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1.
STAR Protoc ; 5(1): 102843, 2024 Mar 15.
Article in English | MEDLINE | ID: mdl-38294909

ABSTRACT

Ubiquitin-like protein ISG15 plays an important role in an array of cellular functions via its covalent attachment to target proteins (ISGylation). Here, we present a protocol for the identification of ISGylated proteins that avoids the caveats associated with ISG15 overexpression and minimizes the likelihood of false positives. We describe steps for the tagging of endogenous ISG15, followed by genotyping and clone selection. We then detail steps for ISGylation induction, the isolation of ISGylated proteins, and their identification via quantitative mass spectrometry. For complete details on the use and execution of this protocol, please refer to Wardlaw and Petrini.1.


Subject(s)
Cytokines , Ubiquitins , Animals , Cytokines/genetics , Cytokines/metabolism , Ubiquitins/genetics , Ubiquitins/chemistry , Ubiquitins/metabolism , Cell Line , Mammals/metabolism
2.
Bioessays ; 45(7): e2300042, 2023 07.
Article in English | MEDLINE | ID: mdl-37147792

ABSTRACT

Interferon stimulated gene 15 (ISG15) encodes a ubiquitin-like protein that is highly induced upon activation of interferon signaling and cytoplasmic DNA sensing pathways. As part of the innate immune system ISG15 acts to inhibit viral replication and particle release via the covalent conjugation to both viral and host proteins. Unlike ubiquitin, unconjugated ISG15 also functions as an intracellular and extra-cellular signaling molecule to modulate the immune response. Several recent studies have shown ISG15 to also function in a diverse array of cellular processes and pathways outside of the innate immune response. This review explores the role of ISG15 in maintaining genome stability, particularly during DNA replication, and how this relates to cancer biology. It puts forth the hypothesis that ISG15, along with DNA sensors, function within a DNA replication fork surveillance pathway to help maintain genome stability.


Subject(s)
Cytokines , Interferons , DNA , DNA Replication , Immunity, Innate , Ubiquitins/genetics , Ubiquitins/metabolism , Humans , Animals
3.
Nat Commun ; 13(1): 5971, 2022 10 10.
Article in English | MEDLINE | ID: mdl-36216822

ABSTRACT

The pathways involved in suppressing DNA replication stress and the associated DNA damage are critical to maintaining genome integrity. The Mre11 complex is unique among double strand break (DSB) repair proteins for its association with the DNA replication fork. Here we show that Mre11 complex inactivation causes DNA replication stress and changes in the abundance of proteins associated with nascent DNA. One of the most highly enriched proteins at the DNA replication fork upon Mre11 complex inactivation was the ubiquitin like protein ISG15. Mre11 complex deficiency and drug induced replication stress both led to the accumulation of cytoplasmic DNA and the subsequent activation of innate immune signaling via cGAS-STING-Tbk1. This led to ISG15 induction and protein ISGylation, including constituents of the replication fork. ISG15 plays a direct role in preventing replication stress. Deletion of ISG15 was associated with replication fork stalling, tonic ATR activation, genomic aberrations, and sensitivity to aphidicolin. These data reveal a previously unrecognized role for ISG15 in mitigating DNA replication stress and promoting genomic stability.


Subject(s)
DNA Repair , DNA Replication , Aphidicolin , DNA/genetics , DNA Damage , DNA Replication/genetics , Nucleotidyltransferases/genetics , Ubiquitins/genetics
4.
Elife ; 112022 10 03.
Article in English | MEDLINE | ID: mdl-36190107

ABSTRACT

During the development of humoral immunity, activated B lymphocytes undergo vigorous proliferative, transcriptional, metabolic, and DNA remodeling activities; hence, their genomes are constantly exposed to an onslaught of genotoxic agents and processes. Branched DNA intermediates generated during replication and recombinational repair pose genomic threats if left unresolved and so, they must be eliminated by structure-selective endonucleases to preserve the integrity of these DNA transactions for the faithful duplication and propagation of genetic information. To investigate the role of two such enzymes, GEN1 and MUS81, in B cell biology, we established B-cell conditional knockout mouse models and found that deletion of GEN1 and MUS81 in early B-cell precursors abrogates the development and maturation of B-lineage cells while the loss of these enzymes in mature B cells inhibit the generation of robust germinal centers. Upon activation, these double-null mature B lymphocytes fail to proliferate and survive while exhibiting transcriptional signatures of p53 signaling, apoptosis, and type I interferon response. Metaphase spreads of these endonuclease-deficient cells showed severe and diverse chromosomal abnormalities, including a preponderance of chromosome breaks, consistent with a defect in resolving recombination intermediates. These observations underscore the pivotal roles of GEN1 and MUS81 in safeguarding the genome to ensure the proper development and proliferation of B lymphocytes.


Subject(s)
Endonucleases , Interferon Type I , Animals , Mice , B-Lymphocytes/metabolism , DNA , Endonucleases/genetics , Endonucleases/metabolism , Holliday Junction Resolvases/genetics , Holliday Junction Resolvases/metabolism , Interferon Type I/metabolism , Tumor Suppressor Protein p53 , Genome
5.
Nat Commun ; 12(1): 3016, 2021 05 21.
Article in English | MEDLINE | ID: mdl-34021146

ABSTRACT

Telomere repeat containing RNAs (TERRAs) are a family of long non-coding RNAs transcribed from the subtelomeric regions of eukaryotic chromosomes. TERRA transcripts can form R-loops at chromosome ends; however the importance of these structures or the regulation of TERRA expression and retention in telomeric R-loops remain unclear. Here, we show that the RTEL1 (Regulator of Telomere Length 1) helicase influences the abundance and localization of TERRA in human cells. Depletion of RTEL1 leads to increased levels of TERRA RNA while reducing TERRA-containing R loops at telomeres. In vitro, RTEL1 shows a strong preference for binding G-quadruplex structures which form in TERRA. This binding is mediated by the C-terminal region of RTEL1, and is independent of the RTEL1 helicase domain. RTEL1 binding to TERRA appears to be essential for cell viability, underscoring the importance of this function. Degradation of TERRA-containing R-loops by overexpression of RNAse H1 partially recapitulates the increased TERRA levels and telomeric instability associated with RTEL1 deficiency. Collectively, these data suggest that regulation of TERRA is a key function of the RTEL1 helicase, and that loss of that function may contribute to the disease phenotypes of patients with RTEL1 mutations.


Subject(s)
DNA Helicases/metabolism , DNA-Binding Proteins/metabolism , Transcription Factors/metabolism , DNA Helicases/chemistry , DNA Helicases/genetics , DNA-Binding Proteins/genetics , Gene Knockout Techniques , HEK293 Cells , Humans , Protein Domains , R-Loop Structures , RNA , Ribonuclease H , Sequence Alignment , Telomere , Transcription Factors/genetics
6.
Cell Rep ; 33(13): 108559, 2020 12 29.
Article in English | MEDLINE | ID: mdl-33378670

ABSTRACT

The MRE11-RAD50-NBS1 complex plays a central role in response to DNA double-strand breaks. Here, we identify a patient with bone marrow failure and developmental defects caused by biallelic RAD50 mutations. One of the mutations creates a null allele, whereas the other (RAD50E1035Δ) leads to the loss of a single residue in the heptad repeats within the RAD50 coiled-coil domain. This mutation represents a human RAD50 separation-of-function mutation that impairs DNA repair, DNA replication, and DNA end resection without affecting ATM-dependent DNA damage response. Purified recombinant proteins indicate that RAD50E1035Δ impairs MRE11 nuclease activity. The corresponding mutation in Saccharomyces cerevisiae causes severe thermosensitive defects in both DNA repair and Tel1ATM-dependent signaling. These findings demonstrate that a minor heptad break in the RAD50 coiled coil suffices to impede MRE11 complex functions in human and yeast. Furthermore, these results emphasize the importance of the RAD50 coiled coil to regulate MRE11-dependent DNA end resection in humans.


Subject(s)
Acid Anhydride Hydrolases/genetics , Acid Anhydride Hydrolases/metabolism , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Endodeoxyribonucleases/metabolism , Exodeoxyribonucleases/metabolism , MRE11 Homologue Protein/metabolism , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/physiology , Bone Marrow Failure Disorders/genetics , Child , Child, Preschool , DNA Breaks, Double-Stranded , DNA Repair , DNA Replication , Developmental Disabilities/genetics , Humans , Protein Binding , Protein Domains , Sequence Analysis, Protein , Sequence Deletion , Signal Transduction
7.
J Clin Invest ; 130(11): 5668-5670, 2020 11 02.
Article in English | MEDLINE | ID: mdl-32986019

ABSTRACT

Growth hormone-secreting (GH-secreting) pituitary tumors are driven by oncogenes that induce cAMP signaling. In this issue of the JCI, Ben-Shlomo et al. performed a whole-exome study of pituitary adenomas. GH-secreting tumors had a high frequency of whole chromosome or chromosome arm copy number alterations and were associated with an increase in the tumor protein p53 and the cyclin-dependent kinase inhibitor p21WAF1/CIP1, which are findings consistent with induction of a response to DNA damage. Further, treatment of mouse pituitary cells with cAMP pathway agonists in vitro and in vivo elicited biomarkers of DNA replication stress or double-strand breaks. The findings of Ben Shlomo et al. indicate that oncoproteins that drive constitutively high cAMP signaling pathway output in susceptible cell types can elicit DNA replication stress and may promote genomic instability.


Subject(s)
Adenoma , Growth Hormone-Secreting Pituitary Adenoma , Pituitary Neoplasms , Adenoma/genetics , Animals , Cyclic AMP , DNA Damage , Growth Hormone/genetics , Growth Hormone-Secreting Pituitary Adenoma/genetics , Mice , Oncogenes/genetics , Pituitary Neoplasms/genetics
8.
Nat Rev Cancer ; 20(9): 533-549, 2020 09.
Article in English | MEDLINE | ID: mdl-32472073

ABSTRACT

Cell division and organismal development are exquisitely orchestrated and regulated processes. The dysregulation of the molecular mechanisms underlying these processes may cause cancer, a consequence of cell-intrinsic and/or cell-extrinsic events. Cellular DNA can be damaged by spontaneous hydrolysis, reactive oxygen species, aberrant cellular metabolism or other perturbations that cause DNA damage. Moreover, several environmental factors may damage the DNA, alter cellular metabolism or affect the ability of cells to interact with their microenvironment. While some environmental factors are well established as carcinogens, there remains a large knowledge gap of others owing to the difficulty in identifying them because of the typically long interval between carcinogen exposure and cancer diagnosis. DNA damage increases in cells harbouring mutations that impair their ability to correctly repair the DNA. Tumour predisposition syndromes in which cancers arise at an accelerated rate and in different organs - the equivalent of a sensitized background - provide a unique opportunity to examine how gene-environment interactions influence cancer risk when the initiating genetic defect responsible for malignancy is known. Understanding the molecular processes that are altered by specific germline mutations, environmental exposures and related mechanisms that promote cancer will allow the design of novel and effective preventive and therapeutic strategies.


Subject(s)
Gene-Environment Interaction , Genetic Predisposition to Disease , Neoplasms/genetics , Animals , Germ-Line Mutation , Humans
9.
Nat Struct Mol Biol ; 27(5): 424-437, 2020 05.
Article in English | MEDLINE | ID: mdl-32398827

ABSTRACT

Oncogene activation during tumorigenesis generates DNA replication stress, a known driver of genome rearrangements. In response to replication stress, certain loci, such as common fragile sites and telomeres, remain under-replicated during interphase and subsequently complete locus duplication in mitosis in a process known as 'MiDAS'. Here, we demonstrate that RTEL1 (regulator of telomere elongation helicase 1) has a genome-wide role in MiDAS at loci prone to form G-quadruplex-associated R-loops, in a process that is dependent on its helicase function. We reveal that SLX4 is required for the timely recruitment of RTEL1 to the affected loci, which in turn facilitates recruitment of other proteins required for MiDAS, including RAD52 and POLD3. Our findings demonstrate that RTEL1 is required for MiDAS and suggest that RTEL1 maintains genome stability by resolving conflicts that can arise between the replication and transcription machineries.


Subject(s)
DNA Helicases/genetics , DNA Helicases/metabolism , G-Quadruplexes , Genome, Human/genetics , Mitosis , Animals , Cell Line , DNA Helicases/chemistry , DNA Polymerase III/genetics , DNA Polymerase III/metabolism , Genomic Instability , Humans , Immunoprecipitation , Mice , Multifunctional Enzymes/genetics , Multifunctional Enzymes/metabolism , Nucleic Acid Conformation , RNA Helicases/genetics , RNA Helicases/metabolism , Rad52 DNA Repair and Recombination Protein/genetics , Rad52 DNA Repair and Recombination Protein/metabolism , Recombinases/genetics , Recombinases/metabolism , Ribonuclease H/genetics , Ribonuclease H/metabolism
10.
PLoS Genet ; 16(3): e1008422, 2020 03.
Article in English | MEDLINE | ID: mdl-32187176

ABSTRACT

The DNA damage response (DDR) comprises multiple functions that collectively preserve genomic integrity and suppress tumorigenesis. The Mre11 complex and ATM govern a major axis of the DDR and several lines of evidence implicate that axis in tumor suppression. Components of the Mre11 complex are mutated in approximately five percent of human cancers. Inherited mutations of complex members cause severe chromosome instability syndromes, such as Nijmegen Breakage Syndrome, which is associated with strong predisposition to malignancy. And in mice, Mre11 complex mutations are markedly more susceptible to oncogene- induced carcinogenesis. The complex is integral to all modes of DNA double strand break (DSB) repair and is required for the activation of ATM to effect DNA damage signaling. To understand which functions of the Mre11 complex are important for tumor suppression, we undertook mining of cancer genomic data from the clinical sequencing program at Memorial Sloan Kettering Cancer Center, which includes the Mre11 complex among the 468 genes assessed. Twenty five mutations in MRE11 and RAD50 were modeled in S. cerevisiae and in vitro. The mutations were chosen based on recurrence and conservation between human and yeast. We found that a significant fraction of tumor-borne RAD50 and MRE11 mutations exhibited separation of function phenotypes wherein Tel1/ATM activation was severely impaired while DNA repair functions were mildly or not affected. At the molecular level, the gene products of RAD50 mutations exhibited defects in ATP binding and hydrolysis. The data reflect the importance of Rad50 ATPase activity for Tel1/ATM activation and suggest that inactivation of ATM signaling confers an advantage to burgeoning tumor cells.


Subject(s)
Ataxia Telangiectasia Mutated Proteins/genetics , Carcinogenesis/genetics , Saccharomyces cerevisiae/genetics , Animals , DNA Damage/genetics , DNA Repair/genetics , DNA Repair Enzymes/genetics , Genomics/methods , MRE11 Homologue Protein/genetics , Mutation/genetics , Sf9 Cells , Signal Transduction/genetics , Tumor Suppressor Proteins/genetics
11.
Cell Rep ; 30(5): 1385-1399.e7, 2020 02 04.
Article in English | MEDLINE | ID: mdl-32023457

ABSTRACT

The Mre11-Rad50-Nbs1 complex is a DNA double-strand break sensor that mediates a tumor-suppressive DNA damage response (DDR) in cells undergoing oncogenic stress, yet the mechanisms underlying this effect are poorly understood. Using a genetically inducible primary mammary epithelial cell model, we demonstrate that Mre11 suppresses proliferation and DNA damage induced by diverse oncogenic drivers through a p53-independent mechanism. Breast tumorigenesis models engineered to express a hypomorphic Mre11 allele exhibit increased levels of oncogene-induced DNA damage, R-loop accumulation, and chromosomal instability with a characteristic copy number loss phenotype. Mre11 complex dysfunction is identified in a subset of human triple-negative breast cancers and is associated with increased sensitivity to DNA-damaging therapy and inhibitors of ataxia telangiectasia and Rad3 related (ATR) and poly (ADP-ribose) polymerase (PARP). Thus, deficiencies in the Mre11-dependent DDR drive proliferation and genome instability patterns in p53-deficient breast cancers and represent an opportunity for therapeutic exploitation.


Subject(s)
Carcinogenesis/pathology , DNA Damage , Genomic Instability , Tumor Suppressor Protein p53/metabolism , Animals , Ataxia Telangiectasia Mutated Proteins/antagonists & inhibitors , Ataxia Telangiectasia Mutated Proteins/metabolism , Breast Neoplasms/pathology , Cell Line, Tumor , Cell Proliferation , Cells, Cultured , Chromosomal Instability , Epithelial Cells/metabolism , Gene Dosage , HEK293 Cells , Humans , MRE11 Homologue Protein/metabolism , Mammary Glands, Animal/pathology , Mice , Models, Biological , Oncogenes , Phenotype , Poly(ADP-ribose) Polymerase Inhibitors/pharmacology , R-Loop Structures
12.
J Biol Chem ; 294(49): 18846-18852, 2019 12 06.
Article in English | MEDLINE | ID: mdl-31640985

ABSTRACT

Saccharomyces cerevisiae Tel1 is the ortholog of human ATM kinase and initiates a cell cycle checkpoint in response to dsDNA breaks (DSBs). Tel1ATM kinase is activated synergistically by naked dsDNA and the Mre11-Rad50-Xrs2NBS1 complex (MRX). A multisubunit protein complex, which is related to human shelterin, protects telomeres from being recognized as DSBs, thereby preventing a Tel1ATM checkpoint response. However, at very short telomeres, Tel1ATM can be recruited and activated by the MRX complex, resulting in telomere elongation. Conversely, at long telomeres, Rap1-interacting-factor 2 (Rif2) is instrumental in suppressing Tel1 activity. Here, using an in vitro reconstituted Tel1 kinase activation assay, we show that Rif2 inhibits MRX-dependent Tel1 kinase activity. Rif2 discharges the ATP-bound form of Rad50, which is essential for all MRX-dependent activities. This conclusion is further strengthened by experiments with a Rad50 allosteric ATPase mutant that maps outside the conserved ATP binding pocket. We propose a model in which Rif2 attenuates Tel1 activity at telomeres by acting directly on Rad50 and discharging its activated ATP-bound state, thereby rendering the MRX complex incompetent for Tel1 activation. These findings expand our understanding of the mechanism by which Rif2 controls telomere length.


Subject(s)
DNA-Binding Proteins/metabolism , Intracellular Signaling Peptides and Proteins/metabolism , Protein Serine-Threonine Kinases/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/metabolism , Telomere-Binding Proteins/metabolism , Telomere/metabolism
13.
Cell Rep ; 28(6): 1564-1573.e3, 2019 08 06.
Article in English | MEDLINE | ID: mdl-31390569

ABSTRACT

Non-homologous end joining (NHEJ) and homologous recombination (HR) are the two major pathways of DNA double-strand break (DSB) repair and both are highly conserved from yeast to mammals. Nej1 has a role in DNA end-tethering at a DSB, and the Mre11/Rad50/Xrs2 (MRX) complex is important for its recruitment to the break. Nej1 and Dna2-Sgs1 interact with the C-terminal end of Mre11, which also includes the region where Rad50 binds. By characterizing the functionality of Nej1 in two rad50 mutants, which alter the structural features of MRX, we demonstrate that Nej1 inhibits the binding of Dna2 to Mre11 and Sgs1. Nej1 interactions with Mre11 promote tethering and inhibit hyper-resection, and when these events are compromised, large deletions develop at a DSB. The work indicates that Nej1 provides a layer of regulation to repair pathway choice and is consistent with its role in NHEJ.


Subject(s)
DNA Breaks, Double-Stranded , DNA Helicases/metabolism , DNA Repair , DNA-Binding Proteins/metabolism , Endodeoxyribonucleases/metabolism , Exodeoxyribonucleases/metabolism , Saccharomyces cerevisiae Proteins/metabolism , DNA, Fungal/metabolism , Multiprotein Complexes/metabolism , RecQ Helicases/metabolism , Saccharomyces cerevisiae
14.
Proc Natl Acad Sci U S A ; 116(30): 15178-15183, 2019 07 23.
Article in English | MEDLINE | ID: mdl-31285322

ABSTRACT

We derived a mouse model in which a mutant form of Nbn/Nbs1mid8 (hereafter Nbnmid8) exhibits severely impaired binding to the Mre11-Rad50 core of the Mre11 complex. The Nbnmid8 allele was expressed exclusively in hematopoietic lineages (in Nbn-/mid8vav mice). Unlike Nbnflox/floxvav mice with Nbn deficiency in the bone marrow, Nbn-/mid8vav mice were viable. Nbn-/mid8vav mice hematopoiesis was profoundly defective, exhibiting reduced cellularity of thymus and bone marrow, and stage-specific blockage of B cell development. Within 6 mo, Nbn-/mid8 mice developed highly penetrant T cell leukemias. Nbn-/mid8vav leukemias recapitulated mutational features of human T cell acute lymphoblastic leukemia (T-ALL), containing mutations in NOTCH1, TP53, BCL6, BCOR, and IKZF1, suggesting that Nbnmid8 mice may provide a venue to examine the relationship between the Mre11 complex and oncogene activation in the hematopoietic compartment. Genomic analysis of Nbn-/mid8vav malignancies showed focal amplification of 9qA2, causing overexpression of MRE11 and CHK1 We propose that overexpression of MRE11 compensates for the metastable Mre11-Nbnmid8 interaction, and that selective pressure for overexpression reflects the essential role of Nbn in promoting assembly and activity of the Mre11 complex.


Subject(s)
Acid Anhydride Hydrolases/genetics , Cell Cycle Proteins/genetics , DNA-Binding Proteins/genetics , Gene Expression Regulation, Leukemic , MRE11 Homologue Protein/genetics , Precursor T-Cell Lymphoblastic Leukemia-Lymphoma/genetics , T-Lymphocytes/immunology , Acid Anhydride Hydrolases/immunology , Animals , B-Lymphocytes/immunology , B-Lymphocytes/pathology , Bone Marrow/immunology , Bone Marrow/pathology , Cell Cycle Proteins/deficiency , Cell Cycle Proteins/immunology , Checkpoint Kinase 1/genetics , Checkpoint Kinase 1/immunology , DNA-Binding Proteins/deficiency , DNA-Binding Proteins/immunology , Disease Models, Animal , Genomic Instability/immunology , Hematopoiesis/genetics , Hematopoiesis/immunology , Humans , Ikaros Transcription Factor/genetics , Ikaros Transcription Factor/immunology , MRE11 Homologue Protein/immunology , Mice , Mice, Knockout , Mutation , Precursor T-Cell Lymphoblastic Leukemia-Lymphoma/immunology , Precursor T-Cell Lymphoblastic Leukemia-Lymphoma/pathology , Precursor T-Cell Lymphoblastic Leukemia-Lymphoma/prevention & control , Protein Binding , Proto-Oncogene Proteins c-bcl-6/genetics , Proto-Oncogene Proteins c-bcl-6/immunology , Receptor, Notch1/genetics , Receptor, Notch1/immunology , Repressor Proteins/genetics , Repressor Proteins/immunology , Signal Transduction , T-Lymphocytes/pathology , Tumor Suppressor Protein p53/genetics , Tumor Suppressor Protein p53/immunology
15.
PLoS One ; 14(1): e0209995, 2019.
Article in English | MEDLINE | ID: mdl-30653527

ABSTRACT

Squamous cell carcinoma-related oncogene (SCCRO, also known as DCUN1D1) is a component of the E3 for neddylation. As such, DCUN1D1 regulates the neddylation of cullin family members. Targeted inactivation of DCUN1D1 in mice results in male-specific infertility. Infertility in DCUN1D1-/- mice is secondary to primary defects in spermatogenesis. Time-dam experiments mapped the onset of the defect in spermatogenesis to 5.5 to 6 weeks of age, which temporally corresponds to defects in spermiogenesis. Although the first round of spermatogenesis progressed normally, the number of spermatozoa released into the seminiferous lumen and epididymis of DCUN1D1-/- mice was significantly reduced. Spermatozoa in DCUN1D1-/- mice had multiple abnormalities, including globozoospermia, macrocephaly, and multiple flagella. Many of the malformed spermatozoa in DCUN1D1-/- mice were multinucleated, with supernumerary and malpositioned centrioles, suggesting a defect in the resolution of intercellular bridges. The onset of the defect in spermatogenesis in DCUN1D1-/- mice corresponds to an increase in DCUN1D1 expression observed during normal spermatogenesis. Moreover, consistent with its known function as a component of the E3 in neddylation, the pattern of DCUN1D1 expression temporally correlates with an increase in the neddylated cullin fraction and stage-specific increases in the total ubiquitinated protein pool in wild-type mice. Levels of neddylated Cul3 were decreased in DCUN1D1-/- mice, and ubiquitinated proteins did not accumulate during the stages in which DCUN1D1 expression peaks during spermatogenesis in wild-type mice. Combined, these findings suggest that DCUN1D1-/- mice fail to release mature spermatozoa into the seminiferous lumen, possibly due to unresolved intercellular bridges. Furthermore, the effects of DCUN1D1 on spermatogenesis likely involve its regulation of cullin-RING-ligase (CRL)-type ubiquitin E3 activity during spermiogenesis through its role in promoting Cul3 neddylation. The specific CRLs required for spermiogenesis and their protein targets require identification.


Subject(s)
Gene Deletion , Proto-Oncogene Proteins/genetics , Spermatogenesis , Spermatozoa/pathology , Animals , Cells, Cultured , Cullin Proteins/metabolism , Gene Targeting , Infertility, Male/genetics , Infertility, Male/metabolism , Infertility, Male/pathology , Intracellular Signaling Peptides and Proteins , Male , Mice , Proto-Oncogene Proteins/metabolism , Spermatozoa/cytology , Spermatozoa/metabolism , Ubiquitination
16.
Sci Transl Med ; 9(414)2017 Nov 01.
Article in English | MEDLINE | ID: mdl-29093183

ABSTRACT

Despite intense efforts, the cure rates of childhood and adult solid tumors are not satisfactory. Resistance to intensive chemotherapy is common, and targets for molecular therapies are largely undefined. We have found that the majority of childhood solid tumors, including rhabdoid tumors, neuroblastoma, medulloblastoma, and Ewing sarcoma, express an active DNA transposase, PGBD5, that can promote site-specific genomic rearrangements in human cells. Using functional genetic approaches, we discovered that mouse and human cells deficient in nonhomologous end joining (NHEJ) DNA repair cannot tolerate the expression of PGBD5. In a chemical screen of DNA damage signaling inhibitors, we identified AZD6738 as a specific sensitizer of PGBD5-dependent DNA damage and apoptosis. We found that expression of PGBD5, but not its nuclease activity-deficient mutant, was sufficient to induce sensitivity to AZD6738. Depletion of endogenous PGBD5 conferred resistance to AZD6738 in human tumor cells. PGBD5-expressing tumor cells accumulated unrepaired DNA damage in response to AZD6738 treatment and underwent apoptosis in both dividing and G1-phase cells in the absence of immediate DNA replication stress. Accordingly, AZD6738 exhibited nanomolar potency against most neuroblastoma, medulloblastoma, Ewing sarcoma, and rhabdoid tumor cells tested while sparing nontransformed human and mouse embryonic fibroblasts in vitro. Finally, treatment with AZD6738 induced apoptosis and regression of human neuroblastoma and medulloblastoma tumors engrafted in immunodeficient mice in vivo. This effect was potentiated by combined treatment with cisplatin, including substantial antitumor activity against patient-derived primary neuroblastoma xenografts. These findings delineate a therapeutically actionable synthetic dependency induced in PGBD5-expressing solid tumors.


Subject(s)
DNA Repair/drug effects , Molecular Targeted Therapy , Neoplasms/drug therapy , Neoplasms/pathology , Pyrimidines/therapeutic use , Sulfoxides/therapeutic use , Transposases/antagonists & inhibitors , Animals , Apoptosis/drug effects , Cell Line, Tumor , Child , DNA Damage , DNA End-Joining Repair/drug effects , Drug Synergism , Humans , Indoles , Mice , Mice, Nude , Models, Biological , Morpholines , Pyrimidines/pharmacology , Signal Transduction , Sulfonamides , Sulfoxides/pharmacology , Transposases/metabolism , Xenograft Model Antitumor Assays
17.
Nat Struct Mol Biol ; 24(3): 248-257, 2017 03.
Article in English | MEDLINE | ID: mdl-28134932

ABSTRACT

The Rad50 hook interface is crucial for assembly and various functions of the Mre11 complex. Previous analyses suggested that Rad50 molecules interact within (intracomplex) or between (intercomplex) dimeric complexes. In this study, we determined the structure of the human Rad50 hook and coiled-coil domains. The data suggest that the predominant structure is the intracomplex, in which the two parallel coiled coils proximal to the hook form a rod shape, and that a novel interface within the coiled-coil domains of Rad50 stabilizes the interaction of Rad50 protomers in the dimeric assembly. In yeast, removal of the coiled-coil interface compromised Tel1 activation without affecting DNA repair, while simultaneous disruption of that interface and the hook phenocopied a null mutation. The results demonstrate that the hook and coiled-coil interfaces coordinately promote intracomplex assembly and define the intracomplex as the functional form of the Mre11 complex.


Subject(s)
DNA Repair Enzymes/chemistry , DNA Repair Enzymes/metabolism , DNA-Binding Proteins/chemistry , DNA-Binding Proteins/metabolism , Eukaryotic Cells/metabolism , Protein Multimerization , Acid Anhydride Hydrolases , Amino Acid Sequence , Cell Cycle Checkpoints , Crystallography, X-Ray , DNA Breaks, Double-Stranded , DNA Repair , Fluorescence Resonance Energy Transfer , Humans , Meiosis , Models, Biological , Mutant Proteins/chemistry , Mutant Proteins/metabolism , Protein Domains , Protein Structure, Secondary , Saccharomyces cerevisiae/metabolism , Signal Transduction , Solutions , Zinc/metabolism
18.
Cell Rep ; 18(2): 496-507, 2017 01 10.
Article in English | MEDLINE | ID: mdl-28076792

ABSTRACT

The Mre11 complex (Mre11, Rad50, and Nbs1) is integral to both DNA repair and ataxia telangiectasia mutated (ATM)-dependent DNA damage signaling. All three Mre11 complex components are essential for viability at the cellular and organismal levels. To delineate essential and non-essential Mre11 complex functions that are mediated by Nbs1, we used TALEN-based genome editing to derive Nbs1 mutant mice (Nbs1mid mice), which harbor mutations in the Mre11 interaction domain of Nbs1. Nbs1mid alleles that abolished interaction were incompatible with viability. Conversely, a 108-amino-acid Nbs1 fragment comprising the Mre11 interface was sufficient to rescue viability and ATM activation in cultured cells and support differentiation of hematopoietic cells in vivo. These data indicate that the essential role of Nbs1 is via its interaction with Mre11 and that most of the Nbs1 protein is dispensable for Mre11 complex functions and suggest that Mre11 and Rad50 directly activate ATM.


Subject(s)
Cell Cycle Proteins/metabolism , MRE11 Homologue Protein/metabolism , Nuclear Proteins/metabolism , Tumor Suppressor Proteins/metabolism , Amino Acid Motifs , Amino Acid Sequence , Animals , Carcinogenesis/pathology , Cell Cycle Proteins/chemistry , Cell Cycle Proteins/deficiency , Cell Survival , Conserved Sequence , DNA Damage , DNA Repair , DNA-Binding Proteins , Embryonic Development , Evolution, Molecular , Fetus/cytology , Hematopoiesis , Liver/embryology , Mice , Nuclear Proteins/chemistry , Nuclear Proteins/deficiency , Protein Binding , Protein Multimerization
19.
J Pathol ; 238(4): 508-18, 2016 Mar.
Article in English | MEDLINE | ID: mdl-26832993

ABSTRACT

Phyllodes tumours (PTs) are breast fibroepithelial lesions that are graded based on histological criteria as benign, borderline or malignant. PTs may recur locally. Borderline PTs and malignant PTs may metastasize to distant sites. Breast fibroepithelial lesions, including PTs and fibroadenomas, are characterized by recurrent MED12 exon 2 somatic mutations. We sought to define the repertoire of somatic genetic alterations in PTs and whether these may assist in the differential diagnosis of these lesions. We collected 100 fibroadenomas, 40 benign PTs, 14 borderline PTs and 22 malignant PTs; six, six and 13 benign, borderline and malignant PTs, respectively, and their matched normal tissue, were subjected to targeted massively parallel sequencing (MPS) using the MSK-IMPACT sequencing assay. Recurrent MED12 mutations were found in 56% of PTs; in addition, mutations affecting cancer genes (eg TP53, RB1, SETD2 and EGFR) were exclusively detected in borderline and malignant PTs. We found a novel recurrent clonal hotspot mutation in the TERT promoter (-124 C>T) in 52% and TERT gene amplification in 4% of PTs. Laser capture microdissection revealed that these mutations were restricted to the mesenchymal component of PTs. Sequencing analysis of the entire cohort revealed that the frequency of TERT alterations increased from benign (18%) to borderline (57%) and to malignant PTs (68%; p < 0.01), and TERT alterations were associated with increased levels of TERT mRNA (p < 0.001). No TERT alterations were observed in fibroadenomas. An analysis of TERT promoter sequencing and gene amplification distinguished PTs from fibroadenomas with a sensitivity and a positive predictive value of 100% (CI 95.38-100%) and 100% (CI 85.86-100%), respectively, and a sensitivity and a negative predictive value of 39% (CI 28.65-51.36%) and 68% (CI 60.21-75.78%), respectively. Our results suggest that TERT alterations may drive the progression of PTs, and may assist in the differential diagnosis between PTs and fibroadenomas. Copyright © 2015 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.


Subject(s)
Breast Neoplasms/genetics , Breast Neoplasms/pathology , Fibroadenoma/pathology , Mutation/genetics , Neoplasm Recurrence, Local/pathology , Phyllodes Tumor/pathology , Promoter Regions, Genetic , Telomerase/genetics , Diagnosis, Differential , Female , Fibroadenoma/diagnosis , Gene Amplification/genetics , High-Throughput Nucleotide Sequencing/methods , Humans , Neoplasm Recurrence, Local/diagnosis , Neoplasm Recurrence, Local/genetics , Phyllodes Tumor/diagnosis
20.
Mol Cancer Res ; 14(2): 185-95, 2016 Feb.
Article in English | MEDLINE | ID: mdl-26538284

ABSTRACT

UNLABELLED: The Mre11 complex (Mre11, Rad50, and Nbs1) occupies a central node of the DNA damage response (DDR) network and is required for ATM activation in response to DNA damage. Hypomorphic alleles of MRE11 and NBS1 confer embryonic lethality in ATM-deficient mice, indicating that the complex exerts ATM-independent functions that are essential when ATM is absent. To delineate those functions, a conditional ATM allele (ATM(flox)) was crossed to hypomorphic NBS1 mutants (Nbs1(ΔB/ΔB) mice). Nbs1(ΔB/ΔB) Atm(-/-) hematopoietic cells derived by crossing to vav(cre) were viable in vivo. Nbs1(ΔB/ΔB) Atm(-/-) (VAV) mice exhibited a pronounced defect in double-strand break repair and completely penetrant early onset lymphomagenesis. In addition to repair defects observed, fragile site instability was noted, indicating that the Mre11 complex promotes genome stability upon replication stress in vivo. The data suggest combined influences of the Mre11 complex on DNA repair, as well as the responses to DNA damage and DNA replication stress. IMPLICATIONS: A novel mouse model was developed, by combining a vav(cre)-inducible ATM knockout mouse with an NBS1 hypomorphic mutation, to analyze ATM-independent functions of the Mre11 complex in vivo. These data show that the DNA repair, rather than DDR signaling functions of the complex, is acutely required in the context of ATM deficiency to suppress genome instability and lymphomagenesis.


Subject(s)
Cell Cycle Proteins/genetics , Chromosome Fragile Sites , DNA Repair , Disease Models, Animal , Lymphoma/genetics , Nuclear Proteins/genetics , Age of Onset , Animals , Ataxia Telangiectasia Mutated Proteins/genetics , DNA Breaks, Double-Stranded , DNA Repair Enzymes/genetics , DNA Repair Enzymes/metabolism , DNA Replication , DNA-Binding Proteins , Mice , Mice, Knockout , Mutation
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