GEO series

Mega-scale single-cell profiling reveals novel biomarkers associated with acute GvHD after allogeneic hematopoietic stem cell transplantation

GSE295359 Homo sapiens (human) Single-cell RNA-seq 15 samples Submitted 2025/12/03 Platform GPL24676

At a glance

Single-cell RNA-seq · human · 15 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Homo sapiens (human)
Samples: 15 samples: 15 × G-CSF mobilized graft and PBMC post-alloHSCT sublibGroups are read from the sample names, not from the paper. Check the list below.
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper: Mega-scale single-cell profiling reveals novel biomarkers associated with acute GvHD after allogeneic hematopoietic stem cell transplantationBiomarker research · 2025

Summary (written by the submitters)

Alloreactive T cells mediate graft-versus-leukemia (GvL) reactions and acute graft-versus-host disease (aGvHD) in AML patients following allogeneic hematopoietic stem cell transplantation. To investigate biomarkers that identify alloreactive T cells associated with either beneficial GvL or detrimental aGvHD, we collected graft samples and two post-transplant follow-up blood samples (day 30 and day 100) of ten AML patients undergoing hematopoietic stem cell transplantation

Read the full summary ↓

and profiled over 777,000 CD45+ leukocytes in total by combinatorial barcoding-based mega-scale single-cell RNA sequencing. Using immune receptor sequences as intrinsic clonal barcodes, we observed that especially CD8+ graft-derived T cells persisted and displayed enhanced proliferation, clonal expansion, and likely alloreactivity. Notably, patient-derived peripheral leukocytes that survived the conditioning, as identified by sex-chromosome-related genes, were primarily CD4+ T helper cells. MDGA1 expression on T cells and NK cells emerged as a novel biomarker potentially associated with aGvHD. Additionally, we observed a significant deficiency of ADGRG1 expression, a marker of alloreactive cytotoxic T cells, by αβ and γδ T cells from relapsed patients. In conclusion, mega-scale single-cell monitoring of graft and hematopoietic immune cell reconstitution allowed us to demonstrate that MDGA1 and ADGRG1 may function as complementary biomarkers expressed by distinct circulating T cells that are associated with divergent outcomes in AML patients, enabling precise risk stratification of alloHSCT outcomes and presenting potential therapeutic targets.

Published in

Mega-scale single-cell profiling reveals novel biomarkers associated with acute GvHD after allogeneic hematopoietic stem cell transplantation

Song Z, Klyuchnikov E, Badbaran A et al. · Biomarker research 2025 · PMID 41327488 · doi:10.1186/s40364-025-00868-x

This dataset

Open GSE295359 in finder → Find more human RNA-seq datasets →

Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE295359_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1254272 and SRA study SRP580608. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41327488) ↗

Study design

15 × G-CSF mobilized graft and PBMC post-alloHSCT sublib

Supports a between-group comparison across 15 samples.

How we read this: 1 replicated groups read from 15 sample titles; they account for 15 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

GSM8946498 G-CSF mobilized graft and PBMC post-alloHSCT sublib 1 G-CSF mobilized graft a…
GSM8946499 G-CSF mobilized graft and PBMC post-alloHSCT sublib 2 G-CSF mobilized graft a…
GSM8946500 G-CSF mobilized graft and PBMC post-alloHSCT sublib 3 G-CSF mobilized graft a…
GSM8946501 G-CSF mobilized graft and PBMC post-alloHSCT sublib 4 G-CSF mobilized graft a…
GSM8946502 G-CSF mobilized graft and PBMC post-alloHSCT sublib 5 G-CSF mobilized graft a…
GSM8946503 G-CSF mobilized graft and PBMC post-alloHSCT sublib 6 G-CSF mobilized graft a…
GSM8946504 G-CSF mobilized graft and PBMC post-alloHSCT sublib 7 G-CSF mobilized graft a…
GSM8946505 G-CSF mobilized graft and PBMC post-alloHSCT sublib 8 G-CSF mobilized graft a…
GSM8946506 G-CSF mobilized graft and PBMC post-alloHSCT sublib 9 G-CSF mobilized graft a…
GSM8946507 G-CSF mobilized graft and PBMC post-alloHSCT sublib 10 G-CSF mobilized graft a…
GSM8946508 G-CSF mobilized graft and PBMC post-alloHSCT sublib 11 G-CSF mobilized graft a…
GSM8946509 G-CSF mobilized graft and PBMC post-alloHSCT sublib 12 G-CSF mobilized graft a…
GSM8946510 G-CSF mobilized graft and PBMC post-alloHSCT sublib 13 G-CSF mobilized graft a…
GSM8946511 G-CSF mobilized graft and PBMC post-alloHSCT sublib 14 G-CSF mobilized graft a…
GSM8946512 G-CSF mobilized graft and PBMC post-alloHSCT sublib 15 G-CSF mobilized graft a…

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