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Wyatt NJ, Watson H, Anderson CA, Kennedy NA, Raine T, Ahmad T, Allerton D, Bardgett M, Clark E, Clewes D, Cotobal Martin C, Doona M, Doyle JA, Frith K, Hancock HC, Hart AL, Hildreth V, Irving PM, Iqbal S, Kennedy C, King A, Lawrence S, Lees CW, Lees R, Letchford L, Liddle T, Lindsay JO, Maier RH, Mansfield JC, Marchesi JR, McGregor N, McIntyre RE, Ostermayer J, Osunnuyi T, Powell N, Prescott NJ, Satsangi J, Sharma S, Shrestha T, Speight A, Strickland M, Wason JM, Whelan K, Wood R, Young GR, Zhang X, Parkes M, Stewart CJ, Jostins-Dean L, Lamb CA. Defining predictors of responsiveness to advanced therapies in Crohn's disease and ulcerative colitis: protocol for the IBD-RESPONSE and nested CD-metaRESPONSE prospective, multicentre, observational cohort study in precision medicine. BMJ Open 2024; 14:e073639. [PMID: 38631839 PMCID: PMC11029295 DOI: 10.1136/bmjopen-2023-073639] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 02/20/2024] [Indexed: 04/19/2024] Open
Abstract
INTRODUCTION Characterised by chronic inflammation of the gastrointestinal tract, inflammatory bowel disease (IBD) symptoms including diarrhoea, abdominal pain and fatigue can significantly impact patient's quality of life. Therapeutic developments in the last 20 years have revolutionised treatment. However, clinical trials and real-world data show primary non-response rates up to 40%. A significant challenge is an inability to predict which treatment will benefit individual patients.Current understanding of IBD pathogenesis implicates complex interactions between host genetics and the gut microbiome. Most cohorts studying the gut microbiota to date have been underpowered, examined single treatments and produced heterogeneous results. Lack of cross-treatment comparisons and well-powered independent replication cohorts hampers the ability to infer real-world utility of predictive signatures.IBD-RESPONSE will use multi-omic data to create a predictive tool for treatment response. Future patient benefit may include development of biomarker-based treatment stratification or manipulation of intestinal microbial targets. IBD-RESPONSE and downstream studies have the potential to improve quality of life, reduce patient risk and reduce expenditure on ineffective treatments. METHODS AND ANALYSIS This prospective, multicentre, observational study will identify and validate a predictive model for response to advanced IBD therapies, incorporating gut microbiome, metabolome, single-cell transcriptome, human genome, dietary and clinical data. 1325 participants commencing advanced therapies will be recruited from ~40 UK sites. Data will be collected at baseline, week 14 and week 54. The primary outcome is week 14 clinical response. Secondary outcomes include clinical remission, loss of response in week 14 responders, corticosteroid-free response/remission, time to treatment escalation and change in patient-reported outcome measures. ETHICS AND DISSEMINATION Ethical approval was obtained from the Wales Research Ethics Committee 5 (ref: 21/WA/0228). Recruitment is ongoing. Following study completion, results will be submitted for publication in peer-reviewed journals and presented at scientific meetings. Publications will be summarised at www.ibd-response.co.uk. TRIAL REGISTRATION NUMBER ISRCTN96296121.
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Affiliation(s)
- Nicola J Wyatt
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Department of Gastroenterology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Hannah Watson
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Carl A Anderson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Nicholas A Kennedy
- Department of Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Tim Raine
- Department of Gastroenterology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Tariq Ahmad
- Department of Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Dean Allerton
- Newcastle Clinical Trials Unit, Newcastle University, Newcastle upon Tyne, UK
| | - Michelle Bardgett
- Newcastle Clinical Trials Unit, Newcastle University, Newcastle upon Tyne, UK
| | - Emma Clark
- Newcastle Clinical Trials Unit, Newcastle University, Newcastle upon Tyne, UK
| | - Dawn Clewes
- Newcastle Clinical Trials Unit, Newcastle University, Newcastle upon Tyne, UK
| | | | - Mary Doona
- Department of Gastroenterology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Jennifer A Doyle
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Katherine Frith
- Newcastle Clinical Trials Unit, Newcastle University, Newcastle upon Tyne, UK
| | - Helen C Hancock
- Newcastle Clinical Trials Unit, Newcastle University, Newcastle upon Tyne, UK
| | - Ailsa L Hart
- Department of Gastroenterology, St Mark's Hospital and Academic Institute, London, UK
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Victoria Hildreth
- Newcastle Clinical Trials Unit, Newcastle University, Newcastle upon Tyne, UK
| | - Peter M Irving
- Department of Gastroenterology, Guy's and St Thomas' NHS Foundation Trust, London, UK
- School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Sameena Iqbal
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Ciara Kennedy
- Newcastle Clinical Trials Unit, Newcastle University, Newcastle upon Tyne, UK
| | - Andrew King
- Department of Gastroenterology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Sarah Lawrence
- Newcastle Clinical Trials Unit, Newcastle University, Newcastle upon Tyne, UK
| | - Charlie W Lees
- Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Edinburgh IBD Unit, Western General Hospital, NHS Lothian, Edinburgh, UK
| | - Robert Lees
- Department of Gastroenterology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Laura Letchford
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Trevor Liddle
- Research Informatics Team, Clinical Research, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - James O Lindsay
- Department of Gastroenterology, Barts Health NHS Trust, London, UK
- Centre for Immunobiology, Blizard Institute, Barts and the London School of Medicine, Queen Mary University of London, London, UK
| | - Rebecca H Maier
- Newcastle Clinical Trials Unit, Newcastle University, Newcastle upon Tyne, UK
| | - John C Mansfield
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Department of Gastroenterology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Julian R Marchesi
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, St Mary's Hospital, Imperial College London, London, UK
| | - Naomi McGregor
- Newcastle Clinical Trials Unit, Newcastle University, Newcastle upon Tyne, UK
| | | | | | | | - Nick Powell
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, St Mary's Hospital, Imperial College London, London, UK
- Department of Gastroenterology, Imperial College Healthcare NHS Trust, London, UK
| | - Natalie J Prescott
- Department of Medical and Molecular Genetics, Guy's Hospital, King's College London, London, UK
| | - Jack Satsangi
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Shriya Sharma
- Newcastle Clinical Trials Unit, Newcastle University, Newcastle upon Tyne, UK
| | - Tara Shrestha
- Newcastle Clinical Trials Unit, Newcastle University, Newcastle upon Tyne, UK
| | - Ally Speight
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Department of Gastroenterology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | | | - James Ms Wason
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Kevin Whelan
- Department of Nutritional Sciences, King's College London, London, UK
| | - Ruth Wood
- Newcastle Clinical Trials Unit, Newcastle University, Newcastle upon Tyne, UK
| | - Gregory R Young
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Xinyue Zhang
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Miles Parkes
- Department of Gastroenterology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Christopher J Stewart
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | | | - Christopher A Lamb
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Department of Gastroenterology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
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Henson S, Rish AJ, Anik Alam M, Liu Y, Drennen JK, Anderson CA. Development of iterative optimization technology: Selecting pure component spectra using a small-scale feed frame simulator. Int J Pharm 2024:124079. [PMID: 38574955 DOI: 10.1016/j.ijpharm.2024.124079] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/19/2024] [Accepted: 04/02/2024] [Indexed: 04/06/2024]
Abstract
The application of spectroscopic process analytical technology (PAT) for in-line data collection offers advantages to modern pharmaceutical manufacturing. Partial least squares (PLS) models are the preferred approach for predicting API potency from PAT data, particularly near-infrared (NIR) spectra. However, the calibration burden of PLS models is sometimes considered prohibitive. Pure component approaches, such as iterative optimization technology (IOT), have a reduced calibration burden for PAT applications. The IOT algorithm is dependent on several assumptions, including the harmonization of spectral collection conditions for pure component and mixture spectra. Collecting pure components under identical conditions to mixture spectra does not guarantee accurate predictions, and not all pure components are suitable for individual processing. This IOT assumption must be addressed to facilitate IOT application in PAT systems. In this work, IOT predicted API potency from in-line NIR spectra using combinations of stagnant and dynamic pure component spectra. A small number of mixture samples called a development set guided the selection of representative pure component spectral sets. Several model performance metrics from the development set predictions identified optimal pure component spectral sets for prediction of test sets. The combination of IOT and a development set generated accurate API potency predictions and potentiates the application of IOT in challenging pharmaceutical manufacturing settings. The IOT assumption of similar collection conditions should not be regarded as an assumption, but rather a consideration that the pure component spectral collection conditions should be representative of the mixture spectra to ensure appropriate predictions.
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Affiliation(s)
- Samuel Henson
- Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, PA 15282, USA
| | - Adam J Rish
- Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, PA 15282, USA
| | - Md Anik Alam
- Worldwide Research and Development, Pfizer Inc., Groton, CT 06340, USA
| | - Yang Liu
- Worldwide Research and Development, Pfizer Inc., Groton, CT 06340, USA
| | - James K Drennen
- Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, PA 15282, USA; Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, PA 15282, USA
| | - Carl A Anderson
- Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, PA 15282, USA; Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, PA 15282, USA.
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Wu S, Ketcham SA, Corredor C, Both D, Zhao Y, Drennen JK, Anderson CA. Adaptive modeling optimized by the data fusion strategy: Real-time dying cell percentage prediction using capacitance spectroscopy. Biotechnol Prog 2024; 40:e3424. [PMID: 38178645 DOI: 10.1002/btpr.3424] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 11/20/2023] [Accepted: 12/19/2023] [Indexed: 01/06/2024]
Abstract
The previous research showcased a partial least squares (PLS) regression model accurately predicting cell death percentages using in-line capacitance spectra. The current study advances the model accuracy through adaptive modeling employing a data fusion approach. This strategy enhances prediction performance by incorporating variables from the Cole-Cole model, conductivity and its derivatives over time, and Mahalanobis distance into the predictor matrix (X-matrix). Firstly, the Cole-Cole model, a mechanistic model with parameters linked to early cell death onset, was integrated to enhance prediction performance. Secondly, the inclusion of conductivity and its derivatives over time in the X-matrix mitigated prediction fluctuations resulting from abrupt conductivity changes during process operations. Thirdly, Mahalanobis distance, depicting spectral changes relative to a reference spectrum from a previous time point, improved model adaptability to independent test sets, thereby enhancing performance. The final data fusion model substantially decreased root-mean squared error of prediction (RMSEP) by around 50%, which is a significant boost in prediction accuracy compared to the prior PLS model. Robustness against reference spectrum selection was confirmed by consistent performance across various time points. In conclusion, this study illustrates that the data fusion strategy substantially enhances the model accuracy compared to the previous model relying solely on capacitance spectra.
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Affiliation(s)
- Suyang Wu
- Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, Pennsylvania, USA
- Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, Pennsylvania, USA
| | - Stephanie A Ketcham
- Manufascutring Science and Technology, Bristol-Myers Squibb, Devens, Massachusetts, USA
| | - Claudia Corredor
- Pharmaceutical Development, Bristol-Myers Squibb, New Brunswick, New Jersey, USA
| | - Douglas Both
- Pharmaceutical Development, Bristol-Myers Squibb, New Brunswick, New Jersey, USA
| | - Yuxiang Zhao
- Global Product Development and Supply, Bristol-Myers Squibb, Devens, Massachusetts, USA
| | - James K Drennen
- Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, Pennsylvania, USA
- Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, Pennsylvania, USA
| | - Carl A Anderson
- Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, Pennsylvania, USA
- Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, Pennsylvania, USA
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Bai BYH, Reppell M, Smaoui N, Waring JF, Pivorunas V, Guay H, Lin S, Chanchlani N, Bewshea C, Goodhand JR, Kennedy NA, Ahmad T, Anderson CA. Baseline Expression of Immune Gene Modules in Blood is Associated With Primary Response to Anti-TNF Therapy in Crohn's Disease Patients. J Crohns Colitis 2024; 18:431-445. [PMID: 37776235 PMCID: PMC10906954 DOI: 10.1093/ecco-jcc/jjad166] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/22/2023] [Accepted: 09/28/2023] [Indexed: 10/02/2023]
Abstract
BACKGROUND AND AIMS Anti-tumour necrosis factor [anti-TNF] therapy is widely used for the treatment of inflammatory bowel disease, yet many patients are primary non-responders, failing to respond to induction therapy. We aimed to identify blood gene expression differences between primary responders and primary non-responders to anti-TNF monoclonal antibodies [infliximab and adalimumab], and to predict response status from blood gene expression and clinical data. METHODS The Personalised Anti-TNF Therapy in Crohn's Disease [PANTS] study is a UK-wide prospective observational cohort study of anti-TNF therapy outcome in anti-TNF-naive Crohn's disease patients [ClinicalTrials.gov identifier: NCT03088449]. Blood gene expression in 324 unique patients was measured by RNA-sequencing at baseline [week 0], and at weeks 14, 30, and 54 after treatment initiation [total sample size = 814]. RESULTS After adjusting for clinical covariates and estimated blood cell composition, baseline expression of major histocompatibility complex, antigen presentation, myeloid cell enriched receptor, and other innate immune gene modules was significantly higher in anti-TNF responders vs non-responders. Expression changes from baseline to week 14 were generally of consistent direction but greater magnitude [i.e. amplified] in responders, but interferon-related genes were upregulated uniquely in non-responders. Expression differences between responders and non-responders observed at week 14 were maintained at weeks 30 and 54. Prediction of response status from baseline clinical data, cell composition, and module expression was poor. CONCLUSIONS Baseline gene module expression was associated with primary response to anti-TNF therapy in PANTS patients. However, these baseline expression differences did not predict response with sufficient sensitivity for clinical use.
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Affiliation(s)
- Benjamin Y H Bai
- Genomics of Inflammation and Immunity Group, Wellcome Sanger Institute, Hinxton, UK
- Postgraduate School of Life Sciences, University of Cambridge, Cambridge, UK
| | | | | | | | | | | | - Simeng Lin
- Department of Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Neil Chanchlani
- Department of Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Claire Bewshea
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - James R Goodhand
- Department of Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Nicholas A Kennedy
- Department of Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Tariq Ahmad
- Department of Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Carl A Anderson
- Genomics of Inflammation and Immunity Group, Wellcome Sanger Institute, Hinxton, UK
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Velez-Silva NL, Drennen JK, Anderson CA. Continuous manufacturing of pharmaceutical products: A density-insensitive near infrared method for the in-line monitoring of continuous powder streams. Int J Pharm 2024; 650:123699. [PMID: 38081558 DOI: 10.1016/j.ijpharm.2023.123699] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/05/2023] [Accepted: 12/08/2023] [Indexed: 12/19/2023]
Abstract
Near infrared (NIR) spectroscopy is a valuable analytical technique for monitoring chemical composition of powder blends in continuous pharmaceutical processes. However, the variation in density captured by NIR during spectral collection of dynamic powder streams at different flow rates often reduces the performance and robustness of NIR models. To overcome this challenge, quantitative NIR measurements are commonly collected across all potential manufacturing conditions, including multiple flow rates to account for the physical variations. The utility of this approach is limited by the considerable quantity of resources required to run and analyze an extensive calibration design at variable flow rates in a continuous manufacturing (CM) process. It is hypothesized that the primary variation introduced to NIR spectra from changing flow rates is a change in the density of the powder from which NIR spectra are collected. In this work, powder stream density was used as an efficient surrogate for flow rate in developing a quantitative NIR method with enhanced robustness against process rate variation. A density design space of two process parameters was generated to determine the conditions required to encompass the apparent density and spectral variance from increases in process rate. This apparent density variance was included in calibration at a constant low flow rate to enable the development of a density-insensitive NIR quantitative model with limited consumption of materials. The density-insensitive NIR model demonstrated comparable prediction performance and flow rate robustness to a traditional NIR model including flow rate variation ("gold standard" model) when applied to monitoring drug content in continuous runs at varying flow rates. The proposed platform for the development of in-line density-insensitive NIR methods is expected to facilitate robust analytical model performance across variable continuous manufacturing production scales while improving the material efficiency over traditional robust modeling approaches for calibration development.
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Affiliation(s)
- Natasha L Velez-Silva
- Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, PA 15282, United States; Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, PA 15282, United States
| | - James K Drennen
- Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, PA 15282, United States; Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, PA 15282, United States
| | - Carl A Anderson
- Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, PA 15282, United States; Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, PA 15282, United States.
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Olafsson S, Rodriguez E, Lawson ARJ, Abascal F, Huber AR, Suembuel M, Jones PH, Gerdes S, Martincorena I, Weidinger S, Campbell PJ, Anderson CA. Effects of psoriasis and psoralen exposure on the somatic mutation landscape of the skin. Nat Genet 2023; 55:1892-1900. [PMID: 37884686 PMCID: PMC10632143 DOI: 10.1038/s41588-023-01545-1] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 09/20/2023] [Indexed: 10/28/2023]
Abstract
Somatic mutations are hypothesized to play a role in many non-neoplastic diseases. We performed whole-exome sequencing of 1,182 microbiopsies dissected from lesional and nonlesional epidermis from 111 patients with psoriasis to search for evidence that somatic mutations in keratinocytes may influence the disease process. Lesional skin remained highly polyclonal, showing no evidence of large-scale spread of clones carrying potentially pathogenic mutations. The mutation rate of keratinocytes was similarly only modestly affected by the disease. We found evidence of positive selection in previously reported driver genes NOTCH1, NOTCH2, TP53, FAT1 and PPM1D and also identified mutations in four genes (GXYLT1, CHEK2, ZFP36L2 and EEF1A1) that we hypothesize are selected for in squamous epithelium irrespective of disease status. Finally, we describe a mutational signature of psoralens-a class of chemicals previously found in some sunscreens and which are used as part of PUVA (psoralens and ultraviolet-A) photochemotherapy treatment for psoriasis.
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Affiliation(s)
| | - Elke Rodriguez
- Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Kiel, Germany
| | | | | | | | - Melike Suembuel
- Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Kiel, Germany
| | | | - Sascha Gerdes
- Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Kiel, Germany
| | | | - Stephan Weidinger
- Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Kiel, Germany
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Velez-Silva NL, Drennen JK, Anderson CA. Influence of powder stream density on near infrared measurements upon scale-up of a simulated continuous process. Int J Pharm 2023; 645:123354. [PMID: 37647977 DOI: 10.1016/j.ijpharm.2023.123354] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 08/17/2023] [Accepted: 08/26/2023] [Indexed: 09/01/2023]
Abstract
Near-infrared (NIR) spectroscopy is a powerful process analytical tool for monitoring chemical constituents in continuous pharmaceutical processes. However, the density variation introduced when quantitative NIR measurements are performed on powder streams at different flow rates is a potential source of a lack of model robustness. Since different flow rates are often required to meet the production requirements (e.g., during scale-up) of a continuous process, the development of efficient strategies to characterize, understand, and mitigate the impact of powder density on NIR measurements is highly desirable. This study focused on assessing the effect of powder physical variation on NIR by enabling the in-line characterization of powder stream density in a simulated continuous system. The in-line measurements of powder stream density were facilitated through a unique analytical interface to a flowing process. Powder streams delivered at various design levels of flow rate and tube angle were monitored simultaneously by NIR diffuse reflectance spectroscopy, live imaging, and dynamic mass characterization. Statistical analysis and multivariate modeling confirmed powder density as a significant source of spectral variability due to flow rate. Besides providing broader process understanding, results elucidated potential mitigation strategies to facilitate effective continuous process scale-up while ensuring NIR model robustness against density.
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Affiliation(s)
- Natasha L Velez-Silva
- Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, PA 15282, United States; Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, PA 15282, United States
| | - James K Drennen
- Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, PA 15282, United States; Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, PA 15282, United States
| | - Carl A Anderson
- Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, PA 15282, United States; Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, PA 15282, United States.
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8
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Rish AJ, Henson SR, Velez-Silva NL, Nahid Hasan M, Drennen JK, Anderson CA. Application of a wavelength angle mapper for variable selection in iterative optimization technology predictions of drug content in pharmaceutical powder mixtures. Int J Pharm 2023; 643:123261. [PMID: 37479099 DOI: 10.1016/j.ijpharm.2023.123261] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/11/2023] [Accepted: 07/18/2023] [Indexed: 07/23/2023]
Abstract
Process analytical technology (PAT) is an essential tool within pharmaceutical manufacturing to ensure consistent quality and maintain process control. Near-infrared (NIR) spectroscopy is one of the most popular PAT techniques, particularly for monitoring active pharmaceutical ingredient (API) concentrations. To interpret the spectral outputs of NIR spectroscopy, advanced multivariate models are required. Calibration-free models such as iterative optimization technology (IOT) algorithms are increasingly of interest, due primarily to their reduced material and time burdens. Variable/wavelength selection is a common method to improve prediction performance and robustness for IOT by focusing on spectral regions with the most relevant information. However, currently proposed wavelength selection approaches rely on training sets for optimization, therefore reducing or removing the advantages of IOT over empirical calibration-dependent models. In this work, a true calibration-free wavelength selection method is proposed based on measuring the difference between individual wavelengths of a mixture spectra and the net analyte signals via a wavelength angle mapper (WAM). An extension of the WAM utilizing a spectral window of wavelength instead of individual wavelengths, called SWAM, was also developed. However, the SWAM method does require a small training set to optimize wavelength selection parameters. The WAM and SWAM methods showed similar prediction performance for API in pharmaceutical powder blends when compared against other calibration-dependent models and the base IOT algorithm.
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Affiliation(s)
- Adam J Rish
- Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, PA 15282, USA
| | - Samuel R Henson
- Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, PA 15282, USA
| | - Natasha L Velez-Silva
- Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, PA 15282, USA
| | - Md Nahid Hasan
- Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, PA 15282, USA
| | - James K Drennen
- Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, PA 15282, USA; Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, PA 15282, USA
| | - Carl A Anderson
- Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, PA 15282, USA; Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, PA 15282, USA.
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9
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Rish AJ, Siddiquee K, Huang Z, Xu J, Anderson CA, Borys MC, Khetan A. Strategies for Controlling Afucosylation in Monoclonal Antibodies during Upstream Manufacturing. Biotechnol J 2023:e2200604. [PMID: 37029472 DOI: 10.1002/biot.202200604] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/14/2023] [Accepted: 04/04/2023] [Indexed: 04/09/2023]
Abstract
Core fucosylation is a highly prevalent and significant feature of N-glycosylation in therapeutic monoclonal antibodies produced by mammalian cells where its absence (afucosylation) plays a key role in treatment safety and efficacy. Notably, even slight changes in the level of afucosylation can have a considerable impact on the antibody-dependent cell-mediated cytotoxicity. Therefore, implementing control over afucosylation levels is important in upstream manufacturing to maintain consistent quality across batches of product, since standard downstream processing does not change afucosylation. In this review, the influences and strategies to control afucosylation are presented. In particular, there is emphasis on upstream manufacturing culture parameters and media supplementation, as these offer particular advantages as control strategies over alternative approaches such as cell line engineering and chemical inhibitors. The review discusses the relationship between the afucosylation influences and the underlying cellular metabolism to promote increased process understanding. Also, briefly highlighted is the value of empirical and mechanistic models in evaluating and designing control methods for core fucosylation. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Adam J Rish
- Biologics Development, Global Product Development and Supply, Bristol Myers Squibb, Devens, Massachusetts, USA
- Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, PA, USA
| | - Khandaker Siddiquee
- Biologics Development, Global Product Development and Supply, Bristol Myers Squibb, Devens, Massachusetts, USA
| | - Zhuangrong Huang
- Biologics Development, Global Product Development and Supply, Bristol Myers Squibb, Devens, Massachusetts, USA
| | - Jianlin Xu
- Biologics Development, Global Product Development and Supply, Bristol Myers Squibb, Devens, Massachusetts, USA
| | - Carl A Anderson
- Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, PA, USA
- Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, PA, USA
| | - Michael C Borys
- Biologics Development, Global Product Development and Supply, Bristol Myers Squibb, Devens, Massachusetts, USA
| | - Anurag Khetan
- Biologics Development, Global Product Development and Supply, Bristol Myers Squibb, Devens, Massachusetts, USA
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10
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Wu S, Ketcham SA, Corredor CC, Both D, Drennen JK, Anderson CA. Capacitance spectroscopy enables real-time monitoring of early cell death in mammalian cell culture. Biotechnol J 2023; 18:e2200231. [PMID: 36479620 DOI: 10.1002/biot.202200231] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/21/2022] [Accepted: 09/06/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND/AIMS Previous work developed a quantitative model using capacitance spectroscopy in an at-line setup to predict the dying cell percentage measured from a flow cytometer. This work aimed to transfer the at-line model to monitor lab-scale bioreactors in real-time, waiving the need for frequent sampling and enabling precise controls. METHODS AND RESULTS Due to the difference between the at-line and in-line capacitance probes, direct application of the at-line model resulted in poor accuracy and high prediction bias. A new model with a variable range and offering similar spectral shape across all probes was first constructed, improving prediction accuracy. Moreover, the global calibration method included the variance of different probes and scales in the model, reducing prediction bias. External parameter orthogonalization, a preprocessing method, also mitigated the interference from feeding, which further improved model performance. The root-mean-square error of prediction of the final model was 6.56% (8.42% of the prediction range) with an R2 of 92.4%. CONCLUSION The culture evolution trajectory predicted by the in-line model captured the cell death and alarmed cell death onset earlier than the trypan blue exclusion test. Additionally, the incorporation of at-line spectra following orthogonal design into the calibration set was shown to generate calibration models that are more robust than the calibration models constructed using the in-line spectra only. This is advantageous, as at-line spectral collection is easier, faster, and more material-sparing than in-line spectra collection.
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Affiliation(s)
- Suyang Wu
- Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, Pennsylvania, USA.,Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, Pennsylvania, USA
| | - Stephanie A Ketcham
- Manufacturing Science and Technology, Bristol-Myers Squibb, Devens, Massachusetts, USA
| | - Claudia C Corredor
- Pharmaceutical Development, Bristol-Myers Squibb, New Brunswick, New Jersey, USA
| | - Douglas Both
- Pharmaceutical Development, Bristol-Myers Squibb, New Brunswick, New Jersey, USA
| | - James K Drennen
- Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, Pennsylvania, USA.,Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, Pennsylvania, USA
| | - Carl A Anderson
- Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, Pennsylvania, USA.,Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, Pennsylvania, USA
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11
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Barrio-Hernandez I, Schwartzentruber J, Shrivastava A, Del-Toro N, Gonzalez A, Zhang Q, Mountjoy E, Suveges D, Ochoa D, Ghoussaini M, Bradley G, Hermjakob H, Orchard S, Dunham I, Anderson CA, Porras P, Beltrao P. Network expansion of genetic associations defines a pleiotropy map of human cell biology. Nat Genet 2023; 55:389-398. [PMID: 36823319 PMCID: PMC10011132 DOI: 10.1038/s41588-023-01327-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [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: 07/19/2021] [Accepted: 01/30/2023] [Indexed: 02/25/2023]
Abstract
Interacting proteins tend to have similar functions, influencing the same organismal traits. Interaction networks can be used to expand the list of candidate trait-associated genes from genome-wide association studies. Here, we performed network-based expansion of trait-associated genes for 1,002 human traits showing that this recovers known disease genes or drug targets. The similarity of network expansion scores identifies groups of traits likely to share an underlying genetic and biological process. We identified 73 pleiotropic gene modules linked to multiple traits, enriched in genes involved in processes such as protein ubiquitination and RNA processing. In contrast to gene deletion studies, pleiotropy as defined here captures specifically multicellular-related processes. We show examples of modules linked to human diseases enriched in genes with known pathogenic variants that can be used to map targets of approved drugs for repurposing. Finally, we illustrate the use of network expansion scores to study genes at inflammatory bowel disease genome-wide association study loci, and implicate inflammatory bowel disease-relevant genes with strong functional and genetic support.
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Affiliation(s)
- Inigo Barrio-Hernandez
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
- Open Targets, Cambridge, UK
| | - Jeremy Schwartzentruber
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
- Open Targets, Cambridge, UK
- Wellcome Sanger Institute, Cambridge, UK
| | - Anjali Shrivastava
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
- Open Targets, Cambridge, UK
| | - Noemi Del-Toro
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
- Open Targets, Cambridge, UK
| | - Asier Gonzalez
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
- Open Targets, Cambridge, UK
| | - Qian Zhang
- Wellcome Sanger Institute, Cambridge, UK
| | - Edward Mountjoy
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
- Open Targets, Cambridge, UK
| | - Daniel Suveges
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
- Open Targets, Cambridge, UK
| | - David Ochoa
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
- Open Targets, Cambridge, UK
| | - Maya Ghoussaini
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
- Open Targets, Cambridge, UK
| | - Glyn Bradley
- Computational Biology, Genomic Sciences, GSK, Stevenage, UK
| | - Henning Hermjakob
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
- Open Targets, Cambridge, UK
| | - Sandra Orchard
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
- Open Targets, Cambridge, UK
| | - Ian Dunham
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
- Open Targets, Cambridge, UK
- Wellcome Sanger Institute, Cambridge, UK
| | - Carl A Anderson
- Open Targets, Cambridge, UK
- Wellcome Sanger Institute, Cambridge, UK
| | - Pablo Porras
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
- Open Targets, Cambridge, UK
| | - Pedro Beltrao
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK.
- Open Targets, Cambridge, UK.
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland.
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12
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Kammermeier J, Lamb CA, Jones KDJ, Anderson CA, Baple EL, Bolton C, Braggins H, Coulter TI, Gilmour KC, Gregory V, Hambleton S, Hartley D, Hawthorne AB, Hearn S, Laurence A, Parkes M, Russell RK, Speight RA, Travis S, Wilson DC, Uhlig HH. Genomic diagnosis and care co-ordination for monogenic inflammatory bowel disease in children and adults: consensus guideline on behalf of the British Society of Gastroenterology and British Society of Paediatric Gastroenterology, Hepatology and Nutrition. Lancet Gastroenterol Hepatol 2023; 8:271-286. [PMID: 36634696 DOI: 10.1016/s2468-1253(22)00337-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 01/11/2023]
Abstract
Genomic medicine enables the identification of patients with rare or ultra-rare monogenic forms of inflammatory bowel disease (IBD) and supports clinical decision making. Patients with monogenic IBD frequently experience extremely early onset of treatment-refractory disease, with complex extraintestinal disease typical of immunodeficiency. Since more than 100 monogenic disorders can present with IBD, new genetic disorders and variants are being discovered every year, and as phenotypic expression of the gene defects is variable, adaptive genomic technologies are required. Monogenic IBD has become a key area to establish the concept of precision medicine. Clear guidance and standardised, affordable applications of genomic technologies are needed to implement exome or genome sequencing in clinical practice. This joint British Society of Gastroenterology and British Society of Paediatric Gastroenterology, Hepatology and Nutrition guideline aims to ensure that testing resources are appropriately applied to maximise the benefit to patients on a national scale, minimise health-care disparities in accessing genomic technologies, and optimise resource use. We set out the structural requirements for genomic medicine as part of a multidisciplinary team approach. Initiation of genomic diagnostics should be guided by diagnostic criteria for the individual patient, in particular the age of IBD onset and the patient's history, and potential implications for future therapies. We outline the diagnostic care pathway for paediatric and adult patients. This guideline considers how to handle clinically actionable findings in research studies and the impact of consumer-based genomics for monogenic IBD. This document was developed by multiple stakeholders, including UK paediatric and adult gastroenterology physicians, immunologists, transplant specialists, clinical geneticists, scientists, and research leads of UK genetic programmes, in partnership with patient representatives of several IBD and rare disease charities.
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Affiliation(s)
- Jochen Kammermeier
- Department of Paediatric Gastroenterology, Evelina London Children's Hospital, London, UK
| | - Christopher A Lamb
- Translational & Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK; Department of Gastroenterology, Royal Victoria Infirmary, Newcastle upon Tyne, UK
| | - Kelsey D J Jones
- Department of Gastroenterology, Great Ormond Street Hospital for Children, London, UK; Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, University of Oxford, Oxford, UK
| | | | - Emma L Baple
- University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, UK
| | - Chrissy Bolton
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Helen Braggins
- Department of Immunology, Great Ormond Street Hospital of Children NHS Foundation Trust and NIHR Great Ormond Street Hospital Biomedical Research Centre, London, UK; Chronic Granulomatous Disorder Society, Dartford, UK
| | - Tanya I Coulter
- Regional Immunology Service for Northern Ireland, Belfast, UK
| | - Kimberly C Gilmour
- Clinical Immunology Laboratory, Great Ormond Street Hospital of Children NHS Foundation Trust and NIHR Great Ormond Street Hospital Biomedical Research Centre, London, UK
| | | | - Sophie Hambleton
- Translational & Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK; Department of Paediatric Immunology, Great North Children's Hospital, Newcastle upon Tyne, UK
| | | | - A Barney Hawthorne
- Department of Gastroenterology, University Hospital of Wales, Cardiff, UK
| | - Sarah Hearn
- Translational Gastroenterology Unit and Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Arian Laurence
- Department of Clinical Immunology, Royal Free Hospital, London, UK; Department of Haematology and Bone Marrow Transplantation, University College Hospital, London, UK
| | - Miles Parkes
- Department of Gastroenterology, Addenbrooke's Hospital, Cambridge, UK
| | - Richard K Russell
- Child Life and Health, University of Edinburgh, The Royal Hospital for Children & Young People, Edinburgh, UK; Department of Paediatric Gastroenterology, The Royal Hospital for Children & Young People, Edinburgh, UK; Department of Paediatric Gastroenterology, The Royal Hospital for Children & Young People, Edinburgh, UK
| | - R Alexander Speight
- Translational & Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK; Department of Gastroenterology, Royal Victoria Infirmary, Newcastle upon Tyne, UK
| | - Simon Travis
- Translational Gastroenterology Unit and Biomedical Research Centre, University of Oxford, Oxford, UK
| | - David C Wilson
- Child Life and Health, University of Edinburgh, The Royal Hospital for Children & Young People, Edinburgh, UK; Department of Paediatric Gastroenterology, The Royal Hospital for Children & Young People, Edinburgh, UK; Department of Paediatric Gastroenterology, The Royal Hospital for Children & Young People, Edinburgh, UK
| | - Holm H Uhlig
- Translational Gastroenterology Unit and Biomedical Research Centre, University of Oxford, Oxford, UK; Department of Paediatrics, University of Oxford, Oxford, UK.
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13
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Sazonovs A, Stevens CR, Venkataraman GR, Yuan K, Avila B, Abreu MT, Ahmad T, Allez M, Ananthakrishnan AN, Atzmon G, Baras A, Barrett JC, Barzilai N, Beaugerie L, Beecham A, Bernstein CN, Bitton A, Bokemeyer B, Chan A, Chung D, Cleynen I, Cosnes J, Cutler DJ, Daly A, Damas OM, Datta LW, Dawany N, Devoto M, Dodge S, Ellinghaus E, Fachal L, Farkkila M, Faubion W, Ferreira M, Franchimont D, Gabriel SB, Ge T, Georges M, Gettler K, Giri M, Glaser B, Goerg S, Goyette P, Graham D, Hämäläinen E, Haritunians T, Heap GA, Hiltunen M, Hoeppner M, Horowitz JE, Irving P, Iyer V, Jalas C, Kelsen J, Khalili H, Kirschner BS, Kontula K, Koskela JT, Kugathasan S, Kupcinskas J, Lamb CA, Laudes M, Lévesque C, Levine AP, Lewis JD, Liefferinckx C, Loescher BS, Louis E, Mansfield J, May S, McCauley JL, Mengesha E, Mni M, Moayyedi P, Moran CJ, Newberry RD, O'Charoen S, Okou DT, Oldenburg B, Ostrer H, Palotie A, Paquette J, Pekow J, Peter I, Pierik MJ, Ponsioen CY, Pontikos N, Prescott N, Pulver AE, Rahmouni S, Rice DL, Saavalainen P, Sands B, Sartor RB, Schiff ER, Schreiber S, Schumm LP, Segal AW, Seksik P, Shawky R, Sheikh SZ, Silverberg MS, Simmons A, Skeiceviciene J, Sokol H, Solomonson M, Somineni H, Sun D, Targan S, Turner D, Uhlig HH, van der Meulen AE, Vermeire S, Verstockt S, Voskuil MD, Winter HS, Young J, Duerr RH, Franke A, Brant SR, Cho J, Weersma RK, Parkes M, Xavier RJ, Rivas MA, Rioux JD, McGovern DPB, Huang H, Anderson CA, Daly MJ. Large-scale sequencing identifies multiple genes and rare variants associated with Crohn's disease susceptibility. Nat Genet 2022; 54:1275-1283. [PMID: 36038634 PMCID: PMC9700438 DOI: 10.1038/s41588-022-01156-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [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: 07/01/2021] [Accepted: 07/12/2022] [Indexed: 01/18/2023]
Abstract
Genome-wide association studies (GWASs) have identified hundreds of loci associated with Crohn's disease (CD). However, as with all complex diseases, robust identification of the genes dysregulated by noncoding variants typically driving GWAS discoveries has been challenging. Here, to complement GWASs and better define actionable biological targets, we analyzed sequence data from more than 30,000 patients with CD and 80,000 population controls. We directly implicate ten genes in general onset CD for the first time to our knowledge via association to coding variation, four of which lie within established CD GWAS loci. In nine instances, a single coding variant is significantly associated, and in the tenth, ATG4C, we see additionally a significantly increased burden of very rare coding variants in CD cases. In addition to reiterating the central role of innate and adaptive immune cells as well as autophagy in CD pathogenesis, these newly associated genes highlight the emerging role of mesenchymal cells in the development and maintenance of intestinal inflammation.
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Affiliation(s)
- Aleksejs Sazonovs
- Genomics of Inflammation and Immunity Group, Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Christine R Stevens
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Kai Yuan
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Brandon Avila
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Maria T Abreu
- Crohn's and Colitis Center, Leonard M. Miller School of Medicine, University of Miami, Miami, FL, USA
| | | | - Matthieu Allez
- Hopital Saint-Louis, APHP, Universite de Paris, INSERM U1160, Paris, France
| | - Ashwin N Ananthakrishnan
- Division of Gastroenterology, Crohn's and Colitis Center, Massachusetts General Hospital, Boston, MA, USA
| | - Gil Atzmon
- Department for Human Biology, University of Haifa, Haifa, Israel
- Departments of Medicine and Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Aris Baras
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Jeffrey C Barrett
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Nir Barzilai
- Departments of Medicine and Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- The Institute for Aging Research, The Nathan Shock Center of Excellence in the Basic Biology of Aging and the Paul F. Glenn Center for the Biology of Human Aging Research at Albert Einstein College of Medicine of Yeshiva University, Bronx, NY, USA
| | - Laurent Beaugerie
- Gastroenterology Department, Sorbonne Universite, Saint Antoine Hospital, Paris, France
| | - Ashley Beecham
- John P. Hussman Institute for Human Genomics, Leonard M. Miller School of Medicine, University of Miami, Miami, FL, USA
- The Dr. John T. Macdonald Foundation Department of Human Genetics, Leonard M. Miller School of Medicine, University of Miami, Miami, FL, USA
| | | | - Alain Bitton
- McGill University and McGill University Health Centre, Montreal, Quebec, Canada
| | - Bernd Bokemeyer
- Department of Internal Medicine, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Andrew Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Womens Hospital, Boston, MA, USA
| | | | | | - Jacques Cosnes
- Professeur Chef de Service chez APHP and Universite Paris-6, Paris, France
| | - David J Cutler
- Department of Human Genetics, Emory University, Atlanta, GA, USA
- Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Allan Daly
- Human Genetics Informatics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Lisa W Datta
- Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Noor Dawany
- Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
| | - Marcella Devoto
- Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
- University of Rome Sapienza, Rome, Italy
- IRGB - CNR, Cagliari, Italy
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Sheila Dodge
- Genomics Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eva Ellinghaus
- Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Laura Fachal
- Genomics of Inflammation and Immunity Group, Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | | | | | | | - Stacey B Gabriel
- Genomics Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Tian Ge
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Precision Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | | | - Kyle Gettler
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mamta Giri
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Benjamin Glaser
- Department of Endocrinology and Metabolism, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Philippe Goyette
- Research Center Montreal Heart Institute, Montreal, Quebec, Canada
| | - Daniel Graham
- Infectious Disease and Microbiome Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Eija Hämäläinen
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | | | - Mikko Hiltunen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Marc Hoeppner
- Christian-Albrechts-University of Kiel, Kiel, Germany
| | | | - Peter Irving
- Department of Gastroenterology, Guys and Saint Thomas Hospital, London, UK
- School of Immunology and Microbial Sciences, Kings College London, London, UK
| | - Vivek Iyer
- Human Genetics Informatics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Chaim Jalas
- Director of Genetic Resources and Services, Center for Rare Jewish Genetic Disorders, Bonei Olam, Brooklyn, NY, USA
| | - Judith Kelsen
- Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
| | - Hamed Khalili
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Barbara S Kirschner
- Department of Gastroenterology, University of Chicago Medicine, Chicago, IL, USA
| | - Kimmo Kontula
- Department of Medicine, Helsinki University Hospital, and Research Program for Clinical and Molecular Metabolism, University of Helsinki, Helsinki, Finland
| | - Jukka T Koskela
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Subra Kugathasan
- Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Juozas Kupcinskas
- Department of Gastroenterology and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Christopher A Lamb
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Department of Gastroenterology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | | | - Chloé Lévesque
- Research Center Montreal Heart Institute, Montreal, Quebec, Canada
| | | | - James D Lewis
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
- Crohn's and Colitis Foundation, New York, NY, USA
| | | | - Britt-Sabina Loescher
- Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | | | - John Mansfield
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Department of Gastroenterology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Sandra May
- Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Jacob L McCauley
- John P. Hussman Institute for Human Genomics, Leonard M. Miller School of Medicine, University of Miami, Miami, FL, USA
- The Dr. John T. Macdonald Foundation Department of Human Genetics, Leonard M. Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Emebet Mengesha
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Myriam Mni
- University of Liège, ULG, Liège, Belgium
| | | | | | | | | | - David T Okou
- Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
- Institut National de Sante Publique (INSP), Abidjan, Côte d'Ivoire
| | - Bas Oldenburg
- Department of Gastroenterology and Hepatology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Harry Ostrer
- Albert Einstein College of Medicine, Bronx, NY, USA
| | - Aarno Palotie
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Jean Paquette
- Research Center Montreal Heart Institute, Montreal, Quebec, Canada
| | - Joel Pekow
- Department of Gastroenterology, University of Chicago Medicine, Chicago, IL, USA
| | - Inga Peter
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marieke J Pierik
- Department of Gastroenterology and Hepatology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Cyriel Y Ponsioen
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centres, Amsterdam, The Netherlands
| | | | - Natalie Prescott
- Department of Medical and Molecular Genetics, Kings College London, London, UK
| | - Ann E Pulver
- School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | | | - Daniel L Rice
- Genomics of Inflammation and Immunity Group, Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Päivi Saavalainen
- Research Programs Unit, Immunobiology, University of Helsinki, Helsinki, Finland
| | - Bruce Sands
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - R Balfour Sartor
- Center for Gastrointestinal Biology and Disease, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | | | - Stefan Schreiber
- Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - L Philip Schumm
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | | | - Philippe Seksik
- Gastroenterology Department, Sorbonne Universite, Saint Antoine Hospital, Paris, France
| | - Rasha Shawky
- IBD BioResource, NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Shehzad Z Sheikh
- Center for Gastrointestinal Biology and Disease, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | | | - Alison Simmons
- MRC Human Immunology Unit, NIHR Biomedical Research Centre, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jurgita Skeiceviciene
- Department of Gastroenterology and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Harry Sokol
- Gastroenterology Department, Sorbonne Universite, Saint Antoine Hospital, Paris, France
| | - Matthew Solomonson
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hari Somineni
- Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Dylan Sun
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Stephan Targan
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Dan Turner
- Shaare Zedek Medical Center, Jerusalem, Israel
| | - Holm H Uhlig
- Translational Gastroenterology Unit and Biomedical Research Centre, Nuffield Department of Clinical Medicine, Experimental Medicine Division, University of Oxford, Oxford, UK
- Department of Pediatrics, John Radcliffe Hospital, Oxford, UK
| | - Andrea E van der Meulen
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Séverine Vermeire
- University Hospitals Leuven, Leuven, Belgium
- Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Sare Verstockt
- Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Michiel D Voskuil
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | | | | | | | - Andre Franke
- Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Steven R Brant
- Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Crohn's Colitis Center of New Jersey, Department of Medicine, Rutgers Robert Wood Johnson Medical School and Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University, New Brunswick and Piscataway, NJ, USA
| | - Judy Cho
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Miles Parkes
- Department of Gastroenterology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Ramnik J Xavier
- Infectious Disease and Microbiome Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Kurt Isselbacher Professor of Medicine at Harvard Medical School, Cambridge, MA, USA
- Core Institute Member, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Klarman Cell Observatory, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Immunology Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Microbiome Informatics and Therapeutics at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Manuel A Rivas
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - John D Rioux
- Research Center Montreal Heart Institute, Montreal, Quebec, Canada
- Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Hailiang Huang
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
| | - Carl A Anderson
- Genomics of Inflammation and Immunity Group, Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
| | - Mark J Daly
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland.
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14
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Rish AJ, Henson SR, Alam MA, Liu Y, Drennen JK, Anderson CA. Comparison Between Pure Component Modeling Approaches for Monitoring Pharmaceutical Powder Blends with Near-Infrared Spectroscopy in Continuous Manufacturing Schemes. AAPS J 2022; 24:82. [PMID: 35821538 DOI: 10.1208/s12248-022-00725-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 06/07/2022] [Indexed: 11/30/2022] Open
Abstract
Near-infrared (NIR) spectroscopy has become an important process analytical technology (PAT) for monitoring and implementing control in continuous manufacturing (CM) schemes. However, NIR requires complex multivariate models to properly extract the relevant information and the traditional model of choice, partial least squares, can be unfavorable on account of its high material and time investments for generating calibrations. To account for this, pure component-based approaches have been gaining attention due to their higher flexibility and ease of development. In the present study, the application of two pure component approaches, classical least squares (CLS) models and iterative optimization technology (IOT) algorithms, to pharmaceutical powder blends in a continuous feed frame was considered. The approaches were compared from both a model performance and practical implementation perspective. IOT were found to demonstrate superior performance in predicting drug content compared to CLS. The practical implementation of each modelling approach was also given consideration.
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Affiliation(s)
- Adam J Rish
- Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, PA, 15282, USA.,Duquesne Center for Pharmaceutical Technology, Duquesne University, 600 Forbes Ave, Pittsburgh, PA, 15282, USA
| | - Samuel R Henson
- Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, PA, 15282, USA.,Duquesne Center for Pharmaceutical Technology, Duquesne University, 600 Forbes Ave, Pittsburgh, PA, 15282, USA
| | - Md Anik Alam
- Worldwide Research and Development, Pfizer Inc., Groton, CT, 06340, USA
| | - Yang Liu
- Worldwide Research and Development, Pfizer Inc., Groton, CT, 06340, USA
| | - James K Drennen
- Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, PA, 15282, USA.,Duquesne Center for Pharmaceutical Technology, Duquesne University, 600 Forbes Ave, Pittsburgh, PA, 15282, USA
| | - Carl A Anderson
- Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, PA, 15282, USA. .,Duquesne Center for Pharmaceutical Technology, Duquesne University, 600 Forbes Ave, Pittsburgh, PA, 15282, USA.
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15
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Kundu K, Tardaguila M, Mann AL, Watt S, Ponstingl H, Vasquez L, Von Schiller D, Morrell NW, Stegle O, Pastinen T, Sawcer SJ, Anderson CA, Walter K, Soranzo N. Genetic associations at regulatory phenotypes improve fine-mapping of causal variants for 12 immune-mediated diseases. Nat Genet 2022; 54:251-262. [PMID: 35288711 DOI: 10.1038/s41588-022-01025-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 01/31/2022] [Indexed: 12/11/2022]
Abstract
The resolution of causal genetic variants informs understanding of disease biology. We used regulatory quantitative trait loci (QTLs) from the BLUEPRINT, GTEx and eQTLGen projects to fine-map putative causal variants for 12 immune-mediated diseases. We identify 340 unique loci that colocalize with high posterior probability (≥98%) with regulatory QTLs and apply Bayesian frameworks to fine-map associations at each locus. We show that fine-mapping credible sets derived from regulatory QTLs are smaller compared to disease summary statistics. Further, they are enriched for more functionally interpretable candidate causal variants and for putatively causal insertion/deletion (INDEL) polymorphisms. Finally, we use massively parallel reporter assays to evaluate candidate causal variants at the ITGA4 locus associated with inflammatory bowel disease. Overall, our findings suggest that fine-mapping applied to disease-colocalizing regulatory QTLs can enhance the discovery of putative causal disease variants and enhance insights into the underlying causal genes and molecular mechanisms.
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Affiliation(s)
- Kousik Kundu
- Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Manuel Tardaguila
- Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Alice L Mann
- Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Stephen Watt
- Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Hannes Ponstingl
- Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Louella Vasquez
- Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Dominique Von Schiller
- Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Nicholas W Morrell
- Division of Respiratory Medicine, Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's and Papworth Hospitals, Cambridge, UK
| | - Oliver Stegle
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Division of Computational Genomics and Systems Genetics, German Cancer Research Center, Heidelberg, Germany.,Cellular Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Tomi Pastinen
- Genomic Medicine Center, Children's Mercy Kansas City and Children's Mercy Research Institute, Kansas City, MO, USA
| | - Stephen J Sawcer
- Department of Clinical Neurosciences, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Carl A Anderson
- Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Klaudia Walter
- Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Nicole Soranzo
- Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK. .,Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK. .,British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK. .,National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK. .,Genomics Research Centre, Human Technopole, Milan, Italy.
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16
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Bolton C, Smillie CS, Pandey S, Elmentaite R, Wei G, Argmann C, Aschenbrenner D, James KR, McGovern DPB, Macchi M, Cho J, Shouval DS, Kammermeier J, Koletzko S, Bagalopal K, Capitani M, Cavounidis A, Pires E, Weidinger C, McCullagh J, Arkwright PD, Haller W, Siegmund B, Peters L, Jostins L, Travis SPL, Anderson CA, Snapper S, Klein C, Schadt E, Zilbauer M, Xavier R, Teichmann S, Muise AM, Regev A, Uhlig HH. An Integrated Taxonomy for Monogenic Inflammatory Bowel Disease. Gastroenterology 2022; 162:859-876. [PMID: 34780721 DOI: 10.1053/j.gastro.2021.11.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 10/18/2021] [Accepted: 11/08/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Monogenic forms of inflammatory bowel disease (IBD) illustrate the essential roles of individual genes in pathways and networks safeguarding immune tolerance and gut homeostasis. METHODS To build a taxonomy model, we assessed 165 disorders. Genes were prioritized based on penetrance of IBD and disease phenotypes were integrated with multi-omics datasets. Monogenic IBD genes were classified by (1) overlapping syndromic features, (2) response to hematopoietic stem cell transplantation, (3) bulk RNA-sequencing of 32 tissues, (4) single-cell RNA-sequencing of >50 cell subsets from the intestine of healthy individuals and patients with IBD (pediatric and adult), and (5) proteomes of 43 immune subsets. The model was validated by addition of newly identified monogenic IBD defects. As a proof-of-concept, we explore the intersection between immunometabolism and antimicrobial activity for a group of disorders (G6PC3/SLC37A4). RESULTS Our quantitative integrated taxonomy defines the cellular landscape of monogenic IBD gene expression across 102 genes with high and moderate penetrance (81 in the model set and 21 genes in the validation set). We illustrate distinct cellular networks, highlight expression profiles across understudied cell types (e.g., CD8+ T cells, neutrophils, epithelial subsets, and endothelial cells) and define genotype-phenotype associations (perianal disease and defective antimicrobial activity). We illustrate processes and pathways shared across cellular compartments and phenotypic groups and highlight cellular immunometabolism with mammalian target of rapamycin activation as one of the converging pathways. There is an overlap of genes and enriched cell-specific expression between monogenic and polygenic IBD. CONCLUSION Our taxonomy integrates genetic, clinical and multi-omic data; providing a basis for genomic diagnostics and testable hypotheses for disease functions and treatment responses.
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Affiliation(s)
- Chrissy Bolton
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK; Institute of Child Health, University College London, London, UK
| | - Christopher S Smillie
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Sumeet Pandey
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Rasa Elmentaite
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Gabrielle Wei
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Carmen Argmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Kylie R James
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK; Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, Australia
| | - Dermot P B McGovern
- F. Widjaja Foundation, Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Marina Macchi
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Judy Cho
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Dror S Shouval
- Institute of Gastroenterology, Nutrition and Liver Diseases, Schneider Children's Medical Center of Israel, Petah-Tiqva, Israel, affiliated with Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Jochen Kammermeier
- Gastroenterology Department, Evelina London Children's Hospital, London, UK
| | - Sibylle Koletzko
- Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital, LMU Munich, Munich, Germany; Department of Pediatrics, Gastroenterology and Nutrition, School of Medicine Collegium Medicum University of Warmia and Mazury, Olsztyn, Poland
| | | | - Melania Capitani
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Athena Cavounidis
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Elisabete Pires
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, UK
| | - Carl Weidinger
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health Department of Gastroenterology, Rheumatology and Infectious Disease, Campus Benjamin Franklin, Berlin, Germany
| | - James McCullagh
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, UK
| | - Peter D Arkwright
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, UK
| | - Wolfram Haller
- Department of Gastroenterology and Nutrition, Birmingham Children's Hospital, Birmingham, UK
| | - Britta Siegmund
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health Department of Gastroenterology, Rheumatology and Infectious Disease, Campus Benjamin Franklin, Berlin, Germany
| | - Lauren Peters
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Luke Jostins
- The Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Simon P L Travis
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK; Biomedical Research Center, University of Oxford, Oxford, UK
| | - Carl A Anderson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Scott Snapper
- Division of Gastroenterology and Nutrition, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Christoph Klein
- Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital, LMU Munich, Munich, Germany
| | - Eric Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Matthias Zilbauer
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Addenbrooke's Hospital, Cambridge, UK; Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Ramnik Xavier
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Sarah Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK; Theory of Condensed Matter, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK; European Molecular Biology Laboratory, European Bioinformatics Institute (EBI), Wellcome Genome Campus, Hinxton UK
| | - Aleixo M Muise
- Gastroenterology Division, The Hospital for Sick Children, Toronto, Ontario, Canada; SickKids Inflammatory Bowel Disease Center and Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada; Department of Pediatrics and Biochemistry, University of Toronto, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Holm H Uhlig
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK; The Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK; Department of Paediatrics, University of Oxford, Oxford, United Kingdom.
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17
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Rish AJ, Henson SR, Anik Alam M, Liu Y, Drennen JK, Anderson CA. Development of calibration-free/minimal calibration wavelength selection for iterative optimization technology algorithms toward process analytical technology application. Int J Pharm 2022; 614:121463. [PMID: 35026311 DOI: 10.1016/j.ijpharm.2022.121463] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 10/19/2022]
Abstract
As continuous manufacturing (CM) processes are developed, process analytical technology (PAT) via NIR spectroscopy has become an integral tool in process monitoring. NIR spectroscopy requires the deployment of complex multivariate models to extract the relevant information. The model of choice for the pharmaceutical industry is Partial Least Squares (PLS). However, the development of PLS can be burdensome due to the time and resource intensive requirements of calibration. To overcome this challenge, calibration-free/minimal calibration approaches have become of increasing interest. Iterative optimization technology (IOT) algorithms are a favorable calibration-free/minimal calibration approach with only the requirement of pure component spectra for successful active pharmaceutical ingredient (API) quantification. IOT algorithms were utilized to monitor potency trends (qualitative) and API content (quantitative) in a CM system and compared to a traditional PLS model. To overcome the reduced prediction performance of IOT during non-steady state conditions, a novel wavelength method based on variable importance in projection scores was employed. Overall, the success and value of IOT algorithms for application in CM settings was demonstrated.
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Affiliation(s)
- Adam J Rish
- Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, PA 15282, USA
| | - Samuel R Henson
- Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, PA 15282, USA
| | - Md Anik Alam
- Worldwide Research and Development, Pfizer Inc., Groton, CT 06340, USA
| | - Yang Liu
- Worldwide Research and Development, Pfizer Inc., Groton, CT 06340, USA
| | - James K Drennen
- Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, PA 15282, USA; Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, PA 15282, USA
| | - Carl A Anderson
- Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, PA 15282, USA; Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, PA 15282, USA.
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18
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Velez NL, Drennen JK, Anderson CA. Challenges, opportunities and recent advances in near infrared spectroscopy applications for monitoring blend uniformity in the continuous manufacturing of solid oral dosage forms. Int J Pharm 2022; 615:121462. [PMID: 35026317 DOI: 10.1016/j.ijpharm.2022.121462] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/20/2021] [Accepted: 01/07/2022] [Indexed: 10/19/2022]
Abstract
Near infrared (NIR) spectroscopy has been widely recognized as a powerful PAT tool for monitoring blend uniformity in continuous manufacturing (CM) processes. However, the dynamic nature of the powder stream and the fast rate at which it moves, compared to batch processes, introduces challenges to NIR quantitative methods for monitoring blend uniformity. For instance, defining the effective sample size interrogated by NIR, selecting the best sampling location for blend monitoring, and ensuring NIR model robustness against influential sources of variability are challenges commonly reported for NIR applications in CM. This article reviews the NIR applications for powder blend monitoring in the continuous manufacturing of solid oral dosage forms, with a particular focus on the challenges, opportunities for method optimization and recent advances with respect three main aspects: effective sample size measured by NIR, probe location and method robustness.
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Affiliation(s)
- Natasha L Velez
- Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, PA 15282, United States; Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, PA 15282, United States.
| | - James K Drennen
- Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, PA 15282, United States; Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, PA 15282, United States.
| | - Carl A Anderson
- Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, PA 15282, United States; Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, PA 15282, United States.
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19
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Wu S, Ketcham SA, Corredor CC, Both D, Drennen JK, Anderson CA. Rapid At-line Early Cell Death Quantification using Capacitance Spectroscopy. Biotechnol Bioeng 2021; 119:857-867. [PMID: 34927241 DOI: 10.1002/bit.28011] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 11/10/2022]
Abstract
Cell death is one of the failure modes of mammalian cell culture. Apoptosis is a regulated cell death process mainly observed in cell culture. Timely detection of apoptosis onset allows opportunities for preventive controls that ensure high productivity and consistent product quality. Capacitance spectroscopy captures the apoptosis-related cellular properties changes and thus quantifies the percentage of dying cells. This work demonstrated a quantification model that measures the percentage of apoptotic cells using a capacitance spectrometer in an at-line setup. When predicting the independent test set collected from bench-scale bioreactors, the root-mean-squared error of prediction (RMSEP) was 8.8% (equivalent to 9.9% of the prediction range). The predicted culture evolution trajectory aligned with measured values from the flow cytometer. Furthermore, this method alarms cell death onset earlier than the traditional viability test, i.e., trypan blue exclusion test. Comparing to flow cytometry (the traditional early cell death detection method), this method is rapid, simple, and less labor-intensive. Additionally, this at-line setup can be easily transferred between scales (e.g., lab-scale for development to manufacturing-scale), which benefits process transfers between facilities, scale-up, and other process transitions. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Suyang Wu
- Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, Pennsylvania, 15282.,Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, Pennsylvania, 15282
| | - Stephanie A Ketcham
- Manufacutring Science and Technology, Bristol-Myers Squibb, Devens, Massachusetts, 01434
| | - Claudia C Corredor
- Pharmaceutical Development, Bristol-Myers Squibb, New Brunswick, New Jersey, 08903
| | - Douglas Both
- Pharmaceutical Development, Bristol-Myers Squibb, New Brunswick, New Jersey, 08903
| | - James K Drennen
- Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, Pennsylvania, 15282.,Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, Pennsylvania, 15282
| | - Carl A Anderson
- Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, Pennsylvania, 15282.,Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, Pennsylvania, 15282
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20
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Eijsbouts C, Zheng T, Kennedy NA, Bonfiglio F, Anderson CA, Moutsianas L, Holliday J, Shi J, Shringarpure S, Voda AI, Farrugia G, Franke A, Hübenthal M, Abecasis G, Zawistowski M, Skogholt AH, Ness-Jensen E, Hveem K, Esko T, Teder-Laving M, Zhernakova A, Camilleri M, Boeckxstaens G, Whorwell PJ, Spiller R, McVean G, D'Amato M, Jostins L, Parkes M. Genome-wide analysis of 53,400 people with irritable bowel syndrome highlights shared genetic pathways with mood and anxiety disorders. Nat Genet 2021; 53:1543-1552. [PMID: 34741163 PMCID: PMC8571093 DOI: 10.1038/s41588-021-00950-8] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 09/08/2021] [Indexed: 12/19/2022]
Abstract
Irritable bowel syndrome (IBS) results from disordered brain-gut interactions. Identifying susceptibility genes could highlight the underlying pathophysiological mechanisms. We designed a digestive health questionnaire for UK Biobank and combined identified cases with IBS with independent cohorts. We conducted a genome-wide association study with 53,400 cases and 433,201 controls and replicated significant associations in a 23andMe panel (205,252 cases and 1,384,055 controls). Our study identified and confirmed six genetic susceptibility loci for IBS. Implicated genes included NCAM1, CADM2, PHF2/FAM120A, DOCK9, CKAP2/TPTE2P3 and BAG6. The first four are associated with mood and anxiety disorders, expressed in the nervous system, or both. Mirroring this, we also found strong genome-wide correlation between the risk of IBS and anxiety, neuroticism and depression (rg > 0.5). Additional analyses suggested this arises due to shared pathogenic pathways rather than, for example, anxiety causing abdominal symptoms. Implicated mechanisms require further exploration to help understand the altered brain-gut interactions underlying IBS.
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Affiliation(s)
- Chris Eijsbouts
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Tenghao Zheng
- Center for Molecular Medicine & Clinical Epidemiology Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Nicholas A Kennedy
- IBD Pharmacogenetics, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Ferdinando Bonfiglio
- Center for Molecular Medicine & Clinical Epidemiology Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Carl A Anderson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Loukas Moutsianas
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- William Harvey Research Institute, Barts & The London School of Medicine & Dentistry, Queen Mary University of London, London, UK
| | - Joanne Holliday
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | | | | | - Alexandru-Ioan Voda
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
- Saint Edmund Hall, University of Oxford, Oxford, UK
| | - Gianrico Farrugia
- Enteric NeuroScience Program, Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Matthias Hübenthal
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
- Department of Dermatology, Quincke Research Center, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Gonçalo Abecasis
- Department of Biostatistics, University of Michigan, School of Public Health, Ann Arbor, MI, USA
| | - Matthew Zawistowski
- Department of Biostatistics, University of Michigan, School of Public Health, Ann Arbor, MI, USA
| | - Anne Heidi Skogholt
- Department of Laboratory Medicine, Children's and Women's Health, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
| | - Eivind Ness-Jensen
- Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Medicine, Levanger Hospital, Nord-Trøndelag Hospital Trust, Levanger, Norway
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Kristian Hveem
- Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
| | - Tõnu Esko
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Maris Teder-Laving
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, Groningen, the Netherlands
| | - Michael Camilleri
- Clinical Enteric Neuroscience Translational and Epidemiological Research and Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Guy Boeckxstaens
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Peter J Whorwell
- Neurogastroenterology Unit, Wythenshawe Hospital, Centre for Gastrointestinal Sciences, University of Manchester, Manchester, UK
| | - Robin Spiller
- Nottingham Digestive Diseases Centre, National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
| | - Gil McVean
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Mauro D'Amato
- Center for Molecular Medicine & Clinical Epidemiology Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden.
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia.
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany.
- Biodonostia Health Research Institute, San Sebastian, Spain.
- Gastrointestinal Genetics Lab, CIC bioGUNE - Basque Research and Technology Alliance, Derio, Spain.
- IKERBASQUE, The Basque Science Foundation, Bilbao, Spain.
| | - Luke Jostins
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK.
- Christ Church, University of Oxford, Oxford, UK.
| | - Miles Parkes
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Cambridge, UK.
- Department of Gastroenterology, Cambridge University Hospital, Cambridge, UK.
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21
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Rish AJ, Drennen JK, Anderson CA. Metabolic trends of Chinese hamster ovary cells in biopharmaceutical production under batch and fed-batch conditions. Biotechnol Prog 2021; 38:e3220. [PMID: 34676699 DOI: 10.1002/btpr.3220] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/05/2021] [Accepted: 10/19/2021] [Indexed: 11/07/2022]
Abstract
Extensive knowledge of Chinese hamster ovary (CHO) cell metabolism is required to improve process productivity and culture performance in biopharmaceutical manufacturing. However, CHO cells show a dynamic metabolism during culturing in batch and fed-batch bioreactors. CHO cell metabolism is generally described as taking place in three stages: exponential growth phase, stationary phase, and death phase. This review aims to summarize the trends of central metabolism for CHO cells during each stage. Additional insights into how culture conditions are related to phase transitions and force metabolic rewiring are provided. Understanding of CHO cell metabolism lends itself to improving culture qualities by, for example, identifying sources of toxic byproducts and pathways for cellular engineering. In summary, this review describes the changes in CHO cell central metabolism over the course of the culture.
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Affiliation(s)
- Adam J Rish
- Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, Pennsylvania, USA
| | - James K Drennen
- Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, Pennsylvania, USA
- Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, Pennsylvania, USA
| | - Carl A Anderson
- Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, Pennsylvania, USA
- Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, Pennsylvania, USA
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22
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Olafsson S, Anderson CA. Somatic mutations provide important and unique insights into the biology of complex diseases. Trends Genet 2021; 37:872-881. [PMID: 34226062 DOI: 10.1016/j.tig.2021.06.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 10/20/2022]
Abstract
Somatic evolution of cells within the body is well known to lead to cancers. However, spread of somatic mutations within a tissue over time may also contribute to the pathogenesis of non-neoplastic diseases. Recent years have seen the publication of many studies aiming to characterize somatic evolution in healthy tissues. A logical next step is to extend such work to diseased conditions. As our understanding of the interplay between somatic mutations and non-neoplastic disease grows, opportunities for the joint study of germline and somatic variants will present themselves. Here, we present our thoughts on the utility of somatic mutations for understanding both the causes and consequences of common complex disease and the challenges that remain for the joint study of the soma and germline.
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Affiliation(s)
| | - Carl A Anderson
- Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK.
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23
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Wu S, Rish AJ, Skomo A, Zhao Y, Drennen JK, Anderson CA. Rapid serum-free/suspension adaptation: Medium development using a definitive screening design for Chinese hamster ovary cells. Biotechnol Prog 2021; 37:e3154. [PMID: 33864359 DOI: 10.1002/btpr.3154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 02/02/2021] [Revised: 03/20/2021] [Accepted: 04/10/2021] [Indexed: 12/17/2022]
Abstract
The biopharmaceutical industry prefers to culture the mammalian cells in suspension with a serum-free media (SFM) due to improved productivity and process consistency. However, mammalian cells preferentially grow as adherent cells in a complete medium (CM) containing serum. Therefore, cells require adaptation from adherence in CM to suspension culture in SFM. This work proposes an adaptation method that includes media supplementation during the adaption of Chinese hamster ovary cells. As a result, the adaptation was accelerated compared to the traditional repetitive subculturing. Ca2+ /Mg2+ supplementation significantly reduced the doubling time compared to the adaptation without supplementation during the adaptation of adherent cells from 100% CM to 75% CM (p < 0.05). Furthermore, a definitive screening design (DSD) was applied to select essential nutrients during the adaptation from 10% CM to 0% CM. The main effects of Ca2+ and Dulbecco's modified essential medium (DMEM) were found significant to both viable cell density and viability at harvest. Additionally, the interaction term between Ca2+ and DMEM was found significant, which highlights the ability of DSD to capture interaction terms. Eventually, the media supplementation method resulted in adaptation SFM in 27 days, compared to the previously reported 66 days. Additionally, the membrane surface integrin expression was found significantly decreased when adherent cells were adapted to suspension. Moreover, the Ca2+ /Mg2+ supplementation correlated with faster integrin recovery after trypsinization. However, faster integrin recovery did not contribute to the accelerated cell growth when subculturing from 100% CM to 75% CM.
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Affiliation(s)
- Suyang Wu
- Graduate School for Pharmaceutical Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA
| | - Adam J Rish
- Graduate School for Pharmaceutical Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA
| | - Alec Skomo
- Rangos School of Health Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA
| | - Yuxiang Zhao
- Graduate School for Pharmaceutical Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA
| | - James K Drennen
- Graduate School for Pharmaceutical Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA.,Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, Pennsylvania, USA
| | - Carl A Anderson
- Graduate School for Pharmaceutical Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA.,Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, Pennsylvania, USA
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24
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Gettler K, Levantovsky R, Moscati A, Giri M, Wu Y, Hsu NY, Chuang LS, Sazonovs A, Venkateswaran S, Korie U, Chasteau C, Duerr RH, Silverberg MS, Snapper SB, Daly MJ, McGovern DP, Brant SR, Rioux JD, Kugathasan S, Anderson CA, Itan Y, Cho JH. Common and Rare Variant Prediction and Penetrance of IBD in a Large, Multi-ethnic, Health System-based Biobank Cohort. Gastroenterology 2021; 160:1546-1557. [PMID: 33359885 PMCID: PMC8237248 DOI: 10.1053/j.gastro.2020.12.034] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 11/24/2020] [Accepted: 12/10/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND AND AIMS Polygenic risk scores (PRS) may soon be used to predict inflammatory bowel disease (IBD) risk in prevention efforts. We leveraged exome-sequence and single nucleotide polymorphism (SNP) array data from 29,358 individuals in the multiethnic, randomly ascertained health system-based BioMe biobank to define effects of common and rare IBD variants on disease prediction and pathophysiology. METHODS PRS were calculated from European, African American, and Ashkenazi Jewish (AJ) reference case-control studies, and a meta-GWAS run using all three association datasets. PRS were then combined using regression to assess which combination of scores best predicted IBD status in European, AJ, Hispanic, and African American cohorts in BioMe. Additionally, rare variants were assessed in genes associated with very early-onset IBD (VEO-IBD), by estimating genetic penetrance in each BioMe population. RESULTS Combining risk scores based on association data from distinct ancestral populations improved IBD prediction for every population in BioMe and significantly improved prediction among European ancestry UK Biobank individuals. Lower predictive power for non-Europeans was observed, reflecting in part substantially lower African IBD case-control reference sizes. We replicated associations for two VEO-IBD genes, ADAM17 and LRBA, with high dominant model penetrance in BioMe. Autosomal recessive LRBA risk alleles are associated with severe, early-onset autoimmunity; we show that heterozygous carriage of an African-predominant LRBA protein-altering allele is associated with significantly decreased LRBA and CTLA-4 expression with T-cell activation. CONCLUSIONS Greater genetic diversity in African populations improves prediction across populations, and generalizes some VEO-IBD genes. Increasing African American IBD case-collections should be prioritized to reduce health disparities and enhance pathophysiological insight.
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Affiliation(s)
- Kyle Gettler
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Rachel Levantovsky
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Arden Moscati
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Mamta Giri
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Yiming Wu
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Nai-Yun Hsu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ling-Shiang Chuang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Aleksejs Sazonovs
- Human Genetics, Wellcome Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Suresh Venkateswaran
- Division of Pediatric Gastroenterology, Hepatology & Nutrition, Emory University School of Medicine, Atlanta, Georgia
| | - Ujunwa Korie
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Colleen Chasteau
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Richard H Duerr
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Mark S Silverberg
- Division of Gastroenterology, Mount Sinai Hospital Inflammatory Bowel Disease Centre, Toronto, Ontario, Canada
| | - Scott B Snapper
- Division of Gastroenterology, Hepatology & Nutrition, Boston Children's Hospital, Boston, Massachusetts
| | - Mark J Daly
- Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts; Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Dermot P McGovern
- Medicine and Biomedical Sciences, Cedars-Sinai, Los Angeles, California
| | - Steven R Brant
- Division of Gastroenterology and Hepatology, Department of Medicine, Rutgers Robert Wood Johnson Medical School, and Department of Genetics and The Human Genetics Institute of New Jersey, Rutgers University, New Brunswick, New Jersey; Harvey M. and Lyn P. Meyerhoff Inflammatory Bowel Disease Center, Division of Gastroenterology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - John D Rioux
- Montreal Heart Institute, University of Montreal, Montreal, Canada
| | - Subra Kugathasan
- Division of Pediatric Gastroenterology, Hepatology & Nutrition, Emory University School of Medicine, Atlanta, Georgia; Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Carl A Anderson
- Human Genetics, Wellcome Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Yuval Itan
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Judy H Cho
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York.
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25
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Sazonovs A, Ahmad T, Anderson CA. Underpowered PANTS: A Response to the Conclusions of "Extended Analysis Identifies Drug-Specific Association of Two Distinct HLA Class II Haplotypes for Development of Immunogenicity to Adalimumab and Infliximab". Gastroenterology 2021; 160:470-471. [PMID: 33022279 DOI: 10.1053/j.gastro.2020.05.102] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 05/10/2020] [Indexed: 01/07/2023]
Affiliation(s)
| | - Tariq Ahmad
- Department of Gastroenterology, Royal Devon and Exeter Hospital National Health Service Foundation Trust; Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Carl A Anderson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
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26
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Olafsson S, McIntyre RE, Coorens T, Butler T, Jung H, Robinson PS, Lee-Six H, Sanders MA, Arestang K, Dawson C, Tripathi M, Strongili K, Hooks Y, Stratton MR, Parkes M, Martincorena I, Raine T, Campbell PJ, Anderson CA. Somatic Evolution in Non-neoplastic IBD-Affected Colon. Cell 2020; 182:672-684.e11. [PMID: 32697969 PMCID: PMC7427325 DOI: 10.1016/j.cell.2020.06.036] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 05/01/2020] [Accepted: 06/24/2020] [Indexed: 12/16/2022]
Abstract
Inflammatory bowel disease (IBD) is a chronic inflammatory disease associated with increased risk of gastrointestinal cancers. We whole-genome sequenced 446 colonic crypts from 46 IBD patients and compared these to 412 crypts from 41 non-IBD controls from our previous publication on the mutation landscape of the normal colon. The average mutation rate of affected colonic epithelial cells is 2.4-fold that of healthy colon, and this increase is mostly driven by acceleration of mutational processes ubiquitously observed in normal colon. In contrast to the normal colon, where clonal expansions outside the confines of the crypt are rare, we observed widespread millimeter-scale clonal expansions. We discovered non-synonymous mutations in ARID1A, FBXW7, PIGR, ZC3H12A, and genes in the interleukin 17 and Toll-like receptor pathways, under positive selection in IBD. These results suggest distinct selection mechanisms in the colitis-affected colon and that somatic mutations potentially play a causal role in IBD pathogenesis.
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Affiliation(s)
| | | | - Tim Coorens
- Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Timothy Butler
- Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Hyunchul Jung
- Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Philip S Robinson
- Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK; University of Cambridge, Department of Paediatrics, Cambridge CB2 0QQ, UK
| | - Henry Lee-Six
- Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Mathijs A Sanders
- Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK; Department of Hematology, Erasmus University Medical Center, Postbus 2040, 3000 CA Rotterdam, the Netherlands
| | - Kenneth Arestang
- Department of Gastroenterology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridgeshire CB2 0QQ, UK
| | - Claire Dawson
- Department of Gastroenterology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridgeshire CB2 0QQ, UK
| | - Monika Tripathi
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridgeshire CB2 0QQ, UK
| | - Konstantina Strongili
- Department of Gastroenterology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridgeshire CB2 0QQ, UK
| | - Yvette Hooks
- Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | | | - Miles Parkes
- Department of Gastroenterology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridgeshire CB2 0QQ, UK
| | | | - Tim Raine
- Department of Gastroenterology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridgeshire CB2 0QQ, UK
| | | | - Carl A Anderson
- Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK.
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27
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Petrova VN, Sawatsky B, Han AX, Laksono BM, Walz L, Parker E, Pieper K, Anderson CA, de Vries RD, Lanzavecchia A, Kellam P, von Messling V, de Swart RL, Russell CA. Incomplete genetic reconstitution of B cell pools contributes to prolonged immunosuppression after measles. Sci Immunol 2020; 4:4/41/eaay6125. [PMID: 31672862 DOI: 10.1126/sciimmunol.aay6125] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 10/01/2019] [Indexed: 12/24/2022]
Abstract
Measles is a disease caused by the highly infectious measles virus (MeV) that results in both viremia and lymphopenia. Lymphocyte counts recover shortly after the disappearance of measles-associated rash, but immunosuppression can persist for months to years after infection, resulting in increased incidence of secondary infections. Animal models and in vitro studies have proposed various immunological factors underlying this prolonged immune impairment, but the precise mechanisms operating in humans are unknown. Using B cell receptor (BCR) sequencing of human peripheral blood lymphocytes before and after MeV infection, we identified two immunological consequences from measles underlying immunosuppression: (i) incomplete reconstitution of the naïve B cell pool leading to immunological immaturity and (ii) compromised immune memory to previously encountered pathogens due to depletion of previously expanded B memory clones. Using a surrogate model of measles in ferrets, we investigated the clinical consequences of morbillivirus infection and demonstrated a depletion of vaccine-acquired immunity to influenza virus, leading to a compromised immune recall response and increased disease severity after secondary influenza virus challenge. Our results show that MeV infection causes changes in naïve and memory B lymphocyte diversity that persist after the resolution of clinical disease and thus contribute to compromised immunity to previous infections or vaccinations. This work highlights the importance of MeV vaccination not only for the control of measles but also for the maintenance of herd immunity to other pathogens, which can be compromised after MeV infection.
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Affiliation(s)
| | - Bevan Sawatsky
- Veterinary Medicine Division, Paul-Ehrlich-Institut, Federal Institute for Vaccines and Biomedicines and DZIF TTU Emerging Infections, Langen, Germany
| | - Alvin X Han
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Laboratory of Applied Evolutionary Biology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Brigitta M Laksono
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, Netherlands
| | - Lisa Walz
- Veterinary Medicine Division, Paul-Ehrlich-Institut, Federal Institute for Vaccines and Biomedicines and DZIF TTU Emerging Infections, Langen, Germany
| | - Edyth Parker
- Laboratory of Applied Evolutionary Biology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Kathrin Pieper
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Carl A Anderson
- Department of Human Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - Rory D de Vries
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, Netherlands
| | - Antonio Lanzavecchia
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Paul Kellam
- Department of Medicine, Division of Infectious Diseases, Imperial College Faculty of Medicine, Wright Fleming Institute, St Mary's Campus, London, UK.,Kymab Ltd., The Bennet Building, Babraham Research Campus, Cambridge, UK
| | - Veronika von Messling
- Veterinary Medicine Division, Paul-Ehrlich-Institut, Federal Institute for Vaccines and Biomedicines and DZIF TTU Emerging Infections, Langen, Germany
| | - Rik L de Swart
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, Netherlands
| | - Colin A Russell
- Laboratory of Applied Evolutionary Biology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands.
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28
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Westerdahl BB, Giraud D, Riddle LJ, Anderson CA. Essential oils for managing Pratylenchus penetrans on Easter lilies. J Nematol 2020; 52:1-7. [PMID: 32180376 PMCID: PMC7265903 DOI: 10.21307/jofnem-2020-010] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Indexed: 11/21/2022] Open
Abstract
Easter lily bulbs for greenhouse forcing are produced in Del Norte County, California and Curry County, Oregon, USA. Pratylenchus penetrans infestation seriously affects growth of field grown bulbs. During two consecutive years of field trials containing 22 treatments, commercially prepared formulations of essential oils (EOs) were compared to an untreated control and to a standard chemical fumigant treatment (FU) (1,3-dichloropropene and metam sodium) applied preplant followed by phorate (PH) at planting to determine their value in the management of lesion nematode, and in improving plant health. The EO products Duogard, EF400, EF300, and Cinnamite were tested as preplant dips to bulblet planting stock. The treated bulblets were tested either alone, in combination with PH at-planting, at planting following FU or in combination with PH at planting following FU. The organophosphates ethoprop and fosthiazate were also tested either alone, or at a reduced rate in combination with a reduced rate of PH. With respect to bulb circumference, ten treatments consistently outperformed the control. In consecutive years, three treatments had healthier looking roots than the control. At harvest, levels of lesion nematode within roots were consistently lower in nine treatments. EOs were beneficial in mitigating nematode damage.
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Affiliation(s)
- B B Westerdahl
- Department of Entomology and Nematology, University of California , Davis, CA 95616
| | - D Giraud
- University of California Cooperative Extension , Eureka, CA 95501
| | - L J Riddle
- Easter Lily Research Foundation, Brookings, OR 97415
| | - C A Anderson
- Department of Entomology and Nematology, University of California , Davis, CA 95616
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29
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Mohan S, Odani N, Hossain MN, Feng H, Li Y, Kato E, Drennen JK, Anderson CA. Terahertz Time of Flight Spectroscopy as a Coating Thickness Reference Method for Partial Least Squares Near Infrared Spectroscopy Models. Anal Chem 2020; 92:3658-3665. [PMID: 32020798 DOI: 10.1021/acs.analchem.9b04750] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Near infrared spectroscopy (NIRS) is often used during the tablet coating process to assess coating thickness. As the coating process proceeds, the increase and decrease in NIRS signal from both the coating formulation and tablet core has been related to coating thickness. Partial least-squares models are often generated relating NIRS spectra to reference coating thickness measurements for in-line and/or at-line monitoring of the coating process. This study investigated the effect of the reference coating thickness measurements on the accuracy of the model. The two primary reference techniques used were weight gain-based coating thickness and terahertz-based coating thickness. Most NIRS coating thickness models currently use weight gain-based reference values; however, terahertz-time-of-flight spectroscopy (THz-TOF) offers a more direct reference coating thickness measurement. Results showed that the accuracy of the NIRS coating thickness model significantly improved when terahertz-based coating thickness measurements were used as reference when compared to weight gain-based coating thickness measurements. Therefore, the application of THz-TOF as a reference method is further demonstrated.
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Affiliation(s)
- Shikhar Mohan
- Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, Pennsylvania 15282, United States.,Duquesne University, Graduate School for Pharmaceutical Sciences, Pittsburgh, Pennsylvania 15282, United States
| | - Noritaka Odani
- Manufacturing Technology Department, Towa Pharmaceutical Co., Ltd., Ichiban-cho, Kadoma, Osaka 571-0033, Japan
| | - Md Nayeem Hossain
- Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, Pennsylvania 15282, United States.,Duquesne University, Graduate School for Pharmaceutical Sciences, Pittsburgh, Pennsylvania 15282, United States
| | - Hanzhou Feng
- Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, Pennsylvania 15282, United States.,Duquesne University, Graduate School for Pharmaceutical Sciences, Pittsburgh, Pennsylvania 15282, United States
| | - Yi Li
- Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, Pennsylvania 15282, United States.,Duquesne University, Graduate School for Pharmaceutical Sciences, Pittsburgh, Pennsylvania 15282, United States
| | - Eiji Kato
- New Concept Product Initiative, Advantest Corporation, Sendai 989-3124 Japan
| | - James K Drennen
- Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, Pennsylvania 15282, United States.,Duquesne University, Graduate School for Pharmaceutical Sciences, Pittsburgh, Pennsylvania 15282, United States
| | - Carl A Anderson
- Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, Pennsylvania 15282, United States.,Duquesne University, Graduate School for Pharmaceutical Sciences, Pittsburgh, Pennsylvania 15282, United States
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30
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Serra EG, Schwerd T, Moutsianas L, Cavounidis A, Fachal L, Pandey S, Kammermeier J, Croft NM, Posovszky C, Rodrigues A, Russell RK, Barakat F, Auth MKH, Heuschkel R, Zilbauer M, Fyderek K, Braegger C, Travis SP, Satsangi J, Parkes M, Thapar N, Ferry H, Matte JC, Gilmour KC, Wedrychowicz A, Sullivan P, Moore C, Sambrook J, Ouwehand W, Roberts D, Danesh J, Baeumler TA, Fulga TA, Carrami EM, Ahmed A, Wilson R, Barrett JC, Elkadri A, Griffiths AM, Snapper SB, Shah N, Muise AM, Wilson DC, Uhlig HH, Anderson CA. Somatic mosaicism and common genetic variation contribute to the risk of very-early-onset inflammatory bowel disease. Nat Commun 2020; 11:995. [PMID: 32081864 PMCID: PMC7035382 DOI: 10.1038/s41467-019-14275-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 12/20/2019] [Indexed: 12/19/2022] Open
Abstract
Very-early-onset inflammatory bowel disease (VEO-IBD) is a heterogeneous phenotype associated with a spectrum of rare Mendelian disorders. Here, we perform whole-exome-sequencing and genome-wide genotyping in 145 patients (median age-at-diagnosis of 3.5 years), in whom no Mendelian disorders were clinically suspected. In five patients we detect a primary immunodeficiency or enteropathy, with clinical consequences (XIAP, CYBA, SH2D1A, PCSK1). We also present a case study of a VEO-IBD patient with a mosaic de novo, pathogenic allele in CYBB. The mutation is present in ~70% of phagocytes and sufficient to result in defective bacterial handling but not life-threatening infections. Finally, we show that VEO-IBD patients have, on average, higher IBD polygenic risk scores than population controls (99 patients and 18,780 controls; P < 4 × 10-10), and replicate this finding in an independent cohort of VEO-IBD cases and controls (117 patients and 2,603 controls; P < 5 × 10-10). This discovery indicates that a polygenic component operates in VEO-IBD pathogenesis.
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Affiliation(s)
| | - Tobias Schwerd
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
- Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital, Ludwig Maximilians University, Munich, Germany
| | | | - Athena Cavounidis
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Laura Fachal
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Sumeet Pandey
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | | | - Nicholas M Croft
- Blizard Institute, Barts and the London School of Medicine, Queen Mary University of London, London, UK
- The Royal London Children's Hospital, Barts Health NHS Trust, London, UK
| | | | | | | | - Farah Barakat
- Blizard Institute, Barts and the London School of Medicine, Queen Mary University of London, London, UK
- The Royal London Children's Hospital, Barts Health NHS Trust, London, UK
| | | | | | | | - Krzysztof Fyderek
- Department of Paediatrics, Gastroenterology and Nutrition, Jagiellonian University Medical College, Krakow, Poland
| | - Christian Braegger
- Division of Gastroenterology and Nutrition and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Simon P Travis
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Jack Satsangi
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Scotland, UK
| | - Miles Parkes
- IBD Research Unit, Department of Gastroenterology, Addenbrooke's Hospital, Cambridge, UK
| | | | - Helen Ferry
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Julie C Matte
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Andrzej Wedrychowicz
- Department of Paediatrics, Gastroenterology and Nutrition, Jagiellonian University Medical College, Krakow, Poland
| | - Peter Sullivan
- Department of Paediatrics, University of Oxford, Oxford, UK
| | - Carmel Moore
- NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- INTERVAL Coordinating Centre, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jennifer Sambrook
- INTERVAL Coordinating Centre, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Willem Ouwehand
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- INTERVAL Coordinating Centre, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - David Roberts
- NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- NHS Blood and Transplant - Oxford Centre, Level 2, John Radcliffe Hospital, Oxford, UK
- Biomedical Research Centre, Oxford - Haematology Theme, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - John Danesh
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- INTERVAL Coordinating Centre, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Toni A Baeumler
- Weatherall Institute of Molecular Medicine and the Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Tudor A Fulga
- Weatherall Institute of Molecular Medicine and the Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Eli M Carrami
- Weatherall Institute of Molecular Medicine and the Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Ahmed Ahmed
- Weatherall Institute of Molecular Medicine and the Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
- National Institute of Health Research Oxford Biomedical Research Centre, Surgical Innovation and Evaluation and Molecular Diagnostics Themes, University of Oxford, Oxford, UK
| | - Rachel Wilson
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | | | - Abdul Elkadri
- Department of Biochemistry and Pediatrics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- SickKids Inflammatory Bowel Disease Centre and Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, ON, Canada
| | - Anne M Griffiths
- Department of Biochemistry and Pediatrics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- SickKids Inflammatory Bowel Disease Centre and Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, ON, Canada
| | - Scott B Snapper
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Brigham and Women's Hospital, Boston, MA, USA
| | - Neil Shah
- Great Ormond Street Hospital, London, UK
| | - Aleixo M Muise
- Department of Biochemistry and Pediatrics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- SickKids Inflammatory Bowel Disease Centre and Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, ON, Canada
| | - David C Wilson
- Child Life and Health, University of Edinburgh, Edinburgh, UK
| | - Holm H Uhlig
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK.
- Department of Paediatrics, University of Oxford, Oxford, UK.
| | - Carl A Anderson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
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Sazonovs A, Kennedy NA, Moutsianas L, Heap GA, Rice DL, Reppell M, Bewshea CM, Chanchlani N, Walker GJ, Perry MH, McDonald TJ, Lees CW, Cummings JRF, Parkes M, Mansfield JC, Irving PM, Barrett JC, McGovern D, Goodhand JR, Anderson CA, Ahmad T. HLA-DQA1*05 Carriage Associated With Development of Anti-Drug Antibodies to Infliximab and Adalimumab in Patients With Crohn's Disease. Gastroenterology 2020; 158:189-199. [PMID: 31600487 DOI: 10.1053/j.gastro.2019.09.041] [Citation(s) in RCA: 222] [Impact Index Per Article: 55.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 09/24/2019] [Accepted: 09/29/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Anti-tumor necrosis factor (anti-TNF) therapies are the most widely used biologic drugs for treating immune-mediated diseases, but repeated administration can induce the formation of anti-drug antibodies. The ability to identify patients at increased risk for development of anti-drug antibodies would facilitate selection of therapy and use of preventative strategies. METHODS We performed a genome-wide association study to identify variants associated with time to development of anti-drug antibodies in a discovery cohort of 1240 biologic-naïve patients with Crohn's disease starting infliximab or adalimumab therapy. Immunogenicity was defined as an anti-drug antibody titer ≥10 AU/mL using a drug-tolerant enzyme-linked immunosorbent assay. Significant association signals were confirmed in a replication cohort of 178 patients with inflammatory bowel disease. RESULTS The HLA-DQA1*05 allele, carried by approximately 40% of Europeans, significantly increased the rate of immunogenicity (hazard ratio [HR], 1.90; 95% confidence interval [CI], 1.60-2.25; P = 5.88 × 10-13). The highest rates of immunogenicity, 92% at 1 year, were observed in patients treated with infliximab monotherapy who carried HLA-DQA1*05; conversely the lowest rates of immunogenicity, 10% at 1 year, were observed in patients treated with adalimumab combination therapy who did not carry HLA-DQA1*05. We confirmed this finding in the replication cohort (HR, 2.00; 95% CI, 1.35-2.98; P = 6.60 × 10-4). This association was consistent for patients treated with adalimumab (HR, 1.89; 95% CI, 1.32-2.70) or infliximab (HR, 1.92; 95% CI, 1.57-2.33), and for patients treated with anti-TNF therapy alone (HR, 1.75; 95% CI, 1.37-2.22) or in combination with an immunomodulator (HR, 2.01; 95% CI, 1.57-2.58). CONCLUSIONS In an observational study, we found a genome-wide significant association between HLA-DQA1*05 and the development of antibodies against anti-TNF agents. A randomized controlled biomarker trial is required to determine whether pretreatment testing for HLA-DQA1*05 improves patient outcomes by helping physicians select anti-TNF and combination therapies. ClinicalTrials.gov ID: NCT03088449.
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Affiliation(s)
| | - Nicholas A Kennedy
- Department of Gastroenterology, Royal Devon and Exeter Hospital National Health Service Foundation Trust, Exeter, UK; Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | | | - Graham A Heap
- Department of Gastroenterology, Royal Devon and Exeter Hospital National Health Service Foundation Trust, Exeter, UK; AbbVie Inc, North Chicago, Illinois
| | - Daniel L Rice
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Claire M Bewshea
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Neil Chanchlani
- Department of Gastroenterology, Royal Devon and Exeter Hospital National Health Service Foundation Trust, Exeter, UK; Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Gareth J Walker
- Department of Gastroenterology, Royal Devon and Exeter Hospital National Health Service Foundation Trust, Exeter, UK; Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Mandy H Perry
- Department of Blood Science, Royal Devon and Exeter Hospital National Health Service Foundation Trust, Exeter, UK
| | - Timothy J McDonald
- Department of Blood Science, Royal Devon and Exeter Hospital National Health Service Foundation Trust, Exeter, UK
| | - Charlie W Lees
- Department of Gastroenterology, Western General Hospital, National Health Service Lothian, Edinburgh, UK
| | - J R Fraser Cummings
- Department of Gastroenterology, University Hospital Southampton National Health Service Foundation Trust, Southampton, UK; Faculty of Experimental Medicine, University of Southampton, Southampton, UK
| | - Miles Parkes
- Department of Gastroenterology, Addenbrooke's Hospital, Cambridge University Hospitals National Health Service Foundation Trust, Cambridge, UK
| | - John C Mansfield
- Department of Gastroenterology, Newcastle Upon Tyne Hospitals National Health Service Foundation Trust, Newcastle upon Tyne, UK
| | - Peter M Irving
- Department of Gastroenterology, Guy's and St Thomas' NHS Foundation, Trust, London, UK
| | | | - Dermot McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - James R Goodhand
- Department of Gastroenterology, Royal Devon and Exeter Hospital National Health Service Foundation Trust, Exeter, UK; Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Carl A Anderson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
| | - Tariq Ahmad
- Department of Gastroenterology, Royal Devon and Exeter Hospital National Health Service Foundation Trust, Exeter, UK; Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK.
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Mohan S, Kato E, Drennen JK, Anderson CA. Refractive Index Measurement of Pharmaceutical Solids: A Review of Measurement Methods and Pharmaceutical Applications. J Pharm Sci 2019; 108:3478-3495. [DOI: 10.1016/j.xphs.2019.06.029] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 06/20/2019] [Indexed: 11/29/2022]
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Odani N, Mohan S, Kato E, Feng H, Li Y, Hossain MN, Drennen JK, Anderson CA. Determining the effect of photodegradation on film coated nifedipine tablets with terahertz based coating thickness measurements. Eur J Pharm Biopharm 2019; 145:35-41. [PMID: 31568821 DOI: 10.1016/j.ejpb.2019.09.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 05/03/2019] [Revised: 08/02/2019] [Accepted: 09/26/2019] [Indexed: 11/17/2022]
Abstract
Film coating of nifedipine tablets is commonly performed to reduce photo-degradation. The coating thickness of these tablets is a primary dictating factor of photo-stability. Terahertz spectroscopy enables accurate measurement of coating thickness. This study identifies a method to determine an end-point of a photo-protective coating process by using coating thickness measurements from terahertz time of flight spectroscopy (THz-TOF). For this method, nifedipine tablets, at different coating thicknesses, were placed in a photostability chamber. The illumination conditions of the coated tablets were adjusted based on the time duration of these tablets inside the chamber. A multiple linear regression model was developed with the coating thickness estimates from THz-TOF and illumination conditions information to predict the amount of drug remaining after photo-degradation (percent label claim). The prediction error of this model was 1.03% label claim in the range of 88.4-100.6% label claim. According to this model, acceptable levels of photo-protection in illumination conditions of up to approximately 700,000 lx hours was achieved at the end of the coating process (approximately 50 µm coating thickness) performed in this study. These results suggest THz-TOF as a viable process analytical technology tool for process understanding and end-point determination of a photo-protective coating process.
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Affiliation(s)
- Noritaka Odani
- Manufacturing Technology Department, Towa Pharmaceutical CO., LTD, Ichiban-cho, Kadoma, Osaka 571-0033, Japan
| | - Shikhar Mohan
- Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, PA 15282, United States; Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, PA 15282, United States
| | - Eiji Kato
- New Concept Product Initiative, Advantest Corporation, Sendai 989-3124, Japan
| | - Hanzhou Feng
- Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, PA 15282, United States; Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, PA 15282, United States
| | - Yi Li
- Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, PA 15282, United States; Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, PA 15282, United States
| | - Md Nayeem Hossain
- Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, PA 15282, United States; Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, PA 15282, United States
| | - James K Drennen
- Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, PA 15282, United States; Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, PA 15282, United States
| | - Carl A Anderson
- Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, PA 15282, United States; Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, PA 15282, United States.
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Li Y, Anderson CA, Drennen JK, Airiau C, Igne B. Development of an In-Line Near-Infrared Method for Blend Content Uniformity Assessment in a Tablet Feed Frame. Appl Spectrosc 2019; 73:1028-1040. [PMID: 30990067 DOI: 10.1177/0003702819842189] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Process analytical technology (PAT) has shown great potential for in-line tableting process monitoring. The study focuses on the development and validation of an in-line near-infrared (NIR) spectroscopic method for the determination of content uniformity of blends in a tablet feed frame. An in-line NIR method was developed after careful evaluation of the impact of potential experimental factors on the robustness and model accuracy and precision. The NIR method was validated according to the principles outlined in International Conference on Harmonization-Q2 for validation of analytical procedures and was demonstrated to be suitable for monitoring blend content for the formulation under evaluation. Reliable measurements of blend homogeneity rely on representative sampling. To reach the appropriate scale of scrutiny for a unit dose, the study assessed factors that influence the effective sample size measured by NIR. Spectral averaging, integration time, and feed frame paddle wheel speed were found to influence the effective sample size measured by the NIR probe. The effective sampling size was also estimated by comparing the distribution of predicted values with the reference values. The development of a robust, in-line PAT method was facilitated by thorough understanding of the sensitivity of PAT sensors to factors affecting pharmaceutical processes and products.
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Affiliation(s)
- Yi Li
- Duquesne University, Graduate School of Pharmaceutical Sciences, Pittsburgh, PA, USA
| | - Carl A Anderson
- Duquesne University, Graduate School of Pharmaceutical Sciences, Pittsburgh, PA, USA
| | - James K Drennen
- Duquesne University, Graduate School of Pharmaceutical Sciences, Pittsburgh, PA, USA
| | - Christian Airiau
- GlaxoSmithKline, Analytical Sciences and Development, Collegeville, PA, USA
| | - Benoît Igne
- GlaxoSmithKline, Analytical Sciences and Development, Collegeville, PA, USA
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35
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Zhao Y, Li W, Shi Z, Drennen JK, Anderson CA. Prediction of Dissolution Profiles From Process Parameters, Formulation, and Spectroscopic Measurements. J Pharm Sci 2019; 108:2119-2127. [DOI: 10.1016/j.xphs.2019.01.023] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 01/04/2019] [Accepted: 01/17/2019] [Indexed: 11/25/2022]
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Rivas MA, Avila BE, Koskela J, Huang H, Stevens C, Pirinen M, Haritunians T, Neale BM, Kurki M, Ganna A, Graham D, Glaser B, Peter I, Atzmon G, Barzilai N, Levine AP, Schiff E, Pontikos N, Weisburd B, Lek M, Karczewski KJ, Bloom J, Minikel EV, Petersen BS, Beaugerie L, Seksik P, Cosnes J, Schreiber S, Bokemeyer B, Bethge J, Heap G, Ahmad T, Plagnol V, Segal AW, Targan S, Turner D, Saavalainen P, Farkkila M, Kontula K, Palotie A, Brant SR, Duerr RH, Silverberg MS, Rioux JD, Weersma RK, Franke A, Jostins L, Anderson CA, Barrett JC, MacArthur DG, Jalas C, Sokol H, Xavier RJ, Pulver A, Cho JH, McGovern DPB, Daly MJ. Correction: Insights into the genetic epidemiology of Crohn's and rare diseases in the Ashkenazi Jewish population. PLoS Genet 2019; 15:e1008190. [PMID: 31145742 PMCID: PMC6542503 DOI: 10.1371/journal.pgen.1008190] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pgen.1007329.].
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37
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Goode EC, Clark AB, Mells GF, Srivastava B, Spiess K, Gelson WT, Trivedi PJ, Lynch KD, Castren E, Vesterhus MN, Karlsen TH, Ji S, Anderson CA, Thorburn D, Hudson M, Heneghan MA, Aldersley MA, Bathgate A, Sandford RN, Alexander GJ, Chapman RW, Walmsley M, Hirschfield GM, Rushbrook SM. Factors Associated With Outcomes of Patients With Primary Sclerosing Cholangitis and Development and Validation of a Risk Scoring System. Hepatology 2019; 69:2120-2135. [PMID: 30566748 PMCID: PMC6519245 DOI: 10.1002/hep.30479] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 12/02/2018] [Indexed: 12/15/2022]
Abstract
We sought to identify factors that are predictive of liver transplantation or death in patients with primary sclerosing cholangitis (PSC), and to develop and validate a contemporaneous risk score for use in a real-world clinical setting. Analyzing data from 1,001 patients recruited to the UK-PSC research cohort, we evaluated clinical variables for their association with 2-year and 10-year outcome through Cox-proportional hazards and C-statistic analyses. We generated risk scores for short-term and long-term outcome prediction, validating their use in two independent cohorts totaling 451 patients. Thirty-six percent of the derivation cohort were transplanted or died over a cumulative follow-up of 7,904 years. Serum alkaline phosphatase of at least 2.4 × upper limit of normal at 1 year after diagnosis was predictive of 10-year outcome (hazard ratio [HR] = 3.05; C = 0.63; median transplant-free survival 63 versus 108 months; P < 0.0001), as was the presence of extrahepatic biliary disease (HR = 1.45; P = 0.01). We developed two risk scoring systems based on age, values of bilirubin, alkaline phosphatase, albumin, platelets, presence of extrahepatic biliary disease, and variceal hemorrhage, which predicted 2-year and 10-year outcomes with good discrimination (C statistic = 0.81 and 0.80, respectively). Both UK-PSC risk scores were well-validated in our external cohort and outperformed the Mayo Clinic and aspartate aminotransferase-to-platelet ratio index (APRI) scores (C statistic = 0.75 and 0.63, respectively). Although heterozygosity for the previously validated human leukocyte antigen (HLA)-DR*03:01 risk allele predicted increased risk of adverse outcome (HR = 1.33; P = 0.001), its addition did not improve the predictive accuracy of the UK-PSC risk scores. Conclusion: Our analyses, based on a detailed clinical evaluation of a large representative cohort of participants with PSC, furthers our understanding of clinical risk markers and reports the development and validation of a real-world scoring system to identify those patients most likely to die or require liver transplantation.
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Affiliation(s)
- Elizabeth C. Goode
- Norfolk and Norwich University HospitalNorwichUnited Kingdom,Academic Department of Medical GeneticsAddenbrooke's Hospital, University of CambridgeCambridgeUnited Kingdom,Wellcome Trust Sanger InstituteHinxton, CambridgeUnited Kingdom,Norwich Medical SchoolUniversity of East AngliaNorwichUnited Kingdom,Cambridge Transplant CentreAddenbrooke's HospitalCambridgeUnited Kingdom
| | - Allan B. Clark
- Norwich Medical SchoolUniversity of East AngliaNorwichUnited Kingdom
| | - George F. Mells
- Academic Department of Medical GeneticsAddenbrooke's Hospital, University of CambridgeCambridgeUnited Kingdom
| | - Brijesh Srivastava
- Academic Department of Medical GeneticsAddenbrooke's Hospital, University of CambridgeCambridgeUnited Kingdom
| | - Kelly Spiess
- Academic Department of Medical GeneticsAddenbrooke's Hospital, University of CambridgeCambridgeUnited Kingdom
| | | | - Palak J. Trivedi
- National Institute for Health Research (NIHR) Birmingham Biomedical Research CentreBirminghamUnited Kingdom,Institute of Immunology & ImmunotherapyUniversity of BirminghamBirminghamUnited Kingdom,Centre for Rare Diseases, Institute of Translational MedicineUniversity Hospitals BirminghamBirminghamUnited Kingdom
| | - Kate D. Lynch
- Translational Gastroenterology UnitJohn Radcliffe Hospital, and Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Edit Castren
- Norfolk and Norwich University HospitalNorwichUnited Kingdom
| | - Mette N. Vesterhus
- Norwegian PSC Research Center, Department of Transplantation MedicineOslo University Hospital RikshospitaletOsloNorway,Institute of Clinical Medicine, Faculty of MedicineUniversity of OsloOsloNorway
| | - Tom H. Karlsen
- Norwegian PSC Research Center, Department of Transplantation MedicineOslo University Hospital RikshospitaletOsloNorway,Institute of Clinical Medicine, Faculty of MedicineUniversity of OsloOsloNorway
| | - Sun‐Gou Ji
- Wellcome Trust Sanger InstituteHinxton, CambridgeUnited Kingdom
| | | | - Douglas Thorburn
- Sheila Sherlock Liver Centre, Royal Free HospitalLondonUnited Kingdom
| | - Mark Hudson
- Liver Medicine and Transplantation ServiceFreeman HospitalNewcastleUnited Kingdom
| | | | | | - Andrew Bathgate
- Scottish Liver Transplant UnitRoyal Infirmary of EdinburghEdinburghUnited Kingdom
| | - Richard N. Sandford
- Academic Department of Medical GeneticsAddenbrooke's Hospital, University of CambridgeCambridgeUnited Kingdom
| | - Graeme J. Alexander
- Cambridge Transplant CentreAddenbrooke's HospitalCambridgeUnited Kingdom,Sheila Sherlock Liver Centre, Royal Free HospitalLondonUnited Kingdom
| | - Roger W. Chapman
- Translational Gastroenterology UnitJohn Radcliffe Hospital, and Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | | | | | - Gideon M. Hirschfield
- National Institute for Health Research (NIHR) Birmingham Biomedical Research CentreBirminghamUnited Kingdom,Institute of Immunology & ImmunotherapyUniversity of BirminghamBirminghamUnited Kingdom,Centre for Rare Diseases, Institute of Translational MedicineUniversity Hospitals BirminghamBirminghamUnited Kingdom,Toronto Centre for Liver DiseaseUniversity Health Network and University of TorontoTorontoCanada
| | - Simon M. Rushbrook
- Norfolk and Norwich University HospitalNorwichUnited Kingdom,Norwich Medical SchoolUniversity of East AngliaNorwichUnited Kingdom
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38
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Zhao Y, Drennen JK, Mohan S, Wu S, Anderson CA. Feedforward and Feedback Control of a Pharmaceutical Coating Process. AAPS PharmSciTech 2019; 20:157. [PMID: 30937727 DOI: 10.1208/s12249-019-1348-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 02/19/2019] [Indexed: 01/08/2023] Open
Abstract
This work demonstrates the use of a combination of feedforward and feedback loops to control the controlled release coating of theophylline granules. Feedforward models are based on the size distribution of incoming granules and are used to set values for the airflow in the fluid bed processor and the target coat weight to be applied to the granules. The target coat weight of the granules is controlled by a feedback loop using NIR spectroscopy to monitor the progress of the process. By combining feedforward and feedback loops, significant variation in the size distributions and ambient conditions were accommodated in the fluid bed coating of the granules and a desired dissolution profile was achieved. The feedforward component of the control system was specifically tested by comparing the performance of the control system with and without this element by Monte Carlo simulation.
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Walker GJ, Harrison JW, Heap GA, Voskuil MD, Andersen V, Anderson CA, Ananthakrishnan AN, Barrett JC, Beaugerie L, Bewshea CM, Cole AT, Cummings FR, Daly MJ, Ellul P, Fedorak RN, Festen EAM, Florin TH, Gaya DR, Halfvarson J, Hart AL, Heerasing NM, Hendy P, Irving PM, Jones SE, Koskela J, Lindsay JO, Mansfield JC, McGovern D, Parkes M, Pollok RCG, Ramakrishnan S, Rampton DS, Rivas MA, Russell RK, Schultz M, Sebastian S, Seksik P, Singh A, So K, Sokol H, Subramaniam K, Todd A, Annese V, Weersma RK, Xavier R, Ward R, Weedon MN, Goodhand JR, Kennedy NA, Ahmad T. Association of Genetic Variants in NUDT15 With Thiopurine-Induced Myelosuppression in Patients With Inflammatory Bowel Disease. JAMA 2019; 321:773-785. [PMID: 30806694 PMCID: PMC6439872 DOI: 10.1001/jama.2019.0709] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
IMPORTANCE Use of thiopurines may be limited by myelosuppression. TPMT pharmacogenetic testing identifies only 25% of at-risk patients of European ancestry. Among patients of East Asian ancestry, NUDT15 variants are associated with thiopurine-induced myelosuppression (TIM). OBJECTIVE To identify genetic variants associated with TIM among patients of European ancestry with inflammatory bowel disease (IBD). DESIGN, SETTING, AND PARTICIPANTS Case-control study of 491 patients affected by TIM and 679 thiopurine-tolerant unaffected patients who were recruited from 89 international sites between March 2012 and November 2015. Genome-wide association studies (GWAS) and exome-wide association studies (EWAS) were conducted in patients of European ancestry. The replication cohort comprised 73 patients affected by TIM and 840 thiopurine-tolerant unaffected patients. EXPOSURES Genetic variants associated with TIM. MAIN OUTCOMES AND MEASURES Thiopurine-induced myelosuppression, defined as a decline in absolute white blood cell count to 2.5 × 109/L or less or a decline in absolute neutrophil cell count to 1.0 × 109/L or less leading to a dose reduction or drug withdrawal. RESULTS Among 1077 patients (398 affected and 679 unaffected; median age at IBD diagnosis, 31.0 years [interquartile range, 21.2 to 44.1 years]; 540 [50%] women; 602 [56%] diagnosed as having Crohn disease), 919 (311 affected and 608 unaffected) were included in the GWAS analysis and 961 (328 affected and 633 unaffected) in the EWAS analysis. The GWAS analysis confirmed association of TPMT (chromosome 6, rs11969064) with TIM (30.5% [95/311] affected vs 16.4% [100/608] unaffected patients; odds ratio [OR], 2.3 [95% CI, 1.7 to 3.1], P = 5.2 × 10-9). The EWAS analysis demonstrated an association with an in-frame deletion in NUDT15 (chromosome 13, rs746071566) and TIM (5.8% [19/328] affected vs 0.2% [1/633] unaffected patients; OR, 38.2 [95% CI, 5.1 to 286.1], P = 1.3 × 10-8), which was replicated in a different cohort (2.7% [2/73] affected vs 0.2% [2/840] unaffected patients; OR, 11.8 [95% CI, 1.6 to 85.0], P = .03). Carriage of any of 3 coding NUDT15 variants was associated with an increased risk (OR, 27.3 [95% CI, 9.3 to 116.7], P = 1.1 × 10-7) of TIM, independent of TPMT genotype and thiopurine dose. CONCLUSIONS AND RELEVANCE Among patients of European ancestry with IBD, variants in NUDT15 were associated with increased risk of TIM. These findings suggest that NUDT15 genotyping may be considered prior to initiation of thiopurine therapy; however, further study including additional validation in independent cohorts is required.
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Affiliation(s)
- Gareth J. Walker
- Department of Gastroenterology, Royal Devon and Exeter Hospital NHS Foundation Trust, Exeter, England
- IBD Pharmacogenetics Group, University of Exeter, Exeter, England
| | | | - Graham A. Heap
- Department of Gastroenterology, Royal Devon and Exeter Hospital NHS Foundation Trust, Exeter, England
- IBD Pharmacogenetics Group, University of Exeter, Exeter, England
| | - Michiel D. Voskuil
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, the Netherlands
| | - Vibeke Andersen
- Medical Department, Regional Hospital Viborg, Viborg, Denmark
| | | | | | | | - Laurent Beaugerie
- Department of Gastroenterology, Saint-Antoine Hospital and Sorbonne Universite, Paris, France
| | | | - Andy T. Cole
- Derby Digestive Diseases Centre, Royal Derby Hospital, Derby Teaching Hospitals NHS Foundation Trust, Derby, England
| | - Fraser R. Cummings
- Department of Gastroenterology, Southampton General Hospital, University Hospital Southampton NHS Foundation Trust, Southampton, England
| | - Mark J. Daly
- Broad Institute, Harvard University, Cambridge, Massachusetts
| | - Pierre Ellul
- Department of Gastroenterology, Mater Dei Hospital, Msida, Malta
| | | | - Eleonora A. M. Festen
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, the Netherlands
| | - Timothy H. Florin
- Mater Research Institute, University of Queensland, South Brisbane, Australia
| | - Daniel R. Gaya
- Department of Gastroenterology, Glasgow Royal Infirmary, NHS Greater Glasgow and Clyde, Glasgow, Scotland
| | | | - Ailsa L. Hart
- Department of Gastroenterology, St Mark’s Hospital, London North West Healthcare NHS Trust, Harrow, England
| | - Neel M. Heerasing
- Department of Gastroenterology, Royal Devon and Exeter Hospital NHS Foundation Trust, Exeter, England
- IBD Pharmacogenetics Group, University of Exeter, Exeter, England
| | - Peter Hendy
- Department of Gastroenterology, Royal Devon and Exeter Hospital NHS Foundation Trust, Exeter, England
- IBD Pharmacogenetics Group, University of Exeter, Exeter, England
| | - Peter M. Irving
- Department of Gastroenterology, Guy’s and St Thomas’ NHS Foundation Trust, London, England
| | | | - Jukka Koskela
- Broad Institute, Harvard University, Cambridge, Massachusetts
| | - James O. Lindsay
- Centre for Immunobiology, Blizard Institute, Barts and the London School of Medicine, Queen Mary University of London, London, England
| | - John C. Mansfield
- Department of Gastroenterology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, England
| | - Dermot McGovern
- F. Widjaja Foundation Inflammatory Bowel Disease and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Miles Parkes
- Department of Gastroenterology, Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, England
| | - Richard C. G. Pollok
- Department of Gastroenterology, St George’s Healthcare NHS Trust, Tooting, England
| | - Subramaniam Ramakrishnan
- Gastrointestinal and Liver Services, Warrington and Halton Hospitals NHS Foundation Trust, Warrington, England
| | - David S. Rampton
- Department of Gastroenterology, Royal London Hospital, Barts Health NHS Trust, London, England
| | - Manuel A. Rivas
- Broad Institute, Harvard University, Cambridge, Massachusetts
| | - Richard K. Russell
- Department of Paediatric Gastroenterology, Royal Hospital for Children, NHS Greater Glasgow and Clyde, Glasgow, Scotland
| | | | - Shaji Sebastian
- Gastroenterology and Hepatology, Hull and East Yorkshire Hospitals NHS Trust, Hull, England
| | - Philippe Seksik
- Department of Gastroenterology, Saint-Antoine Hospital and Sorbonne Universite, Paris, France
| | - Abhey Singh
- Department of Gastroenterology, Royal Devon and Exeter Hospital NHS Foundation Trust, Exeter, England
| | - Kenji So
- Department of Gastroenterology, Royal Devon and Exeter Hospital NHS Foundation Trust, Exeter, England
| | - Harry Sokol
- Department of Gastroenterology, Saint-Antoine Hospital and Sorbonne Universite, Paris, France
| | | | - Anthony Todd
- Department of Haematology, Royal Devon and Exeter Hospital NHS Foundation Trust, Exeter, England
| | - Vito Annese
- Division of Gastroenterology, Azienda Ospedaliero Universitaria Careggi, Florence, Italy
| | - Rinse K. Weersma
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, the Netherlands
| | - Ramnik Xavier
- Broad Institute, Harvard University, Cambridge, Massachusetts
| | - Rebecca Ward
- University of Exeter Medical School, Exeter, England
| | | | - James R. Goodhand
- Department of Gastroenterology, Royal Devon and Exeter Hospital NHS Foundation Trust, Exeter, England
- IBD Pharmacogenetics Group, University of Exeter, Exeter, England
| | - Nicholas A. Kennedy
- Department of Gastroenterology, Royal Devon and Exeter Hospital NHS Foundation Trust, Exeter, England
- IBD Pharmacogenetics Group, University of Exeter, Exeter, England
| | - Tariq Ahmad
- Department of Gastroenterology, Royal Devon and Exeter Hospital NHS Foundation Trust, Exeter, England
- IBD Pharmacogenetics Group, University of Exeter, Exeter, England
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Hossain MN, Igne B, Anderson CA, Drennen JK. Influence of moisture variation on the performance of Raman spectroscopy in quantitative pharmaceutical analyses. J Pharm Biomed Anal 2019; 164:528-535. [DOI: 10.1016/j.jpba.2018.10.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 10/12/2018] [Accepted: 10/12/2018] [Indexed: 10/28/2022]
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Darlay R, Ayers KL, Mells GF, Hall LS, Liu JZ, Almarri MA, Alexander GJ, Jones DE, Sandford RN, Anderson CA, Cordell HJ. Amino acid residues in five separate HLA genes can explain most of the known associations between the MHC and primary biliary cholangitis. PLoS Genet 2018; 14:e1007833. [PMID: 30507971 PMCID: PMC6292650 DOI: 10.1371/journal.pgen.1007833] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 12/13/2018] [Accepted: 11/13/2018] [Indexed: 12/15/2022] Open
Abstract
Primary Biliary Cholangitis (PBC) is a chronic autoimmune liver disease characterised by progressive destruction of intrahepatic bile ducts. The strongest genetic association is with HLA-DQA1*04:01, but at least three additional independent HLA haplotypes contribute to susceptibility. We used dense single nucleotide polymorphism (SNP) data in 2861 PBC cases and 8514 controls to impute classical HLA alleles and amino acid polymorphisms using state-of-the-art methodologies. We then demonstrated through stepwise regression that association in the HLA region can be largely explained by variation at five separate amino acid positions. Three-dimensional modelling of protein structures and calculation of electrostatic potentials for the implicated HLA alleles/amino acid substitutions demonstrated a correlation between the electrostatic potential of pocket P6 in HLA-DP molecules and the HLA-DPB1 alleles/amino acid substitutions conferring PBC susceptibility/protection, highlighting potential new avenues for future functional investigation. Primary Biliary Cholangitis (PBC) is a chronic autoimmune liver disease that exhibits strong genetic associations, especially with variants in the human leukocyte antigen (HLA) gene region. Here we use dense single nucleotide polymorphism (SNP) data from the largest PBC study to date (2861 cases, 8514 controls) to investigate the likely underlying causes of this association, via performing imputation of HLA classical alleles and amino acids. We show that the HLA association can be largely explained by variation at five separate amino acid positions, one of which shows functional relevance to electrostatic potentials of HLA-DP molecules.
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Affiliation(s)
- Rebecca Darlay
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Kristin L. Ayers
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - George F. Mells
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Lynsey S. Hall
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Jimmy Z. Liu
- Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Mohamed A. Almarri
- Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
- Department of Forensic Science and Criminology, Dubai Police HQ, Dubai, United Arab Emirates
| | - Graeme J. Alexander
- Department of Hepatology, Cambridge University Hospitals National Health Service (NHS) Foundation Trust, Cambridge, United Kingdom
| | - David E. Jones
- Institute of Cellular Medicine, Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Richard N. Sandford
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Carl A. Anderson
- Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Heather J. Cordell
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
- * E-mail:
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42
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Cangul H, Liao XH, Schoenmakers E, Kero J, Barone S, Srichomkwun P, Iwayama H, Serra EG, Saglam H, Eren E, Tarim O, Nicholas AK, Zvetkova I, Anderson CA, Frankl FEK, Boelaert K, Ojaniemi M, Jääskeläinen J, Patyra K, Löf C, Williams ED, Soleimani M, Barrett T, Maher ER, Chatterjee VK, Refetoff S, Schoenmakers N. Homozygous loss-of-function mutations in SLC26A7 cause goitrous congenital hypothyroidism. JCI Insight 2018; 3:99631. [PMID: 30333321 DOI: 10.1172/jci.insight.99631] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [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: 01/04/2018] [Accepted: 09/06/2018] [Indexed: 12/27/2022] Open
Abstract
Defects in genes mediating thyroid hormone biosynthesis result in dyshormonogenic congenital hypothyroidism (CH). Here, we report homozygous truncating mutations in SLC26A7 in 6 unrelated families with goitrous CH and show that goitrous hypothyroidism also occurs in Slc26a7-null mice. In both species, the gene is expressed predominantly in the thyroid gland, and loss of function is associated with impaired availability of iodine for thyroid hormone synthesis, partially corrected in mice by iodine supplementation. SLC26A7 is a member of the same transporter family as SLC26A4 (pendrin), an anion exchanger with affinity for iodide and chloride (among others), whose gene mutations cause congenital deafness and dyshormonogenic goiter. However, in contrast to pendrin, SLC26A7 does not mediate cellular iodide efflux and hearing in affected individuals is normal. We delineate a hitherto unrecognized role for SLC26A7 in thyroid hormone biosynthesis, for which the mechanism remains unclear.
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Affiliation(s)
- Hakan Cangul
- Department of Medical Genetics, Istanbul Medipol University, International School of Medicine, Istanbul, Turkey
| | - Xiao-Hui Liao
- Department of Medicine, The University of Chicago, Chicago, Illinois, USA
| | - Erik Schoenmakers
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, Addenbrooke's Hospital, University of Cambridge, Cambridge, United Kingdom (UK)
| | - Jukka Kero
- Research Centre for Integrative Physiology and Pharmacology, Institute of Biomedicine, University of Turku, Turku, Finland.,Department of Paediatrics, Turku University Hospital, Turku, Finland
| | - Sharon Barone
- University of Cincinnati and Veterans Administration Hospital, Cincinnati, Ohio, USA
| | | | - Hideyuki Iwayama
- Department of Medicine, The University of Chicago, Chicago, Illinois, USA
| | - Eva G Serra
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Halil Saglam
- Uludag University School of Medicine, Department of Paediatric Endocrinology, Bursa, Turkey
| | - Erdal Eren
- Uludag University School of Medicine, Department of Paediatric Endocrinology, Bursa, Turkey
| | - Omer Tarim
- Uludag University School of Medicine, Department of Paediatric Endocrinology, Bursa, Turkey
| | - Adeline K Nicholas
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, Addenbrooke's Hospital, University of Cambridge, Cambridge, United Kingdom (UK)
| | - Ilona Zvetkova
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, Addenbrooke's Hospital, University of Cambridge, Cambridge, United Kingdom (UK)
| | - Carl A Anderson
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Fiona E Karet Frankl
- Department of Medical Genetics and Division of Renal Medicine, University of Cambridge, Cambridge, UK
| | - Kristien Boelaert
- Institute of Metabolism and Systems Research, University of Birmingham and Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Edgbaston, Birmingham, UK
| | - Marja Ojaniemi
- PEDEGO Research Center and MRC Oulu, University of Oulu, and Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland
| | - Jarmo Jääskeläinen
- Department of Pediatrics, University of Eastern Finland and Kuopio University, Hospital, Kuopio, Finland
| | - Konrad Patyra
- Research Centre for Integrative Physiology and Pharmacology, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Christoffer Löf
- Research Centre for Integrative Physiology and Pharmacology, Institute of Biomedicine, University of Turku, Turku, Finland
| | - E Dillwyn Williams
- Thyroid Carcinogenesis Group, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | | | - Manoocher Soleimani
- University of Cincinnati and Veterans Administration Hospital, Cincinnati, Ohio, USA
| | - Timothy Barrett
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham and Department of Endocrinology, Birmingham Children's Hospital, Birmingham, UK
| | - Eamonn R Maher
- Department of Medical Genetics, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - V Krishna Chatterjee
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, Addenbrooke's Hospital, University of Cambridge, Cambridge, United Kingdom (UK)
| | - Samuel Refetoff
- Department of Medicine, The University of Chicago, Chicago, Illinois, USA.,Department of Pediatrics and the Committee on Genetics, The University of Chicago, Chicago, Illinois, USA
| | - Nadia Schoenmakers
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, Addenbrooke's Hospital, University of Cambridge, Cambridge, United Kingdom (UK)
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Petrova VN, Muir L, McKay PF, Vassiliou GS, Smith KGC, Lyons PA, Russell CA, Anderson CA, Kellam P, Bashford-Rogers RJM. Combined Influence of B-Cell Receptor Rearrangement and Somatic Hypermutation on B-Cell Class-Switch Fate in Health and in Chronic Lymphocytic Leukemia. Front Immunol 2018; 9:1784. [PMID: 30147686 PMCID: PMC6095981 DOI: 10.3389/fimmu.2018.01784] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 07/19/2018] [Indexed: 01/21/2023] Open
Abstract
A diverse B-cell receptor (BCR) repertoire is required to bind a wide range of antigens. BCRs are generated through genetic recombination and can be diversified through somatic hypermutation (SHM) or class-switch recombination (CSR). Patterns of repertoire diversity can vary substantially between different health conditions. We use isotype-resolved BCR sequencing to compare B-cell evolution and class-switch fate in healthy individuals and in patients with chronic lymphocytic leukemia (CLL). We show that the patterns of SHM and CSR in B-cells from healthy individuals are distinct from CLL. We identify distinct properties of clonal expansion that lead to the generation of antibodies of different classes in healthy, malignant, and non-malignant CLL BCR repertoires. We further demonstrate that BCR diversity is affected by relationships between antibody variable and constant regions leading to isotype-specific signatures of variable gene usage. This study provides powerful insights into the mechanisms underlying the evolution of the adaptive immune responses in health and their aberration during disease.
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MESH Headings
- B-Lymphocytes/immunology
- B-Lymphocytes/metabolism
- B-Lymphocytes/pathology
- Gene Rearrangement, B-Lymphocyte
- Humans
- Immunoglobulin Class Switching/genetics
- Immunoglobulin Isotypes/genetics
- Immunoglobulin Joining Region/genetics
- Immunoglobulin Variable Region/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/immunology
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Leukocytes, Mononuclear/immunology
- Leukocytes, Mononuclear/metabolism
- Leukocytes, Mononuclear/pathology
- Multigene Family
- Receptors, Antigen, B-Cell/genetics
- Somatic Hypermutation, Immunoglobulin
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Affiliation(s)
| | - Luke Muir
- Department of Medicine, Division of Infectious Diseases, Imperial College London, London, United Kingdom
| | - Paul F. McKay
- Department of Medicine, Division of Infectious Diseases, Imperial College London, London, United Kingdom
| | | | | | - Paul A. Lyons
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Colin A. Russell
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | | | - Paul Kellam
- Department of Medicine, Division of Infectious Diseases, Imperial College London, London, United Kingdom
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Alberts R, de Vries EMG, Goode EC, Jiang X, Sampaziotis F, Rombouts K, Böttcher K, Folseraas T, Weismüller TJ, Mason AL, Wang W, Alexander G, Alvaro D, Bergquist A, Björkström NK, Beuers U, Björnsson E, Boberg KM, Bowlus CL, Bragazzi MC, Carbone M, Chazouillères O, Cheung A, Dalekos G, Eaton J, Eksteen B, Ellinghaus D, Färkkilä M, Festen EAM, Floreani A, Franceschet I, Gotthardt DN, Hirschfield GM, van Hoek B, Holm K, Hohenester S, Hov JR, Imhann F, Invernizzi P, Juran BD, Lenzen H, Lieb W, Liu JZ, Marschall HU, Marzioni M, Melum E, Milkiewicz P, Müller T, Pares A, Rupp C, Rust C, Sandford RN, Schramm C, Schreiber S, Schrumpf E, Silverberg MS, Srivastava B, Sterneck M, Teufel A, Vallier L, Verheij J, Vila AV, de Vries B, Zachou K, Chapman RW, Manns MP, Pinzani M, Rushbrook SM, Lazaridis KN, Franke A, Anderson CA, Karlsen TH, Ponsioen CY, Weersma RK. Genetic association analysis identifies variants associated with disease progression in primary sclerosing cholangitis. Gut 2018; 67:1517-1524. [PMID: 28779025 PMCID: PMC5797498 DOI: 10.1136/gutjnl-2016-313598] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 04/28/2017] [Accepted: 05/19/2017] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Primary sclerosing cholangitis (PSC) is a genetically complex, inflammatory bile duct disease of largely unknown aetiology often leading to liver transplantation or death. Little is known about the genetic contribution to the severity and progression of PSC. The aim of this study is to identify genetic variants associated with PSC disease progression and development of complications. DESIGN We collected standardised PSC subphenotypes in a large cohort of 3402 patients with PSC. After quality control, we combined 130 422 single nucleotide polymorphisms of all patients-obtained using the Illumina immunochip-with their disease subphenotypes. Using logistic regression and Cox proportional hazards models, we identified genetic variants associated with binary and time-to-event PSC subphenotypes. RESULTS We identified genetic variant rs853974 to be associated with liver transplant-free survival (p=6.07×10-9). Kaplan-Meier survival analysis showed a 50.9% (95% CI 41.5% to 59.5%) transplant-free survival for homozygous AA allele carriers of rs853974 compared with 72.8% (95% CI 69.6% to 75.7%) for GG carriers at 10 years after PSC diagnosis. For the candidate gene in the region, RSPO3, we demonstrated expression in key liver-resident effector cells, such as human and murine cholangiocytes and human hepatic stellate cells. CONCLUSION We present a large international PSC cohort, and report genetic loci associated with PSC disease progression. For liver transplant-free survival, we identified a genome-wide significant signal and demonstrated expression of the candidate gene RSPO3 in key liver-resident effector cells. This warrants further assessments of the role of this potential key PSC modifier gene.
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Affiliation(s)
- Rudi Alberts
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Elisabeth M G de Vries
- Department of Gastroenterology and Hepatology, Academic Medical Center, Amsterdam, The Netherlands
| | - Elizabeth C Goode
- Norwich Medical School, Faculty of Medicine and Health Sciences, University of East Anglia, Norwich, UK,Academic Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Xiaojun Jiang
- Norwegian PSC Research Center, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway,Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Fotis Sampaziotis
- Department of Surgery, Wellcome Trust-Medical Research Council Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, UK,Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Krista Rombouts
- Institute for Liver and Digestive Health, University College London, Royal Free Hospital, London, UK
| | - Katrin Böttcher
- Institute for Liver and Digestive Health, University College London, Royal Free Hospital, London, UK
| | - Trine Folseraas
- Norwegian PSC Research Center, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway,Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Tobias J Weismüller
- Department of Gastroenterology Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany,Integrated Research and Treatment Center-Transplantation (IFB-tx) Hannover Medical School, Hannover, Germany
| | - Andrew L Mason
- Division of Gastroenterology and Hepatology, University of Alberta, Edmonton, Alberta, Canada
| | - Weiwei Wang
- Division of Gastroenterology and Hepatology, University of Alberta, Edmonton, Alberta, Canada
| | - Graeme Alexander
- Department of Medicine, Division of Hepatology, University of Cambridge, Cambridge, UK
| | - Domenico Alvaro
- Department of Clinical Medicine, Division of Gastroenterology, Sapienza University of Rome, Rome, Italy
| | - Annika Bergquist
- Center for Digestive Diseases, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Niklas K Björkström
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Ulrich Beuers
- Department of Gastroenterology and Hepatology, Academic Medical Center, Amsterdam, The Netherlands
| | - Einar Björnsson
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Landspitali University Hospital, Reykjavik, Iceland
| | - Kirsten Muri Boberg
- Norwegian PSC Research Center, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway,K G Jebsen Inflammation Research Centre and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Christopher L Bowlus
- Division of Gastroenterology and Hepatology, University of California Davis, Davis, California, USA
| | - Maria C Bragazzi
- Sapienza University of Rome, Medico-Surgical Sciences and Biotechnologies, Rome, Italy
| | - Marco Carbone
- Department of Medicine and Surgery, Program for Autoimmune Liver Diseases, International Center for Digestive Health, University of Milan-Bicocca, Milan, Italy
| | | | - Angela Cheung
- General Internal Medicine, University Health Network, Toronto General Hospital, Toronto, Canada
| | - Georgios Dalekos
- Department of Medicine and Research Laboratory of Internal Medicine, Medical School, University of Thessaly, Larissa, Greece
| | - John Eaton
- Division of Gastroenterology and Hepatology, Mayo Clinic Minnesota, Rochester, Minnesota, USA
| | - Bertus Eksteen
- Department of Medicine, Snyder Institute of Chronic Diseases, University of Calgary, Calgary, Canada
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Martti Färkkilä
- Department of Medicine, Division of Gastroenterology, Helsinki University Hospital, Helsinki, Finland
| | - Eleonora A M Festen
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Annarosa Floreani
- Department of Surgical Oncological and Gastroenterological Sciences, University of Padova, Padova, Italy
| | - Irene Franceschet
- Department of Surgery Oncology and Gastroenterology, University of Padova, Padova, Italy
| | | | - Gideon M Hirschfield
- Centre for Liver Research, NIHR Biomedical Research Unit, University of Birmingham, Birmingham, UK
| | - Bart van Hoek
- Department of Gastroenterology and Hepatology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Kristian Holm
- Norwegian PSC Research Center, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway,Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Simon Hohenester
- Department of Medicine II, Liver Center Munich, University of Munich, Munich, Germany
| | - Johannes Roksund Hov
- Norwegian PSC Research Center, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway,Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Floris Imhann
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Pietro Invernizzi
- Department of Medicine and Surgery, Program for Autoimmune Liver Diseases, International Center for Digestive Health, University of Milan-Bicocca, Milan, Italy
| | - Brian D Juran
- Division of Gastroenterology and Hepatology, Mayo Clinic Minnesota, Rochester, Minnesota, USA
| | - Henrike Lenzen
- Department of Gastroenterology Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Wolfgang Lieb
- Popgen Biobank, University Hospital Schleswig-Holstein, Christian-Albrechts-University, Kiel, Germany,Institute for Epidemiology, Christian-Albrechts University, Kiel, Germany
| | - Jimmy Z Liu
- Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Cambridge, UK
| | - Hanns-Ulrich Marschall
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, Gothenburg, Sweden
| | - Marco Marzioni
- Department of Gastroenterology, Università Politecnica delle Marche, Ospedali Riuniti University Hospital, Ancona, Italy
| | - Espen Melum
- Norwegian PSC Research Center, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway,Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Piotr Milkiewicz
- Liver and Internal Medicine Unit, Medical University of Warsaw, Warsaw, Poland
| | - Tobias Müller
- Department of Internal Medicine Hepatology and Gastroenterology, Charité Universitätsmedizin Berlin, Campus Virchow Klinikum, Berlin, Germany
| | - Albert Pares
- Liver Unit Hospital Clinic, IDIBAPS, CIBERehd, University of Barcelona, Barcelona, Spain
| | - Christian Rupp
- Department of Internal Medicine IV, University Hospital of Heidelberg, Heidelberg, Germany
| | - Christian Rust
- Department of Medicine I, Krankenhaus Barmherzige Brüder, Munich, Germany
| | - Richard N Sandford
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Christoph Schramm
- 1st Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany,Department for General Internal Medicine, Christian-Albrechts-University, Kiel, Germany
| | - Erik Schrumpf
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway,Section of Gastroenterology, Department of Transplantation Medicine, Division of Cancer, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Mark S Silverberg
- Inflammatory Bowel Disease (IBD) Group Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital Toronto, Ontario, Canada
| | - Brijesh Srivastava
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Martina Sterneck
- Department of Hepatobiliary Surgery and Transplantation, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Andreas Teufel
- 1st Department of Medicine, University of Mainz, Mainz, Germany
| | - Ludovic Vallier
- Department of Surgery, Wellcome Trust-Medical Research Council Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, UK,Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Cambridge, UK
| | - Joanne Verheij
- Department of Pathology, Academic Medical Center, Amsterdam, The Netherlands
| | - Arnau Vich Vila
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Boudewijn de Vries
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Kalliopi Zachou
- Department of Internal Medicine, University of Thessaly, Larissa, Greece
| | | | - Roger W Chapman
- Department of Hepatology, John Radcliffe University Hospitals NHS Trust, Cambridge, UK
| | - Michael P Manns
- Department of Gastroenterology Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany,Integrated Research and Treatment Center-Transplantation (IFB-tx) Hannover Medical School, Hannover, Germany
| | - Massimo Pinzani
- Institute for Liver and Digestive Health, University College London, Royal Free Hospital, London, UK
| | - Simon M Rushbrook
- Norwich Medical School, Faculty of Medicine and Health Sciences, University of East Anglia, Norwich, UK
| | | | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Carl A Anderson
- Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Cambridge, UK
| | - Tom H Karlsen
- Norwegian PSC Research Center, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway,Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Cyriel Y Ponsioen
- Department of Gastroenterology and Hepatology, Academic Medical Center, Amsterdam, The Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
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Quaranta M, Wilson R, Gonçalves Serra E, Pandey S, Schwerd T, Gilmour K, Klenerman P, Powrie F, Keshav S, Travis SPL, Anderson CA, Uhlig HH. Consequences of Identifying XIAP Deficiency in an Adult Patient With Inflammatory Bowel Disease. Gastroenterology 2018; 155:231-234. [PMID: 29894681 DOI: 10.1053/j.gastro.2018.03.069] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 03/26/2018] [Indexed: 12/02/2022]
Affiliation(s)
- Maria Quaranta
- Translational Gastroenterology Unit, Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Rachel Wilson
- Translational Gastroenterology Unit, Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | | | - Sumeet Pandey
- Translational Gastroenterology Unit, Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Tobias Schwerd
- Translational Gastroenterology Unit, Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | | | - Paul Klenerman
- Translational Gastroenterology Unit, Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Fiona Powrie
- Translational Gastroenterology Unit, Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital and Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Satish Keshav
- Translational Gastroenterology Unit, Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Simon P L Travis
- Translational Gastroenterology Unit, Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | | | - Holm H Uhlig
- Department of Paediatrics, University of Oxford, John Radcliffe Hospital, Oxford, UK; Translational Gastroenterology Unit, Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
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46
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Li Y, Anderson CA, Drennen JK, Airiau C, Igne B. Method Development and Validation of an Inline Process Analytical Technology Method for Blend Monitoring in the Tablet Feed Frame Using Raman Spectroscopy. Anal Chem 2018; 90:8436-8444. [DOI: 10.1021/acs.analchem.8b01009] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yi Li
- Duquesne University, Graduate School of Pharmaceutical Sciences, Pittsburgh, Pennsylvania 15282, United States
| | - Carl A. Anderson
- Duquesne University, Graduate School of Pharmaceutical Sciences, Pittsburgh, Pennsylvania 15282, United States
| | - James K. Drennen
- Duquesne University, Graduate School of Pharmaceutical Sciences, Pittsburgh, Pennsylvania 15282, United States
| | - Christian Airiau
- GlaxoSmithKline, Analytical Sciences and Development, King of Prussia, Pennsylvania 19406, United States
| | - Benoît Igne
- GlaxoSmithKline, Analytical Sciences and Development, King of Prussia, Pennsylvania 19406, United States
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Rivas MA, Avila BE, Koskela J, Huang H, Stevens C, Pirinen M, Haritunians T, Neale BM, Kurki M, Ganna A, Graham D, Glaser B, Peter I, Atzmon G, Barzilai N, Levine AP, Schiff E, Pontikos N, Weisburd B, Lek M, Karczewski KJ, Bloom J, Minikel EV, Petersen BS, Beaugerie L, Seksik P, Cosnes J, Schreiber S, Bokemeyer B, Bethge J, Heap G, Ahmad T, Plagnol V, Segal AW, Targan S, Turner D, Saavalainen P, Farkkila M, Kontula K, Palotie A, Brant SR, Duerr RH, Silverberg MS, Rioux JD, Weersma RK, Franke A, Jostins L, Anderson CA, Barrett JC, MacArthur DG, Jalas C, Sokol H, Xavier RJ, Pulver A, Cho JH, McGovern DPB, Daly MJ. Insights into the genetic epidemiology of Crohn's and rare diseases in the Ashkenazi Jewish population. PLoS Genet 2018; 14:e1007329. [PMID: 29795570 PMCID: PMC5967709 DOI: 10.1371/journal.pgen.1007329] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 03/22/2018] [Indexed: 02/05/2023] Open
Abstract
As part of a broader collaborative network of exome sequencing studies, we developed a jointly called data set of 5,685 Ashkenazi Jewish exomes. We make publicly available a resource of site and allele frequencies, which should serve as a reference for medical genetics in the Ashkenazim (hosted in part at https://ibd.broadinstitute.org, also available in gnomAD at http://gnomad.broadinstitute.org). We estimate that 34% of protein-coding alleles present in the Ashkenazi Jewish population at frequencies greater than 0.2% are significantly more frequent (mean 15-fold) than their maximum frequency observed in other reference populations. Arising via a well-described founder effect approximately 30 generations ago, this catalog of enriched alleles can contribute to differences in genetic risk and overall prevalence of diseases between populations. As validation we document 148 AJ enriched protein-altering alleles that overlap with "pathogenic" ClinVar alleles (table available at https://github.com/macarthur-lab/clinvar/blob/master/output/clinvar.tsv), including those that account for 10-100 fold differences in prevalence between AJ and non-AJ populations of some rare diseases, especially recessive conditions, including Gaucher disease (GBA, p.Asn409Ser, 8-fold enrichment); Canavan disease (ASPA, p.Glu285Ala, 12-fold enrichment); and Tay-Sachs disease (HEXA, c.1421+1G>C, 27-fold enrichment; p.Tyr427IlefsTer5, 12-fold enrichment). We next sought to use this catalog, of well-established relevance to Mendelian disease, to explore Crohn's disease, a common disease with an estimated two to four-fold excess prevalence in AJ. We specifically attempt to evaluate whether strong acting rare alleles, particularly protein-truncating or otherwise large effect-size alleles, enriched by the same founder-effect, contribute excess genetic risk to Crohn's disease in AJ, and find that ten rare genetic risk factors in NOD2 and LRRK2 are enriched in AJ (p < 0.005), including several novel contributing alleles, show evidence of association to CD. Independently, we find that genomewide common variant risk defined by GWAS shows a strong difference between AJ and non-AJ European control population samples (0.97 s.d. higher, p<10-16). Taken together, the results suggest coordinated selection in AJ population for higher CD risk alleles in general. The results and approach illustrate the value of exome sequencing data in case-control studies along with reference data sets like ExAC (sites VCF available via FTP at ftp.broadinstitute.org/pub/ExAC_release/release0.3/) to pinpoint genetic variation that contributes to variable disease predisposition across populations.
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Affiliation(s)
- Manuel A. Rivas
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Department of Biomedical Data Science, Stanford University, Stanford, CA, United States of America
| | - Brandon E. Avila
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Jukka Koskela
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Hailiang Huang
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Christine Stevens
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
| | - Matti Pirinen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Talin Haritunians
- Translational Genomics Unit, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States of America
| | - Benjamin M. Neale
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Mitja Kurki
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Andrea Ganna
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Daniel Graham
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
| | - Benjamin Glaser
- Hadassah-Hebrew University Medical Center, Endocrinology and Metabolism Service Department of Internal Medicine, Jerusalem, Israel
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Gil Atzmon
- Department of Genetics and Medicine, Albert Einstein College of Medicine, Bronx, NY, United States of America
- Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Nir Barzilai
- Department of Genetics and Medicine, Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Adam P. Levine
- Division of Medicine, University College London, London, United Kingdom
| | - Elena Schiff
- Division of Medicine, University College London, London, United Kingdom
| | - Nikolas Pontikos
- Division of Medicine, University College London, London, United Kingdom
- UCL Genetics Institute, University College London, London, United Kingdom
| | - Ben Weisburd
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Monkol Lek
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Konrad J. Karczewski
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Jonathan Bloom
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Eric V. Minikel
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Britt-Sabina Petersen
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Laurent Beaugerie
- Gastroenterology Department, Saint-Antoine Hospital, AP-HP, UPMC Univ Paris, Paris, France
| | - Philippe Seksik
- Gastroenterology Department, Saint-Antoine Hospital, AP-HP, UPMC Univ Paris, Paris, France
| | - Jacques Cosnes
- Gastroenterology Department, Saint-Antoine Hospital, AP-HP, UPMC Univ Paris, Paris, France
| | - Stefan Schreiber
- Department of Internal Medicine, University Hospital Schleswig-Holstein, Kiel, Germany
| | | | - Johannes Bethge
- Department of Internal Medicine, University Hospital Schleswig-Holstein, Kiel, Germany
| | | | | | | | - Graham Heap
- IBD Pharmacogenetics, Royal Devon and Exeter NHS Trust, Exeter, United Kingdom
| | - Tariq Ahmad
- Peninsula College of Medicine and Dentistry, Exeter, United Kingdom
| | - Vincent Plagnol
- UCL Genetics Institute, University College London, London, United Kingdom
| | - Anthony W. Segal
- Division of Medicine, University College London, London, United Kingdom
| | - Stephan Targan
- Translational Genomics Unit, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States of America
| | - Dan Turner
- Juliet Keidan Institute of Pediatric Gastroenterology and Nutrition, Shaare Zedek Medical Center, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Paivi Saavalainen
- Research Programs Unit, Immunobiology, and Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Martti Farkkila
- Department of Medicine, Division of Gastroenterology, Helsinki University Hospital, Helsinki, Finland
| | - Kimmo Kontula
- Department of Medicine, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Aarno Palotie
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Department of Neurology, Massachusetts General Hospital, Boston, MA, United States of America
| | - Steven R. Brant
- Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, United States of America
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States of America
| | - Richard H. Duerr
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, United States of America
| | - Mark S. Silverberg
- Inflammatory Bowel Disease Centre, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - John D. Rioux
- Research Center, Montreal Heart Institute, Montréal, Québec, Canada
- Department of Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Rinse K. Weersma
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, The Netherlands
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Luke Jostins
- Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, United Kingdom
| | - Carl A. Anderson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Jeffrey C. Barrett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Daniel G. MacArthur
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Chaim Jalas
- Bonei Olam, Center for Rare Jewish Genetic Disorders, Brooklyn, NY, United States of America
| | - Harry Sokol
- Gastroenterology Department, Saint-Antoine Hospital, AP-HP, UPMC Univ Paris, Paris, France
| | - Ramnik J. Xavier
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease and Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Ann Pulver
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Judy H. Cho
- Icahn School of Medicine at Mount Sinai, Dr Henry D. Janowitz Division of Gastroenterology, New York, NY, United States of America
| | - Dermot P. B. McGovern
- Translational Genomics Unit, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States of America
| | - Mark J. Daly
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
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48
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Mohan S, Momose W, Katz JM, Hossain MN, Velez N, Drennen JK, Anderson CA. A robust quantitative near infrared modeling approach for blend monitoring. J Pharm Biomed Anal 2018; 148:51-57. [DOI: 10.1016/j.jpba.2017.09.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/05/2017] [Accepted: 09/06/2017] [Indexed: 10/18/2022]
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Dunn DH, Johnson EM, Anderson CA, Krueger JL, DeFor TE, Morphew JA, Banerji N. Operative and survival outcomes in a series of 100 consecutive cases of robot-assisted transhiatal esophagectomies. Dis Esophagus 2017; 30:1-7. [PMID: 28859385 DOI: 10.1093/dote/dox045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 04/04/2017] [Indexed: 12/11/2022]
Abstract
Robotic-assisted transhiatal esophagectomy (RATE) is a technically complex procedure with potential for improved postoperative outcomes. In this report, we describe our experience with RATE in a large case series. A retrospective review was conducted to collect clinical, outcomes, and survival data for 100 consecutive patients with esophageal cancer (n = 98) and benign (n = 2) conditions undergoing RATE between March 2007 and December 2014. Progression-free (PFS) and overall (OS) survival were estimated using the Kaplan-Meier curves with comparisons by log-rank tests. Median operative time and estimated blood loss were 264 minutes and 75 mL, respectively. Median intensive care unit stay was 1 day and median length of hospital stay was 8 days. Postoperative complications commonly observed were nonmalignant pleural effusion (38%) and recurrent laryngeal nerve injury (33%); 30 day mortality rate was 2%. Median number of lymph nodes removed during RATE was 17 and R0 resection was achieved in 97.8% patients. At the end of the median follow-up period of 27.7 months, median PFS was 41 months and median OS was 54 months. 1-year and 3-year PFS rates were 82% (95% CI, 75%-89%) and 53% (95% CI, 42%-62%), respectively, and OS rates were 95% (95% CI, 91%-99%) and 57% (95% CI, 46%-67%). In our experience, RATE is an effective and safe oncologic surgical procedure in a carefully selected group of patients with acceptable operative time, minimal blood loss, standard postoperative morbidity and adequate PFS and OS profiles.
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Affiliation(s)
- D H Dunn
- VPCI Esophageal and Gastric Cancer Program
| | | | | | | | - T E DeFor
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | | | - N Banerji
- JNNI Research, Abbott Northwestern Hospital
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50
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Talwar S, Roopwani R, Anderson CA, Buckner IS, Drennen JK. Determination of Spatially Resolved Tablet Density and Hardness Using Near-Infrared Chemical Imaging (NIR-CI). Appl Spectrosc 2017; 71:1906-1914. [PMID: 28756700 DOI: 10.1177/0003702817693856] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Near-infrared chemical imaging (NIR-CI) combines spectroscopy with digital imaging, enabling spatially resolved analysis and characterization of pharmaceutical samples. Hardness and relative density are critical quality attributes (CQA) that affect tablet performance. Intra-sample density or hardness variability can reveal deficiencies in formulation design or the tableting process. This study was designed to develop NIR-CI methods to predict spatially resolved tablet density and hardness. The method was implemented using a two-step procedure. First, NIR-CI was used to develop a relative density/solid fraction (SF) prediction method for pure microcrystalline cellulose (MCC) compacts only. A partial least squares (PLS) model for predicting SF was generated by regressing the spectra of certain representative pixels selected from each image against the compact SF. Pixel selection was accomplished with a threshold based on the Euclidean distance from the median tablet spectrum. Second, micro-indentation was performed on the calibration compacts to obtain hardness values. A univariate model was developed by relating the empirical hardness values to the NIR-CI predicted SF at the micro-indented pixel locations: this model generated spatially resolved hardness predictions for the entire tablet surface.
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Affiliation(s)
- Sameer Talwar
- 1 Graduate School of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA, USA
| | - Rahul Roopwani
- 1 Graduate School of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA, USA
| | - Carl A Anderson
- 1 Graduate School of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA, USA
- 2 Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, PA, USA
| | - Ira S Buckner
- 1 Graduate School of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA, USA
- 2 Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, PA, USA
| | - James K Drennen
- 1 Graduate School of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA, USA
- 2 Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, PA, USA
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