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Lee JS, Karthikeyan D, Fini M, Vincent BG, Rubinsteyn A. ACE configurator for ELISpot: optimizing combinatorial design of pooled ELISpot assays with an epitope similarity model. Brief Bioinform 2023; 25:bbad495. [PMID: 38180831 PMCID: PMC10768796 DOI: 10.1093/bib/bbad495] [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: 08/22/2023] [Revised: 11/16/2023] [Accepted: 12/01/2023] [Indexed: 01/07/2024] Open
Abstract
The enzyme-linked immunosorbent spot (ELISpot) assay is a powerful in vitro immunoassay that enables cost-effective quantification of antigen-specific T-cell reactivity. It is used widely in the context of cancer and infectious diseases to validate the immunogenicity of predicted epitopes. While technological advances have kept pace with the demand for increased throughput, efforts to increase scale are bottlenecked by current assay design and deconvolution methods, which have remained largely unchanged. Current methods for designing pooled ELISpot experiments offer limited flexibility of assay parameters, lack support for high-throughput scenarios and do not consider peptide identity during pool assignment. We introduce the ACE Configurator for ELISpot (ACE) to address these gaps. ACE generates optimized peptide-pool assignments from highly customizable user inputs and handles the deconvolution of positive peptides using assay readouts. In this study, we present a novel sequence-aware pooling strategy, powered by a fine-tuned ESM-2 model that groups immunologically similar peptides, reducing the number of false positives and subsequent confirmatory assays compared to existing combinatorial approaches. To validate ACE's performance on real-world datasets, we conducted a comprehensive benchmark study, contextualizing design choices with their impact on prediction quality. Our results demonstrate ACE's capacity to further increase precision of identified immunogenic peptides, directly optimizing experimental efficiency. ACE is freely available as an executable with a graphical user interface and command-line interfaces at https://github.com/pirl-unc/ace.
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Affiliation(s)
- Jin Seok Lee
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Computational Medicine Program, UNC School of Medicine, Chapel Hill, NC, USA
- Curriculum in Bioinformatics and Computational Biology, UNC School of Medicine, Chapel Hill, NC, USA
| | - Dhuvarakesh Karthikeyan
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Computational Medicine Program, UNC School of Medicine, Chapel Hill, NC, USA
- Curriculum in Bioinformatics and Computational Biology, UNC School of Medicine, Chapel Hill, NC, USA
| | - Misha Fini
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA
| | - Benjamin G Vincent
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Division of Hematology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA
- Computational Medicine Program, UNC School of Medicine, Chapel Hill, NC, USA
- Curriculum in Bioinformatics and Computational Biology, UNC School of Medicine, Chapel Hill, NC, USA
| | - Alex Rubinsteyn
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Computational Medicine Program, UNC School of Medicine, Chapel Hill, NC, USA
- Curriculum in Bioinformatics and Computational Biology, UNC School of Medicine, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
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Lima-Junior JDC, Morgado FN, Conceição-Silva F. How Can Elispot Add Information to Improve Knowledge on Tropical Diseases? Cells 2017; 6:cells6040031. [PMID: 28961208 PMCID: PMC5755491 DOI: 10.3390/cells6040031] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 09/12/2017] [Accepted: 09/14/2017] [Indexed: 01/04/2023] Open
Abstract
Elispot has been used as an important tool for detecting immune cells' products and functions and has facilitated the understanding of host-pathogen interaction. Despite the incredible diversity of possibilities, two main approaches have been developed: the immunopathogenesis and diagnosis/prognosis of infectious diseases as well as cancer research. Much has been described on the topics of allergy, autoimmune diseases, and HIV-Aids, however, Elispot can also be applied to other infectious diseases, mainly leishmaniasis, malaria, some viruses, helminths and mycosis usually classified as tropical diseases. The comprehension of the function, concentration and diversity of the immune response in the infectious disease is pointed out as crucial to the development of infection or disease in humans and animals. In this review we will describe the knowledge already obtained using Elispot as a method for accessing the profile of immune response as well as the recent advances in information about host-pathogen interaction in order to better understand the clinical outcome of a group of tropical and neglected diseases.
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Affiliation(s)
- Josué da Costa Lima-Junior
- Laboratório de Imunoparasitologia, Instituto Oswaldo Cruz/FIOCRUZ, Pavilhão 26-4° andar, sala 406-C, Av. Brasil 4365, Manguinhos, 21045-900 Rio de Janeiro, Brazil.
| | - Fernanda Nazaré Morgado
- Laboratório de Pesquisa em Leishmaniose, Instituto Oswaldo Cruz/FIOCRUZ, Pavilhão 26-5° andar, sala 509, Av. Brasil 4365, Manguinhos, 21045-900 Rio de Janeiro, Brazil.
| | - Fátima Conceição-Silva
- Laboratório de Imunoparasitologia, Instituto Oswaldo Cruz/FIOCRUZ, Pavilhão 26-4° andar, sala 406-C, Av. Brasil 4365, Manguinhos, 21045-900 Rio de Janeiro, Brazil.
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