Disrupted DNA repair and oxidative stress responses underlie hematopoietic stem cell failure after spinal cord injury

Abstract Hematopoietic stem cells (HSCs) sustain lifelong blood and immune cell production through tightly regulated transitions between dormancy, proliferation, and differentiation. While intrinsic and niche-derived signals guiding these transitions are widely studied, more remains to be understood about how the nervous system influences hematopoiesis. Spinal cord injury (SCI) has been shown to disrupt hematopoiesis and is associated with persistent immune dysfunction and increased infection risk, yet the mechanisms linking neural trauma to hematopoietic failure remain poorly defined. Because hematopoietic recovery from stress requires rapid HSC activation and robust DNA repair and oxidative stress responses, we hypothesized that SCI would impair HSC function by disrupting transcriptional and epigenetic programs essential for stress-responsive hematopoiesis. Transcriptomic analysis revealed that SCI suppresses key stress-response pathways in HSCs, including those involved in cell cycle progression, DNA repair, and oxidative stress regulation. Over 500 genes were downregulated, including Brca1, Fen1, and Lig1, along with antioxidant enzymes such as thioredoxins and peroxiredoxins. Chromatin accessibility profiling showed reduced promoter accessibility at some of these loci (e.g., Fen1 and Lig1), suggesting epigenetic silencing and impaired transcriptional activation of genome maintenance programs. To test the functional consequences of these changes, we performed serial competitive transplantation assays using bone marrow isolated from SCI, sham-operated, and naïve (anesthesia-only) mice at just 1 day after surgery. Sham mice received a laminectomy (i.e., vertebral fracture without perturbation of the spinal cord) and were included to assess the normal hematopoietic response to acute surgical stress. Despite retaining short-term hematopoietic output, SCI-derived HSCs failed to activate and showed impaired long-term repopulating capacity even when introduced into mice with intact nervous systems. Lineage-Sca1⁺cKit⁺ HSPCs (LSKs) from SCI donors exhibited reduced chimerism at endpoint in primary recipients, and secondary and tertiary transplants confirmed durable, cell-intrinsic HSC defects in self-renewal and multilineage output. To validate the transcriptional and epigenetic findings, we used the DNA comet assay on FACS- purified HSCs to quantify DNA damage and stimulated HSCs with H₂O₂, based on the observed downregulation of H₂O₂- handling genes in the scRNA- seq dataset. SCI- derived HSCs exhibited elevated baseline DNA damage, failed to resolve oxidative stress following H₂O₂ exposure, and underwent apoptosis in response to irradiation- induced genotoxic insult. These defects were absent in sham controls, which mounted a canonical stress- induced transcriptional and antioxidant response. In summary, our findings demonstrate that acute disruption of nervous system signaling impairs HSC activation and function by suppressing transcriptional and epigenetic programs required for hematopoietic recovery. These results highlight an underappreciated neuroendocrine axis of regulation. Further studies are focused on what SCI- induced changes drive this phenotype.