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1.
Nat Immunol ; 22(6): 711-722, 2021 06.
Article in English | MEDLINE | ID: mdl-34017121

ABSTRACT

Chromatin undergoes extensive reprogramming during immune cell differentiation. Here we report the repression of controlled histone H3 amino terminus proteolytic cleavage (H3ΔN) during monocyte-to-macrophage development. This abundant histone mark in human peripheral blood monocytes is catalyzed by neutrophil serine proteases (NSPs) cathepsin G, neutrophil elastase and proteinase 3. NSPs are repressed as monocytes mature into macrophages. Integrative epigenomic analysis reveals widespread H3ΔN distribution across the genome in a monocytic cell line and primary monocytes, which becomes largely undetectable in fully differentiated macrophages. H3ΔN is enriched at permissive chromatin and actively transcribed genes. Simultaneous NSP depletion in monocytic cells results in H3ΔN loss and further increase in chromatin accessibility, which likely primes the chromatin for gene expression reprogramming. Importantly, H3ΔN is reduced in monocytes from patients with systemic juvenile idiopathic arthritis, an autoinflammatory disease with prominent macrophage involvement. Overall, we uncover an epigenetic mechanism that primes the chromatin to facilitate macrophage development.


Subject(s)
Arthritis, Juvenile/immunology , Cell Differentiation/immunology , Epigenesis, Genetic/immunology , Histones/metabolism , Leukocytes, Mononuclear/metabolism , Macrophages/immunology , Adolescent , Arthritis, Juvenile/blood , Arthritis, Juvenile/genetics , CRISPR-Cas Systems/genetics , Cathepsin G/genetics , Cathepsin G/metabolism , Cell Differentiation/genetics , Cell Nucleus/metabolism , Child , Child, Preschool , Chromatin/metabolism , Enzyme Assays , Epigenomics , Female , Gene Knockout Techniques , Humans , Jurkat Cells , Leukocyte Elastase/genetics , Leukocyte Elastase/metabolism , Leukocytes, Mononuclear/immunology , Macrophages/metabolism , Male , Myeloblastin/genetics , Myeloblastin/metabolism , Primary Cell Culture , Proteolysis , RNA-Seq , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , THP-1 Cells , Young Adult
2.
Mol Cell ; 83(22): 4017-4031.e9, 2023 Nov 16.
Article in English | MEDLINE | ID: mdl-37820732

ABSTRACT

The MCM motor of the replicative helicase is loaded onto origin DNA as an inactive double hexamer before replication initiation. Recruitment of activators GINS and Cdc45 upon S-phase transition promotes the assembly of two active CMG helicases. Although work with yeast established the mechanism for origin activation, how CMG is formed in higher eukaryotes is poorly understood. Metazoan Downstream neighbor of Son (DONSON) has recently been shown to deliver GINS to MCM during CMG assembly. What impact this has on the MCM double hexamer is unknown. Here, we used cryoelectron microscopy (cryo-EM) on proteins isolated from replicating Xenopus egg extracts to identify a double CMG complex bridged by a DONSON dimer. We find that tethering elements mediating complex formation are essential for replication. DONSON reconfigures the MCM motors in the double CMG, and primordial dwarfism patients' mutations disrupting DONSON dimerization affect GINS and MCM engagement in human cells and DNA synthesis in Xenopus egg extracts.


Subject(s)
Cell Cycle Proteins , DNA Helicases , Nuclear Proteins , Animals , Humans , Cell Cycle Proteins/chemistry , Cell Cycle Proteins/metabolism , Cryoelectron Microscopy , DNA/genetics , DNA/metabolism , DNA Helicases/metabolism , DNA Replication , Minichromosome Maintenance Proteins/genetics , Minichromosome Maintenance Proteins/metabolism , Nuclear Proteins/chemistry , Nuclear Proteins/metabolism , Saccharomyces cerevisiae/genetics , Enzyme Activation
3.
Mol Cell ; 82(10): 1924-1939.e10, 2022 05 19.
Article in English | MEDLINE | ID: mdl-35439434

ABSTRACT

The 53BP1-RIF1-shieldin pathway maintains genome stability by suppressing nucleolytic degradation of DNA ends at double-strand breaks (DSBs). Although RIF1 interacts with damaged chromatin via phospho-53BP1 and facilitates recruitment of the shieldin complex to DSBs, it is unclear whether other regulatory cues contribute to this response. Here, we implicate methylation of histone H3 at lysine 4 by SETD1A-BOD1L in the recruitment of RIF1 to DSBs. Compromising SETD1A or BOD1L expression or deregulating H3K4 methylation allows uncontrolled resection of DNA ends, impairs end-joining of dysfunctional telomeres, and abrogates class switch recombination. Moreover, defects in RIF1 localization to DSBs are evident in patient cells bearing loss-of-function mutations in SETD1A. Loss of SETD1A-dependent RIF1 recruitment in BRCA1-deficient cells restores homologous recombination and leads to resistance to poly(ADP-ribose)polymerase inhibition, reinforcing the clinical relevance of these observations. Mechanistically, RIF1 binds directly to methylated H3K4, facilitating its recruitment to, or stabilization at, DSBs.


Subject(s)
DNA Breaks, Double-Stranded , Telomere-Binding Proteins , BRCA1 Protein/genetics , DNA/metabolism , DNA End-Joining Repair , DNA Repair , Histone-Lysine N-Methyltransferase/genetics , Histone-Lysine N-Methyltransferase/metabolism , Humans , Methylation , Telomere-Binding Proteins/genetics , Telomere-Binding Proteins/metabolism , Tumor Suppressor p53-Binding Protein 1/genetics , Tumor Suppressor p53-Binding Protein 1/metabolism
4.
Nature ; 620(7974): 516-520, 2023 Aug.
Article in English | MEDLINE | ID: mdl-37488359

ABSTRACT

Terrestrial and sub-Neptune planets are expected to form in the inner (less than 10 AU) regions of protoplanetary disks1. Water plays a key role in their formation2-4, although it is yet unclear whether water molecules are formed in situ or transported from the outer disk5,6. So far Spitzer Space Telescope observations have only provided water luminosity upper limits for dust-depleted inner disks7, similar to PDS 70, the first system with direct confirmation of protoplanet presence8,9. Here we report JWST observations of PDS 70, a benchmark target to search for water in a disk hosting a large (approximately 54 AU) planet-carved gap separating an inner and outer disk10,11. Our findings show water in the inner disk of PDS 70. This implies that potential terrestrial planets forming therein have access to a water reservoir. The column densities of water vapour suggest in-situ formation via a reaction sequence involving O, H2 and/or OH, and survival through water self-shielding5. This is also supported by the presence of CO2 emission, another molecule sensitive to ultraviolet photodissociation. Dust shielding, and replenishment of both gas and small dust from the outer disk, may also play a role in sustaining the water reservoir12. Our observations also reveal a strong variability of the mid-infrared spectral energy distribution, pointing to a change of inner disk geometry.

5.
Nature ; 603(7901): 439-444, 2022 03.
Article in English | MEDLINE | ID: mdl-35296845

ABSTRACT

The introduction of molecular complexity in an atom- and step-efficient manner remains an outstanding goal in modern synthetic chemistry. Artificial biosynthetic pathways are uniquely able to address this challenge by using enzymes to carry out multiple synthetic steps simultaneously or in a one-pot sequence1-3. Conducting biosynthesis ex vivo further broadens its applicability by avoiding cross-talk with cellular metabolism and enabling the redesign of key biosynthetic pathways through the use of non-natural cofactors and synthetic reagents4,5. Here we describe the discovery and construction of an enzymatic cascade to MK-1454, a highly potent stimulator of interferon genes (STING) activator under study as an immuno-oncology therapeutic6,7 (ClinicalTrials.gov study NCT04220866 ). From two non-natural nucleotide monothiophosphates, MK-1454 is assembled diastereoselectively in a one-pot cascade, in which two thiotriphosphate nucleotides are simultaneously generated biocatalytically, followed by coupling and cyclization catalysed by an engineered animal cyclic guanosine-adenosine synthase (cGAS). For the thiotriphosphate synthesis, three kinase enzymes were engineered to develop a non-natural cofactor recycling system in which one thiotriphosphate serves as a cofactor in its own synthesis. This study demonstrates the substantial capacity that currently exists to use biosynthetic approaches to discover and manufacture complex, non-natural molecules.


Subject(s)
Guanosine , Nucleotidyltransferases , Adenosine , Animals , Interferons , Membrane Proteins/genetics , Membrane Proteins/metabolism , Nucleotidyltransferases/metabolism , Signal Transduction
6.
Am J Hum Genet ; 110(3): 499-515, 2023 03 02.
Article in English | MEDLINE | ID: mdl-36724785

ABSTRACT

Telomere maintenance 2 (TELO2), Tel2 interacting protein 2 (TTI2), and Tel2 interacting protein 1 (TTI1) are the three components of the conserved Triple T (TTT) complex that modulates activity of phosphatidylinositol 3-kinase-related protein kinases (PIKKs), including mTOR, ATM, and ATR, by regulating the assembly of mTOR complex 1 (mTORC1). The TTT complex is essential for the expression, maturation, and stability of ATM and ATR in response to DNA damage. TELO2- and TTI2-related bi-allelic autosomal-recessive (AR) encephalopathies have been described in individuals with moderate to severe intellectual disability (ID), short stature, postnatal microcephaly, and a movement disorder (in the case of variants within TELO2). We present clinical, genomic, and functional data from 11 individuals in 9 unrelated families with bi-allelic variants in TTI1. All present with ID, and most with microcephaly, short stature, and a movement disorder. Functional studies performed in HEK293T cell lines and fibroblasts and lymphoblastoid cells derived from 4 unrelated individuals showed impairment of the TTT complex and of mTOR pathway activity which is improved by treatment with Rapamycin. Our data delineate a TTI1-related neurodevelopmental disorder and expand the group of disorders related to the TTT complex.


Subject(s)
Microcephaly , Movement Disorders , Neurodevelopmental Disorders , Humans , Intracellular Signaling Peptides and Proteins , HEK293 Cells , TOR Serine-Threonine Kinases
7.
Mol Cell ; 71(1): 25-41.e6, 2018 07 05.
Article in English | MEDLINE | ID: mdl-29937342

ABSTRACT

Components of the Fanconi anemia and homologous recombination pathways play a vital role in protecting newly replicated DNA from uncontrolled nucleolytic degradation, safeguarding genome stability. Here we report that histone methylation by the lysine methyltransferase SETD1A is crucial for protecting stalled replication forks from deleterious resection. Depletion of SETD1A sensitizes cells to replication stress and leads to uncontrolled DNA2-dependent resection of damaged replication forks. The ability of SETD1A to prevent degradation of these structures is mediated by its ability to catalyze methylation on Lys4 of histone H3 (H3K4) at replication forks, which enhances FANCD2-dependent histone chaperone activity. Suppressing H3K4 methylation or expression of a chaperone-defective FANCD2 mutant leads to loss of RAD51 nucleofilament stability and severe nucleolytic degradation of replication forks. Our work identifies epigenetic modification and histone mobility as critical regulatory mechanisms in maintaining genome stability by restraining nucleases from irreparably damaging stalled replication forks.


Subject(s)
DNA/biosynthesis , Fanconi Anemia Complementation Group D2 Protein/metabolism , Histone-Lysine N-Methyltransferase/metabolism , Histones/metabolism , Molecular Chaperones/metabolism , Nucleosomes/metabolism , A549 Cells , DNA/genetics , DNA Replication/physiology , Epigenesis, Genetic/physiology , Fanconi Anemia Complementation Group D2 Protein/genetics , HeLa Cells , Histone-Lysine N-Methyltransferase/genetics , Histones/genetics , Humans , Methylation , Molecular Chaperones/genetics , Nucleosomes/genetics , Rad51 Recombinase/genetics , Rad51 Recombinase/metabolism
8.
J Virol ; 98(7): e0070724, 2024 Jul 23.
Article in English | MEDLINE | ID: mdl-38953655

ABSTRACT

Human norovirus was discovered more than five decades ago and is a widespread cause of outbreaks of acute gastroenteritis. There are no approved vaccines or antivirals currently available. However, norovirus inhibitors, including capsid-specific monoclonal antibodies (Mabs) and nanobodies, have recently shown promising results. Several Mabs and nanobodies were found to inhibit norovirus replication using a human intestinal enteroid (HIE) culture system and/or could block norovirus attachment to histo-blood group antigen (HBGA) co-factors. In our pursuit to develop a single broad-spectrum norovirus therapeutic, we continued our analysis and development of a cross-reactive and HBGA interfering nanobody (NB26). To improve NB26 binding capacity and therapeutic potential, we conjugated NB26 onto a human IgG Fc domain (Fc-NB26). We confirmed that Fc-NB26 cross-reacts with genetically diverse GII genotype capsid protruding (P) domains (GII.8, GII.14, GII.17, GII.24, GII.26, and GII.NA1) using a direct enzyme-linked immunosorbent assay. Furthermore, X-ray crystallography structures of these P domains and structures of other GII genotypes reveal that the NB26 binding site is largely conserved, validating its broad reactivity. We showed that Fc-NB26 has ~100-fold higher affinity toward the norovirus P domain compared to native NB26. We also found that both NB26 and Fc-NB26 neutralize human norovirus replication in the HIE culture system. Furthermore, the mode of inhibition confirmed that like NB26, Fc-NB26 caused norovirus particle disassembly and aggregation. Overall, these new findings demonstrate that structural modifications to nanobodies can improve their therapeutic potential.IMPORTANCEDeveloping vaccines and antivirals against norovirus remains a challenge, mainly due to the constant genetic and antigenic evolution. Moreover, re-infection with genetically related and/or antigenic variants is not uncommon. We further developed our leading norovirus nanobody (NB26) that indirectly interfered with norovirus binding to HBGAs, by converting NB26 into a dimeric Fc-linked Nanobody (Fc-NB26). We found that Fc-NB26 had improved binding affinity and neutralization capacity compared with native NB26. Using X-ray crystallography, we showed this nanobody engaged highly conserved capsid residues among genetically diverse noroviruses. Development of such broadly reactive potent therapeutic nanobodies delivered as a slow-releasing prophylactic could be of exceptional value for norovirus outbreaks, especially for the prevention or treatment of severe acute gastroenteritis in high-risk groups such as the young, elderly, and immunocompromised.


Subject(s)
Caliciviridae Infections , Capsid Proteins , Norovirus , Single-Domain Antibodies , Norovirus/genetics , Norovirus/drug effects , Norovirus/immunology , Humans , Single-Domain Antibodies/immunology , Single-Domain Antibodies/pharmacology , Single-Domain Antibodies/chemistry , Capsid Proteins/immunology , Capsid Proteins/metabolism , Capsid Proteins/chemistry , Capsid Proteins/genetics , Caliciviridae Infections/immunology , Caliciviridae Infections/virology , Caliciviridae Infections/therapy , Antiviral Agents/pharmacology , Immunoglobulin Fc Fragments/immunology , Immunoglobulin Fc Fragments/chemistry , Antibodies, Viral/immunology , Cross Reactions , Capsid/metabolism , Capsid/immunology , Blood Group Antigens/metabolism , Virus Replication/drug effects , Gastroenteritis/virology , Immunoglobulin G/immunology , Antibodies, Monoclonal/immunology , Antibodies, Neutralizing/immunology
9.
Nature ; 571(7766): 521-527, 2019 07.
Article in English | MEDLINE | ID: mdl-31270457

ABSTRACT

The integrity of genomes is constantly threatened by problems encountered by the replication fork. BRCA1, BRCA2 and a subset of Fanconi anaemia proteins protect stalled replication forks from degradation by nucleases, through pathways that involve RAD51. The contribution and regulation of BRCA1 in replication fork protection, and how this role relates to its role in homologous recombination, is unclear. Here we show that BRCA1 in complex with BARD1, and not the canonical BRCA1-PALB2 interaction, is required for fork protection. BRCA1-BARD1 is regulated by a conformational change mediated by the phosphorylation-directed prolyl isomerase PIN1. PIN1 activity enhances BRCA1-BARD1 interaction with RAD51, thereby increasing the presence of RAD51 at stalled replication structures. We identify genetic variants of BRCA1-BARD1 in patients with cancer that exhibit poor protection of nascent strands but retain homologous recombination proficiency, thus defining domains of BRCA1-BARD1 that are required for fork protection and associated with cancer development. Together, these findings reveal a BRCA1-mediated pathway that governs replication fork protection.


Subject(s)
BRCA1 Protein/chemistry , BRCA1 Protein/metabolism , DNA Replication , Tumor Suppressor Proteins/metabolism , Ubiquitin-Protein Ligases/metabolism , BRCA1 Protein/genetics , Cell Line, Tumor , DNA Replication/genetics , Genomic Instability/genetics , Humans , Isomerism , Mutation , NIMA-Interacting Peptidylprolyl Isomerase/metabolism , Phosphorylation , Phosphoserine/metabolism , Protein Binding , Rad51 Recombinase/metabolism
10.
Mol Cell ; 65(5): 900-916.e7, 2017 Mar 02.
Article in English | MEDLINE | ID: mdl-28238654

ABSTRACT

Protein post-translation modification plays an important role in regulating DNA repair; however, the role of arginine methylation in this process is poorly understood. Here we identify the arginine methyltransferase PRMT5 as a key regulator of homologous recombination (HR)-mediated double-strand break (DSB) repair, which is mediated through its ability to methylate RUVBL1, a cofactor of the TIP60 complex. We show that PRMT5 targets RUVBL1 for methylation at position R205, which facilitates TIP60-dependent mobilization of 53BP1 from DNA breaks, promoting HR. Mechanistically, we demonstrate that PRMT5-directed methylation of RUVBL1 is critically required for the acetyltransferase activity of TIP60, promoting histone H4K16 acetylation, which facilities 53BP1 displacement from DSBs. Interestingly, RUVBL1 methylation did not affect the ability of TIP60 to facilitate ATM activation. Taken together, our findings reveal the importance of PRMT5-mediated arginine methylation during DSB repair pathway choice through its ability to regulate acetylation-dependent control of 53BP1 localization.


Subject(s)
Carrier Proteins/metabolism , DNA Breaks, Double-Stranded , DNA Helicases/metabolism , Histone Acetyltransferases/metabolism , Protein Processing, Post-Translational , Protein-Arginine N-Methyltransferases/metabolism , Recombinational DNA Repair , ATPases Associated with Diverse Cellular Activities , Acetylation , Animals , Arginine , Ataxia Telangiectasia Mutated Proteins/metabolism , Carrier Proteins/genetics , DNA Helicases/genetics , Genomic Instability , HEK293 Cells , HeLa Cells , Histone Acetyltransferases/genetics , Histones/metabolism , Humans , Lysine Acetyltransferase 5 , Methylation , Mice , Mice, Transgenic , Protein-Arginine N-Methyltransferases/genetics , RNA Interference , Time Factors , Transfection , Tumor Suppressor p53-Binding Protein 1/genetics , Tumor Suppressor p53-Binding Protein 1/metabolism
11.
Biochem J ; 481(14): 923-944, 2024 Jul 17.
Article in English | MEDLINE | ID: mdl-38985307

ABSTRACT

Maintenance of genome stability is of paramount importance for the survival of an organism. However, genomic integrity is constantly being challenged by various endogenous and exogenous processes that damage DNA. Therefore, cells are heavily reliant on DNA repair pathways that have evolved to deal with every type of genotoxic insult that threatens to compromise genome stability. Notably, inherited mutations in genes encoding proteins involved in these protective pathways trigger the onset of disease that is driven by chromosome instability e.g. neurodevelopmental abnormalities, neurodegeneration, premature ageing, immunodeficiency and cancer development. The ability of cells to regulate the recruitment of specific DNA repair proteins to sites of DNA damage is extremely complex but is primarily mediated by protein post-translational modifications (PTMs). Ubiquitylation is one such PTM, which controls genome stability by regulating protein localisation, protein turnover, protein-protein interactions and intra-cellular signalling. Over the past two decades, numerous ubiquitin (Ub) E3 ligases have been identified to play a crucial role not only in the initiation of DNA replication and DNA damage repair but also in the efficient termination of these processes. In this review, we discuss our current understanding of how different Ub E3 ligases (RNF168, TRAIP, HUWE1, TRIP12, FANCL, BRCA1, RFWD3) function to regulate DNA repair and replication and the pathological consequences arising from inheriting deleterious mutations that compromise the Ub-dependent DNA damage response.


Subject(s)
DNA Damage , DNA Repair , DNA Replication , Ubiquitin-Protein Ligases , Humans , Ubiquitin-Protein Ligases/metabolism , Ubiquitin-Protein Ligases/genetics , Ubiquitination , Neoplasms/genetics , Neoplasms/metabolism , Genomic Instability , Protein Processing, Post-Translational , Animals , Tumor Suppressor Proteins/genetics , Tumor Suppressor Proteins/metabolism
12.
Nucleic Acids Res ; 51(12): 6337-6354, 2023 07 07.
Article in English | MEDLINE | ID: mdl-37224534

ABSTRACT

Accurate genome replication is essential for all life and a key mechanism of disease prevention, underpinned by the ability of cells to respond to replicative stress (RS) and protect replication forks. These responses rely on the formation of Replication Protein A (RPA)-single stranded (ss) DNA complexes, yet this process remains largely uncharacterized. Here, we establish that actin nucleation-promoting factors (NPFs) associate with replication forks, promote efficient DNA replication and facilitate association of RPA with ssDNA at sites of RS. Accordingly, their loss leads to deprotection of ssDNA at perturbed forks, impaired ATR activation, global replication defects and fork collapse. Supplying an excess of RPA restores RPA foci formation and fork protection, suggesting a chaperoning role for actin nucleators (ANs) (i.e. Arp2/3, DIAPH1) and NPFs (i.e, WASp, N-WASp) in regulating RPA availability upon RS. We also discover that ß-actin interacts with RPA directly in vitro, and in vivo a hyper-depolymerizing ß-actin mutant displays a heightened association with RPA and the same dysfunctional replication phenotypes as loss of ANs/NPFs, which contrasts with the phenotype of a hyper-polymerizing ß-actin mutant. Thus, we identify components of actin polymerization pathways that are essential for preventing ectopic nucleolytic degradation of perturbed forks by modulating RPA activity.


Subject(s)
Actins , DNA Replication , Actins/genetics , Replication Protein A/genetics , Replication Protein A/metabolism , DNA, Single-Stranded/genetics , Molecular Chaperones/genetics
13.
Nucleic Acids Res ; 51(9): 4341-4362, 2023 05 22.
Article in English | MEDLINE | ID: mdl-36928661

ABSTRACT

BRCA1 mutations are associated with increased breast and ovarian cancer risk. BRCA1-mutant tumors are high-grade, recurrent, and often become resistant to standard therapies. Herein, we performed a targeted CRISPR-Cas9 screen and identified MEPCE, a methylphosphate capping enzyme, as a synthetic lethal interactor of BRCA1. Mechanistically, we demonstrate that depletion of MEPCE in a BRCA1-deficient setting led to dysregulated RNA polymerase II (RNAPII) promoter-proximal pausing, R-loop accumulation, and replication stress, contributing to transcription-replication collisions. These collisions compromise genomic integrity resulting in loss of viability of BRCA1-deficient cells. We also extend these findings to another RNAPII-regulating factor, PAF1. This study identifies a new class of synthetic lethal partners of BRCA1 that exploit the RNAPII pausing regulation and highlight the untapped potential of transcription-replication collision-inducing factors as unique potential therapeutic targets for treating cancers associated with BRCA1 mutations.


Subject(s)
BRCA1 Protein , DNA Replication , Hereditary Breast and Ovarian Cancer Syndrome , Mutation , Transcription, Genetic , Humans , BRCA1 Protein/deficiency , BRCA1 Protein/genetics , DNA Replication/genetics , Hereditary Breast and Ovarian Cancer Syndrome/genetics , Hereditary Breast and Ovarian Cancer Syndrome/pathology , Hereditary Breast and Ovarian Cancer Syndrome/physiopathology , RNA Polymerase II/metabolism , Transcription, Genetic/genetics , Promoter Regions, Genetic , Methyltransferases/deficiency , Methyltransferases/genetics , R-Loop Structures , Cell Death
14.
Nucleic Acids Res ; 51(19): 10484-10505, 2023 10 27.
Article in English | MEDLINE | ID: mdl-37697435

ABSTRACT

Breast cancer linked with BRCA1/2 mutations commonly recur and resist current therapies, including PARP inhibitors. Given the lack of effective targeted therapies for BRCA1-mutant cancers, we sought to identify novel targets to selectively kill these cancers. Here, we report that loss of RNF8 significantly protects Brca1-mutant mice against mammary tumorigenesis. RNF8 deficiency in human BRCA1-mutant breast cancer cells was found to promote R-loop accumulation and replication fork instability, leading to increased DNA damage, senescence, and synthetic lethality. Mechanistically, RNF8 interacts with XRN2, which is crucial for transcription termination and R-loop resolution. We report that RNF8 ubiquitylates XRN2 to facilitate its recruitment to R-loop-prone genomic loci and that RNF8 deficiency in BRCA1-mutant breast cancer cells decreases XRN2 occupancy at R-loop-prone sites, thereby promoting R-loop accumulation, transcription-replication collisions, excessive genomic instability, and cancer cell death. Collectively, our work identifies a synthetic lethal interaction between RNF8 and BRCA1, which is mediated by a pathological accumulation of R-loops.


Subject(s)
BRCA1 Protein , Breast Neoplasms , Animals , Female , Humans , Mice , BRCA1 Protein/metabolism , BRCA2 Protein/genetics , Breast Neoplasms/genetics , DNA Damage , DNA-Binding Proteins/metabolism , Exoribonucleases/metabolism , Genomic Instability , Neoplasm Recurrence, Local , R-Loop Structures , Ubiquitin-Protein Ligases/genetics , Ubiquitin-Protein Ligases/metabolism , Ubiquitination
15.
Proc Natl Acad Sci U S A ; 119(41): e2210094119, 2022 10 11.
Article in English | MEDLINE | ID: mdl-36194629

ABSTRACT

Understanding the activated transport of penetrant or tracer atoms and molecules in condensed phases is a challenging problem in chemistry, materials science, physics, and biophysics. Many angstrom- and nanometer-scale features enter due to the highly variable shape, size, interaction, and conformational flexibility of the penetrant and matrix species, leading to a dramatic diversity of penetrant dynamics. Based on a minimalist model of a spherical penetrant in equilibrated dense matrices of hard spheres, a recent microscopic theory that relates hopping transport to local structure has predicted a novel correlation between penetrant diffusivity and the matrix thermodynamic dimensionless compressibility, S0(T) (which also quantifies the amplitude of long wavelength density fluctuations), as a consequence of a fundamental statistical mechanical relationship between structure and thermodynamics. Moreover, the penetrant activation barrier is predicted to have a factorized/multiplicative form, scaling as the product of an inverse power law of S0(T) and a linear/logarithmic function of the penetrant-to-matrix size ratio. This implies an enormous reduction in chemical complexity that is verified based solely on experimental data for diverse classes of chemically complex penetrants dissolved in molecular and polymeric liquids over a wide range of temperatures down to the kinetic glass transition. The predicted corollary that the penetrant diffusion constant decreases exponentially with inverse temperature raised to an exponent determined solely by how S0(T) decreases with cooling is also verified experimentally. Our findings are relevant to fundamental questions in glassy dynamics, self-averaging of angstrom-scale chemical features, and applications such as membrane separations, barrier coatings, drug delivery, and self-healing.


Subject(s)
Glass , Physics , Diffusion , Glass/chemistry , Phase Transition , Thermodynamics
16.
J Biol Chem ; 299(2): 102805, 2023 02.
Article in English | MEDLINE | ID: mdl-36529287

ABSTRACT

EmrE, a small multidrug resistance transporter from Escherichia coli, confers broad-spectrum resistance to polyaromatic cations and quaternary ammonium compounds. Previous transport assays demonstrate that EmrE transports a +1 and a +2 substrate with the same stoichiometry of two protons:one cationic substrate. This suggests that EmrE substrate binding capacity is limited to neutralization of the two essential glutamates, E14A and E14B (one from each subunit in the antiparallel homodimer), in the primary binding site. Here, we explicitly test this hypothesis, since EmrE has repeatedly broken expectations for membrane protein structure and transport mechanism. We previously showed that EmrE can bind a +1 cationic substrate and proton simultaneously, with cationic substrate strongly associated with one E14 residue, whereas the other remains accessible to bind and transport a proton. Here, we demonstrate that EmrE can bind a +2 cation substrate and a proton simultaneously using NMR pH titrations of EmrE saturated with divalent substrates, for a net +1 charge in the transport pore. Furthermore, we find that EmrE can alternate access and transport a +2 substrate and proton at the same time. Together, these results lead us to conclude that E14 charge neutralization does not limit the binding and transport capacity of EmrE.


Subject(s)
Antiporters , Catalytic Domain , Escherichia coli Proteins , Escherichia coli , Glutamates , Static Electricity , Antiporters/chemistry , Antiporters/metabolism , Escherichia coli/chemistry , Escherichia coli/metabolism , Escherichia coli Proteins/chemistry , Escherichia coli Proteins/metabolism , Glutamates/chemistry , Glutamates/metabolism , Protons , Substrate Specificity , Protein Binding , Nuclear Magnetic Resonance, Biomolecular , Hydrogen-Ion Concentration , Drug Resistance, Multiple, Bacterial , Ion Transport
17.
J Neurophysiol ; 132(2): 527-530, 2024 Aug 01.
Article in English | MEDLINE | ID: mdl-38985940

ABSTRACT

Ischemic preconditioning (IPC) can enhance maximal strength likely due to neural priming. Cruz et al. (Cruz R, Tramontin AF, Oliveira AS, Caputo F, Denadai BS, Greco CC. Scand J Med Sci Sports 34: e14591, 2024) examined the neurophysiological mechanisms responsible for the ergogenic effect. Although key neurophysiological measures remained largely unchanged, voluntary activation and maximal strength were greater following IPC than sham-IPC. Although the mechanistic evidence remains inconclusive, the greater maximal strength provides further evidence of the ergogenic benefit of IPC. Researchers should continue examining the broader functional implications of IPC.


Subject(s)
Ischemic Preconditioning , Ischemic Preconditioning/methods , Humans , Muscle Strength/physiology , Muscle, Skeletal/physiology
18.
J Virol ; 97(4): e0183322, 2023 04 27.
Article in English | MEDLINE | ID: mdl-36971561

ABSTRACT

Noroviruses are the leading cause of outbreaks of acute gastroenteritis. These viruses usually interact with histo-blood group antigens (HBGAs), which are considered essential cofactors for norovirus infection. This study structurally characterizes nanobodies developed against the clinically important GII.4 and GII.17 noroviruses with a focus on the identification of novel nanobodies that efficiently block the HBGA binding site. Using X-ray crystallography, we have characterized nine different nanobodies that bound to the top, side, or bottom of the P domain. The eight nanobodies that bound to the top or side of the P domain were mainly genotype specific, while one nanobody that bound to the bottom cross-reacted against several genotypes and showed HBGA blocking potential. The four nanobodies that bound to the top of the P domain also inhibited HBGA binding, and structural analysis revealed that these nanobodies interacted with several GII.4 and GII.17 P domain residues that commonly engaged HBGAs. Moreover, these nanobody complementarity-determining regions (CDRs) extended completely into the cofactor pockets and would likely impede HBGA engagement. The atomic level information for these nanobodies and their corresponding binding sites provide a valuable template for the discovery of additional "designer" nanobodies. These next-generation nanobodies would be designed to target other important genotypes and variants, while maintaining cofactor interference. Finally, our results clearly demonstrate for the first time that nanobodies directly targeting the HBGA binding site can function as potent norovirus inhibitors. IMPORTANCE Human noroviruses are highly contagious and a major problem in closed institutions, such as schools, hospitals, and cruise ships. Reducing norovirus infections is challenging on multiple levels and includes the frequent emergence of antigenic variants, which complicates designing effective, broadly reactive capsid therapeutics. We successfully developed and characterized four norovirus nanobodies that bound at the HBGA pockets. Compared with previously developed norovirus nanobodies that inhibited HBGA through disrupted particle stability, these four novel nanobodies directly inhibited HBGA engagement and interacted with HBGA binding residues. Importantly, these new nanobodies specifically target two genotypes that have caused the majority of outbreaks worldwide and consequently would have an enormous benefit if they could be further developed as norovirus therapeutics. To date, we have structurally characterized 16 different GII nanobody complexes, a number of which block HBGA binding. These structural data could be used to design multivalent nanobody constructs with improved inhibition properties.


Subject(s)
Blood Group Antigens , Norovirus , Single-Domain Antibodies , Blood Group Antigens/chemistry , Blood Group Antigens/metabolism , Norovirus/drug effects , Norovirus/metabolism , Single-Domain Antibodies/chemistry , Single-Domain Antibodies/pharmacology , Binding Sites/drug effects , Cross Reactions , Thermodynamics , Crystallography, X-Ray , Protein Domains , Protein Binding , Models, Molecular
19.
Ann Rheum Dis ; 2024 Aug 20.
Article in English | MEDLINE | ID: mdl-38849152

ABSTRACT

OBJECTIVES: We report the safety, tolerability and efficacy of tofacitinib in patients with juvenile idiopathic arthritis (JIA) in an ongoing long-term extension (LTE) study. METHODS: Patients (2-<18 years) with JIA who completed phase 1/3 index studies or discontinued for reasons excluding treatment-related serious adverse events (AEs) entered the LTE study and received tofacitinib 5 mg two times per day or equivalent weight-based doses. Safety outcomes included AEs, serious AEs and AEs of special interest. Efficacy outcomes included improvement since tofacitinib initiation per the JIA-American College of Rheumatology (ACR)70/90 criteria, JIA flare rate and disease activity measured by Juvenile Arthritis Disease Activity Score (JADAS)27, with inactive disease corresponding to JADAS ≤1.0. RESULTS: Of 225 patients with JIA (median (range) duration of treatment, 41.6 (1-103) months), 201 (89.3%) had AEs; 34 (15.1%) had serious AEs. 10 patients developed serious infections; three had herpes zoster. Two patients newly developed uveitis. Among patients with polyarticular course JIA, JIA-ACR70/90 response rates were 60.0% (78 of 130) and 33.6% (47 of 140), respectively, at month 1, and generally improved over time. JIA flare events generally occurred in <5% of patients through to month 48. Observed mean (SE) JADAS27 was 22.0 (0.6) at baseline, 6.2 (0.7) at month 1 and 2.8 (0.5) at month 48, with inactive disease in 28.8% (36 of 125) of patients at month 1 and 46.8% (29 of 82) at month 48. CONCLUSIONS: In this interim analysis of LTE study data in patients with JIA, safety findings were consistent with the known profile of tofacitinib, and efficacy was maintained up to month 48. TRIAL REGISTRATION NUMBER: NCT01500551.

20.
Psychosom Med ; 86(8): 720-729, 2024 Oct 01.
Article in English | MEDLINE | ID: mdl-39132972

ABSTRACT

OBJECTIVE: Prenatal stress physiology is often posited as a predictor of birth outcomes, including gestational age at birth and birthweight. However, research has predominantly relied on indicators in the maternal system, with few studies examining hormones of the fetal system. The current study focuses on fetal cortisol in the third trimester, as measured in neonatal hair, as a biological factor that might be associated with birth outcomes (gestational age at birth and birthweight). We report findings from two studies: a longitudinal cohort (Study 1), and a meta-analysis of the existing literature (Study 2). METHODSSTUDY: Hair was collected for cortisol analysis from 168 neonates (55.95% female) shortly after birth. Gestational age at birth and birthweight were abstracted from medical records. METHODSSTUDY: An exhaustive search of four databases was conducted, yielding 155 total studies for screening. Papers reporting neonatal hair cortisol (collection <2 weeks postpartum) and birth outcomes among human neonates were retained for analysis, including Study 1 results ( k = 9). RESULTSSTUDY: Higher neonatal hair cortisol was related to longer gestation ( r = 0.28, p < .001) and higher birthweight, r = 0.16, p = .040. Sex did not moderate either association. RESULTSSTUDY: Across the nine studies, higher neonatal hair cortisol predicted both longer gestation ( r = 0.35, p < .001, 95% confidence interval = 0.24-0.45) and higher birthweight ( r = 0.18, p = .001, 95% confidence interval = 0.07-0.28). Neonatal sex did not moderate these associations. CONCLUSIONS: Fetal cortisol exposure in the third trimester plays a role in normative maturation of the fetus, and findings reveal that higher cortisol is associated with positive birth outcomes.


Subject(s)
Birth Weight , Gestational Age , Hair , Hydrocortisone , Humans , Hydrocortisone/metabolism , Hydrocortisone/analysis , Hair/chemistry , Hair/metabolism , Infant, Newborn , Female , Pregnancy , Birth Weight/physiology , Male , Adult , Pregnancy Trimester, Third/metabolism , Pregnancy Outcome , Longitudinal Studies
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