Spatiotemporal Single-Cell Analysis Reveals T Cell Clonal Dynamics and Phenotypic Plasticity in Human...

Area of Science:

• Immunology
• Hematology
• Computational Biology

Background:

• Allogeneic hematopoietic cell transplantation (alloHCT) offers cures for hematologic diseases but carries risks of acute graft-versus-host disease (GVHD).
• GVHD is a complex T-cell-mediated pathology that requires deeper understanding for improved patient outcomes.

Purpose of the Study:

• To dissect the T-cell-mediated pathology of acute GVHD using a multi-omics approach.
• To identify T-cell clonal expansion programs and their association with GVHD severity and clinical outcomes.
• To investigate the role of gut-resident immune cells in GVHD pathogenesis.

Main Methods:

• Integration of pre-transplant alloreactive T-cell identification with longitudinal tracking in blood and gut.
• Utilized mixed lymphocyte reaction-based clonal fingerprinting, TCR clonotyping, and single-cell RNA/TCR sequencing.
• Employed DecompTCR, a novel computational tool for longitudinal TCR analysis, and spatial transcriptomics of gut biopsies.

Main Results:

• Identified dynamic clonal expansion programs linked to GVHD severity and clinical outcome.
• Revealed enrichment and expansion of CD8+ effector and ZNF683(Hobit)+ resident memory T-cells in the gut during GVHD.
• Demonstrated localization of CD8+ effector T-cells near intestinal stem cells, correlating with epithelial injury.

Conclusions:

• The study defines dynamic immune circuit rewiring and phenotypic plasticity in GVHD.
• Findings have implications for developing novel biomarkers and therapeutic strategies for GVHD.
• Highlights the utility of integrated multi-omics and computational tools for dissecting complex immune responses.