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Series GSE155724 Query DataSets for GSE155724
Status Public on Dec 01, 2023
Title Spatial coupling of microbes and immune cells in solid malignancies [LCM_cold_hot_tumor_nest]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Solid tumors are composed of cancer cells and host immune cells that are distributed in a non-uniform pattern. Although this spatial heterogeneity may reflect mutational variations in cancer cells, mechanisms that direct the recruitment of immune cells to distinct regions within a tumor remain poorly understood. Here, we show that microbial-host interactions define tumor nests enriched in immune cells, and the distribution of microbes within tumors parallels the spatial heterogeneity of intratumoral lymphoid and myeloid cell populations. Analysis of human solid tumors revealed that the spatial distribution of immune cells, particularly CD8+ T cells, is markedly heterogeneous. Compared to T cell-poor (“cold”) tumor nests, T cell-rich (“hot”) tumor nests displayed a significantly higher number of myeloid cells, B cells, and plasma cells. We performed laser capture microdissection (LCM) followed by RNA sequencing to identify unique gene signatures that define tumor epithelium and stroma of cold and hot tumor nests. Cold tumor nests expressed genes that promote tumor proliferation and fibrosis, whereas hot tumor stroma and epithelium showed upregulation of immune-related processes, including responses to bacteria, and receptors that mediate mucosal immune responses to microbes, respectively. Consistent with these findings, we detected elevated levels of microbes within hot tumor nests in human pancreatic and lung cancers. Our data implicate host immune responses to microbes in defining intratumoral immune heterogeneity and highlight a potential role for crosstalks between microbes, cancer cells, and the host immune system in regulating cancer immunogenicity.
 
Overall design RNA isolated from cold and hot tumor nests of human pancreatic ductal adenocarcinoma was analyzed using SMARTer stranded total RNA sequencing.
 
Contributor(s) Li Y, Chang RB, Lee JW, Beatty GL
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Submission date Aug 05, 2020
Last update date Dec 01, 2023
Contact name Gregory L. Beatty
E-mail(s) gregory.beatty@pennmedicine.upenn.edu
Phone (215) 746-7764
Organization name University of Pennsylvania
Department Medicine
Street address 3400 Civic Center Blvd, South Pavilion, Rm 8-107
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (20)
GSM4711260 PDAC_Cold_epithelium_1
GSM4711261 PDAC_Cold_epithelium_2
GSM4711262 PDAC_Cold_epithelium_3
This SubSeries is part of SuperSeries:
GSE155725 Spatial coupling of microbes and immune cells in solid malignancies
Relations
BioProject PRJNA655412
SRA SRP276053

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE155724_LCM_cold_hot_tumor_nest.tpm.txt.gz 1.3 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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