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Bloise N, Giannaccari M, Guagliano G, Peluso E, Restivo E, Strada S, Volpini C, Petrini P, Visai L. Growing Role of 3D In Vitro Cell Cultures in the Study of Cellular and Molecular Mechanisms: Short Focus on Breast Cancer, Endometriosis, Liver and Infectious Diseases. Cells 2024; 13:1054. [PMID: 38920683 PMCID: PMC11201503 DOI: 10.3390/cells13121054] [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: 04/16/2024] [Revised: 06/10/2024] [Accepted: 06/12/2024] [Indexed: 06/27/2024] Open
Abstract
Over the past decade, the development of three-dimensional (3D) models has increased exponentially, facilitating the unravelling of fundamental and essential cellular mechanisms by which cells communicate with each other, assemble into tissues and organs and respond to biochemical and biophysical stimuli under both physiological and pathological conditions. This section presents a concise overview of the most recent updates on the significant contribution of different types of 3D cell cultures including spheroids, organoids and organ-on-chip and bio-printed tissues in advancing our understanding of cellular and molecular mechanisms. The case studies presented include the 3D cultures of breast cancer (BC), endometriosis, the liver microenvironment and infections. In BC, the establishment of 3D culture models has permitted the visualization of the role of cancer-associated fibroblasts in the delivery of exosomes, as well as the significance of the physical properties of the extracellular matrix in promoting cell proliferation and invasion. This approach has also become a valuable tool in gaining insight into general and specific mechanisms of drug resistance. Given the considerable heterogeneity of endometriosis, 3D models offer a more accurate representation of the in vivo microenvironment, thereby facilitating the identification and translation of novel targeted therapeutic strategies. The advantages provided by 3D models of the hepatic environment, in conjunction with the high throughput characterizing various platforms, have enabled the elucidation of complex molecular mechanisms underlying various threatening hepatic diseases. A limited number of 3D models for gut and skin infections have been developed. However, a more profound comprehension of the spatial and temporal interactions between microbes, the host and their environment may facilitate the advancement of in vitro, ex vivo and in vivo disease models. Additionally, it may pave the way for the development of novel therapeutic approaches in diverse research fields. The interested reader will also find concluding remarks on the challenges and prospects of using 3D cell cultures for discovering cellular and molecular mechanisms in the research areas covered in this review.
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Affiliation(s)
- Nora Bloise
- Molecular Medicine Department (DMM), Centre for Health Technologies (CHT), Unità di Ricerca (UdR) INSTM, University of Pavia, 27100 Pavia, Italy; (M.G.); (E.P.); (E.R.); (S.S.); (C.V.)
- UOR6 Nanotechnology Laboratory, Department of Prevention and Rehabilitation in Occupational Medicine and Specialty Medicine, Istituti Clinici Scientifici Maugeri IRCCS, Via Maugeri 4, 27100 Pavia, Italy
- Interuniversity Center for the Promotion of the 3Rs Principles in Teaching and Research (Centro 3R), Operative Unit (OU) of University of Pavia, 27100 Pavia, Italy
| | - Marialaura Giannaccari
- Molecular Medicine Department (DMM), Centre for Health Technologies (CHT), Unità di Ricerca (UdR) INSTM, University of Pavia, 27100 Pavia, Italy; (M.G.); (E.P.); (E.R.); (S.S.); (C.V.)
| | - Giuseppe Guagliano
- Department of Chemistry, Materials, and Chemical Engineering “G. Natta”, Politecnico di Milano, P.zza L. Da Vinci 32, 20133 Milan, Italy; (G.G.); (P.P.)
| | - Emanuela Peluso
- Molecular Medicine Department (DMM), Centre for Health Technologies (CHT), Unità di Ricerca (UdR) INSTM, University of Pavia, 27100 Pavia, Italy; (M.G.); (E.P.); (E.R.); (S.S.); (C.V.)
| | - Elisa Restivo
- Molecular Medicine Department (DMM), Centre for Health Technologies (CHT), Unità di Ricerca (UdR) INSTM, University of Pavia, 27100 Pavia, Italy; (M.G.); (E.P.); (E.R.); (S.S.); (C.V.)
| | - Silvia Strada
- Molecular Medicine Department (DMM), Centre for Health Technologies (CHT), Unità di Ricerca (UdR) INSTM, University of Pavia, 27100 Pavia, Italy; (M.G.); (E.P.); (E.R.); (S.S.); (C.V.)
- UOR6 Nanotechnology Laboratory, Department of Prevention and Rehabilitation in Occupational Medicine and Specialty Medicine, Istituti Clinici Scientifici Maugeri IRCCS, Via Maugeri 4, 27100 Pavia, Italy
| | - Cristina Volpini
- Molecular Medicine Department (DMM), Centre for Health Technologies (CHT), Unità di Ricerca (UdR) INSTM, University of Pavia, 27100 Pavia, Italy; (M.G.); (E.P.); (E.R.); (S.S.); (C.V.)
- UOR6 Nanotechnology Laboratory, Department of Prevention and Rehabilitation in Occupational Medicine and Specialty Medicine, Istituti Clinici Scientifici Maugeri IRCCS, Via Maugeri 4, 27100 Pavia, Italy
| | - Paola Petrini
- Department of Chemistry, Materials, and Chemical Engineering “G. Natta”, Politecnico di Milano, P.zza L. Da Vinci 32, 20133 Milan, Italy; (G.G.); (P.P.)
- Interuniversity Center for the Promotion of the 3Rs Principles in Teaching and Research (Centro 3R), Operative Unit (OU) of Politecnico di Milano, 20133 Milan, Italy
| | - Livia Visai
- Molecular Medicine Department (DMM), Centre for Health Technologies (CHT), Unità di Ricerca (UdR) INSTM, University of Pavia, 27100 Pavia, Italy; (M.G.); (E.P.); (E.R.); (S.S.); (C.V.)
- UOR6 Nanotechnology Laboratory, Department of Prevention and Rehabilitation in Occupational Medicine and Specialty Medicine, Istituti Clinici Scientifici Maugeri IRCCS, Via Maugeri 4, 27100 Pavia, Italy
- Interuniversity Center for the Promotion of the 3Rs Principles in Teaching and Research (Centro 3R), Operative Unit (OU) of University of Pavia, 27100 Pavia, Italy
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Fasciano AC, Dasanayake GS, Estes MK, Zachos NC, Breault DT, Isberg RR, Tan S, Mecsas J. Yersinia pseudotuberculosis YopE prevents uptake by M cells and instigates M cell extrusion in human ileal enteroid-derived monolayers. Gut Microbes 2022; 13:1988390. [PMID: 34793276 PMCID: PMC8604394 DOI: 10.1080/19490976.2021.1988390] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Many pathogens use M cells to access the underlying Peyer's patches and spread to systemic sites via the lymph as demonstrated by ligated loop murine intestinal models. However, the study of interactions between M cells and microbial pathogens has stalled due to the lack of cell culture systems. To overcome this obstacle, we use human ileal enteroid-derived monolayers containing five intestinal cell types including M cells to study the interactions between the enteric pathogen, Yersinia pseudotuberculosis (Yptb), and M cells. The Yptb type three secretion system (T3SS) effector Yops inhibit host defenses including phagocytosis and are critical for colonization of the intestine and Peyer's patches. Therefore, it is not understood how Yptb traverses through M cells to breach the epithelium. By growing Yptb under two physiological conditions that mimic the early infectious stage (low T3SS-expression) or host-adapted stage (high T3SS-expression), we found that large numbers of Yptb specifically associated with M cells, recapitulating murine studies. Transcytosis through M cells was significantly higher by Yptb expressing low levels of T3SS, because YopE and YopH prevented Yptb uptake. YopE also caused M cells to extrude from the epithelium without inducing cell-death or disrupting monolayer integrity. Sequential infection with early infectious stage Yptb reduced host-adapted Yptb association with M cells. These data underscore the strength of enteroids as a model by discovering that Yops impede M cell function, indicating that early infectious stage Yptb more effectively penetrates M cells while the host may defend against M cell penetration of host-adapted Yptb.
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Affiliation(s)
- Alyssa C. Fasciano
- Graduate Program in Immunology, Tufts Graduate School of Biomedical Sciences, Boston, USA
| | - Gaya S. Dasanayake
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, USA
| | - Mary K. Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, USA
| | - Nicholas C. Zachos
- Department of Medicine, Division of Gastroenterology and Hepatology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - David T. Breault
- Division of Endocrinology, Boston Children’s Hospital, Department of Pediatrics, Harvard Medical School, Boston, USA
| | - Ralph R. Isberg
- Graduate Program in Immunology, Tufts Graduate School of Biomedical Sciences, Boston, USA,Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, USA
| | - Shumin Tan
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, USA
| | - Joan Mecsas
- Graduate Program in Immunology, Tufts Graduate School of Biomedical Sciences, Boston, USA,Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, USA,CONTACT Joan Mecsas Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, USA
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Phillips SMB, Bergstrom C, Walker B, Wang G, Alfaro T, Stromberg ZR, Hess BM. Engineered Cell Line Imaging Assay Differentiates Pathogenic from Non-Pathogenic Bacteria. Pathogens 2022; 11:pathogens11020209. [PMID: 35215152 PMCID: PMC8874627 DOI: 10.3390/pathogens11020209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/31/2022] [Accepted: 02/02/2022] [Indexed: 01/27/2023] Open
Abstract
Cell culture systems have greatly expanded our understanding of how bacterial pathogens target signaling pathways to manipulate the host and cause infection. Advances in genetic engineering have allowed for the creation of fluorescent protein readouts within signaling pathways, but these techniques have been underutilized in pathogen biology. Here, we genetically engineered a lung cell line with fluorescent reporters for extracellular signal-related kinase (ERK) and the downstream transcription factor FOS-related antigen 1 (Fra1) and evaluated signaling after inoculation with pathogenic and non-pathogenic bacteria. Cells were inoculated with 100 colony-forming units of Acinetobacter baylyi, Klebsiella pneumoniae, Pseudomonas aeruginosa, Streptococcus agalactiae, or Staphylococcus epidermidis and imaged in a multi-mode reader. The alamarBlue cell viability assay was used as a reference test and showed that pathogenic P. aeruginosa induced significant (p < 0.05) cell death after 8 h in both wild-type and engineered cell lines compared to non-pathogenic S. epidermidis. In engineered cells, we found that Fra1 signaling was disrupted in as little as 4 h after inoculation with bacterial pathogens compared to delayed disruption in signaling by non-pathogenic S. epidermidis. Overall, we demonstrate that low levels of pathogenic versus non-pathogenic bacteria can be rapidly and sensitively screened based on ERK-Fra1 signaling.
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Aguilar C, Alves da Silva M, Saraiva M, Neyazi M, Olsson IAS, Bartfeld S. Organoids as host models for infection biology - a review of methods. Exp Mol Med 2021; 53:1471-1482. [PMID: 34663936 PMCID: PMC8521091 DOI: 10.1038/s12276-021-00629-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/26/2021] [Accepted: 02/24/2021] [Indexed: 01/10/2023] Open
Abstract
Infectious diseases are a major threat worldwide. With the alarming rise of antimicrobial resistance and emergence of new potential pathogens, a better understanding of the infection process is urgently needed. Over the last century, the development of in vitro and in vivo models has led to remarkable contributions to the current knowledge in the field of infection biology. However, applying recent advances in organoid culture technology to research infectious diseases is now taking the field to a higher level of complexity. Here, we describe the current methods available for the study of infectious diseases using organoid cultures.
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Affiliation(s)
- Carmen Aguilar
- grid.8379.50000 0001 1958 8658Research Centre for Infectious Diseases, Institute for Molecular Infection Biology, Julius Maximilians Universität Wuerzburg, Wuerzburg, Germany
| | - Marta Alves da Silva
- grid.5808.50000 0001 1503 7226i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226IBMC- Instituto de Biologia Celular e Molecular, Universidade do Porto, Porto, Portugal
| | - Margarida Saraiva
- grid.5808.50000 0001 1503 7226i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226IBMC- Instituto de Biologia Celular e Molecular, Universidade do Porto, Porto, Portugal
| | - Mastura Neyazi
- grid.8379.50000 0001 1958 8658Research Centre for Infectious Diseases, Institute for Molecular Infection Biology, Julius Maximilians Universität Wuerzburg, Wuerzburg, Germany
| | - I. Anna S. Olsson
- grid.5808.50000 0001 1503 7226i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226IBMC- Instituto de Biologia Celular e Molecular, Universidade do Porto, Porto, Portugal
| | - Sina Bartfeld
- grid.8379.50000 0001 1958 8658Research Centre for Infectious Diseases, Institute for Molecular Infection Biology, Julius Maximilians Universität Wuerzburg, Wuerzburg, Germany
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Baddal B, Marrazzo P. Refining Host-Pathogen Interactions: Organ-on-Chip Side of the Coin. Pathogens 2021; 10:203. [PMID: 33668558 PMCID: PMC7918822 DOI: 10.3390/pathogens10020203] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/09/2021] [Accepted: 02/11/2021] [Indexed: 02/07/2023] Open
Abstract
Bioinspired organ-level in vitro platforms that recapitulate human organ physiology and organ-specific responses have emerged as effective technologies for infectious disease research, drug discovery, and personalized medicine. A major challenge in tissue engineering for infectious diseases has been the reconstruction of the dynamic 3D microenvironment reflecting the architectural and functional complexity of the human body in order to more accurately model the initiation and progression of host-microbe interactions. By bridging the gap between in vitro experimental models and human pathophysiology and providing alternatives for animal models, organ-on-chip microfluidic devices have so far been implemented in multiple research areas, contributing to major advances in the field. Given the emergence of the recent pandemic, plug-and-play organ chips may hold the key for tackling an unmet clinical need in the development of effective therapeutic strategies. In this review, latest studies harnessing organ-on-chip platforms to unravel host-pathogen interactions are presented to highlight the prospects for the microfluidic technology in infectious diseases research.
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Affiliation(s)
- Buket Baddal
- Department of Medical Microbiology and Clinical Microbiology, Faculty of Medicine, Near East University, Nicosia 99138, Cyprus
| | - Pasquale Marrazzo
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum University of Bologna, 40126 Bologna, Italy;
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Lallemant L, Lebreton C, Garfa-Traoré M. Comparison of different clearing and acquisition methods for 3D imaging of murine intestinal organoids. J Biol Methods 2020; 7:e141. [PMID: 33564693 PMCID: PMC7865078 DOI: 10.14440/jbm.2020.334] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 08/17/2020] [Accepted: 08/17/2020] [Indexed: 01/17/2023] Open
Abstract
An organoid is a three-dimensional multicellular structure that shows realistic micro-anatomy of an organ. This in vitro model mimics the in vivo environment, architecture and multi-lineage differentiation of the original organs and allows to answer many interesting biological questions. For these reasons, they are widely used in stem cell, regenerative medicine, toxicology, pharmacology, and host-microbe interactions research. In order to study organoids, microscopy is very useful: It is possible to make three-dimensional reconstruction of serial sections but it is time consuming and error-prone. Here we propose an alternative solution: Tissue clearing reduces the dispersion of light because it homogenizes the refractive index of the tissue, allowing sample observation throughout its thickness. We have compared different clearing techniques on mouse intestinal organoids using different acquisition methods.
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Affiliation(s)
- Louison Lallemant
- Cell Imaging Platform, INSERM-US24-CNRS UMS 3633 Structure Fédérative de Recherche Necker, Paris University, Paris 75015, France
| | - Corinne Lebreton
- Université de Paris, Imagine Institute, Laboratory of Intestinal Immunity, INSERM UMR1163, Paris 75015, France
| | - Meriem Garfa-Traoré
- Cell Imaging Platform, INSERM-US24-CNRS UMS 3633 Structure Fédérative de Recherche Necker, Paris University, Paris 75015, France
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Son YS, Ki SJ, Thanavel R, Kim JJ, Lee MO, Kim J, Jung CR, Han TS, Cho HS, Ryu CM, Kim SH, Park DS, Son MY. Maturation of human intestinal organoids in vitro facilitates colonization by commensal lactobacilli by reinforcing the mucus layer. FASEB J 2020; 34:9899-9910. [PMID: 32602623 DOI: 10.1096/fj.202000063r] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 04/20/2020] [Accepted: 04/26/2020] [Indexed: 12/14/2022]
Abstract
Lactobacilli, which are probiotic commensal bacteria that mainly reside in the human small intestine, have attracted attention for their ability to exert health-promoting effects and beneficially modulate host immunity. However, host epithelial-commensal bacterial interactions are still largely unexplored because of limited access to human small intestinal tissues. Recently, we described an in vitro maturation technique for generating adult-like, mature human intestinal organoids (hIOs) from human pluripotent stem cells (hPSCs) that closely resemble the in vivo tissue structure and cellular diversity. Here, we established an in vitro human model to study the response to colonization by commensal bacteria using luminal microinjection into mature hIOs, allowing for the direct examination of epithelial-bacterial interactions. Lactobacillus reuteri and Lactobacillus plantarum were more likely to survive and colonize when microinjected into the lumen of mature hIOs than when injected into immature hIOs, as determined by scanning electron microscopy, colony formation assay, immunofluorescence, and real-time imaging with L plantarum expressing red fluorescent protein. The improved mature hIO-based host epithelium system resulted from enhanced intestinal epithelial integrity via upregulation of mucus secretion and tight junction proteins. Our study indicates that mature hIOs are a physiologically relevant in vitro model system for studying commensal microorganisms.
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Affiliation(s)
- Ye Seul Son
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.,KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Soo Jin Ki
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.,Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, Republic of Korea
| | - Rajangam Thanavel
- Center for Biomaterials, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea
| | - Jong-Jin Kim
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.,KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Mi-Ok Lee
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.,KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Janghwan Kim
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.,KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Cho-Rok Jung
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.,KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Tae-Su Han
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Hyun-Soo Cho
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.,KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Choong-Min Ryu
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.,KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Sang-Heon Kim
- Center for Biomaterials, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea.,Department of Biomedical Engineering, KIST school, UST, Daejeon, Republic of Korea
| | - Doo-Sang Park
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.,KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea.,Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, Republic of Korea
| | - Mi-Young Son
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.,KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
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