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Cortés‐Llanos B, Jain V, Cooper‐Volkheimer A, Browne EP, Murdoch DM, Allbritton NL. Automated microarray platform for single-cell sorting and collection of lymphocytes following HIV reactivation. Bioeng Transl Med 2023; 8:e10551. [PMID: 37693052 PMCID: PMC10487311 DOI: 10.1002/btm2.10551] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 04/29/2023] [Accepted: 05/04/2023] [Indexed: 09/12/2023] Open
Abstract
A promising strategy to cure HIV-infected individuals is to use latency reversing agents (LRAs) to reactivate latent viruses, followed by host clearance of infected reservoir cells. However, reactivation of latent proviruses within infected cells is heterogeneous and often incomplete. This fact limits strategies to cure HIV which may require complete elimination of viable virus from all cellular reservoirs. For this reason, understanding the mechanism(s) of reactivation of HIV within cellular reservoirs is critical to achieve therapeutic success. Methodologies enabling temporal tracking of single cells as they reactivate followed by sorting and molecular analysis of those cells are urgently needed. To this end, microraft arrays were adapted to image T-lymphocytes expressing mCherry under the control of the HIV long terminal repeat (LTR) promoter, in response to the application of LRAs (prostratin, iBET151, and SAHA). In response to prostratin, iBET151, and SAHA, 30.5%, 11.2%, and 12.1% percentage of cells, respectively. The arrays enabled large numbers of single cells (>25,000) to be imaged over time. mCherry fluorescence quantification identified cell subpopulations with differing reactivation kinetics. Significant heterogeneity was observed at the single-cell level between different LRAs in terms of time to reactivation, rate of mCherry fluorescence increase upon reactivation, and peak fluorescence attained. In response to prostratin, subpopulations of T lymphocytes with slow and fast reactivation kinetics were identified. Single T-lymphocytes that were either fast or slow reactivators were sorted, and single-cell RNA-sequencing was performed. Different genes associated with inflammation, immune activation, and cellular and viral transcription factors were found.
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Affiliation(s)
- Belén Cortés‐Llanos
- Department of BioengineeringUniversity of WashingtonWashingtonUSA
- Department of MedicineDuke UniversityNorth CarolinaUSA
| | - Vaibhav Jain
- Department of Molecular PhysiologyDuke UniversityNorth CarolinaUSA
| | | | - Edward P. Browne
- Department of MedicineUniversity of North CarolinaNorth CarolinaUSA
- Department of Microbiology and ImmunologyUniversity of North CarolinaNorth CarolinaUSA
- UNC HIV Cure CenterUniversity of North CarolinaNorth CarolinaUSA
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LaBelle CA, Zhang RJ, Hunsucker SA, Armistead PM, Allbritton NL. Microraft arrays for serial-killer CD19 chimeric antigen receptor T cells and single cell isolation. Cytometry A 2023; 103:208-220. [PMID: 35899783 PMCID: PMC9883594 DOI: 10.1002/cyto.a.24678] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 04/30/2022] [Accepted: 07/21/2022] [Indexed: 01/31/2023]
Abstract
Chimeric antigen receptor T (CAR-T) cell immunotherapies have seen success in treating hematological malignancies in recent years; however, the results can be highly variable. Single cell heterogeneity plays a key role in the variable efficacy of CAR-T cell treatments yet is largely unexplored. A major challenge is to understand the killing behavior and phenotype of individual CAR-T cells, which are able to serially kill targets. Thus, a platform capable of measuring time-dependent CAR-T cell mediated killing and then isolating single cells for downstream assays would be invaluable in characterizing CAR-T cells. An automated microraft array platform was designed to track CD19 CAR-T cell killing of CD19+ target cells and CAR-T cell motility over time followed by CAR-T cell collection based on killing behavior. The platform demonstrated automated CAR-T cell counting with up to 98% specificity and 96% sensitivity, and single cells were isolated with 89% efficiency. On average, 2.3% of single CAR-T cells were shown to participate in serial-killing of target cells, killing a maximum of three target cells in a 6 h period. The cytotoxicity and motility of >7000 individual CAR-T cells was tracked across four microraft arrays. The automated microraft array platform measured temporal cell-mediated cytotoxicity, CAR-T cell motility, CAR-T cell death, and CAR-T cell to target cell distances, followed by the capability to sort any desired CAR-T cell. The pipeline has the potential to further our understanding of T cell-based cancer immunotherapies and improve cell-therapy products for better patient outcomes.
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Affiliation(s)
- Cody A. LaBelle
- Joint Department of Biomedical Engineering, University of North Carolina, Chapel Hill, NC, and North Carolina State University, Raleigh, NC
- Department of Bioengineering, University of Washington, Seattle, WA
| | - Raymond J. Zhang
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
| | - Sally A. Hunsucker
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
| | - Paul M. Armistead
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
- Department of Medicine, Division of Hematology, University of North Carolina, Chapel Hill, NC
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3
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Cortés-Llanos B, Jain V, Volkheimer A, Browne EP, Murdoch DM, Allbritton NL. Automated microarray for single-cell sorting and collection of lymphocytes following HIV reactivation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.02.526757. [PMID: 36778314 PMCID: PMC9915582 DOI: 10.1101/2023.02.02.526757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
A promising strategy to cure HIV infected individuals is to use latency reversing agents (LRAs) to reactivate latent viruses, followed by host clearance of infected reservoir cells. However, reactivation of latent proviruses within infected cells is heterogeneous and often incomplete. This fact limits strategies to cure HIV which may require complete elimination of viable virus from all cellular reservoirs. For this reason, understanding the mechanism(s) of reactivation of HIV within cellular reservoirs is critical to achieve therapeutic success. Methodologies enabling temporal tracking of single cells as they reactivate followed by sorting and molecular analysis of those cells are urgently needed. To this end, microraft arrays were adapted to image T-lymphocytes expressing mCherry under the control of the HIV long terminal repeat (LTR) promoter, in response to the application of various LRAs (prostratin, iBET151, and SAHA). In response to prostratin, iBET151, and SAHA, 30.5 %, 11.2 %, and 12.1 % percentage of cells respectively, reactivated similar to that observed in other experimental systems. The arrays enabled large numbers of single cells (>25,000) to be imaged over time. mCherry fluorescence quantification identified cell subpopulations with differing reactivation kinetics. Significant heterogeneity was observed at the single cell level between different LRAs in terms of time to reactivation, rate of mCherry fluorescence increase upon reactivation, and peak fluorescence attained. In response to prostratin, subpopulations of T lymphocytes with slow and fast reactivation kinetics were identified. Single T-lymphocytes that were either fast or slow reactivators were sorted, and single-cell RNA-sequencing was performed. Different genes associated with inflammation, immune activation, and cellular and viral transcription factors were found. These results advance our conceptual understanding of HIV reactivation dynamics at the single-cell level toward a cure for HIV.
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DiSalvo M, Cortés-Llanos B, LaBelle CA, Murdoch DM, Allbritton NL. Scalable Additive Construction of Arrayed Microstructures with Encoded Properties for Bioimaging. MICROMACHINES 2022; 13:1392. [PMID: 36144015 PMCID: PMC9500771 DOI: 10.3390/mi13091392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/20/2022] [Accepted: 08/23/2022] [Indexed: 06/16/2023]
Abstract
Microarrays are essential components of analytical instruments. The elements of microarrays may be imbued with additional functionalities and encodings using composite materials and structures, but traditional microfabrication methods present substantial barriers to fabrication, design, and scalability. In this work, a tool-free technique was reported to additively batch-construct micromolded, composite, and arrayed microstructures. The method required only a compatible carrier fluid to deposit a material onto a substrate with some topography. Permutations of this basic fabrication approach were leveraged to gain control over the volumes and positions of deposited materials within the microstructures. As a proof of concept, cell micro-carrier arrays were constructed to demonstrate a range of designs, compositions, functionalities, and applications for composite microstructures. This approach is envisioned to enable the fabrication of complex composite biological and synthetic microelements for biosensing, cellular analysis, and biochemical screening.
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Affiliation(s)
- Matthew DiSalvo
- Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Belén Cortés-Llanos
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA
- Department of Medicine, Duke University Medical Center, Durham, NC 27705, USA
| | - Cody A. LaBelle
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA
| | - David M. Murdoch
- Department of Medicine, Duke University Medical Center, Durham, NC 27705, USA
| | - Nancy L. Allbritton
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA
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Cortés-Llanos B, Wang Y, Sims CE, Allbritton NL. A technology of a different sort: microraft arrays. LAB ON A CHIP 2021; 21:3204-3218. [PMID: 34346456 PMCID: PMC8387436 DOI: 10.1039/d1lc00506e] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A common procedure performed throughout biomedical research is the selection and isolation of biological entities such as organelles, cells and organoids from a mixed population. In this review, we describe the development and application of microraft arrays, an analysis and isolation platform which enables a vast range of criteria and strategies to be used when separating biological entities. The microraft arrays are comprised of elastomeric microwells with detachable polymer bases (microrafts) that act as capture and culture sites as well as supporting carriers during cell isolation. The technology is elegant in its simplicity and can be implemented for samples possessing tens to millions of objects yielding a flexible platform for applications such as single-cell RNA sequencing, subcellular organelle capture and assay, high-throughput screening and development of CRISPR gene-edited cell lines, and organoid manipulation and selection. The transparent arrays are compatible with a multitude of imaging modalities enabling selection based on 2D or 3D spatial phenotypes or temporal properties. Each microraft can be individually isolated on demand with retention of high viability due to the near zero hydrodynamic stress imposed upon the cells during microraft release, capture and deposition. The platform has been utilized as a simple manual add-on to a standard microscope or incorporated into fully automated instruments that implement state-of-the-art imaging algorithms and machine learning. The vast array of selection criteria enables separations not possible with conventional sorting methods, thus garnering widespread interest in the biological and pharmaceutical sciences.
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Liu L, Dong X, Tu Y, Miao G, Zhang Z, Zhang L, Wei Z, Yu D, Qiu X. Methods and platforms for analysis of nucleic acids from single-cell based on microfluidics. MICROFLUIDICS AND NANOFLUIDICS 2021; 25:87. [PMID: 34580578 PMCID: PMC8457033 DOI: 10.1007/s10404-021-02485-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 08/30/2021] [Indexed: 05/14/2023]
Abstract
Single-cell nucleic acid analysis aims at discovering the genetic differences between individual cells which is well known as the cellular heterogeneity. This technology facilitates cancer diagnosis, stem cell research, immune system analysis, and other life science applications. The conventional platforms for single-cell nucleic acid analysis more rely on manual operation or bulky devices. Recently, the emerging microfluidic technology has provided a perfect platform for single-cell nucleic acid analysis with the characteristic of accurate and automatic single-cell manipulation. In this review, we briefly summarized the procedure of single-cell nucleic acid analysis including single-cell isolation, single-cell lysis, nucleic acid amplification, and genetic analysis. And then, three representative microfluidic platforms for single-cell nucleic acid analysis are concluded as valve-, microwell-, and droplet-based platforms. Furthermore, we described the state-of-the-art integrated single-cell nucleic acid analysis systems based on the three platforms. Finally, the future development and challenges of microfluidics-based single-cell nucleic acid analysis are discussed as well.
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Affiliation(s)
- Luyao Liu
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029 China
| | - Xiaobin Dong
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029 China
| | - Yunping Tu
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029 China
| | - Guijun Miao
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029 China
| | - Zhongping Zhang
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029 China
| | - Lulu Zhang
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029 China
| | - Zewen Wei
- Department of Biomedical Engineering, School of Life Science, Beijing Institute of Technology, Beijing, 100081 China
| | - Duli Yu
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029 China
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing, 100029 China
| | - Xianbo Qiu
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029 China
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Wheeler EC, Vu AQ, Einstein JM, DiSalvo M, Ahmed N, Van Nostrand EL, Shishkin AA, Jin W, Allbritton NL, Yeo GW. Pooled CRISPR screens with imaging on microraft arrays reveals stress granule-regulatory factors. Nat Methods 2020; 17:636-642. [PMID: 32393832 PMCID: PMC7357298 DOI: 10.1038/s41592-020-0826-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 04/06/2020] [Indexed: 12/12/2022]
Abstract
Genetic screens using pooled CRISPR-based approaches are scalable and inexpensive, but restricted to standard readouts, including survival, proliferation and sortable markers. However, many biologically relevant cell states involve cellular and subcellular changes that are only accessible by microscopic visualization, and are currently impossible to screen with pooled methods. Here we combine pooled CRISPR-Cas9 screening with microraft array technology and high-content imaging to screen image-based phenotypes (CRaft-ID; CRISPR-based microRaft followed by guide RNA identification). By isolating microrafts that contain genetic clones harboring individual guide RNAs (gRNA), we identify RNA-binding proteins (RBPs) that influence the formation of stress granules, the punctate protein-RNA assemblies that form during stress. To automate hit identification, we developed a machine-learning model trained on nuclear morphology to remove unhealthy cells or imaging artifacts. In doing so, we identified and validated previously uncharacterized RBPs that modulate stress granule abundance, highlighting the applicability of our approach to facilitate image-based pooled CRISPR screens.
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Affiliation(s)
- Emily C Wheeler
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA, USA
| | - Anthony Q Vu
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA, USA
| | - Jaclyn M Einstein
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA, USA
| | - Matthew DiSalvo
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill and Raleigh, NC, USA
| | - Noorsher Ahmed
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA, USA
| | - Eric L Van Nostrand
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA, USA
| | - Alexander A Shishkin
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Eclipse BioInnovations, San Diego, CA, USA
| | - Wenhao Jin
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA, USA
| | - Nancy L Allbritton
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill and Raleigh, NC, USA
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA, USA.
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Nowotarski HL, Attayek PJ, Allbritton NL. Automated platform for cell selection and separation based on four-dimensional motility and matrix degradation. Analyst 2020; 145:2731-2742. [PMID: 32083265 PMCID: PMC7716803 DOI: 10.1039/c9an02224d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Motility and invasion are key steps in the metastatic cascade, enabling cells to move through normal tissue borders into the surrounding stroma. Most available in vitro assays track cell motility or cell invasion but lack the ability to measure both simultaneously and then separate single cells with unique behaviors. In this work, we developed a cell-separation platform capable of tracking cell movement (chemokinesis) and invasion through an extracellular matrix in space and time. The platform utilized a collagen scaffold with embedded tumor cells overlaid onto a microraft array. Confocal microscopy enabled high resolution (0.4 × 0.4 × 3.5 µm voxel) monitoring of cell movement within the scaffolds. Two pancreatic cancer cell lines with known differing invasiveness were characterized on this platform, with median motilities of 14 ± 6 μm and 10 ± 4 μm over 48 h. Within the same cell line, cells demonstrated highly variable motility, with XYZ movement ranging from 144 μm to 2 μm over 24 h. The ten lowest and highest motility cells, with median movements of 33 ± 11 μm and 3 ± 1 μm, respectively, were separated and sub-cultured. After 6 weeks of culture, the cell populations were assayed on a Transwell invasion assay and 227 ± 56 cells were invasive in the high motility population while only 48 ± 10 cells were invasive in the low motility population, indicating that the resulting offspring possessed a motility phenotype reflective of the parental cells. This work demonstrates the feasibility of sorting single cells based on complex phenotypes along with the capability to further probe those cells and explore biological phenomena.
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Affiliation(s)
- Hannah L Nowotarski
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, USA.
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LaBelle CA, Zhang RJ, Armistead PM, Allbritton NL. Assay and Isolation of Single Proliferating CD4+ Lymphocytes Using an Automated Microraft Array Platform. IEEE Trans Biomed Eng 2019; 67:2166-2175. [PMID: 31794384 DOI: 10.1109/tbme.2019.2956081] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
OBJECTIVE While T lymphocytes have been employed as a cancer immunotherapy, the development of effective and specific T-cell-based therapeutics remains challenging. A key obstacle is the difficulty in identifying T cells reactive to cancer-associated antigens. The objective of this research was to develop a versatile platform for single cell analysis and isolation that can be applied in immunology research and clinical therapy development. METHODS An automated microscopy and cell sorting system was developed to track the proliferative behavior of single-cell human primary CD4+ lymphocytes in response to stimulation using allogeneic lymphoblastoid feeder cells. RESULTS The system identified single human T lymphocytes with a sensitivity of 98% and specificity of 99% and possessed a cell collection efficiency of 86%. Time-lapse imaging simultaneously tracked 4,534 alloreactive T cells on a single array; 19% of the arrayed cells formed colonies of ≥2 cells. From the array, 130 clonal colonies were isolated and 7 grew to colony sizes of >10,000 cells, consistent with the known proliferative capacity of T cells in vitro and their tendency to become exhausted with prolonged stimulation. The isolated colonies underwent ELISA assay to detect interferon-γ secretion and Sanger sequencing to determine T cell receptor β sequences with a 100% success rate. CONCLUSION The platform is capable of both identification and isolation of proliferative T cells in an automated manner. SIGNIFICANCE This novel technology enables the identification of TCR sequences based on T cell proliferation which is expected to speed the development of future cancer immunotherapies.
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DiSalvo M, Harris DM, Kantesaria S, Peña AN, Allbritton-King JD, Cole JH, Allbritton NL. Characterization of Tensioned PDMS Membranes for Imaging Cytometry on Microraft Arrays. Anal Chem 2018; 90:4792-4800. [PMID: 29510027 DOI: 10.1021/acs.analchem.8b00176] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Polydimethylsiloxane (PDMS) membranes can act as sensing elements, barriers, and substrates, yet the low rigidity of the elastomeric membranes can limit their practical use in devices. Microraft arrays rely on a freestanding PDMS membrane as a substrate for cell arrays used in imaging cytometry and cellular isolation. However, the underlying PDMS membrane deforms under the weight of the cell media, making automated analytical microscopy (and thus cytometry and cell isolation) challenging. Here we report the development of microfabrication strategies and physically motivated mathematical modeling of membrane deformation of PDMS microarrays. Microraft arrays were fabricated with mechanical tension stored within the PDMS substrate. These membranes deformed 20× less than that of arrays fabricated using prior methods. Modeling of the deformation of pretensioned arrays using linear membrane theory yielded ≤15% error in predicting the array deflection and predicted the impact of cure temperatures up to 120 °C. A mathematical approach was developed to fit models of microraft shape to sparse real-world shape measurements. Automated imaging of cells on pretensioned microarrays using the focal planes predicted by the model produced high quality fluorescence images of cells, enabling accurate cell area quantification (<4% error) at increased speed (13×) relative to conventional methods. Our microfabrication method and simplified, linear modeling approach is readily applicable to control the deformation of similar membranes in MEMs devices, sensors, and microfluidics.
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Affiliation(s)
- Matthew DiSalvo
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States and North Carolina State University, Raleigh, North Carolina 27607, United States
| | | | - Saurin Kantesaria
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States and North Carolina State University, Raleigh, North Carolina 27607, United States
| | | | - Jules D Allbritton-King
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States and North Carolina State University, Raleigh, North Carolina 27607, United States
| | - Jacqueline H Cole
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States and North Carolina State University, Raleigh, North Carolina 27607, United States
| | - Nancy L Allbritton
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States and North Carolina State University, Raleigh, North Carolina 27607, United States
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Samsa LA, Williamson IA, Magness ST. Quantitative Analysis of Intestinal Stem Cell Dynamics Using Microfabricated Cell Culture Arrays. Methods Mol Biol 2018; 1842:139-166. [PMID: 30196407 DOI: 10.1007/978-1-4939-8697-2_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Regeneration of intestinal epithelium is fueled by a heterogeneous population of rapidly proliferating stem cells (ISCs) found in the base of the small intestine and colonic crypts. ISCs populations can be enriched by fluorescence-activated cell sorting (FACS) based on expression of combinatorial cell surface markers, and fluorescent transgenes. Conventional ISC culture is performed by embedding single ISCs or whole crypt units in a matrix and culturing in conditions that stimulate or repress key pathways to recapitulate ISC niche signaling. Cultured ISCs form organoid, which are spherical, epithelial monolayers that are self-renewing, self-patterning, and demonstrate the full complement of intestinal epithelial cell lineages. However, this conventional "bulk" approach to studying ISC biology is often semiquantitative, low throughput, and masks clonal effects and ISC phenotypic heterogeneity. Our group has recently reported the construction, long-term biocompatibility, and use of microfabricated cell raft arrays (CRA) for high-throughput analysis of single ISCs and organoids. CRAs are composed of thousands of indexed and independently retrievable microwells, which in combination with time-lapse microscopy and/or gene-expression analyses are a powerful tool for studying clonal ISC dynamics and micro-niches. In this protocol, we describe how CRAs are used as an adaptable experimental platform to study the effect of exogenous factors on clonal stem cell behavior.
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Affiliation(s)
- Leigh A Samsa
- Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ian A Williamson
- Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- NC State/UNC Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Scott T Magness
- Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- NC State/UNC Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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Attayek PJ, Waugh JP, Hunsucker SA, Grayeski PJ, Sims CE, Armistead PM, Allbritton NL. Automated microraft platform to identify and collect non-adherent cells successfully gene-edited with CRISPR-Cas9. Biosens Bioelectron 2016; 91:175-182. [PMID: 28006686 DOI: 10.1016/j.bios.2016.12.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Revised: 12/06/2016] [Accepted: 12/08/2016] [Indexed: 11/16/2022]
Abstract
Microraft arrays have been used to screen and then isolate adherent and non-adherent cells with very high efficiency and excellent viability; however, manual screening and isolation limits the throughput and utility of the technology. In this work, novel hardware and software were developed to automate the microraft array platform. The developed analysis software identified microrafts on the array with greater than 99% sensitivity and cells on the microrafts with 100% sensitivity. The software enabled time-lapse imaging and the use of temporally varying characteristics as sort criteria. The automated hardware released microrafts with 98% efficiency and collected released microrafts with 100% efficiency. The automated system was used to examine the temporal variation in EGFP expression in cells transfected with CRISPR-Cas9 components for gene editing. Of 11,499 microrafts possessing a single cell, 220 microrafts were identified as possessing temporally varying EGFP-expression. Candidate cells (n=172) were released and collected from the microraft array and screened for the targeted gene mutation. Two cell colonies were successfully gene edited demonstrating the desired mutation.
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Affiliation(s)
- Peter J Attayek
- Department of Biomedical Engineering, University of North Carolina, Chapel Hill NC and North Carolina State University, Raleigh, NC, United States
| | - Jennifer P Waugh
- Department of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Sally A Hunsucker
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, United States
| | - Philip J Grayeski
- Department of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Christopher E Sims
- Department of Medicine, University of North Carolina, Chapel Hill, NC, United States; Department of Chemistry, University of North Carolina, Chapel Hill, NC, United States
| | - Paul M Armistead
- Department of Medicine, University of North Carolina, Chapel Hill, NC, United States; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, United States
| | - Nancy L Allbritton
- Department of Biomedical Engineering, University of North Carolina, Chapel Hill NC and North Carolina State University, Raleigh, NC, United States; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, United States; Department of Chemistry, University of North Carolina, Chapel Hill, NC, United States.
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Attayek PJ, Hunsucker SA, Sims CE, Allbritton NL, Armistead PM. Identification and isolation of antigen-specific cytotoxic T lymphocytes with an automated microraft sorting system. Integr Biol (Camb) 2016; 8:1208-1220. [PMID: 27853786 PMCID: PMC5138107 DOI: 10.1039/c6ib00168h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The simultaneous measurement of T cell function with recovery of individual T cells would greatly facilitate characterizing antigen-specific responses both in vivo and in model systems. We have developed a microraft array methodology that automatically measures the ability of individual T cells to kill a population of target cells and viably sorts specific cells into a 96-well plate for expansion. A human T cell culture was generated against the influenza M1p antigen. Individual microrafts on a 70 × 70 array were loaded with on average 1 CD8+ cell from the culture and a population of M1p presenting target cells. Target cell killing, measured by fluorescence microscopy, was quantified in each microraft. The rates of target cell death among the individual CD8+ T cells varied greatly; however, individual T cells maintained their rates of cytotoxicity throughout the time course of the experiment enabling rapid identification of highly cytotoxic CD8+ T cells. Microrafts with highly active CD8+ T cells were individually transferred to wells of a 96-well plate, using a needle-release device coupled to the microscope. Three sorted T cells clonally expanded. All of these expressed high-avidity T cell receptors for M1p/HLA*02:01 tetramers, and 2 of the 3 receptors were sequenced. While this study investigated single T cell cytotoxicity rates against simple targets with subsequent cell sorting, future studies will involve measuring T cell mediated cytotoxicity in more complex cellular environments, enlarging the arrays to identify very rare antigen specific T cells, and measuring single cell CD4+ and CD8+ T cell proliferation.
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Affiliation(s)
- Peter J. Attayek
- Department of Biomedical Engineering, University of North Carolina, Chapel Hill NC and North Carolina State University, Raleigh NC
| | - Sally A. Hunsucker
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
| | - Christopher E. Sims
- Department of Chemistry, University of North Carolina, Chapel Hill, NC
- Department of Medicine, University of North Carolina, Chapel Hill, NC
| | - Nancy L. Allbritton
- Department of Biomedical Engineering, University of North Carolina, Chapel Hill NC and North Carolina State University, Raleigh NC
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
- Department of Chemistry, University of North Carolina, Chapel Hill, NC
| | - Paul M. Armistead
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
- Department of Medicine, University of North Carolina, Chapel Hill, NC
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Welch JD, Williams LA, DiSalvo M, Brandt AT, Marayati R, Sims CE, Allbritton NL, Prins JF, Yeh JJ, Jones CD. Selective single cell isolation for genomics using microraft arrays. Nucleic Acids Res 2016; 44:8292-301. [PMID: 27530426 PMCID: PMC5041489 DOI: 10.1093/nar/gkw700] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 07/29/2016] [Indexed: 12/13/2022] Open
Abstract
Genomic methods are used increasingly to interrogate the individual cells that compose specific tissues. However, current methods for single cell isolation struggle to phenotypically differentiate specific cells in a heterogeneous population and rely primarily on the use of fluorescent markers. Many cellular phenotypes of interest are too complex to be measured by this approach, making it difficult to connect genotype and phenotype at the level of individual cells. Here we demonstrate that microraft arrays, which are arrays containing thousands of individual cell culture sites, can be used to select single cells based on a variety of phenotypes, such as cell surface markers, cell proliferation and drug response. We then show that a common genomic procedure, RNA-seq, can be readily adapted to the single cells isolated from these rafts. We show that data generated using microrafts and our modified RNA-seq protocol compared favorably with the Fluidigm C1. We then used microraft arrays to select pancreatic cancer cells that proliferate in spite of cytotoxic drug treatment. Our single cell RNA-seq data identified several expected and novel gene expression changes associated with early drug resistance.
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Affiliation(s)
- Joshua D Welch
- Curriculum in Bioinformatics and Computational Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA Department of Computer Science, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA
| | - Lindsay A Williams
- iBGS-Integrative Program for Biological & Genome Sciences,3356 Genome Sciences Bldg, CB #7100 Chapel Hill, NC 27599-7100, USA Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA
| | - Matthew DiSalvo
- Joint Biomedical Engineering Program, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA
| | - Alicia T Brandt
- Department of Biology, Campus Box 3280, Coker Hall, UNC-Chapel Hill, Chapel Hill, NC 27599-3280, USA
| | - Raoud Marayati
- iBGS-Integrative Program for Biological & Genome Sciences,3356 Genome Sciences Bldg, CB #7100 Chapel Hill, NC 27599-7100, USA
| | - Christopher E Sims
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA
| | - Nancy L Allbritton
- iBGS-Integrative Program for Biological & Genome Sciences,3356 Genome Sciences Bldg, CB #7100 Chapel Hill, NC 27599-7100, USA Joint Biomedical Engineering Program, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA
| | - Jan F Prins
- Curriculum in Bioinformatics and Computational Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA Department of Computer Science, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA
| | - Jen Jen Yeh
- iBGS-Integrative Program for Biological & Genome Sciences,3356 Genome Sciences Bldg, CB #7100 Chapel Hill, NC 27599-7100, USA Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA Department of Surgery, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA
| | - Corbin D Jones
- Curriculum in Bioinformatics and Computational Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA Department of Biology, Campus Box 3280, Coker Hall, UNC-Chapel Hill, Chapel Hill, NC 27599-3280, USA Department of Surgery, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA
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15
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Decrop D, Brans T, Gijsenbergh P, Lu J, Spasic D, Kokalj T, Beunis F, Goos P, Puers R, Lammertyn J. Optical Manipulation of Single Magnetic Beads in a Microwell Array on a Digital Microfluidic Chip. Anal Chem 2016; 88:8596-603. [PMID: 27448015 DOI: 10.1021/acs.analchem.6b01734] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The detection of single molecules in magnetic microbead microwell array formats revolutionized the development of digital bioassays. However, retrieval of individual magnetic beads from these arrays has not been realized until now despite having great potential for studying captured targets at the individual level. In this paper, optical tweezers were implemented on a digital microfluidic platform for accurate manipulation of single magnetic beads seeded in a microwell array. Successful optical trapping of magnetic beads was found to be dependent on Brownian motion of the beads, suggesting a 99% chance of trapping a vibrating bead. A tailor-made experimental design was used to screen the effect of bead type, ionic buffer strength, surfactant type, and concentration on the Brownian activity of beads in microwells. With the optimal conditions, the manipulation of magnetic beads was demonstrated by their trapping, retrieving, transporting, and repositioning to a desired microwell on the array. The presented platform combines the strengths of digital microfluidics, digital bioassays, and optical tweezers, resulting in a powerful dynamic microwell array system for single molecule and single cell studies.
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Affiliation(s)
- Deborah Decrop
- Department of Biosystems, MEBIOS-Biosensors, KU Leuven , Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Toon Brans
- Department of Electronics and Information Systems (ELIS) and Center for Nano and Biophotonics (NB-Photonics), UGent , Sint-Pietersnieuwstraat 41, 9000 Gent, Belgium
| | - Pieter Gijsenbergh
- Department of Electrotechnical Engineering (ESAT-MICAS), KU Leuven , Kasteelpark Arenberg 10 Postbus 2440, 3001 Leuven, Belgium
| | - Jiadi Lu
- Department of Biosystems, MEBIOS-Biosensors, KU Leuven , Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Dragana Spasic
- Department of Biosystems, MEBIOS-Biosensors, KU Leuven , Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Tadej Kokalj
- Department of Biosystems, MEBIOS-Biosensors, KU Leuven , Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Filip Beunis
- Department of Electronics and Information Systems (ELIS) and Center for Nano and Biophotonics (NB-Photonics), UGent , Sint-Pietersnieuwstraat 41, 9000 Gent, Belgium
| | - Peter Goos
- Department of Biosystems, MEBIOS-Biosensors, KU Leuven , Willem de Croylaan 42, 3001 Leuven, Belgium.,Faculty of Applied Economics, University of Antwerp, Stadscampus , Prinsstraat 13, 2000 Antwerp, Belgium
| | - Robert Puers
- Department of Electrotechnical Engineering (ESAT-MICAS), KU Leuven , Kasteelpark Arenberg 10 Postbus 2440, 3001 Leuven, Belgium
| | - Jeroen Lammertyn
- Department of Biosystems, MEBIOS-Biosensors, KU Leuven , Willem de Croylaan 42, 3001 Leuven, Belgium
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