A (DNMT3A) mutations are associated with chemoresistance and poor prognosis, especially in advanced-age patients. Gene expression studies in DNMT3A-mutated cells identified signatures implicated in deregulated DNA damage response and replication fork integrity, suggesting sensitivity to replication stress. Here, we tested whether pharmacologically-induced replication fork stalling such as with cytarabine creates a therapeutic vulnerability in cells with DNMT3A(R882) mutations.EXPERIMENTAL DESIGN: Leukemia cell lines, genetic mouse models, and isogenic cells with and without DNMT3A(mut) were used to evaluate sensitivity to nucleoside analogs such as cytarabine in vitro and in vivo, followed by analysis of DNA damage and signaling, replication restart, and cell cycle progression on treatment and after drug removal. Transcriptome profiling identified pathways deregulated by DNMT3A(mut) expression.
    RESULTS: We found increased sensitivity to pharmacologically-induced replication stress in cells expressing DNMT3A(R882)-mutant, with persistent intra-S phase checkpoint activation, impaired PARP1 recruitment, and elevated DNA damage, which was incompletely resolved after drug removal and carried through mitosis. Pulse-chase double-labeling experiments with EdU and BrdU after cytarabine wash-out demonstrated a higher rate of fork collapse in DNMT3A(mut)-expressing cells. RNA-seq studies supported deregulated cell cycle progression and p53 activation, along with splicing, ribosome biogenesis, and metabolism.
    CONCLUSIONS: Together, our studies show that DNMT3A mutations underlie a defect in recovery from replication fork arrest with subsequent accumulation of unresolved DNA damage, which may have therapeutic tractability. These results demonstrate that, in addition to its role in epigenetic control, DNMT3A contributes to preserving genome integrity during replication stress.
    DOI:  https://doi.org/10.1158/1078-0432.CCR-21-2863
  4. Int J Radiat Oncol Biol Phys. 2021 Nov 01. pii: S0360-3016(21)01075-0. [Epub ahead of print]111(3S): S86
      PURPOSE/OBJECTIVE(S): Despite high prevalence of IDH1-R132H mutations in grade II-III gliomas, effective therapies remain limited. We sought to identify tumor-specific vulnerabilities induced by the IDH1-R132H oncogene and test the translational relevance of targeting them using a new genetically engineered mouse model (GEMM) of IDH1 mutant anaplastic astrocytoma.MATERIALS/METHODS: We conducted a synthetic lethality screen using isogenic IDH1 mutant and IDH1 wild-type (WT) glioma cells and a novel drug screening platform developed by our group, called MAPS. To create a GEMM of anaplastic astrocytoma, we developed a strategy to engineer Tp53, Atrx, Pik3ca, and Idh1 mutations in the brains of adult mice. We intracranially injected adeno-associated virus (AAV) expressing Cre recombinase and CRISPR sgRNAs targeting murine Atrx and Tp53 genes into 4 mouse strains: 1) LSL-Cas9; 2) LSL-Cas9; LSL-Pik3caH1047R, 3) LSL-Cas9; LSL-Idh1R132H, and 4) LSL-Cas9; LSL-Idh1R132H; LSL-Pik3caH1047R.
    RESULTS: Our screen revealed that IDH1 mutant cells are hypersensitive to drugs targeting enzymes in the de novo pyrimidine nucleotide synthesis pathway, including dihydroorotate dehydrogenase (DHODH). We demonstrated that these cytotoxic effects are on-target and are associated with increased DNA damage in IDH1 mutant cells. Next, we showed that IDH1 mutant patient-derived glioma stem-like cell lines (GSCs) are also hyperdependent on de novo pyrimidine synthesis compared to IDH1 WT lines. In addition, we found that the novel brain penetrant DHODH inhibitor, BAY2402234 (currently undergoing testing in leukemia patients), decreased tumor growth in an orthotopic xenograft model of IDH1 mutant, but not IDH1 WT, glioblastoma. We then sought to create and use a GEMM of IDH1 mutant anaplastic astrocytoma to test whether dependence on de novo pyrimidine synthesis manifests across tumor grade. Following intracranial AAV injection (see methods), astrocytomas preferentially formed after 9-14 months in mice carrying both Idh1 and Pik3ca conditional alleles. These tumors histologically resembled grade III astrocytomas, expressed astrocytoma lineage markers, and displayed elevated (R)-2-hydroxyglutarate. To create an additional model with shorter tumor latency, we performed secondary transplants of GSCs derived from our GEMM into recipient mice. We found that BAY2402234 blocked tumor growth in these orthotopic astrocytoma allografts.
    CONCLUSION: Our findings establish IDH1 mutations as predictive biomarkers of DHODH inhibitor efficacy in gliomas across tumor grade, highlight BAY2402234 as a candidate glioma therapeutic, and unveil new genetically faithful mouse models of IDH1 mutant glioma. In addition, we show that BAY2402234 induces preferential DNA damage in IDH1 mutant cells, thereby supporting evaluation of BAY2402234 as a potential tumor-selective radiosensitizer.
    DOI:  https://doi.org/10.1016/j.ijrobp.2021.07.205
  5. FEBS J. 2021 Oct 25.
      De novo thymidylate synthesis is a crucial pathway for normal and cancer cells. Deoxythymidine monophosphate (dTMP) is synthesized by the combined action of three enzymes: serine hydroxymethyltransferase (SHMT), dihydrofolate reductase (DHFR) and thymidylate synthase (TYMS), with the latter two being targets of widely used chemotherapeutics such as antifolates and 5-fluorouracil. These proteins translocate to the nucleus after SUMOylation and are suggested to assemble in this compartment into the thymidylate synthesis complex (dTMP-SC). We report the intracellular dynamics of the complex in cancer cells by in situ proximity ligation assay, showing that it is also detected in the cytoplasm. This result indicates that the role of the dTMP-SC assembly may go beyond dTMP synthesis. We have successfully assembled the dTMP synthesis complex in vitro, employing tetrameric SHMT1 and a bifunctional chimeric enzyme comprising human TYMS and DHFR. We show that the SHMT1 tetrameric state is required for efficient complex assembly, indicating that this aggregation state is evolutionarily selected in eukaryotes to optimize protein-protein interactions. Lastly, our results on the activity of the complete thymidylate cycle in vitro, may provide a useful tool to develop drugs targeting the entire complex instead of the individual components.
    Keywords:  cancer metabolism; protein-protein complex; purine synthesis; thymidylate synthesis; transient interactions
    DOI:  https://doi.org/10.1111/febs.16248
  6. Front Genet. 2021 ;12 742434
      The fine tuning of the DNA double strand break repair pathway choice relies on different regulatory layers that respond to environmental and local cues. Among them, the presence of non-canonical nucleic acids structures seems to create challenges for the repair of nearby DNA double strand breaks. In this review, we focus on the recently published effects of G-quadruplexes and R-loops on DNA end resection and homologous recombination. Finally, we hypothesized a connection between those two atypical DNA structures in inhibiting the DNA end resection step of HR.
    Keywords:  DNA double strand break repair; DNA end resection; G-quadruplex; R-loops; homologous recombination (HR)
    DOI:  https://doi.org/10.3389/fgene.2021.742434
  7. Int J Radiat Oncol Biol Phys. 2021 Nov 01. pii: S0360-3016(21)01659-X. [Epub ahead of print]111(3S): e230-e231
      PURPOSE/OBJECTIVE(S): TTFields is a novel non-invasive physical modality of cancer therapy which was initially thought to interfere with cancer cell mitosis to induce cell death. Genomics and proteomic results suggested the additional mechanisms of action underlying TTFields induced cell death as increased DNA replication stress and DNA damage while decreasing DNA repair through the downregulation of Fanconi's Anemia (FA) pathway genes, chromosome maintenance genes and others. The current study focused on exploiting the conditional vulnerabilities caused by TTFields exposure to test novel combination therapies that target DNA replication fork stability combined with radiation.MATERIALS/METHODS: Human NSCLC cell lines (H157, H4006, H549 and H1299) and pancreatic cancer cell lines (PANC-1 and Panc 04.03) were used in this study. A laboratory research system was used to generate TTFields. TTFields, radiation and drug combination efficacy were tested using clonogenic cell survival assays while the Highest Single Agent approach was used to assess the combinatorial efficacy.
    RESULTS: Comparative analysis of genomics and proteomics data revealed dysregulation of pathways including cell cycle, DNA damage repair and replication, and transcriptional and translational regulation under TTFields exposure. Functional characterization studies confirmed the downregulation of FA pathway proteins there by increased replication stress, DNA damage and impaired DNA damage repair. To exploit the conditional vulnerability environment induced by TTFields exposure different chemo agents that target and increase replication stress were tested in novel combination therapy options. It was found that the effect of TTFields exposure concomitant with the PARP1 inhibitor olaparib followed by irradiation (IR) was synergistic compared to IR or olaparib alone or in combination. In addition, TTFields synergistically enhanced the cell killing efficacy of the ATR inhibitor AZD6738 followed by IR.
    CONCLUSION: Expression of FA pathway genes/proteins is modulated by TTFields exposure and likely explains the reduced DNA repair capacity and replication fork maintenance. Hence, targeting DNA damage repair and the DNA replication stress pathway using inhibitors of PARP1 and ATR could be used in combination with TTFields with or without radiation for cancer therapy.
    DOI:  https://doi.org/10.1016/j.ijrobp.2021.07.789
  8. DNA Repair (Amst). 2021 Oct 13. pii: S1568-7864(21)00196-8. [Epub ahead of print]108 103240
      Unlike all other biological molecules that are degraded and replaced if damaged, DNA must be repaired as chromosomes cannot be replaced. Indeed, DNA endures a wide variety of structural damage that need to be repaired accurately to maintain genomic stability and proper functioning of cells and to prevent mutation leading to disease. Given that the genome is packaged into chromatin within eukaryotic cells, it has become increasingly evident that the chromatin context of DNA both facilitates and regulates DNA repair processes. In this review, we discuss mechanisms involved in removal of histones (chromatin disassembly) from around DNA lesions, by histone chaperones and chromatin remodelers, that promotes accessibility of the DNA repair machinery. We also elaborate on how the deposition of core histones and specific histone variants onto DNA (chromatin assembly) during DNA repair promotes repair processes, the role of histone post translational modifications in these processes and how chromatin structure is reestablished after DNA repair is complete.
    DOI:  https://doi.org/10.1016/j.dnarep.2021.103240
  9. Nat Commun. 2021 Oct 26. 12(1): 6176
      Serine is a non-essential amino acid that is critical for tumour proliferation and depletion of circulating serine results in reduced tumour growth and increased survival in various cancer models. While many cancer cells cultured in a standard tissue culture medium depend on exogenous serine for optimal growth, here we report that these cells are less sensitive to serine/glycine depletion in medium containing physiological levels of metabolites. The lower requirement for exogenous serine under these culture conditions reflects both increased de novo serine synthesis and the use of hypoxanthine (not present in the standard medium) to support purine synthesis. Limiting serine availability leads to increased uptake of extracellular hypoxanthine, sparing available serine for other pathways such as glutathione synthesis. Taken together these results improve our understanding of serine metabolism in physiologically relevant nutrient conditions and allow us to predict interventions that may enhance the therapeutic response to dietary serine/glycine limitation.
    DOI:  https://doi.org/10.1038/s41467-021-26395-5
  10. Mol Carcinog. 2021 Oct 28.
      Poly(ADP-ribose) polymerases (PARP) act as DNA damage sensors that produce poly(ADP-ribose) (PAR) chains at double-strand breaks, facilitating the recruitment of repair factors. Cancers with homologous recombination defects are sensitive to small molecule PARP inhibitors. Despite PARP5B gene copy number changes in many cancers, the effects of this genetic alteration on tumor phenotype are largely unknown. To better understand this clinical finding, we characterized a PARP5B null mutation in a carcinogen-induced in vivo head and neck squamous cell carcinoma (SCC) model. Reduced PARP5B expression inhibited tumor growth, induced primary tumor differentiation and apoptosis, and inhibited cell proliferation and metastasis. Loss of PARP5B expression-induced ataxia telangiectasia and Rad3 related (ATR) activation and depleted the cancer stem cell fraction. PARP5B null tumor cells lacked 53BP1+ double-strand break foci, ATM activation, and p53 induction compared to PARP5B+/+ cancers. PARP5B null SCC expresses a multiprotein complex containing PML, pRPA, Rad50, Rad51, XRCC1, proliferating cell nuclear antigen (PCNA), and Mcm2, suggesting an HR-mediated repair mechanism at DNA replication foci. Low doses of etoposide combined with the PARP5B inhibitor XAV939 induced senescence and apoptosis in human SCC lines. NBS1 overexpression in these cells inhibited the effects of low-dose etoposide/XAV939 treatment. Our results indicate that PARP5B inhibition is new targeted cancer therapy.
    Keywords:  DNA damage signaling; apoptosis; cancer stem cell; homologous recombination; metastasis
    DOI:  https://doi.org/10.1002/mc.23363
  11. Sci Total Environ. 2021 Oct 26. pii: S0048-9697(21)06156-8. [Epub ahead of print] 151078
      Cadmium (Cd) is a well-known carcinogenic metal and widespread environmental pollutant. The effect of Cd-induced carcinogenesis is partly due to accumulated DNA damage and chromosomal aberrations, but the exact mechanisms underlying the genotoxicity of Cd have not been clearly understood. Here, we found that one long non-coding RNA MT1DP is participated in Cd-induced DNA damage and replication stress. Through analyzing the residents from Cd-contaminated area in Southern China, we found that blood DNA repair genes are down-regulated in individuals with high urine Cd values compared to those with low urine Cd values, which contrast to the blood MT1DP levels. Through in vitro experiments, we found that MT1DP promotes Cd-induced DNA damage response, genome instability and replication fork stalling. Mechanically, upon Cd treatment, ATR is activated to enhance HIF-1α expression, which in turn promotes the transcription level of MT1DP. Subsequently MT1DP is recruited on the chromatin and binds to SMARCAL1 to competitive inhibit latter's interaction with RPA complexes, finally leading to increased replication stress and DNA damage. In summary, this study provides clear evidence for the role of epigenetic regulation on the genotoxic effect of Cd, and MT1DP-mediated replication stress may represent a novel mechanism for Cd-induced carcinogenesis.
    Keywords:  ATR;SMARCAL1; Cd; DNA damage; MT1DP; Replication stress
    DOI:  https://doi.org/10.1016/j.scitotenv.2021.151078
  12. Mol Pharmacol. 2021 Oct 23. pii: MOLPHARM-MR-2021-000374. [Epub ahead of print]
      DNA topoisomerases regulate the topological state of DNA, relaxing DNA supercoils and resolving catenanes and knots that result from biological processes such as transcription and replication. DNA topoisomerase II (TOP2) enzymes achieve this by binding DNA and introducing an enzyme-bridged DNA double-strand break (DSB) where each protomer of the dimeric enzyme is covalently attached to the 5' end of the cleaved DNA via an active site tyrosine phosphodiester linkage. The enzyme then passes a second DNA duplex though the DNA break, before religation and release of the enzyme. However, this activity is potentially hazardous to the cell, as failure to complete religation leads to persistent TOP2 protein-DNA covalent complexes which are cytotoxic. Indeed, this property of topoisomerase has been exploited in cancer therapy in the form of topoisomerase poisons which block the religation stage of the reaction cycle, leading to an accumulation of topoisomerase-DNA adducts. A number of parallel cellular processes have been identified that lead to removal of these covalent TOP2-DNA complexes facilitating repair of the resulting protein-free DSB by standard DNA repair pathways. These pathways presumably arose to repair spontaneous stalled or poisoned TOP2-DNA complexes, but understanding their mechanisms also has implications for cancer therapy, particularly resistance to anti-cancer TOP2 poisons and the genotoxic side effects of these drugs. Here we review recent progress in the understanding of the processing to TOP2 DNA covalent complexes., The basic components and mechanisms plus the additional layer of complexity posed by the post-translational modifications that modulate these pathways. Significance Statement Multiple pathways have been reported for removal and repair of TOP2-DNA covalent complexes to ensure the timely and efficient repair of TOP2-DNA covalent adducts to protect the genome. Post-translational modifications such as ubiquitination and SUMOylation are involved in the regulation of TOP2-DNA complex repair. Small molecule inhibitors of these post translational modifications may help to improve outcomes of TOP2 poison chemotherapy, for example by increasing TOP2 poison cytotoxicity and reducing genotoxicity, but this remains to be determined.
    Keywords:  DNA damage and repair; Proteasome-mediated protein degradation; Sumoylation; Topoisomerases; Ubiquitination
    DOI:  https://doi.org/10.1124/molpharm.121.000374
  13. Sci Rep. 2021 Oct 25. 11(1): 21008
      The cytidine deaminase, APOBEC3A (A3A), is a prominent source of mutations in multiple cancer types. These APOBEC-signature mutations are non-uniformly distributed across cancer genomes, associating with single-stranded (ss) DNA formed during DNA replication and hairpin-forming sequences. The biochemical and cellular factors that influence these specificities are unclear. We measured A3A's cytidine deaminase activity in vitro on substrates that model potential sources of ssDNA in the cell and found that A3A is more active on hairpins containing 4 nt ssDNA loops compared to hairpins with larger loops, bubble structures, replication fork mimics, ssDNA gaps, or linear DNA. Despite pre-bent ssDNAs being expected to fit better in the A3A active site, we determined A3A favors a 4 nt hairpin substrate only 2- to fivefold over linear ssDNA substrates. Addition of whole cell lysates or purified RPA to cytidine deaminase assays more severely reduced A3A activity on linear ssDNA (45 nt) compared to hairpin substrates. These results indicate that the large enrichment of A3A-driven mutations in hairpin-forming sequences in tumor genomes is likely driven in part by other proteins that preferentially bind longer ssDNA regions, which limit A3A's access. Furthermore, A3A activity is reduced at ssDNA associated with a stalled T7 RNA polymerase, suggesting that potential protein occlusion by RNA polymerase also limits A3A activity. These results help explain the small transcriptional strand bias for APOBEC mutation signatures in cancer genomes and the general targeting of hairpin-forming sequences in the lagging strand template during DNA replication.
    DOI:  https://doi.org/10.1038/s41598-021-00435-y
  14. Nat Commun. 2021 Oct 27. 12(1): 6207
      Cyclic guanosine monophosphate-adenosine monophosphate (cGAMP), produced by cyclic GMP-AMP synthase (cGAS), stimulates the production of type I interferons (IFN). Here we show that cGAMP activates DNA damage response (DDR) signaling independently of its canonical IFN pathways. Loss of cGAS dampens DDR signaling induced by genotoxic insults. Mechanistically, cGAS activates DDR in a STING-TBK1-dependent manner, wherein TBK1 stimulates the autophosphorylation of the DDR kinase ATM, with the consequent activation of the CHK2-p53-p21 signal transduction pathway and the induction of G1 cell cycle arrest. Despite its stimulatory activity on ATM, cGAMP suppresses homology-directed repair (HDR) through the inhibition of polyADP-ribosylation (PARylation), in which cGAMP reduces cellular levels of NAD+; meanwhile, restoring NAD+ levels abrogates cGAMP-mediated suppression of PARylation and HDR. Finally, we show that cGAMP also activates DDR signaling in invertebrate species lacking IFN (Crassostrea virginica and Nematostella vectensis), suggesting that the genome surveillance mechanism of cGAS predates metazoan interferon-based immunity.
    DOI:  https://doi.org/10.1038/s41467-021-26240-9
  15. J Clin Immunol. 2021 Oct 30.
      DNA damage is a constant event in every cell caused by exogenous factors such as ultraviolet and ionizing radiation (UVR/IR) and intercalating drugs, or endogenous metabolic and replicative stress. Proteins of the DNA damage response (DDR) network sense DNA lesions and induce cell cycle arrest, DNA repair, and apoptosis. Genetic defects of DDR or DNA repair proteins can be associated with immunodeficiency, bone marrow failure syndromes, and cancer susceptibility. Although various diagnostic tools are available to evaluate DNA damage, their quality to identify DNA repair deficiencies differs enormously and depends on affected pathways. In this study, we investigated the DDR biomarkers γH2AX (Ser139), p-ATM (Ser1981), and p-CHK2 (Thr68) using flow cytometry on peripheral blood cells obtained from patients with combined immunodeficiencies due to non-homologous end-joining (NHEJ) defects and ataxia telangiectasia (AT) in response to low-dose IR. Significantly reduced induction of all three markers was observed in AT patients compared to controls. However, delayed downregulation of γH2AX was found in patients with NHEJ defects. In contrast to previous reports of DDR in cellular models, these biomarkers were not sensitive enough to identify ARTEMIS deficiency with sufficient reliability. In summary, DDR biomarkers are suitable for diagnosing NHEJ defects and AT, which can be useful in neonates with abnormal TREC levels (T cell receptor excision circles) identified by newborn screening. We conclude that DDR biomarkers have benefits and some limitations depending on the underlying DNA repair deficiency.
    Keywords:  Cancer susceptibility; DNA damage response; DNA repair; Immunodeficiency; Radiosensitivity
    DOI:  https://doi.org/10.1007/s10875-021-01156-7
  16. Int J Radiat Oncol Biol Phys. 2021 Nov 01. pii: S0360-3016(21)01658-8. [Epub ahead of print]111(3S): e230
      PURPOSE/OBJECTIVE(S): Radiotherapy (RT) controls tumors primarily by inducing DNA damage. However, some tumor cells can repair RT-induced DNA damage and are thus radioresistant. RT could be made more effective by combining it with inhibitors of DNA damage response proteins (DDRi) to selectively render tumor cells more susceptible to RT-induced DNA damage. There are several DDRi currently approved by the FDA or in clinical trials for use as monotherapy, including inhibitors of DNA-PKcs, PARP, Rad 51, ATR and ATM. These proteins function in non-homologous end-joining (classical and alternative), homologous recombination, base excision repair or cell cycle checkpoint and disrupting any of which may enhance RT effectiveness. Because protons produce much more complex DNA lesion compared to x-rays, protons may amplify the effect of DDRis and further enhance potential activation of anti-tumor immune signaling. Our hypothesis is that DDRis sensitize cancer cells to RT and the sensitization effect is amplified by protons more so than x-rays with an enhancement in upstream immune signaling.MATERIALS/METHODS: We used 4 cancer cell lines: H460, H1299, PANC-1 and Panc 10.05 and 5 DDRis targeting DNA-PKcs (NU7441), PARP (AZD2281), Rad 51 (B02), ATR (AZD6738) and ATM (KU55933) at various concentrations (0.1-10 µM). We irradiated cells with 6 MV x-rays or 9.9 keV/µm protons (dose-weighted LET in water) alone or with DDRis at various dose levels to assess cell survival via clonogenic assay, DNA damage via gH2AX and 53BP1 foci, micronuclei (MN) and cGAS-positive micronuclei (NM-cGAS+), the latter two being precursors of antitumor immunity.
    RESULTS: We observed that DDRis sensitized both x-rays and protons. Protons+ATMi (10 µM) sensitization relative to x-rays alone was increased 3.51-fold (± 0.09). The RBE ranged from 0.79 ± 0.03 to 1.54 ± 0.09 and were negatively correlated with x-rays sensitivity (r = -0.6160), suggesting that the greater the DDRi-induced sensitization, the less benefit there will be from the proton LET effect. Nonetheless, the sensitization relative to x-rays alone from combining DDRi with protons was generally larger (30 ± 3% on average). Generally, the combination of DDRi with RT increased gH2AX and 53BP1 foci at 24 h after radiation, and MN and MN-cGAS+ at 24 and 72 h after radiation with protons+DDRi having a higher increase relative to x-rays alone than x-rays+DDRi.
    CONCLUSION: Inhibition of DNA-PKcs, PARP, Rad 51, ATR and ATM substantially sensitized several cancer cell lines to x-rays and protons. Although protons+DDRi reduced proton RBE, the inhibitor-induced sensitization outweighs the RBE loss, resulting in a net sensitization beyond x-rays+DDRi. The increased MN number indicates that pairing RT with DDRis may provide an additional benefit of antitumor immune stimulation. Additional preclinical work is warranted to elucidate the complex interaction of DDRi and RT in vivo.
    DOI:  https://doi.org/10.1016/j.ijrobp.2021.07.788
  17. Leuk Lymphoma. 2021 Oct 27. 1-8
      Cancer cells reprogram their metabolism to maintain sustained proliferation, which creates unique metabolic dependencies between malignant and healthy cells that can be exploited for therapy. In acute myeloid leukemia (AML), mitochondrial inhibitors that block tricarboxylic acid cycle enzymes or electron transport chain complexes have recently shown clinical promise. The isocitrate dehydrogenase 1 inhibitor ivosidenib, the isocitrate dehydrogenase 2 inhibitor enasidenib, and the BH3 mimetic venetoclax received FDA approval for treatment of AML in the last few years. Other mitochondrial inhibitors including CPI-613, CB-839, dihydroorotate dehydrogenase inhibitors, IACS-010759, and mubritinib, have shown encouraging preclinical efficacy and are currently being evaluated in clinical trials. In this review, we summarize recent metabolism-based therapies and their ability to target altered cancer metabolism in AML.
    Keywords:  Targeted therapy; acute myeloid leukemia; mitochondrial metabolism
    DOI:  https://doi.org/10.1080/10428194.2021.1992759
  18. Vaccines (Basel). 2021 Sep 22. pii: 1050. [Epub ahead of print]9(10):
      The availability and adequate balance of deoxyribonucleoside triphosphate (dNTP) is an important determinant of both the fidelity and the processivity of DNA polymerases. Therefore, maintaining an optimal balance of the dNTP pool is critical for genomic stability in replicating and quiescent cells. Since DNA synthesis is required not only in genomic replication but also in DNA damage repair and recombination, the abnormalities in the dNTP pool affect a wide range of chromosomal activities. The generation of antibody diversity relies on antigen-independent V(D)J recombination, as well as antigen-dependent somatic hypermutation and class switch recombination. These processes involve diverse sets of DNA polymerases, which are affected by the dNTP pool imbalances. This review discusses the role of the optimal dNTP pool balance in the diversification of antibody encoding genes.
    Keywords:  CSR; SAMHD1; SHM; V(D)J recombination; antibody; dNTP
    DOI:  https://doi.org/10.3390/vaccines9101050
  19. BMC Cancer. 2021 Oct 28. 21(1): 1154
      Homologous recombination and DNA repair are important for genome maintenance. Genetic variations in essential homologous recombination genes, including BRCA1 and BRCA2 results in homologous recombination deficiency (HRD) and can be a target for therapeutic strategies including poly (ADP-ribose) polymerase inhibitors (PARPi). However, response is limited in patients who are not HRD, highlighting the need for reliable and robust HRD testing. This manuscript will review BRCA1/2 function and homologous recombination proficiency in respect to breast and ovarian cancer. The current standard testing methods for HRD will be discussed as well as trials leading to approval of PARPi's. Finally, standard of care treatment and synthetic lethality will be reviewed.
    Keywords:  BRCA; Breast cancer; Homologous recombination; Homologous recombination deficient; Homologous recombination proficient; Ovarian cancer; PARP inhibitor
    DOI:  https://doi.org/10.1186/s12885-021-08863-9
  20. DNA Repair (Amst). 2021 Oct 21. pii: S1568-7864(21)00199-3. [Epub ahead of print]108 103243
      The phosphorylation of histone variant H2AX and formation of γH2AX is a primary response to the DNA double-strand breaks (DSBs). Detection of γH2AX is a robust and sensitive tool for diagnosis of DNA damage and repair in pre-clinical drug discovery investigations. In addition, the replication stress also leads to the formation of γH2AX and cell death and so γH2AX can serve as a surrogate marker of drug-induced cytotoxicity. Recent advances in genomic research offer an opportunity to detect γH2AX as a specific biomarker for quantitative analysis of DNA damages and repair using high content screening technology and quantitative imaging analysis. The proposed approaches identify a wide range of genetic disorders and are applied in combination with other assays in drug discovery and also for the evaluation of the efficacy of various developmental drugs. In the current review, we provide recent insights into the potential of γH2AX biomarker as a powerful tool in genotoxicity analyses for the monitoring and managing of cancer diseases.
    Keywords:  DNA damage; Genetic imaging; Genotoxicity; H2A histone family; γH2AX
    DOI:  https://doi.org/10.1016/j.dnarep.2021.103243
  21. Cell Rep. 2021 Oct 26. pii: S2211-1247(21)01349-8. [Epub ahead of print]37(4): 109879
      SLX4/FANCP is a key Fanconi anemia (FA) protein and a DNA repair scaffold for incision around a DNA interstrand crosslink (ICL) by its partner XPF nuclease. The tandem UBZ4 ubiquitin-binding domains of SLX4 are critical for the recruitment of SLX4 to damage sites, likely by binding to K63-linked polyubiquitin chains. However, the identity of the ubiquitin E3 ligase that mediates SLX4 recruitment remains unknown. Using small interfering RNA (siRNA) screening with a GFP-tagged N-terminal half of SLX4 (termed SLX4-N), we identify the RNF168 E3 ligase as a critical factor for mitomycin C (MMC)-induced SLX4 foci formation. RNF168 and GFP-SLX4-N colocalize in MMC-induced ubiquitin foci. Accumulation of SLX4-N at psoralen-laser ICL tracks or of endogenous SLX4 at Digoxigenin-psoralen/UVA ICL is dependent on RNF168. Finally, we find that RNF168 is epistatic with SLX4 in promoting MMC tolerance. We conclude that RNF168 is a critical component of the signal transduction that recruits SLX4 to ICL damage.
    Keywords:  Fanconi anemia; RNF168; SLX4; interstrand crosslink repair; ubiquitination
    DOI:  https://doi.org/10.1016/j.celrep.2021.109879
  22. Open Biol. 2021 Oct;11(10): 210121
      Treslin/Ticrr is required for the initiation of DNA replication and binds to MTBP (Mdm2 Binding Protein). Here, we show that in Xenopus egg extract, MTBP forms an elongated tetramer with Treslin containing two molecules of each protein. Immunodepletion and add-back experiments show that Treslin-MTBP is rate limiting for replication initiation. It is recruited onto chromatin before S phase starts and recruitment continues during S phase. We show that DDK activity both increases and strengthens the interaction of Treslin-MTBP with licensed chromatin. We also show that DDK activity cooperates with CDK activity to drive the interaction of Treslin-MTBP with TopBP1 which is a regulated crucial step in pre-initiation complex formation. These results suggest how DDK works together with CDKs to regulate Treslin-MTBP and plays a crucial in selecting which origins will undergo initiation.
    Keywords:  DDK; MTBP; PP1; TopBP1; Treslin; simurosertib
    DOI:  https://doi.org/10.1098/rsob.210121
  23. Exp Mol Med. 2021 Oct 25.
      Transcription-replication conflicts lead to DNA damage and genomic instability, which are closely related to human diseases. A major source of these conflicts is the formation of R-loops, which consist of an RNA-DNA hybrid and a displaced single-stranded DNA. Although these structures have been studied, many aspects of R-loop biology and R-loop-mediated genome instability remain unclear. Here, we demonstrate that thyroid hormone receptor-associated protein 3 (Thrap3) plays a critical role in regulating R-loop resolution. In cancer cells, Thrap3 interacts with DEAD-box helicase 5 (DDX5) and localizes to R-loops. Arginine-mediated methylation of DDX5 is required for its interaction with Thrap3, and the Thrap3-DDX5 axis induces the recruitment of 5'-3' exoribonuclease 2 (XRN2) into R-loops. Loss of Thrap3 increases R-loop accumulation and DNA damage. These findings suggest that Thrap3 mediates resistance to cell death by preventing R-loop accumulation in cancer cells.
    DOI:  https://doi.org/10.1038/s12276-021-00689-6
  24. Cell Chem Biol. 2021 Oct 22. pii: S2451-9456(21)00441-4. [Epub ahead of print]
      Efforts to target glucose metabolism in cancer have been limited by the poor potency and specificity of existing anti-glycolytic agents and a poor understanding of the glucose dependence of cancer subtypes in vivo. Here, we present an extensively characterized series of potent, orally bioavailable inhibitors of the class I glucose transporters (GLUTs). The representative compound KL-11743 specifically blocks glucose metabolism, triggering an acute collapse in NADH pools and a striking accumulation of aspartate, indicating a dramatic shift toward oxidative phosphorylation in the mitochondria. Disrupting mitochondrial metabolism via chemical inhibition of electron transport, deletion of the malate-aspartate shuttle component GOT1, or endogenous mutations in tricarboxylic acid cycle enzymes, causes synthetic lethality with KL-11743. Patient-derived xenograft models of succinate dehydrogenase A (SDHA)-deficient cancers are specifically sensitive to KL-11743, providing direct evidence that TCA cycle-mutant tumors are vulnerable to GLUT inhibitors in vivo.
    Keywords:  GLUT inhibitor; PDX models; electron transport chain inhibitors; glycolysis; imaging; malate-aspartate shuttle; mitochondrial inhibitors; pharmacology; redox biology; toxicology
    DOI:  https://doi.org/10.1016/j.chembiol.2021.10.007
  25. Mol Ther Oncolytics. 2021 Dec 17. 23 107-123
      Metabolic reprogramming is a core hallmark of cancer and is key for tumorigenesis and tumor progression. Investigation of metabolic perturbation by anti-cancer compounds would allow a thorough understanding of the underlying mechanisms of these agents and identification of new anti-cancer targets. Here, we demonstrated that the administration of oleanolic acid (OA) rapidly altered cancer metabolism, particularly suppressing the purine salvage pathway (PSP). PSP restoration significantly opposed OA-induced DNA replication and cell proliferation arrest, underscoring the importance of this pathway for the anti-cancer activity of OA. Hypoxanthine-guanine phosphoribosyltransferase (HGPRT) and 5'-nucleotidase (5'-NT), two metabolic enzymes essential for PSP activity, were promptly degraded by OA via the lysosome pathway. Mechanistically, OA selectively targeted superoxide dismutase 1 (SOD1) and yielded reactive oxygen species (ROS) to activate the AMP-activated protein kinase (AMPK)/mammalian target of rapamycin complex 1 (mTORC1)/macroautophagy pathway, thus eliciting lysosomal degradation of HGPRT and 5'-NT. Furthermore, we found that the PSP was overactivated in human lung and breast cancers, with a negative correlation with patient survival. The results of this study elucidated a new anti-cancer mechanism of OA by restraining the PSP via the SOD1/ROS/AMPK/mTORC1/macroautophagy/lysosomal pathway. We also identified the PSP as a new target for cancer treatment and highlighted OA as a potential therapeutic agent for cancers with high PSP activity.
    Keywords:  5′-nucleotidase; hypoxanthine-guanine phosphoribosyltransferase; lysosomal degradation; macroautophagy; oleanolic acid; purine salvage pathway; superoxide dismutase 1
    DOI:  https://doi.org/10.1016/j.omto.2021.08.013
  26. Oxid Med Cell Longev. 2021 ;2021 7753857
      Hydroxyurea (HU) is a water-soluble antiproliferative agent used for decades in neoplastic and nonneoplastic conditions. HU is considered an essential medicine because of its cytoreduction functions. HU is an antimetabolite that inhibits ribonucleotide reductase, which causes a depletion of the deoxyribonucleotide pool and dramatically reduces cell proliferation. The proliferation arrest, depending on drug concentration and exposure, may promote a cellular senescence phenotype associated with cancer cell therapy resistance and inflammation, influencing neighboring cell functions, immunosuppression, and potential cancer relapse. HU can induce cellular senescence in both healthy and transformed cells in vitro, in part, because of increased reactive oxygen species (ROS). Here, we analyze the main molecular mechanisms involved in cytotoxic/genotoxic HU function, the potential to increase intracellular ROS levels, and the principal features of cellular senescence induction. Understanding the mechanisms involved in HU's ability to induce cellular senescence may help to improve current chemotherapy strategies and control undesirable treatment effects in cancer patients and other diseases.
    DOI:  https://doi.org/10.1155/2021/7753857
  27. Nat Biotechnol. 2021 Oct 28.
      Gene amplification drives oncogenesis in a broad spectrum of cancers. A number of drugs have been developed to inhibit the protein products of amplified driver genes, but their clinical efficacy is often hampered by drug resistance. Here, we introduce a therapeutic strategy for targeting cancer-associated gene amplifications by activating the DNA damage response with triplex-forming oligonucleotides (TFOs), which drive the induction of apoptosis in tumors, whereas cells without amplifications process lower levels of DNA damage. Focusing on cancers driven by HER2 amplification, we find that TFOs targeting HER2 induce copy number-dependent DNA double-strand breaks (DSBs) and activate p53-independent apoptosis in HER2-positive cancer cells and human tumor xenografts via a mechanism that is independent of HER2 cellular function. This strategy has demonstrated in vivo efficacy comparable to that of current precision medicines and provided a feasible alternative to combat drug resistance in HER2-positive breast and ovarian cancer models. These findings offer a general strategy for targeting tumors with amplified genomic loci.
    DOI:  https://doi.org/10.1038/s41587-021-01057-5
  28. Life Sci. 2021 Oct 21. pii: S0024-3205(21)01059-6. [Epub ahead of print] 120072
      AIMS: 5-Fluorouracil (5-FU), a thymidylate synthase (TS) inhibitor, has been used as the first-line chemotherapeutic drug for cholangiocarcinoma (CCA). The side effects and drug resistance have developed the limits of the clinical application of 5-FU in CCA treatment. Upregulation of Forkhead box M1 (FOXM1) and TS were shown to play a significant role in 5-FU resistance. In this study, the effect of Siomycin A (SioA), a FOXM1 inhibitor, on enhancing 5-FU cytotoxicity and reversing 5-FU resistance in CCA cell lines were demonstrated.MAIN METHODS: Human CCA cell lines, KKU-100 and KKU-213A were used. Cell viability was determined using MTT assay. Expression of FOXM1 and TS proteins were determined using Western blotting. FOXM1 mRNA expression was quantitated using real-time PCR. The combination and dose reduction (DRI) were analyzed according to the Chou and Talalay method.
    KEY FINDING: Single drug treatment of 5-FU and SioA effectively inhibited CCA cell growth in dose and time dependent fashions. The two CCA cell lines had different responses to 5-FU but exhibited similar sensitivity to SioA. FOXM1 and TS expression were increased in the 5-FU treated cells but were suppressed in the SioA treated cells. A direct binding of SioA, to TS and 5,10-methylene-tetrahydrofolate as an inactive ternary complex was simulated. The combined treatment of 5-FU with SioA showed a synergistic effect with a high DRI and restored 5-FU sensitivity in the 5-FU resistant cells.
    SIGNIFICANCE: Targeting FOXM1 using SioA in combination with 5-FU might be a strategy to overcome the 5-FU resistance in CCA.
    Keywords:  5-Florouracil; Bile duct cancer; FOXM1; Isobologram; Siomycin A; Synergistic effect
    DOI:  https://doi.org/10.1016/j.lfs.2021.120072
  29. Cell. 2021 Oct 28. pii: S0092-8674(21)01179-X. [Epub ahead of print]184(22): 5503-5505
      Diverse DNA repair pathways correct ranging types of damage and play central roles in genome editing. In this issue of Cell, two publications leverage a new high-throughput screen that links pathway genes with the outcomes of repair, yielding mechanistic insights into the repair process as well as means to shape editing outcomes.
    DOI:  https://doi.org/10.1016/j.cell.2021.10.005
  30. Blood Adv. 2021 Oct 28. pii: bloodadvances.2021006139. [Epub ahead of print]
      Secondary myelodysplastic syndromes and acute myeloid leukemia (sMDS/AML) are rare in children/adolescents and have a dismal prognosis. The mainstay therapy is hematopoietic cell transplantation (HCT) but there has been no innovation in cytoreductive regimens. CPX-351, a fixed 5:1 molar ratio of liposomal cytarabine/daunorubicin, has shown favorable safety and efficacy in elderly individuals with sAML and children with relapsed de novo AML. We report the outcomes of seven young patients (six with newly diagnosed sMDS/AML and one with primary MDS/AML) uniformly treated with CPX-351. Five patients had previously received chemotherapy for osteosarcoma, Ewing sarcoma, neuroblastoma, or T-ALL; one had predisposing genomic instability disorder (Cornelia de Lange); and one MDS-related AML and multi-organ failure. The median age at diagnosis of myeloid malignancy was 17 (13-23) years. Patients received 1-3 cycles of CPX-351 (cytarabine 100mg/m2 plus daunorubicin 44mg/m2) on days 1, 3, and 5, resulting in complete morphologic remission without overt toxicity or treatment-related mortality. This approach allowed for adding FLT3 inhibitor as individualized therapy in one patient. Six patients were alive and leukemia-free at 0.5-3.3 years after HCT. One patient died from disease progression before HCT. Concluding, CPX-351 is an effective and well-tolerated regimen for cytoreduction in pediatric sMDS/AML warranting prospective studies.
    DOI:  https://doi.org/10.1182/bloodadvances.2021006139
  31. Br J Cancer. 2021 Oct 23.
      BACKGROUND: The TIMELESS-TIPIN complex protects the replication fork from replication stress induced by chemotherapeutic drugs. We hypothesised genetic polymorphisms of the TIMELESS-TIPIN complex may affect the response, progression-free survival (PFS), and overall survival (OS) of cytotoxic drugs in patients with metastatic colorectal cancer (mCRC).METHODS: We analysed data from the MAVERICC trial, which compared FOLFOX/bevacizumab and FOLFIRI/bevacizumab in untreated patients with mCRC. Genomic DNA extracted from blood samples was genotyped using an OncoArray. Eight functional single nucleotide polymorphisms (SNPs) in TIMELESS and TIPIN were tested for associations with clinical outcomes.
    RESULTS: In total, 324 patients were included (FOLFOX/bevacizumab arm, n = 161; FOLFIRI/bevacizumab arm, n = 163). In the FOLFOX/bevacizumab arm, no SNPs displayed confirmed associations with survival outcomes. In the FOLFIRI/bevacizumab arm, TIMELESS rs2291739 was significantly associated with OS in multivariate analysis (G/G vs. any A allele, hazard ratio = 3.06, 95% confidence interval = 1.49-6.25, p = 0.004). TIMELESS rs2291739 displayed significant interactions with treatment regarding both PFS and OS.
    CONCLUSIONS: TIMELESS rs2291739 might have different effects on therapeutic efficacy between oxaliplatin- and irinotecan-based chemotherapies. Upon further validation, our findings may be useful for personalised approaches in the first-line treatment of mCRC.
    DOI:  https://doi.org/10.1038/s41416-021-01592-7
  32. iScience. 2021 Oct 22. 24(10): 103173
      Schlafen11 (SLFN11) is referred to as interferon (IFN)-inducible. Based on cancer genomic databases, we identified human acute myeloid and lymphoblastic leukemia cells with gain-of-function mutations in the Janus kinase (JAK) family as exhibiting high SLFN11 expression. In these cells, the clinical JAK inhibitors cerdulatinib, ruxolitinib, and tofacitinib reduced SLFN11 expression, but IFN did not further induce SLFN11 despite phosphorylated STAT1. We provide evidence that suppression of SLFN11 by JAK inhibitors is caused by inactivation of the non-canonical IFN pathway controlled by AKT and ERK. Accordingly, the AKT and ERK inhibitors MK-2206 and SCH77284 suppressed SLFN11 expression. Both also suppressed the E26 transformation-specific (ETS)-family genes ETS-1 and FLI-1 that act as transcription factors for SLFN11. Moreover, SLFN11 expression was inhibited by the ETS inhibitor TK216. Our study reveals that SLFN11 expression is regulated via the JAK, AKT and ERK, and ETS axis. Pharmacological suppression of SLFN11 warrants future studies.
    Keywords:  Cell biology; Immunology; Molecular biology
    DOI:  https://doi.org/10.1016/j.isci.2021.103173