Proteomic Analysis of Serum Small Extracellular Vesicles Identifies Diagnostic Biomarkers for Neuroblastoma

Overview

Journal Front Oncol

Specialty Oncology

Date 2024 Sep 4

PMID 39228987

Authors

Juan Cheng

Dongrui Ji

Jing Ma

Qinghua Zhang

Wanglin Zhang

Lin Yang

Affiliations

Soon will be listed here.

Abstract

Background: Neuroblastoma (NB) primarily arises in children who are <10 years of age, and originates from developing sympathetic nervous system, which results in tumors in adrenal glands and/or sympathetic ganglia. The diagnosis of NB involves a combination of laboratory and imaging tests, and biopsies. Small extracellular vesicles (sEVs) have gained attention as potential biomarkers for various types of tumors. Here, we performed proteomic analysis of serum sEVs and identified potential biomarkers for NB.

Methods: Label-free proteomics of serum sEVs were performed in the discovery phase. A bulk RNA-seq dataset of NB tissues was used to analyze the association between genes encoding sEVs proteins and prognosis. Potential biomarkers were validated via multiple reaction monitoring (MRM) or western blot analysis in the validation phase. A public single-cell RNA-seq (scRNA-seq) dataset was integrated to analyze the tissue origin of sEVs harboring biomarkers.

Results: A total of 104 differentially expressed proteins were identified in NB patients with label-free proteomics, and 26 potential biomarkers were validated with MRM analysis. Seven proteins BSG, HSP90AB1, SLC44A1, CHGA, ATP6V0A1, ITGAL and SELL showed the strong ability to distinguish NB patients from healthy controls and non-NB patients as well. Integrated analysis of scRNA-seq and sEVs proteomics revealed that these sEVs-derived biomarkers originated from different cell populations in tumor tissues.

Conclusion: sEVs-based biomarkers may aid the molecular diagnosis of NB, representing an innovative strategy to improve NB detection and management.

References

Chen J, Li P, Zhang T, Xu Z, Huang X, Wang R . Review on Strategies and Technologies for Exosome Isolation and Purification. Front Bioeng Biotechnol. 2022; 9:811971. PMC: 8766409. DOI: 10.3389/fbioe.2021.811971. View

Huang T, Huang H, Dong S, Chen J, Zhang B, Li H . ATP6V0A1-dependent cholesterol absorption in colorectal cancer cells triggers immunosuppressive signaling to inactivate memory CD8 T cells. Nat Commun. 2024; 15(1):5680. PMC: 11227557. DOI: 10.1038/s41467-024-50077-7. View

Monypenny J, Milewicz H, Flores-Borja F, Weitsman G, Cheung A, Chowdhury R . ALIX Regulates Tumor-Mediated Immunosuppression by Controlling EGFR Activity and PD-L1 Presentation. Cell Rep. 2018; 24(3):630-641. PMC: 6077252. DOI: 10.1016/j.celrep.2018.06.066. View

Zhao Z, McGill J, Gamero-Kubota P, He M . Microfluidic on-demand engineering of exosomes towards cancer immunotherapy. Lab Chip. 2019; 19(10):1877-1886. PMC: 6520140. DOI: 10.1039/c8lc01279b. View

Henrich K, Bender S, Saadati M, Dreidax D, Gartlgruber M, Shao C . Integrative Genome-Scale Analysis Identifies Epigenetic Mechanisms of Transcriptional Deregulation in Unfavorable Neuroblastomas. Cancer Res. 2016; 76(18):5523-37. DOI: 10.1158/0008-5472.CAN-15-2507. View

McKiernan J, Donovan M, ONeill V, Bentink S, Noerholm M, Belzer S . A Novel Urine Exosome Gene Expression Assay to Predict High-grade Prostate Cancer at Initial Biopsy. JAMA Oncol. 2016; 2(7):882-9. DOI: 10.1001/jamaoncol.2016.0097. View

Vermeulen J, De Preter K, Naranjo A, Vercruysse L, Van Roy N, Hellemans J . Predicting outcomes for children with neuroblastoma using a multigene-expression signature: a retrospective SIOPEN/COG/GPOH study. Lancet Oncol. 2009; 10(7):663-71. PMC: 3045079. DOI: 10.1016/S1470-2045(09)70154-8. View

Li W, Hu Y, Jiang T, Han Y, Han G, Chen J . Rab27A regulates exosome secretion from lung adenocarcinoma cells A549: involvement of EPI64. APMIS. 2014; 122(11):1080-7. DOI: 10.1111/apm.12261. View

Brady S, Liu Y, Ma X, Gout A, Hagiwara K, Zhou X . Pan-neuroblastoma analysis reveals age- and signature-associated driver alterations. Nat Commun. 2020; 11(1):5183. PMC: 7560655. DOI: 10.1038/s41467-020-18987-4. View

10.

Cheng J, Ji D, Yin Y, Wang S, Song K, Pan Q . Proteomic profiling of serum small extracellular vesicles reveals immune signatures of children with pneumonia. Transl Pediatr. 2022; 11(6):891-908. PMC: 9253949. DOI: 10.21037/tp-22-134. View

11.

Li Y, Zhao J, Yu S, Wang Z, He X, Su Y . Extracellular Vesicles Long RNA Sequencing Reveals Abundant mRNA, circRNA, and lncRNA in Human Blood as Potential Biomarkers for Cancer Diagnosis. Clin Chem. 2019; 65(6):798-808. DOI: 10.1373/clinchem.2018.301291. View

12.

Shi A, Kasumova G, Michaud W, Cintolo-Gonzalez J, Diaz-Martinez M, Ohmura J . Plasma-derived extracellular vesicle analysis and deconvolution enable prediction and tracking of melanoma checkpoint blockade outcome. Sci Adv. 2020; 6(46). PMC: 7673759. DOI: 10.1126/sciadv.abb3461. View

13.

Pinto N, Applebaum M, Volchenboum S, Matthay K, London W, Ambros P . Advances in Risk Classification and Treatment Strategies for Neuroblastoma. J Clin Oncol. 2015; 33(27):3008-17. PMC: 4567703. DOI: 10.1200/JCO.2014.59.4648. View

14.

. A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. Nat Biotechnol. 2014; 32(9):903-14. PMC: 4321899. DOI: 10.1038/nbt.2957. View

15.

LeBleu V, Kalluri R . Exosomes as a Multicomponent Biomarker Platform in Cancer. Trends Cancer. 2020; 6(9):767-774. DOI: 10.1016/j.trecan.2020.03.007. View

16.

Lin K, Baenke F, Lai X, Helm D, Polster H, Rao V . Comprehensive proteomic profiling of serum extracellular vesicles in patients with colorectal liver metastases identifies a signature for non-invasive risk stratification and early-response evaluation. Mol Cancer. 2022; 21(1):91. PMC: 8973547. DOI: 10.1186/s12943-022-01562-4. View

17.

Sun S, Zhou X, Zhang W, Gallick G, Kuang J . Unravelling the pivotal role of Alix in MVB sorting and silencing of the activated EGFR. Biochem J. 2014; 466(3):475-87. PMC: 4495973. DOI: 10.1042/BJ20141156. View

18.

Hong C, Funk S, Muller L, Boyiadzis M, Whiteside T . Isolation of biologically active and morphologically intact exosomes from plasma of patients with cancer. J Extracell Vesicles. 2016; 5:29289. PMC: 4808740. DOI: 10.3402/jev.v5.29289. View

19.

Hou L, Yuki K . CD11a regulates hematopoietic stem and progenitor cells. Front Immunol. 2023; 14:1219953. PMC: 10537941. DOI: 10.3389/fimmu.2023.1219953. View

20.

Li K, Lin Y, Zhou Y, Xiong X, Wang L, Li J . Salivary Extracellular MicroRNAs for Early Detection and Prognostication of Esophageal Cancer: A Clinical Study. Gastroenterology. 2023; 165(4):932-945.e9. DOI: 10.1053/j.gastro.2023.06.021. View