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Lee JH, LeCher JC, Parigoris E, Shinagawa N, Sentosa J, Manfredi C, Goh SL, De R, Tao S, Zandi K, Amblard F, Sorscher EJ, Spence JR, Tirouvanziam R, Schinazi RF, Takayama S. Development of robust antiviral assays using relevant apical-out human airway organoids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.02.573939. [PMID: 38260306 PMCID: PMC10802305 DOI: 10.1101/2024.01.02.573939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
While breakthroughs with organoids have emerged as next-generation in vitro tools, standardization for drug discovery remains a challenge. This work introduces human airway organoids with reversed biopolarity (AORBs), cultured and analyzed in a high-throughput, single-organoid-per-well format, enabling milestones towards standardization. AORBs exhibit a spatio-temporally stable apical-out morphology, facilitating high-yield direct intact-organoid virus infection. Single-cell RNA sequencing and immunohistochemistry confirm the physiologically relevant recapitulation of differentiated human airway epithelia. The cellular tropism of five severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains along with host response differences between Delta, Washington, and Omicron variants, as observed in transcriptomic profiles, also suggest clinical relevance. Dose-response analysis of three well-studied SARS-CoV-2 antiviral compounds (remdesivir, bemnifosbuvir, and nirmatrelvir) demonstrates that AORBs efficiently predict human efficacy, comparable to gold-standard air-liquid interface cultures, but with higher throughput (~10-fold) and fewer cells (~100-fold). This combination of throughput and relevance allows AORBs to robustly detect false negative results in efficacy, preventing irretrievable loss of promising lead compounds. While this work leverages the SARS-CoV-2 study as a proof-of-concept application, the standardization capacity of AORB holds broader implications in line with regulatory efforts to push alternatives to animal studies.
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Affiliation(s)
- Ji-Hoon Lee
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA 30332, USA
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Julia C. LeCher
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Eric Parigoris
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA 30332, USA
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Noriyuki Shinagawa
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA 30332, USA
| | - Jason Sentosa
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA 30332, USA
| | - Candela Manfredi
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
- Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Shu Ling Goh
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ramyani De
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Sijia Tao
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Keivan Zandi
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Franck Amblard
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Eric J. Sorscher
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
- Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Jason R. Spence
- Division of Gastroenterology, Department of Internal Medicine, Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI 48109, USA
| | - Rabindra Tirouvanziam
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA 30332, USA
- Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
- Center for Cystic Fibrosis & Airways Disease Research, Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Raymond F. Schinazi
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Shuichi Takayama
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA 30332, USA
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
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Han Z, Yao L, Fang Y, Chen S, Lian R, Yao Y, Chen H, Ji X, Yu W, Wang Z, Wang R, Liang S. Patient-derived organoid elucidates the identical clonal origin of bilateral breast cancer with diverse molecular subtypes. Front Oncol 2024; 14:1361603. [PMID: 38800414 PMCID: PMC11116675 DOI: 10.3389/fonc.2024.1361603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 04/25/2024] [Indexed: 05/29/2024] Open
Abstract
Bilateral breast cancer (BBC), an infrequent breast cancer subtype, has primarily been studied in terms of incidence, prognosis, and through comparative analysis of synchronous (SBBC) and metachronous (MBBC) manifestations. The advent and application of organoid technology hold profound implications for tumor research and clinical management. This study represents the pioneering use of organoid models in BBC research. We established organoid lines from two surgical tumor specimens of a BBC patient, with one line undergoing detailed pathological and genomic analysis. The BBC organoid from the right breast demonstrated a marker expression profile of ER (-), PR (-), HER-2 (0), and Ki67 index 10%, indicating that it may derived from the TNBC tissue. Whole Exome Sequencing (WES) displayed consistent set of Top10 cancer driver genes affected by missense mutations, frameshift mutation, or splice site mutations in three tumor tissues and the organoid samples. The organoids' single nucleotide polymorphisms (SNPs) were more closely aligned with the TNBC tissue than other tumor tissues. Evolutionary analysis suggested that different tumor regions might evolve from a common ancestral layer. In this case, the development of BBC organoids indicated that simultaneous lesions with diverse molecular profiles shared a high degree of consistency in key tumor-driving mutations. These findings suggest the feasibility of generating BBC organoids representing various molecular types, accurately replicating significant markers and driver mutations of the originating tumor. Consequently, organoids serve as a valuable in vitro model for exploring treatment strategies and elucidating the underlying mechanisms of BBC.
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Affiliation(s)
- Zhongbin Han
- The Key Laboratory of Biomarker High Throughput Screening And Target Translation of Breast and Gastrointestinal Tumor, Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning, China
- Breast and Thyroid Surgery, Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning, China
| | - Liangxue Yao
- The Key Laboratory of Biomarker High Throughput Screening And Target Translation of Breast and Gastrointestinal Tumor, Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning, China
| | - Yanhua Fang
- The Key Laboratory of Biomarker High Throughput Screening And Target Translation of Breast and Gastrointestinal Tumor, Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning, China
| | - Sijing Chen
- The Key Laboratory of Biomarker High Throughput Screening And Target Translation of Breast and Gastrointestinal Tumor, Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning, China
- Breast and Thyroid Surgery, Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning, China
| | - Ruiqing Lian
- Pathology Department, Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning, China
| | - Yongqiang Yao
- Breast and Thyroid Surgery, Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning, China
| | - Hongsheng Chen
- Breast and Thyroid Surgery, Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning, China
| | - Xuening Ji
- Oncology Department, Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning, China
| | - Weiting Yu
- The Key Laboratory of Biomarker High Throughput Screening And Target Translation of Breast and Gastrointestinal Tumor, Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning, China
| | - Zhe Wang
- Oncology Department, Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning, China
| | - Ruoyu Wang
- The Key Laboratory of Biomarker High Throughput Screening And Target Translation of Breast and Gastrointestinal Tumor, Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning, China
- Oncology Department, Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning, China
| | - Shanshan Liang
- The Key Laboratory of Biomarker High Throughput Screening And Target Translation of Breast and Gastrointestinal Tumor, Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning, China
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Tong K, Bandari M, Carrick JN, Zenkevich A, Kothari OA, Shamshad E, Stefanik K, Haro KS, Perekatt AO, Verzi MP. In Vitro Organoid-Based Assays Reveal SMAD4 Tumor-Suppressive Mechanisms for Serrated Colorectal Cancer Invasion. Cancers (Basel) 2023; 15:5820. [PMID: 38136364 PMCID: PMC10742020 DOI: 10.3390/cancers15245820] [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: 11/21/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
Colon cancer is the third most prominent cancer and second leading cause of cancer-related deaths in the United States. Up to 20% of colon cancers follow the serrated tumor pathway driven by mutations in the MAPK pathway. Loss of SMAD4 function occurs in the majority of late-stage colon cancers and is associated with aggressive cancer progression. Therefore, it is important to develop technology to accurately model and better understand the genetic mechanisms behind cancer invasion. Organoids derived from tumors found in the Smad4KO BRAFV600E/+ mouse model present multiple phenotypes characteristic of invasion both in ex vivo and in vivo systems. Smad4KO BRAFV600E/+ tumor organoids can migrate through 3D culture and infiltrate through transwell membranes. This invasive behavior can be suppressed when SMAD4 is re-expressed in the tumor organoids. RNA-Seq analysis reveals that SMAD4 expression in organoids rapidly regulates transcripts associated with extracellular matrix and secreted proteins, suggesting that the mechanisms employed by SMAD4 to inhibit invasion are associated with regulation of extracellular matrix and secretory pathways. These findings indicate new models to study SMAD4 regulation of tumor invasion and an additional layer of complexity in the tumor-suppressive function of the SMAD4/Tgfβ pathway.
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Affiliation(s)
- Kevin Tong
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA (A.O.P.)
- Human Genetics Institute of New Jersey, Piscataway, NJ 08854, USA
- Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ 07110, USA
- Department of Medical Sciences, Hackensack Meridian Health School of Medicine, Nutley, NJ 07110, USA
| | - Manisha Bandari
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA (A.O.P.)
| | - Jillian N. Carrick
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA (A.O.P.)
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ 07110, USA
| | - Anastasia Zenkevich
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ 07110, USA
| | - Om A. Kothari
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA (A.O.P.)
| | - Eman Shamshad
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA (A.O.P.)
| | - Katarina Stefanik
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA (A.O.P.)
- Department of Biology, The College of New Jersey, Ewing Township, NJ 08618, USA
| | - Katherine S. Haro
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA (A.O.P.)
| | - Ansu O. Perekatt
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA (A.O.P.)
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, Hoboken, NJ 07030, USA
| | - Michael P. Verzi
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA (A.O.P.)
- Human Genetics Institute of New Jersey, Piscataway, NJ 08854, USA
- Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
- Rutgers Center for Lipid Research, New Brunswick, NJ 08901, USA
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4
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Huang Y, Lee S, Liu W, Takayama S, Jia S. OctoShaker: A versatile robotic biomechanical agitator for cellular and organoid research. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2023; 94:124104. [PMID: 38126811 PMCID: PMC10746356 DOI: 10.1063/5.0174526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/03/2023] [Indexed: 12/23/2023]
Abstract
Mechanical forces have increasingly been recognized as a key regulator in the fate of cellular development and functionality. Different mechanical transduction methods, such as substrate stiffness and magnetic bead vibration, have been experimented with to understand the interaction between the biophysical cues and cellular outcome. In the exploration and utilization of the intrinsic cellular mechanism, bio-shakers, traditionally invented for stirring liquid, have garnered more interest as a tool to provide precise mechanical stimuli to aid in this study. Nonetheless, despite the usefulness of current bio-shaking technology, each type of shaker often offers a single mode of motion, insufficient for generating complex force dynamics needed to resemble the actual physical condition that occurs inside living organisms. In this study, we present OctoShaker, a robotic instrument capable of creating a multitude of motions that could be sequenced or programmed to mimic sophisticated hemodynamics in vivo. We demonstrated the programmed motion of circular convection and investigated its influence on micro-particle distribution in 96-well culture microplates. Biological samples, including HeLa cells and organoids, were tested, and unique resultant patterns were observed. We anticipate the open-source dissemination of OctoShaker in diverse biological applications, encompassing biomechanical studies for cellular and organoid research, as well as other disciplines that demand dynamic mechanical force generation.
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Affiliation(s)
- Yan Huang
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, USA
| | - Soojung Lee
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, USA
| | - Wenhao Liu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, USA
| | | | - Shu Jia
- Author to whom correspondence should be addressed:
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Mandracchia B, Liu W, Hua X, Forghani P, Lee S, Hou J, Nie S, Xu C, Jia S. Optimal sparsity allows reliable system-aware restoration of fluorescence microscopy images. SCIENCE ADVANCES 2023; 9:eadg9245. [PMID: 37647399 PMCID: PMC10468132 DOI: 10.1126/sciadv.adg9245] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 07/31/2023] [Indexed: 09/01/2023]
Abstract
Fluorescence microscopy is one of the most indispensable and informative driving forces for biological research, but the extent of observable biological phenomena is essentially determined by the content and quality of the acquired images. To address the different noise sources that can degrade these images, we introduce an algorithm for multiscale image restoration through optimally sparse representation (MIRO). MIRO is a deterministic framework that models the acquisition process and uses pixelwise noise correction to improve image quality. Our study demonstrates that this approach yields a remarkable restoration of the fluorescence signal for a wide range of microscopy systems, regardless of the detector used (e.g., electron-multiplying charge-coupled device, scientific complementary metal-oxide semiconductor, or photomultiplier tube). MIRO improves current imaging capabilities, enabling fast, low-light optical microscopy, accurate image analysis, and robust machine intelligence when integrated with deep neural networks. This expands the range of biological knowledge that can be obtained from fluorescence microscopy.
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Affiliation(s)
- Biagio Mandracchia
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Scientific-Technical Central Units, Instituto de Salud Carlos III (ISCIII), Majadahonda, Spain
- ETSI Telecomunicación, Universidad de Valladolid, Valladolid, Spain
| | - Wenhao Liu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Xuanwen Hua
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Parvin Forghani
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Soojung Lee
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Jessica Hou
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Shuyi Nie
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
| | - Chunhui Xu
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
| | - Shu Jia
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
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6
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Mertz DR, Parigoris E, Sentosa J, Lee JH, Lee S, Kleer CG, Luker G, Takayama S. Triple-negative breast cancer cells invade adipocyte/preadipocyte-encapsulating geometrically inverted mammary organoids. Integr Biol (Camb) 2023; 15:zyad004. [PMID: 37015816 PMCID: PMC10155781 DOI: 10.1093/intbio/zyad004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 02/25/2023] [Indexed: 04/06/2023]
Abstract
This paper describes the manufacture of geometrically inverted mammary organoids encapsulating primary mammary preadipocytes and adipocytes. Material manipulation in an array of 192 hanging drops induces cells to self-assemble into inside-out organoids where an adipose tissue core is enveloped by a cell-produced basement membrane, indicated by laminin V staining and then a continuous layer of mammary epithelial cells. This inverted tissue structure enables investigation of multiple mammary cancer subtypes, with a significantly higher extent of invasion by triple-negative MDA-MB-231 breast cancer cells compared to MCF7 cells. By seeding cancer cells into co-culture around pre-formed organoids with encapsulated preadipocytes/adipocytes, invasion through the epithelium, then into the adipose core is observable through acquisition of confocal image stacks of whole mount specimens. Furthermore, in regions of the connective tissue core where invasion occurs, there is an accumulation of collagen in the microenvironment. Suggesting that this collagen may be conducive to increased invasiveness, the anti-fibrotic drug pirfenidone shows efficacy in this model by slowing invasion. Comparison of adipose tissue derived from three different donors shows method consistency as well as the potential to evaluate donor cell-based biological variability. Insight box Geometrically inverted mammary organoids encapsulating primary preadipocytes/adipocytes (P/As) are bioengineered using a minimal amount of Matrigel scaffolding. Use of this eversion-free method is key to production of adipose mammary organoids (AMOs) where not only the epithelial polarity but also the entire self-organizing arrangement, including adipose position, is inside-out. While an epithelial-only structure can analyze cancer cell invasion, P/As are required for invasion-associated collagen deposition and efficacy of pirfenidone to counteract collagen deposition and associated invasion. The methods described strike a balance between repeatability and preservation of biological variability: AMOs form consistently across multiple adipose cell donors while revealing cancer cell invasion differences.
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Affiliation(s)
- David R Mertz
- Wallace H. Coulter Department of Biomedical Engineering , Georgia Institute of Technology and Emory School of Medicine, Atlanta, GA, USA
| | - Eric Parigoris
- Wallace H. Coulter Department of Biomedical Engineering , Georgia Institute of Technology and Emory School of Medicine, Atlanta, GA, USA
| | - Jason Sentosa
- Wallace H. Coulter Department of Biomedical Engineering , Georgia Institute of Technology and Emory School of Medicine, Atlanta, GA, USA
| | - Ji-Hoon Lee
- Wallace H. Coulter Department of Biomedical Engineering , Georgia Institute of Technology and Emory School of Medicine, Atlanta, GA, USA
| | - Soojung Lee
- Wallace H. Coulter Department of Biomedical Engineering , Georgia Institute of Technology and Emory School of Medicine, Atlanta, GA, USA
| | - Celina G Kleer
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Gary Luker
- Center for Molecular Imaging, Department of Radiology, University of Michigan, Ann Arbor, MI, USA
| | - Shuichi Takayama
- Wallace H. Coulter Department of Biomedical Engineering , Georgia Institute of Technology and Emory School of Medicine, Atlanta, GA, USA
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7
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Han K, Hua X, Vasani V, Kim GAR, Liu W, Takayama S, Jia S. 3D super-resolution live-cell imaging with radial symmetry and Fourier light-field microscopy. BIOMEDICAL OPTICS EXPRESS 2022; 13:5574-5584. [PMID: 36733732 PMCID: PMC9872894 DOI: 10.1364/boe.471967] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 06/18/2023]
Abstract
Live-cell imaging reveals the phenotypes and mechanisms of cellular function and their dysfunction that underscore cell physiology, development, and pathology. Here, we report a 3D super-resolution live-cell microscopy method by integrating radiality analysis and Fourier light-field microscopy (rad-FLFM). We demonstrated the method using various live-cell specimens, including actins in Hela cells, microtubules in mammary organoid cells, and peroxisomes in COS-7 cells. Compared with conventional wide-field microscopy, rad-FLFM realizes scanning-free, volumetric 3D live-cell imaging with sub-diffraction-limited resolution of ∼150 nm (x-y) and 300 nm (z), milliseconds volume acquisition time, six-fold extended depth of focus of ∼6 µm, and low photodamage. The method provides a promising avenue to explore spatiotemporal-challenging subcellular processes in a wide range of cell biological research.
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Affiliation(s)
- Keyi Han
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA
| | - Xuanwen Hua
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA
| | - Vishwa Vasani
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Ge-Ah R. Kim
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Wenhao Liu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA
| | - Shuichi Takayama
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Shu Jia
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA
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8
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Ginga NJ, Slyman R, Kim GA, Parigoris E, Huang S, Yadagiri VK, Young VB, Spence JR, Takayama S. Perfusion System for Modification of Luminal Contents of Human Intestinal Organoids and Realtime Imaging Analysis of Microbial Populations. MICROMACHINES 2022; 13:131. [PMID: 35056297 PMCID: PMC8779378 DOI: 10.3390/mi13010131] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/08/2022] [Accepted: 01/11/2022] [Indexed: 02/01/2023]
Abstract
Intestinal organoids are 3D cell structures that replicate some aspects of organ function and are organized with a polarized epithelium facing a central lumen. To enable more applications, new technologies are needed to access the luminal cavity and apical cell surface of organoids. We developed a perfusion system utilizing a double-barrel glass capillary with a pressure-based pump to access and modify the luminal contents of a human intestinal organoid for extended periods of time while applying cyclic cellular strain. Cyclic injection and withdrawal of fluorescent FITC-Dextran coupled with real-time measurement of fluorescence intensity showed discrete changes of intensity correlating with perfusion cycles. The perfusion system was also used to modify the lumen of organoids injected with GFP-expressing E. coli. Due to the low concentration and fluorescence of the E. coli, a novel imaging analysis method utilizing bacteria enumeration and image flattening was developed to monitor E. coli within the organoid. Collectively, this work shows that a double-barrel perfusion system provides constant luminal access and allows regulation of luminal contents and luminal mixing.
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Affiliation(s)
- Nicholas J. Ginga
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory School of Medicine, Atlanta, GA 30332, USA; (N.J.G.); (R.S.); (G.-A.K.); (E.P.)
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Raleigh Slyman
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory School of Medicine, Atlanta, GA 30332, USA; (N.J.G.); (R.S.); (G.-A.K.); (E.P.)
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Ge-Ah Kim
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory School of Medicine, Atlanta, GA 30332, USA; (N.J.G.); (R.S.); (G.-A.K.); (E.P.)
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Eric Parigoris
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory School of Medicine, Atlanta, GA 30332, USA; (N.J.G.); (R.S.); (G.-A.K.); (E.P.)
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Sha Huang
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA; (S.H.); (J.R.S.)
| | - Veda K. Yadagiri
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA; (V.K.Y.); (V.B.Y.)
| | - Vincent B. Young
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA; (V.K.Y.); (V.B.Y.)
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Jason R. Spence
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA; (S.H.); (J.R.S.)
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Shuichi Takayama
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory School of Medicine, Atlanta, GA 30332, USA; (N.J.G.); (R.S.); (G.-A.K.); (E.P.)
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
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9
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Lee S, Chang J, Kang SM, Parigoris E, Lee JH, Huh YS, Takayama S. High-throughput formation and image-based analysis of basal-in mammary organoids in 384-well plates. Sci Rep 2022; 12:317. [PMID: 35013350 PMCID: PMC8748891 DOI: 10.1038/s41598-021-03739-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 12/09/2021] [Indexed: 01/02/2023] Open
Abstract
This manuscript describes a new method for forming basal-in MCF10A organoids using commercial 384-well ultra-low attachment (ULA) microplates and the development of associated live-cell imaging and automated analysis protocols. The use of a commercial 384-well ULA platform makes this method more broadly accessible than previously reported hanging drop systems and enables in-incubator automated imaging. Therefore, time points can be captured on a more frequent basis to improve tracking of early organoid formation and growth. However, one major challenge of live-cell imaging in multi-well plates is the rapid accumulation of large numbers of images. In this paper, an automated MATLAB script to handle the increased image load is developed. This analysis protocol utilizes morphological image processing to identify cellular structures within each image and quantify their circularity and size. Using this script, time-lapse images of aggregating and non-aggregating culture conditions are analyzed to profile early changes in size and circularity. Moreover, this high-throughput platform is applied to widely screen concentration combinations of Matrigel and epidermal growth factor (EGF) or heparin-binding EGF-like growth factor (HB-EGF) for their impact on organoid formation. These results can serve as a practical resource, guiding future research with basal-in MCF10A organoids.
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Affiliation(s)
- Soojung Lee
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
| | - Jonathan Chang
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
| | - Sung-Min Kang
- Department of Green Chemical Engineering, Sangmyung University, Cheonan, Chungnam, 31066, Republic of Korea
| | - Eric Parigoris
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
| | - Ji-Hoon Lee
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
| | - Yun Suk Huh
- Department of Biological Engineering, NanoBio High-Tech Materials Research Center, Inha University, 100 Inha-ro, Incheon, 22212, Republic of Korea
| | - Shuichi Takayama
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA.
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA.
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10
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Kang SM, Kim D, Lee JH, Takayama S, Park JY. Engineered Microsystems for Spheroid and Organoid Studies. Adv Healthc Mater 2021; 10:e2001284. [PMID: 33185040 PMCID: PMC7855453 DOI: 10.1002/adhm.202001284] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/01/2020] [Indexed: 01/09/2023]
Abstract
3D in vitro model systems such as spheroids and organoids provide an opportunity to extend the physiological understanding using recapitulated tissues that mimic physiological characteristics of in vivo microenvironments. Unlike 2D systems, 3D in vitro systems can bridge the gap between inadequate 2D cultures and the in vivo environments, providing novel insights on complex physiological mechanisms at various scales of organization, ranging from the cellular, tissue-, to organ-levels. To satisfy the ever-increasing need for highly complex and sophisticated systems, many 3D in vitro models with advanced microengineering techniques have been developed to answer diverse physiological questions. This review summarizes recent advances in engineered microsystems for the development of 3D in vitro model systems. The relationship between the underlying physics behind the microengineering techniques, and their ability to recapitulate distinct 3D cellular structures and functions of diverse types of tissues and organs are highlighted and discussed in detail. A number of 3D in vitro models and their engineering principles are also introduced. Finally, current limitations are summarized, and perspectives for future directions in guiding the development of 3D in vitro model systems using microengineering techniques are provided.
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Affiliation(s)
- Sung-Min Kang
- Department of Green Chemical Engineering, Sangmyung University, Cheonan, Chungnam, 31066, Republic of Korea
| | - Daehan Kim
- Department of Mechanical Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Ji-Hoon Lee
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory School of Medicine, Atlanta, GA, 30332, USA
- The Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Shuichi Takayama
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory School of Medicine, Atlanta, GA, 30332, USA
- The Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Joong Yull Park
- Department of Mechanical Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea
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11
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Mertz D, Sentosa J, Luker G, Takayama S. Studying Adipose Tissue in the Breast Tumor Microenvironment In Vitro: Progress and Opportunities. Tissue Eng Regen Med 2020; 17:773-785. [PMID: 32939672 DOI: 10.1007/s13770-020-00299-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 08/14/2020] [Accepted: 08/28/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The breast cancer microenvironment contains a variety of stromal cells that are widely implicated in worse patient outcomes. While many in vitro models of the breast tumor microenvironment have been published, only a small fraction of these feature adipocytes. Adipocytes are a cell type increasingly recognized to have complex functions in breast cancer. METHODS In this review, we examine findings from recent examples of in vitro experiments modeling adipocytes within the local breast tumor microenvironment. RESULTS Both two-dimensional and three-dimensional models of adipocytes in the breast tumor microenvironment are covered in this review and both have uncovered interesting phenomena related to breast tumor progression. CONCLUSION Certain aspects of breast cancer and associated adipocyte biology: extracellular matrix effects, cell-cell contact, and physiological mass transport can only be examined with a three-dimensional culture platform. Opportunities remain for innovative improvements to be made to in vitro models that further increase what is known about adipocytes during breast cancer progression.
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Affiliation(s)
- David Mertz
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Dr NW, Atlanta, GA, 30332, USA
| | - Jason Sentosa
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Dr NW, Atlanta, GA, 30332, USA
| | - Gary Luker
- Departments of Radiology, Biomedical Engineering, Microbiology and Immunology, University of Michigan, 500 S State St, Ann Arbor, MI, 48109, USA
| | - Shuichi Takayama
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Dr NW, Atlanta, GA, 30332, USA. .,Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, 313 Ferst Dr NW, Atlanta, GA, 30332, USA.
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