Multi-targeted therapy resistance via drug-induced secretome fucosylation

  1. Mark Borris D Aldonza
  2. Junghwa Cha
  3. Insung Yong
  4. Jayoung Ku
  5. Pavel Sinitcyn
  6. Dabin Lee
  7. Ryeong-Eun Cho
  8. Roben D Delos Reyes
  9. Dongwook Kim
  10. Soyeon Kim
  11. Minjeong Kang
  12. Yongsuk Ku
  13. Geonho Park
  14. Hye-Jin Sung
  15. Han Suk Ryu
  16. Sukki Cho
  17. Tae Min Kim
  18. Pilnam Kim  Is a corresponding author
  19. Je-Yoel Cho  Is a corresponding author
  20. Yoosik Kim  Is a corresponding author
  1. Seoul National University, Republic of Korea
  2. Korea Advanced Institute of Science and Technology, Republic of Korea
  3. Max Planck Institute of Biochemistry, Germany
  4. Seoul National University Hospital, Republic of Korea
  5. Seoul National University Bundang Hospital, Republic of Korea

Abstract

Cancer secretome is a reservoir for aberrant glycosylation. How therapies alter this post- translational cancer hallmark and the consequences thereof remain elusive. Here we show that an elevated secretome fucosylation is a pan-cancer signature of both response and resistance to multiple targeted therapies. Large-scale pharmacogenomics revealed that fucosylation genes display widespread association with resistance to these therapies. In cancer cell cultures, xenograft mouse models, and patients, targeted kinase inhibitors distinctively induced core fucosylation of secreted proteins less than 60 kDa. Label-free proteomics of N-glycoproteomes identified fucosylation of the antioxidant PON1 as a critical component of the therapy-induced secretome (TIS). N-glycosylation of TIS and target core fucosylation of PON1 are mediated by the fucose salvage-FUT8-SLC35C1 axis with PON3 directly modulating GDP-Fuc transfer on PON1 scaffolds. Core fucosylation in the Golgi impacts PON1 stability and folding prior to secretion, promoting a more degradation-resistant PON1. Global and PON1-specific secretome de-N-glycosylation both limited the expansion of resistant clones in a tumor regression model. We defined the resistance-associated transcription factors (TFs) and genes modulated by the N-glycosylated TIS via a focused and transcriptome-wide analyses. These genes characterize the oxidative stress, inflammatory niche, and unfolded protein response as important factors for this modulation. Our findings demonstrate that core fucosylation is a common modification indirectly induced by targeted therapies that paradoxically promotes resistance.

Data availability

All sequencing data produced for this publication has been deposited to the NCBI Gene Expression Omnibus (GEO) database under the accession number GSE160205. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD022240. Source Data 1 contains raw images of blots and gels. Other data associated with this study are present in the paper, Supplementary Materials, or source data files. Additional data related to this paper may be requested from M.B.D.A., Yoosik K., or J.Y.C. Reagents, and cell lines described here are accessible through a materials transfer agreement.

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Mark Borris D Aldonza

    Department of Biochemistry, Seoul National University, Seoul, Republic of Korea
    Competing interests
    Mark Borris D Aldonza, There is currently a pending patent filing for the biomarker signature revealed in this study for which MBDA is listed as an inventor (application number: 10-2021-0048888 (2021-04-15)). The authors declare that they have no other competing interests..
  2. Junghwa Cha

    Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
    Competing interests
    Junghwa Cha, There is currently a pending patent filing for the biomarker signature revealed in this study for which JC is listed as an inventor (application number: 10-2021-0048888 (2021-04-15)). The authors declare that they have no other competing interests..
  3. Insung Yong

    Computational Systems Biochemistry Research Group, Max Planck Institute of Biochemistry, Martinsried, Germany
    Competing interests
    Insung Yong, There is currently a pending patent filing for the biomarker signature revealed in this study for which IY is listed as an inventor (application number: 10-2021-0048888 (2021-04-15)). The authors declare that they have no other competing interests..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7828-4264
  4. Jayoung Ku

    Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4112-4582
  5. Pavel Sinitcyn

    Computational Systems Biochemistry Research Group, Max Planck Institute of Biochemistry, Martinsried, Germany
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2653-1702
  6. Dabin Lee

    Comparative Medicine Disease Research Center, Seoul National University, Seoul, Republic of Korea
    Competing interests
    No competing interests declared.
  7. Ryeong-Eun Cho

    Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
    Competing interests
    No competing interests declared.
  8. Roben D Delos Reyes

    Department of Electrical Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1368-6817
  9. Dongwook Kim

    Department of Biochemistry, Seoul National University, Seoul, Republic of Korea
    Competing interests
    Dongwook Kim, is currently employed at ProtanBio Inc., a disease biomarker venture company of Seoul National University. The authors declare that they have no other competing interests..
  10. Soyeon Kim

    Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
    Competing interests
    No competing interests declared.
  11. Minjeong Kang

    Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
    Competing interests
    No competing interests declared.
  12. Yongsuk Ku

    Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
    Competing interests
    No competing interests declared.
  13. Geonho Park

    Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
    Competing interests
    No competing interests declared.
  14. Hye-Jin Sung

    Department of Biochemistry, Seoul National University, Seoul, Republic of Korea
    Competing interests
    Hye-Jin Sung, is currently employed at ProtanBio Inc., a disease biomarker venture company of Seoul National University. The authors declare that they have no other competing interests..
  15. Han Suk Ryu

    Department of Pathology, Seoul National University Hospital, Seoul, Republic of Korea
    Competing interests
    No competing interests declared.
  16. Sukki Cho

    Department of Thoracic and Cardiovascular Surgery, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
    Competing interests
    No competing interests declared.
  17. Tae Min Kim

    Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
    Competing interests
    No competing interests declared.
  18. Pilnam Kim

    Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
    For correspondence
    pkim@kaist.ac.kr
    Competing interests
    Pilnam Kim, There is currently a pending patent filing for the biomarker signature revealed in this study for which PK is listed as an inventor (application number: 10-2021-0048888 (2021-04-15)). The authors declare that they have no other competing interests..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5592-4599
  19. Je-Yoel Cho

    Department of Biochemistry, Seoul National University, Seoul, Republic of Korea
    For correspondence
    jeycho@snu.ac.kr
    Competing interests
    Je-Yoel Cho, There is currently a pending patent filing for the biomarker signature revealed in this study for which J-YC is listed as an inventor (application number: 10-2021-0048888 (2021-04-15)). J-YC is CEO of ProtanBio Inc., a disease biomarker venture company of Seoul National University. The authors declare that they have no other competing interests..
  20. Yoosik Kim

    Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
    For correspondence
    ysyoosik@kaist.ac.kr
    Competing interests
    Yoosik Kim, There is currently a pending patent filing for the biomarker signature revealed in this study for which Yoosik K is listed as an inventor (application number: 10-2021-0048888 (2021-04-15)). The authors declare that they have no other competing interests..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3064-4643

Funding

Korea Advanced Institute of Science and Technology (N11190234)

  • Yoosik Kim

National Research Foundation of Korea (NRF-2019R1C1C1006672)

  • Yoosik Kim

National Research Foundation of Korea (NRF-2018R1A6A3A01012494)

  • Pilnam Kim

National Research Foundation of Korea (NRF-2016M3A9B6026771)

  • Je-Yoel Cho

National Research Foundation of Korea (NRF-2021R1A5A1033157)

  • Je-Yoel Cho

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

Ethics

Human subjects: All human blood and tissues from three cohorts of patients diagnosed to have lung adenocarcinoma or squamous cell carcinoma or breast carcinoma were collected and analyzed with approved protocols in accordance with the ethical requirements and regulations of the Institutional Review Board of Seoul National University Hospital after securing written informed consent (IRB Nos. 1104-086-359 and B-1201/143-003).

Copyright

© 2023, Aldonza et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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