Systemic proteomics and miRNA profile analysis of exosomes derived from human pluripotent stem cells

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Abstract

Background

Increasing studies have reported the therapeutic effect of mesenchymal stem cell (MSC)-derived exosomes by which protein and miRNA are clearly characterized. However, the proteomics and miRNA profiles of exosomes derived from human embryonic stem cells (hESCs) and human-induced pluripotent stem cells (hiPSCs) remain unclear.

Methods

In this study, we isolated exosomes from hESCs, hiPSCs, and human umbilical cord mesenchymal stem cells (hUC-MSCs) via classic ultracentrifugation and a 0.22-μm filter, followed by the conservative identification. Tandem mass tag labeling and label-free relative peptide quantification together defined their proteomics. High-throughput sequencing was performed to determine miRNA profiles. Then, we conducted a bioinformatics analysis to identify the dominant biological processes and pathways modulated by exosome cargos. Finally, the western blot and RT-qPCR were performed to detect the actual loads of proteins and miRNAs in three types of exosomes.

Results

Based on our study, the cargos from three types of exosomes contribute to sophisticated biological processes. In comparison, hESC exosomes (hESC-Exos) were superior in regulating development, metabolism, and anti-aging, and hiPSC exosomes (hiPSC-Exos) had similar biological functions as hESC-Exos, whereas hUC-MSCs exosomes (hUC-MSC-Exos) contributed more to immune regulation.

Conclusions

The data presented in our study help define the protein and miRNA landscapes of three exosomes, predict their biological functions via systematic and comprehensive network analysis at the system level, and reveal their respective potential applications in different fields so as to optimize exosome selection in preclinical and clinical trials.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13287-022-03142-1.

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Most cited references 62

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Minimal information for studies of extracellular vesicles 2018 (MISEV2018): a position statement of the International Society for Extracellular Vesicles and update of the MISEV2014 guidelines

Clotilde Théry, Kenneth W Witwer, Elena Aikawa … (2019)

ABSTRACT The last decade has seen a sharp increase in the number of scientific publications describing physiological and pathological functions of extracellular vesicles (EVs), a collective term covering various subtypes of cell-released, membranous structures, called exosomes, microvesicles, microparticles, ectosomes, oncosomes, apoptotic bodies, and many other names. However, specific issues arise when working with these entities, whose size and amount often make them difficult to obtain as relatively pure preparations, and to characterize properly. The International Society for Extracellular Vesicles (ISEV) proposed Minimal Information for Studies of Extracellular Vesicles (“MISEV”) guidelines for the field in 2014. We now update these “MISEV2014” guidelines based on evolution of the collective knowledge in the last four years. An important point to consider is that ascribing a specific function to EVs in general, or to subtypes of EVs, requires reporting of specific information beyond mere description of function in a crude, potentially contaminated, and heterogeneous preparation. For example, claims that exosomes are endowed with exquisite and specific activities remain difficult to support experimentally, given our still limited knowledge of their specific molecular machineries of biogenesis and release, as compared with other biophysically similar EVs. The MISEV2018 guidelines include tables and outlines of suggested protocols and steps to follow to document specific EV-associated functional activities. Finally, a checklist is provided with summaries of key points.

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Shedding light on the cell biology of extracellular vesicles

Guillaume van Niel, Gisela D'Angelo, Graça Raposo (2018)

Extracellular vesicles are a heterogeneous group of cell-derived membranous structures comprising exosomes and microvesicles, which originate from the endosomal system or which are shed from the plasma membrane, respectively. They are present in biological fluids and are involved in multiple physiological and pathological processes. Extracellular vesicles are now considered as an additional mechanism for intercellular communication, allowing cells to exchange proteins, lipids and genetic material. Knowledge of the cellular processes that govern extracellular vesicle biology is essential to shed light on the physiological and pathological functions of these vesicles as well as on clinical applications involving their use and/or analysis. However, in this expanding field, much remains unknown regarding the origin, biogenesis, secretion, targeting and fate of these vesicles.

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Extracellular vesicles: Exosomes, microvesicles, and friends

Graça Raposo, Willem Stoorvogel (2013)

Cells release into the extracellular environment diverse types of membrane vesicles of endosomal and plasma membrane origin called exosomes and microvesicles, respectively. These extracellular vesicles (EVs) represent an important mode of intercellular communication by serving as vehicles for transfer between cells of membrane and cytosolic proteins, lipids, and RNA. Deficiencies in our knowledge of the molecular mechanisms for EV formation and lack of methods to interfere with the packaging of cargo or with vesicle release, however, still hamper identification of their physiological relevance in vivo. In this review, we focus on the characterization of EVs and on currently proposed mechanisms for their formation, targeting, and function.

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Author and article information

Contributors

Ying Zhang: zy730302@aliyun.com

Guangju Ji:

ORCID: http://orcid.org/0000-0001-8626-3490

gj28@ibp.ac.cn

Journal

Journal ID (nlm-ta): Stem Cell Res Ther

Journal ID (iso-abbrev): Stem Cell Res Ther

Title: Stem Cell Research & Therapy

Publisher: BioMed Central (London )

ISSN (Electronic): 1757-6512

Publication date (Electronic): 5 September 2022

Publication date PMC-release: 5 September 2022

Publication date Collection: 2022

Volume: 13

Electronic Location Identifier: 449

Affiliations

[1 ]GRID grid.9227.e, ISNI 0000000119573309, Key Laboratory of Interdisciplinary Research, Institute of Biophysics, , Chinese Academy of Sciences, ; Beijing, 100101 China

[2 ]GRID grid.410726.6, ISNI 0000 0004 1797 8419, University of Chinese Academy of Sciences, ; Beijing, 100049 China

[3 ]GRID grid.452828.1, ISNI 0000 0004 7649 7439, Department of Medical Oncology, , The Second Affiliated Hospital of Dalian Medical University, ; Dalian, 116023 China

[4 ]GRID grid.411971.b, ISNI 0000 0000 9558 1426, Sixth Department of Liver Disease, Dalian Public Health Clinical Center, , Dalian Medical University, ; Dalian, 116023 China

Author information

Guangju Ji http://orcid.org/0000-0001-8626-3490

Article

Publisher ID: 3142

DOI: 10.1186/s13287-022-03142-1

PMC ID: 9444124

PubMed ID: 36064647

SO-VID: 90b09f68-041e-4593-adf4-7d85becc0294

License:

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

History

Date received : 23 May 2022

Date accepted : 16 August 2022

Funding

Funded by: National Key Research and Development Project

Award ID: 2019YFA0100400

Award Recipient : Guangju Ji

Funded by: National Foundation of Sciences and Technology

Award ID: 31971051

Award ID: 31771562

Award Recipient : Guangju Ji

Funded by: Dalian municipal Dengfeng Clinical Medicine Grant

Award ID: 2021024

Award Recipient : Ying Zhang

Custom metadata

ScienceOpen disciplines: Molecular medicine

Keywords: human embryonic stem cells,human-induced pluripotent stem cells,human umbilical cord mesenchymal stem cells,exosomes,proteomics,mirna

Data availability:

ScienceOpen disciplines: Molecular medicine

Keywords: human embryonic stem cells, human-induced pluripotent stem cells, human umbilical cord mesenchymal stem cells, exosomes, proteomics, mirna

Systemic proteomics and miRNA profile analysis of exosomes derived from human pluripotent stem cells

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Abstract

Background

Methods

Results

Conclusions

Supplementary Information

Related collections

Bacterial extracellular vesicles

Most cited references 62

Minimal information for studies of extracellular vesicles 2018 (MISEV2018): a position statement of the International Society for Extracellular Vesicles and update of the MISEV2014 guidelines

Shedding light on the cell biology of extracellular vesicles

Extracellular vesicles: Exosomes, microvesicles, and friends

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