GEO series
Spatial biology reveals macrophage dysfunction in immunosuppressed non-melanoma skin cancer
GSE308361
Homo sapiens
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
16 samples
Submitted 2026/08/07
Platform GPL34284
Summary
The rising incidence of non-melanoma skin cancer (NMSC), including basal cell carcinoma (BCC) and cutaneous squamous cell carcinoma (cSCC), particularly among immunosuppressed individuals, underscores the need for a deeper understanding of the tumor microenvironment (TME) to develop effective and safe immunotherapies. This study employed single-cell multi-omic analyses to investigate the spatial distribution and transcriptional profiles of immune cells in NMSC from both immunocompetent and immunosuppressed patients. Our results challenge the prevailing notion that immunosuppression is primarily driven by reduced immune cell abundance or lymphocytic dysfunction. Instead, we identified a critical deficiency in antigen presentation by macrophages, leading to impaired T-cell diversity and clonal expansion. Additionally, a spatial epigenomic atlas of the NMSC TME revealed distinct spatial niches and epigenetic programs associated with immunosuppression. These findings highlight the central role of innate immunity in shaping anti-tumor responses and offer potential therapeutic targets to enhance immunotherapy in this vulnerable patient population.
Published in
Naara S, Kochat V, Rao X et al.
· Cell 2026
· PMID 42556334
· doi:10.1016/j.cell.2026.07.031
This dataset
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Direct links to NCBI, no account and no request form: the whole study as GSE308361_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 16 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1330270. Searching any of these in the dataset finder brings you back here.
Study design
16 conditions, each sampled once — no replicated groups
Read from 16 sample titles: 16 distinct titles with little repetition. Check it against the sample list below before relying on it.
Samples in this study
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- GSM9244045 SC10-64_BCC_IS_scATAC-seq
- GSM9244046 SC3-38_BCC_IC_scATAC-seq
- GSM9244047 SC4-25_BCC_IC_scATAC-seq
- GSM9244048 SC5-60_SCC_IS_scATAC-seq
- GSM9244049 SC6-68_BCC_IS_scATAC-seq
- GSM9244050 SC7-19_SCC_IS_scATAC-seq
- GSM9244051 SC8-4R_BCC_IC_scATAC-seq
- GSM9244052 SC9-54_BCC_IC_scATAC-seq
- GSM9244053 SC10-64_BCC_IS_scRNA-seq
- GSM9244054 SC3-38_BCC_IC_scRNA-seq
- GSM9244055 SC4-25_BCC_IC_scRNA-seq
- GSM9244056 SC5-60_SCC_IS_scRNA-seq
- GSM9244057 SC6-68_BCC_IS_scRNA-seq
- GSM9244058 SC7-19_SCC_IS_scRNA-seq
- GSM9244059 SC8-4R_BCC_IC_scRNA-seq
- GSM9244060 SC9-54_BCC_IC_scRNA-seq
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