Biology subjects

Libby, R. T.

Publications and source records attributed to Libby, R. T..

6 recordsLinked to original sources

bioRxiv2026

Genetic context alters central nervous system compartment dependent responses to lipopolysaccharide

Systemic inflammation drives neurodegeneration, yet its differential effects across neural tissues and genetic backgrounds remain poorly understood. We performed RNA-sequencing on brain, optic nerve head (ONH), and retina from four genetically diverse mouse strains (B6, CAST, NZO, WSB) following lipopolysaccharide (LPS)-induced systemic inflammation. The ONH mounted the largest response to LPS (9510 DEGs), followed by retina (5152) and brain (4586). A conserved core of 1444 DEGs across all tissues was enriched for innate immune and acute-phase pathways. Tissue-specific responses were apparent; the retina downregulated phototransduction and visual perception genes; ONH exhibited bidirectional remodeling with upregulated proteasome and ribosome biogenesis and suppressed lipid metabolism and lysosomal function; yet the brain displayed no significant pathway level enrichment. Genetic background strongly modulated the LPS response across the three tissues; the retina exhibited the greatest strain-dependent divergence. Interestingly, differing genetic context affected the ONH response to LPS the least despite its markedly larger response to LPS overall. In totality, both genetic and physical context dictate the neuroinflammatory response to LPS.

neuroscience↗

bioRxiv2025

Optimizing the Characterization and Quantification of Retinal Ganglion Cell Somas in Healthy and Injured Retinas Using Cellpose

Quantification of retinal ganglion cell (RGC) soma number and characterization of somal features are commonly used output metrics for investigation of optic neuropathies. Many investigators still perform these quantifications by hand, which is time consuming and prone to bias. Cellpose is an open-source Python package that can perform cellular segmentation and holds promise for automating somal analyses. Here, we designed a custom script incorporating the Cellpose package and custom-trained Cellpose models that are capable of automatic characterization and quantification of RGC somas. Our script, using our models, is capable of automatically counting RGC somas, along with characterizing RGC somal size. Further, we show that Cellpose can quantify RGCs using multiple cell-type specific markers and has the potential to quantify RGCs across the entire retina. Together, our custom Cellpose models and script which generates and analyzes Cellpose outputs provides a powerful tool for all-in-one RGC somal analysis.

neuroscience↗

bioRxiv2024

MKK4 and MKK7 control degeneration of retinal ganglion cell somas and axons after glaucoma-relevant injury.

Glaucoma is characterized by programmed cell death of retinal ganglion cells (RGCs) after axonal injury. Several studies have shown the cell-intrinsic drivers of RGC degeneration act in a compartment-specific manor. Recently, the transcription factors JUN and DDIT3 were identified as critical hubs regulating RGC somal loss after mechanical axonal injury. It is possible somal DDIT3/JUN activity initiates axonal degeneration mechanisms in glaucoma. Alternatively, DDIT3/JUN may act downstream of inciting degenerative mechanisms and only drive RGC somal loss. The MAP2Ks MKK4 and MKK7 control all JNK/JUN activity and can indirectly activate DDIT3. Furthermore, MKK4/7 have been shown to drive RGC axonal degeneration after mechanical axonal injury. The present work investigated whether JUN and DDIT3, or their upstream activators MKK4 and MKK7, control degeneration of RGC axons and somas after glaucoma-relevant injury. Ddit3/Jun deletion did not prevent axonal degeneration in ocular hypertensive DBA/2J mice but prevented nearly all RGC somal loss. Despite robust somal survival, Ddit3/Jun deletion did not preserve RGC somal viability (as assessed by PERG decline and soma shrinkage) in DBA/2J mice or after glaucoma-relevant mechanical axonal injury. In contrast, Mkk4/7 deletion significantly lessened degeneration of RGC somas and axons, and preserved somal function and size after axonal injury. In summary, activation of MKK4 and MKK7 appears to be the inciting mechanism governing death of the entire RGC after glaucoma-relevant injury; driving death of the RGC soma (likely through activation of DDIT3 and JUN), decline in somal viability, and axonal degeneration via DDIT3/JUN-independent mechanisms.

pathology↗

bioRxiv2019

The Ocular Glymphatic Clearance System

Despite high metabolic activity, the retina and optic nerve head lack traditional lymphatic drainage. We here identified a novel ocular glymphatic clearance route for fluid and wastes via the proximal optic nerve. Amyloid-{beta} (A{beta}) was cleared from the vitreous via a pathway driven by the ocular-cranial pressure difference. After traversing the lamina barrier, intra-axonal A{beta} was cleared via the perivenous space and subsequently drained to lymphatic vessels. Light-induced pupil constriction enhanced, while atropine or raising intracranial pressure blocked efflux. In two distinct murine models of glaucoma, A{beta} leaked from the eye via defects in the lamina barrier instead of directional axonal efflux. The discovery of a novel pathway for removal of fluid and metabolites from the intraocular space prompts a reevaluation of the core principles governing eye physiology and provides a framework for new therapeutic approaches to treat common eye diseases, including glaucoma. One Sentence SummaryGlymphatic pathway clears ocular amyloid-{beta} via optic nerve and fails in glaucoma.

physiology↗

bioRxiv2019

DDIT3 (CHOP) contributes to retinal ganglion cell somal loss but not axonal degeneration in DBA/2J mice

Glaucoma is an age-related neurodegenerative disease characterized by the progressive loss of retinal ganglion cells (RGCs). Chronic ocular hypertension, an important risk factor for glaucoma, leads to RGC axonal injury at the optic nerve head. This insult triggers molecularly distinct cascades governing RGC somal apoptosis and axonal degeneration. The molecular mechanisms activated by ocular hypertensive insult that drive both RGC somal apoptosis and axonal degeneration are incompletely understood. The cellular response to endoplasmic reticulum stress and induction of pro-apoptotic DNA damage inducible transcript 3 (DDIT3, also known as CHOP) has been implicated as a driver of neurodegeneration in many disease models, including glaucoma. RGCs express DDIT3 upon glaucoma-relevant insults, and importantly, DDIT3 has been shown to contribute to both RGC somal apoptosis and axonal degeneration after acute induction of ocular hypertension. However, the role of DDIT3 in RGC somal and axonal degeneration has not been critically tested in a model of age-related chronic ocular hypertension. Here, we investigated the role of DDIT3 in glaucomatous RGC death using an age-related, naturally occurring ocular hypertensive mouse model of glaucoma, DBA/2J mice (D2). To accomplish this, a null allele of Ddit3 was backcrossed onto the D2 background. Homozygous Ddit3 deletion did not alter gross retinal or optic nerve head morphology, nor did it change the ocular hypertensive profile of D2 mice. In D2 mice, Ddit3 deletion conferred mild protection to RGC somas but did not significantly prevent RGC axonal degeneration. Together, these data suggest that DDIT3 plays a minor role in perpetuating RGC somal apoptosis caused by chronic ocular hypertension-induced axonal injury, but does not significantly contribute to distal axonal degeneration.

neuroscience↗

bioRxiv2018

Mkk4 and Mkk7 are important for retinal development and axonal injury-induced retinal ganglion cell death

The mitogen activated protein kinase (MAPK) pathway has been shown to be involved in both neurodevelopment and neurodegeneration. c-Jun N-terminal kinase (JNK), a MAPK shown to be important in retinal development and after optic nerve crush injury, is regulated by two upstream kinases: MKK4 and MKK7. The specific requirements of MKK4 and MKK7 in retinal development and retinal ganglion cell (RGC) death after axonal injury, however, are currently undefined. Optic nerve injury is an important insult in many neurologic conditions including traumatic, ischemic, inflammatory, and glaucomatous optic neuropathies. Mice deficient in Mkk4, Mkk7, and both Mkk4 and Mkk7 were generated. Immunohistochemistry was used to study the distribution and structure of retinal cell types and to assess RGC survival after optic nerve injury (mechanical controlled optic nerve crush; CONC). Adult Mkk4 and Mkk7 deficient retinas had all retinal cell types. With the exception of small areas of lamination defects with photoreceptors in Mkk4 deficient mice, the retinas of both mutants were grossly normal. Deficiency of Mkk4 or Mkk7 reduced JNK signaling after axonal injury in RGCs. Mkk4 and Mkk7 deficient retinas had a significantly greater percentage of surviving RGCs 35 days after CONC as compared to wildtype controls (Mkk4: 51.5%, Mkk7: 29.1% WT: 15.2%; p<0.001). Combined deficiency of Mkk4 and Mkk7 caused failure of optic nerve formation, irregular retinal axonal trajectories, disruption of retinal lamination, clumping of RGC cell bodies, and dendritic fasciculation of dopaminergic amacrine cells. These results suggest that MKK4 and MKK7 may serve redundant and unique roles in molecular signaling important for retinal development and injury response following axonal insult.

neuroscience↗