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Connor K, Conroy E, White K, Shiels LP, Keek S, Ibrahim A, Gallagher WM, Sweeney KJ, Clerkin J, O'Brien D, Cryan JB, O'Halloran PJ, Heffernan J, Brett F, Lambin P, Woodruff HC, Byrne AT. A clinically relevant computed tomography (CT) radiomics strategy for intracranial rodent brain tumour monitoring. Sci Rep 2024; 14:2720. [PMID: 38302657 PMCID: PMC10834979 DOI: 10.1038/s41598-024-52960-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 01/25/2024] [Indexed: 02/03/2024] Open
Abstract
Here, we establish a CT-radiomics based method for application in invasive, orthotopic rodent brain tumour models. Twenty four NOD/SCID mice were implanted with U87R-Luc2 GBM cells and longitudinally imaged via contrast enhanced (CE-CT) imaging. Pyradiomics was employed to extract CT-radiomic features from the tumour-implanted hemisphere and non-tumour-implanted hemisphere of acquired CT-scans. Inter-correlated features were removed (Spearman correlation > 0.85) and remaining features underwent predictive analysis (recursive feature elimination or Boruta algorithm). An area under the curve of the receiver operating characteristic curve was implemented to evaluate radiomic features for their capacity to predict defined outcomes. Firstly, we identified a subset of radiomic features which distinguish the tumour-implanted hemisphere and non- tumour-implanted hemisphere (i.e, tumour presence from normal tissue). Secondly, we successfully translate preclinical CT-radiomic pipelines to GBM patient CT scans (n = 10), identifying similar trends in tumour-specific feature intensities (E.g. 'glszm Zone Entropy'), thereby suggesting a mouse-to-human species conservation (a conservation of radiomic features across species). Thirdly, comparison of features across timepoints identify features which support preclinical tumour detection earlier than is possible by visual assessment of CT scans. This work establishes robust, preclinical CT-radiomic pipelines and describes the application of CE-CT for in-depth orthotopic brain tumour monitoring. Overall we provide evidence for the role of pre-clinical 'discovery' radiomics in the neuro-oncology space.
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Affiliation(s)
- Kate Connor
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, York Street, Dublin 2, Ireland
- National Pre-Clinical Imaging Centre (NPIC), Dublin, Ireland
| | - Emer Conroy
- National Pre-Clinical Imaging Centre (NPIC), Dublin, Ireland
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Kieron White
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, York Street, Dublin 2, Ireland
- National Pre-Clinical Imaging Centre (NPIC), Dublin, Ireland
| | - Liam P Shiels
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, York Street, Dublin 2, Ireland
- National Pre-Clinical Imaging Centre (NPIC), Dublin, Ireland
| | - Simon Keek
- The D-Lab: Department of Precision Medicine, GROW - School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Abdalla Ibrahim
- The D-Lab: Department of Precision Medicine, GROW - School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - William M Gallagher
- National Pre-Clinical Imaging Centre (NPIC), Dublin, Ireland
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | | | - James Clerkin
- Department of Neurosurgery, Beaumont Hospital, Dublin, Ireland
| | - David O'Brien
- Department of Neurosurgery, Beaumont Hospital, Dublin, Ireland
| | - Jane B Cryan
- Department of Neurosurgery, Queen Elizabeth Hospital, Birmingham, UK
| | - Philip J O'Halloran
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, York Street, Dublin 2, Ireland
- Department of Neurosurgery, Queen Elizabeth Hospital, Birmingham, UK
| | | | - Francesca Brett
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - Philippe Lambin
- The D-Lab: Department of Precision Medicine, GROW - School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
- Department of Radiology and Nuclear Medicine, GROW - School for Oncology and Reproduction, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Henry C Woodruff
- The D-Lab: Department of Precision Medicine, GROW - School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
- Department of Radiology and Nuclear Medicine, GROW - School for Oncology and Reproduction, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Annette T Byrne
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, York Street, Dublin 2, Ireland.
- National Pre-Clinical Imaging Centre (NPIC), Dublin, Ireland.
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland.
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Effects of empagliflozin on progression of chronic kidney disease: a prespecified secondary analysis from the empa-kidney trial. Lancet Diabetes Endocrinol 2024; 12:39-50. [PMID: 38061371 PMCID: PMC7615591 DOI: 10.1016/s2213-8587(23)00321-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Sodium-glucose co-transporter-2 (SGLT2) inhibitors reduce progression of chronic kidney disease and the risk of cardiovascular morbidity and mortality in a wide range of patients. However, their effects on kidney disease progression in some patients with chronic kidney disease are unclear because few clinical kidney outcomes occurred among such patients in the completed trials. In particular, some guidelines stratify their level of recommendation about who should be treated with SGLT2 inhibitors based on diabetes status and albuminuria. We aimed to assess the effects of empagliflozin on progression of chronic kidney disease both overall and among specific types of participants in the EMPA-KIDNEY trial. METHODS EMPA-KIDNEY, a randomised, controlled, phase 3 trial, was conducted at 241 centres in eight countries (Canada, China, Germany, Italy, Japan, Malaysia, the UK, and the USA), and included individuals aged 18 years or older with an estimated glomerular filtration rate (eGFR) of 20 to less than 45 mL/min per 1·73 m2, or with an eGFR of 45 to less than 90 mL/min per 1·73 m2 with a urinary albumin-to-creatinine ratio (uACR) of 200 mg/g or higher. We explored the effects of 10 mg oral empagliflozin once daily versus placebo on the annualised rate of change in estimated glomerular filtration rate (eGFR slope), a tertiary outcome. We studied the acute slope (from randomisation to 2 months) and chronic slope (from 2 months onwards) separately, using shared parameter models to estimate the latter. Analyses were done in all randomly assigned participants by intention to treat. EMPA-KIDNEY is registered at ClinicalTrials.gov, NCT03594110. FINDINGS Between May 15, 2019, and April 16, 2021, 6609 participants were randomly assigned and then followed up for a median of 2·0 years (IQR 1·5-2·4). Prespecified subgroups of eGFR included 2282 (34·5%) participants with an eGFR of less than 30 mL/min per 1·73 m2, 2928 (44·3%) with an eGFR of 30 to less than 45 mL/min per 1·73 m2, and 1399 (21·2%) with an eGFR 45 mL/min per 1·73 m2 or higher. Prespecified subgroups of uACR included 1328 (20·1%) with a uACR of less than 30 mg/g, 1864 (28·2%) with a uACR of 30 to 300 mg/g, and 3417 (51·7%) with a uACR of more than 300 mg/g. Overall, allocation to empagliflozin caused an acute 2·12 mL/min per 1·73 m2 (95% CI 1·83-2·41) reduction in eGFR, equivalent to a 6% (5-6) dip in the first 2 months. After this, it halved the chronic slope from -2·75 to -1·37 mL/min per 1·73 m2 per year (relative difference 50%, 95% CI 42-58). The absolute and relative benefits of empagliflozin on the magnitude of the chronic slope varied significantly depending on diabetes status and baseline levels of eGFR and uACR. In particular, the absolute difference in chronic slopes was lower in patients with lower baseline uACR, but because this group progressed more slowly than those with higher uACR, this translated to a larger relative difference in chronic slopes in this group (86% [36-136] reduction in the chronic slope among those with baseline uACR <30 mg/g compared with a 29% [19-38] reduction for those with baseline uACR ≥2000 mg/g; ptrend<0·0001). INTERPRETATION Empagliflozin slowed the rate of progression of chronic kidney disease among all types of participant in the EMPA-KIDNEY trial, including those with little albuminuria. Albuminuria alone should not be used to determine whether to treat with an SGLT2 inhibitor. FUNDING Boehringer Ingelheim and Eli Lilly.
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Ryder M, Sabarai A, Saccà C, Sachson R, Sadler E, Safiee NS, Sahani M, Saillant A, Saini J, Saito C, Saito S, Sakaguchi K, Sakai M, Salim H, Salviani C, Sammons E, Sampson A, Samson F, Sandercock P, Sanguila S, Santorelli G, Santoro D, Sarabu N, Saram T, Sardell R, Sasajima H, Sasaki T, Satko S, Sato A, Sato D, Sato H, Sato H, Sato J, Sato T, Sato Y, Satoh M, Sawada K, Schanz M, Scheidemantel F, Schemmelmann M, Schettler E, Schettler V, Schlieper GR, Schmidt C, Schmidt G, Schmidt U, Schmidt-Gurtler H, Schmude M, Schneider A, Schneider I, Schneider-Danwitz C, Schomig M, Schramm T, Schreiber A, Schricker S, Schroppel B, Schulte-Kemna L, Schulz E, Schumacher B, Schuster A, Schwab A, Scolari F, Scott A, Seeger W, Seeger W, Segal M, Seifert L, Seifert M, Sekiya M, Sellars R, Seman MR, Shah S, Shah S, Shainberg L, Shanmuganathan M, Shao F, Sharma K, Sharpe C, Sheikh-Ali M, Sheldon J, Shenton C, Shepherd A, Shepperd M, Sheridan R, Sheriff Z, Shibata Y, Shigehara T, Shikata K, Shimamura K, Shimano H, Shimizu Y, Shimoda H, Shin K, Shivashankar G, Shojima N, Silva R, Sim CSB, Simmons K, Sinha S, Sitter T, Sivanandam S, Skipper M, Sloan K, Sloan L, Smith R, Smyth J, Sobande T, Sobata M, Somalanka S, Song X, Sonntag F, Sood B, Sor SY, Soufer J, Sparks H, Spatoliatore G, Spinola T, Squyres S, Srivastava A, Stanfield J, Staplin N, Staylor K, Steele A, Steen O, Steffl D, Stegbauer J, Stellbrink C, Stellbrink E, Stevens W, Stevenson A, Stewart-Ray V, Stickley J, Stoffler D, Stratmann B, Streitenberger S, Strutz F, Stubbs J, Stumpf J, Suazo N, Suchinda P, Suckling R, Sudin A, Sugamori K, Sugawara H, Sugawara K, Sugimoto D, Sugiyama H, Sugiyama H, Sugiyama T, Sullivan M, Sumi M, Suresh N, Sutton D, Suzuki H, Suzuki R, Suzuki Y, Suzuki Y, Suzuki Y, Swanson E, Swift P, Syed S, Szerlip H, Taal M, Taddeo M, Tailor C, Tajima K, Takagi M, Takahashi K, Takahashi K, Takahashi M, Takahashi T, Takahira E, Takai T, Takaoka M, Takeoka J, Takesada A, Takezawa M, Talbot M, Taliercio J, Talsania T, Tamori Y, Tamura R, Tamura Y, Tan CHH, Tan EZZ, Tanabe A, Tanabe K, Tanaka A, Tanaka A, Tanaka N, Tang S, Tang Z, Tanigaki K, Tarlac M, Tatsuzawa A, Tay JF, Tay LL, Taylor J, Taylor K, Taylor K, Te A, Tenbusch L, Teng KS, Terakawa A, Terry J, Tham ZD, Tholl S, Thomas G, Thong KM, Tietjen D, Timadjer A, Tindall H, Tipper S, Tobin K, Toda N, Tokuyama A, Tolibas M, Tomita A, Tomita T, Tomlinson J, Tonks L, Topf J, Topping S, Torp A, Torres A, Totaro F, Toth P, Toyonaga Y, Tripodi F, Trivedi K, Tropman E, Tschope D, Tse J, Tsuji K, Tsunekawa S, Tsunoda R, Tucky B, Tufail S, Tuffaha A, Turan E, Turner H, Turner J, Turner M, Tuttle KR, Tye YL, Tyler A, Tyler J, Uchi H, Uchida H, Uchida T, Uchida T, Udagawa T, Ueda S, Ueda Y, Ueki K, Ugni S, Ugwu E, Umeno R, Unekawa C, Uozumi K, Urquia K, Valleteau A, Valletta C, van Erp R, Vanhoy C, Varad V, Varma R, Varughese A, Vasquez P, Vasseur A, Veelken R, Velagapudi C, Verdel K, Vettoretti S, Vezzoli G, Vielhauer V, Viera R, Vilar E, Villaruel S, Vinall L, Vinathan J, Visnjic M, Voigt E, von-Eynatten M, Vourvou M, Wada J, Wada J, Wada T, Wada Y, Wakayama K, Wakita Y, Wallendszus K, Walters T, Wan Mohamad WH, Wang L, Wang W, Wang X, Wang X, Wang Y, Wanner C, Wanninayake S, Watada H, Watanabe K, Watanabe K, Watanabe M, Waterfall H, Watkins D, Watson S, Weaving L, Weber B, Webley Y, Webster A, Webster M, Weetman M, Wei W, Weihprecht H, Weiland L, Weinmann-Menke J, Weinreich T, Wendt R, Weng Y, Whalen M, Whalley G, Wheatley R, Wheeler A, Wheeler J, Whelton P, White K, Whitmore B, Whittaker S, Wiebel J, Wiley J, Wilkinson L, Willett M, Williams A, Williams E, Williams K, Williams T, Wilson A, Wilson P, Wincott L, Wines E, Winkelmann B, Winkler M, Winter-Goodwin B, Witczak J, Wittes J, Wittmann M, Wolf G, Wolf L, Wolfling R, Wong C, Wong E, Wong HS, Wong LW, Wong YH, Wonnacott A, Wood A, Wood L, Woodhouse H, Wooding N, Woodman A, Wren K, Wu J, Wu P, Xia S, Xiao H, Xiao X, Xie Y, Xu C, Xu Y, Xue H, Yahaya H, Yalamanchili H, Yamada A, Yamada N, Yamagata K, Yamaguchi M, Yamaji Y, Yamamoto A, Yamamoto S, Yamamoto S, Yamamoto T, Yamanaka A, Yamano T, Yamanouchi Y, Yamasaki N, Yamasaki Y, Yamasaki Y, Yamashita C, Yamauchi T, Yan Q, Yanagisawa E, Yang F, Yang L, Yano S, Yao S, Yao Y, Yarlagadda S, Yasuda Y, Yiu V, Yokoyama T, Yoshida S, Yoshidome E, Yoshikawa H, Young A, Young T, Yousif V, Yu H, Yu Y, Yuasa K, Yusof N, Zalunardo N, Zander B, Zani R, Zappulo F, Zayed M, Zemann B, Zettergren P, Zhang H, Zhang L, Zhang L, Zhang N, Zhang X, Zhao J, Zhao L, Zhao S, Zhao Z, Zhong H, Zhou N, Zhou S, Zhu D, Zhu L, Zhu S, Zietz M, Zippo M, Zirino F, Zulkipli FH. Impact of primary kidney disease on the effects of empagliflozin in patients with chronic kidney disease: secondary analyses of the EMPA-KIDNEY trial. Lancet Diabetes Endocrinol 2024; 12:51-60. [PMID: 38061372 DOI: 10.1016/s2213-8587(23)00322-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND The EMPA-KIDNEY trial showed that empagliflozin reduced the risk of the primary composite outcome of kidney disease progression or cardiovascular death in patients with chronic kidney disease mainly through slowing progression. We aimed to assess how effects of empagliflozin might differ by primary kidney disease across its broad population. METHODS EMPA-KIDNEY, a randomised, controlled, phase 3 trial, was conducted at 241 centres in eight countries (Canada, China, Germany, Italy, Japan, Malaysia, the UK, and the USA). Patients were eligible if their estimated glomerular filtration rate (eGFR) was 20 to less than 45 mL/min per 1·73 m2, or 45 to less than 90 mL/min per 1·73 m2 with a urinary albumin-to-creatinine ratio (uACR) of 200 mg/g or higher at screening. They were randomly assigned (1:1) to 10 mg oral empagliflozin once daily or matching placebo. Effects on kidney disease progression (defined as a sustained ≥40% eGFR decline from randomisation, end-stage kidney disease, a sustained eGFR below 10 mL/min per 1·73 m2, or death from kidney failure) were assessed using prespecified Cox models, and eGFR slope analyses used shared parameter models. Subgroup comparisons were performed by including relevant interaction terms in models. EMPA-KIDNEY is registered with ClinicalTrials.gov, NCT03594110. FINDINGS Between May 15, 2019, and April 16, 2021, 6609 participants were randomly assigned and followed up for a median of 2·0 years (IQR 1·5-2·4). Prespecified subgroupings by primary kidney disease included 2057 (31·1%) participants with diabetic kidney disease, 1669 (25·3%) with glomerular disease, 1445 (21·9%) with hypertensive or renovascular disease, and 1438 (21·8%) with other or unknown causes. Kidney disease progression occurred in 384 (11·6%) of 3304 patients in the empagliflozin group and 504 (15·2%) of 3305 patients in the placebo group (hazard ratio 0·71 [95% CI 0·62-0·81]), with no evidence that the relative effect size varied significantly by primary kidney disease (pheterogeneity=0·62). The between-group difference in chronic eGFR slopes (ie, from 2 months to final follow-up) was 1·37 mL/min per 1·73 m2 per year (95% CI 1·16-1·59), representing a 50% (42-58) reduction in the rate of chronic eGFR decline. This relative effect of empagliflozin on chronic eGFR slope was similar in analyses by different primary kidney diseases, including in explorations by type of glomerular disease and diabetes (p values for heterogeneity all >0·1). INTERPRETATION In a broad range of patients with chronic kidney disease at risk of progression, including a wide range of non-diabetic causes of chronic kidney disease, empagliflozin reduced risk of kidney disease progression. Relative effect sizes were broadly similar irrespective of the cause of primary kidney disease, suggesting that SGLT2 inhibitors should be part of a standard of care to minimise risk of kidney failure in chronic kidney disease. FUNDING Boehringer Ingelheim, Eli Lilly, and UK Medical Research Council.
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Kelleher M, Colling R, Browning L, Roskell D, Roberts-Gant S, Shah KA, Hemsworth H, White K, Rees G, Dolton M, Soares MF, Verrill C. Department Wide Validation in Digital Pathology-Experience from an Academic Teaching Hospital Using the UK Royal College of Pathologists' Guidance. Diagnostics (Basel) 2023; 13:2144. [PMID: 37443538 DOI: 10.3390/diagnostics13132144] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/08/2023] [Accepted: 06/14/2023] [Indexed: 07/15/2023] Open
Abstract
AIM we describe our experience of validating departmental pathologists for digital pathology reporting, based on the UK Royal College of Pathologists (RCPath) "Best Practice Recommendations for Implementing Digital Pathology (DP)," at a large academic teaching hospital that scans 100% of its surgical workload. We focus on Stage 2 of validation (prospective experience) prior to full validation sign-off. METHODS AND RESULTS twenty histopathologists completed Stage 1 of the validation process and subsequently completed Stage 2 validation, prospectively reporting a total of 3777 cases covering eight specialities. All cases were initially viewed on digital whole slide images (WSI) with relevant parameters checked on glass slides, and discordances were reconciled before the case was signed out. Pathologists kept an electronic log of the cases, the preferred reporting modality used, and their experiences. At the end of each validation, a summary was compiled and reviewed with a mentor. This was submitted to the DP Steering Group who assessed the scope of cases and experience before sign-off for full validation. A total of 1.3% (49/3777) of the cases had a discordance between WSI and glass slides. A total of 61% (30/49) of the discordances were categorised as a minor error in a supplementary parameter without clinical impact. The most common reasons for diagnostic discordances across specialities included identification and grading of dysplasia, assessment of tumour invasion, identification of small prognostic or diagnostic objects, interpretation of immunohistochemistry/special stains, and mitotic count assessment. Pathologists showed similar mean diagnostic confidences (on Likert scale from 0 to 7) with a mean of 6.8 on digital and 6.9 on glass slide reporting. CONCLUSION we describe one of the first real-world experiences of a department-wide effort to implement, validate, and roll out digital pathology reporting by applying the RCPath Recommendations for Implementing DP. We have shown a very low rate of discordance between WSI and glass slides.
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Affiliation(s)
- Mai Kelleher
- Department of Cellular Pathology, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Richard Colling
- Department of Cellular Pathology, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
- Nuffield Department of Surgical Sciences, Oxford University, Oxford OX3 9DU, UK
| | - Lisa Browning
- Department of Cellular Pathology, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Derek Roskell
- Department of Cellular Pathology, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Sharon Roberts-Gant
- Department of Cellular Pathology, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Ketan A Shah
- Department of Cellular Pathology, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Helen Hemsworth
- Department of Cellular Pathology, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Kieron White
- Department of Cellular Pathology, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Gabrielle Rees
- Department of Cellular Pathology, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Monica Dolton
- Nuffield Department of Surgical Sciences, Oxford University, Oxford OX3 9DU, UK
| | - Maria Fernanda Soares
- Department of Cellular Pathology, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Clare Verrill
- Department of Cellular Pathology, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
- Nuffield Department of Surgical Sciences, Oxford University, Oxford OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
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White K, Connor K, Meylan M, Bougoüin A, Salvucci M, Bielle F, O'Farrell AC, Sweeney K, Weng L, Bergers G, Dicker P, Ashley DM, Lipp ES, Low JT, Zhao J, Wen P, Prins R, Verreault M, Idbaih A, Biswas A, Prehn JHM, Lambrechts D, Arijs I, Lodi F, Dilcan G, Lamfers M, Leenstra S, Fabro F, Ntafoulis I, Kros JM, Cryan J, Brett F, Quissac E, Beausang A, MacNally S, O'Halloran P, Clerkin J, Bacon O, Kremer A, Chi Yen RT, Varn FS, Verhaak RGW, Sautès-Fridman C, Fridman WH, Byrne AT. Identification, validation and biological characterisation of novel glioblastoma tumour microenvironment subtypes: implications for precision immunotherapy. Ann Oncol 2023; 34:300-314. [PMID: 36494005 DOI: 10.1016/j.annonc.2022.11.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND New precision medicine therapies are urgently required for glioblastoma (GBM). However, to date, efforts to subtype patients based on molecular profiles have failed to direct treatment strategies. We hypothesised that interrogation of the GBM tumour microenvironment (TME) and identification of novel TME-specific subtypes could inform new precision immunotherapy treatment strategies. MATERIALS AND METHODS A refined and validated microenvironment cell population (MCP) counter method was applied to >800 GBM patient tumours (GBM-MCP-counter). Specifically, partition around medoids (PAM) clustering of GBM-MCP-counter scores in the GLIOTRAIN discovery cohort identified three novel patient clusters, uniquely characterised by TME composition, functional orientation markers and immune checkpoint proteins. Validation was carried out in three independent GBM-RNA-seq datasets. Neoantigen, mutational and gene ontology analysis identified mutations and uniquely altered pathways across subtypes. The longitudinal Glioma Longitudinal AnalySiS (GLASS) cohort and three immunotherapy clinical trial cohorts [treatment with neoadjuvant/adjuvant anti-programmed cell death protein 1 (PD-1) or PSVRIPO] were further interrogated to assess subtype alterations between primary and recurrent tumours and to assess the utility of TME classifiers as immunotherapy biomarkers. RESULTS TMEHigh tumours (30%) displayed elevated lymphocyte, myeloid cell immune checkpoint, programmed cell death protein 1 (PD-1) and cytotoxic T-lymphocyte-associated protein 4 transcripts. TMEHigh/mesenchymal+ patients featured tertiary lymphoid structures. TMEMed (46%) tumours were enriched for endothelial cell gene expression profiles and displayed heterogeneous immune populations. TMELow (24%) tumours were manifest as an 'immune-desert' group. TME subtype transitions upon recurrence were identified in the longitudinal GLASS cohort. Assessment of GBM immunotherapy trial datasets revealed that TMEHigh patients receiving neoadjuvant anti-PD-1 had significantly increased overall survival (P = 0.04). Moreover, TMEHigh patients treated with adjuvant anti-PD-1 or oncolytic virus (PVSRIPO) showed a trend towards improved survival. CONCLUSIONS We have established a novel TME-based classification system for application in intracranial malignancies. TME subtypes represent canonical 'termini a quo' (starting points) to support an improved precision immunotherapy treatment approach.
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Affiliation(s)
- K White
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - K Connor
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - M Meylan
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC, Université de Paris, Paris, France
| | - A Bougoüin
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC, Université de Paris, Paris, France
| | - M Salvucci
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - F Bielle
- Paris Brain Institute (ICM), CNRS UMR 7225, Inserm U 1127, UPMC-P6 UMR S 1127, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - A C O'Farrell
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - K Sweeney
- National Centre of Neurosurgery, Beaumont Hospital, Dublin, Ireland
| | - L Weng
- VIB-KU Leuven Center for Cancer Biology, Department of Oncology, Leuven, Belgium
| | - G Bergers
- VIB-KU Leuven Center for Cancer Biology, Department of Oncology, Leuven, Belgium
| | - P Dicker
- Epidemiology & Public Health, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - D M Ashley
- Duke Cancer Institute, Duke University, Durham, USA
| | - E S Lipp
- Duke Cancer Institute, Duke University, Durham, USA
| | - J T Low
- Duke Cancer Institute, Duke University, Durham, USA
| | - J Zhao
- Department of Systems Biology at Columbia University, New York, USA
| | - P Wen
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - R Prins
- Department of Medical and Molecular Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - M Verreault
- Paris Brain Institute (ICM), CNRS UMR 7225, Inserm U 1127, UPMC-P6 UMR S 1127, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - A Idbaih
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Paris Brain Institute (ICM), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière-Charles Foix, Paris, France
| | - A Biswas
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - J H M Prehn
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - D Lambrechts
- Laboratory for Translational Genetics, Department of Human Genetics, Leuven, Belgium; VIB Center for Cancer Biology, Leuven, Belgium
| | - I Arijs
- Laboratory for Translational Genetics, Department of Human Genetics, Leuven, Belgium; VIB Center for Cancer Biology, Leuven, Belgium
| | - F Lodi
- Laboratory for Translational Genetics, Department of Human Genetics, Leuven, Belgium; VIB Center for Cancer Biology, Leuven, Belgium
| | - G Dilcan
- Laboratory for Translational Genetics, Department of Human Genetics, Leuven, Belgium; VIB Center for Cancer Biology, Leuven, Belgium
| | - M Lamfers
- Department of Neurosurgery, Brain Tumor Center, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - S Leenstra
- Department of Neurosurgery, Brain Tumor Center, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - F Fabro
- Department of Neurosurgery, Brain Tumor Center, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - I Ntafoulis
- Department of Neurosurgery, Brain Tumor Center, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - J M Kros
- Department of Pathology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - J Cryan
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - F Brett
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - E Quissac
- Paris Brain Institute (ICM), CNRS UMR 7225, Inserm U 1127, UPMC-P6 UMR S 1127, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - A Beausang
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - S MacNally
- National Centre of Neurosurgery, Beaumont Hospital, Dublin, Ireland
| | - P O'Halloran
- National Centre of Neurosurgery, Beaumont Hospital, Dublin, Ireland
| | - J Clerkin
- National Centre of Neurosurgery, Beaumont Hospital, Dublin, Ireland
| | - O Bacon
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - A Kremer
- Information Technology for Translational Medicine (ITTM), Luxembourg, Luxembourg
| | - R T Chi Yen
- Information Technology for Translational Medicine (ITTM), Luxembourg, Luxembourg
| | - F S Varn
- The Jackson Laboratory for Genomic Medicine, Farmington, USA
| | - R G W Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, USA; Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Centers, VU University Medical Center, Amsterdam, the Netherlands
| | - C Sautès-Fridman
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC, Université de Paris, Paris, France
| | - W H Fridman
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC, Université de Paris, Paris, France
| | - A T Byrne
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland.
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Thornton A, Peterson E, Thomas A, Regouski M, Liu Y, White K, Davies C, Polejaeva I, Rutigliano H. 86 The role of extracellular vesicles in immunomodulation during bovine pregnancy. Reprod Fertil Dev 2022. [DOI: 10.1071/rdv35n2ab86] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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White K, Arey W, Whitfield B, Vizcarra E, Dane'el A, Dixon L, Potter JE, Ogburn T, Beasley A. 002Abortion patients’ priorities and tradeoffs deciding where to obtain out-of-state care following texas 2021 abortion ban. Contraception 2022. [DOI: 10.1016/j.contraception.2022.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Nagle AC, Lerma K, Sierra G, White K. P072Preferred contraceptive use and barriers to care in mississippi. Contraception 2022. [DOI: 10.1016/j.contraception.2022.09.096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Anakwe A, Majee W, White K, BeLue R. P066“Using an adult mindset”: An examination of fertility desires and reproductive planning among low-income black fathers. Contraception 2022. [DOI: 10.1016/j.contraception.2022.09.090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Clerkin J, Connor K, White K, Sweeney K, Shiels L, Van Brussel T, Arijs I, Lambrechts D, Maher S, Marignol L, Prehn J, O'Brien D, Byrne A. MODL-27. PRECLINICAL INTERROGATION OF IMMUNOTHERAPY TREATMENT STRATEGIES IN GLIOBLASTOMA (GBM) USING A CLINICALLY RELEVANT DISEASE MODEL. Neuro Oncol 2022. [DOI: 10.1093/neuonc/noac209.1154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
Clinically faithful pre-clinical models are essential for screening therapies and studying resistance mechanisms. Historically models have failed to predict response in the clinical setting. Current models seldom incorporate surgical resection, and commonly use young animals whose immune contexture differs from older patients. Here, we have established an orthotopic model, employing the syngeneic, mesenchymal-NFpp10a-cell line, in both young and aged mice. We have characterised the model's response to standard of care resection and temozolomide (TMZ) treatment. We have further studied response to anti-PD1 therapy (adjuvant and neoadjuvant). NFpp10a-Luc2 expressing cells were orthotopically implanted into C57BL/6 mice (aged { > 18months} and young {6-8weeks}) and weekly bioluminescence imaging (BLI) performed to monitor tumour growth. Several therapeutic interventions were assessed to study tumour growth and survival: (1)surgical resection, (2)TMZ, (3)anti-PD1 (4)neoadjuvant anti-PD1. RNAseq, murine microenvironment cell population (mMCP) counter and gene ontology analyses characterised treatment related changed in the TME. We demonstrated survival advantage in aged mice undergoing resection (Resection:33.5 days vs Non-Resection:18 days;p=0.0166). Subsequently, we observed that TMZ and anti-PD1 monotherapy had no impact on NFpp10a-Luc2 growth (TMZ-overall:p=0.9001, and anti-PD1-overall:p = 0.7933) or survival (TMZ-overall:p = 0.3035, anti-PD1-overall:p= 0.6328). Neoadjuvant anti-PD1 treated mice demonstrated no survival advantage compared to IgG control (33-days vs 35-days:p = 0.9429). or BLI signal (p = 0.1703). NFpp10a-Luc2 forms immune-cold TME relative to commonly employed models. mMCP counter analysis demonstrates neoadjuvant anti-PD1 induced influx of CD8+-T cells, B cells, and monocytes into the TME compared to IgG control, and was associated with significantly upregulated CXCR3 chemokine receptor binding pathway on gene ontology analysis (p = 0.0045). Overall, we have, for the first time established and characterised response of the NFpp10a-Luc2-C57BL/6 model to resection, TMZ and anti-PD1 therapies. NFpp10a-Luc2 tumours demonstrate similar therapeutic resistance and TME profile compared to human mesenchymal GBM. The model may therefore be employed in future pre-clinical studies to guide clinical trials in mesenchymal GBM.
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Affiliation(s)
- James Clerkin
- Department of Neurosurgery, Beaumont hospital, Dublin Ireland , Dublin , Ireland
| | - Kate Connor
- Dept Physiology and Medical Physics, Royal College of Surgeons in Ireland , Dublin , Ireland
| | - Kieron White
- Dept Physiology and Medical Physics, Royal College of Surgeons in Ireland , Dublin , Ireland
| | - Kieron Sweeney
- Department of Neurosurgery, Beaumont Hospital, Dublin, Ireland , Dublin , Ireland
| | - Liam Shiels
- Dept Physiology and Medical Physics, Royal College of Surgeons in Ireland , Dublin , Ireland
| | - Thomas Van Brussel
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium , Leuven , Belgium
| | - Ingrid Arijs
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium , Leuven , Belgium
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium , Leuven , Belgium
| | - Stephen Maher
- Trinity Translational Medicine Institute, Trinity St James's Cancer Institute, St. James Hospital Dublin 8. , Dublin , Ireland
| | - Laure Marignol
- Discipline of Radiation Therapy Trinity Centre for Health Sciences St. James's Hospital Dublin 8 , Dublin , Ireland
| | - Jochen Prehn
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, York Street, Dublin 2 , Dublin , Ireland
| | - David O'Brien
- Department of Neurosurgery, Beaumont hospital, Dublin , Dublin , Ireland
| | - Annette Byrne
- Dept Physiology and Medical Physics, Royal College of Surgeons in Ireland , Dublin , Ireland
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11
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White K, Connor K, Meylan M, Bougoüin A, Salvucci M, Bielle F, O’Farrell A, Sweeney K, Weng L, Bergers G, Dicker P, Ashley D, Lipp ES, Low J, Zhao J, Wen PY, Prins R, Verreault M, Idbaih A, Prehn J, Varn F, Verhaak R, Sautès-Fridman C, Fridman W, Byrne A. TMIC-10. IDENTIFICATION, VALIDATION AND BIOLOGICAL CHARACTERIZATION OF NOVEL GLIOBLASTOMA TUMOUR MICROENVIRONMENT SUBTYPES: IMPLICATIONS FOR PRECISION IMMUNOTHERAPY. Neuro Oncol 2022. [PMCID: PMC9661289 DOI: 10.1093/neuonc/noac209.1054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
New precision medicine therapies are urgently required for glioblastoma (GBM). However, to date, efforts to subtype patients based on molecular profiles, have failed to direct treatment strategies. We hypothesized that interrogation of the GBM tumor microenvironment (TME) and identification of novel TME-specific subtypes could inform new precision treatment strategies. To this end, a refined and validated microenvironment cell population (MCP)-counter method was applied to > 800 GBM patient tumours and validated by multiplex-immunohistochemistry. The MCP-counter deconvolution method interrogates the TME composition from transcriptomic data. Using this refined method, we classified the GLIOTRAIN(www.gliotrain.eu) IDHwt GBM cohort (n=123) into 3 novel clusters characterised by differences in TME composition and subsequently validated findings in the TCGA (n=69), CGGA (n=72) and DUKE (unpublished)(n=162) cohorts. TMEHigh tumours (30%) displayed elevated immune populations, functional orientation markers, immune checkpoint genes, and upregulated immunoregulatory pathways. Moreover, tertiary lymphoid structures were a feature of TMEHigh/mesenchymal+ patients. TMEMed (46%) tumours displayed heterogeneous immune populations and upregulated neuronal signalling pathways. TMELow (24%) tumours represented an ‘immune-desert’ group, high EGFR mutation frequency and upregulated EGFR signalling pathways. Longitudinal analysis of the GLASS cohort revealed TME-subtype transitions upon recurrence, influenced by TME composition changes. Finally, assessment of three GBM immunotherapy clinical trial cohorts revealed that TMEHigh patients treated with neo-adjuvant anti-PD1 have a significantly improved survival (P=0.04). Moreover, TMEHigh patients treated with anti-PD1 and an oncolytic virus (PVSRIPO) in the adjuvant setting, showed a trend towards improved survival (P=0.15 and P=0.056 respectively). Overall, we have established a novel TME-based classification system for application in intracranial malignancies. This system may be used to better inform a precision targeting approach in the brain tumour setting. For example, we hypothesise that patients bearing TMELow tumours may be amenable to neoadjuvant anti-TIM3 + EGFR inhibitor, TMEMed to anti-angiogenic immunotherapy, and TMEHigh patients to neoadjuvant anti-PD1 + anti-CTLA4.
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Affiliation(s)
- Kieron White
- Dept Physiology and Medical Physics, Royal College of Surgeons in Ireland , Dublin , Ireland
| | - Kate Connor
- Dept Physiology and Medical Physics, Royal College of Surgeons in Ireland , Dublin , Ireland
| | - Maxime Meylan
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité , 75006 Paris , France
| | - Antoine Bougoüin
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité , 75006 Paris , France
| | - Manuela Salvucci
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland , Dublin , Ireland
| | - Franck Bielle
- Sorbonne Université, Paris Brain Institute , Paris , France
| | - Alice O’Farrell
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland , Dublin , Ireland
| | - Kieron Sweeney
- Department of Neurosurgery, Beaumont hospital , Dublin , Ireland
| | - Linqian Weng
- VIB-KU Leuven Center for Cancer Biology, Department of Oncology, KU Leuven , 3000 Leuven , Belgium
| | - Gabriele Bergers
- VIB-KU Leuven Center for Cancer Biology, Department of Oncology, KU Leuven , 3000 Leuven , Belgium
| | - Patrick Dicker
- Epidemiology & Public Health, Royal College of Surgeons in Ireland, Dublin, Ireland , Dublin , Ireland
| | - David Ashley
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center , Durham, NC , USA
| | - Eric S Lipp
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center , Durham, NC , USA
| | - Justin Low
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center , Durham, NC , USA
| | - Junfei Zhao
- Department of Systems Biology at Columbia University , New York, NY, 10032 , New York, NY , USA
- , USA , New York, NY, 10032 , New York, NY , USA
| | | | - Robert Prins
- University of California, Los Angeles , Los Angeles , USA
| | - Maite Verreault
- Paris Brain Institute (ICM), CNRS UMR 7225, Inserm U 1127, UPMC-P6 UMR S 1127, Hôpital de la Pitié - Salpêtrière - 47, boulevard de l'Hôpital –75013 Paris , Paris , France
| | - Ahmed Idbaih
- Sorbonne Université, AP-HP, ICM, Hôpital Universitaire La Pitié-Salpêtrière , Paris , France
| | - Jochen Prehn
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, York Street, Dublin 2 , Dublin , Ireland
| | | | | | - Catherine Sautès-Fridman
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité , 75006 Paris , France
| | - Wolf Fridman
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité , 75006 Paris , France
| | - Annette Byrne
- Dept Physiology and Medical Physics, Royal College of Surgeons in Ireland , Dublin , Ireland
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12
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Connor K, Conroy E, White K, Shiels L, Keek S, Ibrahim A, Gallagher W, Clerkin J, Sweeney K, O'Brien D, Cryan J, Heffernan J, Brett F, Lambin P, Woodruff H, Byrne A. MODL-24. ESTABLISHING A CLINICALLY RELEVANT CT AND ASSOCIATED RADIOMICS PIPELINE FOR INTRACRANIAL RODENT TUMOUR MODELS. Neuro Oncol 2022. [PMCID: PMC9661278 DOI: 10.1093/neuonc/noac209.1151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
While magnetic resonance imaging (MRI) is the predominant imaging modality for glioblastoma (GBM), pre-clinical MRI scanner availability is limited. As pre-clinical CT is more widely available and cost-effective, this study aimed to 1) establish preclinical-GBM CT and CT-radiomic workflows, 2) identify whether CE-CT could detect murine orthotopic GBM tumours on two CT instruments [TRIUMPHX-O-CT; IVISSPECTRUM-CT], 3) assess whether CT-radiomic features could distinguish tumour from normal tissue, and support earlier detection of tumours, 4) verify translation of pre-clinical CT-radiomic pipelines to, and assess pre-clinical CT-features in, clinical CE-CT scans.U87R-Luc2(n=25) and NFpp10a-Luc2(n=10) orthotopic GBM models were established and tumours monitored via bioluminescence imaging (BLI). Concurrently, mice underwent CE-CT (IV-iodine/300mg/mL/50kV-scan). Extracted radiomic features (PyRadiomics) underwent dimensionality reduction (Spearman correlation; >0.85). Remaining features were analysed (Recursive feature elimination (RFE)/RepeatedCV/randomforest) in normal and tumour tissue and across timepoints (TRIUMPHX-O-CT-Wk3vsWk6,Wk6vsWk9/12; IVISSPECTRUM-CT-Wk6vsWk9/12).CE-CT and radiomic pipelines were successfully established for orthotopic GBM models, using both CT-systems. On visual assessment of images, BLI was significantly more sensitive, with tumours detectable at Wk1 (BLI) vs Wk9 (CE-CT). However, RFE analysis identified CT-radiomic features (first_order&glcm) which differentiated tumour from normal tissue (TRIUMPHX-O-CT). A subsequent feature set (first_order,glcm,gldm&glzm) were identified (TRIUMPHX-O-CT/IVISSPECTRUM-CT), detecting tumours earlier (Wk3&Wk6) than possible by visual assessment of CTs. Preclinical radiomic methods were successfully applied to exploratory clinical CE-CT scans(n=10). Here, several preclinical CT-features (e.g. Zone_Entropy) showed increased intensity in tumour regions. Overall experimental BLI is the most sensitive method for pre-clinical intracranial tumour detection. However, analysis of clinically relevant CT-radiomic features may facilitate tumour identification and earlier tumour detection (Wk3/Wk6-TRIUMPHX-O-CT/Wk6-IVISSPECTRUM-CT) than possible by visual assessment of CT (Wk9). Clinically relevant CT-derived radiomic features may therefore support intracranial rodent tumour assessment. Importantly, preclinical radiomic methods successfully translate to clinical CT-radiomic analysis. Parallel trends in tumour-specific feature intensities across pre-clinical and clinical scans suggest species conservation of features.
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Affiliation(s)
- Kate Connor
- Dept Physiology and Medical Physics, Royal College of Surgeons in Ireland , Dublin , Ireland
| | - Emer Conroy
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, , Dublin , Ireland
| | - Kieron White
- Dept Physiology and Medical Physics, Royal College of Surgeons in Ireland , Dublin , Ireland
| | - Liam Shiels
- Dept Physiology and Medical Physics, Royal College of Surgeons in Ireland , Dublin , Ireland
| | - Simon Keek
- The D-Lab: Department of Precision Medicine, GROW - School for Oncology, Maastricht University, Maastricht , Maastricht , Netherlands
| | - Abdalla Ibrahim
- The D-Lab: Department of Precision Medicine, GROW - School for Oncology, Maastricht University, Maastricht , Maastricht , Netherlands
| | - William Gallagher
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin , Dublin , Ireland
| | - James Clerkin
- Department of Neurosurgery, Beaumont hospital, Dublin Ireland , Dublin , Ireland
| | - Kieron Sweeney
- Department of Neurosurgery, Beaumont hospital , Dublin , Ireland
| | - David O'Brien
- Department of Neurosurgery, Beaumont hospital, Dublin , Dublin , Ireland
| | - Jane Cryan
- Department of Neuropathology, Beaumont Hospital , Dublin , Ireland
| | | | - Francesca Brett
- Department of Neuropathology, Beaumont Hospital , Dublin , Ireland
| | - Philippe Lambin
- The D-Lab: Department of Precision Medicine, GROW - School for Oncology, Maastricht University , Maastricht , Netherlands
| | - Henry Woodruff
- The D-Lab: Department of Precision Medicine, GROW - School for Oncology, Maastricht University, Maastricht , Maastricht , Netherlands
| | - Annette Byrne
- Dept Physiology and Medical Physics, Royal College of Surgeons in Ireland , Dublin , Ireland
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13
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Miller C, White K. UNEXPECTED DIAGNOSIS FOLLOWING IMMUNODEFICIENCY WORK-UP. Ann Allergy Asthma Immunol 2022. [DOI: 10.1016/j.anai.2022.08.857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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14
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van de Wal RSW, Nicholls RJ, Behar D, McInnes K, Stammer D, Lowe JA, Church JA, DeConto R, Fettweis X, Goelzer H, Haasnoot M, Haigh ID, Hinkel J, Horton BP, James TS, Jenkins A, LeCozannet G, Levermann A, Lipscomb WH, Marzeion B, Pattyn F, Payne AJ, Pfeffer WT, Price SF, Seroussi H, Sun S, Veatch W, White K. A High-End Estimate of Sea Level Rise for Practitioners. Earths Future 2022; 10:e2022EF002751. [PMID: 36590252 PMCID: PMC9787942 DOI: 10.1029/2022ef002751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 09/23/2022] [Accepted: 10/03/2022] [Indexed: 06/17/2023]
Abstract
Sea level rise (SLR) is a long-lasting consequence of climate change because global anthropogenic warming takes centuries to millennia to equilibrate for the deep ocean and ice sheets. SLR projections based on climate models support policy analysis, risk assessment and adaptation planning today, despite their large uncertainties. The central range of the SLR distribution is estimated by process-based models. However, risk-averse practitioners often require information about plausible future conditions that lie in the tails of the SLR distribution, which are poorly defined by existing models. Here, a community effort combining scientists and practitioners builds on a framework of discussing physical evidence to quantify high-end global SLR for practitioners. The approach is complementary to the IPCC AR6 report and provides further physically plausible high-end scenarios. High-end estimates for the different SLR components are developed for two climate scenarios at two timescales. For global warming of +2°C in 2100 (RCP2.6/SSP1-2.6) relative to pre-industrial values our high-end global SLR estimates are up to 0.9 m in 2100 and 2.5 m in 2300. Similarly, for a (RCP8.5/SSP5-8.5), we estimate up to 1.6 m in 2100 and up to 10.4 m in 2300. The large and growing differences between the scenarios beyond 2100 emphasize the long-term benefits of mitigation. However, even a modest 2°C warming may cause multi-meter SLR on centennial time scales with profound consequences for coastal areas. Earlier high-end assessments focused on instability mechanisms in Antarctica, while here we emphasize the importance of the timing of ice shelf collapse around Antarctica. This is highly uncertain due to low understanding of the driving processes. Hence both process understanding and emission scenario control high-end SLR.
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Affiliation(s)
- R. S. W. van de Wal
- Institute for Marine and Atmospheric Research UtrechtUtrecht UniversityTA UtrechtThe Netherlands
- Department of Physical GeographyUtrecht UniversityTA UtrechtThe Netherlands
| | - R. J. Nicholls
- Tyndall Centre for Climate Change ResearchUniversity of East AngliaNorwichUK
| | - D. Behar
- San Francisco Public Utilities CommissionSan FranciscoCAUSA
| | - K. McInnes
- Climate Change Research CentreUNSW AustraliaSydneyNSWAustralia
| | - D. Stammer
- Centrum für Erdsystemforschung und NachhaltigkeitUniversität HamburgHamburgGermany
| | - J. A. Lowe
- Met Office Hadley CentreExeterUK
- Priestley CentreUniversity of LeedsLeedsUK
| | - J. A. Church
- Climate Change Research CentreUNSW AustraliaSydneyNSWAustralia
- Australian Centre for Excellence in Antarctic Science (ACEAS)University of TasmaniaHobartTASAustralia
| | - R. DeConto
- Department of GeosciencesUniversity of Massachusetts‐AmherstAmherstMAUSA
| | - X. Fettweis
- Department of GeographySPHERES Research UnitUniversity of LiègeLiègeBelgium
| | - H. Goelzer
- NORCE Norwegian Research CentreBjerknes Centre for Climate ResearchBergenNorway
| | | | - I. D. Haigh
- School of Ocean and Earth ScienceUniversity of SouthamptonNational Oceanography CentreSouthamptonUK
| | - J. Hinkel
- Adaptation and Social LearningGlobal Climate ForumBerlinGermany
| | - B. P. Horton
- Earth Observatory of SingaporeNanyang Technological UniversitySingaporeSingapore
- Asian School of the EnvironmentNanyang Technological UniversitySingaporeSingapore
| | - T. S. James
- Natural Resources CanadaGeological Survey of CanadaSidneyBCCanada
| | - A. Jenkins
- Department of Geography and Environmental SciencesNorthumbria UniversityNewcastle upon TyneUK
| | - G. LeCozannet
- Coastal Risks and Climate Change UnitRisks and Prevention DivisionBRGMOrléansFrance
| | - A. Levermann
- Potsdam Institute for Climate Impact ResearchPotsdamGermany
- LDEOColumbia UniversityNew YorkNYUSA
- Physics InstituteUniversity of PotsdamPotsdamGermany
| | - W. H. Lipscomb
- Climate and Global Dynamics LaboratoryNational Center for Atmospheric ResearchBoulderCOUSA
| | - B. Marzeion
- Institute of Geography and MARUM ‐ Center for Marine Environmental SciencesUniversity of BremenBremenGermany
| | - F. Pattyn
- Laboratoire de GlaciologieUniversité libre de BruxellesBrusselsBelgium
| | - A. J. Payne
- School of Geographical SciencesUniversity of BristolBristolUK
| | - W. T. Pfeffer
- INSTAAR and Department of Civil, Environmental, Architectural EngineeringUniversity of ColoradoBoulderCOUSA
| | - S. F. Price
- Theoretical DivisionLos Alamos National LaboratoryLos AlamosNMUSA
| | - H. Seroussi
- Thayer School of EngineeringDartmouth CollegeHanoverNHUSA
| | - S. Sun
- Coastal Risks and Climate Change UnitRisks and Prevention DivisionBRGMOrléansFrance
| | - W. Veatch
- US Army Corps of Engineers, HeadquartersWashingtonDCUSA
| | - K. White
- US Department of DefenseOffice of the Deputy Assistant Secretary of Defense (Environment and Energy Resilience)DCWashingtonUSA
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15
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Gerdts C, Fuentes L, Grossman D, White K, Keefe-Oates B, Baum SE, Hopkins K, Stolp CW, Potter JE. Impact of Clinic Closures on Women Obtaining Abortion Services After Implementation of a Restrictive Law in Texas. Am J Public Health 2022; 112:1297-1304. [PMID: 35969823 PMCID: PMC9382170 DOI: 10.2105/ajph.2016.303134r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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16
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Witkowski A, Ludzik J, Chung J, White K, Leitenberger J, Lee C, Berry E, Samatham R, Esener S, Pellacani G, Leachman S. LB997 Detecting the world’s smallest solid malignant tumor: The role of reflectance confocal microscopy in the diagnosis and management of a micro-melanoma. J Invest Dermatol 2022. [DOI: 10.1016/j.jid.2022.05.1023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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17
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Browning L, White K, Siiankoski D, Colling R, Roskell D, Fryer E, Hemsworth H, Roberts-Gant S, Roelofsen R, Rittscher J, Verrill C. RFID analysis of the complexity of cellular pathology workflow—An opportunity for digital pathology. Front Med (Lausanne) 2022; 9:933933. [PMID: 35979219 PMCID: PMC9377528 DOI: 10.3389/fmed.2022.933933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 07/07/2022] [Indexed: 12/02/2022] Open
Abstract
Digital pathology (DP) offers potential for time efficiency gains over an analog workflow however, to date, evidence supporting this claim is relatively lacking. Studies available concentrate on specific workflow points such as diagnostic reporting time, rather than overall efficiencies in slide logistics that might be expected. This is in part a result of the complexity and variation in analog working, and the challenge therefore in capturing this. We have utilized RFID technology to conduct a novel study capturing the movement of diagnostic cases within the analog pathway in a large teaching hospital setting, thus providing benchmark data for potential efficiency gains with DP. This technology overcomes the need to manually record data items and has facilitated the capture of both the physical journey of a case and the time associated with relevant components of the analog pathway predicted to be redundant in the digital setting. RFID tracking of 1,173 surgical pathology cases and over 30 staff in an analog cellular pathology workflow illustrates the complexity of the physical movement of slides within the department, which impacts on case traceability within the system. Detailed analysis of over 400 case journeys highlights redundant periods created by batching of slides at workflow points, including potentially 2–3 h for a case to become available for reporting after release from the lab, and variable lag-times prior to collection for reporting, and provides an illustration of patterns of lab and pathologist working within the analog setting. This study supports the challenge in evidencing efficiency gains to be anticipated with DP in the context of the variation and complexity of the analog pathway, but also evidences the efficiency gains that may be expected through a greater understanding of patterns of working and movement of cases. Such data may benefit other departments building a business case for DP.
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Affiliation(s)
- Lisa Browning
- Department of Cellular Pathology, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
- *Correspondence: Lisa Browning
| | - Kieron White
- Department of Cellular Pathology, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Darrin Siiankoski
- Department of Cellular Pathology, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Richard Colling
- Department of Cellular Pathology, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, United Kingdom
- Nuffield Department of Surgical Sciences, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Derek Roskell
- Department of Cellular Pathology, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Eve Fryer
- Department of Cellular Pathology, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Helen Hemsworth
- Department of Cellular Pathology, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Sharon Roberts-Gant
- Department of Cellular Pathology, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Ruud Roelofsen
- Philips Digital and Computational Pathology, Precision Diagnosis Solutions, Best, Netherlands
| | - Jens Rittscher
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
- Department of Engineering Science, Institute of Biomedical Engineering, University of Oxford, Oxford, United Kingdom
| | - Clare Verrill
- Department of Cellular Pathology, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
- Nuffield Department of Surgical Sciences, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
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18
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Varn FS, Johnson KC, Martinek J, Huse JT, Nasrallah MP, Wesseling P, Cooper LA, Malta TM, Wade TE, Sabedot TS, Brat DJ, Gould PV, Wöehrer A, Aldape K, Ismail A, Barthel FP, Kim H, Kocakavuk E, Ahmed N, White K, Sivajothi S, Datta I, Barnholtz-Sloan JS, Bakas S, D'Angelo F, Gan HK, Garofano L, Khasraw M, Migliozzi S, Ormond DR, Paek SH, Van Meir EG, Walenkamp AM, Watts C, Weller M, Weiss T, Palucka K, Stead LF, Poisson LM, Noushmehr H, Iavarone A, Verhaak RG. Abstract 2168: Longitudinal analysis of diffuse glioma reveals cell state dynamics at recurrence associated with changes in genetics and the microenvironment. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-2168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Diffuse glioma is characterized by a poor prognosis and a universal resistance to therapy, though the evolutionary processes behind this resistance remain unclear. The Glioma Longitudinal Analysis (GLASS) Consortium has previously demonstrated that therapy-induced selective pressures shape the genetic evolution of glioma in a stochastic manner. However, single-cell studies have revealed that malignant glioma cells are highly plastic and transition their cell state in response to diverse challenges, including changes in the microenvironment and the administration of standard-of-care therapy. To interrogate the factors driving therapy resistance in diffuse glioma, we collected and analyzed RNA- and/or DNA-sequencing data from temporally separated tumor pairs of over 300 adult patients with IDH-wild-type or IDH-mutant glioma. In a subset of these tumor pairs, we additionally performed multiplex immunofluorescence to capture the spatial relationship between tumor cells and their microenvironment. Recurrent tumors exhibited diverse changes that were attributable to changes in histological features, somatic alterations, and microenvironment interactions. IDH-wild-type tumors overall were more invasive at recurrence and exhibited increased expression of neuronal signaling programs that reflected a possible role for neuronal interactions in promoting glioma progression. In contrast, recurrent IDH-mutant tumors exhibited a significant increase in proliferative expression programs that correlated with discrete genetic changes. Hypermutation and acquired CDKN2A homozygous deletions associated with an increase in proliferating stem-like malignant cells at recurrence in both glioma subtypes, reflecting active tumor expansion. A transition to the mesenchymal phenotype was associated with the presence of a specific myeloid cell state defined by unique ligand-receptor interactions with malignant cells, providing opportunities to target this transition through therapy. Collectively, our results uncover recurrence-associated changes in genetics and the microenvironment that can be targeted to shape disease progression following initial diagnosis.
Citation Format: Frederick S. Varn, Kevin C. Johnson, Jan Martinek, Jason T. Huse, MacLean P. Nasrallah, Pieter Wesseling, Lee A. Cooper, Tathiane M. Malta, Taylor E. Wade, Thais S. Sabedot, Daniel J. Brat, Peter V. Gould, Adelheid Wöehrer, Kenneth Aldape, Azzam Ismail, Floris P. Barthel, Hoon Kim, Emre Kocakavuk, Nazia Ahmed, Kieron White, Santhosh Sivajothi, Indrani Datta, Jill S. Barnholtz-Sloan, Spyridon Bakas, Fulvio D'Angelo, Hui K. Gan, Luciano Garofano, Mustafa Khasraw, Simona Migliozzi, D. Ryan Ormond, Sun Ha Paek, Erwin G. Van Meir, Annemiek M. Walenkamp, Colin Watts, Michael Weller, Tobias Weiss, Karolina Palucka, Lucy F. Stead, Laila M. Poisson, Houtan Noushmehr, Antonio Iavarone, Roel G. Verhaak, The GLASS Consortium. Longitudinal analysis of diffuse glioma reveals cell state dynamics at recurrence associated with changes in genetics and the microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2168.
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Affiliation(s)
| | | | - Jan Martinek
- 1The Jackson Laboratory for Genomic Medicine, Farmington, CT
| | - Jason T. Huse
- 2University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Pieter Wesseling
- 4Amsterdam University Medical Centers/VUmc, Amsterdam, Netherlands
| | - Lee A. Cooper
- 5Feinberg School of Medicine, Northwestern University, Chicago, IL
| | | | - Taylor E. Wade
- 1The Jackson Laboratory for Genomic Medicine, Farmington, CT
| | - Thais S. Sabedot
- 7Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, MI
| | - Daniel J. Brat
- 5Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Peter V. Gould
- 8Hôpital de l’Enfant-Jésus du CHU de Québec - Université Laval, Quebec City, Quebec, Canada
| | | | | | | | | | - Hoon Kim
- 13Sungkyunkwan University, Seoul, Republic of Korea
| | - Emre Kocakavuk
- 1The Jackson Laboratory for Genomic Medicine, Farmington, CT
| | - Nazia Ahmed
- 11University of Leeds, Leeds, United Kingdom
| | - Kieron White
- 14Royal College of Surgeons in Ireland, Dublin, Ireland
| | | | - Indrani Datta
- 7Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, MI
| | - Jill S. Barnholtz-Sloan
- 15Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, OH
| | | | | | - Hui K. Gan
- 17Olivia Newton-John Cancer Research Institute, Austin Health, Melbourne, Australia
| | | | | | | | | | - Sun Ha Paek
- 20Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Erwin G. Van Meir
- 21School of Medicine and O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL
| | | | - Colin Watts
- 23University of Birmingham, Birmingham, United Kingdom
| | | | - Tobias Weiss
- 24University Hospital Zurich, Zurich, Switzerland
| | | | | | - Laila M. Poisson
- 7Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, MI
| | - Houtan Noushmehr
- 7Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, MI
| | | | - Roel G. Verhaak
- 1The Jackson Laboratory for Genomic Medicine, Farmington, CT
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Varn FS, Johnson KC, Martinek J, Huse JT, Nasrallah MP, Wesseling P, Cooper LAD, Malta TM, Wade TE, Sabedot TS, Brat D, Gould PV, Wöehrer A, Aldape K, Ismail A, Sivajothi SK, Barthel FP, Kim H, Kocakavuk E, Ahmed N, White K, Datta I, Moon HE, Pollock S, Goldfarb C, Lee GH, Garofano L, Anderson KJ, Nehar-Belaid D, Barnholtz-Sloan JS, Bakas S, Byrne AT, D'Angelo F, Gan HK, Khasraw M, Migliozzi S, Ormond DR, Paek SH, Van Meir EG, Walenkamp AME, Watts C, Weiss T, Weller M, Palucka K, Stead LF, Poisson LM, Noushmehr H, Iavarone A, Verhaak RGW. Glioma progression is shaped by genetic evolution and microenvironment interactions. Cell 2022; 185:2184-2199.e16. [PMID: 35649412 PMCID: PMC9189056 DOI: 10.1016/j.cell.2022.04.038] [Citation(s) in RCA: 137] [Impact Index Per Article: 68.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 01/22/2022] [Accepted: 04/28/2022] [Indexed: 12/21/2022]
Abstract
The factors driving therapy resistance in diffuse glioma remain poorly understood. To identify treatment-associated cellular and genetic changes, we analyzed RNA and/or DNA sequencing data from the temporally separated tumor pairs of 304 adult patients with isocitrate dehydrogenase (IDH)-wild-type and IDH-mutant glioma. Tumors recurred in distinct manners that were dependent on IDH mutation status and attributable to changes in histological feature composition, somatic alterations, and microenvironment interactions. Hypermutation and acquired CDKN2A deletions were associated with an increase in proliferating neoplastic cells at recurrence in both glioma subtypes, reflecting active tumor growth. IDH-wild-type tumors were more invasive at recurrence, and their neoplastic cells exhibited increased expression of neuronal signaling programs that reflected a possible role for neuronal interactions in promoting glioma progression. Mesenchymal transition was associated with the presence of a myeloid cell state defined by specific ligand-receptor interactions with neoplastic cells. Collectively, these recurrence-associated phenotypes represent potential targets to alter disease progression.
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Affiliation(s)
- Frederick S Varn
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Kevin C Johnson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Jan Martinek
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Jason T Huse
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - MacLean P Nasrallah
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Pieter Wesseling
- Amsterdam University Medical Centers/VUmc, Amsterdam, the Netherlands; Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Lee A D Cooper
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Tathiane M Malta
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, Brazil, Ribeirao Preto, São Paulo, Brazil
| | - Taylor E Wade
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Thais S Sabedot
- Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, MI, USA
| | - Daniel Brat
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Peter V Gould
- service d'anatomopathologie, Hôpital de l'Enfant-Jésus du Centre hospitalier universitaire de Québec, Université Laval, Quebec City, QC, Canada
| | - Adelheid Wöehrer
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria
| | | | - Azzam Ismail
- Department of Cellular and Molecular Pathology, Leeds Teaching Hospital NHS Trust, St James's University Hospital, Leeds, UK
| | | | - Floris P Barthel
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; Cancer and Cell Biology Division, the Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Hoon Kim
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; Department of Biopharmaceutical Convergence, Department of Pharmacy, Sungkyunkwan University, Suwon-si, Gyeong gi-do, South Korea
| | - Emre Kocakavuk
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; Department of Hematology and Stem Cell Transplantation, West German Cancer Center, University Hospital Essen, Essen, Germany
| | | | - Kieron White
- Precision Cancer Medicine Group, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, D02 YN77 Dublin, Ireland
| | - Indrani Datta
- Department of Public Health Sciences, Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, MI, USA
| | - Hyo-Eun Moon
- Seoul National University College of Medicine and Seoul National University Hospital, Seoul, Republic of Korea
| | | | | | - Ga-Hyun Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Luciano Garofano
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, USA
| | - Kevin J Anderson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Jill S Barnholtz-Sloan
- Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, OH, USA; Center for Biomedical Informatics and Information Technology & Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Spyridon Bakas
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Annette T Byrne
- Precision Cancer Medicine Group, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, D02 YN77 Dublin, Ireland
| | - Fulvio D'Angelo
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, USA
| | - Hui K Gan
- Olivia Newton-John Cancer Research Institute, Austin Health, Melbourne, Australia
| | - Mustafa Khasraw
- Preston Robert Tisch Brain Tumor Center at Duke, Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Simona Migliozzi
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, USA
| | - D Ryan Ormond
- Department of Neurosurgery, University of Colorado School of Medicine, Aurora, CO, USA
| | - Sun Ha Paek
- Seoul National University College of Medicine and Seoul National University Hospital, Seoul, Republic of Korea
| | - Erwin G Van Meir
- Department of Neurosurgery, School of Medicine and O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Annemiek M E Walenkamp
- Department of Medical Oncology, University Medical Center Groningen, Groningen, the Netherlands
| | - Colin Watts
- Academic Department of Neurosurgery, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Tobias Weiss
- Department of Neurology, Clinical Neuroscience Center, University Hospital Zurich and University of Zürich, Switzerland
| | - Michael Weller
- Department of Neurology, Clinical Neuroscience Center, University Hospital Zurich and University of Zürich, Switzerland
| | - Karolina Palucka
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Laila M Poisson
- Department of Public Health Sciences, Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, MI, USA
| | - Houtan Noushmehr
- Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, MI, USA
| | - Antonio Iavarone
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, USA; Department of Neurology, Columbia University Medical Center, New York, NY, USA; Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, USA
| | - Roel G W Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; Department of Neurosurgery, Amsterdam University Medical Centers/VUmc, Amsterdam, the Netherlands.
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Matcham F, Leightley D, Siddi S, Lamers F, White K, Annas P, De Girolamo G, Difrancesco S, Haro J, Horsfall M, Ivan A, Lavelle G, Li Q, Lombardini F, Mohr D, Narayan V, Oetzmann C, Penninx B, Simblett S, Bruce S, Nica R, Wykes T, Brasen J, Myin-Germeys I, Rintala A, Conde P, Dobson R, Folarin A, Stewart C, Ranjan Y, Rashid Z, Cummins N, Manyakov N, Vairavan S, Hotopf M. Remote Assessment of Disease and Relapse in Major Depressive Disorder (RADAR-MDD): Recruitment, retention, and data availability in a longitudinal remote measurement study. Eur Psychiatry 2022. [PMCID: PMC9564033 DOI: 10.1192/j.eurpsy.2022.315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Introduction
Major Depressive Disorder (MDD) is prevalent, often chronic, and requires ongoing monitoring of symptoms to track response to treatment and identify early indicators of relapse. Remote Measurement Technologies (RMT) provide an exciting opportunity to transform the measurement and management of MDD, via data collected from inbuilt smartphone sensors and wearable devices alongside app-based questionnaires and tasks.
Objectives
To describe the amount of data collected during a multimodal longitudinal RMT study, in an MDD population.
Methods
RADAR-MDD is a multi-centre, prospective observational cohort study. People with a history of MDD were provided with a wrist-worn wearable, and several apps designed to: a) collect data from smartphone sensors; and b) deliver questionnaires, speech tasks and cognitive assessments and followed-up for a maximum of 2 years.
Results
A total of 623 individuals with a history of MDD were enrolled in the study with 80% completion rates for primary outcome assessments across all timepoints. 79.8% of people participated for the maximum amount of time available and 20.2% withdrew prematurely. Data availability across all RMT data types varied depending on the source of data and the participant-burden for each data type. We found no evidence of an association between the severity of depression symptoms at baseline and the availability of data. 110 participants had > 50% data available across all data types, and thus able to contribute to multiparametric analyses.
Conclusions
RADAR-MDD is the largest multimodal RMT study in the field of mental health. Here, we have shown that collecting RMT data from a clinical population is feasible.
Disclosure
No significant relationships.
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Biggs M, Ehrenreich K, Morris N, Blanchard K, Bustamante C, Choimorrow S, Hauser D, Hernandez Y, Kapp N, Kromenaker T, Moayedi G, Perritt J, Ralph L, Raymond E, Valladares E, White K, Grossman D. Comprehension of an Over-the-counter Drug Facts Label Prototype for a Mifepristone and Misoprostol Medication Abortion Product. Contraception 2022. [DOI: 10.1016/j.contraception.2022.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Dyer A, Lerma K, White K, Davis L. CLINICAL ORAL ABSTRACTS. Contraception 2022. [DOI: 10.1016/j.contraception.2022.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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23
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Williams MR, Welikhe P, Bos J, King K, Akland M, Augustine D, Baffaut C, Beck EG, Bierer A, Bosch DD, Boughton E, Brandani C, Brooks E, Buda A, Cavigelli M, Faulkner J, Feyereisen G, Fortuna A, Gamble J, Hanrahan B, Hussain M, Kohmann M, Kovar J, Lee B, Leytem A, Liebig M, Line D, Macrae M, Moorman T, Moriasi D, Nelson N, Ortega-Pieck A, Osmond D, Pisani O, Ragosta J, Reba M, Saha A, Sanchez J, Silveira M, Smith D, Spiegal S, Swain H, Unrine J, Webb P, White K, Wilson H, Yasarer L. P-FLUX: A phosphorus budget dataset spanning diverse agricultural production systems in the United States and Canada. J Environ Qual 2022; 51:451-461. [PMID: 35373848 DOI: 10.1002/jeq2.20351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
Quantifying spatial and temporal fluxes of phosphorus (P) within and among agricultural production systems is critical for sustaining agricultural production while minimizing environmental impacts. To better understand P fluxes in agricultural landscapes, P-FLUX, a detailed and harmonized dataset of P inputs, outputs, and budgets, as well as estimated uncertainties for each P flux and budget, was developed. Data were collected from 24 research sites and 61 production systems through the Long-term Agroecosystem Research (LTAR) network and partner organizations spanning 22 U.S. states and 2 Canadian provinces. The objectives of this paper are to (a) present and provide a description of the P-FLUX dataset, (b) provide summary analyses of the agricultural production systems included in the dataset and the variability in P inputs and outputs across systems, and (c) provide details for accessing the dataset, dataset limitations, and an example of future use. P-FLUX includes information on select site characteristics (area, soil series), crop rotation, P inputs (P application rate, source, timing, placement, P in irrigation water, atmospheric deposition), P outputs (crop removal, hydrologic losses), P budgets (agronomic budget, overall budget), uncertainties associated with each flux and budget, and data sources. Phosphorus fluxes and budgets vary across agricultural production systems and are useful resources to improve P use efficiency and develop management strategies to mitigate environmental impacts of agricultural systems. P-FLUX is available for download through the USDA Ag Data Commons (https://doi.org/10.15482/USDA.ADC/1523365).
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Affiliation(s)
- M R Williams
- National Soil Erosion Research Laboratory, USDA-ARS, West Lafayette, IN, USA
| | - P Welikhe
- National Soil Erosion Research Laboratory, USDA-ARS, West Lafayette, IN, USA
- Dep. of Agronomy, Purdue Univ., West Lafayette, IN, USA
| | - J Bos
- National Soil Erosion Research Laboratory, USDA-ARS, West Lafayette, IN, USA
| | - K King
- Soil Drainage Research Unit, USDA-ARS, Columbus, OH, USA
| | - M Akland
- Dep. of Plant and Soil Sciences, Univ. of Kentucky, Lexington, KY, USA
| | - D Augustine
- Rangeland Resources Research Unit, USDA-ARS, Fort Collins, CO, USA
| | - C Baffaut
- Cropping Systems and Water Quality Research Unit, USDA-ARS, Columbia, MO, USA
| | - E G Beck
- Kentucky Geological Survey, Univ. of Kentucky, Henderson, KY, USA
| | - A Bierer
- Northwest Irrigation and Soils Research Lab, USDA-ARS, Kimberly, ID, USA
| | - D D Bosch
- Southeast Watershed Research Laboratory, USDA-ARS, Tifton, GA, USA
| | - E Boughton
- Buck Island Ranch, Archbold Biological Station, Lake Placid, FL, USA
| | - C Brandani
- Dep. of Animal and Range Science, New Mexico State Univ., Las Cruces, NM, USA
| | - E Brooks
- Dep. of Soil and Water Resources, Univ. of Idaho, Moscow, ID, USA
| | - A Buda
- Systems and Watershed Management Research Unit, USDA-ARS, University Park, PA, USA
| | - M Cavigelli
- Sustainable Agricultural Systems Laboratory, USDA-ARS, Beltsville, MD, USA
| | - J Faulkner
- Dep. of Plant and Soil Science, Univ. of Vermont, Burlington, VT, USA
| | - G Feyereisen
- Soil and Water Management Unit, USDA-ARS, St. Paul, MN, USA
| | - A Fortuna
- Grazinglands Research Laboratory, USDA-ARS, El Reno, OK, USA
| | - J Gamble
- Soil and Water Management Unit, USDA-ARS, St. Paul, MN, USA
| | - B Hanrahan
- Soil Drainage Research Unit, USDA-ARS, Columbus, OH, USA
| | - M Hussain
- W.K. Kellogg Biological Station, Michigan State Univ., Hickory Corners, MI, USA
| | - M Kohmann
- Range Cattle Research and Education Center, Univ. of Florida, Ona, FL, USA
| | - J Kovar
- Agroecosystems Management Research, USDA-ARS, Ames, IA, USA
| | - B Lee
- Dep. of Plant and Soil Sciences, Univ. of Kentucky, Lexington, KY, USA
| | - A Leytem
- Northwest Irrigation and Soils Research Lab, USDA-ARS, Kimberly, ID, USA
| | - M Liebig
- Northern Great Plains Research Laboratory, USDA-ARS, Mandan, ND, USA
| | - D Line
- Dep. of Crop and Soil Sciences, North Carolina State Univ., Raleigh, NC, USA
| | - M Macrae
- Dep. of Geography and Environmental Management, Univ. of Waterloo, Waterloo, ON, Canada
| | - T Moorman
- Agroecosystems Management Research, USDA-ARS, Ames, IA, USA
| | - D Moriasi
- Grazinglands Research Laboratory, USDA-ARS, El Reno, OK, USA
| | - N Nelson
- Dep. of Agronomy, Kansas State Univ., Manhattan, KS, USA
| | - A Ortega-Pieck
- Dep. of Soil and Water Resources, Univ. of Idaho, Moscow, ID, USA
| | - D Osmond
- Dep. of Crop and Soil Sciences, North Carolina State Univ., Raleigh, NC, USA
| | - O Pisani
- Southeast Watershed Research Laboratory, USDA-ARS, Tifton, GA, USA
| | - J Ragosta
- USDA-ARS, Jornada Experimental Range, Las Cruces, NM, USA
| | - M Reba
- USDA-ARS, Delta Water Management Research Unit, Arkansas State Univ., Jonesboro, AR, USA
| | - A Saha
- Buck Island Ranch, Archbold Biological Station, Lake Placid, FL, USA
| | - J Sanchez
- Range Cattle Research and Education Center, Univ. of Florida, Ona, FL, USA
| | - M Silveira
- Range Cattle Research and Education Center, Univ. of Florida, Ona, FL, USA
| | - D Smith
- Grassland, Soil and Water Research Laboratory, USDA-ARS, Temple, TX, USA
| | - S Spiegal
- USDA-ARS, Jornada Experimental Range, Las Cruces, NM, USA
| | - H Swain
- Buck Island Ranch, Archbold Biological Station, Lake Placid, FL, USA
| | - J Unrine
- Dep. of Plant and Soil Sciences, Univ. of Kentucky, Lexington, KY, USA
| | - P Webb
- Dep. of Crop, Soil, and Environmental Sciences, Univ. of Arkansas, Fayetteville, AR, USA
| | - K White
- Sustainable Agricultural Systems Laboratory, USDA-ARS, Beltsville, MD, USA
| | - H Wilson
- Science and Technology Branch, Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, MB, Canada
| | - L Yasarer
- National Sedimentation Laboratory, USDA-ARS, Oxford, MS, USA
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Bond J, White K, Wise L. Feasibility of adding a sexual function questionnaire to a preconception cohort study. J Sex Med 2022. [DOI: 10.1016/j.jsxm.2022.03.584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Lerma K, Nagie A, Strelitz-Block E, White K. Perceptions of Legality and Availability of Abortion Care in Mississippi. Contraception 2022. [DOI: 10.1016/j.contraception.2022.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Faruqi U, White K, Murray N, Cutler J, Breen K. The impact of COVID-19 vaccination on patients with a history of heparin induced thrombocytopenia. Br J Haematol 2022; 197:422-423. [PMID: 35029298 DOI: 10.1111/bjh.18048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 11/30/2022]
Abstract
The newly classified entity of vaccine induced thrombocytopenia and thrombosis (VITT) following AstraZeneca Vaccination is an area of ongoing investigation. The underlying pathophysiology is considered to have pathological similarities to heparin induced thrombocytopenia (HIT). It is unclear which cohorts may be particularly susceptible to developing VITT. In view of the underlying mechanism of action we undertook a retrospective analysis of patients with a history of HIT to assess whether they had been vaccinated and to assess whether any patients had experienced adverse reactions to the AstraZeneca vaccination. 20 out of 60 patients with a confirmed history of HIT received the AstraZeneca vaccination and none of these reported any features suggestive of VITT.
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Affiliation(s)
- U Faruqi
- Department of Thrombosis and Haemostasis, Guys and St Thomas NHS Foundation Trust
| | - K White
- Department of Thrombosis and Haemostasis, Guys and St Thomas NHS Foundation Trust
| | - N Murray
- Department of Thrombosis and Haemostasis, Guys and St Thomas NHS Foundation Trust
| | - J Cutler
- Haemostasis and Thrombosis Laboratory Viapath Analytics
| | - K Breen
- Department of Thrombosis and Haemostasis, Guys and St Thomas NHS Foundation Trust
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Viotti Perisse I, Abercrombie B, Liu Y, Patrick T, Keim J, Benninghoff A, Polejaeva I, White K. 15 Identification of developmental genes regulated by H3K9me2 and H3K27me3 histone marks in bovine somatic cells and their somatic cell nuclear transfer embryos. Reprod Fertil Dev 2021; 34:241-242. [PMID: 35231357 DOI: 10.1071/rdv34n2ab15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
| | | | - Y Liu
- Utah State University, Logan, UT, USA
| | - T Patrick
- Utah State University, Logan, UT, USA
| | - J Keim
- Utah State University, Logan, UT, USA
| | | | | | - K White
- Utah State University, Logan, UT, USA
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Perisse IV, Fan Z, Liu Y, Leir S, Wettere AV, Harris A, White K, Polejaeva I. 670: F508del and G542X sheep models exhibit a severe cystic fibrosis phenotype, and their tracheal epithelial cells respond to human therapeutics in vitro. J Cyst Fibros 2021. [DOI: 10.1016/s1569-1993(21)02093-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Prewitt B, Weiss S, White K. M095 TAKING CYCLOSPORINE TO NEW HEIGHTS- DELAYED PRESSURE URTICARIA ASSOCIATED WITH ALTITUDE CHAMBER RESPONSIVE TO CYCLOSPORINE. Ann Allergy Asthma Immunol 2021. [DOI: 10.1016/j.anai.2021.08.249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Whitfield B, Vizcarra E, Dane'el A, Palomares L, D'Amore G, Maslowsky J, White K. POSTER ABSTRACTS. Contraception 2021. [DOI: 10.1016/j.contraception.2021.07.092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Jones R, White K, Batey A, Kostenko E. Cell-free DNA testing for prenatal aneuploidy assessment: analysis of professional society statements. Ultrasound Obstet Gynecol 2021; 57:840-841. [PMID: 32530137 DOI: 10.1002/uog.22120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/15/2020] [Accepted: 06/01/2020] [Indexed: 06/11/2023]
Affiliation(s)
- R Jones
- Medical and Scientific Affairs, Roche Sequencing Solutions, San Jose, CA, USA
| | - K White
- Medical and Scientific Affairs, Roche Sequencing Solutions, San Jose, CA, USA
| | - A Batey
- Medical and Scientific Affairs, Roche Sequencing Solutions, San Jose, CA, USA
| | - E Kostenko
- Medical and Scientific Affairs, Roche Sequencing Solutions, San Jose, CA, USA
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Curley K, Brown B, White K, Xiong M, Kovacs M, Shah A. Abstract No. 528 Modeling socioeconomic and demographic variables affecting inferior vena cava filter placement and retrieval: a single-institution retrospective review at a safety net hospital from 2012 to 2019. J Vasc Interv Radiol 2021. [DOI: 10.1016/j.jvir.2021.03.337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Gray AR, Davies OMT, White K, Ortega-Loayza AG. Granuloma annulare following initiation of interleukin-17a antagonist. Clin Exp Dermatol 2021; 46:924-926. [PMID: 33511635 DOI: 10.1111/ced.14579] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 01/21/2021] [Accepted: 01/26/2021] [Indexed: 12/24/2022]
Affiliation(s)
- A R Gray
- Department of Dermatology, Oregon Health and Science University, Portland, OR, USA
| | - O M T Davies
- Medical College of Wisconsin, Milwaukee, WI, USA
| | - K White
- Department of Dermatology, Oregon Health and Science University, Portland, OR, USA
| | - A G Ortega-Loayza
- Department of Dermatology, Oregon Health and Science University, Portland, OR, USA
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Bunch K, Perisse IV, Fan Z, White K, Polejaeva I. 95 Invitro correction of F508del and G542X mutations in sheep fibroblasts of cystic fibrosis models. Reprod Fertil Dev 2021. [DOI: 10.1071/rdv33n2ab95] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Cystic fibrosis (CF) is a human genetic disease caused by mutations in the CF transmembrane conductance regulator (CFTR) gene. Among the ∼2000 known CF mutations, the F508del mutation is found in 84% and G542X in 4.6% of the CF patients in the United States. The F508del mutation occurs in exon 11 and is characterised by deletion of the “CTT” nucleotides, resulting in deletion on the phenylalanine residue at the position 508 of CFTR. This causes misfolding of the CFTR protein, which is further degraded by proteases. The G542X mutation is a nonsense mutation found in exon 12 and associated with nonsense-mediated decay of the mutant transcript causing the absence of protein production. Previously, we generated CFTRF508del/F508del and CFTRG542X/G542X lambs (unpublished) using CRISPR/Cas9 and somatic cell nuclear transfer (SCNT) techniques. We hypothesised that gene editing may be an effective tool to correct these mutations and permanently cure this genetic disease. Thus, in this study, we evaluated the efficiency of CRISPR/Cas9-meditated gene knock-in to correct the F508del and G542X mutations in sheep fibroblasts invitro. We designed single guide (sg)RNAs using the Benchling software (https://benchling.com/academic) and approximately 100bp of single-stranded oligodeoxynucleotides (ssODNs) targeting the mutation sites at exon 11 and 12 to introduce either “CTT” or change the “T” to “G” nucleotide in genome of F508del or G542X CF sheep cells, respectively. Each of Cas9/sgRNA ribonucleoproteins was transfected into sheep fibroblast cells along with ssODNs using the Lonza-4D-NucleofectorTM (Lonza) system for homology-directed repair. The transfected cells were subsequently cultured in Dulbecco’s modified Eagle medium, supplemented with 15% fetal bovine serum and 1% penicillin, and incubated at 38.5°C. DNA was extracted 48h post-transfection to validate mutation efficiency. PCR products of the exons 11 and 12 were ligated into T-vector, and bacterial colonies were selected based on blue/white screening. In total, we isolated 32 single cell bacterial colonies for each mutant. Sequencing results indicate that “CTT” was introduced in 4/26 (15.3%) plasmid colonies, and “T to G” replaced in 13/31 (41.9%) colonies. Therefore, our results indicate that the F508del and G542X mutations can be effectively corrected in CF sheep fibroblasts invitro using a CRISPR/Cas9 approach.
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Schofield P, Gough K, Pascoe M, Bergin R, White K, Mileshkin L, Bernshaw D, Kinnane N, Jackson M, Do V, Brand A, Aranda S, Cheuk R, Drosdowsky A, Penberthy S, Juraskova I. A nurse- and peer-led psycho-educational intervention to support women with gynaecological cancers receiving curative radiotherapy: The PeNTAGOn randomised controlled trial – ANZGOG 1102. Gynecol Oncol 2020; 159:785-793. [DOI: 10.1016/j.ygyno.2020.09.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 09/08/2020] [Indexed: 12/01/2022]
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Findlay M, White K, Stapleton N, Bauer J. Is sarcopenia a predictor of prognosis for patients with head and neck cancer undergoing radiotherapy of curative intent? a systematic review and meta-analysis. Clin Nutr ESPEN 2020. [DOI: 10.1016/j.clnesp.2020.09.058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Connor K, Murray DW, Jarzabek MA, Tran NL, White K, Dicker P, Sweeney KJ, O’Halloran PJ, MacCarthy B, Shiels LP, Lodi F, Lambrechts D, Sarkaria JN, Schiffelers RM, Symons M, Byrne AT. Targeting the RhoGEF βPIX/COOL-1 in Glioblastoma: Proof of Concept Studies. Cancers (Basel) 2020; 12:cancers12123531. [PMID: 33256106 PMCID: PMC7761123 DOI: 10.3390/cancers12123531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/15/2020] [Accepted: 11/19/2020] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Glioblastoma (GBM) is an incurable disease with a 14-month average life-expectancy following diagnosis, and clinical management has not improved in four decades. GBM mortality is due to rapid tumour growth and invasion into surrounding normal brain. Invasive cells make complete surgical removal of the tumour impossible, and result in disease relapse. Thus, it is imperative that any new treatment strategy takes these invading cells into consideration. Bevacizumab (Bev), which prevents the formation of new blood vessels, is an FDA approved therapy, but it has failed to increase overall survival in GBM and has even been shown to increase tumour invasion in some cases. Complementary anti-invasive therapies are therefore urgently required to enhance bevacizumab efficacy. We have identified βPIX/COOL-1, a RhoGEF protein which plays an important role in GBM cell invasion and angiogenesis and could be a useful target in this setting. Abstract Glioblastoma (GBM), a highly invasive and vascular malignancy is shown to rapidly develop resistance and evolve to a more invasive phenotype following bevacizumab (Bev) therapy. Rho Guanine Nucleotide Exchange Factor proteins (RhoGEFs) are mediators of key components in Bev resistance pathways, GBM and Bev-induced invasion. To identify GEFs with enhanced mRNA expression in the leading edge of GBM tumours, a cohort of GEFs was assessed using a clinical dataset. The GEF βPix/COOL-1 was identified, and the functional effect of gene depletion assessed using 3D-boyden chamber, proliferation, and colony formation assays in GBM cells. Anti-angiogenic effects were assessed in endothelial cells using tube formation and wound healing assays. In vivo effects of βPix/COOL-1-siRNA delivered via RGD-Nanoparticle in combination with Bev was studied in an invasive model of GBM. We found that siRNA-mediated knockdown of βPix/COOL-1 in vitro decreased cell invasion, proliferation and increased apoptosis in GBM cell lines. Moreover βPix/COOL-1 mediated endothelial cell migration in vitro. Mice treated with βPix/COOL-1 siRNA-loaded RGD-Nanoparticle and Bev demonstrated a trend towards improved median survival compared with Bev monotherapy. Our hypothesis generating study suggests that the RhoGEF βPix/COOL-1 may represent a target of vulnerability in GBM, in particular to improve Bev efficacy.
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Affiliation(s)
- Kate Connor
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland; (K.C.); (D.W.M.); (M.A.J.); (K.W.); (K.J.S.); (P.J.O.); (B.M.); (L.P.S.)
| | - David W. Murray
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland; (K.C.); (D.W.M.); (M.A.J.); (K.W.); (K.J.S.); (P.J.O.); (B.M.); (L.P.S.)
| | - Monika A. Jarzabek
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland; (K.C.); (D.W.M.); (M.A.J.); (K.W.); (K.J.S.); (P.J.O.); (B.M.); (L.P.S.)
| | - Nhan L. Tran
- Department of Cancer Biology and Neurological Surgery, Mayo Clinic Arizona, Scottsdale, AZ 85054, USA;
| | - Kieron White
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland; (K.C.); (D.W.M.); (M.A.J.); (K.W.); (K.J.S.); (P.J.O.); (B.M.); (L.P.S.)
| | - Patrick Dicker
- Epidemiology & Public Health, Royal College of Surgeons in Ireland, Dublin 2, Ireland;
| | - Kieron J. Sweeney
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland; (K.C.); (D.W.M.); (M.A.J.); (K.W.); (K.J.S.); (P.J.O.); (B.M.); (L.P.S.)
- National Neurosurgical Department, Beaumont Hospital, Dublin 9, Ireland
| | - Philip J. O’Halloran
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland; (K.C.); (D.W.M.); (M.A.J.); (K.W.); (K.J.S.); (P.J.O.); (B.M.); (L.P.S.)
- National Neurosurgical Department, Beaumont Hospital, Dublin 9, Ireland
| | - Brian MacCarthy
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland; (K.C.); (D.W.M.); (M.A.J.); (K.W.); (K.J.S.); (P.J.O.); (B.M.); (L.P.S.)
| | - Liam P. Shiels
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland; (K.C.); (D.W.M.); (M.A.J.); (K.W.); (K.J.S.); (P.J.O.); (B.M.); (L.P.S.)
| | - Francesca Lodi
- Center for Cancer Biology, Laboratory for Translational Genetics, Vlaams Instituut voor Biotechnologie (VIB), B-3000 Leuven, Belgium; (F.L.); (D.L.)
| | - Diether Lambrechts
- Center for Cancer Biology, Laboratory for Translational Genetics, Vlaams Instituut voor Biotechnologie (VIB), B-3000 Leuven, Belgium; (F.L.); (D.L.)
| | - Jann N. Sarkaria
- Department of Radiation Oncology, Mayo Clinic, Rochester, MN 55905, USA;
| | - Raymond M. Schiffelers
- Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, 100 3584 Utrecht, The Netherlands;
| | - Marc Symons
- Department of Oncology & Cell Biology, Feinstein Institute for Medical Research at North Shore-LIJ, Manhasset, NY 11030, USA;
| | - Annette T. Byrne
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland; (K.C.); (D.W.M.); (M.A.J.); (K.W.); (K.J.S.); (P.J.O.); (B.M.); (L.P.S.)
- Correspondence: ; Tel.: +353-1-402-8673
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Clerkin J, Connor K, Sweeney K, White K, Shiels L, Maher S, Marignol L, Prehn JHM, O’Brien D, Byrne A. TMOD-12. ESTABLISHING A CLINICALLY RELEVANT MODEL OF MESENCHYMAL GLIOBLASTOMA (GBM) TO STUDY RESPONSE TO STANDARD OF CARE TREATMENT AND IMMUNE CHECKPOINT INHIBITION (ICI). Neuro Oncol 2020. [DOI: 10.1093/neuonc/noaa215.963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
GBM is a devastating disease with peak incidence in the seventh decade. Pre-clinical models are essential for studying resistance mechanisms and screening novel therapies. However, historically these models have failed to predict response in humans. Current models seldom incorporate surgical resection, and commonly use young animals whose immune contexture differs from older patients. Here, we have established an orthotopic model employing the syngeneic mesenchymal-NFpp10a-cell line which incorporates surgical resection in aged mice. We further characterise response to ICI and temozolomide monotherapy. NFpp10a and GL261-cell lines were exposed in vitro to irradiation (0Gy/2Gy/5Gy) and response assessed using colony formation assays. NFpp10a formed significantly more colonies at 5Gy compared to GL261 at both day 10 (NFpp10a 5.167 vs GL261 1.4; p=0.0017) and day 14 (NFpp10a 3.5 vs GL261 0; p< 0.0001). Hence, NFpp10a displays increased radioresistance. Next, NFpp10a-luciferin expressing cells were orthotopically implanted into young (6-8weeks;n=16) and aged (18months;n=16) C57BL/6-mice. Weekly bioluminescence imaging (BLI) was performed to monitor growth. Mice undergoing resection showed a median 18.47-fold drop in BLI signal. We demonstrated resection survival advantage in aged mice (Resection:33.5 days vs Non-Resection:18 days, p= 0.0166) and showed young age to be a positive prognostic factor (Young:62 days vs Aged:22 days, p=0.0002). Subsequently, we orthotopically implanted NFpp10a-Luc2 cells into C57BL/6 mice and treated with temozolomide (n=24) or PBS control (n=23), and anti-PD1 (n=24) or IgG (n=23). We observed that temozolomide and anti-PD1 monotherapy had no impact on NFpp10-Luc2 growth (temozolomide-overall:p=0.9001, anti-PD1-overall:p=0.7933) or survival (temozolomide-overall:p=0.3035, anti-PD1-overall:p=0.6328). Overall, we have established an NFpp10-Luc2 mesenchymal-GBM model in aged mice which incorporates surgical resection and accurately displays significant resistance to temozolomide and anti-PD1 monotherapy. We are currently employing this model to study the efficacy of neoadjuvant anti-PD1 therapy. Mechanistic analyses with multiplex-immunohistochemistry, scRNA and whole exome sequencing are planned to interrogate treatment effects on the tumor microenvironment.
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Affiliation(s)
- James Clerkin
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Kate Connor
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Kieron Sweeney
- Department of Neurosurgery, Beaumont Hospital, Dublin, Ireland
| | - Kieron White
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Liam Shiels
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Stephen Maher
- Trinity Translational Medicine Institute, Trinity St James’s Cancer Institute, St. James Hospital, Dublin, Ireland
| | - Laure Marignol
- Discipline of Radiation Therapy Trinity Centre for Health Sciences St. James’s Hospital, Dublin, Ireland
| | - Jochen H M Prehn
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - David O’Brien
- Department of Neurosurgery, Beaumont Hospital, Dublin, Ireland
| | - Annette Byrne
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
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Connor K, Conroy E, White K, Shiels L, Gallagher W, Keek S, Ibrahim A, Clerkin J, O’Brien D, Lambin P, Woodruff H, Byrne A. EXTH-30. EXPANDING THE UTILITY OF PRE-CLINICAL CONTRAST ENHANCED CT (CE-CT) FOR TUMOR DETECTION IN ORTHOTOPIC GBM MODELS USING RADIOMICS. Neuro Oncol 2020. [DOI: 10.1093/neuonc/noaa215.384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Despite magnetic resonance imaging (MRI) being the gold-standard imaging modality in the glioblastoma (GBM) setting, the availability of rodent MRI scanners is relatively limited. CT is a clinically relevant alternative which is more widely available in the pre-clinic. To study the utility of contrast-enhanced (CE)-CT in GBM xenograft modelling, we optimized CT protocols on two instruments (IVIS-SPECTRUM-CT;TRIUMPH-PET/CT) with/without delivery of contrast. As radiomics analysis may facilitate earlier detection of tumors by CT alone, allowing for deeper analyses of tumor characteristics, we established a radiomic pipeline for extraction and selection of tumor specific CT-derived radiomic features (inc. first order statistics/texture features). U87R-Luc2 GBM cells were implanted orthotopically into NOD/SCID mice (n=25) and tumor growth monitored via weekly BLI. Concurrently mice underwent four rounds of CE-CT (IV iomeprol/iopamidol; 50kV-scan). N=45 CE-CT images were semi-automatically delineated and radiomic features were extracted (Pyradiomics 2.2.0) at each imaging timepoint. Differences between normal and tumor tissue were analyzed using recursive selection. Using either CT instrument/contrast, tumors > 0.4cm3 were not detectable until week-9 post-implantation. Radiomic analysis identified three features (waveletHHH_firstorder_Median, original_glcm_Correlation and waveletLHL_firstorder_Median) at week-3 and -6 which may be early indicators of tumor presence. These features are now being assessed in CE-CT scans collected pre- and post-temozolomide treatment in a syngeneic model of mesenchymal GBM. Nevertheless, BLI is significantly more sensitive than CE-CT (either visually or using radiomic-enhanced CT feature extraction) with luciferase-positive tumors detectable at week-1. In conclusion, U87R-Luc2 tumors > 0.4cm3 are only detectable by Week-8 using CE-CT and either CT instrument studied. Nevertheless, radiomic analysis has defined features which may allow for earlier tumor detection at Week-3, thus expanding the utility of CT in the preclinical setting. Overall, this work supports the discovery of putative prognostic pre-clinical CT-derived radiomic signatures which may ultimately be assessed as early disease markers in patient datasets.
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Affiliation(s)
- Kate Connor
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Emer Conroy
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Kieron White
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Liam Shiels
- Dept Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - William Gallagher
- bUCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Simon Keek
- The D-Lab: Department of Precision Medicine, GROW - School for Oncology, Maastricht University, Maastricht, Netherlands
| | - Abdalla Ibrahim
- The D-Lab: Department of Precision Medicine, GROW - School for Oncology, Maastricht University, Maastricht, Netherlands
| | - James Clerkin
- Dept Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - David O’Brien
- Department of Neurosurgery, Beaumont Hospital, Dublin, Ireland
| | - Philippe Lambin
- The D-Lab: Department of Precision Medicine, GROW - School for Oncology, Maastricht University, Maastricht, Netherlands
| | - Henry Woodruff
- The D-Lab: Department of Precision Medicine, GROW - School for Oncology, Maastricht University, Maastricht, Netherlands
| | - Annette Byrne
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, York Street, Dublin, Ireland
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White K, Meylan M, Bougoüin A, Connor K, Salvucci M, Bielle F, Prehn JHM, Verreault M, Idbaih A, Sautès-Fridman C, Fridman WH, Byrne A. TAMI-51. IDENTIFYING NEW TUMOR MICROENVIRONMENT (TME) CONTEXTS OF VULNERABILITY IN GLIOBLASTOMA. Neuro Oncol 2020. [DOI: 10.1093/neuonc/noaa215.938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Glioblastoma (GBM) is the most frequent and aggressive adult brain tumor with 85% of patients dying within two years. New effective precision medicine therapies are urgently required, especially for isocitrate dehydrogenase wild-type (IDHwt) disease. Despite efforts to subtype patients based on molecular profiles, this approach has yet failed to direct treatment strategies. Further interrogation of the tumor microenvironment (TME) across molecular subtypes and identification of new TME specific subtypes may guide new directions for future therapies. Here, we analysed transcriptomic data from selected GLIOTRAIN(www.gliotrain.eu)(n=120) and TCGA(n=69) IDHwt patients. Firstly, the microenvironment cell population (MCP)-counter method (a gene-expression-based TME deconvolution tool) was validated for use in the brain tumor setting using quantitative multiplex immunohistochemistry. In this context, immune markers (CD20/CD3/CD68/CD8) were significantly correlated with MCP-counter scores. We are currently optimizing and validating a vessel-density and microglial RNA-signature to provide a more robust representation of brain TME. Next, using MCP-counter, the TME composition of IDHwt tumors was assessed within proneural (24%), classical (38%) and mesenchymal (38%) subtypes. We initially classified the GLIOTRAIN cohort into 3 novel clusters characterised by differences in TME composition and validated our findings in the TCGA cohort. A TME-high group (37%) is characterized by elevated presence of lymphocytes and myeloid cells, and presents a high level of immune checkpoint genes: PDCD1(PD1) and CTLA4. In addition, the presence of tertiary lymphoid structures (TLS) is a feature of TMEhigh/mesenchymal+ patients. This finding has been validated by IHC and RNA-signature. TME-med (38%) displayed heterogenous immune populations and the TME-low (25%) represented an ‘immune-desert’ group. There was no significant difference in OS based on these TME subtypes(p=0.50). We hypothesise that PD1/CTLA4 blockade might be an effective treatment strategy in TME-high patients. These hypotheses will be tested (in the adjuvant setting) using appropriate syngeneic disease models which incorporate surgical resection.
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Affiliation(s)
- Kieron White
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Maxime Meylan
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC, Université de Paris, Paris, France
| | - Antoine Bougoüin
- INSERM UMR_S 1138, Cancer, Immune Control and Escape, Cordeliers Research Centre, Paris, France
| | - Kate Connor
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Manuela Salvucci
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Franck Bielle
- Brain and Spine Institute (ICM), CNRS UMR 7225, Inserm U 1127, UPMC-P6 UMR S 1127, Hôpital de la Pitié - Salpêtrière - Paris, France
| | - Jochen H M Prehn
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Maite Verreault
- INSERM UMR_S 1138, Cancer, Immune Control and Escape, Cordeliers Research Centre, Paris, France
| | - Ahmed Idbaih
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie, Paris, France
| | - Catherine Sautès-Fridman
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC, Université de Paris, Paris, France
| | - Wolf H Fridman
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC, Université de Paris, Paris, France
| | - Annette Byrne
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
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Wiltink L, White K, King M, Rutherford C. PO-1079: Systematic review of colorectal/anal cancer guidelines: managing long-term symptoms and functioning. Radiother Oncol 2020. [DOI: 10.1016/s0167-8140(21)01096-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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O’Farrell AC, Jarzabek MA, Lindner AU, Carberry S, Conroy E, Miller IS, Connor K, Shiels L, Zanella ER, Lucantoni F, Lafferty A, White K, Meyer Villamandos M, Dicker P, Gallagher WM, Keek SA, Sanduleanu S, Lambin P, Woodruff HC, Bertotti A, Trusolino L, Byrne AT, Prehn JHM. Implementing Systems Modelling and Molecular Imaging to Predict the Efficacy of BCL-2 Inhibition in Colorectal Cancer Patient-Derived Xenograft Models. Cancers (Basel) 2020; 12:cancers12102978. [PMID: 33066609 PMCID: PMC7602510 DOI: 10.3390/cancers12102978] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 10/09/2020] [Indexed: 12/24/2022] Open
Abstract
Resistance to chemotherapy often results from dysfunctional apoptosis, however multiple proteins with overlapping functions regulate this pathway. We sought to determine whether an extensively validated, deterministic apoptosis systems model, 'DR_MOMP', could be used as a stratification tool for the apoptosis sensitiser and BCL-2 antagonist, ABT-199 in patient-derived xenograft (PDX) models of colorectal cancer (CRC). Through quantitative profiling of BCL-2 family proteins, we identified two PDX models which were predicted by DR_MOMP to be sufficiently sensitive to 5-fluorouracil (5-FU)-based chemotherapy (CRC0344), or less responsive to chemotherapy but sensitised by ABT-199 (CRC0076). Treatment with ABT-199 significantly improved responses of CRC0076 PDXs to 5-FU-based chemotherapy, but showed no sensitisation in CRC0344 PDXs, as predicted from systems modelling. 18F-Fluorodeoxyglucose positron emission tomography/computed tomography (18F-FDG-PET/CT) scans were performed to investigate possible early biomarkers of response. In CRC0076, a significant post-treatment decrease in mean standard uptake value was indeed evident only in the combination treatment group. Radiomic CT feature analysis of pre-treatment images in CRC0076 and CRC0344 PDXs identified features which could phenotypically discriminate between models, but were not predictive of treatment responses. Collectively our data indicate that systems modelling may identify metastatic (m)CRC patients benefitting from ABT-199, and that 18F-FDG-PET could independently support such predictions.
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Affiliation(s)
- Alice C. O’Farrell
- Precision Cancer Medicine Group, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, D02 YN77 Dublin, Ireland; (A.C.O.); (M.A.J.); (I.S.M.); (K.C.); (L.S.); (A.L.); (K.W.); (A.T.B.)
| | - Monika A. Jarzabek
- Precision Cancer Medicine Group, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, D02 YN77 Dublin, Ireland; (A.C.O.); (M.A.J.); (I.S.M.); (K.C.); (L.S.); (A.L.); (K.W.); (A.T.B.)
| | - Andreas U. Lindner
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, D02 YN77 Dublin, Ireland; (A.U.L.); (S.C.); (F.L.); (M.M.V.)
| | - Steven Carberry
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, D02 YN77 Dublin, Ireland; (A.U.L.); (S.C.); (F.L.); (M.M.V.)
| | - Emer Conroy
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland; (E.C.); (W.M.G.)
| | - Ian S. Miller
- Precision Cancer Medicine Group, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, D02 YN77 Dublin, Ireland; (A.C.O.); (M.A.J.); (I.S.M.); (K.C.); (L.S.); (A.L.); (K.W.); (A.T.B.)
| | - Kate Connor
- Precision Cancer Medicine Group, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, D02 YN77 Dublin, Ireland; (A.C.O.); (M.A.J.); (I.S.M.); (K.C.); (L.S.); (A.L.); (K.W.); (A.T.B.)
| | - Liam Shiels
- Precision Cancer Medicine Group, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, D02 YN77 Dublin, Ireland; (A.C.O.); (M.A.J.); (I.S.M.); (K.C.); (L.S.); (A.L.); (K.W.); (A.T.B.)
| | - Eugenia R. Zanella
- Candiolo Cancer Institute—FPO IRCCS, Candiolo, 10060 Torino, Italy; (E.R.Z.); (A.B.); (L.T.)
- Department of Oncology, University of Torino, Candiolo, 10060 Torino, Italy
| | - Federico Lucantoni
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, D02 YN77 Dublin, Ireland; (A.U.L.); (S.C.); (F.L.); (M.M.V.)
| | - Adam Lafferty
- Precision Cancer Medicine Group, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, D02 YN77 Dublin, Ireland; (A.C.O.); (M.A.J.); (I.S.M.); (K.C.); (L.S.); (A.L.); (K.W.); (A.T.B.)
| | - Kieron White
- Precision Cancer Medicine Group, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, D02 YN77 Dublin, Ireland; (A.C.O.); (M.A.J.); (I.S.M.); (K.C.); (L.S.); (A.L.); (K.W.); (A.T.B.)
| | - Mariangela Meyer Villamandos
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, D02 YN77 Dublin, Ireland; (A.U.L.); (S.C.); (F.L.); (M.M.V.)
| | - Patrick Dicker
- Department of Epidemiology and Public Health Medicine, Royal College of Surgeons in Ireland, D02 YN77 Dublin, Ireland;
| | - William M. Gallagher
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland; (E.C.); (W.M.G.)
| | - Simon A. Keek
- The D-Lab, Department of Precision Medicine, GROW—School for Oncology, Maastricht University, 6229 ER Maastricht, The Netherlands; (S.A.K.); (S.S.); (P.L.); (H.C.W.)
| | - Sebastian Sanduleanu
- The D-Lab, Department of Precision Medicine, GROW—School for Oncology, Maastricht University, 6229 ER Maastricht, The Netherlands; (S.A.K.); (S.S.); (P.L.); (H.C.W.)
| | - Philippe Lambin
- The D-Lab, Department of Precision Medicine, GROW—School for Oncology, Maastricht University, 6229 ER Maastricht, The Netherlands; (S.A.K.); (S.S.); (P.L.); (H.C.W.)
- Department of Radiology and Nuclear Imaging, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands
| | - Henry C. Woodruff
- The D-Lab, Department of Precision Medicine, GROW—School for Oncology, Maastricht University, 6229 ER Maastricht, The Netherlands; (S.A.K.); (S.S.); (P.L.); (H.C.W.)
- Department of Radiology and Nuclear Imaging, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands
| | - Andrea Bertotti
- Candiolo Cancer Institute—FPO IRCCS, Candiolo, 10060 Torino, Italy; (E.R.Z.); (A.B.); (L.T.)
- Department of Oncology, University of Torino, Candiolo, 10060 Torino, Italy
| | - Livio Trusolino
- Candiolo Cancer Institute—FPO IRCCS, Candiolo, 10060 Torino, Italy; (E.R.Z.); (A.B.); (L.T.)
- Department of Oncology, University of Torino, Candiolo, 10060 Torino, Italy
| | - Annette T. Byrne
- Precision Cancer Medicine Group, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, D02 YN77 Dublin, Ireland; (A.C.O.); (M.A.J.); (I.S.M.); (K.C.); (L.S.); (A.L.); (K.W.); (A.T.B.)
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland; (E.C.); (W.M.G.)
| | - Jochen H. M. Prehn
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, D02 YN77 Dublin, Ireland; (A.U.L.); (S.C.); (F.L.); (M.M.V.)
- Correspondence: ; Tel.: +353-1-402-2255
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White K, Sierra G, Baum S, Hopkins K, Potter J, Grossman D. P19 Attitudes about second-trimester abortion and the impact of restrictive laws among reproductive-aged Texas women. Contraception 2020. [DOI: 10.1016/j.contraception.2020.07.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Raifman S, Sierra G, Grossman D, Baum S, Hopkins K, Potter J, White K. O1 Out-of-state abortions increased for Texas residents after House Bill 2. Contraception 2020. [DOI: 10.1016/j.contraception.2020.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Coleman-Minahan K, Ela E, White K, Grossman D. P60 Contraindications to hormonal contraception among postpartum women in Texas. Contraception 2020. [DOI: 10.1016/j.contraception.2020.07.079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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47
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White K, Connor K, Clerkin J, Murphy BM, Salvucci M, O'Farrell AC, Rehm M, O'Brien D, Prehn JHM, Niclou SP, Lamfers MLM, Verreault M, Idbaih A, Verhaak R, Golebiewska A, Byrne AT. New hints towards a precision medicine strategy for IDH wild-type glioblastoma. Ann Oncol 2020; 31:1679-1692. [PMID: 32918998 DOI: 10.1016/j.annonc.2020.08.2336] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 08/18/2020] [Accepted: 08/31/2020] [Indexed: 12/11/2022] Open
Abstract
Glioblastoma represents the most common primary malignancy of the central nervous system in adults and remains a largely incurable disease. The elucidation of disease subtypes based on mutational profiling, gene expression and DNA methylation has so far failed to translate into improved clinical outcomes. However, new knowledge emerging from the subtyping effort in the IDH-wild-type setting may provide directions for future precision therapies. Here, we review recent learnings in the field, and further consider how tumour microenvironment differences across subtypes may reveal novel contexts of vulnerability. We discuss recent treatment approaches and ongoing trials in the IDH-wild-type glioblastoma setting, and propose an integrated discovery stratagem incorporating multi-omics, single-cell technologies and computational approaches.
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Affiliation(s)
- K White
- Precision Cancer Medicine Group, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - K Connor
- Precision Cancer Medicine Group, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - J Clerkin
- Precision Cancer Medicine Group, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland; National Neurosurgical Department, Beaumont Hospital, Dublin, Ireland
| | - B M Murphy
- Centre for Systems Medicine, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - M Salvucci
- Centre for Systems Medicine, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - A C O'Farrell
- Precision Cancer Medicine Group, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - M Rehm
- Institute of Cell Biology and Immunology and Stuttgart Research Center Systems Biology, University of Stuttgart, Stuttgart, Germany
| | - D O'Brien
- National Neurosurgical Department, Beaumont Hospital, Dublin, Ireland
| | - J H M Prehn
- Centre for Systems Medicine, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - S P Niclou
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg
| | - M L M Lamfers
- Department of Neurosurgery, Brain Tumor Center, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - M Verreault
- Sorbonne Université, Institut du Cerveau et de la Moelle Épinière, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie, Paris, France
| | - A Idbaih
- Sorbonne Université, Institut du Cerveau et de la Moelle Épinière, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie, Paris, France
| | - R Verhaak
- Jackson Laboratory for Genomic Medicine, Farmington, USA
| | - A Golebiewska
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg
| | - A T Byrne
- Precision Cancer Medicine Group, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland.
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Abstract
The purpose of this ex post facto study was to determine what personality factors and demographic characteristics are related to acceptance or rejection of mobility training for adventitiously blind adults. The sample consisted of 79 subjects who had accepted mobility training and 60 subjects who had rejected training. The results indicated that the groups varied significantly on 7 of the 13 personality scales of the MMPI. No significant differences were found for any of the demographic variables. Different approaches to service for resistant clients are suggested.
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Affiliation(s)
- K. White
- Northern Arizona University (NAU)
| | - R. Carroll
- Institute for Human Development at Northern Arizona University, NAU/IHD, Box 563, Flagstaff, AZ 86011-5630
| | - W. Martin
- Institute for Human Development and NAU
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49
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Browning L, Fryer E, Roskell D, White K, Colling R, Rittscher J, Verrill C. Role of digital pathology in diagnostic histopathology in the response to COVID-19: results from a survey of experience in a UK tertiary referral hospital. J Clin Pathol 2020; 74:129-132. [PMID: 32616541 PMCID: PMC7841475 DOI: 10.1136/jclinpath-2020-206786] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 06/05/2020] [Indexed: 12/21/2022]
Abstract
The COVID-19 pandemic has challenged our diagnostic services at a time when many histopathology departments already faced a diminishing workforce and increasing workload. Digital pathology (DP) has been hailed as a potential solution to at least some of the challenges faced. We present a survey of pathologists within a UK National Health Service cellular pathology department with access to DP, in which we ascertain the role of DP in clinical services during this current pandemic and explore challenges encountered. This survey indicates an increase in uptake of diagnostic DP during this period, with increased remote access. Half of respondents agreed that DP had facilitated maintenance of diagnostic practice. While challenges have been encountered, these are remediable, and none have impacted on the uptake of DP during this period. We conclude that in our institution, DP has demonstrated current and future potential to increase resilience in diagnostic practice and have highlighted some of the challenges that need to be considered.
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Affiliation(s)
- Lisa Browning
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, Oxfordshire, UK .,NIHR Oxford Biomedical Research Centre, Oxford, Oxfordshire, UK
| | - Eve Fryer
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, Oxfordshire, UK
| | - Derek Roskell
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, Oxfordshire, UK
| | - Kieron White
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, Oxfordshire, UK
| | - Richard Colling
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, Oxfordshire, UK.,Nuffield Department of Surgical Sciences, University of Oxford, Oxford, Oxfordshire, UK
| | - Jens Rittscher
- NIHR Oxford Biomedical Research Centre, Oxford, Oxfordshire, UK.,Department of Engineering Science, University of Oxford, Oxford, Oxfordshire, UK
| | - Clare Verrill
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, Oxfordshire, UK.,NIHR Oxford Biomedical Research Centre, Oxford, Oxfordshire, UK.,Nuffield Department of Surgical Sciences, University of Oxford, Oxford, Oxfordshire, UK
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50
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Findlay M, Brown C, De Abreu Lourenço R, White K, Bauer J. Sarcopenia and myosteatosis in patients undergoing curative radiotherapy for head and neck cancer: Impact on survival, treatment completion, hospital admission and cost. J Hum Nutr Diet 2020; 33:811-821. [PMID: 32609428 DOI: 10.1111/jhn.12788] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
BACKGROUND Computed tomography (CT) is the gold standard of body composition analysis at the tissue-organ level. The present study aimed to determine the impact of CT-defined sarcopenia and myosteatosis on outcomes, including overall survival, unplanned hospital admissions and related costs, in patients who had completed treatment of curative intent for head and neck cancer (HNC). METHODS Retrospective observational study of patients undergoing radiotherapy of curative intent ± other treatment modalities for HNC. Tissue density data derived at the third lumbar vertebra (L3) were evaluated with sarcopenia defined per sex-specific published threshold values for skeletal muscle index, stratified by body mass index and mean skeletal muscle attenuation in HU (Hounsfield units). RESULTS Pre- or post-treatment images were available for 79/98 patients (80.6%) and 61/98 patients (62.2%), respectively. Sarcopenia was present in 42/79 patients pre-treatment and 36/61 patients post-treatment, whereas myosteatosis was present in 63/79 patients pre-treatment and 48/61 patients post-treatment. In patients with pre- and post-treatment images (n = 60), the median (range) percentage weight change was -8.5% (-29.9 to +11.7). On multivariable analysis, a post-treatment sarcopenia hazard ratio of 3.87 (95% confidence interval = 1.22-12.24, P = 0.021) and a pre-treatment myosteatosis hazard ratio of 8.86 (95% confidence interval = 1.12-69.88, P = 0.038) were independent predictors of reduced overall survival. There was no difference in radiotherapy or chemotherapy treatment completion based on pre-treatment sarcopenia status. The mean (SD) difference unplanned hospital admission cost was $15 846 ($17 707) for patients without sarcopenia versus $47 945 ($82 688) for patients with sarcopenia at any time point (P = 0.077). CONCLUSIONS As CT-defined sarcopenia and myosteatosis hold clinically meaningful prognostic value, muscle status evaluation is recommended in routine clinical practice.
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Affiliation(s)
- M Findlay
- Cancer Services, Royal Prince Alfred Hospital, Sydney, NSW, Australia.,Chris O'Brien Lifehouse, Sydney, NSW, Australia.,Cancer Nursing Research Unit, Faculty of Medicine and Health, Susan Wakil School of Nursing and Midwifery, University of Sydney, Sydney, NSW, Australia
| | - C Brown
- National Health and Medical Research Council Clinical Trials Centre, The University of Sydney, Sydney, NSW, Australia
| | - R De Abreu Lourenço
- Centre for Health Economics Research and Evaluation, University of Technology Sydney, Sydney, NSW, Australia
| | - K White
- Cancer Nursing Research Unit, Faculty of Medicine and Health, Susan Wakil School of Nursing and Midwifery, University of Sydney, Sydney, NSW, Australia
| | - J Bauer
- School of Human Movement and Nutrition Sciences, University of Queensland, Brisbane, QLD, Australia
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