Biology subjects

Passino, R.

Publications and source records attributed to Passino, R..

4 recordsLinked to original sources

bioRxiv2026

Single-cell spatial transcriptomics of inherited retinal degeneration reveals broad and focal organization of disease responses

Inherited retinal degenerations are largely monogenic disorders characterized by progressive photoreceptor dysfunction and death. Although the transcriptomic responses to inherited degeneration are well-characterized, how these responses are spatially organized across the retinal axis has not been mapped. Here, we used seqFISH to spatially profile 173 cell identity and degeneration-associated genes with single-cell, single-transcript resolution in male wild-type and LCA5gt/gtmouse retinas at early, intermediate, and advanced disease stages. In early disease, rod injury and stress response markers were enriched in the superior retina, while rod function and identity markers were enriched in the inferior retina. Nested within the broader superior-inferior organization, a coordinated rod injury response comprising Edn2, Fgf2, Socs3, and Stat3 was organized into focal regions on the order of 100 m in width, with high-response regions directly adjacent to low-response regions. These focal regions were locally enriched for markers of Muller reactive gliosis and rod stress responses. Our single-cell spatiotemporal map reveals that transcriptional responses to degeneration vary at both the broad and focal scales, and offers a framework for investigating how local tissue properties and interactions among neighboring cells may contribute to disease progression.

neuroscience↗

bioRxiv2025

AxoMetric: A Rapid and Unbiased Tool for Automated Quantification of Axon Regeneration in Tissue Sections

Recent advances in experimental strategies that promote axon regeneration in adult mammals lay the foundation for future therapies. Reliable and unbiased quantification of regenerated axons is challenging, yet essential for comparing the efficacy of individual treatments and identification of most efficacious combinatorial therapies. Here, we introduce AxoMetric, a user-friendly and freely available software for the rapid quantification of regenerated axons in longitudinal nerve tissue sections. AxoMetric automatically identifies and traces regenerated axons, generating quantitative measurements that closely match conventional manual quantification but with significantly greater speed. Key features include length-dependent axon quantification at defined intervals from the injury site and normalization of axon density to nerve diameter to account for anatomical variability. To facilitate high-throughput analysis, the software includes an image queuing function. Additional features of AxoMetric allow quantification of a range of labeled cellular structures. As a proof of concept, we demonstrate accurate quantification of regenerated axons in the optic nerve, retinal ganglion cells density in retinal flat-mounts, and regenerated axon bundles in injured sciatic nerves. Collectively, we introduce a new platform that is expected to streamline and standardize regenerative outcome assessments across diverse experimental conditions and laboratories. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=102 SRC="FIGDIR/small/662816v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@162d692org.highwire.dtl.DTLVardef@1f52ed4org.highwire.dtl.DTLVardef@1d58f76org.highwire.dtl.DTLVardef@1bdabb1_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2022

The Injured Sciatic Nerve Atlas (iSNAT), Insights into the Cellular and Molecular Basis of Neural Tissue Degeneration and Regeneration

Upon trauma, the adult murine PNS displays a remarkable degree of spontaneous anatomical and functional regeneration. To explore extrinsic mechanisms of neural repair, we carried out single cell analysis of naive mouse sciatic nerve, peripheral blood mononuclear cells, and crushed sciatic nerves at 1-day, 3-days, and 7-days following injury. During the first week, monocytes and macrophages (Mo/Mac) rapidly accumulate in the injured nerve and undergo extensive metabolic reprogramming. Proinflammatory Mo/Mac in the injured nerve show high glycolytic flux compared to Mo/Mac in blood and dominate the early injury response. They subsequently give way to inflammation resolving Mac, programmed toward oxidative phosphorylation. Nerve crush injury causes partial leakiness of the blood-nerve-barrier, proliferation of endoneurial and perineurial stromal cells, and accumulation of select serum proteins. Micro-dissection of the nerve injury site and distal nerve, followed by single-cell RNA-sequencing, identified distinct immune compartments, triggered by mechanical nerve wounding and Wallerian degeneration, respectively. This finding was independently confirmed with Sarm1-/- mice, where Wallerian degeneration is greatly delayed. Experiments with chimeric mice showed that wildtype immune cells readily enter the injury site in Sarm1-/- mice, but are sparse in the distal nerve, except for Mo. We used CellChat to explore intercellular communications in the naive and injured PNS and report on hundreds of ligand-receptor interactions. Our longitudinal analysis represents a new resource for nerve regeneration, reveals location specific immune microenvironments, and reports on large intercellular communication networks. To facilitate mining of scRNAseq datasets, we generated the injured sciatic nerve atlas (iSNAT): https://cdb-rshiny.med.umich.edu/Giger_iSNAT/

neuroscience↗

bioRxiv2020

Analysis of the Immune Response to Sciatic Nerve Injury Identifies Efferocytosis as a Key Mechanism of Nerve Debridement

Sciatic nerve crush injury triggers sterile inflammation within the distal nerve and axotomized dorsal root ganglia (DRGs). Granulocytes and pro-inflammatory Ly6Chigh monocytes infiltrate the nerve first, and rapidly give way to Ly6Cnegative inflammation-resolving macrophages. In axotomized DRGs, few hematogenous leukocytes are detected and resident macrophages acquire a ramified morphology. Single-cell RNA-sequencing of injured sciatic nerve identifies five macrophage subpopulations, repair Schwann cells, and mesenchymal precursor cells. Macrophages at the nerve crush site are molecularly distinct from macrophages associated with Wallerian degeneration. In the injured nerve, macrophages "eat" apoptotic leukocytes, a process called efferocytosis, and thereby promote an anti-inflammatory milieu. Myeloid cells in the injured nerve, but not axotomized DRGs, strongly express receptors for the cytokine GM-CSF. In GM-CSF deficient (Csf2-/-) mice, inflammation resolution is delayed and conditioning-lesion induced regeneration of DRG neuron central axons is abolished. Thus, carefully orchestrated inflammation resolution in the nerve is required for conditioning-lesion induced neurorepair.

neuroscience↗