Abstract

Tumor-initiating cells with reprogramming plasticity or stem-progenitor cell properties (stemness) are thought to be essential for cancer development and metastatic regeneration in many cancers; however, elucidation of the underlying molecular network and pathways remains demanding. Combining machine learning and experimental investigation, here we report CD81, a tetraspanin transmembrane protein known to be enriched in extracellular vesicles (EVs), as a newly identified driver of breast cancer stemness and metastasis. Using protein structure modeling and interface prediction-guided mutagenesis, we demonstrate that membrane CD81 interacts with CD44 through their extracellular regions in promoting tumor cell cluster formation and lung metastasis of triple negative breast cancer (TNBC) in human and mouse models. In-depth global and phosphoproteomic analyses of tumor cells deficient with CD81 or CD44 unveils endocytosis-related pathway alterations, leading to further identification of a quality-keeping role of CD44 and CD81 in EV secretion as well as in EV-associated stemness-promoting function. CD81 is co-expressed along with CD44 in human circulating tumor cells (CTCs) and enriched in clustered CTCs that promote cancer stemness and metastasis, supporting the clinical significance of CD81 in association with patient outcomes. Our study highlights machine learning as a powerful tool in facilitating the molecular understanding of new molecular targets in regulating stemness and metastasis of TNBC.

Data availability

RNA sequencing data have been deposited to GEO database with accession number GSE174087.Mass spec raw data sets have been deposited in the Japan ProteOmeSTandard Repository (https://repository.jpostdb.org/) (98). The accession numbers are PXD029529 for ProteomeXchange (99) and JPST001321 for jPOST. The access link is https://repository.jpostdb.org/preview/1370203119618182ba1c0f2

The following data sets were generated

Article and author information

Author details

  1. Erika K Ramos

    Department of Pharmacology, Northwestern University, Chicago, United States
    Competing interests
    Erika K Ramos, has patents on exosomes which are not related to this manuscript..
  2. Chia-Feng Tsai

    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6514-6911
  3. Yuzhi Jia

    Department of Pharmacology, Northwestern University, Chicago, United States
    Competing interests
    No competing interests declared.
  4. Yue Cao

    Department of Electrical and Computer Engineering, Texas A&M University, College Station, United States
    Competing interests
    No competing interests declared.
  5. Megan Manu

    Department of Pharmacology, Northwestern University, Chicago, United States
    Competing interests
    No competing interests declared.
  6. Rokana Taftaf

    Department of Pharmacology, Northwestern University, Chicago, United States
    Competing interests
    No competing interests declared.
  7. Andrew D Hoffmann

    Department of Pharmacology, Northwestern University, Chicago, United States
    Competing interests
    Andrew D Hoffmann, has patents on exosomes which are not related to the paper..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5479-944X
  8. Lamiaa El-Shennawy

    Department of Pharmacology, Northwestern University, Chicago, United States
    Competing interests
    Lamiaa El-Shennawy, has patents on exosomes which are not related to the paper..
  9. Marina A Gritsenko

    Biological Science Division, Pacific Northwest National Laboratory, Richland, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9992-9829
  10. Valery Adorno-Cruz

    Department of Pharmacology, Northwestern University, Chicago, United States
    Competing interests
    No competing interests declared.
  11. Emma J Schuster

    Department of Pharmacology, Northwestern University, Chicago, United States
    Competing interests
    Emma J Schuster, has patents on exosomes which are not related to the paper..
  12. David Scholten

    Department of Pharmacology, Northwestern University, Chicago, United States
    Competing interests
    No competing interests declared.
  13. Dhwani Patel

    Department of Pharmacology, Northwestern University, Chicago, United States
    Competing interests
    No competing interests declared.
  14. Xia Liu

    Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, United States
    Competing interests
    No competing interests declared.
  15. Priyam Patel

    Quantitative Data Science Core, Northwestern University, Chicago, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9433-5017
  16. Brian Wray

    Quantitative Data Science Core, Northwestern University, Chicago, United States
    Competing interests
    No competing interests declared.
  17. Youbin Zhang

    Department of Medicine, Northwestern University, Chicago, United States
    Competing interests
    No competing interests declared.
  18. Shanshan Zhang

    Pathology Core Facility, Northwestern University, Chicago, United States
    Competing interests
    No competing interests declared.
  19. Ronald J Moore

    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, United States
    Competing interests
    No competing interests declared.
  20. Jeremy V Mathews

    Northwestern University, Chicago, IL, United States
    Competing interests
    No competing interests declared.
  21. Matthew J Schipma

    Quantitative Data Science Core, Northwestern University, Chicago, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0865-1057
  22. Tao Liu

    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9529-6550
  23. Valerie L Tokars

    Department of Pharmacology, Northwestern University, Chicago, United States
    Competing interests
    No competing interests declared.
  24. Massimo Cristofanilli

    Department of Medicine, Northwestern University, Chicago, United States
    Competing interests
    No competing interests declared.
  25. Tujin Shi

    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, United States
    Competing interests
    No competing interests declared.
  26. Yang Shen

    Department of Electrical and Computer Engineering, TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1703-7796
  27. Nurmaa K Dashzeveg

    Department of Pharmacology, Northwestern University, Chicago, United States
    Competing interests
    Nurmaa K Dashzeveg, has patents on exosomes which are not related to this manuscript..
  28. Huiping Liu

    Pathology Core Facility, Northwestern University, Chicago, United States
    For correspondence
    huiping.liu@northwestern.edu
    Competing interests
    Huiping Liu, is scientific co-founder of ExoMira Medicine, Inc and has patents related to exosome therapeutics which are not related to the scientific discoveries of this paper..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4822-7995

Funding

National Cancer Institute (R01CA245699)

  • Erika K Ramos
  • Huiping Liu

National Institute of General Medical Sciences (R35GM124952)

  • Yang Shen

U.S. Department of Defense (W81XWH-16-1-0021)

  • Huiping Liu

Susan G. Komen (CCR18548501)

  • Xia Liu

American Cancer Society (ACS127951-RSG-15-025-01-CSM)

  • Huiping Liu

National Cancer Institute (T32 CA009560)

  • Erika K Ramos

National Cancer Institute (T32GM008061)

  • Emma J Schuster

National Science Foundation (CCF-1943008)

  • Yang Shen

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Animal experimentation: All mice used in this study were kept in specific pathogen-free facilities in the Animal Resources Center at Northwestern University. All animal procedures complied with the NIH Guidelines for the Care and Use of Laboratory Animals and were approved by the respective Institutional Animal Care and Use Committees.

Reviewing Editor

  1. Caigang Liu, Shengjing Hospital of China Medical University, China

Version history

  1. Received: August 14, 2022
  2. Accepted: August 26, 2022
  3. Accepted Manuscript published: October 4, 2022 (version 1)
  4. Version of Record published: October 19, 2022 (version 2)

Copyright

This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

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  1. Erika K Ramos
  2. Chia-Feng Tsai
  3. Yuzhi Jia
  4. Yue Cao
  5. Megan Manu
  6. Rokana Taftaf
  7. Andrew D Hoffmann
  8. Lamiaa El-Shennawy
  9. Marina A Gritsenko
  10. Valery Adorno-Cruz
  11. Emma J Schuster
  12. David Scholten
  13. Dhwani Patel
  14. Xia Liu
  15. Priyam Patel
  16. Brian Wray
  17. Youbin Zhang
  18. Shanshan Zhang
  19. Ronald J Moore
  20. Jeremy V Mathews
  21. Matthew J Schipma
  22. Tao Liu
  23. Valerie L Tokars
  24. Massimo Cristofanilli
  25. Tujin Shi
  26. Yang Shen
  27. Nurmaa K Dashzeveg
  28. Huiping Liu
(2022)
Machine learning-assisted elucidation of CD81-CD44 interactions in promoting cancer stemness and extracellular vesicle integrity
eLife 11:e82669.
https://doi.org/10.7554/eLife.82669

Share this article

https://doi.org/10.7554/eLife.82669

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