ATLAS-seq: a microfluidic single-cell TCR screen for antigen-reactive TCRs
Abstract Discovering antigen-reactive T cell receptors (TCRs) is central to developing effective engineered T cell immunotherapies. However, the conventional technologies for isolating antigen-reactive TCRs (i.e., major histocompatibility complex (MHC) multimer staining) focus on high-affinity inter...
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| Format: | Article |
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Nature Portfolio
2025-01-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-024-54675-3 |
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| author | Siwei Luo Amber Notaro Lan Lin |
| author_facet | Siwei Luo Amber Notaro Lan Lin |
| author_sort | Siwei Luo |
| collection | DOAJ |
| description | Abstract Discovering antigen-reactive T cell receptors (TCRs) is central to developing effective engineered T cell immunotherapies. However, the conventional technologies for isolating antigen-reactive TCRs (i.e., major histocompatibility complex (MHC) multimer staining) focus on high-affinity interactions between the TCR and MHC-antigen complex, and may fail to identify TCRs with high efficacy for activating T cells. Here, we develop a microfluidic single-cell screening method for antigen-reactive T cells named ATLAS-seq (Aptamer-based T Lymphocyte Activity Screening and SEQuencing). This technology isolates and characterizes activated T cells via an aptamer-based fluorescent molecular sensor, which monitors the cytotoxic cytokine IFNγ secretion from single T cells upon antigen stimulation, followed by single-cell RNA and single-cell TCR sequencing. We use ATLAS-seq to screen TCRs reactive to cytomegalovirus (CMV) or prostate specific antigen (PSA) from peripheral blood mononuclear cells (PBMCs). ATLAS-seq identifies distinct TCR clonotype populations with higher T cell activation levels compared to TCRs recovered by MHC multimer staining. Select TCR clonotypes from ATLAS-seq are more efficient in target cell killing than those from MHC multimer staining. Collectively, ATLAS-seq provides an efficient and broadly applicable technology to screen antigen-reactive TCRs for engineered T cell immunotherapy. |
| format | Article |
| id | doaj-art-b603d6d5be06467e9bd90c3cbffb2ed5 |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
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| series | Nature Communications |
| spelling | doaj-art-b603d6d5be06467e9bd90c3cbffb2ed52025-01-05T12:36:59ZengNature PortfolioNature Communications2041-17232025-01-0116111710.1038/s41467-024-54675-3ATLAS-seq: a microfluidic single-cell TCR screen for antigen-reactive TCRsSiwei Luo0Amber Notaro1Lan Lin2Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of PhiladelphiaRaymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of PhiladelphiaRaymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of PhiladelphiaAbstract Discovering antigen-reactive T cell receptors (TCRs) is central to developing effective engineered T cell immunotherapies. However, the conventional technologies for isolating antigen-reactive TCRs (i.e., major histocompatibility complex (MHC) multimer staining) focus on high-affinity interactions between the TCR and MHC-antigen complex, and may fail to identify TCRs with high efficacy for activating T cells. Here, we develop a microfluidic single-cell screening method for antigen-reactive T cells named ATLAS-seq (Aptamer-based T Lymphocyte Activity Screening and SEQuencing). This technology isolates and characterizes activated T cells via an aptamer-based fluorescent molecular sensor, which monitors the cytotoxic cytokine IFNγ secretion from single T cells upon antigen stimulation, followed by single-cell RNA and single-cell TCR sequencing. We use ATLAS-seq to screen TCRs reactive to cytomegalovirus (CMV) or prostate specific antigen (PSA) from peripheral blood mononuclear cells (PBMCs). ATLAS-seq identifies distinct TCR clonotype populations with higher T cell activation levels compared to TCRs recovered by MHC multimer staining. Select TCR clonotypes from ATLAS-seq are more efficient in target cell killing than those from MHC multimer staining. Collectively, ATLAS-seq provides an efficient and broadly applicable technology to screen antigen-reactive TCRs for engineered T cell immunotherapy.https://doi.org/10.1038/s41467-024-54675-3 |
| spellingShingle | Siwei Luo Amber Notaro Lan Lin ATLAS-seq: a microfluidic single-cell TCR screen for antigen-reactive TCRs Nature Communications |
| title | ATLAS-seq: a microfluidic single-cell TCR screen for antigen-reactive TCRs |
| title_full | ATLAS-seq: a microfluidic single-cell TCR screen for antigen-reactive TCRs |
| title_fullStr | ATLAS-seq: a microfluidic single-cell TCR screen for antigen-reactive TCRs |
| title_full_unstemmed | ATLAS-seq: a microfluidic single-cell TCR screen for antigen-reactive TCRs |
| title_short | ATLAS-seq: a microfluidic single-cell TCR screen for antigen-reactive TCRs |
| title_sort | atlas seq a microfluidic single cell tcr screen for antigen reactive tcrs |
| url | https://doi.org/10.1038/s41467-024-54675-3 |
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