GEO series
Spatiotemporal Single-Cell Profiling Reveals T Cell Clonal Dynamics and Phenotypic Plasticity in Human Graft-versus-Host Disease
GSE307215
Homo sapiens
Other; Expression profiling by high throughput sequencing
104 samples
Submitted 2026/06/24
Platform GPL34284
Summary
Allogeneic hematopoietic cell transplantation (alloHCT) cures hematologic disease but is limited by acute graft‑versus‑host disease (GVHD). How human T‑cell clones evolve across blood and gut to injure epithelium remains unclear. We prospectively fingerprinted T cell clones pre‑transplant and tracked them longitudinally in 20 recipients, integrating TCR repertoire profiling with scRNA/TCR‑seq and high‑resolution spatial transcriptomics (Visium HD). We developed DecompTCR to resolve temporal expansion programs in blood and adapted computational tools to map clonotype phenotypes and niches in gut tissue. Severe GVHD was marked by persistent expansion and diversification of alloreactive clones and by shared CD8⁺ clonotypes that acquired Hobit (ZNF683)⁺ tissue‑resident memory (TRM) programs migrating from lamina propria to epithelium. Spatial deconvolution identified CD8⁺ effector/Hobit+ TRM hubs that localized near intestinal stem‑cell (ISC)–rich crypt bases and concentrated in crypt‑loss regions. Post‑transplant cyclophosphamide selectively depletes alloreactive clones, whereas incomplete depletion and early expansion are associated with severe disease. This clonotype‑resolved framework links tissue‑instructed TRM remodeling to ISC‑proximal cytotoxic hubs, nominating early repertoire scores and spatial hub burden as biomarker candidates.
This dataset
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Direct links to NCBI, no account and no request form: the whole study as GSE307215_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 104 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1314770 and SRA study SRP617481. Searching any of these in the dataset finder brings you back here.
Study design
40 conditions, each sampled once — no replicated groups
Read from the first 40 of 104 sample titles: 40 distinct titles with little repetition. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- GSM9219126 RH01 gut scRNA-seq
- GSM9219127 RH01 TCR-seq
- GSM9219128 RH02 gut scRNA-seq
- GSM9219129 RH02 TCR-seq
- GSM9219130 RH03 gut scRNA-seq
- GSM9219131 RH03 TCR-seq
- GSM9219132 RH04 gut scRNA-seq
- GSM9219133 RH04 TCR-seq
- GSM9219134 RH05 gut scRNA-seq
- GSM9219135 RH05 TCR-seq
- GSM9219136 RH06 gut scRNA-seq
- GSM9219137 RH06 TCR-seq
- GSM9219138 RH07 gut scRNA-seq
- GSM9219139 RH07 TCR-seq
- GSM9219140 RH08 gut scRNA-seq
- GSM9219141 RH08 TCR-seq
- GSM9219142 RH09 TCR-seq
- GSM9219143 RH10 gut scRNA-seq
- GSM9219144 RH10 TCR-seq
- GSM9219145 RH11 gut scRNA-seq
- GSM9219146 RH11 TCR-seq
- GSM9219147 RH12 gut scRNA-seq
- GSM9219148 RH12 TCR-seq
- GSM9219149 RH13 gut scRNA-seq
- GSM9219150 RH13 TCR-seq
- GSM9219151 RH14 gut scRNA-seq
- GSM9219152 RH14 TCR-seq
- GSM9219153 RH_09 gut scRNA-seq
- GSM9219154 UA01 gut scRNA-seq
- GSM9219155 UA01 TCR-seq
- GSM9219156 UA02 gut scRNA-seq
- GSM9219157 UA02 TCR-seq
- GSM9219158 UA03 gut scRNA-seq
- GSM9219159 UA03 TCR-seq
- GSM9219160 UA04 gut scRNA-seq
- GSM9219161 UA04 TCR-seq
- GSM9219162 UA05 gut scRNA-seq
- GSM9219163 UA05 TCR-seq
- GSM9219164 UA06 RNA-seq
- GSM9219165 UA06 TCR-seq
+ 64 more — browse all 104 samples with per-sample file links →
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