1
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Ng AHC, Hu H, Wang K, Scherler K, Warren SE, Zollinger DR, McKay-Fleisch J, Sorg K, Beechem JM, Ragaglia E, Lacy JM, Smith KD, Marshall DA, Bundesmann MM, López de Castilla D, Corwin D, Yarid N, Knudsen BS, Lu Y, Goldman JD, Heath JR. Organ-specific immunity: A tissue analysis framework for investigating local immune responses to SARS-CoV-2. Cell Rep 2023; 42:113212. [PMID: 37792533 DOI: 10.1016/j.celrep.2023.113212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 09/03/2023] [Accepted: 09/18/2023] [Indexed: 10/06/2023] Open
Abstract
Local immune activation at mucosal surfaces, mediated by mucosal lymphoid tissues, is vital for effective immune responses against pathogens. While pathogens like severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can spread to multiple organs, patients with coronavirus disease 2019 (COVID-19) primarily experience inflammation and damage in their lungs. To investigate this apparent organ-specific immune response, we develop an analytical framework that recognizes the significance of mucosal lymphoid tissues. This framework combines histology, immunofluorescence, spatial transcript profiling, and mathematical modeling to identify cellular and gene expression differences between the lymphoid tissues of the lung and the gut and predict the determinants of those differences. Our findings indicate that mucosal lymphoid tissues are pivotal in organ-specific immune response to SARS-CoV-2, mediating local inflammation and tissue damage and contributing to immune dysfunction. The framework developed here has potential utility in the study of long COVID and may streamline biomarker discovery and treatment design for diseases with differential pathologies at the organ level.
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Affiliation(s)
- Alphonsus H C Ng
- Department of Molecular Pharmaceutics, University of Utah, Salt Lake City, UT 84112, USA; Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA
| | - Huiqian Hu
- Department of Molecular Pharmaceutics, University of Utah, Salt Lake City, UT 84112, USA
| | - Kai Wang
- Institute for Systems Biology, Seattle, WA 98109, USA
| | | | | | | | | | | | | | - Emily Ragaglia
- CellNetix Pathology and Laboratories, Seattle, WA 98168, USA
| | - J Matthew Lacy
- Snohomish County Medical Examiner's Office, Everett, WA 98204, USA
| | - Kelly D Smith
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Desiree A Marshall
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Michael M Bundesmann
- Division of Pulmonary and Critical Care, Evergreen Health, Kirkland, WA 98034, USA
| | | | - David Corwin
- CellNetix Pathology and Laboratories, Seattle, WA 98168, USA
| | - Nicole Yarid
- King County Medical Examiner's Office, Harborview Medical Center, Seattle, WA 98104, USA
| | - Beatrice S Knudsen
- Huntsman Cancer Institute BMP Core, University of Utah, Salt Lake City, UT 84112, USA; Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA
| | - Yue Lu
- Department of Molecular Pharmaceutics, University of Utah, Salt Lake City, UT 84112, USA.
| | - Jason D Goldman
- Swedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA 98104, USA; Providence St. Joseph Health System, Renton, WA 98057, USA; Division of Infectious Disease, University of Washington, Seattle, WA 98101, USA.
| | - James R Heath
- Institute for Systems Biology, Seattle, WA 98109, USA.
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2
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Chour W, Choi J, Xie J, Chaffee ME, Schmitt TM, Finton K, DeLucia DC, Xu AM, Su Y, Chen DG, Zhang R, Yuan D, Hong S, Ng AHC, Butler JZ, Edmark RA, Jones LC, Murray KM, Peng S, Li G, Strong RK, Lee JK, Goldman JD, Greenberg PD, Heath JR. Large libraries of single-chain trimer peptide-MHCs enable antigen-specific CD8+ T cell discovery and analysis. Commun Biol 2023; 6:528. [PMID: 37193826 PMCID: PMC10186326 DOI: 10.1038/s42003-023-04899-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 05/01/2023] [Indexed: 05/18/2023] Open
Abstract
The discovery and characterization of antigen-specific CD8+ T cell clonotypes typically involves the labor-intensive synthesis and construction of peptide-MHC tetramers. We adapt single-chain trimer (SCT) technologies into a high throughput platform for pMHC library generation, showing that hundreds can be rapidly prepared across multiple Class I HLA alleles. We use this platform to explore the impact of peptide and SCT template mutations on protein expression yield, thermal stability, and functionality. SCT libraries were an efficient tool for identifying T cells recognizing commonly reported viral epitopes. We then construct SCT libraries to capture SARS-CoV-2 specific CD8+ T cells from COVID-19 participants and healthy donors. The immunogenicity of these epitopes is validated by functional assays of T cells with cloned TCRs captured using SCT libraries. These technologies should enable the rapid analyses of peptide-based T cell responses across several contexts, including autoimmunity, cancer, or infectious disease.
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Affiliation(s)
- William Chour
- Institute for Systems Biology, Seattle, WA, 98109, USA
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Jongchan Choi
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | - Jingyi Xie
- Institute for Systems Biology, Seattle, WA, 98109, USA
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, 98195, USA
| | - Mary E Chaffee
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Thomas M Schmitt
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Kathryn Finton
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Diana C DeLucia
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Alexander M Xu
- Institute for Systems Biology, Seattle, WA, 98109, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Yapeng Su
- Institute for Systems Biology, Seattle, WA, 98109, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Daniel G Chen
- Institute for Systems Biology, Seattle, WA, 98109, USA
- Department of Microbiology and Department of Informatics, University of Washington, Seattle, WA, 98195, USA
| | - Rongyu Zhang
- Institute for Systems Biology, Seattle, WA, 98109, USA
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Dan Yuan
- Institute for Systems Biology, Seattle, WA, 98109, USA
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Sunga Hong
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | - Alphonsus H C Ng
- Institute for Systems Biology, Seattle, WA, 98109, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Jonah Z Butler
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Rick A Edmark
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | | | - Kim M Murray
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | | | - Guideng Li
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
- Suzhou Institute of Systems Medicine, Suzhou, 215123, China
- Key Laboratory of Synthetic Biology Regulatory Element, Chinese Academy of Medical Sciences, Beijing, China
| | - Roland K Strong
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - John K Lee
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Jason D Goldman
- Swedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA, 98104, USA
- Division of Infectious Disease, Department of Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Philip D Greenberg
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, WA, 98195, USA
- Department of Immunology, University of Washington, Seattle, WA, 98195, USA
| | - James R Heath
- Institute for Systems Biology, Seattle, WA, 98109, USA.
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA.
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3
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Foy SP, Jacoby K, Bota DA, Hunter T, Pan Z, Stawiski E, Ma Y, Lu W, Peng S, Wang CL, Yuen B, Dalmas O, Heeringa K, Sennino B, Conroy A, Bethune MT, Mende I, White W, Kukreja M, Gunturu S, Humphrey E, Hussaini A, An D, Litterman AJ, Quach BB, Ng AHC, Lu Y, Smith C, Campbell KM, Anaya D, Skrdlant L, Huang EYH, Mendoza V, Mathur J, Dengler L, Purandare B, Moot R, Yi MC, Funke R, Sibley A, Stallings-Schmitt T, Oh DY, Chmielowski B, Abedi M, Yuan Y, Sosman JA, Lee SM, Schoenfeld AJ, Baltimore D, Heath JR, Franzusoff A, Ribas A, Rao AV, Mandl SJ. Non-viral precision T cell receptor replacement for personalized cell therapy. Nature 2023; 615:687-696. [PMID: 36356599 PMCID: PMC9768791 DOI: 10.1038/s41586-022-05531-1] [Citation(s) in RCA: 85] [Impact Index Per Article: 85.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 11/04/2022] [Indexed: 11/12/2022]
Abstract
T cell receptors (TCRs) enable T cells to specifically recognize mutations in cancer cells1-3. Here we developed a clinical-grade approach based on CRISPR-Cas9 non-viral precision genome-editing to simultaneously knockout the two endogenous TCR genes TRAC (which encodes TCRα) and TRBC (which encodes TCRβ). We also inserted into the TRAC locus two chains of a neoantigen-specific TCR (neoTCR) isolated from circulating T cells of patients. The neoTCRs were isolated using a personalized library of soluble predicted neoantigen-HLA capture reagents. Sixteen patients with different refractory solid cancers received up to three distinct neoTCR transgenic cell products. Each product expressed a patient-specific neoTCR and was administered in a cell-dose-escalation, first-in-human phase I clinical trial ( NCT03970382 ). One patient had grade 1 cytokine release syndrome and one patient had grade 3 encephalitis. All participants had the expected side effects from the lymphodepleting chemotherapy. Five patients had stable disease and the other eleven had disease progression as the best response on the therapy. neoTCR transgenic T cells were detected in tumour biopsy samples after infusion at frequencies higher than the native TCRs before infusion. This study demonstrates the feasibility of isolating and cloning multiple TCRs that recognize mutational neoantigens. Moreover, simultaneous knockout of the endogenous TCR and knock-in of neoTCRs using single-step, non-viral precision genome-editing are achieved. The manufacture of neoTCR engineered T cells at clinical grade, the safety of infusing up to three gene-edited neoTCR T cell products and the ability of the transgenic T cells to traffic to the tumours of patients are also demonstrated.
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MESH Headings
- Humans
- Antigens, Neoplasm/genetics
- Antigens, Neoplasm/immunology
- Biopsy
- Cell- and Tissue-Based Therapy/adverse effects
- Cell- and Tissue-Based Therapy/methods
- Cytokine Release Syndrome/complications
- Disease Progression
- Encephalitis/complications
- Gene Editing
- Gene Knock-In Techniques
- Gene Knockout Techniques
- Genes, T-Cell Receptor alpha
- Genes, T-Cell Receptor beta
- Mutation
- Neoplasms/complications
- Neoplasms/genetics
- Neoplasms/immunology
- Neoplasms/therapy
- Patient Safety
- Precision Medicine/adverse effects
- Precision Medicine/methods
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/metabolism
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- Transgenes/genetics
- HLA Antigens/immunology
- CRISPR-Cas Systems
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Affiliation(s)
| | | | - Daniela A Bota
- Department of Neurology and Chao Family Comprehensive Cancer Center, University of California, Irvine, CA, USA
| | | | - Zheng Pan
- PACT Pharma, South San Francisco, CA, USA
| | | | - Yan Ma
- PACT Pharma, South San Francisco, CA, USA
| | - William Lu
- PACT Pharma, South San Francisco, CA, USA
| | | | | | | | | | | | | | | | | | - Ines Mende
- PACT Pharma, South San Francisco, CA, USA
| | | | | | | | | | | | - Duo An
- PACT Pharma, South San Francisco, CA, USA
| | | | | | | | - Yue Lu
- Institute for Systems Biology, Seattle, WA, USA
| | - Chad Smith
- PACT Pharma, South San Francisco, CA, USA
| | - Katie M Campbell
- Department of Medicine, Division of Hematology-Oncology, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | | | | | | | | | | | | | | | | | | | - Roel Funke
- PACT Pharma, South San Francisco, CA, USA
| | | | | | - David Y Oh
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Bartosz Chmielowski
- Department of Medicine, Division of Hematology-Oncology, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center at the University of California, Los Angeles, CA, USA
| | - Mehrdad Abedi
- Division of Hematology/Oncology, Department of Internal Medicine, University of California Davis Comprehensive Cancer Center, Sacramento, CA, USA
| | - Yuan Yuan
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Jeffrey A Sosman
- Department of Medicine and Robert H. Lurie Cancer Center, Northwestern University, Evanston, IL, USA
| | - Sylvia M Lee
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Adam J Schoenfeld
- Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, Weill Cornell Medical College, New York, NY, USA
| | - David Baltimore
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | | | | | - Antoni Ribas
- Department of Medicine, Division of Hematology-Oncology, University of California, Los Angeles (UCLA), Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center at the University of California, Los Angeles, CA, USA.
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4
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Lu Y, Ng AHC, Chow FE, Everson RG, Helmink BA, Tetzlaff MT, Thakur R, Wargo JA, Cloughesy TF, Prins RM, Heath JR. Resolution of tissue signatures of therapy response in patients with recurrent GBM treated with neoadjuvant anti-PD1. Nat Commun 2021; 12:4031. [PMID: 34188042 PMCID: PMC8241935 DOI: 10.1038/s41467-021-24293-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 06/03/2021] [Indexed: 02/06/2023] Open
Abstract
The response of patients with recurrent glioblastoma multiforme to neoadjuvant immune checkpoint blockade has been challenging to interpret due to the inter-patient and intra-tumor heterogeneity. We report on a comparative analysis of tumor tissues collected from patients with recurrent glioblastoma and high-risk melanoma, both treated with neoadjuvant checkpoint blockade. We develop a framework that uses multiplex spatial protein profiling, machine learning-based image analysis, and data-driven computational models to investigate the pathophysiological and molecular factors within the tumor microenvironment that influence treatment response. Using melanoma to guide the interpretation of glioblastoma analyses, we interrogate the protein expression in microscopic compartments of tumors, and determine the correlates of cytotoxic CD8+ T cells, tumor growth, treatment response, and immune cell-cell interaction. This work reveals similarities shared between glioblastoma and melanoma, immunosuppressive factors that are unique to the glioblastoma microenvironment, and potential co-targets for enhancing the efficacy of neoadjuvant immune checkpoint blockade.
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Affiliation(s)
- Yue Lu
- grid.64212.330000 0004 0463 2320Institute for Systems Biology, Seattle, WA USA
| | - Alphonsus H. C. Ng
- grid.64212.330000 0004 0463 2320Institute for Systems Biology, Seattle, WA USA
| | - Frances E. Chow
- grid.19006.3e0000 0000 9632 6718Department of Medical and Molecular Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA USA
| | - Richard G. Everson
- grid.19006.3e0000 0000 9632 6718Department of Medical and Molecular Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA USA
| | - Beth A. Helmink
- grid.240145.60000 0001 2291 4776Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Michael T. Tetzlaff
- grid.240145.60000 0001 2291 4776Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Rohit Thakur
- grid.240145.60000 0001 2291 4776Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Jennifer A. Wargo
- grid.240145.60000 0001 2291 4776Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Timothy F. Cloughesy
- grid.19006.3e0000 0000 9632 6718Department of Medical and Molecular Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA USA
| | - Robert M. Prins
- grid.19006.3e0000 0000 9632 6718Department of Medical and Molecular Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA USA
| | - James R. Heath
- grid.64212.330000 0004 0463 2320Institute for Systems Biology, Seattle, WA USA
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5
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Wells DK, van Buuren MM, Dang KK, Hubbard-Lucey VM, Sheehan KCF, Campbell KM, Lamb A, Ward JP, Sidney J, Blazquez AB, Rech AJ, Zaretsky JM, Comin-Anduix B, Ng AHC, Chour W, Yu TV, Rizvi H, Chen JM, Manning P, Steiner GM, Doan XC, Merghoub T, Guinney J, Kolom A, Selinsky C, Ribas A, Hellmann MD, Hacohen N, Sette A, Heath JR, Bhardwaj N, Ramsdell F, Schreiber RD, Schumacher TN, Kvistborg P, Defranoux NA. Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction. Cell 2020; 183:818-834.e13. [PMID: 33038342 DOI: 10.1016/j.cell.2020.09.015] [Citation(s) in RCA: 223] [Impact Index Per Article: 55.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/08/2020] [Accepted: 09/03/2020] [Indexed: 12/15/2022]
Abstract
Many approaches to identify therapeutically relevant neoantigens couple tumor sequencing with bioinformatic algorithms and inferred rules of tumor epitope immunogenicity. However, there are no reference data to compare these approaches, and the parameters governing tumor epitope immunogenicity remain unclear. Here, we assembled a global consortium wherein each participant predicted immunogenic epitopes from shared tumor sequencing data. 608 epitopes were subsequently assessed for T cell binding in patient-matched samples. By integrating peptide features associated with presentation and recognition, we developed a model of tumor epitope immunogenicity that filtered out 98% of non-immunogenic peptides with a precision above 0.70. Pipelines prioritizing model features had superior performance, and pipeline alterations leveraging them improved prediction performance. These findings were validated in an independent cohort of 310 epitopes prioritized from tumor sequencing data and assessed for T cell binding. This data resource enables identification of parameters underlying effective anti-tumor immunity and is available to the research community.
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Affiliation(s)
- Daniel K Wells
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
| | - Marit M van Buuren
- Division of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Amsterdam, the Netherlands; T Cell Immunology, Biopharmaceutical New Technologies (BioNTech) Corporation, BioNTech US, Cambridge, MA, USA
| | - Kristen K Dang
- Computational Oncology, Sage Bionetworks, Seattle, WA, USA
| | | | - Kathleen C F Sheehan
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, St. Louis, MO, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | - Katie M Campbell
- Division of Hematology and Oncology, Department of Medicine, Johnson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Andrew Lamb
- Computational Oncology, Sage Bionetworks, Seattle, WA, USA
| | - Jeffrey P Ward
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Ana B Blazquez
- Division of Hematology and Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andrew J Rech
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Jesse M Zaretsky
- Division of Hematology and Oncology, Department of Medicine, Johnson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Begonya Comin-Anduix
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Department of Surgery, David Geffen School of Medicine, Johnson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - William Chour
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Thomas V Yu
- Computational Oncology, Sage Bionetworks, Seattle, WA, USA
| | - Hira Rizvi
- Druckenmiller Center for Lung Cancer Research, MSKCC, New York, NY, USA
| | - Jia M Chen
- Division of Hematology and Oncology, Department of Medicine, Johnson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Patrice Manning
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | | | - Xengie C Doan
- Computational Oncology, Sage Bionetworks, Seattle, WA, USA
| | - Taha Merghoub
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Department of Medicine, MSKCC, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Justin Guinney
- Computational Oncology, Sage Bionetworks, Seattle, WA, USA; Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA
| | - Adam Kolom
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Anna-Maria Kellen Clinical Accelerator, Cancer Research Institute, New York, NY, USA
| | - Cheryl Selinsky
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Antoni Ribas
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Division of Hematology and Oncology, Department of Medicine, Johnson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Matthew D Hellmann
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Druckenmiller Center for Lung Cancer Research, MSKCC, New York, NY, USA; Department of Medicine, MSKCC, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Alessandro Sette
- Division of Hematology and Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - James R Heath
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Institute for Systems Biology, Seattle, WA, USA
| | - Nina Bhardwaj
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Division of Hematology and Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Fred Ramsdell
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Robert D Schreiber
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, St. Louis, MO, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | - Ton N Schumacher
- Division of Molecular Oncology and Immunology, Oncode Institute, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Pia Kvistborg
- Division of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Amsterdam, the Netherlands
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6
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Du J, Su Y, Qian C, Yuan D, Miao K, Lee D, Ng AHC, Wijker RS, Ribas A, Levine RD, Heath JR, Wei L. Raman-guided subcellular pharmaco-metabolomics for metastatic melanoma cells. Nat Commun 2020; 11:4830. [PMID: 32973134 PMCID: PMC7518429 DOI: 10.1038/s41467-020-18376-x] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 08/14/2020] [Indexed: 02/06/2023] Open
Abstract
Non-invasively probing metabolites within single live cells is highly desired but challenging. Here we utilize Raman spectro-microscopy for spatial mapping of metabolites within single cells, with the specific goal of identifying druggable metabolic susceptibilities from a series of patient-derived melanoma cell lines. Each cell line represents a different characteristic level of cancer cell de-differentiation. First, with Raman spectroscopy, followed by stimulated Raman scattering (SRS) microscopy and transcriptomics analysis, we identify the fatty acid synthesis pathway as a druggable susceptibility for differentiated melanocytic cells. We then utilize hyperspectral-SRS imaging of intracellular lipid droplets to identify a previously unknown susceptibility of lipid mono-unsaturation within de-differentiated mesenchymal cells with innate resistance to BRAF inhibition. Drugging this target leads to cellular apoptosis accompanied by the formation of phase-separated intracellular membrane domains. The integration of subcellular Raman spectro-microscopy with lipidomics and transcriptomics suggests possible lipid regulatory mechanisms underlying this pharmacological treatment. Our method should provide a general approach in spatially-resolved single cell metabolomics studies. Single-cell metabolomics can offer deep insights into the metabolic reprogramming that accompanies disease states. Here, the authors use Raman spectro-microscopy for non-invasive metabolite analysis and identification of druggable metabolic susceptibilities in single live melanoma cells.
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Affiliation(s)
- Jiajun Du
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Yapeng Su
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.,Institute for Systems Biology, Seattle, WA, USA
| | - Chenxi Qian
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Dan Yuan
- Institute for Systems Biology, Seattle, WA, USA
| | - Kun Miao
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Dongkwan Lee
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | | | - Reto S Wijker
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Antoni Ribas
- Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Raphael D Levine
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
| | | | - Lu Wei
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
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7
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Ng AHC, Peng S, Xu AM, Noh WJ, Guo K, Bethune MT, Chour W, Choi J, Yang S, Baltimore D, Heath JR. MATE-Seq: microfluidic antigen-TCR engagement sequencing. Lab Chip 2019; 19:3011-3021. [PMID: 31502632 DOI: 10.1039/c9lc00538b] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Adaptive immunity is based on peptide antigen recognition. Our ability to harness the immune system for therapeutic gain relies on the discovery of the T cell receptor (TCR) genes that selectively target antigens from infections, mutated proteins, and foreign agents. Here we present a method that selectively labels peptide antigen-specific CD8+ T cells using magnetic nanoparticles functionalized with peptide-MHC tetramers, isolates these specific cells within an integrated microfluidic device, and directly amplifies the TCR genes for sequencing. Critically, the identity of the peptide recognized by the TCR is preserved, providing the link between peptide and gene. The platform requires inputs on the order of just 100 000 CD8+ T cells, can be multiplexed for simultaneous analysis of multiple peptides, and performs sorting and isolation on chip. We demonstrate 1000-fold sensitivity enhancement of detecting antigen-specific TCRs relative to bulk analysis and simultaneous capture of two virus antigen-specific TCRs from a population of T cells.
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Affiliation(s)
- Alphonsus H C Ng
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd, Pasadena, CA 91125, USA
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8
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Peng S, Zaretsky JM, Ng AHC, Chour W, Bethune MT, Choi J, Hsu A, Holman E, Ding X, Guo K, Kim J, Xu AM, Heath JE, Noh WJ, Zhou J, Su Y, Lu Y, McLaughlin J, Cheng D, Witte ON, Baltimore D, Ribas A, Heath JR. Sensitive Detection and Analysis of Neoantigen-Specific T Cell Populations from Tumors and Blood. Cell Rep 2019; 28:2728-2738.e7. [PMID: 31484081 PMCID: PMC6774618 DOI: 10.1016/j.celrep.2019.07.106] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 05/04/2019] [Accepted: 07/29/2019] [Indexed: 12/30/2022] Open
Abstract
Neoantigen-specific T cells are increasingly viewed as important immunotherapy effectors, but physically isolating these rare cell populations is challenging. Here, we describe a sensitive method for the enumeration and isolation of neoantigen-specific CD8+ T cells from small samples of patient tumor or blood. The method relies on magnetic nanoparticles that present neoantigen-loaded major histocompatibility complex (MHC) tetramers at high avidity by barcoded DNA linkers. The magnetic particles provide a convenient handle to isolate the desired cell populations, and the barcoded DNA enables multiplexed analysis. The method exhibits superior recovery of antigen-specific T cell populations relative to literature approaches. We applied the method to profile neoantigen-specific T cell populations in the tumor and blood of patients with metastatic melanoma over the course of anti-PD1 checkpoint inhibitor therapy. We show that the method has value for monitoring clinical responses to cancer immunotherapy and might help guide the development of personalized mutational neoantigen-specific T cell therapies and cancer vaccines.
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Affiliation(s)
- Songming Peng
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - Jesse M Zaretsky
- Department of Medicine, University of California Los Angeles and Jonsson Comprehensive Cancer Center, 10833 Le Conte Avenue, Los Angeles, CA 90095, USA
| | - Alphonsus H C Ng
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA; Institute for Systems Biology, Seattle, WA 98109, USA
| | - William Chour
- Institute for Systems Biology, Seattle, WA 98109, USA; Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Michael T Bethune
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Jongchan Choi
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Alice Hsu
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Elizabeth Holman
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - Xiaozhe Ding
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA; Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Katherine Guo
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - Jungwoo Kim
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - Alexander M Xu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA; Institute for Systems Biology, Seattle, WA 98109, USA
| | - John E Heath
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - Won Jun Noh
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Jing Zhou
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - Yapeng Su
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA; Institute for Systems Biology, Seattle, WA 98109, USA
| | - Yue Lu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA; Institute for Systems Biology, Seattle, WA 98109, USA
| | - Jami McLaughlin
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Donghui Cheng
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Owen N Witte
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA 90095, USA; Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - David Baltimore
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Antoni Ribas
- Department of Medicine, University of California Los Angeles and Jonsson Comprehensive Cancer Center, 10833 Le Conte Avenue, Los Angeles, CA 90095, USA
| | - James R Heath
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA; Institute for Systems Biology, Seattle, WA 98109, USA.
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9
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Su Y, Bintz M, Yang Y, Robert L, Ng AHC, Liu V, Ribas A, Heath JR, Wei W. Phenotypic heterogeneity and evolution of melanoma cells associated with targeted therapy resistance. PLoS Comput Biol 2019; 15:e1007034. [PMID: 31166947 PMCID: PMC6576794 DOI: 10.1371/journal.pcbi.1007034] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 06/17/2019] [Accepted: 04/15/2019] [Indexed: 01/26/2023] Open
Abstract
Phenotypic plasticity is associated with non-genetic drug tolerance in several cancers. Such plasticity can arise from chromatin remodeling, transcriptomic reprogramming, and/or protein signaling rewiring, and is characterized as a cell state transition in response to molecular or physical perturbations. This, in turn, can confound interpretations of drug responses and resistance development. Using BRAF-mutant melanoma cell lines as the prototype, we report on a joint theoretical and experimental investigation of the cell-state transition dynamics associated with BRAF inhibitor drug tolerance. Thermodynamically motivated surprisal analysis of transcriptome data was used to treat the cell population as an entropy maximizing system under the influence of time-dependent constraints. This permits the extraction of an epigenetic potential landscape for drug-induced phenotypic evolution. Single-cell flow cytometry data of the same system were modeled with a modified Fokker-Planck-type kinetic model. The two approaches yield a consistent picture that accounts for the phenotypic heterogeneity observed over the course of drug tolerance development. The results reveal that, in certain plastic cancers, the population heterogeneity and evolution of cell phenotypes may be understood by accounting for the competing interactions of the epigenetic potential landscape and state-dependent cell proliferation. Accounting for such competition permits accurate, experimentally verifiable predictions that can potentially guide the design of effective treatment strategies. Cancer cells exhibit varied degrees of phenotypic heterogeneity. These phenotypes, each of them with unique molecular and functional profiles, display dynamic interconversion in response to drug perturbations, and can evolve to form new drug-tolerant phenotypes. Such phenotypic plasticity, in turn, renders tumor cells extremely difficult to treat. To get a quantitative biophysical understanding of the origins of the phenotypic equilibrium and evolution associated with drug tolerance development in highly plastic patient-derived melanoma cells, we employed joint experimental and computational approaches, using either bulk or single cell measurements as input, to interrogate the epigenetic landscape of the phenotypic evolution. We found that the observed phenotypic equilibria were established via competition between state-dependent net proliferation rates and landscape potential. The results reveal how the tumor cells maintain a phenotypic heterogeneity that facilitates appropriate responses to external cues. They implicate that, in certain phenotypically plastic tumor cells, drug targeting the driver oncogenes may not have sustained efficacy unless the phenotypic plasticity of the tumor is co-targeted.
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Affiliation(s)
- Yapeng Su
- Institute for Systems Biology, Seattle, Washington, United State of America
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United State of America
| | - Marcus Bintz
- Department of Molecular and Medical Pharmacology, University of California – Los Angeles, Los Angeles, California, United State of America
| | - Yezi Yang
- Department of Molecular and Medical Pharmacology, University of California – Los Angeles, Los Angeles, California, United State of America
| | - Lidia Robert
- Department of Medicine, University of California – Los Angeles, Los Angeles, California, United State of America
| | - Alphonsus H. C. Ng
- Institute for Systems Biology, Seattle, Washington, United State of America
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United State of America
| | - Victoria Liu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United State of America
| | - Antoni Ribas
- Department of Molecular and Medical Pharmacology, University of California – Los Angeles, Los Angeles, California, United State of America
- Department of Medicine, University of California – Los Angeles, Los Angeles, California, United State of America
- Department of Surgery, Division of Surgical-Oncology, University of California – Los Angeles, Los Angeles, California, United State of America
- Jonsson Comprehensive Cancer Center, University of California – Los Angeles, Los Angeles, California, United State of America
| | - James R. Heath
- Institute for Systems Biology, Seattle, Washington, United State of America
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United State of America
- Jonsson Comprehensive Cancer Center, University of California – Los Angeles, Los Angeles, California, United State of America
- * E-mail: (J.R.H.); (W.W.)
| | - Wei Wei
- Institute for Systems Biology, Seattle, Washington, United State of America
- Department of Molecular and Medical Pharmacology, University of California – Los Angeles, Los Angeles, California, United State of America
- Jonsson Comprehensive Cancer Center, University of California – Los Angeles, Los Angeles, California, United State of America
- * E-mail: (J.R.H.); (W.W.)
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10
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Ng AHC, Fobel R, Fobel C, Lamanna J, Rackus DG, Summers A, Dixon C, Dryden MDM, Lam C, Ho M, Mufti NS, Lee V, Asri MAM, Sykes EA, Chamberlain MD, Joseph R, Ope M, Scobie HM, Knipes A, Rota PA, Marano N, Chege PM, Njuguna M, Nzunza R, Kisangau N, Kiogora J, Karuingi M, Burton JW, Borus P, Lam E, Wheeler AR. A digital microfluidic system for serological immunoassays in remote settings. Sci Transl Med 2018; 10:10/438/eaar6076. [DOI: 10.1126/scitranslmed.aar6076] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 04/06/2018] [Indexed: 12/29/2022]
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11
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Dixon C, Ng AHC, Fobel R, Miltenburg MB, Wheeler AR. An inkjet printed, roll-coated digital microfluidic device for inexpensive, miniaturized diagnostic assays. Lab Chip 2016; 16:4560-4568. [PMID: 27801455 DOI: 10.1039/c6lc01064d] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The diagnosis of infectious disease is typically carried out at the point-of-care (POC) using the lateral flow assay (LFA). While cost-effective and portable, LFAs often lack the clinical sensitivity and specificity required for accurate diagnoses. In response to this challenge, we introduce a new digital microfluidic (DMF) platform fabricated using a custom inkjet printing and roll-coating process that is scalable to mass production. The performance of the new devices is on par with that of traditional DMF devices fabricated in a cleanroom, with a materials cost for the new devices of only US $0.63 per device. To evaluate the usefulness of the new platform, we performed a 13-step rubella virus (RV) IgG immunoassay on the inkjet printed, roll-coated devices, which yielded a limit of detection of 0.02 IU mL-1, well below the diagnostic cut-off of 10 IU mL-1 for RV infection and immunity. We propose that this represents a breakthrough for DMF, lowering the costs to a level such that the new platforms will be an attractive alternative to LFAs for the diagnosis of infectious disease at the POC.
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Affiliation(s)
- Christopher Dixon
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada.
| | - Alphonsus H C Ng
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3H6, Canada and Institute for Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario M5S 3H6, Canada
| | - Ryan Fobel
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3H6, Canada and Institute for Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario M5S 3H6, Canada
| | - Mark B Miltenburg
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada.
| | - Aaron R Wheeler
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada. and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3H6, Canada and Institute for Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario M5S 3H6, Canada
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12
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Abstract
Digital microfluidics (DMF) is a droplet-based liquid-handling technology that has recently become popular for cell culture and analysis. In DMF, picoliter- to microliter-sized droplets are manipulated on a planar surface using electric fields, thus enabling software-reconfigurable operations on individual droplets, such as move, merge, split, and dispense from reservoirs. Using this technique, multistep cell-based processes can be carried out using simple and compact instrumentation, making DMF an attractive platform for eventual integration into routine biology workflows. In this review, we summarize the state-of-the-art in DMF cell culture, and describe design considerations, types of DMF cell culture, and cell-based applications of DMF.
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Affiliation(s)
- Alphonsus H C Ng
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G9, Canada; .,The Terrence Donnelly Center for Cellular and Biomolecular Research, Toronto, Ontario M5S 3E1, Canada
| | - Bingyu Betty Li
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G9, Canada; .,The Terrence Donnelly Center for Cellular and Biomolecular Research, Toronto, Ontario M5S 3E1, Canada
| | - M Dean Chamberlain
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G9, Canada; .,The Terrence Donnelly Center for Cellular and Biomolecular Research, Toronto, Ontario M5S 3E1, Canada
| | - Aaron R Wheeler
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G9, Canada; .,The Terrence Donnelly Center for Cellular and Biomolecular Research, Toronto, Ontario M5S 3E1, Canada.,Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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13
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Shamsi MH, Choi K, Ng AHC, Chamberlain MD, Wheeler AR. Electrochemiluminescence on digital microfluidics for microRNA analysis. Biosens Bioelectron 2015; 77:845-52. [PMID: 26516684 DOI: 10.1016/j.bios.2015.10.036] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 10/08/2015] [Accepted: 10/12/2015] [Indexed: 01/04/2023]
Abstract
Electrochemiluminescence (ECL) is a sensitive analytical technique with great promise for biological applications, especially when combined with microfluidics. Here, we report the first integration of ECL with digital microfluidics (DMF). ECL detectors were fabricated into the ITO-coated top plates of DMF devices, allowing for the generation of light from electrically excited luminophores in sample droplets. The new system was characterized by making electrochemical and ECL measurements of soluble mixtures of tris(phenanthroline)ruthenium(II) and tripropylamine (TPA) solutions. The system was then validated by application to an oligonucleotide hybridization assay, using magnetic particles bearing 21-mer, deoxyribose analogues of the complement to microRNA-143 (miRNA-143). The system detects single nucleotide mismatches with high specificity, and has a limit of detection of 1.5 femtomoles. The system is capable of detecting miRNA-143 in cancer cell lysates, allowing for the discrimination between the MCF-7 (less aggressive) and MDA-MB-231 (more aggressive) cell lines. We propose that DMF-ECL represents a valuable new tool in the microfluidics toolbox for a wide variety of applications.
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Affiliation(s)
- Mohtashim H Shamsi
- Department of Chemistry, University of Toronto, 80 St George St., Toronto, ON, Canada M5S 3H6; Donnelly Centre for Cellular and Biomolecular Research, 160 College St., Toronto, ON, Canada M5S 3E1
| | - Kihwan Choi
- Department of Chemistry, University of Toronto, 80 St George St., Toronto, ON, Canada M5S 3H6; Donnelly Centre for Cellular and Biomolecular Research, 160 College St., Toronto, ON, Canada M5S 3E1
| | - Alphonsus H C Ng
- Department of Chemistry, University of Toronto, 80 St George St., Toronto, ON, Canada M5S 3H6; Donnelly Centre for Cellular and Biomolecular Research, 160 College St., Toronto, ON, Canada M5S 3E1; Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College St., Toronto, ON, Canada M5S 3G9
| | - M Dean Chamberlain
- Department of Chemistry, University of Toronto, 80 St George St., Toronto, ON, Canada M5S 3H6; Donnelly Centre for Cellular and Biomolecular Research, 160 College St., Toronto, ON, Canada M5S 3E1
| | - Aaron R Wheeler
- Department of Chemistry, University of Toronto, 80 St George St., Toronto, ON, Canada M5S 3H6; Donnelly Centre for Cellular and Biomolecular Research, 160 College St., Toronto, ON, Canada M5S 3E1; Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College St., Toronto, ON, Canada M5S 3G9.
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14
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Affiliation(s)
- Alphonsus H C Ng
- Institute of Biomaterials and Biomedical Engineering and Department of Chemistry, University of Toronto, Toronto, ON, Canada; Donnelly Centre for Cellular and Biomolecular Research, Toronto, ON, Canada.
| | - Aaron R Wheeler
- Institute of Biomaterials and Biomedical Engineering and Department of Chemistry, University of Toronto, Toronto, ON, Canada; Donnelly Centre for Cellular and Biomolecular Research, Toronto, ON, Canada.
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15
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Lafrenière NM, Mudrik JM, Ng AHC, Seale B, Spooner N, Wheeler AR. Attractive Design: An Elution Solvent Optimization Platform for Magnetic-Bead-based Fractionation Using Digital Microfluidics and Design of Experiments. Anal Chem 2015; 87:3902-10. [DOI: 10.1021/ac504697r] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Nelson M. Lafrenière
- Department
of Chemistry, University of Toronto, 80 St George Street, Toronto, Ontario M5S 3H6, Canada
| | - Jared M. Mudrik
- Department
of Chemistry, University of Toronto, 80 St George Street, Toronto, Ontario M5S 3H6, Canada
| | - Alphonsus H. C. Ng
- Institute of Biomaterials and Biomedical Engineering, 164 College Street, Toronto, Ontario M5S 3G9, Canada
| | - Brendon Seale
- Department
of Chemistry, University of Toronto, 80 St George Street, Toronto, Ontario M5S 3H6, Canada
| | - Neil Spooner
- Platform Technologies
and Science Drug Metabolism and Pharmacokinetics, GlaxoSmithKline Research and Development, Ware, Hertfordshire SG12 0DP, United Kingdom
| | - Aaron R. Wheeler
- Department
of Chemistry, University of Toronto, 80 St George Street, Toronto, Ontario M5S 3H6, Canada
- Institute of Biomaterials and Biomedical Engineering, 164 College Street, Toronto, Ontario M5S 3G9, Canada
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16
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Ng AHC, Lee M, Choi K, Fischer AT, Robinson JM, Wheeler AR. Digital microfluidic platform for the detection of rubella infection and immunity: a proof of concept. Clin Chem 2014; 61:420-9. [PMID: 25512641 DOI: 10.1373/clinchem.2014.232181] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Whereas disease surveillance for infectious diseases such as rubella is important, it is critical to identify pregnant women at risk of passing rubella to their offspring, which can be fatal and can result in congenital rubella syndrome (CRS). The traditional centralized model for diagnosing rubella is cost-prohibitive in resource-limited settings, representing a major obstacle to the prevention of CRS. As a step toward decentralized diagnostic systems, we developed a proof-of-concept digital microfluidic (DMF) diagnostic platform that possesses the flexibility and performance of automated immunoassay platforms used in central facilities, but with a form factor the size of a shoebox. METHODS DMF immunoassays were developed with integrated sample preparation for the detection of rubella virus (RV) IgG and IgM. The performance (sensitivity and specificity) of the assays was evaluated with serum and plasma samples from a commercial antirubella mixed-titer performance panel. RESULTS The new platform performed the essential processing steps, including sample aliquoting for 4 parallel assays, sample dilution, and IgG blocking. Testing of performance panel samples yielded diagnostic sensitivity and specificity of 100% and 100% for both RV IgG and RV IgM. With 1.8 μL sample per assay, 4 parallel assays were performed in approximately 30 min with <10% mean CV. CONCLUSIONS This proof of concept establishes DMF-powered immunoassays as being potentially useful for the diagnosis of infectious disease.
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Affiliation(s)
- Alphonsus H C Ng
- Institute of Biomaterials and Biomedical Engineering, Donnelly Centre for Cellular and Biomolecular Research, Toronto, ON, Canada
| | - Misan Lee
- Innis College, and Donnelly Centre for Cellular and Biomolecular Research, Toronto, ON, Canada
| | - Kihwan Choi
- Donnelly Centre for Cellular and Biomolecular Research, Toronto, ON, Canada; Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | | | | | - Aaron R Wheeler
- Institute of Biomaterials and Biomedical Engineering, Donnelly Centre for Cellular and Biomolecular Research, Toronto, ON, Canada; Department of Chemistry, University of Toronto, Toronto, ON, Canada;
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17
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Abstract
The first example of so-called "digital microfluidics" (DMF) implemented on paper by inkjet printing is reported. A sandwich enzyme-linked immunosorbent assay (ELISA) is demonstrated as an example of a complex, multistep protocol that would be difficult to achieve with capillary-driven paper microfluidics. Furthermore, it is shown that paper-based DMF devices have comparable performance to traditional photolithographically patterned DMF devices at a fraction of the cost.
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Affiliation(s)
- Ryan Fobel
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, 164 College St., Toronto, ON, M5S 3E1, Canada
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18
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Abstract
Digital microfluidics (DMF) has emerged as a popular format for implementing quantitative immunoassays for diagnostic biomarkers. All previous reports of such assays have relied on optical detection; here, we introduce the first digital microfluidic immunoassay relying on electrochemical detection. In this system, an indium tin oxide (ITO) based DMF top plate was modified to include gold sensing electrodes and silver counter/pseudoreference electrodes suitable for in-line amperometric measurements. A thyroid stimulating hormone (TSH) immunoassay procedure was developed relying on magnetic microparticles conjugated with primary antibody (Ab1). Antigen molecules are captured followed by capture of a secondary antibody (Ab2) conjugated with horseradish peroxidase enzyme (HRP). HRP catalyzes the oxidation of 3,3',5,5'-tetramethylbenzidine (TMB) which can be detected amperometrically. The limit of detection of the technique (2.4 μIU mL(-1)) is compatible with clinical applications; moreover, the simplicity and the small size of the detector suggest utility in the future for portable analysis.
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Affiliation(s)
- Mohtashim H Shamsi
- Department of Chemistry, University of Toronto, 80 St George St., Toronto, ON M5S 3H6, Canada.
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19
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Choi K, Ng AHC, Fobel R, Chang-Yen DA, Yarnell LE, Pearson EL, Oleksak CM, Fischer AT, Luoma RP, Robinson JM, Audet J, Wheeler AR. Automated Digital Microfluidic Platform for Magnetic-Particle-Based Immunoassays with Optimization by Design of Experiments. Anal Chem 2013; 85:9638-46. [DOI: 10.1021/ac401847x] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Kihwan Choi
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto,
Ontario M5S 3H6, Canada
- Donnelly Centre for Cellular and Biomolecular Research, 160 College Street,
Toronto, Ontario M5S 3E1, Canada
| | - Alphonsus H. C. Ng
- Institute of Biomaterials and
Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario M5S 3G9, Canada
- Donnelly Centre for Cellular and Biomolecular Research, 160 College Street,
Toronto, Ontario M5S 3E1, Canada
| | - Ryan Fobel
- Institute of Biomaterials and
Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario M5S 3G9, Canada
- Donnelly Centre for Cellular and Biomolecular Research, 160 College Street,
Toronto, Ontario M5S 3E1, Canada
| | - David A. Chang-Yen
- AbbVie, 200 Abbott Park Road, Abbott Park,
Illinois 60064, United States
| | - Lyle E. Yarnell
- Abbott Diagnostics, 1921 Hurd Drive, Irving,
Texas 75038, United States
| | - Elroy L. Pearson
- AbbVie, 200 Abbott Park Road, Abbott Park,
Illinois 60064, United States
| | - Carl M. Oleksak
- Abbott Diagnostics, 1921 Hurd Drive, Irving,
Texas 75038, United States
| | - Andrew T. Fischer
- Abbott Diagnostics, 1921 Hurd Drive, Irving,
Texas 75038, United States
| | - Robert P. Luoma
- Abbott Diagnostics, 1921 Hurd Drive, Irving,
Texas 75038, United States
| | - John M. Robinson
- Abbott Diagnostics, 100 Abbott Park Road, Abbott Park,
Illinois 60064, United States
| | - Julie Audet
- Institute of Biomaterials and
Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario M5S 3G9, Canada
- Donnelly Centre for Cellular and Biomolecular Research, 160 College Street,
Toronto, Ontario M5S 3E1, Canada
| | - Aaron R. Wheeler
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto,
Ontario M5S 3H6, Canada
- Institute of Biomaterials and
Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario M5S 3G9, Canada
- Donnelly Centre for Cellular and Biomolecular Research, 160 College Street,
Toronto, Ontario M5S 3E1, Canada
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Affiliation(s)
- Alphonsus H. C. Ng
- Institute of Biomaterials and
Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario M5S 3G9, Canada
- Donnelly Centre for Cellular and Biomolecular Research, 160 College Street,
Toronto, Ontario M5S 3E1, Canada
| | - Kihwan Choi
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto,
Ontario M5S 3H6, Canada
- Donnelly Centre for Cellular and Biomolecular Research, 160 College Street,
Toronto, Ontario M5S 3E1, Canada
| | - Robert P. Luoma
- Abbott Diagnostics, 1921 Hurd Drive, Irving,
Texas 75038, United States
| | - John M. Robinson
- Abbott Diagnostics, 100 Abbott Park Road,
Abbott Park, Illinois 60064, United States
| | - Aaron R. Wheeler
- Institute of Biomaterials and
Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario M5S 3G9, Canada
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto,
Ontario M5S 3H6, Canada
- Donnelly Centre for Cellular and Biomolecular Research, 160 College Street,
Toronto, Ontario M5S 3E1, Canada
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Fiddes LK, Luk VN, Au SH, Ng AHC, Luk V, Kumacheva E, Wheeler AR. Hydrogel discs for digital microfluidics. Biomicrofluidics 2012; 6:14112-1411211. [PMID: 22662096 PMCID: PMC3365348 DOI: 10.1063/1.3687381] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 01/27/2012] [Indexed: 05/10/2023]
Abstract
Hydrogels are networks of hydrophilic polymer chains that are swollen with water, and they are useful for a wide range of applications because they provide stable niches for immobilizing proteins and cells. We report here the marriage of hydrogels with digital microfluidic devices. Until recently, digital microfluidics, a fluid handling technique in which discrete droplets are manipulated electromechanically on the surface of an array of electrodes, has been used only for homogeneous systems involving liquid reagents. Here, we demonstrate for the first time that the cylindrical hydrogel discs can be incorporated into digital microfluidic systems and that these discs can be systematically addressed by droplets of reagents. Droplet movement is observed to be unimpeded by interaction with the gel discs, and gel discs remain stationary when droplets pass through them. Analyte transport into gel discs is observed to be identical to diffusion in cases in which droplets are incubated with gels passively, but transport is enhanced when droplets are continually actuated through the gels. The system is useful for generating integrated enzymatic microreactors and for three-dimensional cell culture. This paper demonstrates a new combination of techniques for lab-on-a-chip systems which we propose will be useful for a wide range of applications.
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Abstract
Digital microfluidics (DMF) is an emerging liquid-handling technology that enables individual control over droplets on an open array of electrodes. These picoliter- to microliter-sized droplets, each serving as an isolated vessel for chemical processes, can be made to move, merge, split, and dispense from reservoirs. Because of its unique advantages, including simple instrumentation, flexible device geometry, and easy coupling with other technologies, DMF is being applied to a wide range of fields. In this review, we summarize the state of the art of DMF technology from the perspective of analytical chemistry in sections describing the theory of droplet actuation, device fabrication and integration, and applications.
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Affiliation(s)
- Kihwan Choi
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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Jebrail MJ, Ng AHC, Rai V, Hili R, Yudin AK, Wheeler AR. Inside Cover: Synchronized Synthesis of Peptide-Based Macrocycles by Digital Microfluidics (Angew. Chem. Int. Ed. 46/2010). Angew Chem Int Ed Engl 2010. [DOI: 10.1002/anie.201004588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Jebrail MJ, Ng AHC, Rai V, Hili R, Yudin AK, Wheeler AR. Innentitelbild: Synchronized Synthesis of Peptide-Based Macrocycles by Digital Microfluidics (Angew. Chem. 46/2010). Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201004588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Jebrail MJ, Ng AHC, Rai V, Hili R, Yudin AK, Wheeler AR. Synchronized Synthesis of Peptide-Based Macrocycles by Digital Microfluidics. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201001604] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Jebrail MJ, Ng AHC, Rai V, Hili R, Yudin AK, Wheeler AR. Synchronized Synthesis of Peptide-Based Macrocycles by Digital Microfluidics. Angew Chem Int Ed Engl 2010; 49:8625-9. [DOI: 10.1002/anie.201001604] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Jebrail MJ, Luk VN, Shih SCC, Fobel R, Ng AHC, Yang H, Freire SLS, Wheeler AR. Digital microfluidics for automated proteomic processing. J Vis Exp 2009:1603. [PMID: 19898419 DOI: 10.3791/1603] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Clinical proteomics has emerged as an important new discipline, promising the discovery of biomarkers that will be useful for early diagnosis and prognosis of disease. While clinical proteomic methods vary widely, a common characteristic is the need for (i) extraction of proteins from extremely heterogeneous fluids (i.e. serum, whole blood, etc.) and (ii) extensive biochemical processing prior to analysis. Here, we report a new digital microfluidics (DMF) based method integrating several processing steps used in clinical proteomics. This includes protein extraction, resolubilization, reduction, alkylation and enzymatic digestion. Digital microfluidics is a microscale fluid-handling technique in which nanoliter-microliter sized droplets are manipulated on an open surface. Droplets are positioned on top of an array of electrodes that are coated by a dielectric layer - when an electrical potential is applied to the droplet, charges accumulate on either side of the dielectric. The charges serve as electrostatic handles that can be used to control droplet position, and by biasing a sequence of electrodes in series, droplets can be made to dispense, move, merge, mix, and split on the surface. Therefore, DMF is a natural fit for carrying rapid, sequential, multistep, miniaturized automated biochemical assays. This represents a significant advance over conventional methods (relying on manual pipetting or robots), and has the potential to be a useful new tool in clinical proteomics.
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