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Hellen DJ, Fay ME, Lee DH, Klindt-Morgan C, Bennett A, Pachura KJ, Grakoui A, Huppert SS, Dawson PA, Lam WA, Karpen SJ. BiliQML: a supervised machine-learning model to quantify biliary forms from digitized whole slide liver histopathological images. Am J Physiol Gastrointest Liver Physiol 2024; 327:G1-G15. [PMID: 38651949 DOI: 10.1152/ajpgi.00058.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/03/2024] [Accepted: 04/09/2024] [Indexed: 04/25/2024]
Abstract
The progress of research focused on cholangiocytes and the biliary tree during development and following injury is hindered by limited available quantitative methodologies. Current techniques include two-dimensional standard histological cell-counting approaches, which are rapidly performed, error prone, and lack architectural context or three-dimensional analysis of the biliary tree in opacified livers, which introduce technical issues along with minimal quantitation. The present study aims to fill these quantitative gaps with a supervised machine-learning model (BiliQML) able to quantify biliary forms in the liver of anti-keratin 19 antibody-stained whole slide images. Training utilized 5,019 researcher-labeled biliary forms, which following feature selection, and algorithm optimization, generated an F score of 0.87. Application of BiliQML on seven separate cholangiopathy models [genetic (Afp-CRE;Pkd1l1null/Fl, Alb-CRE;Rbp-jkfl/fl, and Albumin-CRE;ROSANICD), surgical (bile duct ligation), toxicological (3,5-diethoxycarbonyl-1,4-dihydrocollidine), and therapeutic (Cyp2c70-/- with ileal bile acid transporter inhibition)] allowed for a means to validate the capabilities and utility of this platform. The results from BiliQML quantification revealed biological and pathological differences across these seven diverse models, indicating a highly sensitive, robust, and scalable methodology for the quantification of distinct biliary forms. BiliQML is the first comprehensive machine-learning platform for biliary form analysis, adding much-needed morphologic context to standard immunofluorescence-based histology, and provides clinical and basic science researchers with a novel tool for the characterization of cholangiopathies.NEW & NOTEWORTHY BiliQML is the first comprehensive machine-learning platform for biliary form analysis in whole slide histopathological images. This platform provides clinical and basic science researchers with a novel tool for the improved quantification and characterization of biliary tract disorders.
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Affiliation(s)
- Dominick J Hellen
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, Georgia, United States
| | - Meredith E Fay
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, United States
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, Aflac Cancer Center and Blood Disorders Service of Children's Healthcare of Atlanta, Emory University School of Medicine, Atlanta, Georgia, United States
| | - David H Lee
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, Georgia, United States
| | - Caroline Klindt-Morgan
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, Georgia, United States
| | - Ashley Bennett
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, Georgia, United States
| | - Kimberly J Pachura
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, Georgia, United States
| | - Arash Grakoui
- Emory National Primate Research Center, Division of Microbiology and Immunology, Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia, United States
| | - Stacey S Huppert
- Division of Gastroenterology, Hepatology, and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States
| | - Paul A Dawson
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, Georgia, United States
| | - Wilbur A Lam
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, United States
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, Aflac Cancer Center and Blood Disorders Service of Children's Healthcare of Atlanta, Emory University School of Medicine, Atlanta, Georgia, United States
| | - Saul J Karpen
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, Georgia, United States
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Ling YC, Hsu CT, Chen CY, Tai CS, Chang KC, Wu JF. Performance of Baveno VII criteria for the screening of varices needing treatment in patients with biliary atresia. J Pediatr Gastroenterol Nutr 2024. [PMID: 38828708 DOI: 10.1002/jpn3.12278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/05/2024] [Accepted: 05/25/2024] [Indexed: 06/05/2024]
Abstract
OBJECTIVE Biliary atresia (BA) is the leading cause of liver cirrhosis and chronic liver insufficiency in children in the world. Gastroesophageal varices bleeding is an ominous complication of cirrhosis in BA patients and is associated with high morbidity and mortality. In this study, we aimed to investigate the utility of noninvasive Baveno VI and Baveno VII criteria for the screening of varices need treatment (VNT) and the need for liver transplantation in BA patients. METHODS This study enrolled 48 BA patients (23 females and 25 males) who underwent an esophagogastroduodenoscopy (EGD) and transient elastography at a mean age of 11.18 ± 1.48 years; the clinical data were surveyed in a retrospective design. RESULTS The sensitivity and negative predictive value of Baveno VI and Baveno VII criteria for the prediction of VNT in BA patients are both 100% and 100%, respectively. The VNT missing rate of Baveno VI and Baveno VII criteria are both 0% in our cohort. The Baveno VI, expanded Baveno VI, and Baveno VII criteria are also predictive of the need for liver transplantation in our cohort (OR = 10.33, 4.24, and 21.33; p = 0.009, 0.03, and 0.007, respectively). CONCLUSION The Baveno VI and Baveno VII criteria are useful for the screening of VNT and minimize non-necessary invasive EGD in BA patients with low VNT missing rates. The Baveno VI, expanded Baveno VI, and Baveno VII criteria are associated with the need for liver transplantation.
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Affiliation(s)
- Yu-Chieh Ling
- Departments of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan
- Departments of Pediatrics, New Taipei City Hospital, New Taipei City, Taiwan
| | - Chien-Ting Hsu
- Department of Pediatrics, National Taiwan University BioMedical Park Hospital, Taipei, Taiwan
| | - Cheng-Yu Chen
- Department of Pediatrics, National Taiwan University Hospital Hsin-chu Branch, Taipei, Taiwan
| | - Chi-San Tai
- Departments of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan
| | - Kai-Chi Chang
- Departments of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan
| | - Jia-Feng Wu
- Departments of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan
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Lim YZ, Zhu M, Wang Y, Sharma T, Kelley S, Oertling E, Zhu H, Corbitt N. Pkd1l1-deficiency drives biliary atresia through ciliary dysfunction in biliary epithelial cells. J Hepatol 2024:S0168-8278(24)00151-X. [PMID: 38460793 DOI: 10.1016/j.jhep.2024.02.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 02/07/2024] [Accepted: 02/29/2024] [Indexed: 03/11/2024]
Abstract
BACKGROUND & AIMS Syndromic biliary atresia is a cholangiopathy characterized by fibro-obliterative changes in the extrahepatic bile duct (EHBD) and congenital malformations including laterality defects. The etiology remains elusive and faithful animal models are lacking. Genetic syndromes provide important clues regarding the pathogenic mechanisms underlying the disease. We investigated the role of the gene Pkd1l1 in the pathophysiology of syndromic biliary atresia. METHODS Constitutive and conditional Pkd1l1 knockout mice were generated to explore genetic pathology as a cause of syndromic biliary atresia. We investigated congenital malformations, EHBD and liver pathology, EHBD gene expression, and biliary epithelial cell turnover. Biliary drainage was functionally assessed with cholangiography. Histology and serum chemistries were assessed after DDC (3,5-diethoxycarbony l-1,4-dihydrocollidine) diet treatment and inhibition of the ciliary signaling effector GLI1. RESULTS Pkd1l1-deficient mice exhibited congenital anomalies including malrotation and heterotaxy. Pkd1l1-deficient EHBDs were hypertrophic and fibrotic. Pkd1l1-deficient EHBDs were patent but displayed delayed biliary drainage. Pkd1l1-deficient livers exhibited ductular reaction and periportal fibrosis. After DDC treatment, Pkd1l1-deficient mice exhibited EHBD obstruction and advanced liver fibrosis. Pkd1l1-deficient mice had increased expression of fibrosis and extracellular matrix remodeling genes (Tgfα, Cdkn1a, Hb-egf, Fgfr3, Pdgfc, Mmp12, and Mmp15) and decreased expression of genes mediating ciliary signaling (Gli1, Gli2, Ptch1, and Ptch2). Primary cilia were reduced on biliary epithelial cells and altered expression of ciliogenesis genes occurred in Pkd1l1-deficient mice. Small molecule inhibition of the ciliary signaling effector GLI1 with Gant61 recapitulated Pkd1l1-deficiency. CONCLUSIONS Pkd1l1 loss causes both laterality defects and fibro-proliferative EHBD transformation through disrupted ciliary signaling, phenocopying syndromic biliary atresia. Pkd1l1-deficient mice function as an authentic genetic model for study of the pathogenesis of biliary atresia. IMPACT AND IMPLICATIONS The syndromic form of biliary atresia is characterized by fibro-obliteration of extrahepatic bile ducts and is often accompanied by laterality defects. The etiology is unknown, but Pkd1l1 was identified as a potential genetic candidate for syndromic biliary atresia. We found that loss of the ciliary gene Pkd1l1 contributes to hepatobiliary pathology in biliary atresia, exhibited by bile duct hypertrophy, reduced biliary drainage, and liver fibrosis in Pkd1l1-deficient mice. Pkd1l1-deficient mice serve as a genetic model of biliary atresia and reveal ciliopathy as an etiology of biliary atresia. This model will help scientists uncover new therapeutic approaches for patients with biliary atresia, while pediatric hepatologists should validate the diagnostic utility of PKD1L1 variants.
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Affiliation(s)
- Yi Zou Lim
- Children's Research Institute, Department of Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA
| | - Min Zhu
- Children's Research Institute, Departments of Pediatrics and Internal Medicine, Simmons Comprehensive Cancer Center, Center for Regenerative Science and Medicine, Children's Research Institute Mouse Genome Engineering Core, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yunguan Wang
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229, USA
| | - Tripti Sharma
- Children's Research Institute, Departments of Pediatrics and Internal Medicine, Simmons Comprehensive Cancer Center, Center for Regenerative Science and Medicine, Children's Research Institute Mouse Genome Engineering Core, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shannon Kelley
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Estelle Oertling
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hao Zhu
- Children's Research Institute, Departments of Pediatrics and Internal Medicine, Simmons Comprehensive Cancer Center, Center for Regenerative Science and Medicine, Children's Research Institute Mouse Genome Engineering Core, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Natasha Corbitt
- Children's Research Institute, Department of Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA.
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4
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Trampert DC, Beuers U. A beneficial response of fetal wound healing gone bad in the bile duct: The overarching cause of biliary atresia? J Hepatol 2024; 80:387-389. [PMID: 38181824 DOI: 10.1016/j.jhep.2023.12.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 01/07/2024]
Affiliation(s)
- David C Trampert
- Department of Gastroenterology and Hepatology, Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism (AGEM), Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Ulrich Beuers
- Department of Gastroenterology and Hepatology, Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism (AGEM), Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, the Netherlands.
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Sutton H, Karpen SJ, Kamath BM. Pediatric Cholestatic Diseases: Common and Unique Pathogenic Mechanisms. ANNUAL REVIEW OF PATHOLOGY 2024; 19:319-344. [PMID: 38265882 DOI: 10.1146/annurev-pathmechdis-031521-025623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
Cholestasis is the predominate feature of many pediatric hepatobiliary diseases. The physiologic flow of bile requires multiple complex processes working in concert. Bile acid (BA) synthesis and excretion, the formation and flow of bile, and the enterohepatic reuptake of BAs all function to maintain the circulation of BAs, a key molecule in lipid digestion, metabolic and cellular signaling, and, as discussed in the review, a crucial mediator in the pathogenesis of cholestasis. Disruption of one or several of these steps can result in the accumulation of toxic BAs in bile ducts and hepatocytes leading to inflammation, fibrosis, and, over time, biliary and hepatic cirrhosis. Biliary atresia, progressive familial intrahepatic cholestasis, primary sclerosing cholangitis, and Alagille syndrome are four of the most common pediatric cholestatic conditions. Through understanding the commonalities and differences in these diseases, the important cellular mechanistic underpinnings of cholestasis can be greater appreciated.
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Affiliation(s)
- Harry Sutton
- The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada;
| | - Saul J Karpen
- Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Binita M Kamath
- The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada;
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Hong R, Tian X, Ma H, Ni H, Yang J, Bu W, Li T, Yang S, Li D, Liu M, Tan Y. Primary cilium-mediated signaling cascade suppresses age-related biliary fibrosis. J Cell Physiol 2023; 238:2600-2611. [PMID: 37683035 DOI: 10.1002/jcp.31113] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/19/2023] [Accepted: 08/17/2023] [Indexed: 09/10/2023]
Abstract
The primary cilium is increasingly recognized as a crucial player in the physiology of biliary epithelial cells (BECs). However, the precise role of primary cilia in the development of age-related biliary fibrosis remains unclear. Herein, using cilium-deficient mice, we demonstrate that disruption of ciliary homeostasis in BECs in aged mice leads to significant bile duct proliferation, augmented biliary fibrosis, and heightened indicators of liver injury. Our RNA-sequencing data revealed a dysregulation in genes associated with various biological processes such as bile secretion, fatty acid metabolism, and inflammation. Loss of primary cilia also significantly enhanced signaling pathways driving the development of biliary fibrosis. Our findings collectively suggest that loss of primary cilia in the BECs of aged mice initiates a cascade of signaling events that contribute to biliary fibrosis, highlighting the primary cilium as a potential therapeutic target in the treatment of fibrosing cholangiopathies.
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Affiliation(s)
- Renjie Hong
- State Key Laboratory of Medicinal Chemical Biology, Haihe Laboratory of Cell Ecosystem, College of Life Sciences, Nankai University, Tianjin, China
| | - Xiaoyu Tian
- Center for Cell Structure and Function, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Hongbo Ma
- State Key Laboratory of Medicinal Chemical Biology, Haihe Laboratory of Cell Ecosystem, College of Life Sciences, Nankai University, Tianjin, China
| | - Hua Ni
- State Key Laboratory of Medicinal Chemical Biology, Haihe Laboratory of Cell Ecosystem, College of Life Sciences, Nankai University, Tianjin, China
| | - Jia Yang
- State Key Laboratory of Medicinal Chemical Biology, Haihe Laboratory of Cell Ecosystem, College of Life Sciences, Nankai University, Tianjin, China
| | - Weiwen Bu
- State Key Laboratory of Medicinal Chemical Biology, Haihe Laboratory of Cell Ecosystem, College of Life Sciences, Nankai University, Tianjin, China
| | - Te Li
- State Key Laboratory of Medicinal Chemical Biology, Haihe Laboratory of Cell Ecosystem, College of Life Sciences, Nankai University, Tianjin, China
| | - Song Yang
- State Key Laboratory of Medicinal Chemical Biology, Haihe Laboratory of Cell Ecosystem, College of Life Sciences, Nankai University, Tianjin, China
| | - Dengwen Li
- State Key Laboratory of Medicinal Chemical Biology, Haihe Laboratory of Cell Ecosystem, College of Life Sciences, Nankai University, Tianjin, China
| | - Min Liu
- Laboratory of Tissue Homeostasis, Haihe Laboratory of Cell Ecosystem, Tianjin, China
| | - Yanjie Tan
- Center for Cell Structure and Function, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, China
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7
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Ali RQ, Meyer-Miner A, David-Rachel M, Lee FJH, Wilkins BJ, Karpen SJ, Ciruna B, Ghanekar A, Kamath BM. Loss of zebrafish pkd1l1 causes biliary defects that have implications for biliary atresia splenic malformation. Dis Model Mech 2023; 16:dmm049326. [PMID: 37675454 PMCID: PMC10581383 DOI: 10.1242/dmm.049326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 08/15/2023] [Indexed: 09/08/2023] Open
Abstract
Biliary atresia is a fibroinflammatory neonatal disease with no effective therapies. A subset of cases (10-20%) is associated with laterality defects - labeled biliary atresia splenic malformation (BASM) syndrome. Recently, whole-exome sequencing of patients with BASM identified deleterious variants in PKD1L1. PKD1L1 is involved in left-right axis determination; however, its role in cholangiocytes is unknown. We generated the pkd1l1hsc117 allele using CRISPR/Cas9 mutagenesis in zebrafish to determine the role of Pkd1l1 in biliary development and function. Wild-type and mutant larvae were assessed for laterality defects, biliary function and biliary tree architecture at 5 days post fertilization. pkd1l1hsc117 mutant larvae exhibited early left-right patterning defects. The gallbladder was positioned on the left in 47% of mutants compared to 4% of wild-type larvae. Accumulation of PED6 in the gallbladder, an indicator of hepatobiliary function, was significantly reduced in pkd1l1hsc117 mutants (46%) compared to wild-type larvae (4%). pkd1l1hsc117 larvae exhibited fewer biliary epithelial cells and reduced density of the intrahepatic biliary network compared to those in wild-type larvae. These data highlight the essential role of pkd1l1 in normal development and function of the zebrafish biliary system, supporting a role for this gene as a cause of BASM.
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Affiliation(s)
- Rouknuddin Q. Ali
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Anne Meyer-Miner
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Molecular Genetics, The University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Marie David-Rachel
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Molecular Genetics, The University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Fiona J. H. Lee
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Benjamin J. Wilkins
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Saul J. Karpen
- Department of Pediatrics Emory, University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Brian Ciruna
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Molecular Genetics, The University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Anand Ghanekar
- Division of General Surgery, University Health Network, Toronto, ON M5C 2C4, Canada
- Department of Surgery, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Department of Surgery, University of Toronto, Toronto, ON M5T 1P5, Canada
| | - Binita M. Kamath
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Division of Gastroenterology, Hepatology and Nutrition, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Department of Pediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada
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8
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Hellen DJ, Karpen SJ. LiverQuant: An Improved Method for Quantitative Analysis of Liver Pathology. Bio Protoc 2023; 13:e4776. [PMID: 37497459 PMCID: PMC10367012 DOI: 10.21769/bioprotoc.4776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/01/2023] [Accepted: 06/06/2023] [Indexed: 07/28/2023] Open
Abstract
Current means to quantify cells, gene expression, and fibrosis of liver histological slides are not standardized in the research community and typically rely upon data acquired from a selection of random regions identified in each slide. As such, analyses are subject to selection bias as well as limited subsets of available data elements throughout the slide. A whole-slide analysis of cells and fibrosis would provide for a more accurate and complete quantitative analysis, along with minimization of intra- and inter-experimental variables. Herein, we present LiverQuant, a method for quantifying whole-slide scans of digitized histologic images to render a more comprehensive analysis of presented data elements. After loading images and preparing the project in the QuPath program, researchers are provided with one to two scripts per analysis that generate an average intensity threshold for their staining, automated tissue annotation, and downstream detection of their anticipated cellular matrices. When compared with two standard methodologies for histological quantification, LiverQuant had two significant advantages: increased speed and a 50-fold greater tissue area coverage. Using publicly available open-source code (GitHub), LiverQuant improves the reliability and reproducibility of experimental results while reducing the time scientists require to perform bulk analysis of liver histology. This analytical process is readily adaptable by most laboratories, requires minimal optimization, and its principles and code can be optimized for use in other organs. Graphical overview.
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Affiliation(s)
- Dominick J. Hellen
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, USA
| | - Saul J. Karpen
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, USA
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9
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Otumala AE, Hellen DJ, Luna CA, Delgado P, Dissanayaka A, Ugwumadu C, Oshinowo O, Islam MM, Shen L, Karpen SJ, Myers DR. Opportunities and considerations for studying liver disease with microphysiological systems on a chip. LAB ON A CHIP 2023; 23:2877-2898. [PMID: 37282629 DOI: 10.1039/d2lc00940d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Advances in microsystem engineering have enabled the development of highly controlled models of the liver that better recapitulate the unique in vivo biological conditions. In just a few short years, substantial progress has been made in creating complex mono- and multi-cellular models that mimic key metabolic, structural, and oxygen gradients crucial for liver function. Here we review: 1) the state-of-the-art in liver-centric microphysiological systems and 2) the array of liver diseases and pressing biological and therapeutic challenges which could be investigated with these systems. The engineering community has unique opportunities to innovate with new liver-on-a-chip devices and partner with biomedical researchers to usher in a new era of understanding of the molecular and cellular contributors to liver diseases and identify and test rational therapeutic modalities.
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Affiliation(s)
- Adiya E Otumala
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology & Emory University, 1760 Haygood Dr, Suite E-160, Rm E-156, Atlanta, GA, 30332, USA.
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, Aflac Cancer Center and Blood Disorders Service of Children's Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Dominick J Hellen
- Department of Pediatrics, Division of Pediatric Gastroenterology, Hepatology and Nutrition, Emory University School of Medicine, Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - C Alessandra Luna
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology & Emory University, 1760 Haygood Dr, Suite E-160, Rm E-156, Atlanta, GA, 30332, USA.
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, Aflac Cancer Center and Blood Disorders Service of Children's Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Priscilla Delgado
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology & Emory University, 1760 Haygood Dr, Suite E-160, Rm E-156, Atlanta, GA, 30332, USA.
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, Aflac Cancer Center and Blood Disorders Service of Children's Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Anjana Dissanayaka
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology & Emory University, 1760 Haygood Dr, Suite E-160, Rm E-156, Atlanta, GA, 30332, USA.
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, Aflac Cancer Center and Blood Disorders Service of Children's Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Chidozie Ugwumadu
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology & Emory University, 1760 Haygood Dr, Suite E-160, Rm E-156, Atlanta, GA, 30332, USA.
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, Aflac Cancer Center and Blood Disorders Service of Children's Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Oluwamayokun Oshinowo
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology & Emory University, 1760 Haygood Dr, Suite E-160, Rm E-156, Atlanta, GA, 30332, USA.
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, Aflac Cancer Center and Blood Disorders Service of Children's Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Md Mydul Islam
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology & Emory University, 1760 Haygood Dr, Suite E-160, Rm E-156, Atlanta, GA, 30332, USA.
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, Aflac Cancer Center and Blood Disorders Service of Children's Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Luyao Shen
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology & Emory University, 1760 Haygood Dr, Suite E-160, Rm E-156, Atlanta, GA, 30332, USA.
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, Aflac Cancer Center and Blood Disorders Service of Children's Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Saul J Karpen
- Department of Pediatrics, Division of Pediatric Gastroenterology, Hepatology and Nutrition, Emory University School of Medicine, Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - David R Myers
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology & Emory University, 1760 Haygood Dr, Suite E-160, Rm E-156, Atlanta, GA, 30332, USA.
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, Aflac Cancer Center and Blood Disorders Service of Children's Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA 30322, USA
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Li TF, Ke XY, Zhang YR, Zhan JH. The correlation between rs2501577 gene polymorphism and biliary atresia: a systematic review and meta-analysis. Pediatr Surg Int 2023; 39:206. [PMID: 37248361 DOI: 10.1007/s00383-023-05491-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/23/2023] [Indexed: 05/31/2023]
Abstract
IMPORTANCE Multiple studies indicate a possible correlation between ADD3 rs2501577 and biliary atresia susceptibility; however, a conclusive determination has yet to be made. OBJECTIVE Investigate the role of ADD3 rs2501577 in biliary atresia susceptibility across diverse populations. DATA SOURCES The study protocol has been registered on PROSPERO, an international platform for systematic review registration (PROSPERO ID: CRD42023384641). The following databases will be searched until February 1, 2023: PubMed, Embase, Cochrane, CBM, Web of Science, and CNKI. STUDY SELECTION Eight studies were selected from seven papers to assess the data. A total of 7651 participants were included, consisting of 1662 in the BA group and 5989 in the NC group. DATA EXTRACTION AND SYNTHESIS Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines were followed while conducting the systematic reviews and meta-analyses. Two authors independently assessed the quality of the included studies using the Newcastle-Ottawa Quality Assessment Scale. The significance of the pooled odds ratio (OR) was evaluated with a Z test, and statistical heterogeneity across studies was assessed using the I2 and Q statistics. Publication bias was assessed using Egger's and Begg's tests. MAIN OUTCOME(S) AND MEASURE(S) The primary study outcome was the development of biliary atresia. Subgroup analysis was performed based on race, region, and assessment of Hardy-Weinberg equilibrium (HWE). RESULTS The studies indicate that the ADD3 rs2501577 susceptibility locus increases the risk of developing biliary atresia, regardless of allelic, homozygote, dominant, and recessive gene inheritance models. Furthermore, ADD3 has been found to be associated with apoptosis, cell cycle, and cell damage repair based on functional analysis. CONCLUSIONS AND RELEVANCE The ADD3 rs2501577 polymorphic locus is associated with an increased risk of biliary atresia, particularly in Asian populations. This study recommends further investigation of the ADD3 rs2501577 locus in Asian populations to validate its role in the diagnosis of biliary atresia.
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Affiliation(s)
- Teng-Fei Li
- Graduate School, Tianjin Medical University, Tianjin, 300070, China
- Department of General Surgery, Tianjin Children's Hospital, Tianjin, 300134, China
| | - Xing-Yuan Ke
- School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Yan-Ran Zhang
- School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Jiang-Hua Zhan
- Department of General Surgery, Tianjin Children's Hospital, Tianjin, 300134, China.
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