Background To systematically identify cell types in human ligament, investigate how ligamental cell identities, functions, and interactions participated the process of ligamental degeneration and explore the changes of ligamental microenvironment homeostasis in the disease progression.

Methods Using single-cell RNA sequencing and spatial RNA sequencing of approximately 49356 cells, we created a comprehensive cell atlas of healthy and degenerated human anterior cruciate ligaments. We explored the variations of the cell subtypes’ spatial distributions and the different processes involved in the disease progression, linked them with ligamental degeneration process using computational analysis.

Results We identified new fibroblast subgroups contributed to the disease and mapped out their spatial distribution in the tissue and revealed two stages of the degenerative process. We compared the cellular interactions between different tissue states and identified important signaling pathways may contribute to the disease.

Conclusion This cell atlas provides the molecular foundation for investigating how ligamental cell identities, biochemical functions, and interactions contributed to the ligamental degeneration process. The discoveries revealed the pathogenesis of ligamental degeneration at single-cell and spatial level which is characterized by extracellular matrix remodeling. Our results provide new insights into the control of ligamental degeneration and potential clues to developing novel diagnostic and therapeutic strategies.

Funding This study was funded by the National Natural Science Foundation of China (81972123, 82172508), Sichuan Science and Technology Program (2020YFH0075), Fundamental Research Funds for the Central Universities (2015SCU04A40), Chengdu Science and Technology Bureau Project (2019-YF05-00090-SN), and 1.3.5 Project for Disciplines of Excellence of West China Hospital Sichuan University (ZYJC21030, ZY2017301).

The authors have declared no competing interest.

No clinical trials were involved

This study was funded by the National Natural Science Foundation of China (81972123, 82172508), Sichuan Science and Technology Program (2020YFH0075), Fundamental Research Funds for the Central Universities (2015SCU04A40), Chengdu Science and Technology Bureau Project (2019-YF05-00090-SN), and 1.3.5 Project for Disciplines of Excellence of West China Hospital Sichuan University (ZYJC21030, ZY2017301).

I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.

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The details of the IRB/oversight body that provided approval or exemption for the research described are given below:

This study was reviewed and approved by our University Ethics Committee (Ethics Committee on Biomedical Research, West China Hospital of Sichuan University No. 658 2020-(921)) and all procedures complied with the Helsinki Declaration. Participants gave informed consent to participate in the study.

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Data are available in a public, open-access repository. The single-cell RNA-seq data and cluster annotations are available at GSA for human (https://ngdc.cncb.ac.cn/gsa-human/) with the accession number PRJCA014157.