Spatial transcriptomics of T and B cell receptors uncovers lymphocyte clonal dynamics in human tissue

Abstract

The spatial distribution of lymphocyte clones within tissues is critical to their development, selection, and expansion. We have developed Spatial Transcriptomics of VDJ sequences (Spatial VDJ), which maps immunoglobulin and TR antigen receptors in human tissue sections. Spatial VDJ captures lymphocyte clones matching canonical T, B, and plasma cell distributions in tissues and amplifies clonal sequences confirmed by orthogonal methods. We confirm spatial congruency between paired receptor chains, develop a computational framework to predict receptor pairs, and link the expansion of distinct B cell clones to different tumor-associated gene expression programs. Spatial VDJ delineates B cell clonal diversity, class switch recombination, and lineage trajectories within their spatial context. Taken together, Spatial VDJ captures lymphocyte spatial clonal architecture across tissues, which could have important therapeutic implications.One-Sentence SummarySpatial transcriptomics-based technology co-captures T and B cell receptors within their anatomical niche in human tissue.

Spatial transcriptomics of B cell and T cell receptors reveals lymphocyte clonal dynamics

“…The input to the analysis was demultiplexed consensus reads from the long-read Pacbio sequencing. The analysis was performed using Python programming language, see the Zenodo repository (29): scripts/functions/long-readprocessing-STAR-paper-main.zip. Scripts are also available on GitHub (30).…”

“…After removing spots outside the tissue section (as is standard for the Space Ranger pipeline), we imported the gene expression cluster and follicle annotations in R (version 4.2.0), then calculated UMI, spatial barcode, and overlaps among different clusters, follicles, and sections. Script for clone analysis can be found in the Zenodo repository (29): tonsil: scripts/tonsil/ 1_LR-SpatialVDJ/tonsil LR clonotype analysis. Rmd; breast cancer: scripts/breast_cancer/ 1_LR-SpatialVDJ/BC LR clonotype analysis.Rmd.…”

“…S1C, when applicable, features were collapsed based on antigen receptor chain identity and visualized using the FeatureOverlay() function. Tonsil #1 Space Ranger output data can be found in the Zenodo repository (29): data/tonsil/5_spatial_ GEX/spaceranger_output/. R script for reproducing figures in fig.…”

“…Each modified clonotype count matrix was then loaded as a new assay into its respective Seurat object (tonsil, P1, and P2), whereafter genes and clonotypes were visualized on the tissue images using built-in functions of the STUtility package. Scripts for generating all figure panels are listed as in the Zenodo repository (29): paths in data S5, and Seurat objects with descriptions can be found in:…”

Recent insights into the crosstalk between senescent cells and CD8 T lymphocytes

“…Notably, a fraction of the senescence-associated antigens are not expressed by the parental non-senescent fibroblasts, further reinforcing the existence of senescence-specific MHC-Iassociated peptides or "seno-antigens". Following the advent of novel tools to decipher the immunopeptidome in vivo 22 and characterize T cell receptors even with spatial resolution 23,24 , these observations open exciting avenues towards the identification of "seno-antigens" that can be therapeutically harnessed, for instance in the form of dendritic cell (DC)-based or mRNA vaccines, for educating the adaptive immune system to eliminate pathologic senescent cells in setups of aging or age-related diseases.…”