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Anti-tumor activity of a novelLAIR1antagonist in combination with anti-PD-1to treat collagen-rich solid tumors (GeoMx)

GSE260598 Homo sapiens (human) Spatial transcriptomics 48 samples Submitted 2024/03/04 Platform GPL20301
At a glance

Spatial transcriptomics · human · 48 samples

What it is
Spatial transcriptomicsGene activity measured with its position in a tissue section.
Organism
Homo sapiens (human)
Samples
48 samples: 16 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.
Paper
Antitumor Activity of a Novel LAIR1 Antagonist in Combination with Anti-PD1 to Treat Collagen-Rich Solid TumorsMolecular cancer therapeutics · 2024
Summary (written by the submitters)
We recently reported that resistance to PD-1-blockade in a refractory lung cancer-derived model involved increased collagen deposition and the collagen-binding inhibitory receptor leukocyte-associated immunoglobulin-like receptor 1 (LAIR1), and thus we hypothesized that LAIR1 and collagen cooperated to suppress therapeutic response. Here, we report LAIR1 is associated with tumor stroma and is highly expressed by intratumoral myeloid cells in both human tumors and mouse models of cancer.
Read the full summary ↓
Stroma-associated myeloid cells exhibit a suppressive phenotype and correlate with LAIR1 expression in human cancer. NGM438, a novel humanized LAIR1 antagonist monoclonal antibody, elicits myeloid inflammation and allogeneic T cell responses by binding to LAIR1 and blocking collagen engagement. Further, a mouse-reactive NGM438 surrogate antibody sensitized refractory KP mouse lung tumors to anti-PD-1 therapy and resulted in increased intratumoral CD8+ T cell content and inflammatory gene expression. These data place LAIR1 at the intersection of stroma and suppressive myeloid cells and support the notion that blockade of the LAIR1/collagen axis can potentially address resistance to checkpoint inhibitor therapy in the clinic.
Published in
Antitumor Activity of a Novel LAIR1 Antagonist in Combination with Anti-PD1 to Treat Collagen-Rich Solid Tumors
Rodriguez BL, Huang J, Gibson L et al. · Molecular cancer therapeutics 2024 · PMID 38648067 · doi:10.1158/1535-7163.MCT-23-0866
This dataset
Open GSE260598 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 GSE260598_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 PRJNA1082307 and SRA study SRP492613. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38648067) ↗
Study design
16 conditions, mostly in triplicate
F140509 Gastric cancer stroma CD68+ ROI ×3 F140509 Gastric cancer stroma CD68- ROI ×3 F140509 Gastric cancer tumor nest CD68+ ROI ×3 43728 Lung cancer stroma CD68+ ROI ×3 43728 Lung cancer stroma CD68- ROI ×3 43728 Lung cancer tumor nest CD68+ ROI ×3 43728 Lung cancer tumor nest CD68- ROI ×3 43881 Lung cancer stroma CD68+ ROI ×3 +9 more

Supports a between-group comparison across 47 samples.

How we read this: 16 replicated groups read from 48 sample titles; they account for 47 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

+ 8 more — browse all 48 samples with per-sample file links →

Datasets on a similar topic

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