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Fenton AD, Archin N, Turner AM, Joseph S, Moeser M, Margolis DM, Browne EP. A novel high-throughput microwell outgrowth assay for HIV-infected cells. J Virol 2024; 98:e0179823. [PMID: 38376258 PMCID: PMC10949454 DOI: 10.1128/jvi.01798-23] [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: 11/27/2023] [Accepted: 01/12/2024] [Indexed: 02/21/2024] Open
Abstract
Although antiretroviral therapy (ART) is effective at suppressing HIV replication, a viral reservoir persists that can reseed infection if ART is interrupted. Curing HIV will require elimination or containment of this reservoir, but the size of the HIV reservoir is highly variable between individuals. To evaluate the size of the HIV reservoir, several assays have been developed, including PCR-based assays for viral DNA, the intact proviral DNA assay, and the quantitative viral outgrowth assay (QVOA). QVOA is the gold standard assay for measuring inducible replication-competent proviruses, but this assay is technically challenging and time-consuming. To begin progress toward a more rapid and less laborious tool for quantifying cells infected with replication-competent HIV, we developed the Microwell Outgrowth Assay, in which infected CD4 T cells are co-cultured with an HIV-detecting reporter cell line in a polydimethylsiloxane (PDMS)/polystyrene array of nanoliter-sized wells. Transmission of HIV from infected cells to the reporter cell line induces fluorescent reporter protein expression that is detected by automated scanning across the array. Using this approach, we were able to detect HIV-infected cells from ART-naïve people with HIV (PWH) and from PWH on ART with large reservoirs. Furthermore, we demonstrate that infected cells can be recovered from individual rafts and used to analyze the diversity of viral sequences. Although additional development and optimization will be required for quantifying the reservoir in PWH with small latent reservoirs, this assay may be a useful prototype for microwell assays of infected cells.IMPORTANCEMeasuring the size of the HIV reservoir in people with HIV (PWH) will be important for determining the impact of HIV cure strategies. However, measuring this reservoir is challenging. We report a new method for quantifying HIV-infected cells that involves culturing cells from PWH in an array of microwells with a cell line that detects HIV infection. We show that this approach can detect rare HIV-infected cells and derive detailed virus sequence information for each infected cell.
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Affiliation(s)
- Anthony D. Fenton
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nancie Archin
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Anne-Marie Turner
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sarah Joseph
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Matthew Moeser
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - David M. Margolis
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Edward P. Browne
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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Sockell A, Wong W, Longwell S, Vu T, Karlsson K, Mokhtari D, Schaepe J, Lo YH, Cornelius V, Kuo C, Van Valen D, Curtis C, Fordyce PM. A microwell platform for high-throughput longitudinal phenotyping and selective retrieval of organoids. Cell Syst 2023; 14:764-776.e6. [PMID: 37734323 DOI: 10.1016/j.cels.2023.08.002] [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: 07/29/2022] [Revised: 02/24/2023] [Accepted: 08/22/2023] [Indexed: 09/23/2023]
Abstract
Organoids are powerful experimental models for studying the ontogeny and progression of various diseases including cancer. Organoids are conventionally cultured in bulk using an extracellular matrix mimic. However, bulk-cultured organoids physically overlap, making it impossible to track the growth of individual organoids over time in high throughput. Moreover, local spatial variations in bulk matrix properties make it difficult to assess whether observed phenotypic heterogeneity between organoids results from intrinsic cell differences or differences in the microenvironment. Here, we developed a microwell-based method that enables high-throughput quantification of image-based parameters for organoids grown from single cells, which can further be retrieved from their microwells for molecular profiling. Coupled with a deep learning image-processing pipeline, we characterized phenotypic traits including growth rates, cellular movement, and apical-basal polarity in two CRISPR-engineered human gastric organoid models, identifying genomic changes associated with increased growth rate and changes in accessibility and expression correlated with apical-basal polarity. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Alexandra Sockell
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Wing Wong
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Scott Longwell
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Thy Vu
- Department of Biochemistry, UT Austin, Austin, TX 78712, USA
| | - Kasper Karlsson
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Daniel Mokhtari
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Julia Schaepe
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Yuan-Hung Lo
- Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Vincent Cornelius
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Calvin Kuo
- Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - David Van Valen
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Christina Curtis
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94110, USA.
| | - Polly M Fordyce
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94110, USA; ChEM-H Institute, Stanford University, Stanford, CA 94305, USA.
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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: 0] [Impact Index Per Article: 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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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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Freitas SC, Sanderson D, Caspani S, Magalhães R, Cortés-Llanos B, Granja A, Reis S, Belo JH, Azevedo J, Gómez-Gaviro MV, de Sousa CT. New Frontiers in Colorectal Cancer Treatment Combining Nanotechnology with Photo- and Radiotherapy. Cancers (Basel) 2023; 15:383. [PMID: 36672333 PMCID: PMC9856291 DOI: 10.3390/cancers15020383] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/19/2022] [Accepted: 12/24/2022] [Indexed: 01/11/2023] Open
Abstract
Colorectal cancer is the third most common cancer worldwide. Despite recent advances in the treatment of this pathology, which include a personalized approach using radio- and chemotherapies in combination with advanced surgical techniques, it is imperative to enhance the performance of these treatments and decrease their detrimental side effects on patients' health. Nanomedicine is likely the pathway towards solving this challenge by enhancing both the therapeutic and diagnostic capabilities. In particular, plasmonic nanoparticles show remarkable potential due to their dual therapeutic functionalities as photothermal therapy agents and as radiosensitizers in radiotherapy. Their dual functionality, high biocompatibility, easy functionalization, and targeting capabilities make them potential agents for inducing efficient cancer cell death with minimal side effects. This review aims to identify the main challenges in the diagnosis and treatment of colorectal cancer. The heterogeneous nature of this cancer is also discussed from a single-cell point of view. The most relevant works in photo- and radiotherapy using nanotechnology-based therapies for colorectal cancer are addressed, ranging from in vitro studies (2D and 3D cell cultures) to in vivo studies and clinical trials. Although the results using nanoparticles as a photo- and radiosensitizers in photo- and radiotherapy are promising, preliminary studies showed that the possibility of combining both therapies must be explored to improve the treatment efficiency.
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Affiliation(s)
- Sara C. Freitas
- IFIMUP-Institute of Physics for Advanced Materials, Nanotechnology and Photonics of University of Porto, LaPMET-Laboratory of Physics for Materials and Emergent Technologies, Departamento de Física e Astronomia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Daniel Sanderson
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Doctor Esquerdo 46, 28007 Madrid, Spain
- Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, 28911 Leganés, Spain
| | - Sofia Caspani
- IFIMUP-Institute of Physics for Advanced Materials, Nanotechnology and Photonics of University of Porto, LaPMET-Laboratory of Physics for Materials and Emergent Technologies, Departamento de Física e Astronomia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Ricardo Magalhães
- IFIMUP-Institute of Physics for Advanced Materials, Nanotechnology and Photonics of University of Porto, LaPMET-Laboratory of Physics for Materials and Emergent Technologies, Departamento de Física e Astronomia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | | | - Andreia Granja
- LAQV, REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, R. Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Salette Reis
- LAQV, REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, R. Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - João Horta Belo
- IFIMUP-Institute of Physics for Advanced Materials, Nanotechnology and Photonics of University of Porto, LaPMET-Laboratory of Physics for Materials and Emergent Technologies, Departamento de Física e Astronomia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - José Azevedo
- Colorectal Surgery—Champalimaud Foundation, Champalimaud Centre for the Unknown, Avenida Brasília, 1400-038 Lisboa, Portugal
| | - Maria Victoria Gómez-Gaviro
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Doctor Esquerdo 46, 28007 Madrid, Spain
- Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, 28911 Leganés, Spain
| | - Célia Tavares de Sousa
- IFIMUP-Institute of Physics for Advanced Materials, Nanotechnology and Photonics of University of Porto, LaPMET-Laboratory of Physics for Materials and Emergent Technologies, Departamento de Física e Astronomia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
- Departamento de Física Aplicada, Facultad de Ciencias, Universidad Autonoma de Madrid (UAM), Campus de Cantoblanco, C/ Francisco Tomas y Valiente, 7, 28049 Madrid, Spain
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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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