GEO series

IL-1b+ tumor-associated macrophages fuel pathogenic inflammation in pancreatic cancer

GSE217847 Homo sapiens (human) Single-cell RNA-seq 136 samples Submitted 2023/09/07 Platform GPL24247Platform GPL24676Platform GPL33597

At a glance

Single-cell RNA-seq · human · 136 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: Pancreatic cancerThis series is part of our curated briefing on it.
Samples: 136 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.

Summary (written by the submitters)

Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease with high resistance to therapies. Inflammatory and immunomodulatory signals co-exist in the pancreatic tumor microenvironment (TME), leading to dysregulated repair and cytotoxic responses. Tumor-associated macrophages (TAMs) are key players in PDAC, but their diversity prevented therapeutic exploitation.

Read the full summary ↓

Here, we combined single-cell and spatial genomics with functional experiments to elucidate macrophage functions in pancreatic cancer. We uncovered an inflammatory loop between tumor cells and interleukin (IL)-1B+ TAMs, a subset of macrophages elicited by a local synergy between prostaglandin E2 (PGE2) and tumor necrosis factor (TNF)-A. Physical proximity with IL-1B+ TAMs was associated with inflammatory reprogramming and acquisition of pathogenic properties by a subset of PDAC cells. This occurrence was an early event in pancreatic tumorigenesis and led to persistent transcriptional changes associated with disease progression and poor patient outcome. Blocking PGE2 or IL-1B elicited TAM reprogramming and antagonized tumor cell-intrinsic and -extrinsic inflammation, leading to PDAC control in vivo. Targeting the PGE2-IL-1B axis may enable preventive or therapeutic strategy to reprogramming of immune dynamics in pancreatic cancer.

This dataset

Open GSE217847 in finder → Find more RNA-seq datasets → Pancreatic cancer 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 GSE217847_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 PRJNA901006 and SRA study SRP407589. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 37914939) ↗

Samples in this study

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+ 136 more — browse all 136 samples with per-sample file links →

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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.