RNA N6-methyladenosine modulates endothelial atherogenic responses to disturbed flow in mice

  1. Bochuan Li
  2. Ting Zhang
  3. Mengxia Liu
  4. Zhen Cui
  5. Yanhong Zhang
  6. Mingming Liu
  7. Yanan Liu
  8. Yongqiao Sun
  9. Mengqi Li
  10. Yikui Tian
  11. Ying Yang  Is a corresponding author
  12. Hongfeng Jiang  Is a corresponding author
  13. Degang Liang  Is a corresponding author
  1. Tianjin Medical University, China
  2. Chinese Academy of Sciences, China
  3. Capital Medical University, China

Abstract

Atherosclerosis preferentially occurs in atheroprone vasculature where human umbilical vein endothelial cells (HUVECs) are exposed to disturbed flow. Disturbed flow is associated with vascular inflammation and focal distribution. Recent studies have revealed the involvement of epigenetic regulation in atherosclerosis progression. N6-methyladenosine (m6A) is the most prevalent internal modification of eukaryotic mRNA, but its function in endothelial atherogenic progression remains unclear. Here, we show that m6A mediates the EGFR signaling pathway during EC activation to regulate the atherosclerotic process. Oscillatory stress (OS) reduced the expression of METTL3, the primary m6A methyltransferase. Through m6A sequencing and functional studies, we determined that m6A mediates the mRNA decay of the vascular pathophysiology gene EGFR which leads to EC dysfunction. m6A modification of the EGFR 3'UTR accelerated its mRNA degradation. Double mutation of the EGFR 3'UTR abolished METTL3-induced luciferase activity. Adenovirus-mediated METTL3 overexpression significantly reduced EGFR activation and endothelial dysfunction in the presence of OS. Furthermore, TSP-1, an EGFR ligand, was specifically expressed in atheroprone regions without being affected by METTL3. Inhibition of the TSP-1/EGFR axis by using shRNA and AG1478 significantly ameliorated atherogenesis. Overall, our study revealed that METTL3 alleviates endothelial atherogenic progression through m6A-dependent stabilization of EGFR mRNA, highlighting the important role of RNA transcriptomics in atherosclerosis regulation.

Data availability

RNA-seq and MeRIP-seq data generated in this study have been deposited to the Genome Sequence Archive in BIG Data Center under accession number PRJCA004746.

The following data sets were generated

Article and author information

Author details

  1. Bochuan Li

    Department of Physiology and Pathophysiology, Tianjin Medical University, Tianjin, China
    Competing interests
    The authors declare that no competing interests exist.
  2. Ting Zhang

    CAS Key Laboratory of Genomic and Precision Medicine, Chinese Academy of Sciences, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
  3. Mengxia Liu

    CAS Key Laboratory of Genomic and Precision Medicine, Chinese Academy of Sciences, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
  4. Zhen Cui

    Department of Physiology and Pathophysiology, Tianjin Medical University, Tianjin, China
    Competing interests
    The authors declare that no competing interests exist.
  5. Yanhong Zhang

    Department of Physiology and Pathophysiology, Tianjin Medical University, Tianjin, China
    Competing interests
    The authors declare that no competing interests exist.
  6. Mingming Liu

    Department of Physiology and Pathophysiology, Tianjin Medical University, Tianjin, China
    Competing interests
    The authors declare that no competing interests exist.
  7. Yanan Liu

    Department of Physiology and Pathophysiology, Tianjin Medical University, Tianjin, China
    Competing interests
    The authors declare that no competing interests exist.
  8. Yongqiao Sun

    CAS Key Laboratory of Genomic and Precision Medicine, Chinese Academy of Sciences, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
  9. Mengqi Li

    Tianjin Medical University General Hospital Cardiovascular Department, Tianjin Medical University, Tianjin, China
    Competing interests
    The authors declare that no competing interests exist.
  10. Yikui Tian

    Tianjin Medical University General Hospital Cardiovascular Department, Tianjin Medical University, Tianjin, China
    Competing interests
    The authors declare that no competing interests exist.
  11. Ying Yang

    CAS Key Laboratory of Genomic and Precision Medicine, Chinese Academy of Sciences, Beijing, China
    For correspondence
    yingyang@big.ac.cn
    Competing interests
    The authors declare that no competing interests exist.
  12. Hongfeng Jiang

    Key Laboratory of Remodeling-Related Cardiovascular Diseases, Capital Medical University, Tianjin, China
    For correspondence
    jhf@pku.edu.cn
    Competing interests
    The authors declare that no competing interests exist.
  13. Degang Liang

    Tianjin Medical University General Hospital Cardiovascular Department, Tianjin Medical University, Tianjin, China
    For correspondence
    15922230066@163.com
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2618-6651

Funding

National Natural Science Foundation of China (81900396)

  • Bochuan Li

National Natural Science Foundation of China (82000477)

  • Mengqi Li

National Natural Science Foundation of China (81970392)

  • Hongfeng Jiang

Postdoctoral Research Foundation of China (2019M661041)

  • Bochuan Li

Postdoctoral Research Foundation of China (BX20190235)

  • Bochuan Li

China Association for Science and Technology (Excellent Sino-foreign Youth Exchange Program)

  • Bochuan Li

National Natural Science Foundation of China (91940304)

  • Ying Yang

Chinese Academy of Sciences (2018133)

  • Ying Yang

National Key Research and Development Program of China (2018YFA0801200)

  • Ying Yang

Beijing Nova Program (Z201100006820104)

  • Ying Yang

National Natural Science Foundation of China (81870207)

  • Yikui Tian

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

Ethics

Animal experimentation: The investigation conformed to the Guide for the Care and Use of Laboratory Animals by the US National Institutes of Health (NIH 17 Publication No. 85-23, revised in 2011). All study protocols and the use of animals were approved by the Institutional Animal Care and Use Committee of Tianjin Medical University.

Copyright

© 2022, Li 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.

Metrics

  • 1,040
    views
  • 174
    downloads
  • 18
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Bochuan Li
  2. Ting Zhang
  3. Mengxia Liu
  4. Zhen Cui
  5. Yanhong Zhang
  6. Mingming Liu
  7. Yanan Liu
  8. Yongqiao Sun
  9. Mengqi Li
  10. Yikui Tian
  11. Ying Yang
  12. Hongfeng Jiang
  13. Degang Liang
(2022)
RNA N6-methyladenosine modulates endothelial atherogenic responses to disturbed flow in mice
eLife 11:e69906.
https://doi.org/10.7554/eLife.69906

Share this article

https://doi.org/10.7554/eLife.69906

Further reading

    1. Cell Biology
    Tomoharu Kanie, Roy Ng ... Peter K Jackson
    Research Article

    The primary cilium is a microtubule-based organelle that cycles through assembly and disassembly. In many cell types, formation of the cilium is initiated by recruitment of ciliary vesicles to the distal appendage of the mother centriole. However, the distal appendage mechanism that directly captures ciliary vesicles is yet to be identified. In an accompanying paper, we show that the distal appendage protein, CEP89, is important for the ciliary vesicle recruitment, but not for other steps of cilium formation (Tomoharu Kanie, Love, Fisher, Gustavsson, & Jackson, 2023). The lack of a membrane binding motif in CEP89 suggests that it may indirectly recruit ciliary vesicles via another binding partner. Here, we identify Neuronal Calcium Sensor-1 (NCS1) as a stoichiometric interactor of CEP89. NCS1 localizes to the position between CEP89 and a ciliary vesicle marker, RAB34, at the distal appendage. This localization was completely abolished in CEP89 knockouts, suggesting that CEP89 recruits NCS1 to the distal appendage. Similarly to CEP89 knockouts, ciliary vesicle recruitment as well as subsequent cilium formation was perturbed in NCS1 knockout cells. The ability of NCS1 to recruit the ciliary vesicle is dependent on its myristoylation motif and NCS1 knockout cells expressing a myristoylation defective mutant failed to rescue the vesicle recruitment defect despite localizing properly to the centriole. In sum, our analysis reveals the first known mechanism for how the distal appendage recruits the ciliary vesicles.

    1. Cell Biology
    Tomoharu Kanie, Beibei Liu ... Peter K Jackson
    Research Article

    Distal appendages are nine-fold symmetric blade-like structures attached to the distal end of the mother centriole. These structures are critical for formation of the primary cilium, by regulating at least four critical steps: ciliary vesicle recruitment, recruitment and initiation of intraflagellar transport (IFT), and removal of CP110. While specific proteins that localize to the distal appendages have been identified, how exactly each protein functions to achieve the multiple roles of the distal appendages is poorly understood. Here we comprehensively analyze known and newly discovered distal appendage proteins (CEP83, SCLT1, CEP164, TTBK2, FBF1, CEP89, KIZ, ANKRD26, PIDD1, LRRC45, NCS1, CEP15) for their precise localization, order of recruitment, and their roles in each step of cilia formation. Using CRISPR-Cas9 knockouts, we show that the order of the recruitment of the distal appendage proteins is highly interconnected and a more complex hierarchy. Our analysis highlights two protein modules, CEP83-SCLT1 and CEP164-TTBK2, as critical for structural assembly of distal appendages. Functional assays revealed that CEP89 selectively functions in RAB34+ ciliary vesicle recruitment, while deletion of the integral components, CEP83-SCLT1-CEP164-TTBK2, severely compromised all four steps of cilium formation. Collectively, our analyses provide a more comprehensive view of the organization and the function of the distal appendage, paving the way for molecular understanding of ciliary assembly.