GEO series

Integrative single cell RNA-sequencing and spatial transcriptomics uncovers distinct macrophage-fibroblast cross-talk in human hip synovium between patients with femoroacetabular impingement and osteoarthritis

GSE294277 Homo sapiens (human) Spatial transcriptomics 22 samples Submitted 2026/03/28 Platform GPL24676

At a glance

Spatial transcriptomics · human · 22 samples

What it is: Spatial transcriptomicsGene activity measured with its position in a tissue section.
Organism: Homo sapiens (human)
Samples: 22 samples: 6 × Synovium, FAI, FAI vs 6 × Synovium, hip OA, OA vs 6 × Spatial-Seq, Synovium, hip OA, OA vs 4 × Spatial-Seq, Synovium, FAI, FAIGroups 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: Integrative Single-Cell RNA Sequencing and Spatial Transcriptomics Uncover Distinct Fibroblast-Macrophage Crosstalk in Human Hip Synovium Between Patients With Femoroacetabular Impingement and OsteoarthritisArthritis & rheumatology (Hoboken, N.J.) · 2026

Summary (written by the submitters)

Femoroacetabular impingement (FAI) and synovitis have been recognized as essential factors for developing osteoarthritis (OA) in the hip joints. However, little is known about altered synovial cellular compositions, their associated transcriptomic profiles, and cell-cell interactions between patients with FAI and hip OA. In the current study, by using integrative single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (Spatial-seq), we identified the molecular mechanisms by which synovial cells promote hip OA pathogenesis from FAI.

Read the full summary ↓

Compared to FAI synovium, epiregulin (EREG)-enriched lining fibroblast-like synoviocytes (FLS) were significantly increased in the hip OA synovium. These EREG+ FLS are pro-inflammatory due to their high expression of CXCL1, IL8 (CXCL8), and MMPs. Furthermore, pseudotime analysis predicts that EREG+ FLS are potentially derived from DPP4+PI16+ sublining FLS. Importantly, analysis of cell-cell interactions indicates that fibroblast growth factor 2 (FGF2) secreted from COL1A1+IGFBP5+ fibrotic macrophages may signal through syndecan 4 (SDC4) expressed by EREG+ lining FLS, inducing the expression of IL6, IL8, MMP1, and PTGS2. The GO term analysis of activated genes downstream of FGF2-SDC4 signaling revealed that biological processes associated with inflammation and angiogenesis were upregulated in hip OA, while mechanical stimulus and skeletal muscle differentiation were dominant in FAI. Moreover, we also found that EREG+CCL20+MMP3hi lining FLS as well as most macrophage and monocyte populations are unique to hip OA patients when compared to knee OA and RA patients. The findings of this study offer a groundwork in tailoring novel targets and therapies for FAI and hip OA patients.

Published in

Integrative Single-Cell RNA Sequencing and Spatial Transcriptomics Uncover Distinct Fibroblast-Macrophage Crosstalk in Human Hip Synovium Between Patients With Femoroacetabular Impingement and Osteoarthritis

Kulzhanova G, Klee A, Botros M et al. · Arthritis & rheumatology (Hoboken, N.J.) 2026 · PMID 41524472 · doi:10.1002/art.70033

This dataset

Open GSE294277 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 GSE294277_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: Spatial studies usually ship Space Ranger style folders (count matrix plus tissue images). Look for them among the supplementary files.

Also filed as BioProject PRJNA1248924 and SRA study SRP578083. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41524472) ↗

Study design

6 × Synovium, FAI, FAI vs 6 × Synovium, hip OA, OA vs 6 × Spatial-Seq, Synovium, hip OA, OA vs 4 × Spatial-Seq, Synovium, FAI, FAI

Supports a between-group comparison across 22 samples.

How we read this: 4 replicated groups read from 22 sample titles; they account for 22 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

GSM8901676 Synovium, FAI, FAI001 Synovium, FAI, FAI
GSM8901677 Synovium, FAI, FAI002 Synovium, FAI, FAI
GSM8901678 Synovium, FAI, FAI003 Synovium, FAI, FAI
GSM8901679 Synovium, FAI, FAI004 Synovium, FAI, FAI
GSM8901680 Synovium, FAI, FAI007 Synovium, FAI, FAI
GSM8901681 Synovium, FAI, FAI008 Synovium, FAI, FAI
GSM8901682 Synovium, hip OA, OA001 Synovium, hip OA, OA
GSM8901683 Synovium, hip OA, OA005 Synovium, hip OA, OA
GSM8901684 Synovium, hip OA, OA007 Synovium, hip OA, OA
GSM8901685 Synovium, hip OA, OA008 Synovium, hip OA, OA
GSM8901686 Synovium, hip OA, OA009 Synovium, hip OA, OA
GSM8901687 Synovium, hip OA, OA010 Synovium, hip OA, OA
GSM9262941 Spatial-Seq, Synovium, FAI, FAI001 Spatial-Seq, Synovium, …
GSM9262942 Spatial-Seq, Synovium, FAI, FAI002 Spatial-Seq, Synovium, …
GSM9262943 Spatial-Seq, Synovium, FAI, FAI005 Spatial-Seq, Synovium, …
GSM9262944 Spatial-Seq, Synovium, FAI, FAI006 Spatial-Seq, Synovium, …
GSM9262945 Spatial-Seq, Synovium, hip OA, OA001 Spatial-Seq, Synovium, …
GSM9262946 Spatial-Seq, Synovium, hip OA, OA002 Spatial-Seq, Synovium, …
GSM9262947 Spatial-Seq, Synovium, hip OA, OA003 Spatial-Seq, Synovium, …
GSM9262948 Spatial-Seq, Synovium, hip OA, OA004 Spatial-Seq, Synovium, …
GSM9262949 Spatial-Seq, Synovium, hip OA, OA005 Spatial-Seq, Synovium, …
GSM9262950 Spatial-Seq, Synovium, hip OA, OA006 Spatial-Seq, Synovium, …

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