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McCarthy CM, McKevitt KL, Connolly SA, Andersson I, Leahy FC, Egan S, Moloney MA, Kavanagh EG, Peirce C, Cunnane EM, McGourty KD, Walsh MT, Mulvihill JJE. Microindentation of fresh soft biological tissue: A rapid tissue sectioning and mounting protocol. PLoS One 2024; 19:e0297618. [PMID: 38422111 PMCID: PMC10903917 DOI: 10.1371/journal.pone.0297618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/03/2024] [Indexed: 03/02/2024] Open
Abstract
Microindentation of fresh biological tissues is necessary for the creation of 3D biomimetic models that accurately represent the native extracellular matrix microenvironment. However, tissue must first be precisely sectioned into slices. Challenges exist in the preparation of fresh tissue slices, as they can tear easily and must be processed rapidly in order to mitigate tissue degradation. In this study, we propose an optimised mounting condition for microindentation and demonstrate that embedding tissue in a mixture of 2.5% agarose and 1.5% gelatin is the most favourable method of tissue slice mounting for microindentation. This protocol allows for rapid processing of fresh biological tissue and is applicable to a variety of tissue types.
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Affiliation(s)
- Clíona M. McCarthy
- Biomaterials Cluster, Bernal Institute, University of Limerick, Limerick, Ireland
- School of Engineering, University of Limerick, Limerick, Ireland
| | - Kevin L. McKevitt
- Department of Vascular & Endovascular Surgery, University Hospital Limerick, Limerick, Ireland
| | - Sinéad A. Connolly
- Biomaterials Cluster, Bernal Institute, University of Limerick, Limerick, Ireland
- School of Engineering, University of Limerick, Limerick, Ireland
| | - Isabel Andersson
- Biomaterials Cluster, Bernal Institute, University of Limerick, Limerick, Ireland
- School of Engineering, University of Limerick, Limerick, Ireland
| | - Fiona C. Leahy
- Department of Vascular & Endovascular Surgery, University Hospital Limerick, Limerick, Ireland
| | - Siobhan Egan
- Department of Colorectal Surgery, University Hospital Limerick, Limerick, Ireland
| | - Michael A. Moloney
- Department of Vascular & Endovascular Surgery, University Hospital Limerick, Limerick, Ireland
| | - Eamon G. Kavanagh
- Department of Vascular & Endovascular Surgery, University Hospital Limerick, Limerick, Ireland
| | - Colin Peirce
- Department of Colorectal Surgery, University Hospital Limerick, Limerick, Ireland
| | - Eoghan M. Cunnane
- Biomaterials Cluster, Bernal Institute, University of Limerick, Limerick, Ireland
- School of Engineering, University of Limerick, Limerick, Ireland
- Health Research Institute, University of Limerick, Limerick, Ireland
| | - Kieran D. McGourty
- Biomaterials Cluster, Bernal Institute, University of Limerick, Limerick, Ireland
- School of Engineering, University of Limerick, Limerick, Ireland
- School of Chemical Sciences, University of Limerick, Limerick, Ireland
| | - Michael T. Walsh
- Biomaterials Cluster, Bernal Institute, University of Limerick, Limerick, Ireland
- School of Engineering, University of Limerick, Limerick, Ireland
- Health Research Institute, University of Limerick, Limerick, Ireland
| | - John J. E. Mulvihill
- Biomaterials Cluster, Bernal Institute, University of Limerick, Limerick, Ireland
- School of Engineering, University of Limerick, Limerick, Ireland
- Health Research Institute, University of Limerick, Limerick, Ireland
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2
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Fridrichs J, Hamel B, Kelder W, van den Hoed E, van den Heuvel MC, Hulscher JBF, Olinga P. Human precision-cut cystic duct and gallbladder slices: a novel method for studying cholangiopathies. Front Pediatr 2023; 11:1058319. [PMID: 37528870 PMCID: PMC10387522 DOI: 10.3389/fped.2023.1058319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 05/15/2023] [Indexed: 08/03/2023] Open
Abstract
Background and aims Precision-cut tissue slices (PCTS) are widely used as an ex vivo culture tissue culture technique to study pathogeneses of diseases and drug activities in organs in vitro. A novel application of the PCTS model may be in the field of translational research into cholangiopathies such as biliary atresia. Therefore, the aim of this study was to apply the precision-cut slice technique to human bile duct and gallbladder tissue. Methods Cystic duct and gallbladder tissue derived from patients undergoing a cholecystectomy were collected, preserved and used for preparation of precision-cut cystic duct slices (PCCDS) and precision-cut gallbladder slices (PCGS). The PCCDS and PCGS were prepared using a mechanical tissue slicer and subsequently incubated for 24 and 48 h respectively in William's Medium E (WME) culture medium. Viability was assessed based on ATP/protein content and tissue morphology [hematoxylin and eosin (H&E) staining]. Results It was shown that viability, assessed by the ATP/protein content and morphology, of the PCCDS (n = 8) and PCGS (n = 8) could be maintained over the 24 and 48 h incubation period respectively. ATP/protein content of the PCCDS increased significantly from 0.58 ± 0.13 pmol/µg at 0 h to 2.4 ± 0.29 pmol/µg after 24 h incubation (P = .0003). A similar significant increase from 0.94 ± 0.22 pmol/µg at 0 h to 3.7 ± 0.41 pmol/µg after 24 h (P = .0005) and 4.2 ± 0.47 pmol/µg after 48 h (P = .0002) was observed in the PCGS. Morphological assessment of the PCCDS and PCGS showed viable tissue at 0 h and after 24 and 48 h incubation respectively. Conclusion This study is the first to report on the use of the PCTS model for human gallbladder and cystic duct tissue. PCCDS and PCGS remain viable for an incubation period of at least 24 h, which makes them suitable for research purposes in the field of cholangiopathies, including biliary atresia.
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Affiliation(s)
- Jeske Fridrichs
- Department of Pharmaceutical Technology and Biopharmacy, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, Netherlands
- Division of Pediatric Surgery, Department of Surgery, University Medical Center Groningen, Groningen, Netherlands
| | - Bart Hamel
- Department of Pathology, Martini Hospital, Groningen, Netherlands
| | - Wendy Kelder
- Department of Surgery, Martini Hospital, Groningen, Netherlands
| | | | | | - Jan B. F. Hulscher
- Division of Pediatric Surgery, Department of Surgery, University Medical Center Groningen, Groningen, Netherlands
| | - Peter Olinga
- Department of Pharmaceutical Technology and Biopharmacy, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, Netherlands
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Wu KZ, Adine C, Mitriashkin A, Aw BJJ, Iyer NG, Fong ELS. Making In Vitro Tumor Models Whole Again. Adv Healthc Mater 2023; 12:e2202279. [PMID: 36718949 DOI: 10.1002/adhm.202202279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 01/04/2023] [Indexed: 02/01/2023]
Abstract
As a reductionist approach, patient-derived in vitro tumor models are inherently still too simplistic for personalized drug testing as they do not capture many characteristics of the tumor microenvironment (TME), such as tumor architecture and stromal heterogeneity. This is especially problematic for assessing stromal-targeting drugs such as immunotherapies in which the density and distribution of immune and other stromal cells determine drug efficacy. On the other end, in vivo models are typically costly, low-throughput, and time-consuming to establish. Ex vivo patient-derived tumor explant (PDE) cultures involve the culture of resected tumor fragments that potentially retain the intact TME of the original tumor. Although developed decades ago, PDE cultures have not been widely adopted likely because of their low-throughput and poor long-term viability. However, with growing recognition of the importance of patient-specific TME in mediating drug response, especially in the field of immune-oncology, there is an urgent need to resurrect these holistic cultures. In this Review, the key limitations of patient-derived tumor explant cultures are outlined and technologies that have been developed or could be employed to address these limitations are discussed. Engineered holistic tumor explant cultures may truly realize the concept of personalized medicine for cancer patients.
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Affiliation(s)
- Kenny Zhuoran Wu
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, 119276, Singapore
| | - Christabella Adine
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, 119276, Singapore
| | - Aleksandr Mitriashkin
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, 119276, Singapore
| | - Benjamin Jun Jie Aw
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, 119276, Singapore
| | - N Gopalakrishna Iyer
- Department of Head and Neck Surgery, Division of Surgery and Surgical Oncology, Duke-NUS Medical School, Singapore, 169857, Singapore
- Department of Head and Neck Surgery, National Cancer Centre Singapore, Singapore, 169610, Singapore
| | - Eliza Li Shan Fong
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, 119276, Singapore
- The N.1 Institute for Health, National University of Singapore, Singapore, 117456, Singapore
- Cancer Science Institute (CSI), National University of Singapore, Singapore, 117599, Singapore
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4
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Ito F, Kato K, Yanatori I, Maeda Y, Murohara T, Toyokuni S. Matrigel-based organoid culture of malignant mesothelioma reproduces cisplatin sensitivity through CTR1. BMC Cancer 2023; 23:487. [PMID: 37254056 DOI: 10.1186/s12885-023-10966-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 05/16/2023] [Indexed: 06/01/2023] Open
Abstract
Organoids are a three-dimensional (3D) culture system that simulate actual organs. Therefore, tumor organoids are expected to predict precise response to chemotherapy in patients. However, to date, few studies have studied the drug responses in organoids of malignant mesothelioma (MM). The poor prognosis of MM emphasizes the importance of establishing a protocol for generating MM-organoid for research and clinical use. Here, we established murine MM organoids from p53+/- or wild-type C57BL/6 strain by intraperitoneal injection either with crocidolite or carbon nanotube. Established MM-organoids proliferated in Matrigel as spheroids. Subcutaneous injection assays revealed that the MM-organoids mimicked actual tissue architecture and maintained the original histological features of the primary MM. RNA sequencing and pathway analyses revealed that the significant expressional differences between the 2D- and 3D-culture systems were observed in receptor tyrosine kinases, including IGF1R and EGFR, glycosylation and cholesterol/steroid metabolism. MM-organoids exhibited a more sensitive response to cisplatin through stable plasma membrane localization of a major cisplatin transporter, copper transporter 1/Slc31A1 (Ctr1) in comparison to 2D-cultures, presumably through glycosylation and lipidation. The Matrigel culture system facilitated the localization of CTR1 on the plasma membrane, which simulated the original MMs and the subcutaneous xenografts. These results suggest that the newly developed protocol for MM-organoids is useful to study strategies to overcome chemotherapy resistance to cisplatin.
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Affiliation(s)
- Fumiya Ito
- Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Katsuhiro Kato
- Department of Cardiology, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Izumi Yanatori
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Sakyo-Ku, Kyoto, 606-8501, Japan
| | - Yuki Maeda
- Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Toyoaki Murohara
- Department of Cardiology, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Shinya Toyokuni
- Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan.
- Center for Low-Temperature Plasma Sciences, Nagoya University, Furo-Cho, Chikusa-Ku, Nagoya, 464-8603, Japan.
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5
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Zhang L, Wang L, Yang S, He K, Bao D, Xu M. Quantifying the drug response of patient-derived organoid clusters by aggregated morphological indicators with multi-parameters based on optical coherence tomography. BIOMEDICAL OPTICS EXPRESS 2023; 14:1703-1717. [PMID: 37078050 PMCID: PMC10110317 DOI: 10.1364/boe.486666] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/17/2023] [Accepted: 03/17/2023] [Indexed: 05/03/2023]
Abstract
Patient-derived organoids (PDOs) serve as excellent tools for personalized drug screening to predict clinical outcomes of cancer treatment. However, current methods for efficient quantification of drug response are limited. Herein, we develop a method for label-free, continuous tracking imaging and quantitative analysis of drug efficacy using PDOs. A self-developed optical coherence tomography (OCT) system was used to monitor the morphological changes of PDOs within 6 days of drug administration. OCT image acquisition was performed every 24 h. An analytical method for organoid segmentation and morphological quantification was developed based on a deep learning network (EGO-Net) to simultaneously analyze multiple morphological organoid parameters under the drug's effect. Adenosine triphosphate (ATP) testing was conducted on the last day of drug treatment. Finally, a corresponding aggregated morphological indicator (AMI) was established using principal component analysis (PCA) based on the correlation analysis between OCT morphological quantification and ATP testing. Determining the AMI of organoids allowed quantitative evaluation of the PDOs responses to gradient concentrations and combinations of drugs. Results showed that there was a strong correlation (correlation coefficient >90%) between the results using the AMI of organoids and those from ATP testing, which is the standard test used for bioactivity measurement. Compared with single-time-point morphological parameters, the introduction of time-dependent morphological parameters can reflect drug efficacy with improved accuracy. Additionally, the AMI of organoids was found to improve the efficiency of 5-fluorouracil(5FU) against tumor cells by allowing the determination of the optimum concentration, and the discrepancies in response among different PDOs using the same drug combinations could also be measured. Collectively, the AMI established by OCT system combined with PCA could quantify the multidimensional morphological changes of organoids under the drug's effect, providing a simple and efficient tool for drug screening in PDOs.
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Affiliation(s)
- Linyi Zhang
- Hangzhou Dianzi University, Automation College, Hangzhou, Zhejiang, China
| | - Ling Wang
- Hangzhou Dianzi University, Automation College, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Medical Information and Biological 3D Printing, Hangzhou, Zhejiang, China
| | - Shanshan Yang
- Hangzhou Dianzi University, Automation College, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Medical Information and Biological 3D Printing, Hangzhou, Zhejiang, China
| | - Kangxin He
- First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Di Bao
- Hangzhou Dianzi University, Automation College, Hangzhou, Zhejiang, China
| | - Mingen Xu
- Hangzhou Dianzi University, Automation College, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Medical Information and Biological 3D Printing, Hangzhou, Zhejiang, China
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6
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Meran L, Tullie L, Eaton S, De Coppi P, Li VSW. Bioengineering human intestinal mucosal grafts using patient-derived organoids, fibroblasts and scaffolds. Nat Protoc 2023; 18:108-135. [PMID: 36261633 DOI: 10.1038/s41596-022-00751-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 06/30/2022] [Indexed: 01/14/2023]
Abstract
Tissue engineering is an interdisciplinary field that combines stem cells and matrices to form functional constructs that can be used to repair damaged tissues or regenerate whole organs. Tissue stem cells can be expanded and functionally differentiated to form 'mini-organs' resembling native tissue architecture and function. The choice of the scaffold is also pivotal to successful tissue reconstruction. Scaffolds may be broadly classified into synthetic or biological depending upon the purpose of the engineered organ. Bioengineered intestinal grafts represent a potential source of transplantable tissue for patients with intestinal failure, a condition resulting from extensive anatomical and functional loss of small intestine and therefore digestive and absorptive capacity. Prior strategies in intestinal bioengineering have predominantly used either murine or pluripotent cells and synthetic or decellularized rodent scaffolds, thus limiting their translation. Microscale models of human intestinal epithelium on shaped hydrogels and synthetic scaffolds are more physiological, but their regenerative potential is limited by scale. Here we present a protocol for bioengineering human intestinal grafts using patient-derived materials in a bioreactor culture system. This includes the isolation, expansion and biobanking of patient-derived intestinal organoids and fibroblasts, the generation of decellularized human intestinal scaffolds from native human tissue and providing a system for recellularization to form transplantable grafts. The duration of this protocol is 12 weeks, and it can be completed by scientists with prior experience of organoid culture. The resulting engineered mucosal grafts comprise physiological intestinal epithelium, matrix and surrounding niche, offering a valuable tool for both regenerative medicine and the study of human gastrointestinal diseases.
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Affiliation(s)
- Laween Meran
- Stem Cell and Cancer Biology Laboratory, The Francis Crick Institute, London, UK
- Stem Cell and Regenerative Medicine Section, DBC, Great Ormond Street Institute of Child Health, University College London, London, UK
- Medical Research Council Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Lucinda Tullie
- Stem Cell and Cancer Biology Laboratory, The Francis Crick Institute, London, UK
- Stem Cell and Regenerative Medicine Section, DBC, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Simon Eaton
- Stem Cell and Regenerative Medicine Section, DBC, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Paolo De Coppi
- Stem Cell and Regenerative Medicine Section, DBC, Great Ormond Street Institute of Child Health, University College London, London, UK.
- Specialist Neonatal and Paediatric Surgery Unit, Great Ormond Street Hospital, London, UK.
| | - Vivian S W Li
- Stem Cell and Cancer Biology Laboratory, The Francis Crick Institute, London, UK.
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7
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Extending the viability of human precision-cut intestinal slice model for drug metabolism studies. Arch Toxicol 2022; 96:1815-1827. [PMID: 35428896 PMCID: PMC9095520 DOI: 10.1007/s00204-022-03295-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/24/2022] [Indexed: 11/09/2022]
Abstract
Human Precision-cut intestinal slices (hPCIS) are used to study intestinal physiology, pathophysiology, drug efficacy, toxicology, kinetics, and metabolism. However, the use of this ex vivo model is restricted to approximately a 24 h timeframe because of declining viability of the hPCIS during traditional culture. We hypothesized that we could extend the hPCIS viability by using organoid medium. Therefore, we cultured hPCIS for up to 72 h in organoid media [expansion medium (Emed) and differentiation medium (Dmed)]. After incubation, we assessed culture-induced changes on viability markers, specific cell type markers and we assessed the metabolic activity of enterocytes by measuring midazolam metabolite formation. We show that the adenosine triphosphate (ATP)/protein ratio of Emed-cultured hPCIS and morphology of both Emed- and Dmed-cultured hPCIS was improved compared to WME-cultured hPCIS. Emed-cultured hPCIS showed an increased expression of proliferation and stem cell markers, whereas Dmed-cultured hPCIS showed an increased expression of proliferation and enterocyte markers, along with increased midazolam metabolism. Using the Emed, the viability of hPCIS could be extended for up to 72 h, and proliferating stem cells remained preserved. Using Dmed, hPCS also remained viable for up to 72 h, and specifically rescued the metabolizing enterocytes during culture. In conclusion, by using two different organoid culture media, we could extend the hPCIS viability for up to 72 h of incubation and specifically steer stem cells or enterocytes towards their original function, metabolism, and proliferation, potentially allowing pharmacokinetic and toxicology studies beyond the 24 h timeframe.
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8
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Biel C, Bigaeva E, Hesse M, Bomers JJM, van Summeren K, Teunis MAT, Vaessen S, Ten Klooster JP, Olinga P. Survival and cellular heterogeneity of epithelium in cultured mouse and rat precision-cut intestinal slices. Toxicol In Vitro 2020; 69:104974. [PMID: 32828807 DOI: 10.1016/j.tiv.2020.104974] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/05/2020] [Accepted: 08/19/2020] [Indexed: 11/30/2022]
Abstract
Precision-cut intestinal slices (PCIS) are used to study intestinal (patho)physiology, drug efficacy, toxicity, transport and metabolism ex vivo. One of the factors that limit the use of PCIS is a relatively short life-span. Moreover, culture-induced changes in cellular composition of PCIS remain largely uncharacterized. In this study, we demonstrated the epithelial cell heterogeneity in mouse and rat PCIS and its alterations during culture. In addition, we evaluated whether the presence of niche growth factors impacts the survival of PCIS epithelial cells. We showed that freshly prepared PCIS retained the main epithelial cell types, namely absorptive enterocytes, goblet cells, enteroendocrine cells, stem cells, transit-amplifying cells and Paneth cells. Once placed in culture, PCIS displayed progressive epithelial damage, and loss of these epithelial cell types. Cells comprising the intestinal stem cell niche were especially sensitive to the damage, and the addition of niche growth factors beneficially affected the survival of stem cells and transit-amplifying cells in PCIS during culture. In conclusion, this study provides new insights into the dynamic changes in cellular composition of epithelium in cultured PCIS, paving the way to future toxicological and pharmacological studies in an informed and reliable ex vivo setting.
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Affiliation(s)
- Carin Biel
- Department of Pharmaceutical Technology and Biopharmacy, University of Groningen, the Netherlands
| | - Emilia Bigaeva
- Department of Pharmaceutical Technology and Biopharmacy, University of Groningen, the Netherlands; Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Melanie Hesse
- Department of Pharmaceutical Technology and Biopharmacy, University of Groningen, the Netherlands
| | - Jordy J M Bomers
- Department of Pharmaceutical Technology and Biopharmacy, University of Groningen, the Netherlands; PROdermpath, Labor für Dermatohistopathology, Vreden, Germany
| | - Kitty van Summeren
- Research Centre for Healthy and Sustainable Living, Innovative Testing in Life Sciences and Chemistry, University of Applied Sciences, Utrecht, the Netherlands
| | - Marc A T Teunis
- Research Centre for Healthy and Sustainable Living, Innovative Testing in Life Sciences and Chemistry, University of Applied Sciences, Utrecht, the Netherlands
| | - Stefan Vaessen
- Research Centre for Healthy and Sustainable Living, Innovative Testing in Life Sciences and Chemistry, University of Applied Sciences, Utrecht, the Netherlands
| | - Jean Paul Ten Klooster
- Research Centre for Healthy and Sustainable Living, Innovative Testing in Life Sciences and Chemistry, University of Applied Sciences, Utrecht, the Netherlands
| | - Peter Olinga
- Department of Pharmaceutical Technology and Biopharmacy, University of Groningen, the Netherlands.
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9
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Bigaeva E, Gore E, Simon E, Zwick M, Oldenburger A, de Jong KP, Hofker HS, Schlepütz M, Nicklin P, Boersema M, Rippmann JF, Olinga P. Transcriptomic characterization of culture-associated changes in murine and human precision-cut tissue slices. Arch Toxicol 2019; 93:3549-3583. [PMID: 31754732 DOI: 10.1007/s00204-019-02611-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 11/05/2019] [Indexed: 12/14/2022]
Abstract
Our knowledge of complex pathological mechanisms underlying organ fibrosis is predominantly derived from animal studies. However, relevance of animal models for human disease is limited; therefore, an ex vivo model of human precision-cut tissue slices (PCTS) might become an indispensable tool in fibrosis research and drug development by bridging the animal-human translational gap. This study, presented as two parts, provides comprehensive characterization of the dynamic transcriptional changes in PCTS during culture by RNA sequencing. Part I investigates the differences in culture-induced responses in murine and human PCTS derived from healthy liver, kidney and gut. Part II delineates the molecular processes in cultured human PCTS generated from diseased liver, kidney and ileum. We demonstrated that culture was associated with extensive transcriptional changes and impacted PCTS in a universal way across the organs and two species by triggering an inflammatory response and fibrosis-related extracellular matrix (ECM) remodelling. All PCTS shared mRNA upregulation of IL-11 and ECM-degrading enzymes MMP3 and MMP10. Slice preparation and culturing activated numerous pathways across all PCTS, especially those involved in inflammation (IL-6, IL-8 and HMGB1 signalling) and tissue remodelling (osteoarthritis pathway and integrin signalling). Despite the converging effects of culture, PCTS display species-, organ- and pathology-specific differences in the regulation of genes and canonical pathways. The underlying pathology in human diseased PCTS endures and influences biological processes like cytokine release. Our study reinforces the use of PCTS as an ex vivo fibrosis model and supports future studies towards its validation as a preclinical tool for drug development.
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Affiliation(s)
- Emilia Bigaeva
- Department of Pharmaceutical Technology and Biopharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen, 9713AV, The Netherlands
| | - Emilia Gore
- Department of Pharmaceutical Technology and Biopharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen, 9713AV, The Netherlands
| | - Eric Simon
- Computational Biology, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88397, Biberach an der Riss, Germany
| | - Matthias Zwick
- Computational Biology, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88397, Biberach an der Riss, Germany
| | - Anouk Oldenburger
- Cardiometabolic Disease Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88397, Biberach an der Riss, Germany
| | - Koert P de Jong
- Department of Hepato-Pancreato-Biliary Surgery and Liver Transplantation, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Hendrik S Hofker
- Department of Surgery, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Marco Schlepütz
- Respiratory Diseases, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88397, Biberach an der Riss, Germany
| | - Paul Nicklin
- Research Beyond Borders, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88397, Biberach an der Riss, Germany
| | - Miriam Boersema
- Department of Pharmaceutical Technology and Biopharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen, 9713AV, The Netherlands
| | - Jörg F Rippmann
- Cardiometabolic Disease Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88397, Biberach an der Riss, Germany
| | - Peter Olinga
- Department of Pharmaceutical Technology and Biopharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen, 9713AV, The Netherlands.
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10
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Bigaeva E, Gore E, Mutsaers HAM, Oosterhuis D, Kim YO, Schuppan D, Bank RA, Boersema M, Olinga P. Exploring organ-specific features of fibrogenesis using murine precision-cut tissue slices. Biochim Biophys Acta Mol Basis Dis 2019; 1866:165582. [PMID: 31676376 DOI: 10.1016/j.bbadis.2019.165582] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 10/06/2019] [Accepted: 10/16/2019] [Indexed: 12/14/2022]
Abstract
Fibrosis is the hallmark of pathologic tissue remodelling in most chronic diseases. Despite advances in our understanding of the mechanisms of fibrosis, it remains uncured. Fibrogenic processes share conserved core cellular and molecular pathways across organs. In this study, we aimed to elucidate shared and organ-specific features of fibrosis using murine precision-cut tissue slices (PCTS) prepared from small intestine, liver and kidneys. PCTS displayed substantial differences in their baseline gene expression profiles: 70% of the extracellular matrix (ECM)-related genes were differentially expressed across the organs. Culture for 48 h induced significant changes in ECM regulation and triggered the onset of fibrogenesis in all PCTS in organ-specific manner. TGFβ signalling was activated during 48 h culture in all PCTS. However, the degree of its involvement varied: both canonical and non-canonical TGFβ pathways were activated in liver and kidney slices, while only canonical, Smad-dependent, cascade was involved in intestinal slices. The treatment with galunisertib blocked the TGFβRI/SMAD2 signalling in all PCTS, but attenuated culture-induced dysregulation of ECM homeostasis and mitigated the onset of fibrogenesis with organ-specificity. In conclusion, regardless the many common features in pathophysiology of organ fibrosis, PCTS displayed diversity in culture-induced responses and in response to the treatment with TGFβRI kinase inhibitor galunisertib, even though it targets a core fibrosis pathway. A clear understanding of the common and organ-specific features of fibrosis is the basis for developing novel antifibrotic therapies.
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Affiliation(s)
- Emilia Bigaeva
- Department of Pharmaceutical Technology and Biopharmacy, University of Groningen, the Netherlands
| | - Emilia Gore
- Department of Pharmaceutical Technology and Biopharmacy, University of Groningen, the Netherlands
| | - Henricus A M Mutsaers
- Department of Pharmaceutical Technology and Biopharmacy, University of Groningen, the Netherlands; Department of Clinical Medicine, Aarhus University, Denmark
| | - Dorenda Oosterhuis
- Department of Pharmaceutical Technology and Biopharmacy, University of Groningen, the Netherlands
| | - Yong Ook Kim
- Institute of Translational Immunology and Research Center for Immunotherapy, University Medical Center, Johannes Gutenberg University, Obere Zahlbacherstraße 63, Mainz 55131, Germany
| | - Detlef Schuppan
- Institute of Translational Immunology and Research Center for Immunotherapy, University Medical Center, Johannes Gutenberg University, Obere Zahlbacherstraße 63, Mainz 55131, Germany; Division of Gastroenterology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, 330 Brookline Avenue, MA 02215, USA
| | - Ruud A Bank
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, the Netherlands
| | - Miriam Boersema
- Department of Pharmaceutical Technology and Biopharmacy, University of Groningen, the Netherlands
| | - Peter Olinga
- Department of Pharmaceutical Technology and Biopharmacy, University of Groningen, the Netherlands.
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