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1.
Nat Rev Mol Cell Biol ; 23(6): 407-427, 2022 06.
Article in English | MEDLINE | ID: mdl-35228717

ABSTRACT

Human topoisomerases comprise a family of six enzymes: two type IB (TOP1 and mitochondrial TOP1 (TOP1MT), two type IIA (TOP2A and TOP2B) and two type IA (TOP3A and TOP3B) topoisomerases. In this Review, we discuss their biochemistry and their roles in transcription, DNA replication and chromatin remodelling, and highlight the recent progress made in understanding TOP3A and TOP3B. Because of recent advances in elucidating the high-order organization of the genome through chromatin loops and topologically associating domains (TADs), we integrate the functions of topoisomerases with genome organization. We also discuss the physiological and pathological formation of irreversible topoisomerase cleavage complexes (TOPccs) as they generate topoisomerase DNA-protein crosslinks (TOP-DPCs) coupled with DNA breaks. We discuss the expanding number of redundant pathways that repair TOP-DPCs, and the defects in those pathways, which are increasingly recognized as source of genomic damage leading to neurological diseases and cancer.


Subject(s)
Genomic Instability , Neoplasms , DNA Damage/genetics , DNA Replication/genetics , Humans , Mitochondria/genetics , Neoplasms/genetics
2.
Cell ; 170(3): 507-521.e18, 2017 Jul 27.
Article in English | MEDLINE | ID: mdl-28735753

ABSTRACT

In this study, we show that evolutionarily conserved chromosome loop anchors bound by CCCTC-binding factor (CTCF) and cohesin are vulnerable to DNA double strand breaks (DSBs) mediated by topoisomerase 2B (TOP2B). Polymorphisms in the genome that redistribute CTCF/cohesin occupancy rewire DNA cleavage sites to novel loop anchors. While transcription- and replication-coupled genomic rearrangements have been well documented, we demonstrate that DSBs formed at loop anchors are largely transcription-, replication-, and cell-type-independent. DSBs are continuously formed throughout interphase, are enriched on both sides of strong topological domain borders, and frequently occur at breakpoint clusters commonly translocated in cancer. Thus, loop anchors serve as fragile sites that generate DSBs and chromosomal rearrangements. VIDEO ABSTRACT.


Subject(s)
Chromosome Fragility , DNA Breaks, Double-Stranded , Neoplasms/genetics , Animals , B-Lymphocytes/metabolism , CCCTC-Binding Factor , Cell Line, Tumor , DNA Topoisomerases, Type II/metabolism , DNA-Binding Proteins/metabolism , Humans , Mice , Mice, Inbred C57BL , Poly-ADP-Ribose Binding Proteins , Repressor Proteins/metabolism
3.
Cell ; 165(2): 357-71, 2016 Apr 07.
Article in English | MEDLINE | ID: mdl-27058666

ABSTRACT

We report a mechanism through which the transcription machinery directly controls topoisomerase 1 (TOP1) activity to adjust DNA topology throughout the transcription cycle. By comparing TOP1 occupancy using chromatin immunoprecipitation sequencing (ChIP-seq) versus TOP1 activity using topoisomerase 1 sequencing (TOP1-seq), a method reported here to map catalytically engaged TOP1, TOP1 bound at promoters was discovered to become fully active only after pause-release. This transition coupled the phosphorylation of the carboxyl-terminal-domain (CTD) of RNA polymerase II (RNAPII) with stimulation of TOP1 above its basal rate, enhancing its processivity. TOP1 stimulation is strongly dependent on the kinase activity of BRD4, a protein that phosphorylates Ser2-CTD and regulates RNAPII pause-release. Thus the coordinated action of BRD4 and TOP1 overcame the torsional stress opposing transcription as RNAPII commenced elongation but preserved negative supercoiling that assists promoter melting at start sites. This nexus between transcription and DNA topology promises to elicit new strategies to intercept pathological gene expression.


Subject(s)
DNA Topoisomerases, Type I/metabolism , DNA/metabolism , RNA Polymerase II/metabolism , Transcription, Genetic , DNA/chemistry , DNA Topoisomerases, Type I/genetics , Gene Knockdown Techniques , Humans , Promoter Regions, Genetic , RNA Polymerase II/chemistry , RNA Polymerase II/isolation & purification , Transcription Elongation, Genetic , Transcription Factors/isolation & purification , Transcription Initiation Site
4.
Genes Dev ; 35(3-4): 250-260, 2021 02 01.
Article in English | MEDLINE | ID: mdl-33446567

ABSTRACT

Reactive oxygen species (ROS) produced by NADPH1 oxidase 1 (NOX1) are thought to drive spermatogonial stem cell (SSC) self-renewal through feed-forward production of ROS by the ROS-BCL6B-NOX1 pathway. Here we report the critical role of oxygen on ROS-induced self-renewal. Cultured SSCs proliferated poorly and lacked BCL6B expression under hypoxia despite increase in mitochondria-derived ROS. Due to lack of ROS amplification under hypoxia, NOX1-derived ROS were significantly reduced, and Nox1-deficient SSCs proliferated poorly under hypoxia but normally under normoxia. NOX1-derived ROS also influenced hypoxic response in vivo because Nox1-deficient undifferentiated spermatogonia showed significantly reduced expression of HIF1A, a master transcription factor for hypoxic response. Hypoxia-induced poor proliferation occurred despite activation of MYC and suppression of CDKN1A by HIF1A, whose deficiency exacerbated self-renewal efficiency. Impaired proliferation of Nox1- or Hif1a-deficient SSCs under hypoxia was rescued by Cdkn1a depletion. Consistent with these observations, Cdkn1a-deficient SSCs proliferated actively only under hypoxia but not under normoxia. On the other hand, chemical suppression of mitochondria-derived ROS or Top1mt mitochondria-specific topoisomerase deficiency did not influence SSC fate, suggesting that NOX1-derived ROS play a more important role in SSCs than mitochondria-derived ROS. These results underscore the importance of ROS origin and oxygen tension on SSC self-renewal.


Subject(s)
Adult Germline Stem Cells/cytology , Cell Hypoxia/physiology , Oxygen/metabolism , Reactive Oxygen Species/metabolism , Animals , Cell Division/genetics , Cell Proliferation/genetics , Cells, Cultured , DNA Topoisomerases, Type I/genetics , Gene Expression Regulation, Developmental , Hypoxia-Inducible Factor 1, alpha Subunit/deficiency , Mice , Mice, Knockout , Mitochondria/physiology , NADPH Oxidase 1/metabolism
5.
Nat Rev Mol Cell Biol ; 17(11): 703-721, 2016 11.
Article in English | MEDLINE | ID: mdl-27649880

ABSTRACT

Topoisomerases introduce transient DNA breaks to relax supercoiled DNA, remove catenanes and enable chromosome segregation. Human cells encode six topoisomerases (TOP1, TOP1mt, TOP2α, TOP2ß, TOP3α and TOP3ß), which act on a broad range of DNA and RNA substrates at the nuclear and mitochondrial genomes. Their catalytic intermediates, the topoisomerase cleavage complexes (TOPcc), are therapeutic targets of various anticancer drugs. TOPcc can also form on damaged DNA during replication and transcription, and engage specific repair pathways, such as those mediated by tyrosyl-DNA phosphodiesterase 1 (TDP1) and TDP2 and by endonucleases (MRE11, XPF-ERCC1 and MUS81). Here, we review the roles of topoisomerases in mediating chromatin dynamics, transcription, replication, DNA damage repair and genomic stability, and discuss how deregulation of topoisomerases can cause neurodegenerative diseases, immune disorders and cancer.


Subject(s)
DNA Replication , DNA Topoisomerases/physiology , Genomic Instability , Transcription, Genetic , Animals , DNA Damage , DNA Repair , Humans , Mitochondria/enzymology , Mitochondria/genetics
6.
Mol Cell ; 79(5): 836-845.e7, 2020 09 03.
Article in English | MEDLINE | ID: mdl-32649884

ABSTRACT

The inactive X chromosome (Xi) is inherently susceptible to genomic aberrations. Replication stress (RS) has been proposed as an underlying cause, but the mechanisms that protect from Xi instability remain unknown. Here, we show that macroH2A1.2, an RS-protective histone variant enriched on the Xi, is required for Xi integrity and female survival. Mechanistically, macroH2A1.2 counteracts its structurally distinct and equally Xi-enriched alternative splice variant, macroH2A1.1. Comparative proteomics identified a role for macroH2A1.1 in alternative end joining (alt-EJ), which accounts for Xi anaphase defects in the absence of macroH2A1.2. Genomic instability was rescued by simultaneous depletion of macroH2A1.1 or alt-EJ factors, and mice deficient for both macroH2A1 variants harbor no overt female defects. Notably, macroH2A1 splice variant imbalance affected alt-EJ capacity also in tumor cells. Together, these findings identify macroH2A1 splicing as a modulator of genome maintenance that ensures Xi integrity and may, more broadly, predict DNA repair outcome in malignant cells.


Subject(s)
Alternative Splicing , DNA Repair , Epigenesis, Genetic , Genomic Instability , Histones/physiology , Anaphase , Animals , Cell Line , Chromosomal Instability , Chromosomes, Human, X , Female , Histones/genetics , Humans , Male , Mice , Mice, Inbred C57BL , Mice, Knockout
7.
Nature ; 600(7888): 279-284, 2021 12.
Article in English | MEDLINE | ID: mdl-34837071

ABSTRACT

Confocal microscopy1 remains a major workhorse in biomedical optical microscopy owing to its reliability and flexibility in imaging various samples, but suffers from substantial point spread function anisotropy, diffraction-limited resolution, depth-dependent degradation in scattering samples and volumetric bleaching2. Here we address these problems, enhancing confocal microscopy performance from the sub-micrometre to millimetre spatial scale and the millisecond to hour temporal scale, improving both lateral and axial resolution more than twofold while simultaneously reducing phototoxicity. We achieve these gains using an integrated, four-pronged approach: (1) developing compact line scanners that enable sensitive, rapid, diffraction-limited imaging over large areas; (2) combining line-scanning with multiview imaging, developing reconstruction algorithms that improve resolution isotropy and recover signal otherwise lost to scattering; (3) adapting techniques from structured illumination microscopy, achieving super-resolution imaging in densely labelled, thick samples; (4) synergizing deep learning with these advances, further improving imaging speed, resolution and duration. We demonstrate these capabilities on more than 20 distinct fixed and live samples, including protein distributions in single cells; nuclei and developing neurons in Caenorhabditis elegans embryos, larvae and adults; myoblasts in imaginal disks of Drosophila wings; and mouse renal, oesophageal, cardiac and brain tissues.


Subject(s)
Deep Learning , Microscopy, Confocal/methods , Microscopy, Confocal/standards , Animals , Caenorhabditis elegans/cytology , Caenorhabditis elegans/embryology , Caenorhabditis elegans/growth & development , Cell Line, Tumor , Drosophila melanogaster/cytology , Drosophila melanogaster/growth & development , Humans , Imaginal Discs/cytology , Mice , Myoblasts/cytology , Organ Specificity , Single-Cell Analysis , Tissue Fixation
8.
Mol Cell ; 75(2): 252-266.e8, 2019 07 25.
Article in English | MEDLINE | ID: mdl-31202577

ABSTRACT

Topoisomerase II (TOP2) relieves torsional stress by forming transient cleavage complex intermediates (TOP2ccs) that contain TOP2-linked DNA breaks (DSBs). While TOP2ccs are normally reversible, they can be "trapped" by chemotherapeutic drugs such as etoposide and subsequently converted into irreversible TOP2-linked DSBs. Here, we have quantified etoposide-induced trapping of TOP2ccs, their conversion into irreversible TOP2-linked DSBs, and their processing during DNA repair genome-wide, as a function of time. We find that while TOP2 chromatin localization and trapping is independent of transcription, it requires pre-existing binding of cohesin to DNA. In contrast, the conversion of trapped TOP2ccs to irreversible DSBs during DNA repair is accelerated 2-fold at transcribed loci relative to non-transcribed loci. This conversion is dependent on proteasomal degradation and TDP2 phosphodiesterase activity. Quantitative modeling shows that only two features of pre-existing chromatin structure-namely, cohesin binding and transcriptional activity-can be used to predict the kinetics of TOP2-induced DSBs.


Subject(s)
DNA Breaks, Double-Stranded , DNA Topoisomerases, Type II/chemistry , DNA/genetics , Multiprotein Complexes/chemistry , Poly-ADP-Ribose Binding Proteins/chemistry , Chromosome Breakage , Chromosomes/genetics , DNA/chemistry , DNA Repair/genetics , DNA Topoisomerases, Type II/genetics , DNA-Binding Proteins/chemistry , DNA-Binding Proteins/genetics , Etoposide/chemistry , Gene Conversion/genetics , HCT116 Cells , Humans , Kinetics , Multiprotein Complexes/genetics , Poly-ADP-Ribose Binding Proteins/genetics , Topoisomerase II Inhibitors/chemistry , Topoisomerase II Inhibitors/pharmacology , Torsion, Mechanical , Transcription, Genetic , Translocation, Genetic/genetics
9.
Development ; 150(20)2023 10 15.
Article in English | MEDLINE | ID: mdl-36897562

ABSTRACT

Reactive oxygen species (ROS) are generated from NADPH oxidases and mitochondria; they are generally harmful for stem cells. Spermatogonial stem cells (SSCs) are unique among tissue-stem cells because they undergo ROS-dependent self-renewal via NOX1 activation. However, the mechanism by which SSCs are protected from ROS remains unknown. Here, we demonstrate a crucial role for Gln in ROS protection using cultured SSCs derived from immature testes. Measurements of amino acids required for SSC cultures revealed the indispensable role of Gln in SSC survival. Gln induced Myc expression to drive SSC self-renewal in vitro, whereas Gln deprivation triggered Trp53-dependent apoptosis and impaired SSC activity. However, apoptosis was attenuated in cultured SSCs that lacked NOX1. In contrast, cultured SSCs lacking Top1mt mitochondria-specific topoisomerase exhibited poor mitochondrial ROS production and underwent apoptosis. Gln deprivation reduced glutathione production; supra-molar Asn supplementation allowed offspring production from SSCs cultured without Gln. Therefore, Gln ensures ROS-dependent SSC-self-renewal by providing protection against NOX1 and inducing Myc.


Subject(s)
Glutamine , Spermatogonia , Male , Mice , Animals , Spermatogonia/metabolism , Glutamine/metabolism , Reactive Oxygen Species/metabolism , Cell Proliferation , Stem Cells , Cells, Cultured
10.
Mol Cell ; 69(3): 371-384.e6, 2018 02 01.
Article in English | MEDLINE | ID: mdl-29395061

ABSTRACT

SLFN11 sensitizes cancer cells to a broad range of DNA-targeted therapies. Here we show that, in response to replication stress induced by camptothecin, SLFN11 tightly binds chromatin at stressed replication foci via RPA1 together with the replication helicase subunit MCM3. Unlike ATR, SLFN11 neither interferes with the loading of CDC45 and PCNA nor inhibits the initiation of DNA replication but selectively blocks fork progression while inducing chromatin opening across replication initiation sites. The ATPase domain of SLFN11 is required for chromatin opening, replication block, and cell death but not for the tight binding of SLFN11 to chromatin. Replication stress by the CHK1 inhibitor Prexasertib also recruits SLFN11 to nascent replicating DNA together with CDC45 and PCNA. We conclude that SLFN11 is recruited to stressed replication forks carrying extended RPA filaments where it blocks replication by changing chromatin structure across replication sites.


Subject(s)
Nuclear Proteins/genetics , Ataxia Telangiectasia Mutated Proteins/metabolism , Camptothecin , Cell Cycle Proteins/metabolism , Cell Line, Tumor , Chromatin/metabolism , DNA Damage , DNA Helicases/metabolism , DNA Replication/genetics , DNA Replication/physiology , DNA, Single-Stranded/genetics , DNA, Single-Stranded/metabolism , Humans , Minichromosome Maintenance Proteins/metabolism , Nuclear Proteins/metabolism , Pyrazines , Pyrazoles , Replication Protein A/metabolism
11.
Proc Natl Acad Sci U S A ; 120(34): e2218483120, 2023 08 22.
Article in English | MEDLINE | ID: mdl-37579177

ABSTRACT

We designed and carried out a high-throughput screen for compounds that trap topoisomerase III beta (TOP3B poisons) by developing a Comparative Cellular Cytotoxicity Screen. We found a bisacridine compound NSC690634 and a thiacyanine compound NSC96932 that preferentially sensitize cell lines expressing TOP3B, indicating that they target TOP3B. These compounds trap TOP3B cleavage complex (TOP3Bcc) in cells and in vitro and predominately act on RNA, leading to high levels of RNA-TOP3Bccs. NSC690634 also leads to enhanced R-loops in a TOP3B-dependent manner. Preliminary structural activity studies show that the lengths of linkers between the two aromatic moieties in each compound are critical; altering the linker length completely abolishes the trapping of TOP3Bccs. Both of our lead compounds share a similar structural motif, which can serve as a base for further modification. They may also serve in anticancer, antiviral, and/or basic research applications.


Subject(s)
DNA Topoisomerases, Type I , Topoisomerase I Inhibitors , Cell Line , DNA Topoisomerases, Type I/metabolism , RNA , Topoisomerase I Inhibitors/chemistry
12.
Hum Mol Genet ; 32(15): 2422-2440, 2023 07 20.
Article in English | MEDLINE | ID: mdl-37129502

ABSTRACT

The recognition that cytosolic mitochondrial DNA (mtDNA) activates cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) innate immune signaling has unlocked novel disease mechanisms. Here, an uncharacterized variant predicted to affect TOP1MT function, P193L, was discovered in a family with multiple early onset autoimmune diseases, including Systemic Lupus Erythematosus (SLE). Although there was no previous genetic association between TOP1MT and autoimmune disease, the role of TOP1MT as a regulator of mtDNA led us to investigate whether TOP1MT could mediate the release of mtDNA to the cytosol, where it could then activate the cGAS-STING innate immune pathway known to be activated in SLE and other autoimmune diseases. Through analysis of cells with reduced TOP1MT expression, we show that loss of TOP1MT results in release of mtDNA to the cytosol, which activates the cGAS-STING pathway. We also characterized the P193L variant for its ability to rescue several TOP1MT functions when expressed in TOP1MT knockout cells. We show that the P193L variant is not fully functional, as its re-expression at high levels was unable to rescue mitochondrial respiration deficits, and only showed partial rescue for other functions, including repletion of mtDNA replication following depletion, nucleoid size, steady state mtDNA transcripts levels and mitochondrial morphology. Additionally, expression of P193L at endogenous levels was unable to rescue mtDNA release-mediated cGAS-STING signaling. Overall, we report a link between TOP1MT and mtDNA release leading to cGAS-STING activation. Moreover, we show that the P193L variant has partial loss of function that may contribute to autoimmune disease susceptibility via cGAS-STING mediated activation of the innate immune system.


Subject(s)
Autoimmune Diseases , Lupus Erythematosus, Systemic , Humans , DNA, Mitochondrial/genetics , Immunity, Innate/genetics , Interferons , Nucleotidyltransferases/genetics , Nucleotidyltransferases/metabolism
13.
Mol Cell Proteomics ; 22(8): 100602, 2023 08.
Article in English | MEDLINE | ID: mdl-37343696

ABSTRACT

Treatment and relevant targets for breast cancer (BC) remain limited, especially for triple-negative BC (TNBC). We identified 6091 proteins of 76 human BC cell lines using data-independent acquisition (DIA). Integrating our proteomic findings with prior multi-omics datasets, we found that including proteomics data improved drug sensitivity predictions and provided insights into the mechanisms of action. We subsequently profiled the proteomic changes in nine cell lines (five TNBC and four non-TNBC) treated with EGFR/AKT/mTOR inhibitors. In TNBC, metabolism pathways were dysregulated after EGFR/mTOR inhibitor treatment, while RNA modification and cell cycle pathways were affected by AKT inhibitor. This systematic multi-omics and in-depth analysis of the proteome of BC cells can help prioritize potential therapeutic targets and provide insights into adaptive resistance in TNBC.


Subject(s)
Signal Transduction , Triple Negative Breast Neoplasms , Humans , Proto-Oncogene Proteins c-akt/metabolism , Proteomics , Cell Proliferation , Cell Line, Tumor , Drug Resistance, Neoplasm/genetics , Triple Negative Breast Neoplasms/metabolism , ErbB Receptors/metabolism
14.
Nucleic Acids Res ; 51(18): e97, 2023 10 13.
Article in English | MEDLINE | ID: mdl-37670571

ABSTRACT

Topoisomerases (TOP1, TOP2α, and ß) are nuclear enzymes crucial for virtually all aspects of DNA metabolisms. They also are the targets of important anti-tumor chemotherapeutics that act by trapping the otherwise reversible topoisomerase-DNA covalent complex intermediates (TOPccs) that are formed during their catalytic reactions, resulting in long-lived topoisomerase DNA-protein crosslinks (TOP-DPCs) that interfere with DNA transactions. The Poly(ADP-ribose) polymerase (PARP) family protein PARP1 is activated by DNA damage to recruit DNA repair proteins, and PARP inhibitors are another class of commonly used chemotherapeutics, which bind and trap PARP molecules on DNA. To date, the trapping of TOPccs and PARP by their respective inhibitors can only be measured by immune-biochemical methods in cells. Here, we developed an imaging-based approach enabling real-time monitoring of drug-induced trapping of TOPccs and PARP1 in live cells at the single-molecule level. Capitalizing on this approach, we calculated the fraction of self-fluorescence tag-labeled topoisomerases and PARP single-molecules that are trapped by their respective inhibitors in real time. This novel technique should help elucidate the molecular processes that repair TOPcc and PARP trapping and facilitate the development of novel topoisomerase and PARP inhibitor-based therapies.


Subject(s)
Poly(ADP-ribose) Polymerase Inhibitors , Poly(ADP-ribose) Polymerases , Poly(ADP-ribose) Polymerase Inhibitors/pharmacology , Poly (ADP-Ribose) Polymerase-1/metabolism , Poly(ADP-ribose) Polymerases/metabolism , DNA Damage , DNA Repair , Isomerases/genetics , DNA Topoisomerases, Type I/metabolism , DNA/metabolism
15.
Nucleic Acids Res ; 51(20): 10846-10866, 2023 11 10.
Article in English | MEDLINE | ID: mdl-37850658

ABSTRACT

Apurinic/apyrimidinic (AP) sites, 5-formyluracil (fU) and 5-formylcytosine (fC) are abundant DNA modifications that share aldehyde-type reactivity. Here, we demonstrate that polyamines featuring at least one secondary 1,2-diamine fragment in combination with aromatic units form covalent DNA adducts upon reaction with AP sites (with concomitant cleavage of the AP strand), fU and, to a lesser extent, fC residues. Using small-molecule mimics of AP site and fU, we show that reaction of secondary 1,2-diamines with AP sites leads to the formation of unprecedented 3'-tetrahydrofuro[2,3,4-ef]-1,4-diazepane ('ribodiazepane') scaffold, whereas the reaction with fU produces cationic 2,3-dihydro-1,4-diazepinium adducts via uracil ring opening. The reactivity of polyamines towards AP sites versus fU and fC can be tuned by modulating their chemical structure and pH of the reaction medium, enabling up to 20-fold chemoselectivity for AP sites with respect to fU and fC. This reaction is efficient in near-physiological conditions at low-micromolar concentration of polyamines and tolerant to the presence of a large excess of unmodified DNA. Remarkably, 3'-ribodiazepane adducts are chemically stable and resistant to the action of apurinic/apyrimidinic endonuclease 1 (APE1) and tyrosyl-DNA phosphoesterase 1 (TDP1), two DNA repair enzymes known to cleanse a variety of 3' end-blocking DNA lesions.


Subject(s)
DNA Adducts , Polyamines , DNA/chemistry , DNA Adducts/chemistry , DNA Adducts/metabolism , DNA Damage , DNA Repair , DNA-(Apurinic or Apyrimidinic Site) Lyase/metabolism , Nucleic Acid Conformation , Polyamines/chemistry , Polyamines/metabolism
16.
Mol Carcinog ; 63(6): 1024-1037, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38411275

ABSTRACT

Homologous recombination (HR) and poly ADP-ribosylation are partially redundant pathways for the repair of DNA damage in normal and cancer cells. In cell lines that are deficient in HR, inhibition of poly (ADP-ribose) polymerase (poly (ADP-ribose) polymerase [PARP]1/2) is a proven target with several PARP inhibitors (PARPis) currently in clinical use. Resistance to PARPi often develops, usually involving genetic alterations in DNA repair signaling cascades, but also metabolic rewiring particularly in HR-proficient cells. We surmised that alterations in metabolic pathways by cancer drugs such as Olaparib might be involved in the development of resistance to drug therapy. To test this hypothesis, we conducted a metabolism-focused clustered regularly interspaced short palindromic repeats knockout screen to identify genes that undergo alterations during the treatment of tumor cells with PARPis. Of about 3000 genes in the screen, our data revealed that mitochondrial pyruvate carrier 1 (MPC1) is an essential factor in desensitizing nonsmall cell lung cancer (NSCLC) lung cancer lines to PARP inhibition. In contrast to NSCLC lung cancer cells, triple-negative breast cancer cells do not exhibit such desensitization following MPC1 loss and reprogram the tricarboxylic acid cycle and oxidative phosphorylation pathways to overcome PARPi treatment. Our findings unveil a previously unknown synergistic response between MPC1 loss and PARP inhibition in lung cancer cells.


Subject(s)
Drug Resistance, Neoplasm , Lung Neoplasms , Monocarboxylic Acid Transporters , Poly(ADP-ribose) Polymerase Inhibitors , Humans , Poly(ADP-ribose) Polymerase Inhibitors/pharmacology , Lung Neoplasms/genetics , Lung Neoplasms/drug therapy , Lung Neoplasms/metabolism , Lung Neoplasms/pathology , Drug Resistance, Neoplasm/genetics , Monocarboxylic Acid Transporters/genetics , Monocarboxylic Acid Transporters/metabolism , Cell Line, Tumor , Mitochondrial Membrane Transport Proteins/genetics , Mitochondrial Membrane Transport Proteins/metabolism , Phthalazines/pharmacology , Piperazines/pharmacology , Clustered Regularly Interspaced Short Palindromic Repeats , CRISPR-Cas Systems , Mitochondria/metabolism , Mitochondria/drug effects , Mitochondria/genetics
17.
Proc Natl Acad Sci U S A ; 118(6)2021 02 09.
Article in English | MEDLINE | ID: mdl-33536335

ABSTRACT

Schlafen-11 (SLFN11) inactivation in ∼50% of cancer cells confers broad chemoresistance. To identify therapeutic targets and underlying molecular mechanisms for overcoming chemoresistance, we performed an unbiased genome-wide RNAi screen in SLFN11-WT and -knockout (KO) cells. We found that inactivation of Ataxia Telangiectasia- and Rad3-related (ATR), CHK1, BRCA2, and RPA1 overcome chemoresistance to camptothecin (CPT) in SLFN11-KO cells. Accordingly, we validate that clinical inhibitors of ATR (M4344 and M6620) and CHK1 (SRA737) resensitize SLFN11-KO cells to topotecan, indotecan, etoposide, cisplatin, and talazoparib. We uncover that ATR inhibition significantly increases mitotic defects along with increased CDT1 phosphorylation, which destabilizes kinetochore-microtubule attachments in SLFN11-KO cells. We also reveal a chemoresistance mechanism by which CDT1 degradation is retarded, eventually inducing replication reactivation under DNA damage in SLFN11-KO cells. In contrast, in SLFN11-expressing cells, SLFN11 promotes the degradation of CDT1 in response to CPT by binding to DDB1 of CUL4CDT2 E3 ubiquitin ligase associated with replication forks. We show that the C terminus and ATPase domain of SLFN11 are required for DDB1 binding and CDT1 degradation. Furthermore, we identify a therapy-relevant ATPase mutant (E669K) of the SLFN11 gene in human TCGA and show that the mutant contributes to chemoresistance and retarded CDT1 degradation. Taken together, our study reveals new chemotherapeutic insights on how targeting the ATR pathway overcomes chemoresistance of SLFN11-deficient cancers. It also demonstrates that SLFN11 irreversibly arrests replication by degrading CDT1 through the DDB1-CUL4CDT2 ubiquitin ligase.


Subject(s)
Cell Cycle Proteins/metabolism , Cullin Proteins/metabolism , DNA Damage/genetics , DNA Replication , Nuclear Proteins/metabolism , Protein Kinase Inhibitors/pharmacology , Proteolysis , Synthetic Lethal Mutations/genetics , Ataxia Telangiectasia Mutated Proteins/antagonists & inhibitors , Ataxia Telangiectasia Mutated Proteins/metabolism , Cell Line, Tumor , Checkpoint Kinase 1/antagonists & inhibitors , Checkpoint Kinase 1/metabolism , Chromosomes, Human/genetics , DNA Replication/genetics , DNA-Binding Proteins/metabolism , Drug Resistance, Neoplasm , Enzyme Stability , Genome, Human , Humans , Mitosis , Models, Biological , Molecular Targeted Therapy , Phosphorylation , Protein Binding , RNA Interference , Signal Transduction
18.
J Biol Chem ; 298(10): 102420, 2022 10.
Article in English | MEDLINE | ID: mdl-36030054

ABSTRACT

TOP1MT encodes a mitochondrial topoisomerase that is important for mtDNA regulation and is involved in mitochondrial replication, transcription, and translation. Two variants predicted to affect TOP1MT function (V1 - R198C and V2 - V338L) were identified by exome sequencing of a newborn with hypertrophic cardiomyopathy. As no pathogenic TOP1MT variants had been confirmed previously, we characterized these variants for their ability to rescue several TOP1MT functions in KO cells. Consistent with these TOP1MT variants contributing to the patient phenotype, our comprehensive characterization suggests that both variants had impaired activity. Critically, we determined neither variant was able to restore steady state levels of mitochondrial-encoded proteins nor to rescue oxidative phosphorylation when re-expressed in TOP1MT KO cells. However, we found the two variants behaved differently in some respects; while the V1 variant was more efficient in restoring transcript levels, the V2 variant showed better rescue of mtDNA copy number and replication. These findings suggest that the different TOP1MT variants affect distinct TOP1MT functions. Altogether, these findings begin to provide insight into the many roles that TOP1MT plays in the maintenance and expression of the mitochondrial genome and how impairments in this important protein may lead to human pathology.


Subject(s)
Cardiomyopathy, Hypertrophic , DNA Topoisomerases, Type I , Genome, Mitochondrial , Mitochondria , Humans , Infant, Newborn , Cardiomyopathy, Hypertrophic/genetics , DNA Topoisomerases, Type I/genetics , DNA Topoisomerases, Type I/metabolism , DNA, Mitochondrial/metabolism , Genetic Variation , Mitochondria/enzymology , Mitochondrial Proteins/genetics , Mitochondrial Proteins/metabolism
19.
Oncologist ; 28(5): 460-e298, 2023 05 08.
Article in English | MEDLINE | ID: mdl-37010988

ABSTRACT

BACKGROUND: Multiple preclinical studies have shown cytotoxic synergy involving combinations of poly (ADP-ribose) polymerase (PARP) inhibitors and topoisomerase 1 (TOP1) inhibitors, but such combinations have proven too toxic in clinical trials. Liposomal irinotecan (nal-IRI) achieved similar intratumoral exposure with better antitumor activity than the conventional TOP1 inhibitor irinotecan in preclinical models. Tumor targeted delivery of TOP1 inhibitor using nal-IRI and an intermittent schedule of administration of PARP inhibitor may provide a tolerable combination. METHODS: A phase I study was performed to evaluate the safety and tolerability of escalating doses of nal-IRI and the PARP inhibitor veliparib in patients with solid tumors resistant to standard treatments. Nal-IRI was administered on days 1 and 15 and veliparib on days 5-12 and 19-25 in 28-day cycles. RESULTS: Eighteen patients were enrolled across 3 dose levels. Five patients encountered dose-limiting toxicities, including grade 3 diarrhea lasting more than 72 h in 3 patients and 1 patient each with grade 4 diarrhea and grade 3 hyponatremia. The most common grade 3 or 4 toxicities included diarrhea (50% of patients), nausea (16.6%), anorexia, and vomiting (11.1% each) (Table 1). There was no difference in frequencies of adverse events based on UGT1A1*28 status or prior opioid use (Table 1). CONCLUSION: The clinical trial was terminated due to high frequency of unacceptable gastrointestinal toxicities, which precluded dose escalation of veliparib in combination with nal-IRI (ClinicalTrials.gov Identifier: NCT02631733).


Subject(s)
Antineoplastic Agents , Neoplasms , Humans , Irinotecan/pharmacology , Irinotecan/therapeutic use , Poly(ADP-ribose) Polymerase Inhibitors/adverse effects , Neoplasms/drug therapy , Neoplasms/pathology , Antineoplastic Agents/therapeutic use , Topoisomerase I Inhibitors/adverse effects , Poly(ADP-ribose) Polymerases , Diarrhea/chemically induced , Antineoplastic Combined Chemotherapy Protocols/adverse effects
20.
Biochem Biophys Res Commun ; 657: 43-49, 2023 05 21.
Article in English | MEDLINE | ID: mdl-36972660

ABSTRACT

Adult T-cell leukemia (ATL) is a peripheral T-cell malignancy caused by human T-cell leukemia virus type 1 (HTLV-1). Microsatellite instability (MSI) has been observed in ATL cells. Although MSI results from impaired mismatch repair (MMR) pathway, no null mutations in the genes encoding MMR factors are detectable in ATL cells. Thus, it is unclear whether or not impairment of MMR causes the MSI in ATL cells. HTLV-1 bZIP factor (HBZ) protein interacts with numerous host transcription factors and significantly contributes to disease pathogenesis and progression. Here we investigated the effect of HBZ on MMR in normal cells. The ectopic expression of HBZ in MMR-proficient cells induced MSI, and also suppressed the expression of several MMR factors. We then hypothesized that the HBZ compromises MMR by interfering with a transcription factor, nuclear respiratory factor 1 (NRF-1), and identified the consensus NRF-1 binding site at the promoter of the gene encoding MutS homologue 2 (MSH2), an essential MMR factor. The luciferase reporter assay revealed that NRF-1 overexpression enhanced MSH2 promoter activity, while co-expression of HBZ reversed this enhancement. These results supported the idea that HBZ suppresses the transcription of MSH2 by inhibiting NRF-1. Our data demonstrate that HBZ causes impaired MMR, and may imply a novel oncogenesis driven by HTLV-1.


Subject(s)
Human T-lymphotropic virus 1 , Leukemia-Lymphoma, Adult T-Cell , Adult , Humans , Human T-lymphotropic virus 1/genetics , DNA Mismatch Repair , Retroviridae Proteins/genetics , Retroviridae Proteins/metabolism , MutS Homolog 2 Protein/genetics , MutS Homolog 2 Protein/metabolism , Basic-Leucine Zipper Transcription Factors/genetics , Basic-Leucine Zipper Transcription Factors/metabolism , Leukemia-Lymphoma, Adult T-Cell/pathology
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