Identification of potential plasma biomarkers in early-stage nasopharyngeal carcinoma-derived exosomes based on RNA sequencing

Abstract

Background Early diagnosis of nasopharyngeal carcinoma (NPC) is vital to improve the prognosis of these patients. However, early diagnosis of NPC is typically challenging. Therefore, we explored the pathogenetic roles and associated mechanisms of exosomes in plasma of patients with early-stage NPC. Methods Exosomes in plasma were extracted by ultra-high-speed centrifugation. Western blot and transmission electron microscopy (TEM) were used to verify the purity of exosomes. The sequencing data (6 plasma samples from healthy volunteers vs. 6 NPC plasma samples) were analyzed by principal component analysis (PCA), DESeq2, gene ontology (GO), Kyoto encyclopedia of genes and genomes (KEGG), and TargetScan. The differentially expressed miRNAs (DEmiRNAs) were obtained from the dataset (GSE118720) downloaded from the Gene Expression Omnibus (GEO) repository. Additionally, the datasets downloaded from the GEO database (GSE12452, GSE13597, GSE53819, GSE64634) were used to predict the target genes and functions of hsa-miR-1301-3p. qPCR was applied to verify the differences in the expressions of hsa-miR-1301-3p between 10 normal plasma and 10 NPC plasma samples. Results Western blot, TEM, and Nanoparticle Tracking Analysis showed adequate purity of the extracted exosomes. RNA-seq analysis revealed 21 upregulated miRNAs, and 10 downregulated miRNAs in plasma exosomes of early-stage NPC patients. GO analysis showed that the target genes of DEmiRNAs were mainly enriched in DNA synthesis and transcription regulation. KEGG analysis revealed that DEmiRNAs were mainly enriched in PI3K-Akt and MAPK signaling pathways. Moreover, the expression of hsa-mir-1301-3p was verified to be significantly upregulated in enlarged samples of plasma exosomes. Conclusions We identified several DEmiRNAs extracted from tumor-derived exosomes between normal plasma and early-stage NPC plasma. Bioinformatics analyses indicated that these DEmiRNAs may be related to NPC development. Our study may provide novel insights into underlying biomarkers and mechanisms of plasma exosomes in early-stage NPC.

Integrated Bioinformatics Analysis of Serine Racemase as an Independent Prognostic Biomarker in Endometrial Cancer

“…Similarly, Pu et al (2016) reported that hsa-miR-193a-5p contributes to osteosarcoma metastasis by suppressing SRR expression. Another candidate miRNA, hsa-miR-1301-3p, was upregulated in early-stage nasopharyngeal carcinoma ( Zheng et al, 2021 ). However, no studies have investigated the target genes and mechanisms of both hsa-miR-1301-3p and hsa-miR-193a-5p in the context of UCEC.…”

Nasopharyngeal Carcinoma and Its Microenvironment: Past, Current, and Future Perspectives

“…miR-BART7-3p is a potential prognostic biomarker, whereby prominent levels of pre-treatment miR-BART7-3p in plasma indicated a higher risk of distant metastasis whereas post-treatment miR-BART7-3p is associated with short DMFS and OS ( 191 , 192 ). Significant upregulation of miR-1301-3p was detected in the exosomes from early-stage NPC patients’ plasma, indicating their potential application as diagnostic biomarkers in early-stage NPC ( 193 ).…”

MicroRNAs/LncRNAs Modulate MDSCs in Tumor Microenvironment

“…Exosomes are rich in genetic material and molecules: DNA, miRNA, lncRNAs, proteins and lipids, which are essential for cell-cell communication and physiological status. Moreover, exosomes are also involved in the regulation of tumor progression in the TME ( 11 ). Recently, it has been demonstrated that exosomes secreted by tumor cells play critical roles in cancer progression and invasion, including TME remodeling, tumor metastasis and tumor-associated immunosuppression ( 73 ).…”

“…Tumor MDSCs are mainly divided into two main subtypes according to their phenotypes and origins, which are defined by cell surface markers of MDSCs in both tumor models and cancer patients ( 10 , 11 ). The phenotypes of MDSCs in tumor-bearing mice are defined using Gr1 (ly6G/ly6C)/CD11b and further include two subtypes of MDSCs: Monocyte-MDSCs (M-MDSCs, CD11b+Ly6G−Ly6Chi) and Granulocyte-MDSCs (G-MDSCs, CD11b+Ly6G+Ly6Clo) ( 12 , 13 ).…”

“…MiRNAs are non-coding single-stranded small RNAs of approximately 22-24 nucleotides in length and are highly conserved evolutionarily, and are widely found in eukaryotic cells. They play vital regulatory roles in cells, especially in mRNA post-transcriptional regulation, and reduce mRNA expression levels by binding to the 3'UTR of mRNA and binding to the 5 '-UTR of mRNA to upregulate its transcription (10)(11)(12). MiRNAs are involved in regulating both a wide range of physiological activities such as cell cycle, differentiation, proliferation, maturation and immune response and pathological processes, such as inflammation and cancer (13).…”