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Shi T, Burg AR, Caldwell JT, Roskin KM, Castro-Rojas CM, Chukwuma PC, Gray GI, Foote SG, Alonso JA, Cuda CM, Allman DA, Rush JS, Regnier CH, Wieczorek G, Alloway RR, Shields AR, Baker BM, Woodle ES, Hildeman DA. Single cell transcriptomic analysis of renal allograft rejection reveals insights into intragraft TCR clonality. J Clin Invest 2023:170191. [PMID: 37227784 DOI: 10.1172/jci170191] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023] Open
Abstract
Bulk analysis of renal allograft biopsies (rBx) identified RNA transcripts associated with acute cellular rejection (ACR); however, these lacked cellular context critical to mechanistic understanding of how rejection occurs despite immunosuppression (IS). We performed combined single cell RNA transcriptomic and TCRα/β sequencing on rBx from patients with ACR under differing IS: tacrolimus, iscalimab, and belatacept. We found distinct CD8+ T cell phenotypes (e.g., effector, memory, exhausted) depending upon IS type, particularly within clonally expanded cells (CD8EXP). Gene expression of CD8EXP identified therapeutic targets that were influenced by IS type. TCR analysis revealed a highly restricted number of CD8EXP, independent of HLA mismatch or IS type. Subcloning of TCRα/β cDNAs from CD8EXP into Jurkat76 cells (TCR-/-) conferred alloreactivity by mixed lymphocyte reaction. Analysis of sequential rBx samples revealed persistence of CD8EXP that decreased, but were not eliminated, after successful anti-rejection therapy. In contrast, CD8EXP were maintained in treatment-refractory rejection. Finally, most rBx-derived CD8EXP were also observed in matching urine samples, providing precedent for using urine-derived CD8EXP as a surrogate for those found in the rejecting allograft. Overall, our data define the clonal CD8+ T cell response to ACR, paving the next steps to improve detection, assessment, and treatment of rejection.
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Affiliation(s)
- Tiffany Shi
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - Ashley R Burg
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - J Timothy Caldwell
- Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - Krishna M Roskin
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - Cyd M Castro-Rojas
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - P Chukwunalu Chukwuma
- Department of Chemistry and Biochemistry and the Harper Cancer Research Ins, University of Notre Dame, South Bend, United States of America
| | - George I Gray
- Department of Chemistry and Biochemistry and the Harper Cancer Research Ins, University of Notre Dame, South Bend, United States of America
| | - Sara G Foote
- Department of Chemistry and Biochemistry and the Harper Cancer Research Ins, University of Notre Dame, South Bend, United States of America
| | - Jesus A Alonso
- Department of Chemistry and Biochemistry and the Harper Cancer Research Ins, University of Notre Dame, South Bend, United States of America
| | - Carla M Cuda
- Division of Rheumatology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, United States of America
| | - David A Allman
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States of America
| | - James S Rush
- Immunology Disease Area, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Catherine H Regnier
- Immunology Disease Area, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Grazyna Wieczorek
- Immunology Disease Area, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Rita R Alloway
- Division of Nephrology and Hypertension, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, United States of America
| | - Adele R Shields
- Division of Transplantation, Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, United States of America
| | - Brian M Baker
- Department of Chemistry and Biochemistry and the Harper Cancer Research Ins, University of Notre Dame, South Bend, United States of America
| | - E Steve Woodle
- Division of Transplantation, Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, United States of America
| | - David A Hildeman
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
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Shi T, Burg AR, Caldwell JT, Roskin K, Castro-Rojas CM, Chukwuma PC, Gray GI, Foote SG, Alonso J, Cuda CM, Allman DA, Rush JS, Regnier CH, Wieczorek G, Alloway RR, Shields AR, Baker BM, Woodle ES, Hildeman DA. Single cell transcriptomic analysis of renal allograft rejection reveals novel insights into intragraft TCR clonality. bioRxiv 2023:2023.02.08.524808. [PMID: 36798151 PMCID: PMC9934650 DOI: 10.1101/2023.02.08.524808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Bulk analysis of renal allograft biopsies (rBx) identified RNA transcripts associated with acute cellular rejection (ACR); however, these lacked cellular context critical to mechanistic understanding. We performed combined single cell RNA transcriptomic and TCRα/β sequencing on rBx from patients with ACR under differing immunosuppression (IS): tacrolimus, iscalimab, and belatacept. TCR analysis revealed a highly restricted CD8 + T cell clonal expansion (CD8 EXP ), independent of HLA mismatch or IS type. Subcloning of TCRα/β cDNAs from CD8 EXP into Jurkat76 cells (TCR -/- ) conferred alloreactivity by mixed lymphocyte reaction. scRNAseq analysis of CD8 EXP revealed effector, memory, and exhausted phenotypes that were influenced by IS type. Successful anti-rejection treatment decreased, but did not eliminate, CD8 EXP , while CD8 EXP were maintained during treatment-refractory rejection. Finally, most rBx-derived CD8 EXP were also observed in matching urine samples. Overall, our data define the clonal CD8 + T cell response to ACR, providing novel insights to improve detection, assessment, and treatment of rejection.
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