X inactive specific transcript drives mitochondrial metabolic rewiring and neural stem cell fate after spinal cord injury

Table 1 Multidimensional regulatory landscape of X-inactive specific transcript in spinal cord injury: From mitochondrial metabolism to epigenetic and immune control

Regulatory dimension	Key molecular partners/targets	Core mechanistic action	Functional impact and SCI outcome	Ref.
Epigenetic and chromatin	SAF-A/HNRNPU, PRC1/2, MED14	XIST coating and chromatin anchoring; recruitment of polycomb complexes; suppression of specific enhancers	Maintains XCI integrity and lineage stability in stem cells	Kolpa et al[14], 2016; Bousard et al[15], 2019; Richart et al[16], 2022
Post-transcriptional and metabolic (core axis)	IGF2BP2, CPT1A, NDUFA2	XIST recruits IGF2BP2 (m6A reader) to stabilize CPT1A and NDUFA2 mRNAs; markedly enhances FAO and OXPHOS	Promotes neuronal differentiation of NSCs; increases ATP production and OCR; improves locomotor recovery and reduces neuroinflammation	Zeng et al[1], 2025; Huang et al[4], 2022; Wang et al[11], 2021; Weng et al[17], 2022
Immune-metabolic and ceRNA	miR-124-3p, IRF1	XIST acts as a ceRNA sponge for miR-124-3p, modulating the Irf1 pathway and microglial polarization	Regulates M1/M2 macrophage balance; exerts context-dependent effects on the inflammatory microenvironment	Yang et al[18], 2023
Systemic and intercellular	miR-539-3p, ADAMTS5; MSC-derived exosomes	XIST modulates hepatic mitochondrial injury via Adamts5 axis; XIST-containing EVs facilitate stem-immune crosstalk	Sustains cross-organ energy homeostasis; drives pro-regenerative M2 phenotype through exosomal shuttling of regulatory RNAs	Wu et al[2], 2023; Karpenko[19], 2025; Phinney et al[20], 2015; Arabpour et al[21], 2021

SCI: Spinal cord injury; SAF-A: Scaffold attachment factor A; HNRNPU: Heterogeneous nuclear ribonucleoprotein U; PRC1: Polycom repressive complex 1; PRC2: Polycom repressive complex 2; MED14: Mediator complex subunit 14; XIST: X-inactive specific transcript; XCI: X-chromosome inactivation; IGF2BP2: Insulin-like growth factor 2 mRNA-binding protein 2; CPT1A: Carnitine palmitoyl transferase 1A; NDUFA2: NADH ubiquinone oxidoreductase subunit A2; m⁶A: N6-methyladenosine; FAO: Fatty acid oxidation; OXPHOS: Oxidative phosphorylation; NSCs: Neural stem cells; ATP: Adenosine triphosphate; OCR: Oxygen consumption rate; IRF1: Interferon regulatory factor 1; ceRNA: Competing endogenous RNA; ADAMTS5: A disintegrin and metalloproteinase with thrombospondin motifs 5; MSCs: Mesenchymal stromal/stem cells; EVs: Extracellular vesicles; M1: Classically activated (pro-inflammatory) macrophage phenotype; M2: Alternatively activated (anti-inflammatory/pro-regenerative) macrophage phenotype.

Table 2 Prioritized research agenda and experimental strategies for X-chromosome inactivation-centered metabolic interventions in spinal cord injury

Research priority	Current gap (critique of evidence)	Suggested experimental approach (specific parameters)	Expected outcome	Ref.
Precision histomorphology and lineage specificity	Insufficiency of specialized histological characterization; lack of specific parameters to confirm NSC terminal differentiation	Confocal co-localization analysis (e.g., BrdU/NeuN for neurogenesis; synaptophysin for synaptic integration); integration of snRNA-seq and spatial transcriptomics	High-resolution mapping of XIST-mediated lineage commitment and functional integration across neural/glial subpopulations	Li et al[7], 2024; Zhang et al[32], 2024
Long-term structural and functional stability	Absence of 12-24 week chronic-phase data; limited correlation between short-term metabolic gains and longitudinal functional trajectories	Standardized chronic injury paradigms (compression/contusion); 12-24 weeks follow-up; multiparametric MRI/DTI coupled with composite behavioral metrics (gait analysis, grid walking)	Verification of sustained regenerative benefits, scar-stabilizing effects, and long-term structure-function correlations in chronic SCI	Rosenzweig et al[35], 2018; Chen et al[33], 2023
Metabolic safety and targeted delivery systems	Systemic metabolic risks of non-specific CPT1A intervention; demand for scalable, CNS-oriented and bio-responsive delivery platforms	Cell-type-specific Cpt1a cKO or knock-in models; engineered exosomes (EVs) or LNPs integrated into hydrogel scaffolds	Establishment of an optimized therapeutic window and clinically feasible “gene-cell-vector” platforms for spinal cord repair	Morant-Ferrando et al[12], 2023; Williams et al[34], 2025

NSC: Neural stem cell; BrdU: 5-bromo-2’-deoxyuridine; NeuN: Neuronal nuclei; snRNA-seq: Single-nucleus RNA sequencing; XIST: X-inactive specific transcript; MRI: Magnetic resonance imaging; DTI: Diffusion tensor imaging; SCI: Spinal cord injury; CPT1A: Carnitine palmitoyl transferase 1A; CNS: Central nervous system; cKO: Conditional knockout; EVs: Extracellular vesicles; LNPs: Lipid nanoparticles.