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1.
Chembiochem ; 25(11): e202400085, 2024 Jun 03.
Article in English | MEDLINE | ID: mdl-38574237

ABSTRACT

Over the last three decades, significant advancements have been made in the development of biosensors and bioassays that use RNA-cleaving DNAzymes (RCDs) as molecular recognition elements. While early examples of RCDs were primarily responsive to metal ions, the past decade has seen numerous RCDs reported for more clinically relevant targets such as bacteria, cancer cells, small metabolites, and protein biomarkers. Over the past 5 years several RCD-based biosensors have also been evaluated using either spiked biological matrixes or patient samples, including blood, serum, saliva, nasal mucus, sputum, urine, and faeces, which is a critical step toward regulatory approval and commercialization of such sensors. In this review, an overview of the methods used to generate RCDs and the properties of key RCDs that have been utilized for in vitro testing is first provided. Examples of RCD-based assays and sensors that have been used to test either spiked biological samples or patient samples are then presented, highlighting assay performance in different biological matrixes. A summary of current prospects and challenges for development of in vitro diagnostic tests incorporating RCDs and an overview of future directions of the field is also provided.


Subject(s)
Biosensing Techniques , DNA, Catalytic , DNA, Catalytic/metabolism , DNA, Catalytic/chemistry , Humans , RNA/metabolism , RNA/analysis , RNA Cleavage
2.
J Phys Chem B ; 128(12): 2955-2971, 2024 Mar 28.
Article in English | MEDLINE | ID: mdl-38489758

ABSTRACT

The MSCG/FM (multiscale coarse-graining via force-matching) approach is an efficient supervised machine learning method to develop microscopically informed coarse-grained (CG) models. We present a theory based on the principle of maximum entropy (PME) enveloping the existing MSCG/FM approaches. This theory views the MSCG/FM method as a special case of matching the thermodynamic forces from the extended ensemble described by the set of thermodynamic (relevant) system coordinates. This set may include CG coordinates, the stress tensor, applied external fields, and so forth, and may be characterized by nonequilibrium conditions. Following the presentation of the theory, we discuss the consistent matching of both bonded and nonbonded interactions. The proposed PME formulation is used as a starting point to extend the MSCG/FM method to the constant strain ensemble, which together with the explicit matching of the bonded forces is better suited for coarse-graining anisotropic media at a submolecular resolution. The theory is demonstrated by performing the fine coarse-graining of crystalline 1,3,5-triamino-2,4,6-trinitrobenzene (TATB), a well-known insensitive molecular energetic material, which exhibits highly anisotropic mechanical properties.

3.
BMJ Open Qual ; 13(1)2024 01 08.
Article in English | MEDLINE | ID: mdl-38191216

ABSTRACT

BACKGROUND: Chronic obstructive pulmonary disease (COPD) is the the most common disease-specific cause of adult emergency hospital admissions in Ireland. Preliminary groundwork indicated that treatment of acute exacerbations of COPD (AECOPD) in Ireland is not standardised between public hospitals. Applying Institute for Healthcare Improvement Breakthrough Series and Model for Improvement methodologies, Royal College of Physicians of Ireland designed and conducted a novel flexible and adaptive quality improvement (QI) collaborative which, using embedded evaluation, aimed to deliver QI teaching to enable teams to implement bespoke, locally applicable changes to improve and standardise acute COPD care at presentation, admission and discharge stages within their hospitals. METHODS: Eighteen teams from 19 hospitals across Ireland participated over 13 months. QI teaching was facilitated through inperson learning sessions, site visits, programme manager and coaching support. Teams submitted monthly anonymised patient data (n=10) for 22 measures of AECOPD care for ongoing QI evaluation. A mixed-methods survey was administered at the final learning session to retrospectively evaluate participants' experiences of QI learning and patient care changes. RESULTS: Participants reported that they learnt QI and improved patient care during the collaborative. Barriers included increased workload and lack of stakeholder buy-in. Statistically significant improvements (mean±SD) were seen for 'documented dyspnoea, eosinopenia, consolidation, acidaemia and atrial Fibrillation (DECAF) assessment' (7.3 (±14.4)% month(M)1 (n=15 sites); 49.6 (±37.7)% M13 (n=16 sites); p<0.001, 95% CI (14.3 to 66.7)), 'Documented diagnosis - spirometry' (42.5 (± 30.0)% M1 (n=16 sites); 69.1 (±29.9)% M13 (n=16 sites); p=0.0176, 95% CI 5.0 to 48.2) and 'inhaler technique review completed' (45.6 (± 34.1)% M1 (n=16 sites); 76.3 (±33.7)% M13 (n=16 sites); p=0.0131, 95% CI 10.0 to 65.0). 'First respiratory review' demonstrated improved standardisation. CONCLUSION: This flexible QI collaborative provided adaptive collaborative learning that facilitated participating teams to improve AECOPD patient care based on the unique context of their own hospitals. Findings indicate that involvement in the QI collaborative facilitated teams in achieving their improvements.


Subject(s)
Pulmonary Disease, Chronic Obstructive , Quality Improvement , Adult , Humans , Retrospective Studies , Learning , Pulmonary Disease, Chronic Obstructive/therapy , Hospitals
4.
BJGP Open ; 2024 Feb 20.
Article in English | MEDLINE | ID: mdl-37813473

ABSTRACT

BACKGROUND: It is estimated that each year in Ireland, approximately 29 million consultations occur in general practice with a patient satisfaction level of 90%. To date, research has been lacking on how GPs assess the quality of care. AIM: To examine how GPs assess care quality during routine practice with respect to the following pillars of quality improvement: effectiveness, safety, timeliness, equity, efficiency, sustainability, and person-centredness. DESIGN & SETTING: Qualitative study of GPs in Ireland. METHOD: In this qualitative study, semi-structured interviews were conducted with 10 GPs who were recruited via a snowball sampling strategy. Interviews were recorded, transcribed, and analysed. Quality 'assessment points' were identified and themes were synthesised to produce a theoretical framework. RESULTS: Five female and five male GPs practising in a variety of settings were interviewed. The age range was 33-68 years. In total, 122 assessment points emerged from the data and were collated into the following eight themes: the GP as a professional person factors; the patient and coproduction factors; care team factors; direct care factors; outcome factors; practice environment and organisation factors; external environment factors; and improvement approach factors. CONCLUSION: This is the first study to examine how GPs in Ireland assess care quality as a holistic construct during daily care. The qualitative approach applied yielded rich and diverse insights into the many assessment points that GPs use to inform their approach and actions as clinicians, managers, collaborators, and leaders to maximise patient care. The theory produced is likely useful and applicable for practising GPs, healthcare administration, policymakers, and funders in planning and executing changes for quality improvement.

5.
Surg Endosc ; 38(3): 1306-1315, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38110792

ABSTRACT

AIM/BACKGROUND: Intra-operative colonic perfusion assessment via indocyanine green fluorescence angiography (ICGFA) aims to address malperfusion-related anastomotic complications; however, its interpretation suffers interuser variability (IUV), especially early in ICGFA experience. This work assesses the impact of a protocol developed for both operator-based judgement and computational development on interpretation consistency, focusing on senior surgeons yet to start using ICGFA. METHODS: Experienced and junior gastrointestinal surgeons were invited to complete an ICGFA-experience questionnaire. They subsequently interpreted nine operative ICGFA videos regarding perfusion sufficiency of a surgically prepared distal colon during laparoscopic anterior resection by indicating their preferred site of proximal transection using an online annotation platform (mindstamp.com). Six ICGFA videos had been prepared with a clinical standardisation protocol controlling camera and patient positioning of which three each had monochrome near infrared (NIR) and overlay display. Three others were non-standardised controls with synchronous NIR and overlay picture-in-picture display. Differences in transection level between different cohorts were assessed for intraclass correlation coefficient (ICC) via ImageJ and IBM SPSS. RESULTS: 58 clinicians (12 ICGFA experts, 46 ICGFA inexperienced of whom 23 were either finished or within one year of finishing training and 23 were junior trainees) participated as per power calculations. 63% felt that ICGFA should be routinely deployed with 57% believing interpretative competence requires 11-50 cases. Transection level concordance was generally good (ICC = 0.869) across all videos and levels of expertise (0.833-0.915). However, poor agreement was evident with the standardised protocol videos for overlay presentation (0.208-0.345). Similarly, poor agreement was seen for the monochrome display (0.392-0.517), except for those who were trained but ICG inexperienced (0.877) although even here agreement was less than with unstandardised videos (0.943). CONCLUSION: Colorectal ICGFA acquisition and display standardisation impacts IUV with this specific protocol tending to diminish surgeon interpretation consistency. ICGFA video recording for computational development may require dedicated protocols.


Subject(s)
Colorectal Neoplasms , Colorectal Surgery , Humans , Indocyanine Green , Fluorescein Angiography , Colorectal Neoplasms/diagnostic imaging , Colorectal Neoplasms/surgery , Anastomotic Leak , Colorectal Surgery/methods , Anastomosis, Surgical/methods
6.
Angew Chem Int Ed Engl ; 62(38): e202307451, 2023 09 18.
Article in English | MEDLINE | ID: mdl-37477970

ABSTRACT

The first protein-binding allosteric RNA-cleaving DNAzyme (RCD) obtained by direct in vitro selection against eosinophil peroxidase (EPX), a validated marker for airway eosinophilia, is described. The RCD has nanomolar affinity for EPX, shows high selectivity against related peroxidases and other eosinophil proteins, and is resistant to degradation by mammalian nucleases. An optimized RCD was used to develop both fluorescence and lateral flow assays, which were evaluated using 38 minimally processed patient sputum samples (23 non-eosinophilic, 15 eosinophilic), producing a clinical sensitivity of 100 % and specificity of 96 %. This RCD-based lateral flow assay should allow for rapid evaluation of airway eosinophilia as an aid for guiding asthma therapy.


Subject(s)
DNA, Catalytic , Eosinophil Peroxidase , Eosinophilia , Sputum , Animals , Humans , DNA, Catalytic/metabolism , Eosinophil Peroxidase/metabolism , Eosinophilia/diagnosis , Eosinophils/enzymology , Sputum/chemistry , Sputum/cytology
7.
Cureus ; 15(5): e39095, 2023 May.
Article in English | MEDLINE | ID: mdl-37332422

ABSTRACT

Maffucci syndrome is an extremely rare congenital condition characterized by the development of multiple enchondromas and haemangiomas, primarily on the extremities, and an association with various tumors. Colonic and pelvic floor function has never been explored in patients with Maffucci syndrome. We report a case illustrating the challenges in managing colonic and pelvic floor dysfunction in a female patient secondary to vascular malformations as part of Maffucci syndrome.

8.
Small ; 19(41): e2303007, 2023 10.
Article in English | MEDLINE | ID: mdl-37294164

ABSTRACT

clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems are increasingly used in biosensor development. However, directly translating recognition events for non-nucleic acid targets by CRISPR into effective measurable signals represents an important ongoing challenge. Herein, it is hypothesized and confirmed that CRISPR RNAs (crRNAs) in a circular topology efficiently render Cas12a incapable of both site-specific double-stranded DNA cutting and nonspecific single-stranded DNA trans cleavage. Importantly, it is shown that nucleic acid enzymes (NAzymes) with RNA-cleaving activity can linearize the circular crRNAs, activating CRISPR-Cas12a functions. Using ligand-responsive ribozymes and DNAzymes as molecular recognition elements, it is demonstrated that target-triggered linearization of circular crRNAs offers great versatility for biosensing. This strategy is termed as "NAzyme-Activated CRISPR-Cas12a with Circular CRISPR RNA (NA3C)." Use of NA3C for clinical evaluation of urinary tract infections using an Escherichia coli-responsive RNA-cleaving DNAzyme to test 40 patient urine samples, providing a diagnostic sensitivity of 100% and specificity of 90%, is further demonstrated.


Subject(s)
Biosensing Techniques , Nucleic Acids , Humans , CRISPR-Cas Systems/genetics , RNA, Circular , DNA, Single-Stranded , RNA
9.
Chemistry ; 29(27): e202300075, 2023 May 11.
Article in English | MEDLINE | ID: mdl-36790320

ABSTRACT

A new method for the detection of genomic RNA combines RNA cleavage by the 10-23 DNAzyme and use of the cleavage fragments as primers to initiate rolling circle amplification (RCA). 230 different 10-23 DNAzyme variants were screened to identify those that target accessible RNA sites within the highly structured RNA transcripts of SARS-CoV-2. A total of 28 DNAzymes were identified with >20 % cleavage, 5 with >40 % cleavage and one with >60 % in 10 min. The cleavage fragments from these reactions were then screened for coupling to an RCA reaction, leading to the identification of several cleavage fragments that could efficiently initiate RCA. Using a newly developed quasi-exponential RCA method with a detection limit of 500 aM of RNA, 14 RT-PCR positive and 15 RT-PCR negative patient saliva samples were evaluated for SARS-CoV-2 genomic RNA, achieving a clinical sensitivity of 86 % and specificity of 100 % for detection of the virus in <2.5 h.


Subject(s)
Biosensing Techniques , COVID-19 , DNA, Catalytic , Humans , DNA, Catalytic/metabolism , RNA , SARS-CoV-2/genetics , SARS-CoV-2/metabolism , RNA Cleavage , COVID-19/diagnosis , Nucleic Acid Amplification Techniques/methods , Genomics , Biosensing Techniques/methods
10.
J Chem Phys ; 158(2): 024702, 2023 Jan 14.
Article in English | MEDLINE | ID: mdl-36641383

ABSTRACT

Predictive models for the thermal, chemical, and mechanical response of high explosives at extreme conditions are important for investigating their performance and safety. We introduce a particle-based, reactive model of 1,3,5-trinitro-1,3,5-triazinane (RDX) with molecular resolution utilizing generalized energy-conserving dissipative particle dynamics with reactions. The model is parameterized with respect to the data from atomistic molecular dynamics simulations as well as from quantum mechanical calculations, thus bridging atomic processes to the mesoscales, including microstructures and defects. It accurately captures the response of RDX under a range of thermal loading conditions compared to atomistic simulations. In addition, the Hugoniot response of the CG model in the overdriven regime reasonably matches atomistic simulations and experiments. Exploiting the model's high computational efficiency, we investigate mesoscale systems involving millions of molecules and characterize size-dependent criticality of hotspots in RDX. The combination of accuracy and computational efficiency of our reactive model provides a tool for investigation of mesoscale phenomena, such as the role of microstructures and defects in the shock-to-deflagration transition, through particle-based simulation.

11.
J Am Chem Soc ; 144(51): 23465-23473, 2022 12 28.
Article in English | MEDLINE | ID: mdl-36520671

ABSTRACT

Our previously discovered monomeric aptamer for SARS-CoV-2 (MSA52) possesses a universal affinity for COVID-19 spike protein variants but is ultimately limited by its ability to bind only one subunit of the spike protein. The symmetrical shape of the homotrimeric SARS-CoV-2 spike protein presents the opportunity to create a matching homotrimeric molecular recognition element that is perfectly complementary to its structural scaffold, causing enhanced binding affinity. Here, we describe a branched homotrimeric aptamer with three-fold rotational symmetry, named TMSA52, that not only possesses excellent binding affinity but is also capable of binding several SARS-CoV-2 spike protein variants with picomolar affinity, as well as pseudotyped lentiviruses expressing SARS-CoV-2 spike protein variants with femtomolar affinity. Using Pd-Ir nanocubes as nanozymes in an enzyme-linked aptamer binding assay (ELABA), TMSA52 was capable of sensitively detecting diverse pseudotyped lentiviruses in pooled human saliva with a limit of detection as low as 6.3 × 103 copies/mL. The ELABA was also used to test 50 SARS-CoV-2-positive and 60 SARS-CoV-2-negative patient saliva samples, providing sensitivity and specificity values of 84.0 and 98.3%, respectively, thus highlighting the potential of TMSA52 for the development of future rapid tests.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , COVID-19/diagnosis , Spike Glycoprotein, Coronavirus , Biological Assay , Oligonucleotides
12.
Sci Rep ; 12(1): 22476, 2022 12 28.
Article in English | MEDLINE | ID: mdl-36577785

ABSTRACT

Eosinophils are granulocytes that play a significant role in the pathogenesis of asthma and other airway diseases. Directing patient treatment based on the level of eosinophilia has been shown to be extremely effective in reducing exacerbations and therefore has tremendous potential as a routine clinical test. Herein, we describe the in vitro selection and optimization of DNA aptamers that bind to eosinophil peroxidase (EPX), a protein biomarker unique to eosinophils. Fifteen rounds of magnetic bead aptamer selection were performed prior to high throughput DNA sequencing. The top 10 aptamer candidates were assessed for EPX binding using a mobility shift assay. This process identified a lead aptamer candidate termed EAP1-05 with low nanomolar affinity and high specificity for EPX over other common sputum proteins. This aptamer sequence was further optimized through truncation and used to develop an easy-to-use colourimetric pull-down assay that can detect EPX over a concentration range from 1 - 100 nM in processed sputum. Forty-six clinical samples were processed using a new sputum dispersal method, appropriate for a rapid assessment assay, that avoids centrifugation and lengthy processing times. The assay showed 89% sensitivity and 96% specificity to detect eosinophilia (compared to gold standard sputum cytometry), with results being produced in under an hour. This assay could allow for an easy assessment of eosinophil activity in the airway to guide anti-inflammatory therapy for several airway diseases.


Subject(s)
Asthma , Eosinophilia , Humans , Eosinophil Peroxidase/metabolism , Sputum/metabolism , Eosinophilia/pathology , Eosinophils/metabolism , Asthma/metabolism
13.
J Chem Theory Comput ; 18(12): 7653-7670, 2022 Dec 13.
Article in English | MEDLINE | ID: mdl-36399703

ABSTRACT

We present the second part of a two-part paper series intended to address a gap in computational capability for coarse-grain particle modeling and simulation, namely, the simulation of phenomena in which diffusion via mass transfer is a contributing mechanism. In part 1, we presented a formulation of a dissipative particle dynamics method to simulate interparticle mass transfer, termed generalized energy-conserving dissipative particle dynamics with mass transfer (GenDPDE-M). In the GenDPDE-M method, the mass of each mesoparticle remains constant following the interparticle mass exchange. In part 2 of this series, further verification and demonstrations of the GenDPDE-M method are presented for mesoparticles with embedded binary mixtures using the ideal gas (IG) and van der Waals (vdW) equation-of-state (EoS). The targeted readership of part 2 is toward practitioners, where applications and practical considerations for implementing the GenDPDE-M method are presented and discussed, including a numerical discretisztion algorithm for the equations-of-motion. The GenDPDE-M method is verified by reproducing the particle distributions predicted by Monte Carlo simulations for the IG and vdW fluids, along with several demonstrations under both equilibrium and non-equilibrium conditions. GenDPDE-M can be generally applied to multi-component mixtures and to other fundamental EoS, such as the Lennard-Jones or Exponential-6 models, as well as to more advanced EoS models such as Statistical Associating Fluid Theory.

14.
Aorta (Stamford) ; 10(3): 114-121, 2022 Jun.
Article in English | MEDLINE | ID: mdl-36318932

ABSTRACT

BACKGROUND: Open surgical repair (OSR) of complex abdominal aortic aneurysms (CAAAs) can be challenging. We frequently utilize the retroperitoneal (RP) approach for such cases. We audited our outcomes with the aim of establishing the utility and safety of this approach. METHODS: Retrospective analysis was performed of all patients undergoing OSR of an unruptured CAAA via a RP approach in our center over a 7-year period. Data on repairs via a transperitoneal (TP) approach were collected to provide context. Demographic, operative, radiological, and biochemical data were collected. The primary outcome measure was 30-day/inpatient mortality. Secondary outcomes included the need for reoperation, incidence of postoperative chest infection, acute kidney injury (AKI) and length of stay (LOS). All patients received aortic clamping above at least one main renal artery. RESULTS: One hundred and three patients underwent OSR of an unruptured CAAA; 55 via a RP approach, 48 TP. The RP group demonstrated a more advanced pattern of disease with a larger median maximum diameter (65 vs. 61 mm, p= 0.013) and a more proximal extent. Consequently, the rate of supravisceral clamping was higher in RP repair (66 vs. 15%, p < 0.001). Despite this there were no differences in the observed early mortality (9.1 vs. 10%, NS); incidence of reoperation (10.9 vs. 12.5%, NS), chest infection (32.7 vs. 25%, NS), and AKI (52.7 vs. 45.8%, NS); or median LOS (10 vs. 12 days, NS) following RP and TP repair. CONCLUSION: OSR of CAAAs carries significant 30-day mortality. In patients unsuitable for fenestrated endovascular aortic repair or those desiring a durable long-term solution, OSR can be performed through the RP or TP approach. This study has demonstrated that in our unit RP repair facilitates treatment of more advanced AAA utilizing complex proximal clamp zones with similar perioperative morbidity and mortality compared with TP cases utilizing more distal clamping.

15.
Chem Soc Rev ; 51(21): 9009-9067, 2022 Oct 31.
Article in English | MEDLINE | ID: mdl-36259976

ABSTRACT

Functional nucleic acids (FNAs), including DNA aptamers and DNAzymes, are finding increasing use as molecular recognition elements for point-of-care (POC) assays and sensors. An ongoing challenge in the development of FNA-based POC sensors is the ability to achieve detection of low levels of analyte without compromising assay time and ease of use. Rolling circle amplification (RCA) is a leading nucleic acid (NA) isothermal amplification method which can be coupled with FNAs for the ultrasensitive detection of non-NA targets. Herein we examine the key considerations required when designing FNA-coupled biosensors utilizing RCA. Specifically, we describe methods for using FNAs as inputs to regulate RCA, various modes of RCA amplification, and methods to detect the output of the RCA reaction, along with how these can be combined to allow detection of non-NA targets. Recent progress on development of portable optical and electrochemical POC devices that incorporate RCA is then described, followed by a summary of key challenges and opportunities in the field.


Subject(s)
Aptamers, Nucleotide , Biosensing Techniques , DNA, Catalytic , Biosensing Techniques/methods , Nucleic Acid Amplification Techniques/methods , Aptamers, Nucleotide/chemistry
16.
J Chem Theory Comput ; 18(12): 7639-7652, 2022 Dec 13.
Article in English | MEDLINE | ID: mdl-36306139

ABSTRACT

An extension of the generalized energy-conserving dissipative particle dynamics method (GenDPDE) that allows mass transfer between mesoparticles via a diffusion process is presented. By considering the concept of the mesoparticles as property carriers, the complexity and flexibility of the GenDPDE framework were enhanced to allow for interparticle mass transfer under isoenergetic conditions, notated here as GenDPDE-M. In the formulation, diffusion is described via the theory of mesoscale irreversible processes based on linear relationships between the fluxes and thermodynamic forces, where their fluctuations are described by Langevin-like equations. The mass exchange between mesoparticles is such that the mass of the mesoparticle remains unchanged after the transfer process and requires additional considerations regarding the coupling with other system properties such as the particle internal energy. The proof-of-concept work presented in this article is the first part of a two-part article series. In Part 1, the development of the GenDPDE-M theoretical framework and the derivation of the algorithm are presented in detail. Part 2 of this article series is targeted for practitioners, where applications, demonstrations, and practical considerations for implementing the GenDPDE-M method are presented and discussed.


Subject(s)
Algorithms , Diffusion , Thermodynamics
17.
Anal Sens ; 2(5): e202200035, 2022 Sep.
Article in English | MEDLINE | ID: mdl-35936648

ABSTRACT

The cover feature image shows nucleic acid aptamers armed and ready for our battle against the monstrous SARS-CoV-2 virus. Often thought of as "chemical antibodies", these molecular recognition elements are equipped with several unique benefits and have thus been a popular research subject worldwide. Many aptamers for recognizing the spike and nucleocapsid proteins of SARS-CoV-2 have been developed and examined as diagnostic and therapeutic weaponry for the war against COVID-19 and future pandemics. More information can be found in the Review by J. D. Brennan, Y. Li, and co-workers.

18.
Leukemia ; 36(8): 2032-2041, 2022 08.
Article in English | MEDLINE | ID: mdl-35778533

ABSTRACT

Acute myeloid leukemia (AML) is driven by mutations that occur in numerous combinations. A better understanding of how mutations interact with one another to cause disease is critical to developing targeted therapies. Approximately 50% of patients that harbor a common mutation in NPM1 (NPM1cA) also have a mutation in the cohesin complex. As cohesin and Npm1 are known to regulate gene expression, we sought to determine how cohesin mutation alters the transcriptome in the context of NPM1cA. We utilized inducible Npm1cAflox/+ and core cohesin subunit Smc3flox/+ mice to examine AML development. While Npm1cA/+;Smc3Δ/+ mice developed AML with a similar latency and penetrance as Npm1cA/+ mice, RNA-seq suggests that the Npm1cA/+; Smc3Δ/+ mutational combination uniquely alters the transcriptome. We found that the Rac1/2 nucleotide exchange factor Dock1 was specifically upregulated in Npm1cA/+;Smc3Δ/+ HSPCs. Knockdown of Dock1 resulted in decreased growth and adhesion and increased apoptosis only in Npm1cA/+;Smc3Δ/+ AML. Higher Rac activity was also observed in Npm1cA/+;Smc3Δ/+ vs. Npm1cA/+ AMLs. Importantly, the Dock1/Rac pathway is targetable in Npm1cA/+;Smc3Δ/+ AMLs. Our results suggest that Dock1/Rac represents a potential target for the treatment of patients harboring NPM1cA and cohesin mutations and supports the use of combinatorial genetics to identify novel precision oncology targets.


Subject(s)
Leukemia, Myeloid, Acute , Nuclear Proteins , Animals , Cell Cycle Proteins , Chromosomal Proteins, Non-Histone , Leukemia, Myeloid, Acute/drug therapy , Leukemia, Myeloid, Acute/genetics , Mice , Mutation , Nuclear Proteins/genetics , Nuclear Proteins/metabolism , Nucleophosmin , Precision Medicine , Transcription Factors/genetics , rac GTP-Binding Proteins , Cohesins , RAC2 GTP-Binding Protein
19.
Chem Sci ; 13(22): 6496-6501, 2022 Jun 07.
Article in English | MEDLINE | ID: mdl-35756503

ABSTRACT

We report on a paper-based sensor capable of performing template-independent DNA synthesis by terminal deoxynucleotidyl transferase (TdT). Importantly, we observed that TdT efficiently incorporates fluorescently labeled dUTP on to 3'-OH ends of DNA strands in a strictly controllable manner on cellulose paper, in comparison to its distributive mode of DNA synthesis in solution. Due to the high roughness and porous nature of cellulose paper, we attribute this controllable DNA polymerization to the pore confinement effect on the catalytic behaviour of TdT. Taking advantage of this finding, we proposed a paper-assisted TdT (PAT) assay for absolute quantification of alkylated DNA lesions (N7-methylguanine), DNA deamination (cytosine-to-uracil) and DNA oxidation (8-oxo-7,8-dihydroguanine) by combining various DNA glycosylases. This PAT assay provides a low-cost, high throughput and easy to use method for quantifying the absolute levels of various types of DNA lesions, thus making it well-suited for drug development, genotoxicity testing, and environmental toxicology.

20.
BJGP Open ; 6(3)2022 Sep.
Article in English | MEDLINE | ID: mdl-35728817

ABSTRACT

BACKGROUND: Access to community rectoscopy might help to ease the burden on hospital services and reduce costs for the NHS. To assess this, a prospective multicentre observational phase I feasibility study of a novel digital rectoscope and telestration software for the triage of lower gastrointestinal (GI) symptoms was undertaken. AIM: To determine if digital rectoscopy is feasible, acceptable, and clinically safe. DESIGN & SETTING: Evaluation of clinician case reports and patient questionnaires from patients recruited from five primary care centres. METHOD: Adults meeting 2-week wait (2WW) criteria for suspected lower GI cancer, suspected new diagnosis, or flare-up of inflammatory bowel disease (IBD) were enrolled. Examinations were performed by primary care practitioners using the LumenEye rectoscope. The CHiP platform allowed immediate remote review by secondary care. A prospective analysis was performed of patient and clinician experiences, diagnostic accuracy, and cost. RESULTS: A total of 114 patients were recruited and 110 underwent the procedure (46 [42%] females and 64 [58%] males). No serious adverse events were reported. Eighty-two (74.5%) patients reported that examination was more comfortable than expected, while 104 (94.5%) felt the intervention was most convenient if delivered in the community. Clinicians were confident of their assessment in 100 (87.7%) examinations. Forty-eight (42.1%) patients subsequently underwent colonoscopy, flexible sigmoidoscopy, or computed tomography virtual colonoscopy (CTVC). The overall sensitivity and specificity of LumenEye in identifying rectal pathology was 90.0% and 88.9%. It was 100% and 100% for cancer, and 83.3% and 97.8% for polyps. Following LumenEye examination, 19 (17.3%) patients were discharged, with projected savings of 11 305 GBP. CONCLUSION: Digital rectoscopy in primary care is safe, acceptable, and can reduce referrals. A phase III randomised controlled trial is indicated to define its utility in reducing the burden on hospital diagnostic services.

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