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Single-cell integration and multi-modal profiling reveals phenotypes and spatial organization of neutrophils in colorectal cancer

ABSTRACT: Single-cell integration and multi-modal profiling reveals phenotypes and spatial organization of neutrophils in colorectal cancer

PROVIDER: PRJNA1201197 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR31797222_1.fastq.gz	Fastqsanger.gz
	SRR31797222_2.fastq.gz	Fastqsanger.gz
	SRR31797223_1.fastq.gz	Fastqsanger.gz
	SRR31797223_2.fastq.gz	Fastqsanger.gz
	SRR31797224_1.fastq.gz	Fastqsanger.gz

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Single-cell integration and multi-modal profiling reveals phenotypes and spatial organization of neutrophils in colorectal cancer

Project description:The immune composition of the tumor microenvironment (TME) has a major impact on the therapeutic response and clinical outcome in patients with colorectal cancer (CRC). Here, we comprehensively characterize the TME at the single-cell level by first building a large-scale atlas that integrates 4.27 million single cells from 1,670 patient samples. We then complemented the atlas with single-cell profiles from four CRC cohorts with 266 patients, including cells with low mRNA content, spatial transcriptional profiles from 3.7 million cells, and protein profiles from 0.7 million cells. The analysis of the atlas allows refined tumor classification into four immune phenotypes: immune desert, B cell enriched, T cell enriched, and myeloid cell enriched subtypes. Within the myeloid compartment we uncover distinct subpopulations of neutrophils that acquire new functional properties in blood and in the TME, including anti-tumorigenic capabilities. Further, spatial multimodal single-cell profiling reveals that neutrophils are organized in clusters within distinct functional niches. Finally, using an orthotopic mouse model we show that cancer-derived systemic signals modify neutrophil production in the bone marrow, providing evidence for tumor-induced granulopoiesis. Our study provides a big data resource for the CRC and suggests novel therapeutic strategies targeting neutrophils.

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Project description:<p>Annexin A1 (AnxA1) is an anti-inflammatory protein present in different cells in biological systems, especially expressed in macrophages and neutrophils. Since neutrophils play an important role in infections and inflammatory processes and the AnxA1 and its relation in Candida spp. infections is not well understood, our study highlights a perspective in AnxA1 as a target protein in control the immune response during fungi infection. C57BL/6 wild-type (WT) and AnxA1 knockout (AnxA1-/-) peritoneal neutrophils were coinfected with Candida albicans or Candida auris for 4 hours. High levels of COX-2 were observed in WT and AnxA1-/- neutrophils infected with C. albicans and C. auris coinfection. In addition, AnxA1-/- neutrophils exhibited a marked increase of phosphorylated ERK, p-38 and JNK levels after coinfection with both Candida spp. Lipidomics approach shows that lack of AnxA1 produced a marked difference in lipid profile of control or coinfected neutrophil supernatants compared to WT, especially glycerophospholipids and glycerolipids. In summary, our results showed that endogenous AnxA1 regulates neutrophil response under fungal infection and its lipid membrane organization and metabolism.  </p>

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Monocytes and neutrophils

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Lipopolysaccharide-stimulated neutrophils

Project description:Neutrophil gene transcription following lipopolysaccharide exposure. Microarray analysis of lipopolysaccharide-treated human neutrophils. Neutrophils respond to infection by degranulation, release of reactive oxygen intermediates, and secretion of chemokines and cytokines; however, activation of neutrophil transcriptional machinery has been little appreciated. Recent findings suggest that gene expression may represent an additional neutrophil function after exposure to lipopolysaccharide (LPS). We performed microarray gene expression analysis of 4,608 mostly nonredundant genes on LPS-stimulated human neutrophils. Analysis of three donors indicated some variability but also a high degree of reproducibility in gene expression. Twenty-eight verifiable, distinct genes were induced by 4 h of LPS treatment, and 13 genes were repressed. Genes other than cytokines and chemokines are regulated; interestingly, genes involved in cell growth regulation and survival, transcriptional regulation, and interferon response are among those induced, whereas genes involved in cytoskeletal regulation are predominantly repressed. In addition, we identified monocyte chemoattractant protein-1 as a novel LPS-regulated chemokine in neutrophils. Included in these lists are five clones with no defined function. These data suggest molecular mechanisms by which neutrophils respond to infection and indicate that the transcriptional potential of neutrophils is greater than previously thought.

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