Comprehensive analysis on subchondral bone marrow lesions of human osteoarthritis by integrating bulk and single-cell transcriptomes

Muhui Zeng; Xiaoshuai Wang; Tianyu Chen; Guangfeng Ruan; Jia Li; Song Xue; Yang Zhao; Zhiyang Hu; Ye Xie; Tianxiang Fan; Shibo Chen; Yang Li; Qianyi Wang; Yue Zhang; Rongkai Zhang; Lijun Lin; Changhai Ding; Zhaohua Zhu

doi:10.1186/s12891-023-06676-4

Comprehensive analysis on subchondral bone marrow lesions of human osteoarthritis by integrating bulk and single-cell transcriptomes

BMC Musculoskelet Disord. 2023 Aug 25;24(1):677. doi: 10.1186/s12891-023-06676-4.

Authors

Muhui Zeng^#^{1

2}, Xiaoshuai Wang^#^{1

3}, Tianyu Chen^#⁴, Guangfeng Ruan⁵, Jia Li^{1

3}, Song Xue⁶, Yang Zhao¹, Zhiyang Hu⁷, Ye Xie⁸, Tianxiang Fan¹, Shibo Chen¹, Yang Li¹, Qianyi Wang¹, Yue Zhang⁹, Rongkai Zhang⁴, Lijun Lin³, Changhai Ding^{10

11}, Zhaohua Zhu^{12

13}

Affiliations

¹ Clinical Research Centre, Zhujiang Hospital, Southern Medical University, Guangzhou, 510280, Guangdong, China.
² Department of Orthopedics, General Hospital of Southern Theater Command of PLA, Guangzhou, Guangdong, China.
³ Department of Orthopedics, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
⁴ Department of Orthopedics, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China.
⁵ Clinical Research Centre, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China.
⁶ Department of Rheumatology and Immunology, Arthritis Research Institute, The First Affiliated Hospital of Anhui Medical University, Hefei, China.
⁷ Sun Yat-sen University School of Medicine, Sun Yat-sen University, Shenzhen, China.
⁸ Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
⁹ State Key Laboratory of Organ Failure Research, Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.
¹⁰ Clinical Research Centre, Zhujiang Hospital, Southern Medical University, Guangzhou, 510280, Guangdong, China. changhai.ding@utas.edu.au.
¹¹ Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia. changhai.ding@utas.edu.au.
¹² Clinical Research Centre, Zhujiang Hospital, Southern Medical University, Guangzhou, 510280, Guangdong, China. zhaohua.zhu@utas.edu.au.
¹³ Department of Orthopedics, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China. zhaohua.zhu@utas.edu.au.

^# Contributed equally.

Abstract

Objective: This study aims to demonstrate the cellular composition and underlying mechanisms in subchondral bone marrow lesions (BMLs) of knee osteoarthritis (OA).

Methods: BMLs were assessed by MRI Osteoarthritis Knee Score (MOAKS)≥2. Bulk RNA-sequencing (bulk-seq) and BML-specific differentially expressed genes (DEGs) analysis were performed among subchondral bone samples (including OA-BML=3, paired OA-NBML=3; non-OA=3). The hub genes of BMLs were identified by verifying in independent datasets and multiple bioinformatic analyses. To further estimate cell-type composition of subchondral bone, we utilized two newly developed deconvolution algorithms (MuSiC, MCP-counter) in transcriptomic datasets, based on signatures from open-accessed single-cell RNA sequencing (scRNA-seq). Finally, competing endogenous RNA (ceRNA) and transcription factor (TF) networks were constructed through multiple predictive databases, and validated by public non-coding RNA profiles.

Results: A total of 86 BML-specific DEGs (up 79, down 7) were identified. IL11 and VCAN were identified as core hub genes. The "has-miR-424-5p/lncRNA PVT1" was determined as crucial network, targeting IL11 and VCAN, respectively. More importantly, two deconvolution algorithms produced approximate estimations of cell-type composition, and the cluster of heterotopic-chondrocyte was discovered abundant in BMLs, and positively correlated with the expression of hub genes.

Conclusion: IL11 and VCAN were identified as the core hub genes of BMLs, and their molecular networks were determined as well. We profiled the characteristics of subchondral bone at single-cell level and determined that the heterotopic-chondrocyte was abundant in BMLs and was closely linked to IL11 and VCAN. Our study may provide new insights into the microenvironment and pathological molecular mechanism of BMLs, and could lead to novel therapeutic strategies.

Keywords: Bone marrow lesions; Deconvolution algorithm; Osteoarthritis; Single-cell RNA sequencing; Subchondral bone.

MeSH terms

Bone Diseases*
Bone Marrow
Cartilage Diseases*
Humans
Interleukin-11
Osteoarthritis, Knee* / genetics
Transcriptome

Substances

Interleukin-11

Abstract

MeSH terms

Substances

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