GVHD Data Analysis
Overview
This repository contains the code and data analysis pipeline for our study on acute Graft-versus-Host Disease (GVHD) following allogeneic hematopoietic cell transplantation (allo-HCT) in collaboration with Reshef Lab. Acute GVHD is a potentially fatal complication where donor T cells attack recipient tissues. Our study aims to identify reliable biomarkers and uncover the mechanisms of T cell-mediated damage using a combination of in vitro assays, high-throughput sequencing, and spatial transcriptomics.
Study Design
To understand the interaction between donor T cells and host tissues:
We performed mixed lymphocyte reactions (MLRs) combined with high-throughput TCR sequencing to identify alloreactive T cell fingerprints across 20 patients, with 5–12 timepoints per patient. A subset of patients received Post-Transplant Cyclophosphamide (PTCy). We profiled immune cells in gut biopsies from 14 GVHD patients and two normal donors using paired single-cell transcriptomics and TCR sequencing. We further examined spatial transcriptomics data to elucidate the tissue architecture and cell-cell interactions underlying GvHD.
Data Access
Acknowlegement
This work was made possible by the collaboration between the Azizi Lab and Reshef Lab, as well as our clinical partners at CUIMC and CCTI. We thank all participating patients and acknowledge the funding sources that supported this research.
Citation
Spatiotemporal Single-Cell Analysis Reveals T Cell Clonal Dynamics and Phenotypic Plasticity in Human Graft-versus-Host Disease Lingting Shi, Ajna Uzuni, Ximi K. Wang, Michael Pressler, David W. Harle, Shami Chakrabarti, Rodney Macedo, Kirubel Belay, Christian A. Gordillo, Erik Raps, Jia Yi (Ady) Zhang, Achille Nazaret, Joy L. Fan, Yinuo Jin, Xumin Shen, Joshua S. Fuller, Tamjeed Azad, Jessie Huang, Pranik Chainani, Julian A. Abrams, Armando Del Portillo, Markus Y. Mapara, Mohamed Alhamar, Megan Sykes, José L. McFaline-Figueroa, Elham Azizi, Ran Reshef bioRxiv 2025.05.24.655962; doi: https://doi.org/10.1101/2025.05.24.655962