Single-cell sequencing highlights heterogeneity and malignant progression in actinic keratosis and cutaneous squamous cell carcinoma

  1. Dan-Dan Zou
  2. Ya-Zhou Sun
  3. Xin-Jie Li
  4. Wen-Juan Wu
  5. Dan Xu
  6. Yu-Tong He
  7. Jue Qi
  8. Ying Tu
  9. Yang Tang
  10. Yun-Hua Tu
  11. Xiao-Li Wang
  12. Xing Li
  13. Feng-Yan Lu
  14. Ling Huang
  15. Heng Long
  16. Li He  Is a corresponding author
  17. Xin Li  Is a corresponding author
  1. First Affiliated Hospital of Kunming Medical University, China
  2. Sun Yat-sen University, China
  3. Shanghai Changzheng Hospital, China
  4. People's Hospital of Chuxiong Yi Autonomous Prefecture, China
  5. Qujing Affiliated Hospital of Kunming Medical University, China
  6. First Affiliated Hospital of Dali University, China
  7. Wenshan Zhuang and Miao Autonomous Prefecture Specialist Hospital of Dermatology, China

Abstract

Cutaneous squamous cell carcinoma (cSCC) is the second most frequent of the keratinocyte-derived malignancies with actinic keratosis (AK) as a precancerous lesion. To comprehensively delineate the underlying mechanisms for the whole progression from normal skin to AK to invasive cSCC, we performed single-cell RNA-seq (scRNA-seq) to acquire the transcriptomes of 138,982 cells from 13 samples of six patients including AK, squamous cell carcinoma in situ (SCCIS), cSCC and their matched normal tissues, covering comprehensive clinical courses of cSCC. We identified diverse cell types, including important subtypes with different gene expression profiles and functions in major keratinocytes. In SCCIS, we discovered the malignant subtypes of basal cells with differential proliferative and migration potential. Differentially expressed genes (DEGs) analysis screened out multiple key driver genes including transcription factors (TFs) along AK to cSCC progression. Immunohistochemistry (IHC) / immunofluorescence (IF) experiments and single-cell ATAC sequencing (scATAC-seq) data verified the expression changes of these genes. The functional experiments confirmed the important roles of these genes in regulating cell proliferation, apoptosis, migration and invasion in cSCC tumor. Furthermore, we comprehensively described the tumor microenvironment (TME) landscape and potential keratinocyte-TME crosstalk in cSCC providing theoretical basis for immunotherapy. Together, our findings provide a valuable resource for deciphering the progression from AK to cSCC and identifying potential targets for anticancer treatment of cSCC.

Data availability

The raw data and gene counts table are available from GEO under accession number (GSE193304). All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials.

The following data sets were generated

Article and author information

Author details

  1. Dan-Dan Zou

    Department of Dermatology, First Affiliated Hospital of Kunming Medical University, Kunming, China
    Competing interests
    The authors declare that no competing interests exist.
  2. Ya-Zhou Sun

    School of Medical, Sun Yat-sen University, Shenzhen, China
    Competing interests
    The authors declare that no competing interests exist.
  3. Xin-Jie Li

    School of Medical, Sun Yat-sen University, Shenzhen, China
    Competing interests
    The authors declare that no competing interests exist.
  4. Wen-Juan Wu

    Department of Dermatology, First Affiliated Hospital of Kunming Medical University, Kunming, China
    Competing interests
    The authors declare that no competing interests exist.
  5. Dan Xu

    Department of Dermatology, First Affiliated Hospital of Kunming Medical University, Kunming, China
    Competing interests
    The authors declare that no competing interests exist.
  6. Yu-Tong He

    School of Medical, Sun Yat-sen University, Shenzhen, China
    Competing interests
    The authors declare that no competing interests exist.
  7. Jue Qi

    Department of Dermatology, First Affiliated Hospital of Kunming Medical University, Kunming, China
    Competing interests
    The authors declare that no competing interests exist.
  8. Ying Tu

    Department of Dermatology, First Affiliated Hospital of Kunming Medical University, Kunming, China
    Competing interests
    The authors declare that no competing interests exist.
  9. Yang Tang

    Department of Dermatology, First Affiliated Hospital of Kunming Medical University, Kunming, China
    Competing interests
    The authors declare that no competing interests exist.
  10. Yun-Hua Tu

    Department of Dermatology, First Affiliated Hospital of Kunming Medical University, Kunming, China
    Competing interests
    The authors declare that no competing interests exist.
  11. Xiao-Li Wang

    Department of Dermatology, Shanghai Changzheng Hospital, Shanghai, China
    Competing interests
    The authors declare that no competing interests exist.
  12. Xing Li

    Department of Dermatology, People's Hospital of Chuxiong Yi Autonomous Prefecture, Chuxiong, China
    Competing interests
    The authors declare that no competing interests exist.
  13. Feng-Yan Lu

    Department of Dermatology, Qujing Affiliated Hospital of Kunming Medical University, Qujing, China
    Competing interests
    The authors declare that no competing interests exist.
  14. Ling Huang

    Department of Dermatology, First Affiliated Hospital of Dali University, Dali, China
    Competing interests
    The authors declare that no competing interests exist.
  15. Heng Long

    Wenshan Zhuang and Miao Autonomous Prefecture Dermatology Clinic, Wenshan Zhuang and Miao Autonomous Prefecture Specialist Hospital of Dermatology, Wenshan, China
    Competing interests
    The authors declare that no competing interests exist.
  16. Li He

    Department of Dermatology, First Affiliated Hospital of Kunming Medical University, Kunming, China
    For correspondence
    drheli2662@126.com
    Competing interests
    The authors declare that no competing interests exist.
  17. Xin Li

    School of Medical, Sun Yat-sen University, Shenzhen, China
    For correspondence
    lixin253@mail.sysu.edu.cn
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8328-4894

Funding

Yunnan Science and Technology Leading Talents Project (2017HA010)

  • Li He

National Natural Science Foundation of China (82260517)

  • Xin Li

Yunnan High-level Talents Scientific Research Project (2023-KHRCBZ-B13)

  • Dan-Dan Zou

Yunnan Province Clinical Research Center for Skin Immune Diseases (2019ZF012)

  • Li He

Yunnan Province Clinical Center for Skin Immune Diseases (ZX2019-03-02)

  • Li He

Shenzhen Science and Technology Program (JCYJ20190807160011600)

  • Xin Li

Shenzhen Science and Technology Program (JCYJ20210324124808023)

  • Xin Li

China Postdoctoral Science Foundation (2020M683073)

  • Ya-Zhou Sun

Guangzhou Science Technology Project (201904010007)

  • Xin Li

Guangdong Provincial Key Laboratory of Digestive Cancer Research (2021B1212040006)

  • Xin Li

National Natural Science Foundation of China (81872299)

  • Xin Li

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

Reviewing Editor

  1. Beate Maria Lichtenberger, Medical University of Vienna, Austria

Ethics

Human subjects: The authors are accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved. All procedures performed in this study involving human participants were in accordance with the Declaration of Helsinki (as revised in 2013). This study protocol was approved by the Ethics Committee of the First Affiliated Hospital of Kunming Medical University (Approval Number (2020)-L-29), and written informed consent was obtained from all patients.

Version history

  1. Received: November 30, 2022
  2. Preprint posted: December 22, 2022 (view preprint)
  3. Accepted: December 14, 2023
  4. Accepted Manuscript published: December 15, 2023 (version 1)
  5. Version of Record published: January 11, 2024 (version 2)

Copyright

© 2023, Zou 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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  1. Dan-Dan Zou
  2. Ya-Zhou Sun
  3. Xin-Jie Li
  4. Wen-Juan Wu
  5. Dan Xu
  6. Yu-Tong He
  7. Jue Qi
  8. Ying Tu
  9. Yang Tang
  10. Yun-Hua Tu
  11. Xiao-Li Wang
  12. Xing Li
  13. Feng-Yan Lu
  14. Ling Huang
  15. Heng Long
  16. Li He
  17. Xin Li
(2023)
Single-cell sequencing highlights heterogeneity and malignant progression in actinic keratosis and cutaneous squamous cell carcinoma
eLife 12:e85270.
https://doi.org/10.7554/eLife.85270

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https://doi.org/10.7554/eLife.85270

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