1
|
Gall L, Duckworth C, Jardi F, Lammens L, Parker A, Bianco A, Kimko H, Pritchard DM, Pin C. Homeostasis, injury, and recovery dynamics at multiple scales in a self-organizing mouse intestinal crypt. eLife 2023; 12:e85478. [PMID: 38063302 PMCID: PMC10789491 DOI: 10.7554/elife.85478] [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] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 12/07/2023] [Indexed: 01/16/2024] Open
Abstract
The maintenance of the functional integrity of the intestinal epithelium requires a tight coordination between cell production, migration, and shedding along the crypt-villus axis. Dysregulation of these processes may result in loss of the intestinal barrier and disease. With the aim of generating a more complete and integrated understanding of how the epithelium maintains homeostasis and recovers after injury, we have built a multi-scale agent-based model (ABM) of the mouse intestinal epithelium. We demonstrate that stable, self-organizing behaviour in the crypt emerges from the dynamic interaction of multiple signalling pathways, such as Wnt, Notch, BMP, ZNRF3/RNF43, and YAP-Hippo pathways, which regulate proliferation and differentiation, respond to environmental mechanical cues, form feedback mechanisms, and modulate the dynamics of the cell cycle protein network. The model recapitulates the crypt phenotype reported after persistent stem cell ablation and after the inhibition of the CDK1 cycle protein. Moreover, we simulated 5-fluorouracil (5-FU)-induced toxicity at multiple scales starting from DNA and RNA damage, which disrupts the cell cycle, cell signalling, proliferation, differentiation, and migration and leads to loss of barrier integrity. During recovery, our in silico crypt regenerates its structure in a self-organizing, dynamic fashion driven by dedifferentiation and enhanced by negative feedback loops. Thus, the model enables the simulation of xenobiotic-, in particular chemotherapy-, induced mechanisms of intestinal toxicity and epithelial recovery. Overall, we present a systems model able to simulate the disruption of molecular events and its impact across multiple levels of epithelial organization and demonstrate its application to epithelial research and drug development.
Collapse
Affiliation(s)
- Louis Gall
- Clinical Pharmacology and Quantitative Pharmacology, Clinical Pharmacology and Safety Sciences, R&D, AstraZenecaCambridgeUnited Kingdom
| | - Carrie Duckworth
- Institute of Systems, Molecular and Integrative Biology, University of LiverpoolLiverpoolUnited Kingdom
| | - Ferran Jardi
- Preclinical Sciences and Translational Safety, JanssenBeerseBelgium
| | - Lieve Lammens
- Preclinical Sciences and Translational Safety, JanssenBeerseBelgium
| | - Aimee Parker
- Gut Microbes and Health Programme, Quadram InstituteNorwichUnited Kingdom
| | - Ambra Bianco
- Clinical Pharmacology and Safety Sciences, AstraZenecaCambridgeUnited Kingdom
| | - Holly Kimko
- Clinical Pharmacology and Quantitative Pharmacology, Clinical Pharmacology and Safety Sciences, R&D, AstraZenecaCambridgeUnited Kingdom
| | - David Mark Pritchard
- Institute of Systems, Molecular and Integrative Biology, University of LiverpoolLiverpoolUnited Kingdom
| | - Carmen Pin
- Clinical Pharmacology and Quantitative Pharmacology, Clinical Pharmacology and Safety Sciences, R&D, AstraZenecaCambridgeUnited Kingdom
| |
Collapse
|
2
|
Gall L, Jardi F, Lammens L, Piñero J, Souza TM, Rodrigues D, Jennen DGJ, de Kok TM, Coyle L, Chung S, Ferreira S, Jo H, Beattie KA, Kelly C, Duckworth CA, Pritchard DM, Pin C. A dynamic model of the intestinal epithelium integrates multiple sources of preclinical data and enables clinical translation of drug-induced toxicity. CPT Pharmacometrics Syst Pharmacol 2023; 12:1511-1528. [PMID: 37621010 PMCID: PMC10583244 DOI: 10.1002/psp4.13029] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 07/13/2023] [Accepted: 07/17/2023] [Indexed: 08/26/2023] Open
Abstract
We have built a quantitative systems toxicology modeling framework focused on the early prediction of oncotherapeutic-induced clinical intestinal adverse effects. The model describes stem and progenitor cell dynamics in the small intestinal epithelium and integrates heterogeneous epithelial-related processes, such as transcriptional profiles, citrulline kinetics, and probability of diarrhea. We fitted a mouse-specific version of the model to quantify doxorubicin and 5-fluorouracil (5-FU)-induced toxicity, which included pharmacokinetics and 5-FU metabolism and assumed that both drugs led to cell cycle arrest and apoptosis in stem cells and proliferative progenitors. The model successfully recapitulated observations in mice regarding dose-dependent disruption of proliferation which could lead to villus shortening, decrease of circulating citrulline, increased diarrhea risk, and transcriptional induction of the p53 pathway. Using a human-specific epithelial model, we translated the cytotoxic activity of doxorubicin and 5-FU quantified in mice into human intestinal injury and predicted with accuracy clinical diarrhea incidence. However, for gefitinib, a specific-molecularly targeted therapy, the mice failed to reproduce epithelial toxicity at exposures much higher than those associated with clinical diarrhea. This indicates that, regardless of the translational modeling approach, preclinical experimental settings have to be suitable to quantify drug-induced clinical toxicity with precision at the structural scale of the model. Our work demonstrates the usefulness of translational models at early stages of the drug development pipeline to predict clinical toxicity and highlights the importance of understanding cross-settings differences in toxicity when building these approaches.
Collapse
Affiliation(s)
- Louis Gall
- Clinical Pharmacology and Quantitative Pharmacology, Clinical Pharmacology and Safety Sciences, R&DAstraZenecaCambridgeUK
| | - Ferran Jardi
- Preclinical Sciences & Translational SafetyJanssen Pharmaceutica NVBeerseBelgium
| | - Lieve Lammens
- Preclinical Sciences & Translational SafetyJanssen Pharmaceutica NVBeerseBelgium
| | - Janet Piñero
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM)UPFBarcelonaSpain
| | - Terezinha M. Souza
- Department of Toxicogenomics, GROW School for Oncology and Developmental BiologyMaastricht UniversityMaastrichtThe Netherlands
| | - Daniela Rodrigues
- Department of Toxicogenomics, GROW School for Oncology and Developmental BiologyMaastricht UniversityMaastrichtThe Netherlands
| | - Danyel G. J. Jennen
- Department of Toxicogenomics, GROW School for Oncology and Developmental BiologyMaastricht UniversityMaastrichtThe Netherlands
| | - Theo M. de Kok
- Department of Toxicogenomics, GROW School for Oncology and Developmental BiologyMaastricht UniversityMaastrichtThe Netherlands
| | - Luke Coyle
- Boehringer Ingelheim International GmbHRidgefieldConnecticutUSA
| | | | | | - Heeseung Jo
- Simcyp DivisionCertara UK LimitedSheffieldUK
| | - Kylie A. Beattie
- Target and Systems Safety, Non‐Clinical Safety, In Vivo/In Vitro TranslationGSKStevenageUK
| | - Colette Kelly
- Institute of Systems, Molecular and Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - Carrie A. Duckworth
- Institute of Systems, Molecular and Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - D. Mark Pritchard
- Institute of Systems, Molecular and Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - Carmen Pin
- Clinical Pharmacology and Quantitative Pharmacology, Clinical Pharmacology and Safety Sciences, R&DAstraZenecaCambridgeUK
| |
Collapse
|
3
|
Pin C. S-25-03 Multiscale models, integrating several data types, applied to predict clinical pharmacological adverse events in early stages of drug development. Toxicol Lett 2022. [DOI: 10.1016/j.toxlet.2022.07.183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
4
|
Altera A, Barone V, Kondova I, Langermans JAM, Gentile M, Pin C, Nicoletti C, Bertelli E. Light-Induced Smooth Endoplasmic Reticulum Rearrangement in a Unique Interlaced Compartmental Pattern in Macaca mulatta RPE. Invest Ophthalmol Vis Sci 2021; 62:32. [PMID: 34967853 PMCID: PMC8727310 DOI: 10.1167/iovs.62.15.32] [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] [Indexed: 11/29/2022] Open
Abstract
Purpose To investigate light-induced modifications of the smooth endoplasmic reticulum of the RPE in primates. Methods Eyes of three terminally anesthetized Rhesus monkeys were exposed to 5000 lux for 10 minutes or kept in the dark. Transmission electron microscopy and electron tomography were conducted on small fragments of retina sampled from different regions of the retina. Results RPE cells smooth endoplasmic reticulum shows a previously unknown arrangement characterized by an interlaced compartmental pattern (ICP). Electron tomograms and 3D-modelling demonstrated that the smooth endoplasmic reticulum with an ICP (ICPSER) consisted of four parallel, independent and interwoven networks of tubules arranged as interconnected coiled coils. Its architecture realized a compact labyrinthine structure of tightly packed tubules stabilized by intertubular filamentous tethers. On average, the ICPSER is present in about 14.6% of RPE cells. Although ICPSER was preferentially found in cells located in the peripheral and in the para/perifoveal retina, ICPSER cells significantly increased in number upon light exposure in the para/perifovea and in the fovea. Conclusions An ICPSER is apparently a unique feature to primate RPE. Its rapid appearance in the area centralis of the retina upon light exposure suggests a function related to the foveate structure of primate retina or to the diurnal habits of animals that may require additional protection from photo-oxidation or enhanced requests of visual pigments regeneration.
Collapse
Affiliation(s)
- Annalisa Altera
- Department of Life Sciences, University of Siena, Siena, Italy.,Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Virginia Barone
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Ivanela Kondova
- Division of Pathology and Microbiology, Animal Science Department, Biomedical Primate Research Centre, Rijswijk, the Netherlands
| | - Jan A M Langermans
- Animal Science Department, Biomedical Primate Research Centre, Rijswijk, the Netherlands.,Department Population Health Sciences, Division Animals in Science and Society, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | | | - Carmen Pin
- Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Claudio Nicoletti
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Eugenio Bertelli
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| |
Collapse
|
5
|
Pin C. Mathematical modelling combined with new in-vitro technologies to enablequantitative translation between preclinical and clinical safety. Toxicol Lett 2021. [DOI: 10.1016/s0378-4274(21)00296-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
6
|
Gill SJ, Macdonald R, Pin C, Collins R, Leonard E, Maglennon G, Pike A, Cotton P, Hawthorne G, Pugh J, Sargeant R, Sutton D, Atkinson J, Jones S, Chinery S, Anderton M. Abstract 1374: The novel PARP1-selective inhibitor AZD5305 has reduced hematological toxicity when compared to PARP1/2 inhibitors in pre-clinical models. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-1374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Current clinical poly (ADP-ribose) polymerase (PARP) inhibitors target both PARP1 and PARP2 and they all cause clinical cytopenias with varying severity. Understanding the mechanism underlying the hematological toxicity of these agents is key for the rational design of a best-in-class molecule with greater therapeutic potential, both as monotherapy and in combination with chemotherapy.
We validated the rat as a physiologically competent translational model to investigate PARP inhibitor-driven hematological toxicity. Here we demonstrate that in comparison with a representative PARP1/2 inhibitor, olaparib, the novel highly potent PARP1-selective inhibitor and trapper, AZD5305, does not cause hematological toxicity as a monotherapy in pre-clinical rat models at predicted clinically efficacious exposures. Thus, monotherapy toxicity of PARP1/2 inhibitors likely depends on PARP2 inhibition.
Next, we proceeded to investigate whether PARP1-selective inhibition would be better tolerated in chemotherapy combinations than PARP1/2 inhibition. We performed a rat in vivo study comparing daily olaparib or daily AZD5305 at matched exposures in combination with one cycle of intravenous carboplatin for 14 days. We show that olaparib and PARP1-selective AZD5305 cause comparable exacerbation of carboplatin-induced peripheral blood effects implicating PARP1 inhibition in combination-driven hematological toxicity. Importantly however, AZD5305+carboplatin showed improved hematological tolerability over olaparib+carboplatin because peripheral reticulocytes and bone marrow erythroid precursor cells recover in the presence of continuous AZD5305 but not in the presence of continuous olaparib. Importantly, this differentiation was maintained in a subsequent rat in vivo study, where daily olaparib or daily AZD5305 were combined with two three-weekly cycles of a higher dose of carboplatin to more closely mimic clinical protocol. AZD5305+carboplatin was associated with a more rapid recovery of reticulocytes, red blood cells and hemoglobin following both cycles of carboplatin. In contrast, olaparib+carboplatin was associated with a slower recovery resulting in a more sustained reduction in red cells and hemoglobin during both the first and second cycle of carboplatin.
Thus, in rodents the novel potent PARP1-selective inhibitor AZD5305 has improved hematological tolerability over dual PARP1/2 inhibitors, both as a monotherapy and in carboplatin combinations.
Citation Format: Sonja J. Gill, Ruth Macdonald, Carmen Pin, Rob Collins, Emilyanne Leonard, Gareth Maglennon, Andy Pike, Peter Cotton, Glen Hawthorne, Jordan Pugh, Rebecca Sargeant, Daniel Sutton, James Atkinson, Stewart Jones, Sarah Chinery, Mark Anderton. The novel PARP1-selective inhibitor AZD5305 has reduced hematological toxicity when compared to PARP1/2 inhibitors in pre-clinical models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1374.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Andy Pike
- AstraZeneca, Cambridge, United Kingdom
| | | | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Pin C, Collins T, Gibbs M, Kimko H. Systems Modeling to Quantify Safety Risks in Early Drug Development: Using Bifurcation Analysis and Agent-Based Modeling as Examples. AAPS J 2021; 23:77. [PMID: 34018069 PMCID: PMC8137611 DOI: 10.1208/s12248-021-00580-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 03/09/2021] [Indexed: 11/30/2022]
Abstract
Quantitative Systems Toxicology (QST) models, recapitulating pharmacokinetics and mechanism of action together with the organic response at multiple levels of biological organization, can provide predictions on the magnitude of injury and recovery dynamics to support study design and decision-making during drug development. Here, we highlight the application of QST models to predict toxicities of cancer treatments, such as cytopenia(s) and gastrointestinal adverse effects, where narrow therapeutic indexes need to be actively managed. The importance of bifurcation analysis is demonstrated in QST models of hematologic toxicity to understand how different regions of the parameter space generate different behaviors following cancer treatment, which results in asymptotically stable predictions, yet highly irregular for specific schedules, or oscillating predictions of blood cell levels. In addition, an agent-based model of the intestinal crypt was used to simulate how the spatial location of the injury within the crypt affects the villus disruption severity. We discuss the value of QST modeling approaches to support drug development and how they align with technological advances impacting trial design including patient selection, dose/regimen selection, and ultimately patient safety.
Collapse
Affiliation(s)
- Carmen Pin
- Clinical Pharmacology and Quantitative Pharmacology, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge Science Park, Milton Road, Cambridge, UK
| | - Teresa Collins
- Clinical Pharmacology and Quantitative Pharmacology, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge Science Park, Milton Road, Cambridge, UK
| | - Megan Gibbs
- Clinical Pharmacology and Quantitative Pharmacology, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Gaithersburg, Maryland, USA
| | - Holly Kimko
- Clinical Pharmacology and Quantitative Pharmacology, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Gaithersburg, Maryland, USA.
| |
Collapse
|
8
|
McCallum S, Obata Y, Fourli E, Boeing S, Peddie CJ, Xu Q, Horswell S, Kelsh RN, Collinson L, Wilkinson D, Pin C, Pachnis V, Heanue TA. Enteric glia as a source of neural progenitors in adult zebrafish. eLife 2020; 9:56086. [PMID: 32851974 PMCID: PMC7521928 DOI: 10.7554/elife.56086] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 08/26/2020] [Indexed: 12/23/2022] Open
Abstract
The presence and identity of neural progenitors in the enteric nervous system (ENS) of vertebrates is a matter of intense debate. Here, we demonstrate that the non-neuronal ENS cell compartment of teleosts shares molecular and morphological characteristics with mammalian enteric glia but cannot be identified by the expression of canonical glial markers. However, unlike their mammalian counterparts, which are generally quiescent and do not undergo neuronal differentiation during homeostasis, we show that a relatively high proportion of zebrafish enteric glia proliferate under physiological conditions giving rise to progeny that differentiate into enteric neurons. We also provide evidence that, similar to brain neural stem cells, the activation and neuronal differentiation of enteric glia are regulated by Notch signalling. Our experiments reveal remarkable similarities between enteric glia and brain neural stem cells in teleosts and open new possibilities for use of mammalian enteric glia as a potential source of neurons to restore the activity of intestinal neural circuits compromised by injury or disease.
Collapse
Affiliation(s)
- Sarah McCallum
- Development and Homeostasis of the Nervous System Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Yuuki Obata
- Development and Homeostasis of the Nervous System Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Evangelia Fourli
- Development and Homeostasis of the Nervous System Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Stefan Boeing
- Bionformatics & Biostatistics Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Christopher J Peddie
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Qiling Xu
- Neural Development Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Stuart Horswell
- Bionformatics & Biostatistics Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Robert N Kelsh
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Lucy Collinson
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - David Wilkinson
- Neural Development Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Carmen Pin
- Clinical Pharmacology and Quantitative Pharmacology, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, United Kingdom
| | - Vassilis Pachnis
- Development and Homeostasis of the Nervous System Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Tiffany A Heanue
- Development and Homeostasis of the Nervous System Laboratory, The Francis Crick Institute, London, United Kingdom
| |
Collapse
|
9
|
Fornari C, Pin C, Yates JWT, Mettetal JT, Collins TA. Importance of Stability Analysis When Using Nonlinear Semimechanistic Models to Describe Drug-Induced Hematotoxicity. CPT Pharmacometrics Syst Pharmacol 2020; 9:498-508. [PMID: 32453487 PMCID: PMC7499189 DOI: 10.1002/psp4.12514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 03/31/2020] [Indexed: 12/27/2022]
Abstract
Stability analysis, often overlooked in pharmacometrics, is essential to explore dynamical systems. The model developed by Friberg et al.1 to describe drug‐induced hematotoxicity is widely used to support decisions across drug development, and parameter values are often identified from observed blood counts. We use stability analysis to study the parametric dependence of stable and unstable solutions of several Friberg‐type models and highlight the risks associated with system instability in the context of nonlinear mixed effects modeling. We emphasize the consequences of unstable solutions on prediction performance by demonstrating nonbiological system behaviors in a real case study of drug‐induced thrombocytopenia. Ultimately, we provide simple criteria for identifying parameters associated with stable solutions of Friberg‐type models. For instance, in the original Friberg model, we find that stability depends only on the parameter that governs the feedback from peripheral cells to progenitors and provide the exact range of values that results in stable solutions.
Collapse
Affiliation(s)
- Chiara Fornari
- Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Carmen Pin
- Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - James W T Yates
- Drug Metabolism and Pharmacokinetic, Oncology R&D, AstraZeneca, Cambridge, UK
| | | | - Teresa A Collins
- Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| |
Collapse
|
10
|
Peters MF, Choy AL, Pin C, Leishman DJ, Moisan A, Ewart L, Guzzie-Peck PJ, Sura R, Keller DA, Scott CW, Kolaja KL. Developing in vitro assays to transform gastrointestinal safety assessment: potential for microphysiological systems. Lab Chip 2020; 20:1177-1190. [PMID: 32129356 DOI: 10.1039/c9lc01107b] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Drug-induced gastrointestinal toxicities (DI-GITs) are among the most common adverse events in clinical trials. High prevalence of DI-GIT has persisted among new drugs due in part to the lack of robust experimental tools to allow early detection or to guide optimization of safer molecules. Developing in vitro assays for the leading GI toxicities (nausea, vomiting, diarrhoea, constipation, and abdominal pain) will likely involve recapitulating complex physiological properties that require contributions from diverse cell/tissue types including epithelial, immune, microbiome, nerve, and muscle. While this stipulation may be beyond traditional 2D monocultures of intestinal cell lines, emerging 3D GI microtissues capture interactions between diverse cell and tissue types. These interactions give rise to microphysiologies fundamental to gut biology. For GI microtissues, organoid technology was the breakthrough that introduced intestinal stem cells with the capability of differentiating into each of the epithelial cell types and that self-organize into a multi-cellular tissue proxy with villus- and crypt-like domains. Recently, GI microtissues generated using miniaturized devices with microfluidic flow and cyclic peristaltic strain were shown to induce Caco2 cells to spontaneously differentiate into each of the principle intestinal epithelial cell types. Second generation models comprised of epithelial organoids or microtissues co-cultured with non-epithelial cell types can successfully reproduce cross-'tissue' functional interactions broadening the potential of these models to accurately study drug-induced toxicities. A new paradigm in which in vitro assays become an early part of GI safety assessment could be realized if microphysiological systems (MPS) are developed in alignment with drug-discovery needs. Herein, approaches for assessing GI toxicity of pharmaceuticals are reviewed and gaps are compared with capabilities of emerging GI microtissues (e.g., organoids, organ-on-a-chip, transwell systems) in order to provide perspective on the assay features needed for MPS models to be adopted for DI-GIT assessment.
Collapse
Affiliation(s)
- Matthew F Peters
- Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Boston, USA.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Peters MF, Landry T, Pin C, Maratea K, Dick C, Wagoner MP, Choy AL, Barthlow H, Snow D, Stevens Z, Armento A, Scott CW, Ayehunie S. Human 3D Gastrointestinal Microtissue Barrier Function As a Predictor of Drug-Induced Diarrhea. Toxicol Sci 2020; 168:3-17. [PMID: 30364994 PMCID: PMC6390652 DOI: 10.1093/toxsci/kfy268] [Citation(s) in RCA: 23] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Drug-induced gastrointestinal toxicities (GITs) rank among the most common clinical side effects. Preclinical efforts to reduce incidence are limited by inadequate predictivity of in vitro assays. Recent breakthroughs in in vitro culture methods support intestinal stem cell maintenance and continual differentiation into the epithelial cell types resident in the intestine. These diverse cells self-assemble into microtissues with in vivo-like architecture. Here, we evaluate human GI microtissues grown in transwell plates that allow apical and/or basolateral drug treatment and 96-well throughput. Evaluation of assay utility focused on predictivity for diarrhea because this adverse effect correlates with intestinal barrier dysfunction which can be measured in GI microtissues using transepithelial electrical resistance (TEER). A validation set of widely prescribed drugs was assembled and tested for effects on TEER. When the resulting TEER inhibition potencies were adjusted for clinical exposure, a threshold was identified that distinguished drugs that induced clinical diarrhea from those that lack this liability. Microtissue TEER assay predictivity was further challenged with a smaller set of drugs whose clinical development was limited by diarrhea that was unexpected based on 1-month animal studies. Microtissue TEER accurately predicted diarrhea for each of these drugs. The label-free nature of TEER enabled repeated quantitation with sufficient precision to develop a mathematical model describing the temporal dynamics of barrier damage and recovery. This human 3D GI microtissue is the first in vitro assay with validated predictivity for diarrhea-inducing drugs. It should provide a platform for lead optimization and offers potential for dose schedule exploration.
Collapse
Affiliation(s)
- Matthew F Peters
- Oncology Safety, Drug Safety and Metabolism, IMED Biotech Unit, AstraZeneca, Waltham, MA 02451
| | - Tim Landry
- MatTek Corporation, Ashland, Massachusetts 01721
| | - Carmen Pin
- Mechanistic Safety and ADME Sciences, Drug Safety and Metabolism, IMED Biotech Unit, AstraZeneca, Cambridge, CB4 0WG, UK
| | - Kim Maratea
- Oncology Safety, Drug Safety and Metabolism, IMED Biotech Unit, AstraZeneca, Waltham, MA 02451
| | - Cortni Dick
- Oncology Safety, Drug Safety and Metabolism, IMED Biotech Unit, AstraZeneca, Waltham, MA 02451
| | - Matthew P Wagoner
- Oncology Safety, Drug Safety and Metabolism, IMED Biotech Unit, AstraZeneca, Waltham, MA 02451
| | - Allison L Choy
- Science and Enabling Units IT, AstraZeneca, Waltham, MA 02451
| | - Herb Barthlow
- Oncology Safety, Drug Safety and Metabolism, IMED Biotech Unit, AstraZeneca, Waltham, MA 02451
| | - Deb Snow
- Oncology Safety, Drug Safety and Metabolism, IMED Biotech Unit, AstraZeneca, Waltham, MA 02451
| | | | - Alex Armento
- MatTek Corporation, Ashland, Massachusetts 01721
| | - Clay W Scott
- Oncology Safety, Drug Safety and Metabolism, IMED Biotech Unit, AstraZeneca, Waltham, MA 02451
| | | |
Collapse
|
12
|
Powell N, Pantazi E, Pavlidis P, Tsakmaki A, Li K, Yang F, Parker A, Pin C, Cozzetto D, Minns D, Stolarczyk E, Saveljeva S, Mohamed R, Lavender P, Afzali B, Digby-Bell J, Tjir-Li T, Kaser A, Friedman J, MacDonald TT, Bewick GA, Lord GM. Interleukin-22 orchestrates a pathological endoplasmic reticulum stress response transcriptional programme in colonic epithelial cells. Gut 2020; 69:578-590. [PMID: 31792136 PMCID: PMC7034350 DOI: 10.1136/gutjnl-2019-318483] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 10/15/2019] [Accepted: 10/31/2019] [Indexed: 12/12/2022]
Abstract
OBJECTIVE The functional role of interleukin-22 (IL22) in chronic inflammation is controversial, and mechanistic insights into how it regulates target tissue are lacking. In this study, we evaluated the functional role of IL22 in chronic colitis and probed mechanisms of IL22-mediated regulation of colonic epithelial cells. DESIGN To investigate the functional role of IL22 in chronic colitis and how it regulates colonic epithelial cells, we employed a three-dimentional mini-gut epithelial organoid system, in vivo disease models and transcriptomic datasets in human IBD. RESULTS As well as inducing transcriptional modules implicated in antimicrobial responses, IL22 also coordinated an endoplasmic reticulum (ER) stress response transcriptional programme in colonic epithelial cells. In the colon of patients with active colonic Crohn's disease (CD), there was enrichment of IL22-responsive transcriptional modules and ER stress response modules. Strikingly, in an IL22-dependent model of chronic colitis, targeting IL22 alleviated colonic epithelial ER stress and attenuated colitis. Pharmacological modulation of the ER stress response similarly impacted the severity of colitis. In patients with colonic CD, antibody blockade of IL12p40, which simultaneously blocks IL12 and IL23, the key upstream regulator of IL22 production, alleviated the colonic epithelial ER stress response. CONCLUSIONS Our data challenge perceptions of IL22 as a predominantly beneficial cytokine in IBD and provide novel insights into the molecular mechanisms of IL22-mediated pathogenicity in chronic colitis. Targeting IL22-regulated pathways and alleviating colonic epithelial ER stress may represent promising therapeutic strategies in patients with colitis. TRIAL REGISTRATION NUMBER NCT02749630.
Collapse
Affiliation(s)
- Nick Powell
- School of Immunology and Microbial Sciences, King's College London, London, UK
- National Institute for Health Research Biomedical Research Centre at Guy's and St Thomas' NHS Foundation Trust and King's College London, London, UK
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Eirini Pantazi
- School of Immunology and Microbial Sciences, King's College London, London, UK
| | | | - Anastasia Tsakmaki
- Diabetes Research Group, School of Life Course Sciences, Faculty of Life Sciences and Medicine, Kings College London, London, UK
| | - Katherine Li
- Janssen Research & Development, Spring House, Pennsylvania, USA
| | - Feifei Yang
- Janssen Research & Development, Spring House, Pennsylvania, USA
| | - Aimee Parker
- Quadram Institute Bioscience, Norwich, Norfolk, UK
| | - Carmen Pin
- Quadram Institute Bioscience, Norwich, Norfolk, UK
| | - Domenico Cozzetto
- National Institute for Health Research Biomedical Research Centre at Guy's and St Thomas' NHS Foundation Trust and King's College London, London, UK
- Department of Translational Bioinformatics, National Institute for Health Research Biomedical Research Centre at Guy's and St Thomas' NHS Foundation Trust and King's College London, London, UK
| | - Danielle Minns
- School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Emilie Stolarczyk
- School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Svetlana Saveljeva
- Division of Gastroenterology and Hepatology, Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| | - Rami Mohamed
- School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Paul Lavender
- School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Behdad Afzali
- School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Jonathan Digby-Bell
- School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Tsui Tjir-Li
- School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Arthur Kaser
- Division of Gastroenterology and Hepatology, Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| | - Joshua Friedman
- Janssen Research & Development, Spring House, Pennsylvania, USA
| | - Thomas T MacDonald
- Centre for Immunology and Infectious Disease, Bart's & the London School of Medicine and Dentistry, Blizard Institute of Cell and Molecular Science, London, UK
| | - Gavin A Bewick
- Diabetes Research Group, School of Life Course Sciences, Faculty of Life Sciences and Medicine, Kings College London, London, UK
| | - Graham M Lord
- School of Immunology and Microbial Sciences, King's College London, London, UK
- National Institute for Health Research Biomedical Research Centre at Guy's and St Thomas' NHS Foundation Trust and King's College London, London, UK
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| |
Collapse
|
13
|
Ferreira S, Fisher C, Furlong LI, Laplanche L, Park BK, Pin C, Saez-Rodriguez J, Trairatphisan P. Quantitative Systems Toxicology Modeling To Address Key Safety Questions in Drug Development: A Focus of the TransQST Consortium. Chem Res Toxicol 2020; 33:7-9. [PMID: 31909603 DOI: 10.1021/acs.chemrestox.9b00499] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Omics data have been increasingly generated with limited demonstrated value in drug safety assessment. The TransQST consortium was launched to use omics and other data in mechanistic-based quantitative systems toxicology (QST) models to evaluate their potential use in species translation.
Collapse
Affiliation(s)
- Sofia Ferreira
- Certara UK Limited , Simcyp Division, Level 2-Acero, 1 Concourse Way , Sheffield , S1 2BJ , United Kingdom
| | - Ciarán Fisher
- Certara UK Limited , Simcyp Division, Level 2-Acero, 1 Concourse Way , Sheffield , S1 2BJ , United Kingdom
| | - Laura I Furlong
- Research Programme on Biomedical Informatics (GRIB), IMIM (Hospital del Mar Medical Research Institute) , Pompeu Fabra University (UPF) , Dr. Aiguader 88 , 08003 Barcelona , Spain
| | - Loic Laplanche
- Drug Metabolism Pharmacokinetics and Bioanalysis , AbbVie Deutschland GmbH & Co. KG , D-67008 Ludwigshafen , Germany
| | - Brian Kevin Park
- MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine , University of Liverpool , Liverpool L69 3GE , United Kingdom
| | - Carmen Pin
- Clinical Pharmacology, ADME, and AI, Clinical Pharmacology and Safety Sciences, Biopharmaceuticals R&D , AstraZeneca , Cambridge CB2 0SL , United Kingdom
| | - Julio Saez-Rodriguez
- Faculty of Medicine, Institute of Computational Biomedicine , Heidelberg University , 69120 Heidelberg , Germany
| | - Panuwat Trairatphisan
- Drug Metabolism Pharmacokinetics and Bioanalysis , AbbVie Deutschland GmbH & Co. KG , D-67008 Ludwigshafen , Germany.,Faculty of Medicine, Institute of Computational Biomedicine , Heidelberg University , 69120 Heidelberg , Germany
| |
Collapse
|
14
|
Fornari C, Oplustil O'Connor L, Pin C, Smith A, Yates JW, Cheung SA, Jodrell DI, Mettetal JT, Collins TA. Quantifying Drug-Induced Bone Marrow Toxicity Using a Novel Haematopoiesis Systems Pharmacology Model. CPT Pharmacometrics Syst Pharmacol 2019; 8:858-868. [PMID: 31508894 PMCID: PMC6875710 DOI: 10.1002/psp4.12459] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 07/08/2019] [Accepted: 07/22/2019] [Indexed: 12/19/2022] Open
Abstract
Haematological toxicity associated with cancer therapeutics is monitored by changes in blood cell count, and their primary effect is on proliferative progenitors in the bone marrow. Using observations in rat bone marrow and blood, we characterize a mathematical model that comprises cell proliferation and differentiation of the full haematopoietic phylogeny, with interacting feedback loops between lineages in homeostasis as well as following carboplatin exposure. We accurately predicted the temporal dynamics of several mature cell types related to carboplatin-induced bone marrow toxicity and identified novel insights into haematopoiesis. Our model confirms a significant degree of plasticity within bone marrow cells, with the number and type of both early progenitors and circulating cells affecting cell balance, via feedback mechanisms, through fate decisions of the multipotent progenitors. We also demonstrated cross-species translation of our predictions to patients, applying the same core model structure and considering differences in drug-dependent and physiology-dependent parameters.
Collapse
Affiliation(s)
- Chiara Fornari
- Clinical Pharmacology and Safety SciencesBioPharmaceuticals R&D, AstraZenecaCambridgeUSA
| | | | - Carmen Pin
- Clinical Pharmacology and Safety SciencesBioPharmaceuticals R&D, AstraZenecaCambridgeUSA
| | - Aaron Smith
- Drug Metabolism and PharmacokineticOncology R&D, AstraZenecaCambridgeUK
| | - James W.T. Yates
- Drug Metabolism and PharmacokineticOncology R&D, AstraZenecaCambridgeUK
| | - S.Y. Amy Cheung
- Clinical Pharmacology and Safety SciencesBioPharmaceuticals R&D, AstraZenecaCambridgeUSA
- CertaraPrincetonNew JerseyUSA
| | - Duncan I. Jodrell
- Cancer Research UK Cambridge InstituteLi Ka Shing CentreUniversity of CambridgeCambridgeUK
| | | | - Teresa A. Collins
- Clinical Pharmacology and Safety SciencesBioPharmaceuticals R&D, AstraZenecaCambridgeUSA
| |
Collapse
|
15
|
Muraro D, Parker A, Vaux L, Filippi S, Almet AA, Fletcher AG, Watson AJM, Pin C, Maini PK, Byrne HM. Chronic TNFα-driven injury delays cell migration to villi in the intestinal epithelium. J R Soc Interface 2019; 15:rsif.2018.0037. [PMID: 30068555 DOI: 10.1098/rsif.2018.0037] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 01/15/2018] [Accepted: 07/03/2018] [Indexed: 12/19/2022] Open
Abstract
The intestinal epithelium is a single layer of cells which provides the first line of defence of the intestinal mucosa to bacterial infection. Cohesion of this physical barrier is supported by renewal of epithelial stem cells, residing in invaginations called crypts, and by crypt cell migration onto protrusions called villi; dysregulation of such mechanisms may render the gut susceptible to chronic inflammation. The impact that excessive or misplaced epithelial cell death may have on villus cell migration is currently unknown. We integrated cell-tracking methods with computational models to determine how epithelial homeostasis is affected by acute and chronic TNFα-driven epithelial cell death. Parameter inference reveals that acute inflammatory cell death has a transient effect on epithelial cell dynamics, whereas cell death caused by chronic elevated TNFα causes a delay in the accumulation of labelled cells onto the villus compared to the control. Such a delay may be reproduced by using a cell-based model to simulate the dynamics of each cell in a crypt-villus geometry, showing that a prolonged increase in cell death slows the migration of cells from the crypt to the villus. This investigation highlights which injuries (acute or chronic) may be regenerated and which cause disruption of healthy epithelial homeostasis.
Collapse
Affiliation(s)
- Daniele Muraro
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, UK .,Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - Aimee Parker
- Gut Health and Food Safety Research Programme, Institute of Food Research, Norwich, UK
| | - Laura Vaux
- Gut Health and Food Safety Research Programme, Institute of Food Research, Norwich, UK
| | - Sarah Filippi
- Department of Mathematics, Imperial College London, London, UK.,Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - Axel A Almet
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, UK
| | - Alexander G Fletcher
- School of Mathematics and Statistics and Bateson Centre, University of Sheffield, Sheffield, UK
| | | | - Carmen Pin
- Gut Health and Food Safety Research Programme, Institute of Food Research, Norwich, UK
| | - Philip K Maini
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, UK
| | - Helen M Byrne
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, UK
| |
Collapse
|
16
|
Parker A, Vaux L, Patterson AM, Modasia A, Muraro D, Fletcher AG, Byrne HM, Maini PK, Watson AJM, Pin C. Elevated apoptosis impairs epithelial cell turnover and shortens villi in TNF-driven intestinal inflammation. Cell Death Dis 2019; 10:108. [PMID: 30728350 PMCID: PMC6365534 DOI: 10.1038/s41419-018-1275-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [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: 07/17/2018] [Revised: 11/05/2018] [Accepted: 12/03/2018] [Indexed: 12/27/2022]
Abstract
The intestinal epithelial monolayer, at the boundary between microbes and the host immune system, plays an important role in the development of inflammatory bowel disease (IBD), particularly as a target and producer of pro-inflammatory TNF. Chronic overexpression of TNF leads to IBD-like pathology over time, but the mechanisms driving early pathogenesis events are not clear. We studied the epithelial response to inflammation by combining mathematical models with in vivo experimental models resembling acute and chronic TNF-mediated injury. We found significant villus atrophy with increased epithelial cell death along the crypt-villus axis, most dramatically at the villus tips, in both acute and chronic inflammation. In the acute model, we observed overexpression of TNF receptor I in the villus tip rapidly after TNF injection and concurrent with elevated levels of intracellular TNF and rapid shedding at the tip. In the chronic model, sustained villus atrophy was accompanied by a reduction in absolute epithelial cell turnover. Mathematical modelling demonstrated that increased cell apoptosis on the villus body explains the reduction in epithelial cell turnover along the crypt-villus axis observed in chronic inflammation. Cell destruction in the villus was not accompanied by changes in proliferative cell number or division rate within the crypt. Epithelial morphology and immunological changes in the chronic setting suggest a repair response to cell damage although the villus length is not recovered. A better understanding of how this state is further destabilised and results in clinical pathology resembling IBD will help identify suitable pathways for therapeutic intervention.
Collapse
Affiliation(s)
- Aimée Parker
- Gut Health and Food Safety Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Laura Vaux
- Gut Health and Food Safety Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Angela M Patterson
- Gut Health and Food Safety Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Amisha Modasia
- Gut Health and Food Safety Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | | | - Alexander G Fletcher
- School of Mathematics and Statistics, University of Sheffield, Sheffield, United Kingdom.,Bateson Centre, University of Sheffield, Sheffield, United Kingdom
| | - Helen M Byrne
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, United Kingdom
| | - Philip K Maini
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, United Kingdom
| | | | - Carmen Pin
- Gut Health and Food Safety Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom. .,Drug Safety and Metabolism, IMED Biotech Unit, AstraZeneca, Cambridge, United Kingdom.
| |
Collapse
|
17
|
Parker A, Lawson MAE, Vaux L, Pin C. Host-microbe interaction in the gastrointestinal tract. Environ Microbiol 2018; 20:2337-2353. [PMID: 28892253 PMCID: PMC6175405 DOI: 10.1111/1462-2920.13926] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 08/25/2017] [Accepted: 08/31/2017] [Indexed: 12/13/2022]
Abstract
The gastrointestinal tract is a highly complex organ in which multiple dynamic physiological processes are tightly coordinated while interacting with a dense and extremely diverse microbial population. From establishment in early life, through to host-microbe symbiosis in adulthood, the gut microbiota plays a vital role in our development and health. The effect of the microbiota on gut development and physiology is highlighted by anatomical and functional changes in germ-free mice, affecting the gut epithelium, immune system and enteric nervous system. Microbial colonisation promotes competent innate and acquired mucosal immune systems, epithelial renewal, barrier integrity, and mucosal vascularisation and innervation. Interacting or shared signalling pathways across different physiological systems of the gut could explain how all these changes are coordinated during postnatal colonisation, or after the introduction of microbiota into germ-free models. The application of cell-based in-vitro experimental systems and mathematical modelling can shed light on the molecular and signalling pathways which regulate the development and maintenance of homeostasis in the gut and beyond.
Collapse
Affiliation(s)
- Aimée Parker
- Quadram Institute BioscienceNorwich Research ParkNR4 7UAUK
| | | | - Laura Vaux
- Quadram Institute BioscienceNorwich Research ParkNR4 7UAUK
| | - Carmen Pin
- Quadram Institute BioscienceNorwich Research ParkNR4 7UAUK
| |
Collapse
|
18
|
Pin C, Jager JB, Tardif M, Picard E, Hadji E, de Fornel F, Cluzel B. Optical tweezing using tunable optical lattices along a few-mode silicon waveguide. Lab Chip 2018; 18:1750-1757. [PMID: 29774333 DOI: 10.1039/c8lc00298c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Fourteen years ago, optical lattices and holographic tweezers were considered as a revolution, allowing for trapping and manipulating multiple particles at the same time using laser light. Since then, near-field optical forces have aroused tremendous interest as they enable efficient trapping of a wide range of objects, from living cells to atoms, in integrated devices. Yet, handling at will multiple objects using a guided light beam remains a challenging task for current on-chip optical trapping techniques. We demonstrate here on-chip optical trapping of dielectric microbeads and bacteria using one-dimensional optical lattices created by near-field mode beating along a few-mode silicon nanophotonic waveguide. This approach allows not only for trapping large numbers of particles in periodic trap arrays with various geometries, but also for manipulating them via diverse transport and repositioning techniques. Near-field mode-beating optical lattices may be readily implemented in lab-on-a-chip devices, addressing numerous scientific fields ranging from bio-analysis to nanoparticle processing.
Collapse
Affiliation(s)
- C Pin
- Groupe Optique de Champ Proche, Laboratoire Interdisciplinaire Carnot de Bourgogne UMR CNRS 6303, Université de Bourgogne Franche-Comté, 21078 Dijon, France.
| | | | | | | | | | | | | |
Collapse
|
19
|
Lasrado R, Boesmans W, Kleinjung J, Pin C, Bell D, Bhaw L, McCallum S, Zong H, Luo L, Clevers H, Vanden Berghe P, Pachnis V. Lineage-dependent spatial and functional organization of the mammalian enteric nervous system. Science 2018; 356:722-726. [PMID: 28522527 DOI: 10.1126/science.aam7511] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 04/10/2017] [Indexed: 12/11/2022]
Abstract
The enteric nervous system (ENS) is essential for digestive function and gut homeostasis. Here we show that the amorphous neuroglia networks of the mouse ENS are composed of overlapping clonal units founded by postmigratory neural crest-derived progenitors. The spatial configuration of ENS clones depends on proliferation-driven local interactions of ENS progenitors with lineally unrelated neuroectodermal cells, the ordered colonization of the serosa-mucosa axis by clonal descendants, and gut expansion. Single-cell transcriptomics and mutagenesis analysis delineated dynamic molecular states of ENS progenitors and identified RET as a regulator of neurogenic commitment. Clonally related enteric neurons exhibit synchronous activity in response to network stimulation. Thus, lineage relationships underpin the organization of the peripheral nervous system.
Collapse
Affiliation(s)
- Reena Lasrado
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Werend Boesmans
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.,Laboratory for Enteric Neuroscience (LENS), Translational Research in GastroIntestinal Disorders (TARGID), Department of Clinical and Experimental Medicine, University of Leuven, Leuven, Belgium
| | - Jens Kleinjung
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Carmen Pin
- Institute of Food Research, Norwich NR4 7UA, UK
| | - Donald Bell
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Leena Bhaw
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Sarah McCallum
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Hui Zong
- Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Liqun Luo
- Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Hans Clevers
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Centre Utrecht, 3584 CT Utrecht, Netherlands
| | - Pieter Vanden Berghe
- Laboratory for Enteric Neuroscience (LENS), Translational Research in GastroIntestinal Disorders (TARGID), Department of Clinical and Experimental Medicine, University of Leuven, Leuven, Belgium
| | - Vassilis Pachnis
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
| |
Collapse
|
20
|
Maclaren OJ, Parker A, Pin C, Carding SR, Watson AJM, Fletcher AG, Byrne HM, Maini PK. A hierarchical Bayesian model for understanding the spatiotemporal dynamics of the intestinal epithelium. PLoS Comput Biol 2017; 13:e1005688. [PMID: 28753601 PMCID: PMC5550005 DOI: 10.1371/journal.pcbi.1005688] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [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: 10/29/2016] [Revised: 08/09/2017] [Accepted: 07/18/2017] [Indexed: 01/13/2023] Open
Abstract
Our work addresses two key challenges, one biological and one methodological. First, we aim to understand how proliferation and cell migration rates in the intestinal epithelium are related under healthy, damaged (Ara-C treated) and recovering conditions, and how these relations can be used to identify mechanisms of repair and regeneration. We analyse new data, presented in more detail in a companion paper, in which BrdU/IdU cell-labelling experiments were performed under these respective conditions. Second, in considering how to more rigorously process these data and interpret them using mathematical models, we use a probabilistic, hierarchical approach. This provides a best-practice approach for systematically modelling and understanding the uncertainties that can otherwise undermine the generation of reliable conclusions-uncertainties in experimental measurement and treatment, difficult-to-compare mathematical models of underlying mechanisms, and unknown or unobserved parameters. Both spatially discrete and continuous mechanistic models are considered and related via hierarchical conditional probability assumptions. We perform model checks on both in-sample and out-of-sample datasets and use them to show how to test possible model improvements and assess the robustness of our conclusions. We conclude, for the present set of experiments, that a primarily proliferation-driven model suffices to predict labelled cell dynamics over most time-scales.
Collapse
Affiliation(s)
- Oliver J. Maclaren
- Department of Engineering Science, University of Auckland, Auckland, New Zealand
| | - Aimée Parker
- Gut Health and Food Safety Research Programme, Institute of Food Research, Norwich, United Kingdom
| | - Carmen Pin
- Gut Health and Food Safety Research Programme, Institute of Food Research, Norwich, United Kingdom
| | - Simon R. Carding
- Gut Health and Food Safety Research Programme, Institute of Food Research, Norwich, United Kingdom
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
| | - Alastair J. M. Watson
- Gut Health and Food Safety Research Programme, Institute of Food Research, Norwich, United Kingdom
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
| | - Alexander G. Fletcher
- School of Mathematics and Statistics, University of Sheffield, Sheffield, United Kingdom
- Bateson Centre, University of Sheffield, Sheffield, United Kingdom
| | - Helen M. Byrne
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, United Kingdom
| | - Philip K. Maini
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
21
|
Mañes-Lázaro R, Van Diemen PM, Pin C, Mayer MJ, Stevens MP, Narbad A. Administration of Lactobacillus johnsonii FI9785 to chickens affects colonisation by Campylobacter jejuni and the intestinal microbiota. Br Poult Sci 2017; 58:373-381. [PMID: 28318296 DOI: 10.1080/00071668.2017.1307322] [Citation(s) in RCA: 28] [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] [Indexed: 12/15/2022]
Abstract
1. Campylobacter jejuni is the most common bacterial cause of human food-borne gastroenteritis in the world. A major source of human infection is the consumption of contaminated meat, particularly poultry. New control measures to reduce or eliminate this pathogen from the animal gastrointestinal tract are urgently required, and the use of probiotics as competitive exclusion agents is a promising biocontrol measure to reduce C. jejuni in the food chain. 2. In this study, we assessed the potential of Lactobacillus johnsonii FI9785, which has shown efficacy against Clostridium perfringens, to combat C. jejuni. The effect of prophylactic administration of L. johnsonii on the ability of C. jejuni to colonise chickens was determined. 3. Two doses of L. johnsonii given a week apart led to a reduction in C. jejuni colonisation in the caecal contents, but this biocontrol seemed reliant upon a high level of initial colonisation by the probiotic. 4. The microbial composition in the chicken gut was significantly altered by the probiotic treatment, as shown by denaturing gradient gel electrophoresis of 16S rRNA gene amplicons. 5. Together these results demonstrate the potential of this probiotic strain to be tested further as a competitive exclusion agent in poultry against C. jejuni.
Collapse
Affiliation(s)
- R Mañes-Lázaro
- a Gut Health and Food Safety Institute Strategic Programme , Institute of Food Research , Norwich , UK
| | - P M Van Diemen
- b Enteric Bacterial Pathogens Laboratory , Institute for Animal Health , Compton , Berkshire , UK
| | - C Pin
- a Gut Health and Food Safety Institute Strategic Programme , Institute of Food Research , Norwich , UK
| | - M J Mayer
- a Gut Health and Food Safety Institute Strategic Programme , Institute of Food Research , Norwich , UK
| | - M P Stevens
- b Enteric Bacterial Pathogens Laboratory , Institute for Animal Health , Compton , Berkshire , UK
| | - A Narbad
- a Gut Health and Food Safety Institute Strategic Programme , Institute of Food Research , Norwich , UK
| |
Collapse
|
22
|
Parker A, Maclaren OJ, Fletcher AG, Muraro D, Kreuzaler PA, Byrne HM, Maini PK, Watson AJM, Pin C. Cell proliferation within small intestinal crypts is the principal driving force for cell migration on villi. FASEB J 2016; 31:636-649. [PMID: 27811059 PMCID: PMC5241155 DOI: 10.1096/fj.201601002] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 10/11/2016] [Indexed: 12/05/2022]
Abstract
The functional integrity of the intestinal epithelial barrier relies on tight coordination of cell proliferation and migration, with failure to regulate these processes resulting in disease. It is not known whether cell proliferation is sufficient to drive epithelial cell migration during homoeostatic turnover of the epithelium. Nor is it known precisely how villus cell migration is affected when proliferation is perturbed. Some reports suggest that proliferation and migration may not be related while other studies support a direct relationship. We used established cell-tracking methods based on thymine analog cell labeling and developed tailored mathematical models to quantify cell proliferation and migration under normal conditions and when proliferation is reduced and when it is temporarily halted. We found that epithelial cell migration velocities along the villi are coupled to cell proliferation rates within the crypts in all conditions. Furthermore, halting and resuming proliferation results in the synchronized response of cell migration on the villi. We conclude that cell proliferation within the crypt is the primary force that drives cell migration along the villus. This methodology can be applied to interrogate intestinal epithelial dynamics and characterize situations in which processes involved in cell turnover become uncoupled, including pharmacological treatments and disease models.—Parker, A., Maclaren, O. J., Fletcher, A. G., Muraro, D., Kreuzaler, P. A., Byrne, H. M., Maini, P. K., Watson, A. J. M., Pin, C. Cell proliferation within small intestinal crypts is the principal driving force for cell migration on villi.
Collapse
Affiliation(s)
- Aimee Parker
- Gut Health and Food Safety Research Programme, Institute of Food Research, Norwich, United Kingdom
| | - Oliver J Maclaren
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, United Kingdom
| | - Alexander G Fletcher
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, United Kingdom.,School of Mathematics and Statistics, University of Sheffield, Sheffield, United Kingdom.,Bateson Centre, University of Sheffield, Sheffield, United Kingdom
| | - Daniele Muraro
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, United Kingdom
| | - Peter A Kreuzaler
- Department of Biochemistry, University of Cambridge, United Kingdom; and
| | - Helen M Byrne
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, United Kingdom
| | - Philip K Maini
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, United Kingdom
| | | | - Carmen Pin
- Gut Health and Food Safety Research Programme, Institute of Food Research, Norwich, United Kingdom;
| |
Collapse
|
23
|
Gurresch A, Gerner W, Pin C, Wagner M, Hein I. Evidence of metabolically active but non-culturable Listeria monocytogenes in long-term growth at 10 °C. Res Microbiol 2016; 167:334-343. [DOI: 10.1016/j.resmic.2016.01.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Revised: 11/16/2015] [Accepted: 01/11/2016] [Indexed: 10/22/2022]
|
24
|
Leushacke M, Barker N, Pin C. Quantifying Lgr5-positive stem cell behaviour in the pyloric epithelium. Sci Rep 2016; 6:21923. [PMID: 26916214 PMCID: PMC4768140 DOI: 10.1038/srep21923] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [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: 11/13/2015] [Accepted: 02/02/2016] [Indexed: 02/06/2023] Open
Abstract
Using in-vivo lineage tracing data we quantified clonal expansion as well as proliferation and differentiation of the Lgr5-positive stem cell population in pyloric gastric glands. Fitting clone expansion models, we estimated that there are five effective Lgr5-positive cells able to give rise to monoclonal glands by replacing each other following a pattern of neutral drift dynamics. This analysis is instrumental to assess stem cell performance; however, stem cell proliferation is not quantified by clone expansion analysis. We identified a suitable mathematical model to quantify proliferation and differentiation of the Lgr5-positive population. As expected for populations in steady-state, the proliferation rate of the Lgr5-positive population was equal to its rate of differentiation. This rate was significantly faster than the rate at which effective cells are replaced, estimated by modelling clone expansion/contraction. This suggests that the majority of Lgr5-positive cell divisions serve to renew epithelial cells and only few result in the effective replacement of a neighbour to effect expansion to the entire gland. The application of the model under altered situations with uncoupled differentiation and proliferation was demonstrated. This methodology represents a valuable tool for quantifying stem cell performance in homeostasis and importantly for deciphering altered stem cell behaviour in disease.
Collapse
Affiliation(s)
| | - Nick Barker
- A*STAR Institute of Medical Biology, Singapore.,Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Carmen Pin
- Gut Health and Food Safety Programme. Institute of Food Research, Norwich, UK
| |
Collapse
|
25
|
Pin C, Parker A, Gunning AP, Ohta Y, Johnson IT, Carding SR, Sato T. An individual based computational model of intestinal crypt fission and its application to predicting unrestrictive growth of the intestinal epithelium. Integr Biol (Camb) 2015; 7:213-28. [PMID: 25537618 DOI: 10.1039/c4ib00236a] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Intestinal crypt fission is a homeostatic phenomenon, observable in healthy adult mucosa, but which also plays a pathological role as the main mode of growth of some intestinal polyps. Building on our previous individual based model for the small intestinal crypt and on in vitro cultured intestinal organoids, we here model crypt fission as a budding process based on fluid mechanics at the individual cell level and extrapolated predictions for growth of the intestinal epithelium. Budding was always observed in regions of organoids with abundant Paneth cells. Our data support a model in which buds are biomechanically initiated by single stem cells surrounded by Paneth cells which exhibit greater resistance to viscoelastic deformation, a hypothesis supported by atomic force measurements of single cells. Time intervals between consecutive budding events, as simulated by the model and observed in vitro, were 2.84 and 2.62 days, respectively. Predicted cell dynamics was unaffected within the original crypt which retained its full capability of providing cells to the epithelium throughout fission. Mitotic pressure in simulated primary crypts forced upward migration of buds, which simultaneously grew into new protruding crypts at a rate equal to 1.03 days(-1) in simulations and 0.99 days(-1) in cultured organoids. Simulated crypts reached their final size in 4.6 days, and required 6.2 days to migrate to the top of the primary crypt. The growth of the secondary crypt is independent of its migration along the original crypt. Assuming unrestricted crypt fission and multiple budding events, a maximal growth rate of the intestinal epithelium of 0.10 days(-1) is predicted and thus approximately 22 days are required for a 10-fold increase of polyp size. These predictions are in agreement with the time reported to develop macroscopic adenomas in mice after loss of Apc in intestinal stem cells.
Collapse
Affiliation(s)
- Carmen Pin
- Gut Health and Food Safety Research Programme, Institute of Food Research, Norwich, NR4 7UA, UK.
| | | | | | | | | | | | | |
Collapse
|
26
|
Kober OI, Ahl D, Pin C, Holm L, Carding SR, Juge N. γδ T-cell-deficient mice show alterations in mucin expression, glycosylation, and goblet cells but maintain an intact mucus layer. Am J Physiol Gastrointest Liver Physiol 2014; 306:G582-93. [PMID: 24503767 PMCID: PMC3962592 DOI: 10.1152/ajpgi.00218.2013] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [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] [Indexed: 01/31/2023]
Abstract
Intestinal homeostasis is maintained by a hierarchy of immune defenses acting in concert to minimize contact between luminal microorganisms and the intestinal epithelial cell surface. The intestinal mucus layer, covering the gastrointestinal tract epithelial cells, contributes to mucosal homeostasis by limiting bacterial invasion. In this study, we used γδ T-cell-deficient (TCRδ(-/-)) mice to examine whether and how γδ T-cells modulate the properties of the intestinal mucus layer. Increased susceptibility of TCRδ(-/-) mice to dextran sodium sulfate (DSS)-induced colitis is associated with a reduced number of goblet cells. Alterations in the number of goblet cells and crypt lengths were observed in the small intestine and colon of TCRδ(-/-) mice compared with C57BL/6 wild-type (WT) mice. Addition of keratinocyte growth factor to small intestinal organoid cultures from TCRδ(-/-) mice showed a marked increase in crypt growth and in both goblet cell number and redistribution along the crypts. There was no apparent difference in the thickness or organization of the mucus layer between TCRδ(-/-) and WT mice, as measured in vivo. However, γδ T-cell deficiency led to reduced sialylated mucins in association with increased gene expression of gel-secreting Muc2 and membrane-bound mucins, including Muc13 and Muc17. Collectively, these data provide evidence that γδ T cells play an important role in the maintenance of mucosal homeostasis by regulating mucin expression and promoting goblet cell function in the small intestine.
Collapse
Affiliation(s)
- Olivia I. Kober
- 1Gut Health and Food Safety Institute Strategic Programme, Institute of Food Research, Norwich, United Kingdom;
| | - David Ahl
- 2Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden; and
| | - Carmen Pin
- 1Gut Health and Food Safety Institute Strategic Programme, Institute of Food Research, Norwich, United Kingdom;
| | - Lena Holm
- 2Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden; and
| | - Simon R. Carding
- 1Gut Health and Food Safety Institute Strategic Programme, Institute of Food Research, Norwich, United Kingdom; ,3Faculty of Medical and Health Sciences, Norwich Medical School, University of East Anglia, Norwich, United Kingdom
| | - Nathalie Juge
- 1Gut Health and Food Safety Institute Strategic Programme, Institute of Food Research, Norwich, United Kingdom;
| |
Collapse
|
27
|
Rosenkrantz JT, Aarts H, Abee T, Rolfe MD, Knudsen GM, Nielsen MB, Thomsen LE, Zwietering MH, Olsen JE, Pin C. Non-essential genes form the hubs of genome scale protein function and environmental gene expression networks in Salmonella enterica serovar Typhimurium. BMC Microbiol 2013; 13:294. [PMID: 24345035 PMCID: PMC3878590 DOI: 10.1186/1471-2180-13-294] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 12/10/2013] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Salmonella Typhimurium is an important pathogen of human and animals. It shows a broad growth range and survives in harsh conditions. The aim of this study was to analyze transcriptional responses to a number of growth and stress conditions as well as the relationship of metabolic pathways and/or cell functions at the genome-scale-level by network analysis, and further to explore whether highly connected genes (hubs) in these networks were essential for growth, stress adaptation and virulence. RESULTS De novo generated as well as published transcriptional data for 425 selected genes under a number of growth and stress conditions were used to construct a bipartite network connecting culture conditions and significantly regulated genes (transcriptional network). Also, a genome scale network was constructed for strain LT2. The latter connected genes with metabolic pathways and cellular functions. Both networks were shown to belong to the family of scale-free networks characterized by the presence of highly connected nodes or hubs which are genes whose transcription is regulated when responding to many of the assayed culture conditions or genes encoding products involved in a high number of metabolic pathways and cell functions.The five genes with most connections in the transcriptional network (wraB, ygaU, uspA, cbpA and osmC) and in the genome scale network (ychN, siiF (STM4262), yajD, ybeB and dcoC) were selected for mutations, however mutagenesis of ygaU and ybeB proved unsuccessful. No difference between mutants and the wild type strain was observed during growth at unfavorable temperatures, pH values, NaCl concentrations and in the presence of H2O2. Eight mutants were evaluated for virulence in C57/BL6 mice and none differed from the wild type strain. Notably, however, deviations of phenotypes with respect to the wild type were observed when combinations of these genes were deleted. CONCLUSION Network analysis revealed the presence of hubs in both transcriptional and functional networks of S. Typhimurium. Hubs theoretically confer higher resistance to random mutation but a greater susceptibility to directed attacks, however, we found that genes that formed hubs were dispensable for growth, stress adaptation and virulence, suggesting that evolution favors non-essential genes as main connectors in cellular networks.
Collapse
Affiliation(s)
- Jesper T Rosenkrantz
- Department of Veterinary Disease Biology, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg, C, Denmark
| | - Henk Aarts
- Centre for Infectious disease control, National Institute for Public Health, PO box 1, 3720 BA Bilthoven, The Netherlands
| | - Tjakko Abee
- Wageningen University and Research Centre, Laboratory of Food Microbiology, P.O. Box 17, 6700 AA Wageningen, Netherlands
| | - Matthew D Rolfe
- Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK
| | - Gitte M Knudsen
- Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK
- National Food Institute, Danish Technical University, Soelvtofts Plads, 2800 Kgs. Lyngby, Denmark
| | - Maj-Britt Nielsen
- Department of Veterinary Disease Biology, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg, C, Denmark
- Present address: DANSTEM Laboratory, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, N, Denmark
| | - Line E Thomsen
- Department of Veterinary Disease Biology, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg, C, Denmark
| | - Marcel H Zwietering
- Wageningen University and Research Centre, Laboratory of Food Microbiology, P.O. Box 17, 6700 AA Wageningen, Netherlands
| | - John E Olsen
- Department of Veterinary Disease Biology, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg, C, Denmark
| | - Carmen Pin
- Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK
| |
Collapse
|
28
|
Doxa A, Besnard A, Bechet A, Pin C, Lebreton JD, Sadoul N. Inferring dispersal dynamics from local population demographic modelling: the case of the slender-billed gull in France. Anim Conserv 2013. [DOI: 10.1111/acv.12048] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [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)
- A. Doxa
- Centre d'Ecologie Fonctionnelle et Evolutive (UMR 5175), Ecole Pratique des Hautes Etudes, Biogéographie et Ecologie des Vertébrés, campus CNRS; Montpellier Cedex 5 France
| | - A. Besnard
- Centre d'Ecologie Fonctionnelle et Evolutive (UMR 5175), Ecole Pratique des Hautes Etudes, Biogéographie et Ecologie des Vertébrés, campus CNRS; Montpellier Cedex 5 France
| | - A. Bechet
- Centre de Recherche de la Tour du Valat; Arles France
| | - C. Pin
- Les Amis des Marais du Vigueirat; Arles France
| | - J.-D. Lebreton
- Centre d'Ecologie Fonctionnelle et Evolutive (UMR 5175), campus CNRS; Montpellier Cedex 5 France
| | - N. Sadoul
- Les Amis des Marais du Vigueirat; Arles France
| |
Collapse
|
29
|
Gunning AP, Kirby AR, Fuell C, Pin C, Tailford LE, Juge N. Mining the "glycocode"--exploring the spatial distribution of glycans in gastrointestinal mucin using force spectroscopy. FASEB J 2013; 27:2342-54. [PMID: 23493619 PMCID: PMC3659345 DOI: 10.1096/fj.12-221416] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Mucins are the main components of the gastrointestinal mucus layer. Mucin glycosylation is critical to most intermolecular and intercellular interactions. However, due to the highly complex and heterogeneous mucin glycan structures, the encoded biological information remains largely encrypted. Here we have developed a methodology based on force spectroscopy to identify biologically accessible glycoepitopes in purified porcine gastric mucin (pPGM) and purified porcine jejunal mucin (pPJM). The binding specificity of lectins Ricinus communis agglutinin I (RCA), peanut (Arachis hypogaea) agglutinin (PNA), Maackia amurensis lectin II (MALII), and Ulex europaeus agglutinin I (UEA) was utilized in force spectroscopy measurements to quantify the affinity and spatial distribution of their cognate sugars at the molecular scale. Binding energy of 4, 1.6, and 26 aJ was determined on pPGM for RCA, PNA, and UEA. Binding was abolished by competition with free ligands, demonstrating the validity of the affinity data. The distributions of the nearest binding site separations estimated the number of binding sites in a 200-nm mucin segment to be 4 for RCA, PNA, and UEA, and 1.8 for MALII. Binding site separations were affected by partial defucosylation of pPGM. Furthermore, we showed that this new approach can resolve differences between gastric and jejunum mucins.
Collapse
|
30
|
Pin C, Hansen T, Muñoz-Cuevas M, de Jonge R, Rosenkrantz JT, Löfström C, Aarts H, Olsen JE. The transcriptional heat shock response of Salmonella typhimurium shows hysteresis and heated cells show increased resistance to heat and acid stress. PLoS One 2012; 7:e51196. [PMID: 23236453 PMCID: PMC3517412 DOI: 10.1371/journal.pone.0051196] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Accepted: 10/30/2012] [Indexed: 11/18/2022] Open
Abstract
We investigated if the transcriptional response of Salmonella Typhimurium to temperature and acid variations was hysteretic, i.e. whether the transcriptional regulation caused by environmental stimuli showed memory and remained after the stimuli ceased. The transcriptional activity of non-replicating stationary phase cells of S. Typhimurium caused by the exposure to 45 °C and to pH 5 for 30 min was monitored by microarray hybridizations at the end of the treatment period as well as immediately and 30 minutes after conditions were set back to their initial values, 25 °C and pH 7. One hundred and two out of 120 up-regulated genes during the heat shock remained up-regulated 30 minutes after the temperature was set back to 25 °C, while only 86 out of 293 down regulated genes remained down regulated 30 minutes after the heat shock ceased. Thus, the majority of the induced genes exhibited hysteresis, i.e., they remained up-regulated after the environmental stress ceased. At 25 °C the transcriptional regulation of genes encoding for heat shock proteins was determined by the previous environment. Gene networks constructed with up-regulated genes were significantly more modular than those of down-regulated genes, implying that down-regulation was significantly less synchronized than up-regulation. The hysteretic transcriptional response to heat shock was accompanied by higher resistance to inactivation at 50 °C as well as cross-resistance to inactivation at pH 3; however, growth rates and lag times at 43 °C and at pH 4.5 were not affected. The exposure to pH 5 only caused up-regulation of 12 genes and this response was neither hysteretic nor accompanied of increased resistance to inactivation conditions. Cellular memory at the transcriptional level may represent a mechanism of adaptation to the environment and a deterministic source of variability in gene regulation.
Collapse
Affiliation(s)
- Carmen Pin
- Institute of Food Research, Norwich, United Kingdom.
| | | | | | | | | | | | | | | |
Collapse
|
31
|
Pin C, Watson AJM, Carding SR. Modelling the spatio-temporal cell dynamics reveals novel insights on cell differentiation and proliferation in the small intestinal crypt. PLoS One 2012; 7:e37115. [PMID: 22623982 PMCID: PMC3356410 DOI: 10.1371/journal.pone.0037115] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [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: 12/16/2011] [Accepted: 04/13/2012] [Indexed: 12/25/2022] Open
Abstract
We developed a slow structural relaxation model to describe cellular dynamics in the crypt of the mouse small intestine. Cells are arranged in a three dimensional spiral the size of which dynamically changes according to cell production demands of adjacent villi. Cell differentiation and proliferation is regulated through Wnt and Notch signals, the strength of which depends on the local cell composition. The highest level of Wnt activity is associated with maintaining equipotent stem cells (SC), Paneth cells and common goblet-Paneth cell progenitors (CGPCPs) intermingling at the crypt bottom. Low levels of Wnt signalling area are associated with stem cells giving rise to secretory cells (CGPCPs, enteroendocrine or Tuft cells) and proliferative absorptive progenitors. Deciding between these two fates, secretory and stem/absorptive cells, depends on Notch signalling. Our model predicts that Notch signalling inhibits secretory fate if more than 50% of cells they are in contact with belong to the secretory lineage. CGPCPs under high Wnt signalling will differentiate into Paneth cells while those migrating out from the crypt bottom differentiate into goblet cells. We have assumed that mature Paneth cells migrating upwards undergo anoikis. Structural relaxation explains the localisation of Paneth cells to the crypt bottom in the absence of active forces. The predicted crypt generation time from one SC is 4-5 days with 10-12 days needed to reach a structural steady state. Our predictions are consistent with experimental observations made under altered Wnt and Notch signalling. Mutations affecting stem cells located at the crypt floor have a 50% chance of being propagated throughout the crypt while mutations in cells above are rarely propagated. The predicted recovery time of an injured crypt losing half of its cells is approximately 2 days.
Collapse
Affiliation(s)
- Carmen Pin
- Integrated Biology of the Gastrointestinal Tract, Institute of Food Research, Norwich, United Kingdom.
| | | | | |
Collapse
|
32
|
Martinez O, Salmerón J, Guillén MD, Pin C, Casas C. Physicochemical, sensorial and textural characteristics of liquid-smoked salmon (Salmo salar) as affected by salting treatment and sugar addition. Int J Food Sci Technol 2012. [DOI: 10.1111/j.1365-2621.2012.02945.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
33
|
Pin C, Avendaño-Perez G, Cosciani-Cunico E, Gómez N, Gounadakic A, Nychas GJ, Skandamis P, Barker G. Modelling Salmonella concentration throughout the pork supply chain by considering growth and survival in fluctuating conditions of temperature, pH and aw. Int J Food Microbiol 2011; 145 Suppl 1:S96-102. [DOI: 10.1016/j.ijfoodmicro.2010.09.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2010] [Revised: 09/21/2010] [Accepted: 09/25/2010] [Indexed: 10/19/2022]
|
34
|
Muñoz-Cuevas M, Fernández PS, George S, Pin C. Modeling the lag period and exponential growth of Listeria monocytogenes under conditions of fluctuating temperature and water activity values. Appl Environ Microbiol 2010; 76:2908-15. [PMID: 20208022 PMCID: PMC2863444 DOI: 10.1128/aem.02572-09] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [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: 10/22/2009] [Accepted: 02/22/2010] [Indexed: 11/20/2022] Open
Abstract
The dynamic model for the growth of a bacterial population described by Baranyi and Roberts (J. Baranyi and T. A. Roberts, Int. J. Food Microbiol. 23:277-294, 1994) was applied to model the lag period and exponential growth of Listeria monocytogenes under conditions of fluctuating temperature and water activity (a(w)) values. To model the duration of the lag phase, the dependence of the parameter h(0), which quantifies the amount of work done during the lag period, on the previous and current environmental conditions was determined experimentally. This parameter depended not only on the magnitude of the change between the previous and current environmental conditions but also on the current growth conditions. In an exponentially growing population, any change in the environment requiring a certain amount of work to adapt to the new conditions initiated a lag period that lasted until that work was finished. Observations for several scenarios in which exponential growth was halted by a sudden change in the temperature and/or a(w) were in good agreement with predictions. When a population already in a lag period was subjected to environmental fluctuations, the system was reset with a new lag phase. The work to be done during the new lag phase was estimated to be the workload due to the environmental change plus the unfinished workload from the uncompleted previous lag phase.
Collapse
Affiliation(s)
- Marina Muñoz-Cuevas
- Institute of Food Research, Norwich NR4 7UA, United Kingdom, Departamento Ingeniería Alimentos y del Equipamiento Agrícola, Escuela Técnica Superior de Ingeniería Agronómica, Universidad Politécnica de Cartagena, 30203 Cartagena, Spain
| | - Pablo S. Fernández
- Institute of Food Research, Norwich NR4 7UA, United Kingdom, Departamento Ingeniería Alimentos y del Equipamiento Agrícola, Escuela Técnica Superior de Ingeniería Agronómica, Universidad Politécnica de Cartagena, 30203 Cartagena, Spain
| | - Susan George
- Institute of Food Research, Norwich NR4 7UA, United Kingdom, Departamento Ingeniería Alimentos y del Equipamiento Agrícola, Escuela Técnica Superior de Ingeniería Agronómica, Universidad Politécnica de Cartagena, 30203 Cartagena, Spain
| | - Carmen Pin
- Institute of Food Research, Norwich NR4 7UA, United Kingdom, Departamento Ingeniería Alimentos y del Equipamiento Agrícola, Escuela Técnica Superior de Ingeniería Agronómica, Universidad Politécnica de Cartagena, 30203 Cartagena, Spain
| |
Collapse
|
35
|
Artin I, Mason DR, Pin C, Schelin J, Peck MW, Holst E, Rådström P, Carter AT. Effects of carbon dioxide on growth of proteolytic Clostridium botulinum, its ability to produce neurotoxin, and its transcriptome. Appl Environ Microbiol 2010; 76:1168-72. [PMID: 20038699 PMCID: PMC2820955 DOI: 10.1128/aem.02247-09] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [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: 09/17/2009] [Accepted: 12/14/2009] [Indexed: 01/02/2023] Open
Abstract
The antimicrobial gas carbon dioxide is frequently used in modified atmosphere packaging. In the present study, the effects of CO2 (10 to 70%, vol/vol) on gene expression (measured using quantitative reverse transcription-PCR and a whole-genome DNA microarray) and neurotoxin formation (measured using an enzyme-linked immunosorbent assay [ELISA]) by proteolytic Clostridium botulinum type A1 strain ATCC 3502 were studied during the growth cycle. Interestingly, in marked contrast to the situation with nonproteolytic C. botulinum types B and E, CO2 had little effect on any of these parameters. At all CO2 concentrations, relative expression of neurotoxin cluster genes peaked in the transition between exponential and stationary phases, with evidence of a second rise in expression in late stationary phase. Microarray analysis enabled identification of coding sequences whose expression profiles matched those of the neurotoxin cluster. Further research is needed to determine whether these are connected to neurotoxin formation or are merely growth phase associated.
Collapse
Affiliation(s)
- Ingrid Artin
- Institute of Food Research, Norwich, United Kingdom, Applied Microbiology, Lund Institute of Technology, Lund University, Lund, Sweden, Division of Medical Microbiology, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - David R. Mason
- Institute of Food Research, Norwich, United Kingdom, Applied Microbiology, Lund Institute of Technology, Lund University, Lund, Sweden, Division of Medical Microbiology, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Carmen Pin
- Institute of Food Research, Norwich, United Kingdom, Applied Microbiology, Lund Institute of Technology, Lund University, Lund, Sweden, Division of Medical Microbiology, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Jenny Schelin
- Institute of Food Research, Norwich, United Kingdom, Applied Microbiology, Lund Institute of Technology, Lund University, Lund, Sweden, Division of Medical Microbiology, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Michael W. Peck
- Institute of Food Research, Norwich, United Kingdom, Applied Microbiology, Lund Institute of Technology, Lund University, Lund, Sweden, Division of Medical Microbiology, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Elisabet Holst
- Institute of Food Research, Norwich, United Kingdom, Applied Microbiology, Lund Institute of Technology, Lund University, Lund, Sweden, Division of Medical Microbiology, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Peter Rådström
- Institute of Food Research, Norwich, United Kingdom, Applied Microbiology, Lund Institute of Technology, Lund University, Lund, Sweden, Division of Medical Microbiology, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Andrew T. Carter
- Institute of Food Research, Norwich, United Kingdom, Applied Microbiology, Lund Institute of Technology, Lund University, Lund, Sweden, Division of Medical Microbiology, Department of Laboratory Medicine, Lund University, Lund, Sweden
| |
Collapse
|
36
|
Pin C, Rolfe MD, Muñoz-Cuevas M, Hinton JCD, Peck MW, Walton NJ, Baranyi J. Network analysis of the transcriptional pattern of young and old cells of Escherichia coli during lag phase. BMC Syst Biol 2009; 3:108. [PMID: 19917103 PMCID: PMC2780417 DOI: 10.1186/1752-0509-3-108] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2009] [Accepted: 11/16/2009] [Indexed: 11/18/2022]
Abstract
Background The aging process of bacteria in stationary phase is halted if cells are subcultured and enter lag phase and it is then followed by cellular division. Network science has been applied to analyse the transcriptional response, during lag phase, of bacterial cells starved previously in stationary phase for 1 day (young cells) and 16 days (old cells). Results A genome scale network was constructed for E. coli K-12 by connecting genes with operons, transcription and sigma factors, metabolic pathways and cell functional categories. Most of the transcriptional changes were detected immediately upon entering lag phase and were maintained throughout this period. The lag period was longer for older cells and the analysis of the transcriptome revealed different intracellular activity in young and old cells. The number of genes differentially expressed was smaller in old cells (186) than in young cells (467). Relatively, few genes (62) were up- or down-regulated in both cultures. Transcription of genes related to osmotolerance, acid resistance, oxidative stress and adaptation to other stresses was down-regulated in both young and old cells. Regarding carbohydrate metabolism, genes related to the citrate cycle were up-regulated in young cells while old cells up-regulated the Entner Doudoroff and gluconate pathways and down-regulated the pentose phosphate pathway. In both old and young cells, anaerobic respiration and fermentation pathways were down-regulated, but only young cells up-regulated aerobic respiration while there was no evidence of aerobic respiration in old cells. Numerous genes related to DNA maintenance and replication, translation, ribosomal biosynthesis and RNA processing as well as biosynthesis of the cell envelope and flagellum and several components of the chemotaxis signal transduction complex were up-regulated only in young cells. The genes for several transport proteins for iron compounds were up-regulated in both young and old cells. Numerous genes encoding transporters for carbohydrates and organic alcohols and acids were down-regulated in old cells only. Conclusion Network analysis revealed very different transcriptional activities during the lag period in old and young cells. Rejuvenation seems to take place during exponential growth by replicative dilution of old cellular components.
Collapse
Affiliation(s)
- Carmen Pin
- Institute of Food Research, Norwich NR4 7UA, UK.
| | | | | | | | | | | | | |
Collapse
|
37
|
Man AL, Lodi F, Bertelli E, Regoli M, Pin C, Mulholland F, Satoskar AR, Taussig MJ, Nicoletti C. Macrophage migration inhibitory factor plays a role in the regulation of microfold (M) cell-mediated transport in the gut. J Immunol 2008; 181:5673-80. [PMID: 18832726 DOI: 10.4049/jimmunol.181.8.5673] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
It has been shown previously that certain bacteria rapidly (3 h) up-regulated in vivo microfold cell (M cell)-mediated transport of Ag across the follicle-associated epithelium of intestinal Peyer's patch. Our aim was to determine whether soluble mediators secreted following host-bacteria interaction were involved in this event. A combination of proteomics and immunohistochemical analyses was used to identify molecules produced in the gut in response to bacterial challenge in vivo; their effects were then tested on human intestinal epithelial cells in vitro. Macrophage migration inhibitory factor (MIF) was the only cytokine produced rapidly after in vivo bacterial challenge by CD11c(+) cells located beneath the M cell-rich area of the follicle-associated epithelium of the Peyer's patch. Subsequently, in vitro experiments conducted using human Caco-2 cells showed that, within hours, MIF induced the appearance of cells that showed temperature-dependent transport of microparticles and M cell-specific bacterium Vibrio cholerae, and acquired biochemical features of M cells. Furthermore, using an established in vitro human M cell model, we showed that anti-MIF Ab blocked Raji B cell-mediated conversion of Caco-2 cells into Ag-sampling cells. Finally, we report that MIF(-/-) mice, in contrast to wild-type mice, failed to show increased M cell-mediated transport following in vivo bacterial challenge. These data show that MIF plays a role in M cell-mediated transport, and cross-talk between bacteria, gut epithelium, and immune system is instrumental in regulating key functions of the gut, including M cell-mediated Ag sampling.
Collapse
Affiliation(s)
- Angela L Man
- Programme of Gastrointestinal Tract Biology and Health, Institute of Food Research, Norwich, United Kingdom
| | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Nuin M, Alfaro B, Cruz Z, Argarate N, George S, Le Marc Y, Olley J, Pin C. Modelling spoilage of fresh turbot and evaluation of a time–temperature integrator (TTI) label under fluctuating temperature. Int J Food Microbiol 2008; 127:193-9. [DOI: 10.1016/j.ijfoodmicro.2008.04.010] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2007] [Revised: 04/14/2008] [Accepted: 04/22/2008] [Indexed: 11/25/2022]
|
39
|
Sado Kamdem S, Guerzoni ME, Baranyi J, Pin C. Effect of capric, lauric and alpha-linolenic acids on the division time distributions of single cells of Staphylococcus aureus. Int J Food Microbiol 2008; 128:122-8. [PMID: 18793815 DOI: 10.1016/j.ijfoodmicro.2008.08.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2007] [Revised: 08/04/2008] [Accepted: 08/05/2008] [Indexed: 11/29/2022]
Abstract
The effect of non-inhibitory concentrations of capric, lauric and alpha-linolenic acids (C10:0, C12:0 and C18:3 respectively) on the division time distribution of single cells of Staphylococcus aureus was evaluated at pH 7 and pH 5. The effect of the initial cell concentration on the lag time of growing cell populations was also assessed. The statistical properties of the division times (defined as the time interval from birth to next binary fission for a single cell) were studied using the method of Elfwing et al. [Elfwing, A., Le Marc, Y., Baranyi, J., Ballagi, A., 2004. Observing the growth and division of large number of individual bacteria using image analysis. Applied and Environmental Microbiology 70, 675-678]. The division times were significantly longer in the presence of free fatty acids than in the control. Shorter division intervals were detected at pH 7 than at pH 5 in the control experiment and in the presence of C10:0. However, both C12:0 and C18:3 slowed down the growth, regardless of the pH. The observed division time distributions were used to simulate growth curves from different inoculum sizes using the stochastic birth process described by Pin and Baranyi [Pin, C., Baranyi, J., 2006. Kinetics of single cells: observation and modelling of a stochastic process. Applied and Environmental Microbiology 72, 2163-2169]. The output of the simulation results were compared with observed data. The lag times fitted to simulated growth curves were in good agreement with those fitted to growth curves measured by plate counts. The averaged out effect of the population masked the effect of the free fatty acids and pH on the division times of single cells.
Collapse
Affiliation(s)
- S Sado Kamdem
- Dipartimento di Scienze degli Alimenti (DISA), University of Bologna, Campus Scienze degli Alimenti, Pzza Goidanich, 60, 47023 Cesena, Italy.
| | | | | | | |
Collapse
|
40
|
Ivory K, Chambers SJ, Pin C, Prieto E, Arqués JL, Nicoletti C. Oral delivery of Lactobacillus casei Shirota modifies allergen-induced immune responses in allergic rhinitis. Clin Exp Allergy 2008; 38:1282-9. [PMID: 18510694 DOI: 10.1111/j.1365-2222.2008.03025.x] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.8] [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
BACKGROUND Changes in the composition of the gut microbiota have been implicated in the pathogenesis of allergic disorders, suggesting beneficial interactions between the intestinal immune system and specific bacterial strains. Lactobacilli are naturally present within the complex gastrointestinal microbiota of humans and they are currently present in many probiotic supplements. OBJECTIVE We sought to investigate the role that Lactobacillus casei Shirota (LcS) may play in modulating seasonal allergic rhinitis (SAR). METHODS The study format was double-blinded, placebo-controlled with 10 SAR sufferers in each group. We have documented and compared changes in immune status arising through the daily ingestion of a milk drink with or without live LcS, over a period of 5 months. Pre-, peak- and post-grass pollen season blood samples were collected for determination of plasma total IgE and grass pollen-specific IgG and IgE levels by an enzyme immunoassay. At the same time, cytokine levels were determined by flow cytometric bead array technology following culture of peripheral blood mononuclear cells for 6 days in the presence or absence of specific grass pollen antigens. RESULTS Volunteers treated with LcS showed a significant reduction in levels of antigen-induced IL-5, IL-6 and IFN-gamma production compared with volunteers supplemented with placebo. Meanwhile, levels of specific IgG increased and IgE decreased in the probiotic group. CONCLUSION Changes in antigen-induced production of cytokines were observed in patients treated with probiotics. These data show that probiotic supplementation modulates immune responses in allergic rhinitis and may have the potential to alleviate the severity of symptoms.
Collapse
Affiliation(s)
- K Ivory
- Gastrointestinal Biology and Health Programme, Institute of Food Research, Colney, Norwich, UK.
| | | | | | | | | | | |
Collapse
|
41
|
Gunning AP, Chambers S, Pin C, Man AL, Morris VJ, Nicoletti C. Mapping specific adhesive interactions on living human intestinal epithelial cells with atomic force microscopy. FASEB J 2008; 22:2331-9. [PMID: 18263697 DOI: 10.1096/fj.07-100578] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Specific molecular-receptor interactions with gut epithelium cells are important in understanding bioactivity of food components and drugs, binding of commensal microflora, attachment and initiation of defense mechanisms against pathogenic bacteria and for development of targeted delivery systems to the gut. However, methods for probing such interactions are lacking. Methodology has been developed and validated to measure specific molecular-receptor interactions on living human colorectal cancer cells as in vitro models for the gut epithelium. Atomic force microscopy (AFM) was used to measure ligand-receptor interactions and to map receptor locations on cell surfaces. Measurements were made using silica beads attached to the AFM tip-cantilever assembly, which were functionalized by coupling of ligands to the bead surface. Wheat germ agglutinin (WGA) binds to the glycosylated extracellular domain III of the epidermal growth factor receptor. Methodology was tested by measuring binding of WGA to the surface of confluent monolayers of living Caco-2 human intestinal epithelial cells. The measured modal detachment force of 125 pN is typical of values expected for single molecule interactions. Adhesive events were used to map the location of binding sites on the cell surface revealing heterogeneity in their distribution within and between cells within the monolayer.
Collapse
Affiliation(s)
- A Patrick Gunning
- Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK.
| | | | | | | | | | | |
Collapse
|
42
|
Pin C, Reuter M. Use of genomic DNA control features and predicted operon structure in microarray data analysis: ArrayLeaRNA - a Bayesian approach. BMC Bioinformatics 2007; 8:455. [PMID: 18021437 PMCID: PMC2228326 DOI: 10.1186/1471-2105-8-455] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [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: 01/09/2007] [Accepted: 11/19/2007] [Indexed: 11/17/2022] Open
Abstract
Background Microarrays are widely used for the study of gene expression; however deciding on whether observed differences in expression are significant remains a challenge. Results A computing tool (ArrayLeaRNA) has been developed for gene expression analysis. It implements a Bayesian approach which is based on the Gumbel distribution and uses printed genomic DNA control features for normalization and for estimation of the parameters of the Bayesian model and prior knowledge from predicted operon structure. The method is compared with two other approaches: the classical LOWESS normalization followed by a two fold cut-off criterion and the OpWise method (Price, et al. 2006. BMC Bioinformatics. 7, 19), a published Bayesian approach also using predicted operon structure. The three methods were compared on experimental datasets with prior knowledge of gene expression. With ArrayLeaRNA, data normalization is carried out according to the genomic features which reflect the results of equally transcribed genes; also the statistical significance of the difference in expression is based on the variability of the equally transcribed genes. The operon information helps the classification of genes with low confidence measurements. ArrayLeaRNA is implemented in Visual Basic and freely available as an Excel add-in at Conclusion We have introduced a novel Bayesian model and demonstrated that it is a robust method for analysing microarray expression profiles. ArrayLeaRNA showed a considerable improvement in data normalization, in the estimation of the experimental variability intrinsic to each hybridization and in the establishment of a clear boundary between non-changing and differentially expressed genes. The method is applicable to data derived from hybridizations of labelled cDNA samples as well as from hybridizations of labelled cDNA with genomic DNA and can be used for the analysis of datasets where differentially regulated genes predominate.
Collapse
Affiliation(s)
- Carmen Pin
- Institute of Food Research, Norwich, NR4 7UA, UK.
| | | |
Collapse
|
43
|
Arzel C, Guillemain M, Gurd DB, Elmberg J, Fritz H, Arnaud A, Pin C, Bosca F. Experimental functional response and inter-individual variation in foraging rate of teal (Anas crecca). Behav Processes 2007; 75:66-71. [PMID: 17336000 DOI: 10.1016/j.beproc.2007.01.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2006] [Revised: 01/02/2007] [Accepted: 01/15/2007] [Indexed: 10/23/2022]
Abstract
The functional response, i.e. the change in per capita food intake rate per time unit with changed food availability, is a widely used tool for understanding the ecology and behaviour of animals. However, waterfowl remain poorly explored in this context. In an aviary experiment we derived a functional response curve for teal (Anas crecca) foraging on rice (Oryza sativa) seeds. We found a linear relationship between intake rate and seed density, as expected for a filter-feeder. At high seed densities we found a threshold, above which intake rate still increased linearly but with a lower slope, possibly reflecting a switch from filter-feeding to a scooping foraging mode. The present study shows that food intake rate in teal is linearly related to food availability within the range of naturally occurring seed densities, a finding with major implications for management and conservation of wetland habitats.
Collapse
Affiliation(s)
- C Arzel
- Office National de la Chasse et de la Faune Sauvage, CNERA Avifaune Migratrice, La Tour du Valat, Le Sambuc, F-13200 Arles, France.
| | | | | | | | | | | | | | | |
Collapse
|
44
|
Webb MD, Pin C, Peck MW, Stringer SC. Historical and contemporary NaCl concentrations affect the duration and distribution of lag times from individual spores of nonproteolytic clostridium botulinum. Appl Environ Microbiol 2007; 73:2118-27. [PMID: 17277206 PMCID: PMC1855668 DOI: 10.1128/aem.01744-06] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2006] [Accepted: 01/21/2007] [Indexed: 11/20/2022] Open
Abstract
In this study we determined the effect of NaCl concentration during sporulation (0 or 3.0% [wt/vol] added NaCl) and subsequent growth (0 or 2.0% [wt/vol] added NaCl) on the distributions of times associated with various stages of the lag phase of individual spores of nonproteolytic Clostridium botulinum strain Eklund 17B. The effects of NaCl on the probability of germination and the probability of subsequent growth were also determined. Spore populations exhibited considerable heterogeneity at all stages of lag phase for each condition tested. Germination time did not correlate strongly with the times for later stages in the lag phase, such as outgrowth and doubling time. Addition of NaCl to either the sporulation or growth media increased the mean times for, and variability of, all the measured stages of the lag phase (germination, emergence, time to one mature cell, and time to first doubling). There was a synergistic interaction between the inhibitory effects of NaCl in the sporulation medium and the inhibitory effects of NaCl in the subsequent growth medium on the total lag time and each of its stages. Addition of NaCl to either the sporulation medium or the growth medium reduced both the probability of germination and the probability of a germinated spore developing into a mature cell, but the interaction was not synergistic. Spores formed in medium with added NaCl were not better adapted to subsequent growth in suboptimal osmotic conditions than spores formed in medium with no added NaCl were. Knowledge of the distribution of lag times for individual spores and quantification of the biovariability within lag time distributions may provide insight into the underlying mechanisms and can be used to improve predictions of growth in food and to refine risk assessments.
Collapse
Affiliation(s)
- Martin D Webb
- Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, United Kingdom
| | | | | | | |
Collapse
|
45
|
Yang XJ, Pin C. A NOVEL SOLID-PHASE EXTRACTION SCHEME FOR THE GROUP SEPARATION OF HIGH FIELD STRENGTH ELEMENTS (Nb, Ta, Zr, Hf) FROM Al-, Ti-, AND Fe-RICH GEOLOGICAL MATERIALS. SEP SCI TECHNOL 2007. [DOI: 10.1081/ss-100102947] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
46
|
Fernández M, Ordóñez JA, Cambero I, Santos C, Pin C, Hoz LDL. Fatty acid compositions of selected varieties of Spanish dry ham related to their nutritional implications. Food Chem 2007. [DOI: 10.1016/j.foodchem.2006.01.006] [Citation(s) in RCA: 148] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
47
|
Polley ACJ, Mulholland F, Pin C, Williams EA, Bradburn DM, Mills SJ, Mathers JC, Johnson IT. Proteomic analysis reveals field-wide changes in protein expression in the morphologically normal mucosa of patients with colorectal neoplasia. Cancer Res 2006; 66:6553-62. [PMID: 16818627 DOI: 10.1158/0008-5472.can-06-0534] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Models for the pathogenesis of colorectal cancer tend to focus on the localized lesion, with less attention paid to changes in normal-appearing mucosa. Here we used two-dimensional gel electrophoresis and mass spectrometry to define patterns of protein expression in morphologically normal colonic mucosa from 13 healthy subjects, 9 patients with adenomatous polyps, and 9 with cancer. Tumor samples were also compared with the normal mucosa. Systematic gel comparisons identified a total of 839 spots that differed significantly between one or more groups (P < 0.05). Principle component analysis indicated that the first three components accounted for approximately 37% of the total variation and provided clear evidence that flat mucosa from healthy subjects differed significantly from that of patients with polyps or cancer. Sixty-one proteins differed significantly between mucosa from healthy subjects and all other tissue types, and 206 differed significantly between healthy mucosa and polyp mucosa. Several of the proteins showing significant underexpression in tumor tissue were cytokeratins and other cytoskeletal components. In contrast, cytokeratins, including several isoforms of cytokeratin 8, were overexpressed in apparently normal mucosa from polyp and cancer patients compared with mucosa from healthy subjects. These findings indicate that protein expression in the apparently normal colonic mucosal field is modified in individuals with neoplastic lesions at sites distant from the lesion. Recognition and further characterization of this field effect at the molecular level may provide protein biomarkers of susceptibility to colorectal cancer and facilitate development of hypotheses for the role of diet and other environmental factors in its causation.
Collapse
|
48
|
Friis LM, Pin C, Taylor DE, Pearson BM, Wells JM. A role for the tet(O) plasmid in maintaining Campylobacter plasticity. Plasmid 2006; 57:18-28. [PMID: 16934869 DOI: 10.1016/j.plasmid.2006.06.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2006] [Revised: 05/05/2006] [Accepted: 06/09/2006] [Indexed: 11/23/2022]
Abstract
Genomic sequencing projects are beginning to reveal regions of extensive DNA homology between bacterial genera. Public fears of the spread of genetically modified organisms into the food chain and the increasing prevalence of multi-drug resistant disease in humans highlight the implications of horizontal gene transfer. The striking DNA sequence similarity between the two uniquely identified tetracycline resistant (Tc(R)) Campylobacter plasmids, pCC31 and pTet, suggests their conserved acquisition and maintenance within Campylobacter [Batchelor, R.A., Pearson, B.M., Friis, L.M., Guerry, P., Wells, J.M. 2004. Nucleotide sequences and comparison of two large conjugative plasmids from different Campylobacter species. Microbiology 150, 3507-3517]. It is thus likely that these and other conjugative plasmids are highly prevalent and broadly distributed across several continents. Microarray technology is now enabling fast and extensive genomic comparisons to be made and allows us to investigate intra- and inter-genetic conservation and variability. This study details the development of a microarray specific for genes from Campylobacter plasmids pCC31, pTet and pVir and its application to the analysis of Campylobacter plasmid gene presence and preservation throughout environmental and clinical isolates. Application of the iterative algorithm GENCOM (freely available at ) is used as a rapid and effective way of comparing the content and conservation of plasmids in bacteria and provides details of the Campylobacter flexible gene pool and its contribution to genomic plasticity.
Collapse
Affiliation(s)
- L M Friis
- Institute of Food Research, Colney Lane, Norwich, Norfolk NR4 7UA, UK.
| | | | | | | | | |
Collapse
|
49
|
Pin C, Reuter M, Pearson B, Friis L, Overweg K, Baranyi J, Wells J. Comparison of different approaches for comparative genetic analysis using microarray hybridization. Appl Microbiol Biotechnol 2006; 72:852-9. [PMID: 16933134 DOI: 10.1007/s00253-006-0536-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2006] [Revised: 06/06/2006] [Accepted: 06/07/2006] [Indexed: 10/24/2022]
Abstract
A robust analysis of comparative genomic microarray data is critical for meaningful genomic comparison studies. In this paper, we compare our method (implemented in a new software tool, GENCOM, freely available at http://www.ifr.ac.uk/safety/gencom ) with three commonly used analysis methods: GACK (freely available at http://falkow.stanford.edu ), an empirical cut-off value of twofold difference between the fluorescence intensities after LOWESS normalization or after AVERAGE normalization in which the fluorescence intensity is divided by the average fluorescence intensity of the entire data set. Each method was tested using data sets from real experiments with prior knowledge of conserved and divergent genes. GENCOM and GACK were superior when a high proportion of genes were divergent. GENCOM was the most suitable method for the data set in which the relationship between the fluorescence intensities was not linear. GENCOM has proved robust in an analysis of all the data sets tested.
Collapse
Affiliation(s)
- Carmen Pin
- Institute of Food Research, Norwich Research Park, Coloney Lane, Norwich, NR4 7UA, UK.
| | | | | | | | | | | | | |
Collapse
|
50
|
D'Arrigo M, García de Fernando GD, Velasco de Diego R, Ordóñez JA, George SM, Pin C. Indirect measurement of the lag time distribution of single cells of Listeria innocua in food. Appl Environ Microbiol 2006; 72:2533-8. [PMID: 16597954 PMCID: PMC1449042 DOI: 10.1128/aem.72.4.2533-2538.2006] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The distribution of log counts at a given time during the exponential growth phase of Listeria innocua measured in food samples inoculated with one cell each was applied to estimate the distribution of the single-cell lag times. Three replicate experiments in broth showed that the distribution of the log counts is a linear mapping of the distribution of the detection times measured by optical density. The detection time distribution reflects the lag time distribution but is shifted in time. The log count distribution was applied to estimate the distributions of the lag times in a liquid dairy product and in liver paté after different heat treatments. Two batches of ca. 100 samples of the dairy product were inoculated and heated at 55 degrees C for 45 min or at 62 degrees C for 2 min, and an unheated batch was incubated at 4 degrees C. The final concentration of surviving bacteria was ca. 1 cell per sample. The unheated cells showed the shortest lag times with the smallest variance. The mean and the variance of the lag times of the surviving cells at 62 degrees C were greater than those of the cells treated at 55 degrees C. Three batches of paté samples were heated at 55 degrees C for 25 min, 62 degrees C for 81 s, or 65 degrees C for 20 s. A control batch was inoculated but not heated. All paté samples were incubated at 15 degrees C. The distribution of the lag times of the cells heated at 55 degrees C was not significantly different from that of the unheated cells. However, at the higher temperatures, 62 degrees C and 65 degrees C, the lag duration was longer and its variance greater.
Collapse
Affiliation(s)
- M D'Arrigo
- Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, United Kingdom
| | | | | | | | | | | |
Collapse
|