Evidence map›Paper›PMID 41121424›Full record

ArticleBiomarker research2025

Integrating single-cell RNA sequencing and spatial multi-omics reveals the molecular signature of regeneration after spinal cord injury.

Haoru Dong, Yuanqing Ding, Xingyu Chen, Xiao Xiao, Longnian Zhou, Haiyue Lin, Zezhen Zhang, Yiming Tao, Shiyi Cai, Jianlan Zhao and 2 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Biomarker research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

6 citing papers in PubMed.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

12 authors.

Haoru Dong *Department of Neurosurgery, National Center for Neurological Disorders, Shanghai Clinical Medical Center of Neurosurgery, Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration, Huashan Hospital, Neurosurgical Institute of Fudan University, Fudan University, Shanghai, 200040, China.
Yuanqing Ding *Department of Neurosurgery, National Center for Neurological Disorders, Shanghai Clinical Medical Center of Neurosurgery, Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration, Huashan Hospital, Neurosurgical Institute of Fudan University, Fudan University, Shanghai, 200040, China.
Xingyu Chen *Department of Neurosurgery, National Center for Neurological Disorders, Shanghai Clinical Medical Center of Neurosurgery, Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration, Huashan Hospital, Neurosurgical Institute of Fudan University, Fudan University, Shanghai, 200040, China.
Xiao XiaoDepartment of Neurosurgery, National Center for Neurological Disorders, Shanghai Clinical Medical Center of Neurosurgery, Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration, Huashan Hospital, Neurosurgical Institute of Fudan University, Fudan University, Shanghai, 200040, China.
Longnian ZhouDepartment of Neurosurgery, National Center for Neurological Disorders, Shanghai Clinical Medical Center of Neurosurgery, Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration, Huashan Hospital, Neurosurgical Institute of Fudan University, Fudan University, Shanghai, 200040, China.
Haiyue LinDepartment of Neurosurgery, National Center for Neurological Disorders, Shanghai Clinical Medical Center of Neurosurgery, Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration, Huashan Hospital, Neurosurgical Institute of Fudan University, Fudan University, Shanghai, 200040, China.
Zezhen ZhangDepartment of Neurosurgery, National Center for Neurological Disorders, Shanghai Clinical Medical Center of Neurosurgery, Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration, Huashan Hospital, Neurosurgical Institute of Fudan University, Fudan University, Shanghai, 200040, China.
Yiming TaoDepartment of Neurosurgery, National Center for Neurological Disorders, Shanghai Clinical Medical Center of Neurosurgery, Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration, Huashan Hospital, Neurosurgical Institute of Fudan University, Fudan University, Shanghai, 200040, China.
Shiyi CaiDepartment of Neurosurgery, National Center for Neurological Disorders, Shanghai Clinical Medical Center of Neurosurgery, Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration, Huashan Hospital, Neurosurgical Institute of Fudan University, Fudan University, Shanghai, 200040, China.
Jianlan ZhaoDepartment of Neurosurgery, National Center for Neurological Disorders, Shanghai Clinical Medical Center of Neurosurgery, Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration, Huashan Hospital, Neurosurgical Institute of Fudan University, Fudan University, Shanghai, 200040, China. jlzhao16@fudan.edu.cn.
Xiaomu LiDepartment of Endocrinology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China. li_xiao_mu@163.com.
Rong XieDepartment of Neurosurgery, National Center for Neurological Disorders, Shanghai Clinical Medical Center of Neurosurgery, Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration, Huashan Hospital, Neurosurgical Institute of Fudan University, Fudan University, Shanghai, 200040, China. rongxie@fudan.edu.cn.

Funding

National Key R&D Program of China 2018AAA0100300 and 2018AAA0100302National Natural Science Foundation of China 81870909, 82071315, 82271342, 82171381, 81970695, 82170808, 82371396
6 · The paper itself

Abstract

backgroundA certain degree of self-repair is initiated following spinal cord injury (SCI). Although intraneuronal regeneration and a supportive growth environment are limited, they serve as the foundation for functional recovery after SCI.

methodsIn this study, we conducted single-cell RNA sequencing combined with spatial transcriptomics and spatial metabolomics to reveal the spatial molecular characteristics of self-repair processes after SCI at single-cell resolution.

resultsWe identified three cell subsets-Mic2 (a microglia subset), Mac4 (a macrophage subset), and Fib4 (a fibroblast subset)-that express markers associated with spinal cord repair. Mic2 and Mac4 exhibit clustered spatial distribution patterns, whereas Fib4 is predominantly located around the injured spinal cord. Additionally, Mic2 is predominantly distributed in the white matter, particularly in the dorsal region of the injured spinal cord, and exhibits high expression of taurine. Mac4 and Fib4 exhibit high expression of copalic acid and uridine, respectively.

conclusionsIn this study, we have identified three distinct cell subsets that express markers associated with wound healing and may promote regenerative processes, and we have determined their spatial transcriptional and metabolic features enriched within these regions. Our dataset represents a valuable resource that offers novel mechanistic insights into the pathobiology of spinal cord injury.

Indexed as

RegenerationSingle-cell RNA sequencingSpatial metabolomicsSpatial transcriptomicsSpinal cord injury

Identifiers

PMID41121424
PMCPMC12542165

What OpenQuestion holds

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LicenceCC BY
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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.