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SOURCE OF LIQUID BIOPSY BIOMARKER: EXOSOME VS WHOLE PLASMA, FASTING VS NON-FASTING

ABSTRACT: Purpose: We compare small noncoding RNA (ncRNA) profiles between exosomes and whole plasma to test a better source of small ncRNA biomarkers. We hypothesize that exosome is a better source of small ncRNA biomarkers compared to whole plasma. Methods: Small ncRNA sequencings were done using Illumina NextSeq500. Single-end 76 bp reads were explored using FASTQC. GeneGlobe Data Analysis Center, an online platform from Qiagen was used for the small ncRNA-seq data analysis. The mapped read counts for miRNA, piRNA and tRNA were used for differential expression analysis using DESeq2 Bioconductor in R. The small RNA species with logFC > |1| and adj.P-value <0.05 were called differentially expressed. Conclusion: Small ncRNAs extracted from exosomes were found to have the most consistent profiles among healthy individuals. Whole plasma RNA profiles contain high concentrations of blood-derived miRNAs. These miRNA levels can create batch effects among samples due to different levels of hemolysis. Our finding suggests the importance of using purified exosomes as a better source of small ncRNA biomarkers to avoid the batch effect.

ORGANISM(S): Homo sapiens

PROVIDER: GSE216556 | GEO | 2022/10/28

REPOSITORIES: GEO

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Project description:Introduction: microRNAs are promising candidate breast cancer biomarkers due to their cancer-specific expression profiles. However, efforts to develop circulating breast cancer biomarkers are challenged by the heterogeneity of microRNAs in the blood. To overcome this challenge, we aimed to develop a molecular profile of microRNAs specifically secreted from breast cancer cells. Our first step towards this direction relates to capturing and analyzing the contents of exosomes, which are small secretory vesicles that selectively encapsulate microRNAs indicative of their cell of origin. To our knowledge, circulating exosome microRNAs have not been well evaluated as biomarkers for breast cancer diagnosis or monitoring. Methods: Exosomes were collected from the conditioned media of human breast cancer cell lines, mouse plasma of patient-derived orthotopic xenograft models (PDX), and human plasma samples. Exosomes were verified by electron microscopy, nanoparticle tracking analysis, and western blot. Cellular and exosome microRNAs from breast cancer cell lines were profiled by next-generation small RNA sequencing. Plasma exosome microRNA expression was analyzed by qRT-PCR analysis. Results: Small RNA sequencing and qRT-PCR analysis showed that several microRNAs are selectively encapsulated or highly enriched in breast cancer exosomes. Importantly, the selectively enriched exosome microRNA, human miR-1246, was detected at significantly higher levels in exosomes isolated from PDX mouse plasma, indicating that tumor exosome microRNAs are released into the circulation and can serve as plasma biomarkers for breast cancer. This observation was extended to human plasma samples where miR-1246 and miR-21 were detected at significantly higher levels in the plasma exosomes of 16 breast cancer patients as compared to the plasma exosomes of healthy control subjects. Receiver Operating Characteristic (ROC) curve analysis indicated that the combination of plasma exosome miR-1246 and miR-21 levels is a better indicator of breast cancer than their individual levels. Conclusions: Our results demonstrate that certain microRNA species, such as miR-21 and miR-1246, are selectively enriched in human breast cancer exosomes and significantly elevated in the plasma of breast cancer patients. These findings indicate a potential new strategy to selectively analyze plasma breast cancer microRNAs indicative of the presence of breast cancer.

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SOURCE OF LIQUID BIOPSY BIOMARKER: EXOSOME VS WHOLE PLASMA, FASTING VS NON-FASTING

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