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Pham HN, Pham L, Sato K. Deconvolution analysis identified altered hepatic cell landscape in primary sclerosing cholangitis and primary biliary cholangitis. Front Med (Lausanne) 2024; 11:1327973. [PMID: 38818402 PMCID: PMC11138208 DOI: 10.3389/fmed.2024.1327973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 04/29/2024] [Indexed: 06/01/2024] Open
Abstract
Introduction Primary sclerosing cholangitis (PSC) and primary biliary cholangitis (PBC) are characterized by ductular reaction, hepatic inflammation, and liver fibrosis. Hepatic cells are heterogeneous, and functional roles of different hepatic cell phenotypes are still not defined in the pathophysiology of cholangiopathies. Cell deconvolution analysis estimates cell fractions of different cell phenotypes in bulk transcriptome data, and CIBERSORTx is a powerful deconvolution method to estimate cell composition in microarray data. CIBERSORTx performs estimation based on the reference file, which is referred to as signature matrix, and allows users to create custom signature matrix to identify specific phenotypes. In the current study, we created two custom signature matrices using two single cell RNA sequencing data of hepatic cells and performed deconvolution for bulk microarray data of liver tissues including PSC and PBC patients. Methods Custom signature matrix files were created using single-cell RNA sequencing data downloaded from GSE185477 and GSE115469. Custom signature matrices were validated for their deconvolution performance using validation data sets. Cell composition of each hepatic cell phenotype in the liver, which was identified in custom signature matrices, was calculated by CIBERSORTx and bulk RNA sequencing data of GSE159676. Deconvolution results were validated by analyzing marker expression for the cell phenotype in GSE159676 data. Results CIBERSORTx and custom signature matrices showed comprehensive performance in estimation of population of various hepatic cell phenotypes. We identified increased population of large cholangiocytes in PSC and PBC livers, which is in agreement with previous studies referred to as ductular reaction, supporting the effectiveness and reliability of deconvolution analysis in this study. Interestingly, we identified decreased population of small cholangiocytes, periportal hepatocytes, and interzonal hepatocytes in PSC and PBC liver tissues compared to healthy livers. Discussion Although further studies are required to elucidate the roles of these hepatic cell phenotypes in cholestatic liver injury, our approach provides important implications that cell functions may differ depending on phenotypes, even in the same cell type during liver injury. Deconvolution analysis using CIBERSORTx could provide a novel approach for studies of specific hepatic cell phenotypes in liver diseases.
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Affiliation(s)
- Hoang Nam Pham
- Department of Life Sciences, University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Linh Pham
- Department of Science and Mathematics, Texas A&M University—Central Texas, Killeen, TX, United States
| | - Keisaku Sato
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
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Wang Z, Xing C, van der Laan LJW, Verstegen MMA, Spee B, Masereeuw R. Cholangiocyte organoids to study drug-induced injury. Stem Cell Res Ther 2024; 15:78. [PMID: 38475870 DOI: 10.1186/s13287-024-03692-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 03/07/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND Drug induced bile duct injury is a frequently observed clinical problem leading to a wide range of pathological features. During the past decades, several agents have been identified with various postulated mechanisms of bile duct damage, however, mostly still poorly understood. METHODS Here, we investigated the mechanisms of chlorpromazine (CPZ) induced bile duct injury using advanced in vitro cholangiocyte cultures. Intrahepatic cholangiocyte organoids (ICOs) were driven into mature cholangiocyte like cells (CLCs), which were exposed to CPZ under cholestatic or non-cholestatic conditions through the addition of a bile acid cocktail. RESULTS CPZ caused loss of monolayer integrity by reducing expression levels of tight junction protein 1 (TJP1), E-cadherin 1 (CDH1) and lysyl oxidase homolog 2 (LOXL2). Loss of zonula occuludens-1 (ZO-1) and E-cadherin was confirmed by immunostaining after exposure to CPZ and rhodamine-123 leakage further confirmed disruption of the cholangiocyte barrier function. Furthermore, oxidative stress seemed to play a major role in the early damage response by CPZ. The drug also decreased expression of three main basolateral bile acid transporters, ABCC3 (ATP binding cassette subfamily C member 3), SLC51A/B (solute carrier family 51 subunit alpha/beta) and multidrug resistance transporter ABCB1 (ATP binding cassette subfamily B member 1), thereby contributing to bile acid accumulation. CPZ did not induce an inflammatory response by itself, but addition of TNFα revealed a synergistic effect. CONCLUSION These results show that ICOs present a model to identify toxic drugs affecting the bile ducts while providing mechanistic insights into hepatotoxicity.
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Affiliation(s)
- Zhenguo Wang
- Division of Pharmacology, Faculty of Sciences, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Chen Xing
- Division of Pharmacology, Faculty of Sciences, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Luc J W van der Laan
- Department of Surgery, Erasmus MC Transplant Institute, University Medical Center, Rotterdam, The Netherlands
| | - Monique M A Verstegen
- Department of Surgery, Erasmus MC Transplant Institute, University Medical Center, Rotterdam, The Netherlands
| | - Bart Spee
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Rosalinde Masereeuw
- Division of Pharmacology, Faculty of Sciences, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands.
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Klabukov I, Tenchurin T, Shepelev A, Baranovskii D, Mamagulashvili V, Dyuzheva T, Krasilnikova O, Balyasin M, Lyundup A, Krasheninnikov M, Sulina Y, Gomzyak V, Krasheninnikov S, Buzin A, Zayratyants G, Yakimova A, Demchenko A, Ivanov S, Shegay P, Kaprin A, Chvalun S. Biomechanical Behaviors and Degradation Properties of Multilayered Polymer Scaffolds: The Phase Space Method for Bile Duct Design and Bioengineering. Biomedicines 2023; 11:biomedicines11030745. [PMID: 36979723 PMCID: PMC10044742 DOI: 10.3390/biomedicines11030745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 03/06/2023] Open
Abstract
This article reports the electrospinning technique for the manufacturing of multilayered scaffolds for bile duct tissue engineering based on an inner layer of polycaprolactone (PCL) and an outer layer either of a copolymer of D,L-lactide and glycolide (PLGA) or a copolymer of L-lactide and ε-caprolactone (PLCL). A study of the degradation properties of separate polymers showed that flat PCL samples exhibited the highest resistance to hydrolysis in comparison with PLGA and PLCL. Irrespective of the liquid-phase nature, no significant mass loss of PCL samples was found in 140 days of incubation. The PLCL- and PLGA-based flat samples were more prone to hydrolysis within the same period of time, which was confirmed by the increased loss of mass and a significant reduction of weight-average molecular mass. The study of the mechanical properties of developed multi-layered tubular scaffolds revealed that their strength in the longitudinal and transverse directions was comparable with the values measured for a decellularized bile duct. The strength of three-layered scaffolds declined significantly because of the active degradation of the outer layer made of PLGA. The strength of scaffolds with the PLCL outer layer deteriorated much less with time, both in the axial (p-value = 0.0016) and radial (p-value = 0.0022) directions. A novel method for assessment of the physiological relevance of synthetic scaffolds was developed and named the phase space approach for assessment of physiological relevance. Two-dimensional phase space (elongation modulus and tensile strength) was used for the assessment and visualization of the physiological relevance of scaffolds for bile duct bioengineering. In conclusion, the design of scaffolds for the creation of physiologically relevant tissue-engineered bile ducts should be based not only on biodegradation properties but also on the biomechanical time-related behavior of various compositions of polymers and copolymers.
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Affiliation(s)
- Ilya Klabukov
- Department of Regenerative Medicine, National Medical Research Radiological Centre of the Ministry of Health of the Russian Federation, 249031 Obninsk, Russia
- Department of Urology and Operative Nephrology, Peoples Friendship University of Russia (RUDN University), 117198 Moscow, Russia
- Obninsk Institute for Nuclear Power Engineering, National Research Nuclear University MEPhI, 115409 Obninsk, Russia
- Correspondence:
| | - Timur Tenchurin
- National Research Centre “Kurchatov Institute”, 1, Akademika Kurchatova pl., 123182 Moscow, Russia
| | - Alexey Shepelev
- National Research Centre “Kurchatov Institute”, 1, Akademika Kurchatova pl., 123182 Moscow, Russia
| | - Denis Baranovskii
- Department of Regenerative Medicine, National Medical Research Radiological Centre of the Ministry of Health of the Russian Federation, 249031 Obninsk, Russia
- Department of Urology and Operative Nephrology, Peoples Friendship University of Russia (RUDN University), 117198 Moscow, Russia
| | - Vissarion Mamagulashvili
- National Research Centre “Kurchatov Institute”, 1, Akademika Kurchatova pl., 123182 Moscow, Russia
| | - Tatiana Dyuzheva
- Department of Hospital Surgery, Sklifosovsky Institute of Clinical Medicine, Sechenov First Moscow State Medical University (Sechenov University), 119435 Moscow, Russia
| | - Olga Krasilnikova
- Department of Regenerative Medicine, National Medical Research Radiological Centre of the Ministry of Health of the Russian Federation, 249031 Obninsk, Russia
| | - Maksim Balyasin
- Research and Educational Resource Center for Cellular Technologies, Peoples Friendship University of Russia (RUDN University), 117198 Moscow, Russia
| | - Alexey Lyundup
- Research and Educational Resource Center for Cellular Technologies, Peoples Friendship University of Russia (RUDN University), 117198 Moscow, Russia
- N.P. Bochkov Research Centre for Medical Genetics, 115478 Moscow, Russia
| | - Mikhail Krasheninnikov
- Research and Educational Resource Center for Cellular Technologies, Peoples Friendship University of Russia (RUDN University), 117198 Moscow, Russia
- Lomonosov Institute of Fine Chemical Technologies, Russian Technological University MIREA, 119454 Moscow, Russia
| | - Yana Sulina
- Department of Obstetrics and Gynecology, Sechenov First Moscow State Medical University (Sechenov University), 119435 Moscow, Russia
| | - Vitaly Gomzyak
- National Research Centre “Kurchatov Institute”, 1, Akademika Kurchatova pl., 123182 Moscow, Russia
| | - Sergey Krasheninnikov
- National Research Centre “Kurchatov Institute”, 1, Akademika Kurchatova pl., 123182 Moscow, Russia
| | - Alexander Buzin
- National Research Centre “Kurchatov Institute”, 1, Akademika Kurchatova pl., 123182 Moscow, Russia
- Laboratory of the Structure of Polymer Materials, Enikolopov Institute of Synthetic Polymer Materials RAS, 117393 Moscow, Russia
| | - Georgiy Zayratyants
- Department of Pathology, Moscow State University of Medicine and Dentistry, Delegatskaya st., 20, p. 1, 127473 Moscow, Russia
| | - Anna Yakimova
- Department of Regenerative Medicine, National Medical Research Radiological Centre of the Ministry of Health of the Russian Federation, 249031 Obninsk, Russia
| | - Anna Demchenko
- N.P. Bochkov Research Centre for Medical Genetics, 115478 Moscow, Russia
| | - Sergey Ivanov
- Department of Regenerative Medicine, National Medical Research Radiological Centre of the Ministry of Health of the Russian Federation, 249031 Obninsk, Russia
| | - Peter Shegay
- Department of Regenerative Medicine, National Medical Research Radiological Centre of the Ministry of Health of the Russian Federation, 249031 Obninsk, Russia
- Department of Urology and Operative Nephrology, Peoples Friendship University of Russia (RUDN University), 117198 Moscow, Russia
| | - Andrey Kaprin
- Department of Regenerative Medicine, National Medical Research Radiological Centre of the Ministry of Health of the Russian Federation, 249031 Obninsk, Russia
- Department of Urology and Operative Nephrology, Peoples Friendship University of Russia (RUDN University), 117198 Moscow, Russia
| | - Sergei Chvalun
- National Research Centre “Kurchatov Institute”, 1, Akademika Kurchatova pl., 123182 Moscow, Russia
- Laboratory of the Structure of Polymer Materials, Enikolopov Institute of Synthetic Polymer Materials RAS, 117393 Moscow, Russia
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Florentino RM, Li Q, Coard MC, Haep N, Motomura T, Diaz-Aragon R, Faccioli LAP, Amirneni S, Kocas-Kilicarslan ZN, Ostrowska A, Squires JE, Feranchak AP, Soto-Gutierrez A. Transmembrane channel activity in human hepatocytes and cholangiocytes derived from induced pluripotent stem cells. Hepatol Commun 2022; 6:1561-1573. [PMID: 35289126 PMCID: PMC9234678 DOI: 10.1002/hep4.1920] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 01/06/2022] [Accepted: 01/22/2022] [Indexed: 11/10/2022] Open
Abstract
The initial creation of human-induced pluripotent stem cells (iPSCs) set the foundation for the future of regenerative medicine. Human iPSCs can be differentiated into a variety of cell types in order to study normal and pathological molecular mechanisms. Currently, there are well-defined protocols for the differentiation, characterization, and establishment of functionality in human iPSC-derived hepatocytes (iHep) and iPSC-derived cholangiocytes (iCho). Electrophysiological study on chloride ion efflux channel activity in iHep and iCho cells has not been previously reported. We generated iHep and iCho cells and characterized them based on hepatocyte-specific and cholangiocyte-specific markers. The relevant transmembrane channels were selected: cystic fibrosis transmembrane conductance regulator, leucine rich repeat-containing 8 subunit A, and transmembrane member 16 subunit A. To measure the activity in these channels, we used whole-cell patch-clamp techniques with a standard intracellular and extracellular solution. Our iHep and iCho cells demonstrated definitive activity in the selected transmembrane channels, and this approach may become an important tool for investigating human liver biology of cholestatic diseases.
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Affiliation(s)
- Rodrigo M Florentino
- Department of PathologyUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA.,Pittsburgh Liver Research CenterUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Qin Li
- Department of PediatricsUniversity of Pittsburgh Medical CenterPittsburghPennsylvaniaUSA
| | - Michael C Coard
- Department of PathologyUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Nils Haep
- Department of PathologyUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Takashi Motomura
- Department of PathologyUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Ricardo Diaz-Aragon
- Department of PathologyUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Lanuza A P Faccioli
- Department of PathologyUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Sriram Amirneni
- Department of PathologyUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | | | - Alina Ostrowska
- Department of PathologyUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA.,Pittsburgh Liver Research CenterUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - James E Squires
- Pittsburgh Liver Research CenterUniversity of PittsburghPittsburghPennsylvaniaUSA.,Division of Gastroenterology, Hepatology, and NutritionUniversity of Pittsburgh Medical CenterPittsburghPennsylvaniaUSA
| | - Andrew P Feranchak
- Pittsburgh Liver Research CenterUniversity of PittsburghPittsburghPennsylvaniaUSA.,Department of PediatricsUniversity of Pittsburgh Medical CenterPittsburghPennsylvaniaUSA
| | - Alejandro Soto-Gutierrez
- Department of PathologyUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA.,Pittsburgh Liver Research CenterUniversity of PittsburghPittsburghPennsylvaniaUSA.,McGowan Institute for Regenerative MedicinePittsburghPennsylvaniaUSA
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Wang Z, Faria J, van der Laan LJW, Penning LC, Masereeuw R, Spee B. Human Cholangiocytes Form a Polarized and Functional Bile Duct on Hollow Fiber Membranes. Front Bioeng Biotechnol 2022; 10:868857. [PMID: 35813994 PMCID: PMC9263983 DOI: 10.3389/fbioe.2022.868857] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/12/2022] [Indexed: 12/12/2022] Open
Abstract
Liver diseases affect hundreds of millions of people worldwide; most often the hepatocytes or cholangiocytes are damaged. Diseases of the biliary tract cause severe patient burden, and cholangiocytes, the cells lining the biliary tract, are sensitive to numerous drugs. Therefore, investigations into proper cholangiocyte functions are of utmost importance, which is restricted, in vitro, by the lack of primary human cholangiocytes allowing such screening. To investigate biliary function, including transepithelial transport, cholangiocytes must be cultured as three-dimensional (3D) ductular structures. We previously established murine intrahepatic cholangiocyte organoid-derived cholangiocyte-like cells (CLCs) and cultured them onto polyethersulfone hollow fiber membranes (HFMs) to generate 3D duct structures that resemble native bile ducts at the structural and functional level. Here, we established an efficient, stepwise method for directed differentiation of human intrahepatic cholangiocyte organoids (ICOs) into CLCs. Human ICO-derived CLCs showed key characteristics of cholangiocytes, such as the expression of structural and functional markers, formation of primary cilia, and P-glycoprotein-mediated transport in a polarized fashion. The organoid cultures exhibit farnesoid X receptor (FXR)-dependent functions that are vital to liver bile acid homeostasis in vivo. Furthermore, human ICO-derived CLCs cultured on HFMs in a differentiation medium form tubular architecture with some tight, confluent, and polarized monolayers that better mimic native bile duct characteristics than differentiated cultures in standard 2D or Matrigel-based 3D culture plates. Together, our optimized differentiation protocol to obtain CLC organoids, when applied on HFMs to form bioengineered bile ducts, will facilitate studying cholangiopathies and allow developing therapeutic strategies.
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Affiliation(s)
- Zhenguo Wang
- Division of Pharmacology, Department of Pharmaceutical Sciences, Faculty of Sciences, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - João Faria
- Division of Pharmacology, Department of Pharmaceutical Sciences, Faculty of Sciences, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands
| | | | - Louis C. Penning
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Rosalinde Masereeuw
- Division of Pharmacology, Department of Pharmaceutical Sciences, Faculty of Sciences, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands
- *Correspondence: Rosalinde Masereeuw, ; Bart Spee,
| | - Bart Spee
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
- *Correspondence: Rosalinde Masereeuw, ; Bart Spee,
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