Biology subjects

Khem, S.

Publications and source records attributed to Khem, S..

4 recordsLinked to original sources

bioRxiv2026

Selective collateralization of transcriptomically distinct neurons organizes visual-stream output from the primary visual cortex

Parallel visual streams segregate information into pathways specialized for distinct computations, but how this segregation is achieved by anatomical segregation of primary visual cortex output remains unclear. This problem is complicated because individual neurons frequently send broadcasting projections to multiple cortical areas, and the target choice depends on both topographical location and molecular identity. Here we developed axonal BARseq2 to jointly map gene expression and high-resolution axonal projections from 1,448 neurons spanning the mouse primary visual cortex (VISp). Axonal BARseq2 recapitulated projection patterns observed by bulk tracing and single-neuron reconstruction, and recovered transcriptomic identities consistent with reference snRNA-seq datasets. Retinotopy strongly predicted projections to individual cortical targets, particularly for areas proximal to VISp, but explained little of which areas are frequently co-innervated. Instead, co-innervation patterns defined three preferential output pathways that largely corresponded to the ventral stream and two subdivisions of the dorsal stream. These pathways were associated with fine-grained transcriptional identities of L4/5 intra-telencephalic neurons, which were further validated with an external MERFISH dataset. Thus, VISp output is organized by two distinct rules: retinotopy constrains where neurons project, whereas cell-type-associated collateralization constrains which targets are co-innervated. This selective broadcasting, in which single neurons reach many higher visual areas in cell-type-specific combinations, could provide an anatomical substrate for visual-stream segregation at the level of VISp output in mice.

neuroscience↗

bioRxiv2026

Morphoelectric Diversity and Specialization of Neuronal Cell Types in the Primate Striatum

The basal ganglia are evolutionary ancient subcortical nuclei that form interconnected loops with the neocortex and limbic system to regulate movement, learning, habit formation, emotion, and motivation. Their dysfunction contributes to major neurological and psychiatric disorders, yet most cellular-level insights derive from rodent studies, leaving knowledge gaps in humans and translationally relevant primate species. To address this, we generated multi-modal Patch-seq data linking transcriptomic identity with morphological and electrophysiological properties in macaque striatum, the input nucleus of the basal ganglia. We found underappreciated diversity among medium spiny neurons, including non-canonical types, and variation aligned with functional gradients. Interneurons also exhibited spatial variation and even greater morphoelectric diversity, highlighting their functional modularity. Despite broad evolutionary conservation, we identified primate-specific features and key differences from rodent striatal neurons. By integrating molecular classification with cellular properties that shape network function, our findings provide insights into the functional organization of the primate striatum.

neuroscience↗

bioRxiv2026

Enhancer-based AAV approach for selective AADC delivery reduces motor symptoms and dyskinesia in Parkinson's mouse models

Degeneration of midbrain dopamine (DA) neurons and the resulting loss of striatal dopamine signaling are hallmarks of Parkinsons disease (PD). Although the dopamine precursor levodopa (L-DOPA) provides symptomatic relief, prolonged treatment often leads to abnormal involuntary movements (dyskinesia). Previous adeno-associated virus (AAV) approaches delivering aromatic L-amino acid decarboxylase (AADC) to the striatum under a ubiquitous promoter enhanced local dopamine synthesis and improved PD motor deficits, but this broad targeting strategy limited insight into the cellular populations underlying the behavioral improvements. Here, we engineered enhancer-driven AAVs to direct AADC expression to defined striatal and midbrain cell populations and paired these regulatory elements with a blood-brain barrier-penetrant capsid to enable both systemic and direct delivery. Targeted expression restored motor performance at reduced L-DOPA doses and decreased dyskinesia-like behaviors, producing improvements comparable to or greater than those achieved with ubiquitous expression. Distinct neuronal and non-neuronal populations each supported motor rescue but improved different behavioral domains to different extents, indicating complementary cell type-specific roles within PD-relevant circuits. Together, these findings establish enhancer-driven, cell type-specific AADC delivery as a better-tolerated strategy that enables rescue of motor deficits at lower L-DOPA doses in PD models.

neuroscience↗

bioRxiv2025

Technical and biological sources of noise confound multiplexed enhancer AAV screening

Cis-acting regulatory enhancer elements are valuable tools for gaining cell type-specific genetic access. Leveraging large chromatin accessibility atlases, putative enhancer sequences can be identified and deployed in adeno-associated virus (AAV) delivery platforms. However, a significant bottleneck in enhancer AAV discovery is charting their detailed expression patterns in vivo, a process that currently requires gold-standard one-by-one testing. Here we present a barcoded multiplex strategy for screening enhancer AAVs at cell type resolution using single cell RNA sequencing and taxonomy mapping. We executed a proof-of-concept study using a small pool of validated enhancer AAVs expressing in a variety of neuronal and non-neuronal cell types across the mouse brain. Unexpectedly, we encountered substantial technical and biological noise including chimeric packaging products, necessitating development of novel techniques to accurately deconvolve enhancer expression patterns. These results underscore the need for improved methods to mitigate noise and highlight the complexity of enhancer AAV biology in vivo.

neuroscience↗