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  • Journal article
    Chrisochoidou Y, Roy R, Farahmand P, Gonzalez G, Doig J, Krasny L, Rimmer EF, Willis AE, MacFarlane M, Huang PH, Carragher NO, Munro AF, Murphy DJ, Veselkov K, Seckl MJ, Moffatt MF, Cookson WOC, Pardo OEet al., 2023,

    Crosstalk with lung fibroblasts shapes the growth and therapeutic response of mesothelioma cells.

    , Cell Death Dis, Vol: 14

    Mesothelioma is an aggressive cancer of the mesothelial layer associated with an extensive fibrotic response. The latter is in large part mediated by cancer-associated fibroblasts which mediate tumour progression and poor prognosis. However, understanding of the crosstalk between cancer cells and fibroblasts in this disease is mostly lacking. Here, using co-cultures of patient-derived mesothelioma cell lines and lung fibroblasts, we demonstrate that fibroblast activation is a self-propagated process producing a fibrotic extracellular matrix (ECM) and triggering drug resistance in mesothelioma cells. Following characterisation of mesothelioma cells/fibroblasts signalling crosstalk, we identify several FDA-approved targeted therapies as far more potent than standard-of-care Cisplatin/Pemetrexed in ECM-embedded co-culture spheroid models. In particular, the SRC family kinase inhibitor, Saracatinib, extends overall survival well beyond standard-of-care in a mesothelioma genetically-engineered mouse model. In short, we lay the foundation for the rational design of novel therapeutic strategies targeting mesothelioma/fibroblast communication for the treatment of mesothelioma patients.

  • Journal article
    Ellis T, Blount B, 2023,

    Synthetic yeast chromosome XI design provides a testbed for the study of extrachromosomal circular DNA dynamics

    , Cell Genomics, Vol: 3, ISSN: 2666-979X

    We describe construction of the synthetic yeast chromosome XI (synXI) and reveal the effects of redesign at non-coding DNA elements. The 660-kb synthetic yeast genome project (Sc2.0) chromosome was assembled from synthesized DNA fragments before CRISPR-based methods were used in a process of bug discovery, redesign, and chromosome repair, including precise compaction of 200 kb of repeat sequence. Repaired defects were related to poor centromere function and mitochondrial health and were associated with modifications to non-coding regions. As part of the Sc2.0 design, loxPsym sequences for Cre-mediated recombination are inserted between most genes. Using the GAP1 locus from chromosome XI, we show that these sites can facilitate induced extrachromosomal circular DNA (eccDNA) formation, allowing direct study of the effects and propagation of these important molecules. Construction and characterization of synXI contributes to our understanding of non-coding DNA elements, provides a useful tool for eccDNA study, and will inform future synthetic genome design.

  • Journal article
    Hunter B, Argyros C, Inglese M, Linton-Reid K, Pulzato I, Nicholson AG, Kemp SV, L Shah P, Molyneaux PL, McNamara C, Burn T, Guilhem E, Mestas Nuñez M, Hine J, Choraria A, Ratnakumar P, Bloch S, Jordan S, Padley S, Ridge CA, Robinson G, Robbie H, Barnett J, Silva M, Desai S, Lee RW, Aboagye EO, Devaraj Aet al., 2023,

    Radiomics-based decision support tool assists radiologists in small lung nodule classification and improves lung cancer early diagnosis.

    , Br J Cancer

    BACKGROUND: Methods to improve stratification of small (≤15 mm) lung nodules are needed. We aimed to develop a radiomics model to assist lung cancer diagnosis. METHODS: Patients were retrospectively identified using health records from January 2007 to December 2018. The external test set was obtained from the national LIBRA study and a prospective Lung Cancer Screening programme. Radiomics features were extracted from multi-region CT segmentations using TexLab2.0. LASSO regression generated the 5-feature small nodule radiomics-predictive-vector (SN-RPV). K-means clustering was used to split patients into risk groups according to SN-RPV. Model performance was compared to 6 thoracic radiologists. SN-RPV and radiologist risk groups were combined to generate "Safety-Net" and "Early Diagnosis" decision-support tools. RESULTS: In total, 810 patients with 990 nodules were included. The AUC for malignancy prediction was 0.85 (95% CI: 0.82-0.87), 0.78 (95% CI: 0.70-0.85) and 0.78 (95% CI: 0.59-0.92) for the training, test and external test datasets, respectively. The test set accuracy was 73% (95% CI: 65-81%) and resulted in 66.67% improvements in potentially missed [8/12] or delayed [6/9] cancers, compared to the radiologist with performance closest to the mean of six readers. CONCLUSIONS: SN-RPV may provide net-benefit in terms of earlier cancer diagnosis.

  • Journal article
    Verdross P, Guinchard S, Woodward RT, Bismarck Aet al., 2023,

    Black liquor-based epoxy resin: Thermosets from untreated kraft lignin

    , Chemical Engineering Journal, Vol: 475, ISSN: 1385-8947

    The production of thermosetting resins from lignin is a promising route to upcycle this biomaterial, currently overwhelmingly used as fuel. Raw kraft black liquor with no prior purification or treatment was derivatised using epichlorohydrin and an aniline catalyst to yield a black liquor-based epoxy resin (BLER). BLER is a liquid resin, which can be processed using conventional moulding techniques prior to curing into black liquor-based thermosets using maleic anhydride as hardener. We report the production of liquid lignin-based thermosets containing a biocarbon content of ∼ 16%. These thermosets possess Young's moduli and tensile strengths exceeding 1 GPa and 40 MPa, respectively. The chemical composition of the starting material and BLER were characterised, and the mechanisms of cure as well as the mechanical properties of lignin-based thermosets were determined.

  • Journal article
    McNally P, Lester K, Stone G, Elnazir B, Williamson M, Cox D, Linnane B, Kirwan L, Rea D, O'Regan P, Semple T, Saunders C, Tiddens HAWM, McKone E, Davies JC, RECOVER Study Groupet al., 2023,

    Improvement in Lung Clearance Index and Chest Computed Tomography Scores with Elexacaftor/Tezacaftor/Ivacaftor Treatment in People with Cystic Fibrosis Aged 12 Years and Older - The RECOVER Trial.

    , Am J Respir Crit Care Med, Vol: 208, Pages: 917-929

    Rationale: Clinical trials have shown that use of elexacaftor/tezacaftor/ivacaftor (ETI) is associated with improvements in sweat chloride, pulmonary function, nutrition, and quality of life in people with cystic fibrosis (CF). Little is known about the impact of ETI on ventilation inhomogeneity and lung structure. Objectives: RECOVER is a real-world study designed to measure the impact of ETI in people with CF. The primary endpoints were lung clearance (lung clearance index; LCI2.5) and FEV1. Secondary endpoints included spirometry-controlled chest computed tomography (CT) scores. Methods: The study was conducted in seven sites in Ireland and the United Kingdom. Participants ages 12 years and older who were homozygous for the F508del mutation (F508del/F508del) or heterozygous for F508del and a minimum-function mutation (F508del/MF) were recruited before starting ETI and were followed up over 12 months. LCI2.5 was measured using nitrogen multiple breath washout (MBW) at baseline and at 6 and 12 months. Spirometry was performed as per the criteria of the American Thoracic Society and the European Respiratory Society. Spirometry-controlled chest CT scans were performed at baseline and at 12 months. CT scans were scored using the Perth Rotterdam Annotated Grid Morphometric Analysis (PRAGMA) system. Other outcome measures include weight, height, Cystic Fibrosis Quality of Life Questionnaire-Revised (CFQ-R), and sweat chloride. Measurements and Main Results: One hundred seventeen people with CF ages 12 and older were recruited to the study. Significant improvements were seen in LCI scores (-2.5; 95% confidence interval [CI], -3.0, -2.0) and in the percents predicted for FEV1 (8.9; 95% CI, 7.0, 10.9), FVC (6.6; 95% CI, 4.9, 8.3), and forced expiratory flow between 25% and 75% of expired volume (12.4; 95% CI, 7.8, 17.0). Overall PRAGMA-CF scores reflecting airway disease improved significantly (-3.46; 95% CI, -5.23, -1.69). Scores for trapped air, mucus plugging, an

  • Journal article
    Barnett JL, Maher TM, Quint JK, Adamson A, Wu Z, Smith DJF, Rawal B, Nair A, Walsh SLF, Desai SR, George PM, Kokosi M, Jenkins G, Kouranos V, Renzoni EA, Rice A, Nicholson AG, Chua F, Wells AU, Molyneaux PL, Devaraj Aet al., 2023,

    Combination of BAL and Computed Tomography Differentiates Progressive and Non-progressive Fibrotic Lung Diseases.

    , Am J Respir Crit Care Med, Vol: 208, Pages: 975-982

    Rationale: Identifying patients with pulmonary fibrosis (PF) at risk of progression can guide management. Objectives: To explore the utility of combining baseline BAL and computed tomography (CT) in differentiating progressive and nonprogressive PF. Methods: The derivation cohort consisted of incident cases of PF for which BAL was performed as part of a diagnostic workup. A validation cohort was prospectively recruited with identical inclusion criteria. Baseline thoracic CT scans were scored for the extent of fibrosis and usual interstitial pneumonia (UIP) pattern. The BAL lymphocyte proportion was recorded. Annualized FVC decrease of >10% or death within 1 year was used to define disease progression. Multivariable logistic regression identified the determinants of the outcome. The optimum binary thresholds (maximal Wilcoxon rank statistic) at which the extent of fibrosis on CT and the BAL lymphocyte proportion could distinguish disease progression were identified. Measurements and Main Results: BAL lymphocyte proportion, UIP pattern, and fibrosis extent were significantly and independently associated with disease progression in the derivation cohort (n = 240). Binary thresholds for increased BAL lymphocyte proportion and extensive fibrosis were identified as 25% and 20%, respectively. An increased BAL lymphocyte proportion was rare in patients with a UIP pattern (8 of 135; 5.9%) or with extensive fibrosis (7 of 144; 4.9%). In the validation cohort (n = 290), an increased BAL lymphocyte proportion was associated with a significantly lower probability of disease progression in patients with nonextensive fibrosis or a non-UIP pattern. Conclusions: BAL lymphocytosis is rare in patients with extensive fibrosis or a UIP pattern on CT. In patients without a UIP pattern or with limited fibrosis, a BAL lymphocyte proportion of ⩾25% was associated with a lower likelihood of progression.

  • Journal article
    Muratspahić E, Schöffmann J, Jiang Q, Bismarck Aet al., 2023,

    Micellar aggregation of poly(acrylamide-co-styrene): Towards ‘self-removing’ polymers from solution

    , Reactive and Functional Polymers, Vol: 192, ISSN: 1381-5148

    Polymer drag reducing agents (DRAs) are used in hydraulic fracturing processes to reduce frictional drag developed in fully turbulent pipe-flows. The drag reduction lowers energy consumption required to pump fluids. Removal and/or recovery of DRAs from the fracking fluids remains challenging causing environmental issues. We used model aqueous hydraulic fracturing fluids containing poly(acrylamide-co-styrene) P(AAm-co-St) as DRA and demonstrate an approach to ‘self-remove’/recover the P(AAm-co-St) copolymers by up to 55%. This approach involves foaming of P(AAm-co-St) solutions by sparging gas into fluid (at application relevant conditions) resulting in copolymer enrichment in a generated foam phase and subsequent removal from solution. Our observations suggest a simple method to remove or recover DRAs after drag reduction applications from fracking fluids. Liquid foams containing the P(AAm-co-St) copolymer were dried and redissolved in water offering the potential to be reused for further drag reduction applications or, in case of waste, explored for other applications as emulsifier or in macroporous materials.

  • Journal article
    Sole A, Davies JC, Quintana-Gallego E, 2023,

    Cystic Fibrosis: From Salty Malediction to Possible Cure.

    , Arch Bronconeumol
  • Journal article
    Almond M, Farne HA, Jackson MM, Jha A, Katsoulis O, Pitts O, Tunstall T, Regis E, Dunning J, Byrne AJ, Mallia P, Kon OM, Saunders KA, Simpson KD, Snelgrove RJ, Openshaw PJM, Edwards MR, Barclay WS, Heaney LM, Johnston SL, Singanayagam Aet al., 2023,

    Obesity dysregulates the pulmonary antiviral immune response.

    , Nat Commun, Vol: 14

    Obesity is a well-recognized risk factor for severe influenza infections but the mechanisms underlying susceptibility are poorly understood. Here, we identify that obese individuals have deficient pulmonary antiviral immune responses in bronchoalveolar lavage cells but not in bronchial epithelial cells or peripheral blood dendritic cells. We show that the obese human airway metabolome is perturbed with associated increases in the airway concentrations of the adipokine leptin which correlated negatively with the magnitude of ex vivo antiviral responses. Exogenous pulmonary leptin administration in mice directly impaired antiviral type I interferon responses in vivo and ex vivo in cultured airway macrophages. Obese individuals hospitalised with influenza showed dysregulated upper airway immune responses. These studies provide insight into mechanisms driving propensity to severe influenza infections in obesity and raise the potential for development of leptin manipulation or interferon administration as novel strategies for conferring protection from severe infections in obese higher risk individuals.

  • Journal article
    Southern KW, Burgel P-R, Castellani C, De Boeck K, Davies JC, Dunlevy F, Fajac I, Gramegna A, Lammertyn E, Middleton PG, Ratjen F, van Koningsbruggen-Rietschel Set al., 2023,

    Standards for the care of people with cystic fibrosis (CF).

    , J Cyst Fibros

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