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1.
Nat Commun ; 15(1): 5392, 2024 Jun 25.
Article in English | MEDLINE | ID: mdl-38918391

ABSTRACT

DNA double-strand breaks (DSBs), such as those produced by radiation and radiomimetics, are amongst the most toxic forms of cellular damage, in part because they involve extensive oxidative modifications at the break termini. Prior to completion of DSB repair, the chemically modified termini must be removed. Various DNA processing enzymes have been implicated in the processing of these dirty ends, but molecular knowledge of this process is limited. Here, we demonstrate a role for the metallo-ß-lactamase fold 5'-3' exonuclease SNM1A in this vital process. Cells disrupted for SNM1A manifest increased sensitivity to radiation and radiomimetic agents and show defects in DSB damage repair. SNM1A is recruited and is retained at the sites of DSB damage via the concerted action of its three highly conserved PBZ, PIP box and UBZ interaction domains, which mediate interactions with poly-ADP-ribose chains, PCNA and the ubiquitinated form of PCNA, respectively. SNM1A can resect DNA containing oxidative lesions induced by radiation damage at break termini. The combined results reveal a crucial role for SNM1A to digest chemically modified DNA during the repair of DSBs and imply that the catalytic domain of SNM1A is an attractive target for potentiation of radiotherapy.


Subject(s)
DNA Breaks, Double-Stranded , DNA Repair Enzymes , DNA Repair , Exodeoxyribonucleases , Humans , DNA Breaks, Double-Stranded/radiation effects , Exodeoxyribonucleases/metabolism , Exodeoxyribonucleases/genetics , DNA Repair Enzymes/metabolism , DNA Repair Enzymes/genetics , Proliferating Cell Nuclear Antigen/metabolism , Proliferating Cell Nuclear Antigen/genetics , DNA/metabolism , DNA/genetics , Ubiquitination , Cell Cycle Proteins
2.
Chem Sci ; 15(21): 8227-8241, 2024 May 29.
Article in English | MEDLINE | ID: mdl-38817593

ABSTRACT

The three human SNM1 metallo-ß-lactamase fold nucleases (SNM1A-C) play key roles in DNA damage repair and in maintaining telomere integrity. Genetic studies indicate that they are attractive targets for cancer treatment and to potentiate chemo- and radiation-therapy. A high-throughput screen for SNM1A inhibitors identified diverse pharmacophores, some of which were shown by crystallography to coordinate to the di-metal ion centre at the SNM1A active site. Structure and turnover assay-guided optimization enabled the identification of potent quinazoline-hydroxamic acid containing inhibitors, which bind in a manner where the hydroxamic acid displaces the hydrolytic water and the quinazoline ring occupies a substrate nucleobase binding site. Cellular assays reveal that SNM1A inhibitors cause sensitisation to, and defects in the resolution of, cisplatin-induced DNA damage, validating the tractability of MBL fold nucleases as cancer drug targets.

3.
Chem Sci ; 14(44): 12498-12505, 2023 Nov 15.
Article in English | MEDLINE | ID: mdl-38020377

ABSTRACT

Formaldehyde is a pollutant and human metabolite that is toxic at high concentrations. Biological studies on formaldehyde are hindered by its high reactivity and volatility, which make it challenging to deliver quantitatively to cells. Here, we describe the development and validation of a set of N-acyloxymethyl-phthalimides as cell-relevant formaldehyde delivery agents. These esterase-sensitive compounds were similarly or less inhibitory to human cancer cell growth than free formaldehyde but the lead compound increased intracellular formaldehyde concentrations, increased cellular levels of thymidine derivatives (implying increased formaldehyde-mediated carbon metabolism), induced formation of cellular DNA-protein cross-links and induced cell death in pancreatic cancer cells. Overall, our N-acyloxymethyl-phthalimides and control compounds provide an accessible and broadly applicable chemical toolkit for formaldehyde biological research and have potential as cancer therapeutics.

4.
Bioact Mater ; 26: 437-451, 2023 Aug.
Article in English | MEDLINE | ID: mdl-36993789

ABSTRACT

In this study, the influence of a plasma electrolytic oxidation (PEO) surface treatment on a medical-grade WE43-based magnesium alloy is examined through an experimental and computational framework that considers the effects of localised corrosion features and mechanical properties throughout the corrosion process. First, a comprehensive in-vitro immersion study was performed on WE43-based tensile specimens with and without PEO surface modification, which included fully automated spatial reconstruction of the phenomenological features of corrosion through micro-CT scanning, followed by uniaxial tensile testing. Then the experimental data of both unmodified and PEO-modified groups were used to calibrate parameters of a finite element-based surface corrosion model. In-vitro, it was found that the WE43-PEO modified group had a significantly lower corrosion rate and maintained significantly higher mechanical properties than the unmodified. While corrosion rates were ∼50% lower in the WE43-PEO modified specimens, the local geometric features of corroding surfaces remained similar to the unmodified WE43 group, however evolving after almost the double amount of time. We were also able to quantitatively demonstrate that the PEO surface treatment on magnesium continued to protect samples from corrosion throughout the entire period tested, and not just in the early stages of corrosion. Using the results from the testing framework, the model parameters of the surface-based corrosion model were identified for both groups. This enabled, for the first time, in-silico prediction of the physical features of corrosion and the mechanical performance of both unmodified and PEO modified magnesium specimens. This simulation framework can enable future in-silico design and optimisation of bioabsorbable magnesium devices for load-bearing medical applications.

5.
J Mech Behav Biomed Mater ; 138: 105637, 2023 02.
Article in English | MEDLINE | ID: mdl-36610284

ABSTRACT

This study developed an enhanced phenomenological model for the predictions of surface-based localised corrosion of magnesium alloys for use in medical applications. The modelling framework extended previous surface-based approaches by considering the role of ß-phase components throughout the material volume to better predict spatial and temporal aspects of surface-based corrosion in magnesium alloys. This enhanced surface-based corrosion model offers many advantages as it (i) captures multi-directional pitting, (ii) captures various pit morphologies, (iii) eliminates mesh sizing effects, (iv) reduces computational cost through custom time controls (v) offers control of pit sizing and (vi) produces corrosion rates that are independent of pitting parameter values. The model was fully implemented in three dimensions within the finite element framework and shows excellent potential to enable robust predictions of the long-term performance of magnesium-based implants undergoing corrosion.


Subject(s)
Alloys , Magnesium , Corrosion , Absorbable Implants , Materials Testing
6.
EMBO J ; 42(3): e111998, 2023 02 01.
Article in English | MEDLINE | ID: mdl-36541070

ABSTRACT

The Werner Syndrome helicase, WRN, is a promising therapeutic target in cancers with microsatellite instability (MSI). Long-term MSI leads to the expansion of TA nucleotide repeats proposed to form cruciform DNA structures, which in turn cause DNA breaks and cell lethality upon WRN downregulation. Here we employed biochemical assays to show that WRN helicase can efficiently and directly unfold cruciform structures, thereby preventing their cleavage by the SLX1-SLX4 structure-specific endonuclease. TA repeats are particularly prone to form cruciform structures, explaining why these DNA sequences are preferentially broken in MSI cells upon WRN downregulation. We further demonstrate that the activity of the DNA mismatch repair (MMR) complexes MutSα (MSH2-MSH6), MutSß (MSH2-MSH3), and MutLα (MLH1-PMS2) similarly decreases the level of DNA cruciforms, although the mechanism is different from that employed by WRN. When combined, WRN and MutLα exhibited higher than additive effects in in vitro cruciform processing, suggesting that WRN and the MMR proteins may cooperate. Our data explain how WRN and MMR defects cause genome instability in MSI cells with expanded TA repeats, and provide a mechanistic basis for their recently discovered synthetic-lethal interaction with promising applications in precision cancer therapy.


Subject(s)
DNA Mismatch Repair , DNA, Cruciform , Humans , MutS Homolog 2 Protein/genetics , MutS Homolog 2 Protein/metabolism , Microsatellite Instability , Werner Syndrome Helicase/genetics , Werner Syndrome Helicase/metabolism , MutL Protein Homolog 1/genetics
7.
Bioact Mater ; 21: 32-43, 2023 Mar.
Article in English | MEDLINE | ID: mdl-36017069

ABSTRACT

This study presents a computational framework that investigates the effect of localised surface-based corrosion on the mechanical performance of a magnesium-based alloy. A finite element-based phenomenological corrosion model was used to generate a wide range of corrosion profiles, with subsequent uniaxial tensile test simulations to predict the mechanical response to failure. The python-based detection framework PitScan provides detailed quantification of the spatial phenomenological features of corrosion, including a full geometric tracking of corroding surface. Through this approach, this study is the first to quantitatively demonstrate that a surface-based non-uniform corrosion model can capture both the geometrical and mechanical features of a magnesium alloy undergoing corrosion by comparing to experimental data. Using this verified corrosion modelling approach, a wide range of corrosion scenarios was evaluated and enabled quantitative relationships to be established between the mechanical integrity and key phenomenological corrosion features. In particular, we demonstrated that the minimal cross-sectional area parameter was the strongest predictor of the remaining mechanical strength (R2 = 0.98), with this relationship being independent of the severity or spatial features of localised surface corrosion. Interestingly, our analysis demonstrated that parameters described in ASTM G46-94 showed weaker correlations to the mechanical integrity of corroding specimens, compared to parameters determined by Pitscan. This study establishes new mechanistic insight into the performance of the magnesium-based materials undergoing corrosion.

9.
Bone ; 165: 116544, 2022 Dec.
Article in English | MEDLINE | ID: mdl-36075352

ABSTRACT

Issues with current treatments for osteochondral defects such as mosaicplasty and autologous chondrocyte implantation (ACI) are lack of donor material, problems associated with donor sites, necessity of second surgical intervention and cell expansion, difficult site preparation and implant fitting to match the surrounding tissue. This study presents the development of a patient specific implant system for focal osteochondral defects that addresses these issues. Using computer aided design and manufacturing techniques, computed tomography scans are utilized to design the implant and templates that facilitate site preparation to allow for precise and easy implantation of the designed perfectly fitting tissue replacement. Functionality of the system and accurate restoration of a defect is demonstrated by digital before/after comparison and with a prototype. With the presented implantation system larger defects in curved joint surfaces can be restored to an optimal shape in an easier procedure than for instance mosaicplasty. The proposed system potentially allows for later replacement of worn implants.

10.
Cochrane Database Syst Rev ; 4: CD012926, 2022 04 01.
Article in English | MEDLINE | ID: mdl-35363887

ABSTRACT

BACKGROUND: Thoracoabdominal aortic aneurysms (TAAAs) are a life-threatening condition which remain difficult to treat. Endovascular and open surgical repair (OSR) provide treatment options for patients, however, due to the lack of clinical trials comparing these, the optimum treatment option is unknown. OBJECTIVES: To assess the effectiveness and safety of endovascular repair versus conventional OSR for the treatment of TAAAs. SEARCH METHODS: The Cochrane Vascular Information Specialist searched the Cochrane Vascular Specialised Register, CENTRAL, MEDLINE, Embase, CINAHL and AMED databases and World Health Organization International Clinical Trials Registry Platform and ClinicalTrials.gov trials registers to 26 April 2021. We also searched references of relevant articles retrieved from the electronic search for additional citations. SELECTION CRITERIA: We considered all published and unpublished randomised controlled trials (RCTs) and controlled clinical trials (CCTs) comparing endovascular repair to OSR for TAAAs for inclusion in the review. The main outcomes of interest were prevention of aneurysm rupture (participants without aneurysm rupture up to 5 years from intervention), aneurysm-related mortality (30 days and 12 months), all-cause mortality, spinal cord ischaemia (paraplegia, paraparesis), visceral arterial branch compromise causing mesenteric ischaemia or renal failure, and rate of reintervention. DATA COLLECTION AND ANALYSIS: Two review authors independently screened all titles and abstracts identified from the searches to identify those that met the inclusion criteria. We planned to undertake data collection, risk of bias assessment, and analysis in accordance with Cochrane recommendations. We planned to assess the certainty of the evidence using GRADE. MAIN RESULTS: No RCTs or CCTs met the inclusion criteria for this review. AUTHORS' CONCLUSIONS: Due to the lack of RCTs or CCTs, we were unable to determine the safety and effectiveness of endovascular compared to OSR in patients with TAAAs and are unable to provide any evidence on the optimal surgical intervention for this cohort of patients. High-quality RCTs or CCTs addressing this objective are necessary, however conducting such studies will be logistically and ethically challenging for this life-threatening disease.


Subject(s)
Aortic Aneurysm, Thoracic , Endovascular Procedures , Aortic Aneurysm, Thoracic/surgery , Arteries , Humans
11.
Nucleic Acids Res ; 50(3): 1484-1500, 2022 02 22.
Article in English | MEDLINE | ID: mdl-35037045

ABSTRACT

The SARS-CoV-2 coronavirus is the causal agent of the current global pandemic. SARS-CoV-2 belongs to an order, Nidovirales, with very large RNA genomes. It is proposed that the fidelity of coronavirus (CoV) genome replication is aided by an RNA nuclease complex, comprising the non-structural proteins 14 and 10 (nsp14-nsp10), an attractive target for antiviral inhibition. Our results validate reports that the SARS-CoV-2 nsp14-nsp10 complex has RNase activity. Detailed functional characterization reveals nsp14-nsp10 is a versatile nuclease capable of digesting a wide variety of RNA structures, including those with a blocked 3'-terminus. Consistent with a role in maintaining viral genome integrity during replication, we find that nsp14-nsp10 activity is enhanced by the viral RNA-dependent RNA polymerase complex (RdRp) consisting of nsp12-nsp7-nsp8 (nsp12-7-8) and demonstrate that this stimulation is mediated by nsp8. We propose that the role of nsp14-nsp10 in maintaining replication fidelity goes beyond classical proofreading by purging the nascent replicating RNA strand of a range of potentially replication-terminating aberrations. Using our developed assays, we identify drug and drug-like molecules that inhibit nsp14-nsp10, including the known SARS-CoV-2 major protease (Mpro) inhibitor ebselen and the HIV integrase inhibitor raltegravir, revealing the potential for multifunctional inhibitors in COVID-19 treatment.


Subject(s)
Antiviral Agents/pharmacology , Drug Evaluation, Preclinical , Exoribonucleases/metabolism , Genome, Viral/genetics , Genomic Instability , SARS-CoV-2/enzymology , SARS-CoV-2/genetics , Viral Nonstructural Proteins/metabolism , Viral Regulatory and Accessory Proteins/metabolism , Coronavirus RNA-Dependent RNA Polymerase/metabolism , Exoribonucleases/antagonists & inhibitors , Genome, Viral/drug effects , Genomic Instability/drug effects , Genomic Instability/genetics , HIV Integrase Inhibitors/pharmacology , Isoindoles/pharmacology , Multienzyme Complexes/antagonists & inhibitors , Multienzyme Complexes/metabolism , Organoselenium Compounds/pharmacology , RNA, Viral/biosynthesis , RNA, Viral/genetics , Raltegravir Potassium/pharmacology , SARS-CoV-2/drug effects , Viral Nonstructural Proteins/antagonists & inhibitors , Viral Regulatory and Accessory Proteins/antagonists & inhibitors , Virus Replication/drug effects , Virus Replication/genetics
12.
Ecology ; 103(1): e03545, 2022 01.
Article in English | MEDLINE | ID: mdl-34614210

ABSTRACT

Mechanisms linked to demographic, biogeographic, and food-web processes thought to underpin community stability could be affected by habitat size, but the effects of habitat size on community stability remain relatively unknown. We investigated whether those habitat-size-dependent properties influenced community instability and vulnerability to perturbations caused by disturbance. This is particularly important given that human exploitation is contracting ecosystems, and abiotic perturbations are becoming more severe and frequent. We used a perturbation experiment in which 10 streams, spanning three orders of magnitude in habitat size, were subjected to simulated bed movement akin to a major flood disturbance event. We measured the resistance, resilience, and variability of basal resources, and population and community-level responses across the stream habitat-size gradient immediately before, and at 0.5, 5, 10, 20, and 40 d post-disturbance. Resistance to disturbance consistently increased with stream size in all response variables. In contrast, resilience was significantly higher in smaller streams for some response variables. However, this higher resilience of small ecosystems was insufficient to compensate for their lower resistance, and communities of smaller streams were thus more variable over time than those of larger streams. Compensatory dynamics of populations, especially for predators, stabilized some aspects of communities, but these mechanisms were unrelated to habitat size. Together, our results provide compelling evidence for the links between habitat size and community stability, and should motivate ecologists and managers to consider how changes in the size of habitats will alter the vulnerability of ecosystems to perturbations caused by environmental disturbance.


Subject(s)
Biota , Ecosystem , Rivers , Floods
13.
Bioact Mater ; 8: 545-558, 2022 Feb.
Article in English | MEDLINE | ID: mdl-34541419

ABSTRACT

This study develops a three-dimensional automated detection framework (PitScan) that systematically evaluates the severity and phenomenology of pitting corrosion. This framework uses a python-based algorithm to analyse microcomputer-tomography scans (µCT) of cylindrical specimens undergoing corrosion. The approach systematically identifies several surface-based corrosion features, enabling full spatial characterisation of pitting parameters, including pit density, pit size, pit depth as well as pitting factor according to ASTM G46-94. Furthermore, it is used to evaluate pitting formation in tensile specimens of a Rare Earth Magnesium alloy undergoing corrosion, and relationships between key pitting parameters and mechanical performance are established. Results demonstrated that several of the parameters described in ASTM G46-94, including pit number, pit density and pitting factor, showed little correlation to mechanical performance. However, this study did identify that other parameters showed strong correlations with the ultimate tensile strength and these tended to be directly linked to the reduction of the cross-sectional area of the specimen. Specifically, our results indicate, that parameters directly linked to the loss of the cross-sectional area (e.g. minimum material width), are parameters that are most suited to provide an indication of a specimen's mechanical performance. The automated detection framework developed in this study has the potential to provide a basis to standardise measurements of pitting corrosion across a range of metals and future prediction of mechanical strength over degradation time.

14.
Cochrane Database Syst Rev ; 12: CD012992, 2021 12 14.
Article in English | MEDLINE | ID: mdl-34905228

ABSTRACT

BACKGROUND: Type B aortic dissection can lead to serious and life-threatening complications such as aortic rupture, stroke, renal failure, and paraplegia, all of which require intervention. Traditionally, these complications have been treated with open surgery. Recently however, endovascular repair has been proposed as an alternative. OBJECTIVES: To assess the effectiveness and safety of thoracic aortic endovascular repair versus open surgical repair for treatment of complicated chronic Type B aortic dissection (CBAD). SEARCH METHODS: The Cochrane Vascular Information Specialist searched the Cochrane Vascular Specialised Register, Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, Embase, CINAHL, and AMED databases, as well as the World Health Organization International Clinical Trials Registry Platform and ClinicalTrials.gov trials registers, to 2 August 2021. We searched references of relevant articles retrieved through the electronic search for additional citations. SELECTION CRITERIA: We considered all randomised controlled trials (RCTs) and controlled clinical trials (CCTs) assessing the effects of thoracic aortic endovascular repair (TEVAR) versus open surgical repair (OSR) for treatment of complicated chronic Type B aortic dissection (CBAD). Outcomes of interest were mortality (all-cause, dissection-related), neurological sequelae (stroke, spinal cord ischaemia/paresis-paralysis, vertebral insufficiency), morphological outcomes (false lumen thrombosis, progression of dissection, aortic diameters), acute renal failure, ischaemic symptoms (visceral ischaemia, limb ischaemia), re-intervention, and health-related quality of life. DATA COLLECTION AND ANALYSIS: Two review authors independently screened all titles and abstracts identified by the searches to identify those that met the inclusion criteria. From title and abstract screening, we did not identify any trials (RCTs or CCTs) that required full-text assessment. We planned to undertake data collection and analysis in accordance with recommendations described in the Cochrane Handbook for Systematic Reviews of Interventions. We planned to assess the certainty of evidence using GRADE. MAIN RESULTS: We did not identify any trials (RCTs or CCTs) that met the inclusion criteria for this review. AUTHORS' CONCLUSIONS: Due to lack of RCTs or CCTs investigating the effectiveness and safety of TEVAR compared to OSR for patients with complicated CBAD, we are unable to provide any evidence to inform decision-making on the optimal intervention for these patients. High-quality RCTs or CCTs addressing this objective are necessary. However, conducting such studies will be challenging for this life-threatening disease.


Subject(s)
Aortic Dissection , Aortic Dissection/surgery , Aorta, Thoracic , Humans , Ischemia
15.
Nucleic Acids Res ; 49(16): 9294-9309, 2021 09 20.
Article in English | MEDLINE | ID: mdl-34387694

ABSTRACT

The SNM1 nucleases which help maintain genome integrity are members of the metallo-ß-lactamase (MBL) structural superfamily. Their conserved MBL-ß-CASP-fold SNM1 core provides a molecular scaffold forming an active site which coordinates the metal ions required for catalysis. The features that determine SNM1 endo- versus exonuclease activity, and which control substrate selectivity and binding are poorly understood. We describe a structure of SNM1B/Apollo with two nucleotides bound to its active site, resembling the product state of its exonuclease reaction. The structure enables definition of key SNM1B residues that form contacts with DNA and identifies a 5' phosphate binding pocket, which we demonstrate is important in catalysis and which has a key role in determining endo- versus exonucleolytic activity across the SNM1 family. We probed the capacity of SNM1B to digest past sites of common endogenous DNA lesions and find that base modifications planar to the nucleobase can be accommodated due to the open architecture of the active site, but lesions axial to the plane of the nucleobase are not well tolerated due to constriction around the altered base. We propose that SNM1B/Apollo might employ its activity to help remove common oxidative lesions from telomeres.


Subject(s)
Endonucleases/chemistry , Exodeoxyribonucleases/chemistry , Exonucleases/chemistry , beta-Lactamases/genetics , Binding Sites/genetics , Catalysis , Catalytic Domain/genetics , DNA-Binding Proteins , Endonucleases/genetics , Exodeoxyribonucleases/genetics , Exodeoxyribonucleases/ultrastructure , Exonucleases/genetics , Humans , Metals , Phosphates/chemistry , beta-Lactamases/chemistry
16.
Nucleic Acids Res ; 49(16): 9310-9326, 2021 09 20.
Article in English | MEDLINE | ID: mdl-34387696

ABSTRACT

Artemis (SNM1C/DCLRE1C) is an endonuclease that plays a key role in development of B- and T-lymphocytes and in dsDNA break repair by non-homologous end-joining (NHEJ). Artemis is phosphorylated by DNA-PKcs and acts to open DNA hairpin intermediates generated during V(D)J and class-switch recombination. Artemis deficiency leads to congenital radiosensitive severe acquired immune deficiency (RS-SCID). Artemis belongs to a superfamily of nucleases containing metallo-ß-lactamase (MBL) and ß-CASP (CPSF-Artemis-SNM1-Pso2) domains. We present crystal structures of the catalytic domain of wildtype and variant forms of Artemis, including one causing RS-SCID Omenn syndrome. The catalytic domain of the Artemis has similar endonuclease activity to the phosphorylated full-length protein. Our structures help explain the predominantly endonucleolytic activity of Artemis, which contrasts with the predominantly exonuclease activity of the closely related SNM1A and SNM1B MBL fold nucleases. The structures reveal a second metal binding site in its ß-CASP domain unique to Artemis, which is amenable to inhibition by compounds including ebselen. By combining our structural data with that from a recently reported Artemis structure, we were able model the interaction of Artemis with DNA substrates. The structures, including one of Artemis with the cephalosporin ceftriaxone, will help enable the rational development of selective SNM1 nuclease inhibitors.


Subject(s)
Cell Cycle Proteins/ultrastructure , DNA-Binding Proteins/ultrastructure , Endonucleases/ultrastructure , Exodeoxyribonucleases/ultrastructure , Severe Combined Immunodeficiency/genetics , B-Lymphocytes/enzymology , Catalytic Domain/genetics , Cell Cycle Proteins/chemistry , Cell Cycle Proteins/genetics , Crystallography, X-Ray , DNA End-Joining Repair/genetics , DNA Repair/genetics , DNA-Binding Proteins/antagonists & inhibitors , DNA-Binding Proteins/chemistry , DNA-Binding Proteins/genetics , Endonucleases/antagonists & inhibitors , Endonucleases/chemistry , Endonucleases/genetics , Enzyme Inhibitors/chemistry , Exodeoxyribonucleases/chemistry , Exodeoxyribonucleases/genetics , Humans , Phosphorylation/genetics , Protein Folding , Severe Combined Immunodeficiency/enzymology , Severe Combined Immunodeficiency/pathology , T-Lymphocytes/enzymology
17.
NAR Cancer ; 3(1): zcaa043, 2021 Mar.
Article in English | MEDLINE | ID: mdl-34316696

ABSTRACT

Genome instability is a characteristic enabling factor for carcinogenesis. HelQ helicase is a component of human DNA maintenance systems that prevent or reverse genome instability arising during DNA replication. Here, we provide details of the molecular mechanisms that underpin HelQ function-its recruitment onto ssDNA through interaction with replication protein A (RPA), and subsequent translocation of HelQ along ssDNA. We describe for the first time a functional role for the non-catalytic N-terminal region of HelQ, by identifying and characterizing its PWI-like domain. We present evidence that this domain of HelQ mediates interaction with RPA that orchestrates loading of the helicase domains onto ssDNA. Once HelQ is loaded onto the ssDNA, ATP-Mg2+ binding in the catalytic site activates the helicase core and triggers translocation along ssDNA as a dimer. Furthermore, we identify HelQ-ssDNA interactions that are critical for the translocation mechanism. Our data are novel and detailed insights into the mechanisms of HelQ function relevant for understanding how human cells avoid genome instability provoking cancers, and also how cells can gain resistance to treatments that rely on DNA crosslinking agents.

18.
Biomed Mater ; 16(4)2021 05 24.
Article in English | MEDLINE | ID: mdl-33946056

ABSTRACT

Biomaterials constructed exclusively of sintered microspheres have great potential in tissue engineering scaffold applications, offering the ability to create shape-specific scaffolds with precise controlled release yet to be matched by traditional additive manufacturing methods. The problem is that these microsphere-based scaffolds are limited in their stiffness for applications such as bone regeneration. Our vision to solve this problem was borne from a hierarchical structure perspective, focusing on the individual unit of the structure: the microsphere itself. In a core-shell approach, we envisioned a stiff core to create a stiff microsphere unit, with a polymeric shell that would enable sintering to the other microsphere units. Therefore, the current study provided a comparison of macroscopic biomaterials built on either polymer microspheres or polymer-coated hard glass microspheres. Identical polycaprolactone (PCL) polymer solutions were used to fabricate microspheres and as a thin coating on soda lime glass microspheres (hard phase). The materials were characterized as loose particles and as scaffolds via scanning electron microscopy, thermogravimetry, differential scanning calorimetry, Raman spectroscopy, mechanical testing, and a live/dead analysis with human umbilical cord-derived Wharton's jelly cells. The elastic modulus of the scaffolds with the thinly coated hard phase was about five times higher with glass microspheres (up to about 25 MPa) than pure polymer microspheres, while retaining the structure, cell adhesion, and chemical properties of the PCL polymer. This proof-of-concept study demonstrated the ability to achieve at least a five-fold increase in macroscopic stiffness via altering the core microsphere units with a core-shell approach.


Subject(s)
Coated Materials, Biocompatible/chemistry , Polyesters/chemistry , Tissue Engineering/methods , Tissue Scaffolds/chemistry , Cell Survival/drug effects , Cells, Cultured , Coated Materials, Biocompatible/toxicity , Elastic Modulus , Humans , Mesenchymal Stem Cells/cytology , Mesenchymal Stem Cells/drug effects , Microspheres , Musculoskeletal System/cytology
19.
Nature ; 593(7859): 440-444, 2021 05.
Article in English | MEDLINE | ID: mdl-33767446

ABSTRACT

Defects in DNA repair frequently lead to neurodevelopmental and neurodegenerative diseases, underscoring the particular importance of DNA repair in long-lived post-mitotic neurons1,2. The cellular genome is subjected to a constant barrage of endogenous DNA damage, but surprisingly little is known about the identity of the lesion(s) that accumulate in neurons and whether they accrue throughout the genome or at specific loci. Here we show that post-mitotic neurons accumulate unexpectedly high levels of DNA single-strand breaks (SSBs) at specific sites within the genome. Genome-wide mapping reveals that SSBs are located within enhancers at or near CpG dinucleotides and sites of DNA demethylation. These SSBs are repaired by PARP1 and XRCC1-dependent mechanisms. Notably, deficiencies in XRCC1-dependent short-patch repair increase DNA repair synthesis at neuronal enhancers, whereas defects in long-patch repair reduce synthesis. The high levels of SSB repair in neuronal enhancers are therefore likely to be sustained by both short-patch and long-patch processes. These data provide the first evidence of site- and cell-type-specific SSB repair, revealing unexpected levels of localized and continuous DNA breakage in neurons. In addition, they suggest an explanation for the neurodegenerative phenotypes that occur in patients with defective SSB repair.


Subject(s)
DNA Breaks, Single-Stranded , DNA Repair , Enhancer Elements, Genetic/genetics , Neurons/metabolism , 5-Methylcytosine/metabolism , Cell Line , DNA/biosynthesis , DNA Replication , Humans , Male , Methylation , Poly(ADP-ribose) Polymerases/metabolism , Sequence Analysis, DNA
20.
J Med Genet ; 58(3): 185-195, 2021 03.
Article in English | MEDLINE | ID: mdl-32518175

ABSTRACT

BACKGROUND: Congenital dyserythropoietic anaemia type I (CDA-I) is a hereditary anaemia caused by biallelic mutations in the widely expressed genes CDAN1 and C15orf41. Little is understood about either protein and it is unclear in which cellular pathways they participate. METHODS: Genetic analysis of a cohort of patients with CDA-I identifies novel pathogenic variants in both known causative genes. We analyse the mutation distribution and the predicted structural positioning of amino acids affected in Codanin-1, the protein encoded by CDAN1. Using western blotting, immunoprecipitation and immunofluorescence, we determine the effect of particular mutations on both proteins and interrogate protein interaction, stability and subcellular localisation. RESULTS: We identify six novel CDAN1 mutations and one novel mutation in C15orf41 and uncover evidence of further genetic heterogeneity in CDA-I. Additionally, population genetics suggests that CDA-I is more common than currently predicted. Mutations are enriched in six clusters in Codanin-1 and tend to affect buried residues. Many missense and in-frame mutations do not destabilise the entire protein. Rather C15orf41 relies on Codanin-1 for stability and both proteins, which are enriched in the nucleolus, interact to form an obligate complex in cells. CONCLUSION: Stability and interaction data suggest that C15orf41 may be the key determinant of CDA-I and offer insight into the mechanism underlying this disease. Both proteins share a common pathway likely to be present in a wide variety of cell types; however, nucleolar enrichment may provide a clue as to the erythroid specific nature of CDA-I. The surprisingly high predicted incidence of CDA-I suggests that better ascertainment would lead to improved patient care.


Subject(s)
Anemia, Dyserythropoietic, Congenital/genetics , Genetic Predisposition to Disease , Glycoproteins/genetics , Nuclear Proteins/genetics , Transcription Factors/genetics , Anemia, Dyserythropoietic, Congenital/pathology , Female , Gene Expression Regulation/genetics , Genetic Testing , Genetics, Population , Humans , Male , Multiprotein Complexes/genetics , Mutation/genetics
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