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GPNMB is a potential biomarker for arthroplasty aseptic loosening stages

GSE276597 Homo sapiens (human) RNA-seq (gene expression) 28 samples Submitted 2025/09/17 Platform GPL21697
At a glance

RNA-seq (gene expression) · human · 28 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Homo sapiens (human)
Samples
28 samples
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
Glycoprotein non-metastatic melanoma protein B is a potential biomarker for arthroplasty aseptic looseningScientific reports · 2025
Summary (written by the submitters)
Background: Endoprosthesis loosening is the major cause of arthroplasty failure. Currently, radiography and histo-pathological classification of the periprosthetic membrane are used retrospectively for diagnosis. Prospective options for early diagnosis and prevention of loosening are not available. In order to approach this challenge, the study presented here aimed to identify molecular biomarkers in single-centre prospectively collected cell and plasma samples from patients.
Read the full summary ↓
Methods: Four patient cohorts (primary and revision arthroplasty of hip or knee) were defined. Aseptic loosening of implants was assessed by the standardised approach of the Knee Society Total Knee Arthroplasty Roentgenographic Evaluation and Scoring System (KSRESS) which is based on radiolucent lines. Synovial fluid, bone marrow, and blood were collected from a total of 96 patients. Bulk RNA-sequencing (RNA-seq) of mesenchymal stem cells (MSCs) isolated from the bone marrow of patients was performed for 28 samples. The data was analysed by bioinformatic tools. Quantitative real-time PCR served to validate and extend RNA-seq data. Western blots were performed for molecular differentiation. ELISAs were used to quantitate selected protein targets. Results: RNA-seq of MSCs identified glycoprotein non-metastatic melanoma protein B (GPNMB) as significantly upregulated in the cells from revision patients compared to patients with primary implantations. The protein encoded by this gene is plasma membrane-standing; its extracellular domain may be cleaved and secreted. In synovial fluid plasma, the soluble GPNMB protein exhibited increased levels in patients undergoing revision surgery compared to patients subjected to primary arthroplasty. No significant differences were observed in bone marrow plasma and blood plasma. The molecular species detected by Western blotting were similar in the plasma fractions of synovial fluid, bone marrow and blood. Conclusions: The use of GPNMB as a biomarker may be of prime importance for early detection of implant loosening, ahead of radiographic failure demonstration. Translational potential of this article: GPNMB has the potential to act as a prospective and quantitative parameter to assess different stages of implant loosening. Radiography and histo-pathological classification of the periprosthetic membrane, on the contrary, are used retrospectively for diagnosis and are subjective measures, performed mainly at the end of a full loosening process.
Published in
Glycoprotein non-metastatic melanoma protein B is a potential biomarker for arthroplasty aseptic loosening
Schadzek P, Derksen A, Behrens W et al. · Scientific reports 2025 · PMID 40940329 · doi:10.1038/s41598-025-13922-3
This dataset
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.

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 GSE276597_RAW.tar (it can run to tens of gigabytes).

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.

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1157894 and SRA study SRP531184. Searching any of these in the dataset finder brings you back here.

Samples in this study

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