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Identifying signatures of EV secretion in metastatic breast cancer through functional single-cell profiling

ABSTRACT: Identifying signatures of EV secretion in metastatic breast cancer through functional single-cell profiling

PROVIDER: PRJNA870910 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21124111_1.fastq.gz	Fastqsanger.gz
	SRR21124111_2.fastq.gz	Fastqsanger.gz
	SRR21124112_1.fastq.gz	Fastqsanger.gz
	SRR21124112_2.fastq.gz	Fastqsanger.gz

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Identifying signatures of EV secretion in metastatic breast cancer through functional single-cell profiling

Project description:Extracellular vesicles (EVs) regulate the tumor microenvironment by facilitating transport of biomolecular cargo including RNA, protein, and metabolites. We developed an integrated method to identify individual cells with differences in EV secretion and linked single-cell RNA-sequencing on cloned single cells from MDAMB231 cell line. Additionally, We profiled parental MDAMB231, MCF7 and HCC70 cell lines.

2023-03-27 | GSE211561 | GEO

Identifying signatures of EV secretion in metastatic breast cancer through functional single-cell profiling.

Project description:Extracellular vesicles (EVs) regulate the tumor microenvironment by facilitating transport of biomolecules. Despite extensive investigation, heterogeneity in EV secretion among cancer cells and the mechanisms that support EV secretion are not well characterized. We developed an integrated method to identify individual cells with differences in EV secretion and performed linked single-cell RNA-sequencing on cloned single cells from the metastatic breast cancer cells. Differential gene expression analyses identified a four-gene signature of breast cancer EV secretion: HSP90AA1, HSPH1, EIF5, and DIAPH3. We functionally validated this gene signature by testing it across cell lines with different metastatic potential in vitro. Analysis of the TCGA and METABRIC datasets showed that this signature is associated with poor survival, invasive breast cancer types, and poor CD8+ T cell infiltration in human tumors. We anticipate that our method for directly identifying the molecular determinants of EV secretion will have broad applications across cell types and diseases.

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Extracellular vesicle (EV) miRNome profiling in hiPSC-cardiomyocyte differentiation reveals a stemness-maintenance miRNA cluster driving hiPSC-EV bioactivity

Project description:Extracellular Vesicles (EV) are an attractive therapy to boost cardiac regeneration. Nevertheless, identification of EV and corresponding cell platform(s) suitable for therapeutic application, is still a challenge. Here, we isolated EV from key stages of the human induced pluripotent stem cell-cardiomyocyte (hiPSC-CM) differentiation and maturation, i.e., from hiPSC (hiPSC-EV), cardiac progenitors (CPC-EV), immature (CMi-EV) and mature (CMm-EV) cardiomyocytes, with the aim of identifying a promising cell biofactory for EV production, and pinpoint the genetic signatures of bioactive EV. EV were characterized in terms of expression of specific markers, yield, and size. Bioactivity was assessed in human umbilical vein endothelial cells (HUVEC) and hiPSC-CM. Small RNA-Seq was performed to identify the differentially expressed miRNA in the four EV groups. Bioactivity assays showed increased tube formation and migration in HUVEC treated with hiPSC-EV compared to EV from committed cell populations. hiPSC-EV also significantly increased hiPSC-CM proliferation. Global miRNA expression profiles corroborated an EV-miRNA pattern indicative of stem cell to cardiomyocyte specification. A stemness maintenance miRNA cluster upregulated in hiPSC-EV was found to target the PTEN/PI3K/AKT pathway. Moreover, hiPSC-EV treatment mediated PTEN suppression and increased AKT phosphorylation. Overall, our findings validate hiPSC as suitable cell biofactories for EV production for cardiac regenerative applications.

2022-06-01 | GSE179323 | GEO

Identifying Macrophage-specific L13a Knockout Transcriptomic Signatures

Project description:Identifying Macrophage-specific L13a Knockout Transcriptomic Signatures

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EV-miRome-wide identification of noncoding RNAs for detecting metastatic colorectal cancer and monitoring the therapeutic response

Project description:Molecular composition of circulating small extracellular vesicles (EVs) does not merely reflect the cells of origin, but also is enriched in specific biomolecules directly associated with the cellular transformation. Given their functional and clinical relevance, small EVs have emerged as a promising target among the liquid biopsy approaches for cancer detection. However, while most of the currently identified EV-miRs are only geared towards one-dimensional disease detection, their application for long-term tracking and treatment response monitoring has been largely elusive. In this study, we established and optimized a rapid, sensitive and robust liquid biopsy sampling method, and further used small RNA sequencing to comprehensively catalogue EV-miRomes in association with the progression and outcome of metastatic colorectal cancer (mCRC). By cross-comparison of EV-miRomes (n = 290) from multi-stage and longitundial cohorts, we uncovered 28 EV-miRs for detecting mCRC, and 131 EV-miRs for long-term monitoring of tumor size progression. Among these candidates, we further pinpointed a 15-EV-miR signature with dual detection and monitoring functions for mCRC. From this panel, EV-miR-320c was uncovered as a strong clinical marker – aside from its diagnostic power, its high expression has also been linked to lower overall survival and a greater likelihood of disease recurrence. Furthermore, target spectrum of this 15-EV-miR signature of mCRC suggested an involvement of small EVs in programming the mesenchymal–epithelial transition (MET) transition for distant localization of the metastasized cells and also in creating a tumor-favoring metastatic niche. Our clinically-oriented delineation of the mCRC-associated circulating EV-miRomes revealed the functional significance of these liquid biopsy markers and further strengthen their translational potential in tumor therapeutic monitoring.

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2025-09-04 | PXD068092 | JPOST Repository

Unique structural configuration of EV-DNA primes Kupffer cell-mediated anti-tumor immunity to prevent metastatic progression

Project description:Extracellular vesicles (EVs) transport biomolecules that mediate intercellular communication. We previously showed that EVs contain DNA (EV-DNA) representing the entire genome. However, the mechanism of EV-DNA packaging and its role in cancer remains elusive. Here, we demonstrate that the majority of DNA is localized on the vesicle surface and associated with uniquely modified and cleaved histones. We conducted a genome-wide CRISPR knockout screen, which revealed that immune developmental pathways and genes, including APAF1 and NCF1, regulated EV-DNA packaging. We further demonstrated in colorectal cancer models that uptake of EVs and EV-DNA by Kupffer cells (KC) activated DNA damage responses. This activation re-wired KC cytokine production and generated tertiary lymphoid structures in pre-metastatic livers, thereby suppressing metastasis. Conversely, loss of APAF1 decreased EV-DNA packaging and promoted liver metastasis. Quantifying EV-DNA in colorectal cancer biopsies revealed that EV-DNA could possibly serve as a predictive biomarker for metastatic risk.

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Exosomes dependent immune surveillance at the metastatic niche requires BAG6

Project description:Mice were intravenously injected with extracellular vesicles (EVs) isolated from B16V wt (n=3) or BAG6KO (n=3) cells or with PBS (n=3) as a control for 4 weeks on a weekly basis. Since B-16V melanoma cells colonise the lung upon intravenous injection and referring to current literature, we hypothesise that melanoma EVs alter the (immune-) microenvironment of the lung to prepare a pre-metastatic niche. Based on current literature and own previous experiments identifying BAG6 as an immunoregulatory protein that is also involved in the biogenesis of EVs, we are particularly interested in differences between the immune signature upon wt EV treatment compared to BAG6KO EV treatment.

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Identifying immune signatures of sepsis in very preterm babies

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Highly-metastatic colorectal cancer cell released Nidogen 1-Enriched Extracellular Vesicles promote liver metastasis by activating hepatic stellate cells and forming the neutrophilextracellulartraps

Project description:The liver is frequently affected by metastasis in colorectal cancer patients; however, the precise interaction between the liver microenvironment and metastatic colorectal cancer cells remains elusive. Our study reveals that NID1, present in extracellular vesicles (EVs) derived from metastatic colorectal cancer, plays a pivotal role in promoting colorectal cancer liver metastasis (CRLM). EV-NID1 facilitates epithelial-mesenchymal transition (EMT) in colorectal cancer cells by modulating EMT-associated genes. Moreover, EV-NID1 activates hepatic stellate cells (HSCs), which in turn stimulate neutrophil infiltration and induce the formation of neutrophil extracellular traps (NETs) within the hepatic metastatic microenvironment via interleukin 11 (IL-11) secretion. This process ultimately reshapes the tumor microenvironment (TME) and fosters the establishment of a metastatic niche conducive to CRLM. Notably, targeted inhibition of IL-11 signaling using anti-IL-11 monoclonal antibodies effectively suppresses EV-NID1-induced liver metastasis in a murine model. In summary, our findings elucidate the mechanism underlying EV-NID1-mediated regulation of CRLM, presenting a promising therapeutic target for intervention in this disease.

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