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Transcriptional profiles of the Hodgkin lymphoma tumor-associated macrophage in vitro models

GSE288623 Homo sapiens (human) Single-cell RNA-seq 24 samples Submitted 2026/06/01 Platform GPL21697
At a glance

Single-cell RNA-seq · human · 24 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Homo sapiens (human)
Topic
Hodgkin lymphomaThis series is part of our curated briefing on it.
Samples
24 samples: 8 conditions, mostly in triplicateGroups 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.
Summary (written by the submitters)
Tumor-associated macrophages (TAMs) of classic Hodgkin Lymphoma (cHL) contribute to the development of immunosuppressive tumor microenvironment (TME) and are associated with worse treatment outcome. However, detailed features and functions of cHL TAMs and their therapeutic vulnerabilities remain largely unknown. To gain deeper insight into the biology of TAMs in cHL, we analyzed diagnostic biopsies by Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) and assessed transcriptional, proteomic and metabolic profiles of the in vitro TAM models.
Read the full summary ↓
We show that Reed-Sternberg (RS) cells of cHL induce disease-specific TAM phenotype, characterized by elevated expression of factors involved in chemotaxis, angiogenesis, extracellular matrix remodeling and tumor immune escape. Importantly, RS cell-conditioned TAMs expressed TGFβ, CCL17 and tryptophan catabolizing enzymes, IDO1 and IL4I1, facilitating induction or and/or recruitment of Tregs. In addition, we identified PIM1/2/3 kinases in cHL TAMs. We characterized PIMs as important hubs orchestrating RS-macrophage interactions. Pharmacological PIM blockade attenuated development of TAM transcriptional profile and phenotype induced by RS cells. In established TAMs, PIM inhibition or PROTAC-mediated degradation decreased expression of multiple factors associated with pro-tumoral TAM functions, including IL8, MMP9, CHI3L1/2, CD206, CD209, PD-L1, CCL17, TGFβ, IL4I1 and IDO1. PIM blockade attenuated TAM-dependent eosinophil chemoattraction, extracellular matrix remodelling, angiogenesis and regulatory T cell development. Taken together, our study highlights the role of PIMs in regulation of TAM activities involved in cHL pathogenesis and potentially relevant for response of cHL patients to immunotherapies.
This dataset
Open GSE288623 in finder → Find more human RNA-seq datasets → Hodgkin lymphoma 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 GSE288623_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 PRJNA1218716 and SRA study SRP561294. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
8 conditions, mostly in triplicate
THP-1 derived M0 macrophages ×3 THP-1 derived RS-M generated using L1236 ×3 THP-1 derived RS-M generated using L428 ×3 MdM M0 macrophages ×3 RS-M DMSO_24h ×3 RS-M MEN_24h ×3 MdM RS-M generated using L1236 ×2 MdM RS-M generated using L428 ×2 +2 more

Supports a between-group comparison across 22 samples.

How we read this: 8 replicated groups read from 24 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
More Hodgkin lymphoma datasets

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