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Wen Z, Lin YH, Wang S, Fujiwara N, Rong R, Jin KW, Yang DM, Yao B, Yang S, Wang T, Xie Y, Hoshida Y, Zhu H, Xiao G. Deep-Learning-Based Hepatic Ploidy Quantification Using H&E Histopathology Images. Genes (Basel) 2023; 14:921. [PMID: 37107679 PMCID: PMC10137944 DOI: 10.3390/genes14040921] [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: 03/01/2023] [Revised: 03/28/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
Polyploidy, the duplication of the entire genome within a single cell, is a significant characteristic of cells in many tissues, including the liver. The quantification of hepatic ploidy typically relies on flow cytometry and immunofluorescence (IF) imaging, which are not widely available in clinical settings due to high financial and time costs. To improve accessibility for clinical samples, we developed a computational algorithm to quantify hepatic ploidy using hematoxylin-eosin (H&E) histopathology images, which are commonly obtained during routine clinical practice. Our algorithm uses a deep learning model to first segment and classify different types of cell nuclei in H&E images. It then determines cellular ploidy based on the relative distance between identified hepatocyte nuclei and determines nuclear ploidy using a fitted Gaussian mixture model. The algorithm can establish the total number of hepatocytes and their detailed ploidy information in a region of interest (ROI) on H&E images. This is the first successful attempt to automate ploidy analysis on H&E images. Our algorithm is expected to serve as an important tool for studying the role of polyploidy in human liver disease.
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Affiliation(s)
- Zhuoyu Wen
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yu-Hsuan Lin
- Children’s Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shidan Wang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Naoto Fujiwara
- Division of Digestive and Liver Diseases, Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ruichen Rong
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kevin W. Jin
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Donghan M. Yang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Bo Yao
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shengjie Yang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tao Wang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Center for the Genetics of Host Defense, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yang Xie
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Medicine, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Bioinformatics, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yujin Hoshida
- Division of Digestive and Liver Diseases, Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hao Zhu
- Children’s Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Children’s Research Institute Mouse Genome Engineering Core, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Guanghua Xiao
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Medicine, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Bioinformatics, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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Kulka M, Wagner A, Cho JY, Alam SB, Santos JR, Jovel J, Karamchand L, Marcet-Palacios M. Agarose/crystalline nanocellulose (CNC) composites promote bone marrow-derived mast cell integrity, degranulation and receptor expression but inhibit production of de novo synthesized mediators. Front Bioeng Biotechnol 2023; 11:1160460. [PMID: 37113661 PMCID: PMC10126518 DOI: 10.3389/fbioe.2023.1160460] [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: 02/07/2023] [Accepted: 03/22/2023] [Indexed: 04/29/2023] Open
Abstract
Introduction: Mast cells are highly granulated tissue-resident leukocytes that require a three-dimensional matrix to differentiate and mediate immune responses. However, almost all cultured mast cells rely on two-dimensional suspension or adherent cell culture systems, which do not adequately reflect the complex structure that these cells require for optimal function. Methods: Crystalline nanocellulose (CNC), consisting of rod-like crystals 4-15 nm in diameter and 0.2-1 µm in length, were dispersed in an agarose matrix (12.5% w/v), and bone marrow derived mouse mast cells (BMMC) were cultured on the agarose/CNC composite. BMMC were activated with the calcium ionophore A23187 or immunoglobulin E (IgE) and antigen (Ag) to crosslink high affinity IgE receptors (FcεRI). Results: BMMC cultured on a CNC/agarose matrix remained viable and metabolically active as measured by reduction of sodium 3'-[1-[(phenylamino)-carbony]-3,4-tetrazolium]-bis(4-methoxy-6-nitro) benzene-sulfonic acid hydrate (XTT), and the cells maintained their membrane integrity as analyzed by measuring the release of lactate dehydrogenase (LDH) and propidium iodide exclusion by flow cytometry. Culture on CNC/agarose matrix had no effect on BMMC degranulation in response to IgE/Ag or A23187. However, culture of BMMC on a CNC/agarose matrix inhibited A23187-and IgE/Ag-activated production of tumor necrosis factor (TNF) and other mediators such as IL-1β, IL-4, IL-6, IL-13, MCP-1/CCL2, MMP-9 and RANTES by as much as 95%. RNAseq analysis indicated that BMMC expressed a unique and balanced transcriptome when cultured on CNC/agarose. Discussion: These data demonstrate that culture of BMMCs on a CNC/agarose matrix promotes cell integrity, maintains expression of surface biomarkers such as FcεRI and KIT and preserves the ability of BMMC to release pre-stored mediators in response to IgE/Ag and A23187. However, culture of BMMC on CNC/agarose matrix inhibits BMMC production of de novo synthesized mediators, suggesting that CNC may be altering specific phenotypic characteristics of these cells that are associated with late phase inflammatory responses.
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Affiliation(s)
- Marianna Kulka
- Nanotechnology Research Centre, National Research Council Canada, Edmonton, AB, Canada
- Department of Medical Microbiology and Immunology 6-020 Katz Group Centre, University of Alberta, Edmonton, AB, Canada
- *Correspondence: Marianna Kulka,
| | - Ashley Wagner
- Nanotechnology Research Centre, National Research Council Canada, Edmonton, AB, Canada
| | - Jae-Young Cho
- Nanotechnology Research Centre, National Research Council Canada, Edmonton, AB, Canada
| | - Syed Benazir Alam
- Nanotechnology Research Centre, National Research Council Canada, Edmonton, AB, Canada
| | | | - Juan Jovel
- The Metabolomics Innovation Centre (TMIC), 7-12 Heritage Medical Research Centre, University of Alberta, Edmonton, AB, Canada
| | - Leshern Karamchand
- Nanotechnology Research Centre, National Research Council Canada, Edmonton, AB, Canada
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