374 results on '"Sam M Janes"'
Search Results
2. The SUMMIT Study: Utilising a written ‘Next Steps’ information booklet to prepare participants for potential lung cancer screening results and follow-up
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Amyn Bhamani, Carolyn Horst, Fanta Bojang, Samantha L Quaife, Jennifer L Dickson, Sophie Tisi, Helen Hall, Priyam Verghese, Andrew Creamer, Ruth Prendecki, John McCabe, Kylie Gyertson, Vicky Bowyer, Ethaar El-Emir, Alice Cotton, Simranjit Mehta, Claire Levermore, Anne-Marie Mullin, Jonathan Teague, Laura Farrelly, Arjun Nair, Anand Devaraj, Allan Hackshaw, and Sam M Janes
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Pulmonary and Respiratory Medicine ,Cancer Research ,Oncology - Abstract
Low-Dose Computed Tomography (LDCT) screening for lung cancer can result in several potential outcomes of varying significance. Communication methods used in Lung Cancer Screening (LCS) programmes must, therefore, ensure that participants are prepared for the range of possible results and follow-up. Here, we assess perceptions of a written preparatory information booklet provided to participants in a large LCS cohort designed to convey this information.All participants in the SUMMIT Study (NCT03934866) were provided with a results preparation information booklet, entitled 'The SUMMIT Study: Next Steps' at their baseline appointment which outlined potential results, their significance, and timelines for follow up. Results from the LDCT scan and Lung Health Check were subsequently sent by letter. Perceptions of this booklet were assessed among participants with indeterminate pulmonary findings when they attended a face-to-face appointment immediately before their three-month interval scan. Specifically, questions assessed the perceived usefulness of the booklet and the amount of information contained in it.70.1% (n = 1,412/2,014) participants remembered receiving the booklet at their appointment. Of these participants, 72.0% (n = 1,017/1,412) found it quite or very useful and 68.0% (n = 960/1,412) reported that it contained the right amount of information. Older participants, those from the least deprived socioeconomic quintile and those of Black ethnicity were less likely to report finding the booklet either quite or very useful, or that it contained the right amount of information. Participants who remembered receiving the booklet were more likely to be satisfied with the process of results communication by letter.Providing written information that prepares participants for possible LDCT results and their significance appears to be a useful resource and a helpful adjunct to a written method of results communication for large scale LCS programmes.
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- 2023
3. Uptake of invitations to a lung health check offering low-dose CT lung cancer screening among an ethnically and socioeconomically diverse population at risk of lung cancer in the UK (SUMMIT): a prospective, longitudinal cohort study
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Jennifer L Dickson, Helen Hall, Carolyn Horst, Sophie Tisi, Priyam Verghese, Anne-Marie Mullin, Jon Teague, Laura Farrelly, Vicky Bowyer, Kylie Gyertson, Fanta Bojang, Claire Levermore, Tania Anastasiadis, John McCabe, Neal Navani, Arjun Nair, Anand Devaraj, Allan Hackshaw, Samantha L Quaife, and Sam M Janes
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Public Health, Environmental and Occupational Health - Published
- 2023
4. Utilisation of primary care electronic patient records for identification and targeted invitation of individuals to a lung cancer screening programme
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Jennifer L. Dickson, Helen Hall, Carolyn Horst, Sophie Tisi, Priyam Verghese, Sarah Worboys, Andrew Perugia, James Rusius, Anne-Marie Mullin, Jonathan Teague, Laura Farrelly, Vicky Bowyer, Kylie Gyertson, Fanta Bojang, Claire Levermore, Tania Anastasiadis, John McCabe, Anand Devaraj, Arjun Nair, Neal Navani, Allan Hackshaw, Samantha L. Quaife, and Sam M. Janes
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Pulmonary and Respiratory Medicine ,Cancer Research ,Lung Neoplasms ,Primary Health Care ,Oncology ,Humans ,Electronic Health Records ,Mass Screening ,Tomography, X-Ray Computed ,Early Detection of Cancer - Abstract
Lung cancer screening (LCS) eligibility is largely determined by tobacco consumption. Primary care smoking data could guide LCS invitation and eligibility assessment. We present observational data from the SUMMIT Study, where individual self-reported smoking status was concordant with primary care records in 75.3%. However, 10.3% demonstrated inconsistencies between historic and most recent smoking status documentation. Quantified tobacco consumption was frequently missing, precluding direct LCS eligibility assessment. Primary care recorded "ever-smoker" status, encompassing both recent and historic documentation, can be used to target LCS invitation. Identifying those with missing or erroneous "never-smoker" smoking status is crucial for equitable invitation to LCS.
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- 2022
5. Synthetic data for privacy-preserving clinical risk prediction
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Zhaozhi Qian, Thomas Callender, Bogdan Cebere, Sam M Janes, Neal Navani, and Mihaela van der Schaar
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Synthetic data promise privacy-preserving data sharing for healthcare research and development. Compared with other privacy-enhancing approaches - such as federated learning - analyses performed on synthetic data can be applied downstream without modification, such that synthetic data can act in place of real data for a wide range of use cases. However, the role that synthetic data might play in all aspects of clinical model development remains unknown. In this work, we used state-of-the-art generators explicitly designed for privacy preservation to create a synthetic version of the UK Biobank before building prognostic models for lung cancer under several data release assumptions. We demonstrate that synthetic data can be effectively used throughout the modelling pipeline even without eventual access to the real data. Furthermore, we show the implications of different data release approaches on how synthetic data could be deployed within the healthcare system.
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- 2023
6. Mortality surrogates in combined pulmonary fibrosis and emphysema
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An Zhao, Eyjolfur Gudmundsson, Nesrin Mogulkoc, Coline van Moorsel, Tamera J. Corte, Chiara Romei, Robert Chapman, Tim J.M. Wallis, Emma Denneny, Tinne Goos, Recep Savas, Asia Ahmed, Christopher J. Brereton, Hendrik W. van Es, Helen Jo, Annalisa De Liperi, Mark Duncan, Katarina Pontoppidan, Laurens J. De Sadeleer, Frouke van Beek, Joseph Barnett, Gary Cross, Alex Procter, Marcel Veltkamp, Peter Hopkins, Yuben Moodley, Alessandro Taliani, Magali Taylor, Stijn Verleden, Laura Tavanti, Marie Vermant, Arjun Nair, Iain Stewart, Sam M. Janes, Alexandra L. Young, David Barber, Daniel C. Alexander, Joanna C. Porter, Athol U. Wells, Mark G. Jones, Wim A. Wuyts, and Joseph Jacob
- Abstract
BackgroundIdiopathic pulmonary fibrosis (IPF) with co-existent emphysema, termed combined pulmonary fibrosis and emphysema (CPFE) may be associated with reduced FVC decline compared to non-CPFE IPF patients. We examined associations between mortality and functional measures of disease progression in two IPF cohorts.MethodsVisual emphysema extent (CPFE:non-CPFE: derivation cohort=317:183; replication cohort=358:152), scored on computed tomography imaging subgrouped CPFE patients using either a) 10%, or b) 15% visual emphysema threshold, or c) an unsupervised machine learning model considering emphysema and ILD extents. Baseline characteristics, 1-year forced vital capacity (FVC) and diffusion capacity for carbon monoxide (DLco) decline (linear mixed effects models), and their associations with mortality (multivariable Cox regression models) were compared across CPFE and non-CPFE subgroups.ResultsIn both IPF cohorts, CPFE patients with >10% emphysema had a greater smoking history and lower baseline DLco compared to CPFE patients with 10% emphysema, 1-year DLco decline was a better indicator of mortality than 1-year FVC decline. Results were maintained in patients suitable for therapeutic IPF trials.Results were replicated in the >15% emphysema population and using unsupervised machine learning. Importantly, the unsupervised machine learning approach identified CPFE patients in whom FVC decline did not associate strongly with mortality. In non-CPFE IPF patients, 1-year FVC declines >5% and >10% showed comparable mortality associations.ConclusionWhen assessing disease progression in IPF, DLco decline should be considered in patients with >10% emphysema and a >5% 1-year FVC decline threshold considered in non-CPFE IPF patients.
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- 2023
7. Human SARS-CoV-2 challenge resolves local and systemic response dynamics
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Rik G.H. Lindeboom, Kaylee B. Worlock, Lisa M. Dratva, Masahiro Yoshida, David Scobie, Helen R. Wagstaffe, Laura Richardson, Anna Wilbrey-Clark, Josephine L. Barnes, Krzysztof Polanski, Jessica Allen-Hyttinen, Puja Mehta, Dinithi Sumanaweera, Jacqueline Boccacino, Waradon Sungnak, Ni Huang, Lira Mamanova, Rakesh Kapuge, Liam Bolt, Elena Prigmore, Ben Killingley, Mariya Kalinova, Maria Mayer, Alison Boyers, Alex Mann, Vitor Teixeira, Sam M. Janes, Rachel C. Chambers, Muzlifah Haniffa, Andrew Catchpole, Robert Heyderman, Mahdad Noursadeghi, Benny Chain, Andreas Mayer, Kerstin B. Meyer, Christopher Chiu, Marko Z. Nikolić, and Sarah A. Teichmann
- Abstract
The COVID-19 pandemic is an ongoing global health threat, yet our understanding of the cellular disease dynamics remains limited. In our unique COVID-19 human challenge study we used single cell genomics of nasopharyngeal swabs and blood to temporally resolve abortive, transient and sustained infections in 16 seronegative individuals challenged with preAlpha-SARS-CoV-2. Our analyses revealed rapid changes in cell type proportions and dozens of highly dynamic cellular response states in epithelial and immune cells associated with specific timepoints or infection status. We observed that the interferon response in blood precedes the nasopharynx, and that nasopharyngeal immune infiltration occurred early in transient but later in sustained infection, and thus correlated with preventing sustained infection. Ciliated cells showed an acute response phase, upregulated MHC class II while infected, and were most permissive for viral replication, whilst nasal T cells and macrophages were infected non-productively. We resolve 54 T cell states, including acutely activated T cells that clonally expanded while carrying convergent SARS-CoV-2 motifs. Our novel computational pipeline (Cell2TCR) identifies activated antigen-responding clonotype groups and motifs in any dataset. Together, we show that our detailed time series data (covid19cellatlas.org) can serve as a “Rosetta stone” for the epithelial and immune cell responses, and reveals early dynamic responses associated with protection from infection.
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- 2023
8. Supplementary Figure 1 from Induction of APOBEC3 Exacerbates DNA Replication Stress and Chromosomal Instability in Early Breast and Lung Cancer Evolution
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Charles Swanton, Nnennaya Kanu, Jiri Bartek, Samuel F. Bakhoum, Jirina Bartkova, Sam M. Janes, Reuben S. Harris, Nicholas McGranahan, Mariam Jamal-Hanjani, Vassilis G. Gorgoulis, Robert E. Hynds, Eric Santoni-Rugiu, Apolinar Maya-Mendoza, Robertus A.M. de Bruin, Tim R. Fenton, Cosetta Bertoli, Simon J. Boulton, Michael Howell, Mary Y. Wu, Teresa Marafioti, Ayse U. Akarca, William L. Brown, Brittany B. Campbell, Ersilia Nigro, Adam Pennycuick, Eva Grönroos, Sebastijan Hobor, Maise Al Bakir, Lykourgos-Panagiotis Zalmas, Bryan Ngo, Haiquan Chen, Yue Zhao, Vitor H. Teixeira, Andrew Rowan, Thomas B.K. Watkins, Emilia L. Lim, Roberto Bellelli, Konstantinos Evangelou, Panagiotis Galanos, Michelle Dietzen, Wei-Ting Lu, Deborah R. Caswell, Haoran Zhai, Clare Puttick, Mihaela Angelova, and Subramanian Venkatesan
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Assessing APOBEC3 gene expression using immunohistochemical and bioinformatic approaches.
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- 2023
9. Table S3 from Immune Surveillance in Clinical Regression of Preinvasive Squamous Cell Lung Cancer
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Sam M. Janes, Nicholas McGranahan, Sergio A. Quezada, Yinyin Yuan, Teresa Marafioti, Peter J. Campbell, Christina Thirlwell, Charles Swanton, Jeremy George, Ricky M. Thakrar, Lisa M. Coussens, Courtney Betts, William Larson, Marie-Liesse Asselin-Labat, Claire Marceaux, Bernadette Carroll, Andrew J. Furness, Pascal F. Durrenberger, Sophia Antoniou, David A. Moore, Mary Falzon, Celine Denais, Yeman B. Hagos, Fraser R. Millar, Jake Y. Henry, Kate H.C. Gowers, Robert E. Hynds, Henry Lee-Six, Christodoulos P. Pipinikas, Deepak P. Chandrasekharan, Lukas Kalinke, Rachel Rosenthal, Ayse U. Akarca, Tom Lund, Shan E. Ahmed Raza, Khalid AbdulJabbar, Vitor H. Teixeira, and Adam Pennycuick
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Immune cell deconvolution from molecular data. Relative proportions of immune cell subtypes are predicted from gene expression data using the Danaher method, and from methylation data using methylCIBERSORT. Differences between progressive and regressive groups are reported here.
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- 2023
10. Table S1 from BRCA1/MAD2L1 Deficiency Disrupts the Spindle Assembly Checkpoint to Confer Vinorelbine Resistance in Mesothelioma
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Dean A. Fennell, Andrew M. Fry, Paul Baas, Sam M. Janes, Aaron S. Mansfield, Michael Sheaff, Apostolos Nakas, Naomi Guppy, Laurel M. Schunselaar, Neelam Kumar, Aimee Parsons, Joanna Dzialo, Alan G. Dawson, Annabel J. Sharkey, Anita Singh, Laura O'Regan, and Sara Busacca
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Western blots quantification
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- 2023
11. Table S2 from Immune Surveillance in Clinical Regression of Preinvasive Squamous Cell Lung Cancer
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Sam M. Janes, Nicholas McGranahan, Sergio A. Quezada, Yinyin Yuan, Teresa Marafioti, Peter J. Campbell, Christina Thirlwell, Charles Swanton, Jeremy George, Ricky M. Thakrar, Lisa M. Coussens, Courtney Betts, William Larson, Marie-Liesse Asselin-Labat, Claire Marceaux, Bernadette Carroll, Andrew J. Furness, Pascal F. Durrenberger, Sophia Antoniou, David A. Moore, Mary Falzon, Celine Denais, Yeman B. Hagos, Fraser R. Millar, Jake Y. Henry, Kate H.C. Gowers, Robert E. Hynds, Henry Lee-Six, Christodoulos P. Pipinikas, Deepak P. Chandrasekharan, Lukas Kalinke, Rachel Rosenthal, Ayse U. Akarca, Tom Lund, Shan E. Ahmed Raza, Khalid AbdulJabbar, Vitor H. Teixeira, and Adam Pennycuick
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Markers used to define cell types in quantitative multiplex immunohistochemistry experiments.
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- 2023
12. Figure S2 from BRCA1/MAD2L1 Deficiency Disrupts the Spindle Assembly Checkpoint to Confer Vinorelbine Resistance in Mesothelioma
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Dean A. Fennell, Andrew M. Fry, Paul Baas, Sam M. Janes, Aaron S. Mansfield, Michael Sheaff, Apostolos Nakas, Naomi Guppy, Laurel M. Schunselaar, Neelam Kumar, Aimee Parsons, Joanna Dzialo, Alan G. Dawson, Annabel J. Sharkey, Anita Singh, Laura O'Regan, and Sara Busacca
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Silencing of BRCA1 and MAD2L1 leads to resistance to docetaxel. A) 24 hours following transfection, cells were treated with docetaxel 20 nM for a further 24 hours and caspase 3 activity measured. Data were normalised to untreated siNT control. MSTO-211H: siNT NT vs siNT DOCE p=0.0003; siBRCA1 NT vs siBRCA1 DOCE p=0.0206; siNT DOCE vs siBRCA1 DOCE p=0.0013. REN: siNT NT vs siNT DOCE p
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- 2023
13. Figure S5 from BRCA1/MAD2L1 Deficiency Disrupts the Spindle Assembly Checkpoint to Confer Vinorelbine Resistance in Mesothelioma
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Dean A. Fennell, Andrew M. Fry, Paul Baas, Sam M. Janes, Aaron S. Mansfield, Michael Sheaff, Apostolos Nakas, Naomi Guppy, Laurel M. Schunselaar, Neelam Kumar, Aimee Parsons, Joanna Dzialo, Alan G. Dawson, Annabel J. Sharkey, Anita Singh, Laura O'Regan, and Sara Busacca
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Prognostic effect of MAD2L1 in second line cohort. Kaplan Meier curve for overall survival (OS) in patients treated with vinorelbine second line (n=3) stratified according to MAD2L1 expression
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- 2023
14. Supplementary Figure 2 from Induction of APOBEC3 Exacerbates DNA Replication Stress and Chromosomal Instability in Early Breast and Lung Cancer Evolution
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Charles Swanton, Nnennaya Kanu, Jiri Bartek, Samuel F. Bakhoum, Jirina Bartkova, Sam M. Janes, Reuben S. Harris, Nicholas McGranahan, Mariam Jamal-Hanjani, Vassilis G. Gorgoulis, Robert E. Hynds, Eric Santoni-Rugiu, Apolinar Maya-Mendoza, Robertus A.M. de Bruin, Tim R. Fenton, Cosetta Bertoli, Simon J. Boulton, Michael Howell, Mary Y. Wu, Teresa Marafioti, Ayse U. Akarca, William L. Brown, Brittany B. Campbell, Ersilia Nigro, Adam Pennycuick, Eva Grönroos, Sebastijan Hobor, Maise Al Bakir, Lykourgos-Panagiotis Zalmas, Bryan Ngo, Haiquan Chen, Yue Zhao, Vitor H. Teixeira, Andrew Rowan, Thomas B.K. Watkins, Emilia L. Lim, Roberto Bellelli, Konstantinos Evangelou, Panagiotis Galanos, Michelle Dietzen, Wei-Ting Lu, Deborah R. Caswell, Haoran Zhai, Clare Puttick, Mihaela Angelova, and Subramanian Venkatesan
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APOBEC3 gene expression during senescence and cell cycle progression.
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- 2023
15. Table S1 from Immune Surveillance in Clinical Regression of Preinvasive Squamous Cell Lung Cancer
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Sam M. Janes, Nicholas McGranahan, Sergio A. Quezada, Yinyin Yuan, Teresa Marafioti, Peter J. Campbell, Christina Thirlwell, Charles Swanton, Jeremy George, Ricky M. Thakrar, Lisa M. Coussens, Courtney Betts, William Larson, Marie-Liesse Asselin-Labat, Claire Marceaux, Bernadette Carroll, Andrew J. Furness, Pascal F. Durrenberger, Sophia Antoniou, David A. Moore, Mary Falzon, Celine Denais, Yeman B. Hagos, Fraser R. Millar, Jake Y. Henry, Kate H.C. Gowers, Robert E. Hynds, Henry Lee-Six, Christodoulos P. Pipinikas, Deepak P. Chandrasekharan, Lukas Kalinke, Rachel Rosenthal, Ayse U. Akarca, Tom Lund, Shan E. Ahmed Raza, Khalid AbdulJabbar, Vitor H. Teixeira, and Adam Pennycuick
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Details of molecular investigations performed on each sample. Clinical and outcome data is also presented. In all cases with a previous history of lung cancer, this was of squamous histology.
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- 2023
16. Table S3 from BRCA1/MAD2L1 Deficiency Disrupts the Spindle Assembly Checkpoint to Confer Vinorelbine Resistance in Mesothelioma
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Dean A. Fennell, Andrew M. Fry, Paul Baas, Sam M. Janes, Aaron S. Mansfield, Michael Sheaff, Apostolos Nakas, Naomi Guppy, Laurel M. Schunselaar, Neelam Kumar, Aimee Parsons, Joanna Dzialo, Alan G. Dawson, Annabel J. Sharkey, Anita Singh, Laura O'Regan, and Sara Busacca
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Patient characteristics
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- 2023
17. Figure S7 from BRCA1/MAD2L1 Deficiency Disrupts the Spindle Assembly Checkpoint to Confer Vinorelbine Resistance in Mesothelioma
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Dean A. Fennell, Andrew M. Fry, Paul Baas, Sam M. Janes, Aaron S. Mansfield, Michael Sheaff, Apostolos Nakas, Naomi Guppy, Laurel M. Schunselaar, Neelam Kumar, Aimee Parsons, Joanna Dzialo, Alan G. Dawson, Annabel J. Sharkey, Anita Singh, Laura O'Regan, and Sara Busacca
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Western blot images for replicates. Replicate images for figure 1, figure 2 and figure 3.
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- 2023
18. Figure S4 from BRCA1/MAD2L1 Deficiency Disrupts the Spindle Assembly Checkpoint to Confer Vinorelbine Resistance in Mesothelioma
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Dean A. Fennell, Andrew M. Fry, Paul Baas, Sam M. Janes, Aaron S. Mansfield, Michael Sheaff, Apostolos Nakas, Naomi Guppy, Laurel M. Schunselaar, Neelam Kumar, Aimee Parsons, Joanna Dzialo, Alan G. Dawson, Annabel J. Sharkey, Anita Singh, Laura O'Regan, and Sara Busacca
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Prognostic effect of BRCA1 and MAD2L1. Kaplan Meier curve for overall survival (OS) in patients (n=48) showing survival in patients who were negative for both BRCA1 and MAD2L1 compared to patients positive for either BRCA1 or MAD2L1 and in patients negative for both BRCA1 and MAD2L1 vs patients positive for both BRCA1 and MAD2L1 vs patients negative for either BRCA1 or MAD2L1
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- 2023
19. Figure S1 from BRCA1/MAD2L1 Deficiency Disrupts the Spindle Assembly Checkpoint to Confer Vinorelbine Resistance in Mesothelioma
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Dean A. Fennell, Andrew M. Fry, Paul Baas, Sam M. Janes, Aaron S. Mansfield, Michael Sheaff, Apostolos Nakas, Naomi Guppy, Laurel M. Schunselaar, Neelam Kumar, Aimee Parsons, Joanna Dzialo, Alan G. Dawson, Annabel J. Sharkey, Anita Singh, Laura O'Regan, and Sara Busacca
- Abstract
BRCA2 is not required for vinorelbine-induced cell death MSTO and REN cells were transfected with siNT and siBRCA2. 24 hours following transfection, cells were treated with vinorelbine 100 nM for a further 48 hours and caspase 3 activity measured. Data were normalised to untreated siNT control. Western blots show downregulation of BRCA2 after silencing. MSTO-211H: siNT NT vs siNT VNB p
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- 2023
20. Supplementary Data from Immune Surveillance in Clinical Regression of Preinvasive Squamous Cell Lung Cancer
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Sam M. Janes, Nicholas McGranahan, Sergio A. Quezada, Yinyin Yuan, Teresa Marafioti, Peter J. Campbell, Christina Thirlwell, Charles Swanton, Jeremy George, Ricky M. Thakrar, Lisa M. Coussens, Courtney Betts, William Larson, Marie-Liesse Asselin-Labat, Claire Marceaux, Bernadette Carroll, Andrew J. Furness, Pascal F. Durrenberger, Sophia Antoniou, David A. Moore, Mary Falzon, Celine Denais, Yeman B. Hagos, Fraser R. Millar, Jake Y. Henry, Kate H.C. Gowers, Robert E. Hynds, Henry Lee-Six, Christodoulos P. Pipinikas, Deepak P. Chandrasekharan, Lukas Kalinke, Rachel Rosenthal, Ayse U. Akarca, Tom Lund, Shan E. Ahmed Raza, Khalid AbdulJabbar, Vitor H. Teixeira, and Adam Pennycuick
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Supplementary Methods
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- 2023
21. Table S2 from BRCA1/MAD2L1 Deficiency Disrupts the Spindle Assembly Checkpoint to Confer Vinorelbine Resistance in Mesothelioma
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Dean A. Fennell, Andrew M. Fry, Paul Baas, Sam M. Janes, Aaron S. Mansfield, Michael Sheaff, Apostolos Nakas, Naomi Guppy, Laurel M. Schunselaar, Neelam Kumar, Aimee Parsons, Joanna Dzialo, Alan G. Dawson, Annabel J. Sharkey, Anita Singh, Laura O'Regan, and Sara Busacca
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Patient characteristics (explants cohort, n=20)
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- 2023
22. Table S4 from Immune Surveillance in Clinical Regression of Preinvasive Squamous Cell Lung Cancer
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Sam M. Janes, Nicholas McGranahan, Sergio A. Quezada, Yinyin Yuan, Teresa Marafioti, Peter J. Campbell, Christina Thirlwell, Charles Swanton, Jeremy George, Ricky M. Thakrar, Lisa M. Coussens, Courtney Betts, William Larson, Marie-Liesse Asselin-Labat, Claire Marceaux, Bernadette Carroll, Andrew J. Furness, Pascal F. Durrenberger, Sophia Antoniou, David A. Moore, Mary Falzon, Celine Denais, Yeman B. Hagos, Fraser R. Millar, Jake Y. Henry, Kate H.C. Gowers, Robert E. Hynds, Henry Lee-Six, Christodoulos P. Pipinikas, Deepak P. Chandrasekharan, Lukas Kalinke, Rachel Rosenthal, Ayse U. Akarca, Tom Lund, Shan E. Ahmed Raza, Khalid AbdulJabbar, Vitor H. Teixeira, and Adam Pennycuick
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Gene lists used in this analysis.
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- 2023
23. Supplementary Tables S1-S4 from Induction of APOBEC3 Exacerbates DNA Replication Stress and Chromosomal Instability in Early Breast and Lung Cancer Evolution
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Charles Swanton, Nnennaya Kanu, Jiri Bartek, Samuel F. Bakhoum, Jirina Bartkova, Sam M. Janes, Reuben S. Harris, Nicholas McGranahan, Mariam Jamal-Hanjani, Vassilis G. Gorgoulis, Robert E. Hynds, Eric Santoni-Rugiu, Apolinar Maya-Mendoza, Robertus A.M. de Bruin, Tim R. Fenton, Cosetta Bertoli, Simon J. Boulton, Michael Howell, Mary Y. Wu, Teresa Marafioti, Ayse U. Akarca, William L. Brown, Brittany B. Campbell, Ersilia Nigro, Adam Pennycuick, Eva Grönroos, Sebastijan Hobor, Maise Al Bakir, Lykourgos-Panagiotis Zalmas, Bryan Ngo, Haiquan Chen, Yue Zhao, Vitor H. Teixeira, Andrew Rowan, Thomas B.K. Watkins, Emilia L. Lim, Roberto Bellelli, Konstantinos Evangelou, Panagiotis Galanos, Michelle Dietzen, Wei-Ting Lu, Deborah R. Caswell, Haoran Zhai, Clare Puttick, Mihaela Angelova, and Subramanian Venkatesan
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Supplementary Table 1: Overview of data resource. Supplementary Table 2: List of antibodies used for immunofluorescence. Supplementary Table 3: List of antibodies used for western blotting. Supplementary Table 4. List of primers used for PCR.
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- 2023
24. Supplementary Figure 3 from Induction of APOBEC3 Exacerbates DNA Replication Stress and Chromosomal Instability in Early Breast and Lung Cancer Evolution
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Charles Swanton, Nnennaya Kanu, Jiri Bartek, Samuel F. Bakhoum, Jirina Bartkova, Sam M. Janes, Reuben S. Harris, Nicholas McGranahan, Mariam Jamal-Hanjani, Vassilis G. Gorgoulis, Robert E. Hynds, Eric Santoni-Rugiu, Apolinar Maya-Mendoza, Robertus A.M. de Bruin, Tim R. Fenton, Cosetta Bertoli, Simon J. Boulton, Michael Howell, Mary Y. Wu, Teresa Marafioti, Ayse U. Akarca, William L. Brown, Brittany B. Campbell, Ersilia Nigro, Adam Pennycuick, Eva Grönroos, Sebastijan Hobor, Maise Al Bakir, Lykourgos-Panagiotis Zalmas, Bryan Ngo, Haiquan Chen, Yue Zhao, Vitor H. Teixeira, Andrew Rowan, Thomas B.K. Watkins, Emilia L. Lim, Roberto Bellelli, Konstantinos Evangelou, Panagiotis Galanos, Michelle Dietzen, Wei-Ting Lu, Deborah R. Caswell, Haoran Zhai, Clare Puttick, Mihaela Angelova, and Subramanian Venkatesan
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Generation and characterization of A3A and A3B knockouts in TIIP cells.
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- 2023
25. Figure S3 from BRCA1/MAD2L1 Deficiency Disrupts the Spindle Assembly Checkpoint to Confer Vinorelbine Resistance in Mesothelioma
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Dean A. Fennell, Andrew M. Fry, Paul Baas, Sam M. Janes, Aaron S. Mansfield, Michael Sheaff, Apostolos Nakas, Naomi Guppy, Laurel M. Schunselaar, Neelam Kumar, Aimee Parsons, Joanna Dzialo, Alan G. Dawson, Annabel J. Sharkey, Anita Singh, Laura O'Regan, and Sara Busacca
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ROC curves for BRCA1 and MAD2L1 for explants. The percentage of cleaved PARP was used as a measure of outcome
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- 2023
26. TRACERx Consortium Members from Induction of APOBEC3 Exacerbates DNA Replication Stress and Chromosomal Instability in Early Breast and Lung Cancer Evolution
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Charles Swanton, Nnennaya Kanu, Jiri Bartek, Samuel F. Bakhoum, Jirina Bartkova, Sam M. Janes, Reuben S. Harris, Nicholas McGranahan, Mariam Jamal-Hanjani, Vassilis G. Gorgoulis, Robert E. Hynds, Eric Santoni-Rugiu, Apolinar Maya-Mendoza, Robertus A.M. de Bruin, Tim R. Fenton, Cosetta Bertoli, Simon J. Boulton, Michael Howell, Mary Y. Wu, Teresa Marafioti, Ayse U. Akarca, William L. Brown, Brittany B. Campbell, Ersilia Nigro, Adam Pennycuick, Eva Grönroos, Sebastijan Hobor, Maise Al Bakir, Lykourgos-Panagiotis Zalmas, Bryan Ngo, Haiquan Chen, Yue Zhao, Vitor H. Teixeira, Andrew Rowan, Thomas B.K. Watkins, Emilia L. Lim, Roberto Bellelli, Konstantinos Evangelou, Panagiotis Galanos, Michelle Dietzen, Wei-Ting Lu, Deborah R. Caswell, Haoran Zhai, Clare Puttick, Mihaela Angelova, and Subramanian Venkatesan
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A complete list of investigators in the Tracking Non-Small Cell Lung Cancer Evolution through Therapy (TRACERx) Consortium
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- 2023
27. Supplementary Figure 4 from Induction of APOBEC3 Exacerbates DNA Replication Stress and Chromosomal Instability in Early Breast and Lung Cancer Evolution
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Charles Swanton, Nnennaya Kanu, Jiri Bartek, Samuel F. Bakhoum, Jirina Bartkova, Sam M. Janes, Reuben S. Harris, Nicholas McGranahan, Mariam Jamal-Hanjani, Vassilis G. Gorgoulis, Robert E. Hynds, Eric Santoni-Rugiu, Apolinar Maya-Mendoza, Robertus A.M. de Bruin, Tim R. Fenton, Cosetta Bertoli, Simon J. Boulton, Michael Howell, Mary Y. Wu, Teresa Marafioti, Ayse U. Akarca, William L. Brown, Brittany B. Campbell, Ersilia Nigro, Adam Pennycuick, Eva Grönroos, Sebastijan Hobor, Maise Al Bakir, Lykourgos-Panagiotis Zalmas, Bryan Ngo, Haiquan Chen, Yue Zhao, Vitor H. Teixeira, Andrew Rowan, Thomas B.K. Watkins, Emilia L. Lim, Roberto Bellelli, Konstantinos Evangelou, Panagiotis Galanos, Michelle Dietzen, Wei-Ting Lu, Deborah R. Caswell, Haoran Zhai, Clare Puttick, Mihaela Angelova, and Subramanian Venkatesan
- Abstract
Correlation between APOBEC3 expression and different measures of CIN.
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- 2023
28. Table S5 from Immune Surveillance in Clinical Regression of Preinvasive Squamous Cell Lung Cancer
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Sam M. Janes, Nicholas McGranahan, Sergio A. Quezada, Yinyin Yuan, Teresa Marafioti, Peter J. Campbell, Christina Thirlwell, Charles Swanton, Jeremy George, Ricky M. Thakrar, Lisa M. Coussens, Courtney Betts, William Larson, Marie-Liesse Asselin-Labat, Claire Marceaux, Bernadette Carroll, Andrew J. Furness, Pascal F. Durrenberger, Sophia Antoniou, David A. Moore, Mary Falzon, Celine Denais, Yeman B. Hagos, Fraser R. Millar, Jake Y. Henry, Kate H.C. Gowers, Robert E. Hynds, Henry Lee-Six, Christodoulos P. Pipinikas, Deepak P. Chandrasekharan, Lukas Kalinke, Rachel Rosenthal, Ayse U. Akarca, Tom Lund, Shan E. Ahmed Raza, Khalid AbdulJabbar, Vitor H. Teixeira, and Adam Pennycuick
- Abstract
Pathway analysis comparing the illumina and Affymetrix datasets as described in Supplementary Methods.
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- 2023
29. Data from Induction of APOBEC3 Exacerbates DNA Replication Stress and Chromosomal Instability in Early Breast and Lung Cancer Evolution
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Charles Swanton, Nnennaya Kanu, Jiri Bartek, Samuel F. Bakhoum, Jirina Bartkova, Sam M. Janes, Reuben S. Harris, Nicholas McGranahan, Mariam Jamal-Hanjani, Vassilis G. Gorgoulis, Robert E. Hynds, Eric Santoni-Rugiu, Apolinar Maya-Mendoza, Robertus A.M. de Bruin, Tim R. Fenton, Cosetta Bertoli, Simon J. Boulton, Michael Howell, Mary Y. Wu, Teresa Marafioti, Ayse U. Akarca, William L. Brown, Brittany B. Campbell, Ersilia Nigro, Adam Pennycuick, Eva Grönroos, Sebastijan Hobor, Maise Al Bakir, Lykourgos-Panagiotis Zalmas, Bryan Ngo, Haiquan Chen, Yue Zhao, Vitor H. Teixeira, Andrew Rowan, Thomas B.K. Watkins, Emilia L. Lim, Roberto Bellelli, Konstantinos Evangelou, Panagiotis Galanos, Michelle Dietzen, Wei-Ting Lu, Deborah R. Caswell, Haoran Zhai, Clare Puttick, Mihaela Angelova, and Subramanian Venkatesan
- Abstract
APOBEC3 enzymes are cytosine deaminases implicated in cancer. Precisely when APOBEC3 expression is induced during cancer development remains to be defined. Here we show that specific APOBEC3 genes are upregulated in breast ductal carcinoma in situ, and in preinvasive lung cancer lesions coincident with cellular proliferation. We observe evidence of APOBEC3-mediated subclonal mutagenesis propagated from TRACERx preinvasive to invasive non–small cell lung cancer (NSCLC) lesions. We find that APOBEC3B exacerbates DNA replication stress and chromosomal instability through incomplete replication of genomic DNA, manifested by accumulation of mitotic ultrafine bridges and 53BP1 nuclear bodies in the G1 phase of the cell cycle. Analysis of TRACERx NSCLC clinical samples and mouse lung cancer models revealed APOBEC3B expression driving replication stress and chromosome missegregation. We propose that APOBEC3 is functionally implicated in the onset of chromosomal instability and somatic mutational heterogeneity in preinvasive disease, providing fuel for selection early in cancer evolution.Significance:This study reveals the dynamics and drivers of APOBEC3 gene expression in preinvasive disease and the exacerbation of cellular diversity by APOBEC3B through DNA replication stress to promote chromosomal instability early in cancer evolution.This article is highlighted in the In This Issue feature, p. 2355
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- 2023
30. Data from Immune Surveillance in Clinical Regression of Preinvasive Squamous Cell Lung Cancer
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Sam M. Janes, Nicholas McGranahan, Sergio A. Quezada, Yinyin Yuan, Teresa Marafioti, Peter J. Campbell, Christina Thirlwell, Charles Swanton, Jeremy George, Ricky M. Thakrar, Lisa M. Coussens, Courtney Betts, William Larson, Marie-Liesse Asselin-Labat, Claire Marceaux, Bernadette Carroll, Andrew J. Furness, Pascal F. Durrenberger, Sophia Antoniou, David A. Moore, Mary Falzon, Celine Denais, Yeman B. Hagos, Fraser R. Millar, Jake Y. Henry, Kate H.C. Gowers, Robert E. Hynds, Henry Lee-Six, Christodoulos P. Pipinikas, Deepak P. Chandrasekharan, Lukas Kalinke, Rachel Rosenthal, Ayse U. Akarca, Tom Lund, Shan E. Ahmed Raza, Khalid AbdulJabbar, Vitor H. Teixeira, and Adam Pennycuick
- Abstract
Before squamous cell lung cancer develops, precancerous lesions can be found in the airways. From longitudinal monitoring, we know that only half of such lesions become cancer, whereas a third spontaneously regress. Although recent studies have described the presence of an active immune response in high-grade lesions, the mechanisms underpinning clinical regression of precancerous lesions remain unknown. Here, we show that host immune surveillance is strongly implicated in lesion regression. Using bronchoscopic biopsies from human subjects, we find that regressive carcinoma in situ lesions harbor more infiltrating immune cells than those that progress to cancer. Moreover, molecular profiling of these lesions identifies potential immune escape mechanisms specifically in those that progress to cancer: antigen presentation is impaired by genomic and epigenetic changes, CCL27–CCR10 signaling is upregulated, and the immunomodulator TNFSF9 is downregulated. Changes appear intrinsic to the carcinoma in situ lesions, as the adjacent stroma of progressive and regressive lesions are transcriptomically similar.Significance:Immune evasion is a hallmark of cancer. For the first time, this study identifies mechanisms by which precancerous lesions evade immune detection during the earliest stages of carcinogenesis and forms a basis for new therapeutic strategies that treat or prevent early-stage lung cancer.See related commentary by Krysan et al., p. 1442.This article is highlighted in the In This Issue feature, p. 1426
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- 2023
31. Figure S6 from BRCA1/MAD2L1 Deficiency Disrupts the Spindle Assembly Checkpoint to Confer Vinorelbine Resistance in Mesothelioma
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Dean A. Fennell, Andrew M. Fry, Paul Baas, Sam M. Janes, Aaron S. Mansfield, Michael Sheaff, Apostolos Nakas, Naomi Guppy, Laurel M. Schunselaar, Neelam Kumar, Aimee Parsons, Joanna Dzialo, Alan G. Dawson, Annabel J. Sharkey, Anita Singh, Laura O'Regan, and Sara Busacca
- Abstract
Cyclin B expression is not altered after silencing of BRCA1 or treatment with vinorelbine. Western blots showing expression of cyclin B in MSTO-211H and REN cells 24 hours after silencing, and treatment of parental and resistant cells with vinorelbine 50nM (REN/RVR) or 100 nM (MSTO-211H/MVR) for 48 hours.
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- 2023
32. Supplementary Data from Tumor Heterogeneity and Permeability as Measured on the CT Component of PET/CT Predict Survival in Patients with Non–Small Cell Lung Cancer
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Ashley M. Groves, Peter J. Ell, Irfan Kayani, Simon Wan, Robert I. Shortman, Marie Meagher, Raymondo Endozo, Manu Shastry, Balaji Ganeshan, Sam M. Janes, Kenneth A. Miles, and Thida Win
- Abstract
Supplementary Data from Tumor Heterogeneity and Permeability as Measured on the CT Component of PET/CT Predict Survival in Patients with Non–Small Cell Lung Cancer
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- 2023
33. Automated airway quantification associates with mortality in idiopathic pulmonary fibrosis
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Wing Keung Cheung, Ashkan Pakzad, Nesrin Mogulkoc, Sarah Needleman, Bojidar Rangelov, Eyjolfur Gudmundsson, An Zhao, Mariam Abbas, Davina McLaverty, Dimitrios Asimakopoulos, Robert Chapman, Recep Savas, Sam M Janes, Yipeng Hu, Daniel C. Alexander, John R Hurst, and Joseph Jacob
- Abstract
ObjectivesThe study was to examine whether the airway metrics associate with mortality in IPF patients.MethodsWe performed an observational cohort study (n=90) of IPF patients identified from Ege University Hospital. An airway analysis tool AirQuant calculated median airway segmental intertapering and segmental tortuosity across 2ndto 6thgenerations of IPF airways. Intertapering measures the difference in median diameter between adjacent airway segments. Tortuosity evaluates the ratio of measured segmental length against direct end- to-end segmental length. Univariable linear regression analyses examined relationships between AirQuant variables, clinical variables and lung function tests. Univariable and Multivariable Cox proportional hazards models estimated mortality risk with the latter adjusted for patient age, gender, smoking status, antifibrotic use, CT usual interstitial pneumonia (UIP) pattern and either forced vital capacity (FVC) or diffusion capacity of carbon monoxide (DLco) if obtained within 3 months of the CT.ResultsNo significant collinearity existed between AirQuant variables and clinical or functional variables. On univariable Cox regression analyses, male gender, smoking history, no antifibrotic use, reduced DLco, reduced segmental intertapering and increased segmental tortuosity associated with increased risk of death. On multivariable Cox regression analyses (adjusted using FVC), segmental intertapering (Hazard Ratio (HR)=0.75, 95% CI=0.66-0.85, pConclusionsAirQuant generated measures of segmental intertapering and tortuosity independently associate with mortality in IPF patients. Abnormalities in proximal airway generations, which are not typically considered to be abnormal in IPF, have prognostic value.Key PointsAirQuant generates measures of segmental intertapering and tortuosity.Automated airway quantification associates with mortality in IPF independent of established measures of disease severity.Automated airway analysis could be used to refine patient selection for therapeutic trials in IPF.
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- 2023
34. Supplementary Table 1 from Tumor Heterogeneity and Permeability as Measured on the CT Component of PET/CT Predict Survival in Patients with Non–Small Cell Lung Cancer
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Ashley M. Groves, Peter J. Ell, Irfan Kayani, Simon Wan, Robert I. Shortman, Marie Meagher, Raymondo Endozo, Manu Shastry, Balaji Ganeshan, Sam M. Janes, Kenneth A. Miles, and Thida Win
- Abstract
Supplementary Table 1 - PDF file 38K, Data to supplement Kaplan Meier curve in Supplementary Figure2
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- 2023
35. Supplementary Figure 1 from Tumor Heterogeneity and Permeability as Measured on the CT Component of PET/CT Predict Survival in Patients with Non–Small Cell Lung Cancer
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Ashley M. Groves, Peter J. Ell, Irfan Kayani, Simon Wan, Robert I. Shortman, Marie Meagher, Raymondo Endozo, Manu Shastry, Balaji Ganeshan, Sam M. Janes, Kenneth A. Miles, and Thida Win
- Abstract
Supplementary Figure 1 - PDF file 49K, The 2-D forms of the LoG filter in the spatial and frequency domain at filter value of 2.0
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- 2023
36. Appendix from Tumor Heterogeneity and Permeability as Measured on the CT Component of PET/CT Predict Survival in Patients with Non–Small Cell Lung Cancer
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Ashley M. Groves, Peter J. Ell, Irfan Kayani, Simon Wan, Robert I. Shortman, Marie Meagher, Raymondo Endozo, Manu Shastry, Balaji Ganeshan, Sam M. Janes, Kenneth A. Miles, and Thida Win
- Abstract
Appendix - PDF file 148K, This section contains technical and statistical information regarding textural analysis, as well as supplementary survival analysis
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- 2023
37. Data from Tumor Heterogeneity and Permeability as Measured on the CT Component of PET/CT Predict Survival in Patients with Non–Small Cell Lung Cancer
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Ashley M. Groves, Peter J. Ell, Irfan Kayani, Simon Wan, Robert I. Shortman, Marie Meagher, Raymondo Endozo, Manu Shastry, Balaji Ganeshan, Sam M. Janes, Kenneth A. Miles, and Thida Win
- Abstract
Purpose: We prospectively examined the role of tumor textural heterogeneity on positron emission tomography/computed tomography (PET/CT) in predicting survival compared with other clinical and imaging parameters in patients with non–small cell lung cancer (NSCLC).Experimental Design: The feasibility study consisted of 56 assessed consecutive patients with NSCLC (32 males, 24 females; mean age 67 ± 9.7 years) who underwent combined fluorodeoxyglucose (FDG) PET/CT. The validation study population consisted of 66 prospectively recruited consecutive consenting patients with NSCLC (37 males, 29 females; mean age, 67.5 ± 7.8 years) who successfully underwent combined FDG PET/CT-dynamic contrast-enhanced (DCE) CT. Images were used to derive tumoral PET/CT textural heterogeneity, DCE CT permeability, and FDG uptake (SUVmax). The mean follow-up periods were 22.6 ± 13.3 months and 28.5± 13.2 months for the feasibility and validation studies, respectively. Optimum threshold was determined for clinical stage and each of the above biomarkers (where available) from the feasibility study population. Kaplan–Meier analysis was used to assess the ability of the biomarkers to predict survival in the validation study. Cox regression determined survival factor independence.Results: Univariate analysis revealed that tumor CT-derived heterogeneity (P < 0.001), PET-derived heterogeneity (P = 0.003), CT-derived permeability (P = 0.002), and stage (P < 0·001) were all significant survival predictors. The thresholds used in this study were derived from a previously conducted feasibility study. Tumor SUVmax did not predict survival. Using multivariable analysis, tumor CT textural heterogeneity (P = 0.021), stage (P = 0.001), and permeability (P < 0.001) were independent survival predictors. These predictors were independent of patient treatment.Conclusions: Tumor stage and CT-derived textural heterogeneity were the best predictors of survival in NSCLC. The use of CT-derived textural heterogeneity should assist the management of many patients with NSCLC. Clin Cancer Res; 19(13); 3591–9. ©2013 AACR.
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- 2023
38. Supplementary Figure 2 from Tumor Heterogeneity and Permeability as Measured on the CT Component of PET/CT Predict Survival in Patients with Non–Small Cell Lung Cancer
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Ashley M. Groves, Peter J. Ell, Irfan Kayani, Simon Wan, Robert I. Shortman, Marie Meagher, Raymondo Endozo, Manu Shastry, Balaji Ganeshan, Sam M. Janes, Kenneth A. Miles, and Thida Win
- Abstract
Supplementary Figure 2 - PDF file 34K, Kaplan Meier curve (along with number of patients at risk for each group over time) showing the proportion of patients surviving for treatment in the validation data-set
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- 2023
39. Supplementary Figure 2 from Mesenchymal Stem Cell Delivery of TRAIL Can Eliminate Metastatic Cancer
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Sam M. Janes, Derek Davies, Ayad Eddaoudi, and Michael R. Loebinger
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Supplementary Figure 2 from Mesenchymal Stem Cell Delivery of TRAIL Can Eliminate Metastatic Cancer
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- 2023
40. Supplementary Figure 1 from Mesenchymal Stem Cell Delivery of TRAIL Can Eliminate Metastatic Cancer
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Sam M. Janes, Derek Davies, Ayad Eddaoudi, and Michael R. Loebinger
- Abstract
Supplementary Figure 1 from Mesenchymal Stem Cell Delivery of TRAIL Can Eliminate Metastatic Cancer
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- 2023
41. The role of computer-assisted radiographer reporting in lung cancer screening programmes
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Helen Hall, Mamta Ruparel, Samantha L. Quaife, Jennifer L. Dickson, Carolyn Horst, Sophie Tisi, James Batty, Nicholas Woznitza, Asia Ahmed, Stephen Burke, Penny Shaw, May Jan Soo, Magali Taylor, Neal Navani, Angshu Bhowmik, David R. Baldwin, Stephen W. Duffy, Anand Devaraj, Arjun Nair, and Sam M. Janes
- Subjects
Lung Neoplasms ,Computers ,Humans ,Multiple Pulmonary Nodules ,Radiology, Nuclear Medicine and imaging ,General Medicine ,Tomography, X-Ray Computed ,Sensitivity and Specificity ,Early Detection of Cancer - Abstract
Objectives Successful lung cancer screening delivery requires sensitive, timely reporting of low-dose computed tomography (LDCT) scans, placing a demand on radiology resources. Trained non-radiologist readers and computer-assisted detection (CADe) software may offer strategies to optimise the use of radiology resources without loss of sensitivity. This report examines the accuracy of trained reporting radiographers using CADe support to report LDCT scans performed as part of the Lung Screen Uptake Trial (LSUT). Methods In this observational cohort study, two radiographers independently read all LDCT performed within LSUT and reported on the presence of clinically significant nodules and common incidental findings (IFs), including recommendations for management. Reports were compared against a ‘reference standard’ (RS) derived from nodules identified by study radiologists without CADe, plus consensus radiologist review of any additional nodules identified by the radiographers. Results A total of 716 scans were included, 158 of which had one or more clinically significant pulmonary nodules as per our RS. Radiographer sensitivity against the RS was 68–73.7%, with specificity of 92.1–92.7%. Sensitivity for detection of proven cancers diagnosed from the baseline scan was 83.3–100%. The spectrum of IFs exceeded what could reasonably be covered in radiographer training. Conclusion Our findings highlight the complexity of LDCT reporting requirements, including the limitations of CADe and the breadth of IFs. We are unable to recommend CADe-supported radiographers as a sole reader of LDCT scans, but propose potential avenues for further research including initial triage of abnormal LDCT or reporting of follow-up surveillance scans. Key Points • Successful roll-out of mass screening programmes for lung cancer depends on timely, accurate CT scan reporting, placing a demand on existing radiology resources. • This observational cohort study examines the accuracy of trained radiographers using computer-assisted detection (CADe) software to report lung cancer screening CT scans, as a potential means of supporting reporting workflows in LCS programmes. • CADe-supported radiographers were less sensitive than radiologists at identifying clinically significant pulmonary nodules, but had a low false-positive rate and good sensitivity for detection of confirmed cancers.
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- 2022
42. Hesitancy around low-dose CT screening for lung cancer
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J. Dickson, R. Prendecki, S. Tisi, Arjun Nair, Sam M. Janes, and C. Horst
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Male ,medicine.medical_specialty ,Sputum Cytology ,Lung Neoplasms ,Population ,Disease ,Humans ,Mass Screening ,Medicine ,Overdiagnosis ,Intensive care medicine ,education ,Lung cancer ,Lung ,Early Detection of Cancer ,education.field_of_study ,business.industry ,Hematology ,medicine.disease ,United States ,medicine.anatomical_structure ,Oncology ,National Lung Screening Trial ,Tomography, X-Ray Computed ,business ,Lung cancer screening - Abstract
Lung cancer is the leading cause of cancer death worldwide. The absence of symptoms in early-stage (I/II) disease, when curative treatment is possible, results in >70% of cases being diagnosed at late stage (III/IV), when treatment is rarely curative. This contributes greatly to the poor prognosis of lung cancer, which sees only 16.2% of individuals diagnosed with the disease alive at 5 years. Early detection is key to improving lung cancer survival outcomes. As a result, there has been longstanding interest in finding a reliable screening test. After little success with chest radiography and sputum cytology, in 2011 the United States National Lung Screening Trial demonstrated that annual low-dose computed tomography (LDCT) screening reduced lung cancer-specific mortality by 20%, when compared with annual chest radiography. In 2020, the NELSON study demonstrated an even greater reduction in lung cancer-specific mortality for LDCT screening at 0, 1, 3 and 5.5 years of 24% in men, when compared to no screening. Despite these impressive results, a call to arms in the 2017 European position statement on lung cancer screening (LCS) and the widespread introduction across the United States, there was, until recently, no population-based European national screening programme in place. We address the potential barriers and outstanding concerns including common screening foes, such as false-positive tests, overdiagnosis and the negative psychological impact of screening, as well as others more unique to LDCT LCS, including appropriate risk stratification of potential participants, radiation exposure and incidental findings. In doing this, we conclude that whilst the evidence generated from ongoing work can be used to refine the screening process, for those risks which remain, appropriate and acceptable mitigations are available, and none should serve as barriers to the implementation of national unified LCS programmes across Europe and beyond.
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- 2022
43. Lung viral infection modelling in a bioengineered whole-organ
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Fabio Tommasini, Thomas Benoist, Soichi Shibuya, Maximillian N.J. Woodall, Eleonora Naldi, Jessica C. Orr, Giovanni Giuseppe Giobbe, Elizabeth F. Maughan, Robert E. Hynds, Asllan Gjinovci, J. Ciaran Hutchinson, Owen J. Arthurs, Sam M. Janes, Nicola Elvassore, Claire M. Smith, Federica Michielin, Alessandro Filippo Pellegata, and Paolo De Coppi
- Abstract
Lung infections are one of the leading causes of death worldwide, and this situation has been exacerbated by the emergence of COVID-19. Pre-clinical modelling of viral infections has relied on cell cultures that lack 3D structure and the context of lung extracellular matrices. Here, we propose a bioreactor-based, whole-organ lung model of viral infection. The bioreactor takes advantage of an automated system to achieve efficient decellularization of a whole rat lung, and recellularization of the scaffold using primary human bronchial cells. Automatization allowed for the dynamic culture of airway epithelial cells in a breathing-mimicking setup that led to an even distribution of lung epithelial cells throughout the distal regions. In the sealed bioreactor system, we demonstrate proof-of-concept for viral infection with the engineered lung by infecting primary human airway epithelial cells. Moreover, to assess the possibility of drug screening in this model, we demonstrate the efficacy of the broad-spectrum antiviral Remdesivir. This whole-organ scale lung infection model represents a step towards modelling viral infection of human cells in a 3D context, providing a powerful tool to investigate the mechanisms of the early stages of pathogenic infections and the development of effective treatment strategies for respiratory diseases.
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- 2023
44. Phenotyping of lymphoproliferative tumours generated in xenografts of non-small cell lung cancer
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David R. Pearce, Ayse U. Akarca, Roel P. H. De Maeyer, Emily Kostina, Ariana Huebner, Monica Sivakumar, Takahiro Karasaki, Kavina Shah, Sam M. Janes, Nicholas McGranahan, Venkat Reddy, Arne N. Akbar, David A. Moore, Teresa Marafioti, Charles Swanton, and Robert E. Hynds
- Subjects
Chemical Biology & High Throughput ,Signalling & Oncogenes ,Human Biology & Physiology ,Cancer Research ,Ecology,Evolution & Ethology ,Oncology ,Genome Integrity & Repair ,Tumour Biology ,Genetics & Genomics ,Computational & Systems Biology - Abstract
Patient-derived xenograft (PDX) models involve the engraftment of tumour tissue in immunocompromised mice and represent an important pre-clinixtcal oncology research. A limitation of non-small cell lung cancer (NSCLC) PDX model derivation in NOD-scidIL2Rgammanull(NSG) mice is that a subset of initial engraftments are of lymphocytic, rather than tumour origin. In the lung TRACERx PDX pipeline, lymphoproliferations occurred in 17.8% of lung adenocarcinoma and 10% of lung squamous cell carcinoma transplantations, despite none of these patients having a prior or subsequent clinical history of lymphoproliferative disease. Lymphoproliferations were predominantly human CD20+ B cells and had the immunophenotype expected for post-transplantation diffuse large B cell lymphoma. All lymphoproliferations expressed Epstein-Barr-encoded RNAs (EBER). Analysis of immunoglobulin light chain gene rearrangements in three tumours where multiple tumour regions had resulted in lymphoproliferations suggested that each had independent clonal origins. Overall, these data suggest the presence of B cell clones with lymphoproliferative potential within primary NSCLC tumours that are under continuous immune surveillance. Since these cells can be expanded following transplantation into NSG mice, our data highlight the value of quality control measures to identify lymphoproliferations within xenograft pipelines and support the incorporation of strategies to minimise lymphoproliferations during the early stages of xenograft establishment pipelines. To present the histology data herein, we developed a Python-based tool for generating patient-level pathology overview figures from whole-slide image files; PATHOverview is available on GitHub (https://github.com/EpiCENTR-Lab/PATHOverview).
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- 2023
45. Delineating associations of progressive pleuroparenchymal fibroelastosis in patients with pulmonary fibrosis
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Eyjolfur Gudmundsson, An Zhao, Nesrin Mogulkoc, Frouke van Beek, Tinne Goos, Christopher J. Brereton, Marcel Veltkamp, Robert Chapman, Hendrik W. van Es, Helen Garthwaite, Bahareh Gholipour, Melissa Heightman, Arjun Nair, Katarina Pontoppidan, Recep Savas, Asia Ahmed, Marie Vermant, Omer Unat, Alex Procter, Laurens De Sadeleer, Emma Denneny, Timothy Wallis, Mark Duncan, Magali Taylor, Stijn Verleden, Sam M. Janes, Daniel C. Alexander, Athol U. Wells, Joanna Porter, Mark G. Jones, Iain Stewart, Coline H.M. van Moorsel, Wim Wuyts, and Joseph Jacob
- Subjects
Pulmonary and Respiratory Medicine ,Human medicine - Abstract
BackgroundComputer quantification of baseline computed tomography (CT) radiological pleuroparenchymal fibroelastosis (PPFE) associates with mortality in idiopathic pulmonary fibrosis (IPF). We examined mortality associations of longitudinal change in computer-quantified PPFE-like lesions in IPF and fibrotic hypersensitivity pneumonitis (FHP).MethodsTwo CT scans 6–36 months apart were retrospectively examined in one IPF (n=414) and one FHP population (n=98). Annualised change in computerised upper-zone pleural surface area comprising radiological PPFE-like lesions (Δ-PPFE) was calculated. Δ-PPFE >1.25% defined progressive PPFE above scan noise. Mixed-effects models evaluated Δ-PPFE against change in visual CT interstitial lung disease (ILD) extent and annualised forced vital capacity (FVC) decline. Multivariable models were adjusted for age, sex, smoking history, baseline emphysema presence, antifibrotic use and diffusion capacity of the lung for carbon monoxide. Mortality analyses further adjusted for baseline presence of clinically important PPFE-like lesions and ILD change.ResultsΔ-PPFE associated weakly with ILD and FVC change. 22–26% of IPF and FHP cohorts demonstrated progressive PPFE-like lesions which independently associated with mortality in the IPF cohort (hazard ratio 1.25, 95% CI 1.16–1.34, pInterpretationProgression of PPFE-like lesions independently associates with mortality in IPF and FHP but does not associate strongly with measures of fibrosis progression.
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- 2023
46. Early human lung immune cell development and its role in epithelial cell fate
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Josephine L. Barnes, Peng He, Masahiro Yoshida, Kaylee B. Worlock, Rik G.H. Lindeboom, Chenqu Suo, J. Patrick Pett, Anna Wilbrey-Clark, Emma Dann, Lira Mamanova, Laura Richardson, Amanda J. Oliver, Adam Pennycuick, Jessica Allen-Hyttinen, Iván T. Herczeg, Robert E. Hynds, Vitor H. Teixeira, Muzlifah Haniffa, Kyungtae Lim, Dawei Sun, Emma L. Rawlins, Krzysztof Polanski, Paul A. Lyons, John C. Marioni, Zewen Kelvin Tuong, Menna R. Clatworthy, James L. Reading, Sam M. Janes, Sarah A. Teichmann, Kerstin B. Meyer, and Marko Z. Nikolić
- Abstract
During human development, lungs develop their roles of gas exchange and barrier function. Recent single cell studies have focused on epithelial and mesenchymal cell types, but much less is known about the developing lung immune cells, although the airways are a major site of mucosal immunity after birth. An open question is whether tissue-resident immune cells play a role in shaping the tissue as it developsin utero. In order to address this, we profiled lung immune cells using scRNAseq, smFISH and immunohistochemistry. At the embryonic stage, we observed an early wave of innate immune cells, including ILCs, NK, myeloid cells and lineage progenitors. By the canalicular stage, we detected naive T lymphocytes high in cytotoxicity genes, and mature B lymphocytes, including B1 cells. Our analysis suggests that fetal lungs provide a niche for full B cell maturation. Given the abundance of immune cells, we investigated their possible effect on epithelial maturation and found that IL-1β drives epithelial progenitor exit from self-renewal and differentiation to basal cellsin vitro.In vivo, IL-1β-producing myeloid cells were found adjacent to epithelial tips, suggesting that immune cells may direct the developing lung epithelium.
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- 2022
47. Lung cancer symptom appraisal, help‐seeking and diagnosis – rapid systematic review of differences between patients with and without a smoking history
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Aron Syversen, Katriina L. Whitaker, Samantha L Quaife, Sam M. Janes, Sandra van Os, Mbasan Jallow, and Georgia Black
- Subjects
medicine.medical_specialty ,Lung Neoplasms ,business.industry ,Psycho-oncology ,MEDLINE ,Cancer ,Experimental and Cognitive Psychology ,Prognosis ,medicine.disease ,Help-seeking ,respiratory tract diseases ,Psychiatry and Mental health ,Oncology ,Risk Factors ,Health care ,medicine ,Humans ,Medical diagnosis ,business ,Lung cancer ,Intensive care medicine ,Qualitative research - Abstract
Background Lung cancer is the leading cause of cancer death in the world. A significant minority of lung cancer patients have never smoked (14% in the UK, and ranging from 10% to 25% worldwide). Current evidence suggests that never-smokers encounter delays during the diagnostic pathway, yet it is unclear how their experiences and reasons for delayed diagnoses differ from those of current and former smokers. This rapid review assessed literature about patient experiences in relation to symptom awareness and appraisal, help-seeking, and the lung cancer diagnostic pathway, comparing patients with and without a smoking history. Methods MEDLINE, PsychINFO and Google Scholar were searched for studies (2010-2020) that investigated experiences of the pathway to diagnosis for patients with and without a smoking history. Findings are presented using a narrative synthesis. Results Analysis of seven quantitative and three qualitative studies revealed that some delays during symptom appraisal and diagnosis are unique to never-smokers. Due to the strong link between smoking and lung cancer, and low awareness of non-smoking related lung cancer risk factors and symptoms, never-smokers do not perceive themselves to be at risk. Never-smokers are also likely to evaluate their experiences in comparison with other non-smoking related cancers, where prognosis is likely better, potentially leading to lower satisfaction with healthcare. Conclusion Never-smokers appear to have different experiences in relation to symptom appraisal and diagnosis. However, evidence in relation to help-seeking, and what is driving diagnostic delays for never-smoker patients specifically is lacking.
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- 2021
48. Analysis of the baseline performance of five UK lung cancer screening programmes
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Samantha L Quaife, Anna Sharman, Richard Booton, Sam M. Janes, David R Baldwin, Philip A.J. Crosbie, Stephen W. Duffy, Martin Ledson, Haval Balata, Emma O'Dowd, M. Ruparel, and John K. Field
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Pulmonary and Respiratory Medicine ,Cancer Research ,medicine.medical_specialty ,Lung Neoplasms ,Lung Neoplasms/diagnosis ,Population ,State Medicine ,Screening programme ,Internal medicine ,Humans ,Mass Screening ,Medicine ,Major complication ,Lung cancer ,education ,Early Detection of Cancer ,education.field_of_study ,United Kingdom/epidemiology ,business.industry ,Specific mortality ,medicine.disease ,United Kingdom ,Clinical trial ,Oncology ,False positive rate ,Tomography, X-Ray Computed ,business ,Lung cancer screening - Abstract
INTRODUCTION: Low-dose CT (LDCT) screening reduces lung cancer specific mortality. Several countries, including the UK, are evaluating the clinical impact and cost-effectiveness of LDCT screening using the latest evidence. In this paper we report baseline screening performance from five UK-based lung cancer screening programmes.METHODS: Data was collected at baseline from each screening programme. Measures of performance included prevalence of screen detected lung cancer, rate of surveillance imaging for indeterminate findings and surgical resection rates. Screening related harms were assessed by measuring false positive rates, number of invasive tests with associated complications in individuals without lung cancer and benign surgical resection rates.RESULTS: A total of 11,148 individuals had a baseline LDCT scan during the period of analysis (2011 to 2020). Overall, 84.7% (n = 9,440) of baseline LDCT scans were categorised as negative, 11.1% (n = 1,239) as indeterminate and 4.2% (n = 469) as positive. The prevalence of screen detected lung cancer was 2.2%, ranging between 1.8% and 4.4% for individual programmes. The surgical resection rate was 66% (range 46% to 83%) and post-surgical 90-day mortality for those with lung cancer 1.2% (n = 2/165). The false positive rate was 2% (n = 219/10,898) and of those with a positive result, one in two had lung cancer diagnosed (53.3%). An invasive test was required in 0.6% (n = 61/10,898) of screening attendees without lung cancer; there were no associated major complications or deaths. The benign surgical resection rate was 4.6% (n = 8/173), equating to 0.07% of the screened population.DISCUSSION: The performance of UK-based lung cancer screening programmes, delivered within or aligned to the National Health Service, compares favourably to published clinical trial data. Reported harms, including false positive and benign surgical resection rates are low. Ongoing monitoring of screening performance is vital to ensure standards are maintained and harms minimised.
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- 2021
49. Perspectives on the Treatment of Malignant Pleural Mesothelioma
- Author
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Sam M. Janes, Dean A Fennell, and Doraid Alrifai
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Oncology ,medicine.medical_specialty ,Pleural Neoplasms ,medicine.medical_treatment ,Antineoplastic Agents ,Epigenetic Repression ,medicine.disease_cause ,Asbestos ,Internal medicine ,Humans ,Medicine ,Combined Modality Therapy ,Mesothelioma ,neoplasms ,Radiotherapy ,business.industry ,Pleural mesothelioma ,Incidence (epidemiology) ,Mesothelioma, Malignant ,General Medicine ,Immunotherapy ,respiratory system ,medicine.disease ,respiratory tract diseases ,Radiation therapy ,Pleura ,business - Abstract
Mesothelioma Most mesotheliomas originate in the pleura and are due to asbestos exposure. The incidence is decreasing somewhat with asbestos remediation, but mortality remains high in part because ...
- Published
- 2021
50. Release of Notch activity coordinated by IL-1β signalling confers differentiation plasticity of airway progenitors via Fosl2 during alveolar regeneration
- Author
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Bon-Kyoung Koo, Jinwook Choi, Joo-Hyeon Lee, Jonghwan Kim, Yu Jin Jang, Kelly V. Evans, Benjamin D. Simons, Catherine Dabrowska, H. Hall, Elhadi Iich, Sam M. Janes, Simons, Benjamin [0000-0002-3875-7071], Lee, Joo [0000-0002-7364-6422], and Apollo - University of Cambridge Repository
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JAG2 ,0303 health sciences ,JAG1 ,Regeneration (biology) ,Notch signaling pathway ,Cell Biology ,Biology ,Cell biology ,03 medical and health sciences ,0302 clinical medicine ,StemCellInstitute ,Progenitor cell ,Transcription factor ,Reprogramming ,030217 neurology & neurosurgery ,Progenitor ,030304 developmental biology ,Adult stem cell - Abstract
While the acquisition of cellular plasticity in adult stem cells is essential for rapid regeneration after tissue injury, little is known about the underlying mechanisms governing this process. Our data reveal the coordination of airway progenitor differentiation plasticity by inflammatory signals during alveolar regeneration. Following damage, interleukin-1β (IL-1β) signalling-dependent modulation of Jag1 and Jag2 expression in ciliated cells results in the inhibition of Notch signalling in secretory cells, which drives the reprogramming and acquisition of differentiation plasticity. We identify the transcription factor Fosl2 (also known as Fra2) for secretory cell fate conversion to alveolar type 2 cells that retain the distinct genetic and epigenetic signatures of secretory lineages. We also reveal that human secretory cells positive for KDR (also known as FLK-1) display a conserved capacity to generate alveolar type 2 cells via Notch inhibition. Our results demonstrate the functional role of an IL-1β–Notch–Fosl2 axis in the fate decision of secretory cells during injury repair, proposing a potential therapeutic target for human lung alveolar regeneration. Using human airway organoids and mouse models, Choi et al. show that an IL-1β–Notch–Fosl2 signalling axis regulates the conversion of secretory cells into alveolar type 2 cells after injury.
- Published
- 2021
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