Mark P. Goldberg

Recovery after focal motor cortex stroke relies on structural remodeling of neuronal circuits in the perilesional cortex (PLC) and contralesional cortex (CLC). Although transcriptomic studies have identified distinct reactive glial states after stroke, how their spatial organization relates to processes of tissue degeneration and neuronal circuit remodeling remains poorly understood. We used a custom 347-gene Xenium spatial transcriptomics panel to profile approximately 650,000 cells across both hemispheres of male and female mice 7 days after photothrombotic stroke. We identified injury-associated myeloid populations concentrated within the infarct and reactive astrocytes enriched in the glial scar. Distinct reactive populations also extended into spared cortex, including an interferon-associated myeloid population and a reactive astrocyte population that was present in both PLC and CLC. Spatial mapping further revealed elevated neuronal growth-associated gene expression in both regions, particularly among layer 5 extratelencephalic projection neurons, which include corticospinal neurons. Intriguingly, reactive glial populations were enriched in regions exhibiting elevated neuronal growth-associated gene expression, including areas of the CLC containing axons and presynaptic terminals originating from the PLC. Together, these findings reveal a striking spatial association between reactive glial populations and neurons exhibiting elevated growth-associated gene expression and support glial-neuronal interactions as potential targets for promoting circuit remodeling and functional recovery after stroke.

Stroke induces a transient period of heightened plasticity during which functional recovery is most pronounced. Experimental models have identified repair-associated processes in both the ipsilesional and contralesional cortex, indicating that stroke recovery involves regions both remote and near the lesion. However, most transcriptional studies have focused on the infarct core and peri-lesional cortex (PLC), leaving it unclear whether comparable molecular responses occur in the contralesional cortex (CLC), a region that undergoes substantial remodeling in the absence of direct tissue injury, necrosis, or widespread cellular infiltration. In addition, potential sex-dependent differences in these responses remain incompletely defined, despite known influences of biological sex on post-stroke inflammation and vascular remodeling. To address these gaps, we performed bulk RNA-sequencing of the PLC and CLC at 7 days after photothrombotic stroke, a subacute time point associated with the initiation of repair, in male and female mice. Despite distinct positions relative to the lesion, both regions exhibited robust upregulation of inflammatory signaling, including cytokine-, astrocyte-, and myeloid-lineage-associated pathways. The CLC did not demonstrate a distinct region-specific transcriptional profile; instead, shared signatures between PLC and CLC included genes strongly associated with reactive microglial phenotypes. This shared neuroinflammatory response was largely conserved across sexes. Consistent with these findings, male and female mice exhibited comparable corticospinal tract axonal sprouting originating from the CLC at 6 weeks post-stroke. Together, these findings support a shared neuroinflammatory transcriptional response as a prominent early feature of cortical regions associated with post-stroke plasticity.

Skilled movement relies on descending cortical projections to the brainstem and spinal cord. The brainstem integrates cortical inputs from subcerebral projection neurons (SCPN). Here, we identify a previously unrecognized direct cortico-brainstem circuit that emerges early in development and persists into adulthood. A subset of SCPN project exclusively to the brainstem from the earliest stages of axon extension, never extending to the spinal cord. We find that during development, these cortico-brainstem neurons (CBN) can be prospectively identified by Neuropeptide Y (Npy) expression. In adulthood, Npy⁺ CBN project preferentially to rostral brainstem motor regions. Silencing Npy⁺ CBN impairs the precision and targeting of forelimb movement in a skilled reaching task. Together, these results outline how molecular programs lay the foundation for adult cortico-brainstem circuits underlying skilled movement. Our findings reveal the developmental logic diversifying descending cortical circuits and enable investigation of specific descending projection neuron subsets in motor control.

Aging and age-related diseases like ischemic stroke induce chronic lymphocyte recruitment into the CNS. Conflicting effects on post-stroke functional recovery, however, are secondary to the differences in responding lymphocyte populations that shift immunophenotype with injury and age. To better define CNS-localized B cell subsets, we used flow cytometry, single-cell RNA sequencing, and B cell receptor sequencing on B cells isolated from uninjured and post-stroke brains of aged male and female mice. We identified a novel B1b cell progenitor pool distinct from canonical pleural/peritoneal niches. Trajectory analysis showed progenitor transition into age-associated B cell (ABC) subsets, and clonal expansion of IgM⁺ ABCs (ABC/B1b) and plasma cells following ischemic stroke. We also confirmed analogous ABCs and developing B cell populations in post-mortem human parenchymal tissue isolated from aged brain donors. These studies reveal unique B cell populations that can proliferate within the aging CNS and exhibit a conserved inflammatory signature across species.

Stroke induces a transient period of heightened plasticity during which functional recovery is most pronounced. Work in rodent models of stroke has identified key mechanisms in both the ipsilesional and contralesional cortex that contribute to functional and structural post-stroke plasticity. To date, most gene expression studies have focused on the infarct core and the immediately surrounding tissue, peri-lesional cortex (PLC). We sought to understand whether the contralesional cortex (CLC), a region that shows robust structural and molecular remodeling despite its distance from the lesion, mounts a distinct transcriptional response to stroke. Direct comparisons of molecular pathways governing these regions, particularly across sexes, are limited. To address this gap, we performed bulk RNA sequencing of the PLC and CLC at 7 days post-stroke, a critical time point for initiating repair, in male and female mice. Our results indicate that despite distinct positions from the lesion, both regions share a robust upregulation of inflammatory signaling, with Gene Ontology enrichment indicating activation of cytokine signaling, leukocyte activation, and gliogenesis pathways. Further analysis of this shared gene expression signature revealed reactive microglia signaling as the dominant pathway. Surprisingly, the CLC did not show a distinct transcriptional response. These findings were consistent across males and females, which also showed similar CLC-derived corticospinal tract axonal sprouting at 6 weeks post-stroke. Together, these findings support a shared microglia-centered neuroinflammatory transcriptional response in the PLC and CLC and suggest that microglial reactivity is a key early process for post-stroke cortical plasticity in both male and female mice.

The corticospinal tract (CST) is essential for forelimb-specific fine motor skills. In rodents, it undergoes extensive structural remodeling across development, injury, and disease states, with major implications for motor function. A vast body of literature, spanning numerous injury models, frequently assesses these projections. Despite this, a cohesive imaging modality for rapid, quantitative assessment of the bilateral cervical spinal cord projectome is lacking. To address this, we developed SpinalTRAQ (Spinal cord Tomographic Registration and Automated Quantification), a novel mouse cervical spinal cord volumetric reference atlas and machine learning-based analytical pipeline. Using serial two-photon tomography, SpinalTRAQ enables unbiased, region-specific quantification of fluorescently labeled CST presynaptic terminals. In healthy male mice, the CST exhibits a distinct bilateral synaptic projectome, with the densest innervation in laminae 5 and 7 on the contralateral side and lamina 7 on the ipsilateral side. We additionally observed sparse synaptic input in lamina 9, specifically axial motor neuron pools, which we found was targeted to spinal motoneurons. Following focal motor cortical stroke, the injured CST axons are depleted, and contralesional CST projections are significantly increased after 4 and 6 weeks. By 6 weeks post-stroke, ipsilateral CST synapses were increased by fivefold, with the greatest increases seen in homotopic laminae and all motor neuron pools. SpinalTRAQ offers detailed, level- and lamina-specific quantification of the bilateral cervical spinal cord synaptic projectome, revealing previously unrecognized CST connectivity and plasticity after injury.

Social determinants of health (SDoH) contribute to disparities in SARS-CoV-2 infection, but their associations with long COVID are unknown. To determine associations between SDoH at the time of SARS-CoV-2 infection and risk for long COVID. Prospective observational cohort study. 33 states plus Washington, DC, and Puerto Rico. Adults (aged ≥18 years) enrolled in RECOVER-Adult (Researching COVID to Enhance Recovery) between October 2021 and November 2023 who were within 30 days of SARS-CoV-2 infection; completed baseline SDoH, comorbidity, and pregnancy questionnaires; and were followed prospectively. Social risk factors from SDoH baseline questionnaires, ZIP code poverty and household crowding measures, and a weighted score of 11 or higher on the Long COVID Research Index 6 months after infection. Among 3787 participants, 418 (11%) developed long COVID. After adjustment for demographic characteristics, pregnancy, disability, comorbidities, SARS-CoV-2 severity, and vaccinations, financial hardship (adjusted marginal risk ratio [ARR], 2.36 [95% CI, 1.97 to 2.91]), food insecurity (ARR, 2.36 [CI, 1.83 to 2.98]), less than a college education (ARR, 1.60 [CI, 1.30 to 1.97]), experiences of medical discrimination (ARR, 2.37 [CI, 1.94 to 2.83]), skipped medical care due to cost (ARR, 2.87 [CI, 2.22 to 3.70]), and lack of social support (ARR, 1.79 [CI, 1.50 to 2.17]) were associated with increased risk for long COVID. Living in ZIP codes with the highest (vs. lowest) household crowding was also associated with greater risk (ARR, 1.36 [CI, 1.05 to 1.71]). Selection bias may influence observed associations and generalizability. Participants with social risk factors at the time of SARS-CoV-2 infection had greater risk for subsequent long COVID than those without. Future studies should determine whether social risk factor interventions mitigate long-term effects of SARS-CoV-2 infection. National Institutes of Health.

/Summary: Descending corticospinal tract (CST) connections to the neurons of the cervical spinal cord are vital for performance of forelimb-specific fine motor skills. In rodents, CST axons are almost entirely crossed at the level of the medullary decussation. While specific contralateral axon projections have been well-characterized using anatomic and molecular approaches, the field currently lacks a cohesive imaging modality allowing rapid quantitative assessment of the entire, bilateral cervical cord projectome at the level of individual laminae and cervical levels. This is potentially important as the CST is known to undergo marked structural remodeling in development, injury, and disease. We developed SpinalTRAQ ( S pinal cord T omographic R egistration and A utomated Q uantification), a novel volumetric cervical spinal cord atlas and machine learning-driven microscopy acquisition and analysis pipeline that uses serial two-photon tomography-images to generate unbiased, region-specific quantification of the fluorescent pixels of anterograde AAV-labeled CST pre-synaptic terminals. In adult mice, the CST synaptic projectome densely innervates the contralateral hemicord, particularly in laminae 5 and 7, with sparse, monosynaptic input to motoneurons in lamina 9. Motor pools supplying axial musculature in the upper cervical cord are bilaterally innervated. The remainder of the ipsilateral cord has sparse labeling in a distinct distribution compared to the contralateral side. Following a focal stroke of the motor cortex, there is a complete loss of descending corticospinal axons from the injured side. Consistent with prior reports of axon collateralization, the CST spinal projectome increases at four weeks post-stroke and continues to elevate by six weeks post stroke. At six weeks post-stroke, we observed striking synapse formation in the denervated hemicord from the uninjured CST in a homotopic distribution. Additionally, CST synaptic reinnervation increases in the denervated lamina 9 in nearly all motoneuron pools, exhibiting novel patterns of connectivity. Detailed level- and lamina-specific quantification of the bilateral cervical spinal cord synaptic projectome reveals previously undescribed patterns of CST connectivity in health and injury-related plasticity.