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High-Resolution Single-Cell RNA Sequencing Uncovers Disparate Neutrophil Populations within Metastatic Cancer Lesions Linked to Progression Free Survival in Multiple Myeloma Patients

GSE261171 Homo sapiens (human) Single-cell RNA-seq 28 samples Submitted 2025/10/22 Platform GPL24676
At a glance

Single-cell RNA-seq · human · 28 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)
Topic
Multiple myelomaThis series is part of our curated briefing on it.
Samples
28 samples: 28 samples, each with a distinct title — no replicated groupsGroups 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
Deciphering neutrophil dynamics in the focal lesion tumor microenvironment to overcome immunosuppression in multiple myelomaBlood · 2025
Summary (written by the submitters)
Understanding the myeloid cell biology of the tumor microenvironment (TME) will allow discovery of novel strategies to disrupt the local immunosuppressive milieu and to develop effective immune based therapies. Neutrophils are a major, understudied myeloid cell population in metastatic malignant tumors. Here, we studied myeloid cells freshly sorted from paired focal lesions (FL) (osteolytic lesions and plasmacytomas) and pelvic bone marrow (BM) from multiple myeloma (MM) patients.
Read the full summary ↓
Using single cell RNA sequencing and functional assays, we discovered the emergence and expansion of distinct, late-stage neutrophil subsets with potent immunosuppressive signatures predominantly in FL. The most abundant late-stage neutrophil subset, MM_N_FL1, activates cytokine responses, the IL-8 CXCR2 pathway, and nitrogen compound metabolism while downregulating primary, secondary, and tertiary granule expression. FL neutrophils exhibit transcriptional and functional differences compared to their paired BM counterparts, displaying notably elevated immunosuppressive capacities independent of tumor cell percentage in FL and BM. Furthermore, the gene signature of the FL neutrophils was associated with significantly inferior progression-free survival (PFS) in a defined population of MM patients. The study provides an in-depth analysis of neutrophil dynamics, function, and imbalance in MM patient FL, suggesting promising targets for novel clinical immunomodulatory therapies.
Published in
Deciphering neutrophil dynamics in the focal lesion tumor microenvironment to overcome immunosuppression in multiple myeloma
Rivera J, Yan Q, Daneshmandi S et al. · Blood 2025 · PMID 40758944 · doi:10.1182/blood.2025028963
This dataset
Open GSE261171 in finder → Find more human RNA-seq datasets → Multiple myeloma landscape →
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 GSE261171_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 PRJNA1085686 and SRA study SRP494143. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40758944) ↗
Study design
28 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 28 sample titles: 28 distinct titles with little repetition. 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
More Multiple myeloma datasets

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.