Monitoring of single extracellular vesicle heterogeneity in cancer progression and therapy

Connecting the dots: (RANKL+) extracellular vesicle count in blood plasma in relation to bone metastases, skeletal related events and osimertinib treatment in patients with EGFR mutated non-small cell lung cancer

Background

The biological mechanisms responsible for the different incidences of bone metastases in molecular subgroups of non-small cell lung cancer (NSCLC) are not identified. Extracellular vesicles (EVs) may play a role, as they are involved in organotrophic metastasis. Phosphorylation of epidermal growth factor receptor (EGFR) in exosomes possibly leads to an increase in receptor activator of nuclear factor κB ligand (RANKL) triggering osteoclastogenesis. In search for new biomarkers with focus on EVs and RANKL, we studied in plasma of patients with EGFR + NSCLC the associations between the total concentration of EVs, RANKL+ EVs, RANKL, and osteoprotegerin (OPG) protein levels, osimertinib treatment, presence of bone metastases and skeletal related events (SREs).

Methods

From the prospective biomarker cohort study START-TKI (NCT05221372), including patients with metastatic EGFR + NSCLC, we collected deep frozen plasma samples at initiation and during osimertinib treatment. Imaging flow cytometry (IFC) was used to determine the concentration of tetraspanin positive EVs and detection of RANKL on EVs. RANKL and OPG levels were measured by enzyme-linked immunosorbent assay (ELISA). Data on demographics, date of NSCLC diagnosis, date of initiation of osimertinib, presence of bone metastases and SREs were collected. Primary endpoint was the relation between (RANKL+) EV levels and bone metastases.

Results

Forty unique patients with in total 50 plasma samples (45% at initiation of osimertinib, 55% during osimertinib treatment) were included. Identification of EVs was possible in 38/40 patients, and determination of RANKL and OPG plasma levels in all samples. Of these 40 patients, 25 (63%) had bone metastases at sample collection. Both total EV and RANKL+ EV concentrations were significantly higher in samples at initiation of osimertinib compared to samples during treatment [mean ± standard deviation (SD), 6.3×1012±2.1×1012/mL plasma vs. 3.2×1012±1.9×1012/mL plasma, P≤0.001 for total EV concentrations; and 2.2×1010±9.3×109/mL plasma vs. 1.1×1010±8.0×109/mL plasma, P=0.001 for RANKL+ EVs]. Patients without a SRE had a significantly higher concentration of RANKL+ EVs compared to patients with an SRE (mean ± SD, 1.8×1010±1.1×1010/mL plasma vs. 1.1×1010±7.4×109/mL plasma, P=0.02). No association was found between the total EV concentration or RANKL+ EVs, plasma levels of OPG and RANKL and bone metastases.

Conclusions

No association was found between the presence of bone metastases and the total concentration of EVs, RANKL+ EVs, or plasma values of RANKL and OPG. In patients without SREs the concentration of RANKL+ EVs was significantly increased. Both the total EV and RANKL+ EV concentrations significantly decreased during osimertinib treatment. This opens new perspectives for the role of (RANKL+) EVs as prognostic biomarkers for EGFR + NSCLC disease progression and response to therapy.

Metabolic Reprogramming Into a Glycolysis Phenotype Induced by Extracellular Vesicles Derived From Prostate Cancer Cells

Most cancer cells adopt a less efficient metabolic process of aerobic glycolysis with high level of glucose uptake followed by lactic acid production, known as the Warburg effect. This phenotypic transition enables cancer cells to achieve increased cellular survival and proliferation in a harsh low-oxygen tumor microenvironment. Also, the resulting acidic microenvironment causes inactivation of the immune system such as T-cell impairment that favors escape by immune surveillance. While lots of studies have revealed that tumor-derived EVs can deliver parental materials to adjacent cells and contribute to oncogenic reprogramming, their functionality in energy metabolism is not well addressed. In this study, we established prostate cancer cells PC-3AcT resistant to cellular death in an acidic culture medium driven by lactic acid. Quantitative proteomics between EVs derived from PC-3 and PC-3AcT cells identified 935 confident EV proteins. According to cellular adaptation to lactic acidosis, we revealed 159 regulated EV proteins related to energy metabolism, cellular shape, and extracellular matrix. These EVs contained a high abundance of glycolytic enzymes. In particular, PC-3AcT EVs were enriched with apolipoproteins including apolipoprotein B-100 (APOB). APOB on PC-3AcT EVs could facilitate their endocytic uptake depending on low density lipoprotein receptor of recipient PC-3 cells, encouraging increases of cellular proliferation and survival in acidic culture media via increased activity and expression of hexokinases and phosphofructokinase. The activation of recipient PC-3 cells can increase glucose consumption and ATP generation, representing an acquired metabolic reprogramming into the Warburg phenotype. Our study first revealed that EVs derived from prostate cancer cells could contribute to energy metabolic reprogramming and that the acquired metabolic phenotypic transition of recipient cells could favor cellular survival in tumor microenvironment.

TcEVdb: a database for T-cell-derived small extracellular vesicles from single-cell transcriptomes

T-Cell-derived extracellular vesicles (TcEVs) play key roles in immune regulation and tumor microenvironment modulation. However, the heterogeneity of TcEV remains poorly understood due to technical limitations of EV analysis and the lack of comprehensive data. To address this, we constructed TcEVdb, a comprehensive database that explores the expression and cluster of TcEV by the SEVtras method from T-cell single-cell RNA sequencing data. TcEVdb contains 277 265 EV droplets from 51 T-cell types across 221 samples from 21 projects, covering 9 tissue sources and 23 disease conditions. The database provides two main functional modules. The Browse module enables users to investigate EV secretion activity indices across samples, visualize TcEV clusters, analyze differentially expressed genes (DEGs) and pathway enrichment in TcEV subpopulations, and compare TcEV transcriptomes with their cellular origins. The Search module allows users to query specific genes across all datasets and visualize their expression distribution. Furthermore, our analysis of TcEV in diffuse large B-cell lymphoma revealed increased EV secretion in CD4+ T exhausted cells compared to healthy controls. Subsequent analyses identified distinct droplet clusters with differential expression genes, including clusters enriched for genes associated with cell motility and mitochondrial function. Overall, TcEVdb serves as a comprehensive resource for exploring the transcriptome of TcEV, which will contribute to advancements in EV-based diagnostics and therapeutics across a wide range of diseases. Database URL: https://guolab.wchscu.cn/TcEVdb.

Ultrasensitive Quantification of microRNA Copy Number in Individual Extracellular Vesicles Using DNA Tetrahedron-Based Single-Molecule Imaging

The ultrasensitive detection of microRNAs (miRNAs) in extracellular vesicles (EVs) can accurately reflect the progress and metastasis of miRNA-mediated intercellular communication, providing an unprecedented opportunity for liquid biopsy. However, due to the low abundance and high heterogeneity of miRNAs in EVs, the ultrasensitive quantification and establishment of a distribution model for miRNA within native EVs remain challenging. Here, we have developed a DNA tetrahedron-based single-molecule fluorescence imaging strategy to overcome this challenge. The internalization efficiency of the probe was as high as 70% without disrupting the native structure of EVs, and combined with single-molecule fluorescence imaging, we achieved in situ imaging analysis of single-copy miRNA in individual EVs without amplification for the first time. A new distribution model for miRNAs has been revealed by statistical analysis of the copy number of miRNAs in EVs across multiple cell lines, characterized by low occupancy and a heterogeneous distribution. More importantly, we found that drug resistance cancer cells promote an increase in the number of drug resistance-related miRNAs within EVs without a corresponding increase in the number of EVs secreted, providing new insights into the EV miRNA sorting mechanisms. We anticipate that this technology will rapidly advance miRNA-mediated intercellular communication based on EVs.

Exosomes-mediated CRISPR/Cas delivery: A cutting-edge frontier in cancer gene therapy

Cancer is considered the second most common disease globally. In the past few decades, many approaches have been proposed for cancer treatment. One among those is targeted therapy using CRISPR/Cas system which plays a significant role in translational research through gene editing. However, due to its inability to cope with specific targeting, off-target effects, and limited tumor penetration, it is very challenging to use this approach in cancer studies. To increase its efficacy, CRISPR components are engineered into the extracellular vesicles (EVs), especially exosomes (a subpopulation of EVs). Exosomes have a significant role in cellular communication. Exosomes-based CRISPR/Cas system transport for gene editing enhances specificity, reduces off-target effects, and improves the therapeutic potential. This review highlights the role of exosomes and the CRISPR/Cas system in cancer research, exosomes-based CRISPR delivery for cancer treatment, and its future orientation.

Therapy-induced secretion of spliceosomal components mediates pro-survival crosstalk between ovarian cancer cells

Ovarian cancer often develops resistance to conventional therapies, hampering their effectiveness. Here, using ex vivo paired ovarian cancer ascites obtained before and after chemotherapy and in vitro therapy-induced secretomes, we show that molecules secreted by ovarian cancer cells upon therapy promote cisplatin resistance and enhance DNA damage repair in recipient cancer cells. Even a short-term incubation of chemonaive ovarian cancer cells with therapy-induced secretomes induces changes resembling those that are observed in chemoresistant patient-derived tumor cells after long-term therapy. Using integrative omics techniques, we find that both ex vivo and in vitro therapy-induced secretomes are enriched with spliceosomal components, which relocalize from the nucleus to the cytoplasm and subsequently into the extracellular vesicles upon treatment. We demonstrate that these molecules substantially contribute to the phenotypic effects of therapy-induced secretomes. Thus, SNU13 and SYNCRIP spliceosomal proteins promote therapy resistance, while the exogenous U12 and U6atac snRNAs stimulate tumor growth. These findings demonstrate the significance of spliceosomal network perturbation during therapy and further highlight that extracellular signaling might be a key factor contributing to the emergence of ovarian cancer therapy resistance.

The non-vesicle cell-free DNA (cfDNA) induces cell transformation associated with horizontal DNA transfer

BACKGROUND

Cell-free DNA (cfDNA) is a source for liquid biopsy used for cancer diagnosis, therapy selection, and disease monitoring due to its non-invasive nature and ease of extraction. However, cfDNA also participates in cancer development and progression by horizontal transfer. In humans, cfDNA circulates complexed with extracellular vesicles (EV) and macromolecular complexes such as nucleosomes, lipids, and serum proteins. The present study aimed to demonstrate whether cfDNA not associated with EV induces cell transformation and tumorigenesis.

METHODS

Supernatant of the SW480 human colon cancer cell line was processed by ultracentrifugation to obtain a soluble fraction (SF) and a fraction associated with EV (EVF). Primary murine embryonic fibroblast cells (NIH3T3) underwent passive transfection with these fractions, and cell proliferation, cell cycle, apoptosis, cell transformation, and tumorigenic assays were performed. Next, cfDNA was analyzed by electronic microscopy, and horizontal transfer was assessed by human mutant KRAS in recipient cells via PCR and recipient cell internalization via fluorescence microscopy.

RESULTS

The results showed that the SF but not the EVF of cfDNA induced proliferative and antiapoptotic effects, cell transformation, and tumorigenesis in nude mice, which were reduced by digestion with DNAse I and proteinase K. These effects were associated with horizontal DNA transfer and cfDNA internalization into recipient cells.

CONCLUSIONS

The results suggest pro-tumorigenic effects of cfDNA in the SF that can be offset by enzyme treatment. Further exploration of the horizontal tumor progression phenomenon mediated by cfDNA is needed to determine whether its manipulation may play a role in cancer therapy.