Spatiotemporal R-loop accumulation orchestrates microenvironmental remodeling after spinal cord injury

Zhipeng Jiang; Youwei Guo; Zihan Wang; Jinhao Ouyang; Haoxuan Huang; Tianqian Shen; Lei Wang; Wen Yin; Xingjun Jiang; Caiping Ren

doi:10.1016/j.nbd.2025.107055

Neurobiology of Disease (Oct 2025)

Spatiotemporal R-loop accumulation orchestrates microenvironmental remodeling after spinal cord injury

Zhipeng Jiang,
Youwei Guo,
Zihan Wang,
Jinhao Ouyang,
Haoxuan Huang,
Tianqian Shen,
Lei Wang,
Wen Yin,
Xingjun Jiang,
Caiping Ren

Affiliations

Zhipeng Jiang: Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Cancer Research Institute, Xiangya School of Basic Medical Science, Central South University, Changsha, Hunan Province 410078, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
Youwei Guo: Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Cancer Research Institute, Xiangya School of Basic Medical Science, Central South University, Changsha, Hunan Province 410078, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
Zihan Wang: Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Cancer Research Institute, Xiangya School of Basic Medical Science, Central South University, Changsha, Hunan Province 410078, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
Jinhao Ouyang: Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Cancer Research Institute, Xiangya School of Basic Medical Science, Central South University, Changsha, Hunan Province 410078, China; The NHC Key Laboratory of Carcinogenesis and The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, Hunan Province, 410078, China
Haoxuan Huang: Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Cancer Research Institute, Xiangya School of Basic Medical Science, Central South University, Changsha, Hunan Province 410078, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
Tianqian Shen: Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Cancer Research Institute, Xiangya School of Basic Medical Science, Central South University, Changsha, Hunan Province 410078, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
Lei Wang: Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Cancer Research Institute, Xiangya School of Basic Medical Science, Central South University, Changsha, Hunan Province 410078, China; The NHC Key Laboratory of Carcinogenesis and The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, Hunan Province, 410078, China
Wen Yin: Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Cancer Research Institute, Xiangya School of Basic Medical Science, Central South University, Changsha, Hunan Province 410078, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Corresponding authors at: Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Cancer Research Institute, Xiangya School of Basic Medical Science, Central South University, Changsha, Hunan Province 410078, China.
Xingjun Jiang: Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Cancer Research Institute, Xiangya School of Basic Medical Science, Central South University, Changsha, Hunan Province 410078, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Corresponding authors at: Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Cancer Research Institute, Xiangya School of Basic Medical Science, Central South University, Changsha, Hunan Province 410078, China.
Caiping Ren: Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Cancer Research Institute, Xiangya School of Basic Medical Science, Central South University, Changsha, Hunan Province 410078, China; The NHC Key Laboratory of Carcinogenesis and The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, Hunan Province, 410078, China; Corresponding authors at: Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Cancer Research Institute, Xiangya School of Basic Medical Science, Central South University, Changsha, Hunan Province 410078, China.

DOI: https://doi.org/10.1016/j.nbd.2025.107055
Journal volume & issue: Vol. 214
p. 107055

Abstract

Read online

Spinal cord injury (SCI) induces severe neurological dysfunction through direct mass cell damage and secondary inflammatory molecular cascades. These cascades—initiated by damage—recruit immune cells and amplify cytokine release, exacerbating neuronal death and tissue destruction. We initially report that R-loop accumulation (three-stranded RNA-DNA hybrids with displaced ssDNA) in neural injury contexts drives neurodegeneration via neuroinflammation. Utilizing annotated R-loop-associated genes (loci harboring RNA-DNA hybrids, resolvases, or functionally impacted by R-loops), we characterized fresh spinal cord tissues (50–100 mg) harvested from the cavity of injury (COI) (including gray/white matter) at 0, 1, 3, 7, and 14 days post-injury(dpi) in clip contusion models. Our research characterized dynamic post-injury expression patterns, including stage-specific upregulation of Cdk1, Top2a, Tp53, Tln1, and Flna. Spatial transcriptomics and immunofluorescence revealed significant R-loop accumulation in COI, correlating with tissue damage progression (loss of normal cellular architecture and expanding tissue cavitation quantified by HE/LFB staining). Applying cellular deconvolution—a computational approach inferring the proportional composition of distinct cell types by analyzing bulk-level molecular data—to SCI models, we observed dynamic microenvironment remodeling in COI. This process featured depletion of oligodendrocytes and neurons within post-injury, along with recruitment of diverse immune subsets including peripheral macrophages, bordering leukocytes, and activated microglia. Single-cell analysis and immunofluorescence staining ultimately identified Cdk1 as potentially involved in R-loop-associated microglial (Cd68+) inflammatory infiltration in COI at 7 dpi. These results provide the first evidence of R-loop's potential role in SCI progression, offering new insights for developing therapies aimed at preserving neurological function and promoting repair.

Published in Neurobiology of Disease

ISSN: 0969-9961 (Print); 1095-953X (Online)
Publisher: Elsevier
Country of publisher: United States
LCC subjects: Medicine: Internal medicine: Neurosciences. Biological psychiatry. Neuropsychiatry
Website: https://www.journals.elsevier.com/neurobiology-of-disease

About the journal

Abstract

Keywords