Biology subjects

Heinsbroek, J. A.

Publications and source records attributed to Heinsbroek, J. A..

3 recordsLinked to original sources

bioRxiv2026

nf_xpatial: A Reproducible Framework for Standardized Preprocessing and Clustering of Xenium Data

Recent advances in spatial transcriptomics have enabled the profiling of increasingly larger numbers of genes while retaining single-cell and subcellular resolution in situ. However, standardized bioinformatics workflows for analyzing these datasets have lagged behind, with existing pipelines focusing primarily on image processing and cell segmentation. To address this gap, we present nf_xpatial, a best-practices Nextflow pipeline for the downstream analysis of 10x Genomics Xenium data. The pipeline performs quality control, filtering, log and cell area normalization, multi-sample integration, and both expression-driven and spatially informed clustering across systematic parameter sweeps, allowing users to evaluate and compare clustering resolutions and spatial modeling parameters within a single reproducible run. Overall, nf_xpatial streamlines the processing of Xenium data from platform outputs to integrated single-cell and spatial clustering datasets, providing a standardized starting point from which biologists can fine-tune parameters and proceed to hypothesis-driven spatial analyses.

bioinformatics↗

bioRxiv2026

A conserved population of genetically defined striatal neurons gates opioid reward

A longstanding paradox in striatal circuit architecture is that opioid reward depends on -opioid receptors ({micro}ORs) in nucleus accumbens medium spiny neurons (MSNs), yet {micro}OR function is not explained by the canonical D1/direct and D2/indirect pathway organization. Here, we identify a rare MSN population marked by Chst9 that exhibits exceptionally high expression of the {micro}OR and is conserved across species. Notably, Chst9-MSNs comprise a specialized indirect pathway striatal neuron subtype that is molecularly and spatially distinct from canonical striatal populations. Opioids robustly silence Chst9-MSNs, and selective deletion of Oprm1 from this population abolishes fentanyl-conditioned place preference. These findings establish Chst9-MSNs as a critical substrate for opioid reward and define a new cellular framework for therapies targeting opioid use disorder.

neuroscience↗

bioRxiv2026

Ventral pallidal perineuronal nets regulate opioid relapse

Opioid use disorder remains a major health challenge worldwide. Neuronal activity in the ventral pallidum (VP) regulates opioid reward and relapse to opioid seeking but the underlying cellular mechanisms remain largely unknown. A sizable population of VP neurons previously linked to drug relapse expresses the calcium binding protein parvalbumin (VPPV). Across the brain parvalbumin neurons are often ensheathed by perineuronal nets (PNNs), specialized extracellular structures that regulate intrinsic activity and constrain synaptic plasticity onto these neurons. The VP contains high levels of PNNs but the role of these structures in the neurophysiology of VPPV neurons and in relapse to opioid seeking has not been studied. To investigate whether VP PNNs are altered by opioid exposure, male and female mice were trained to self-administer intravenous heroin. We found that heroin increased the density of PNNs in the VP, and that an intracranial microinfusion of the PNN-degrading enzyme, chondroitinase ABC, prevented cue-induced reinstatement of heroin seeking. VP PNN depletion also reduced the intrinsic excitability of VPPV neurons, potentiated inhibitory synaptic inputs onto these cells, and diminished Fos expression in VPPV neurons following reinstatement. The suppressive effect of VP PNN depletion on heroin seeking was rescued by chemogenetic activation of VPPV neurons and mimicked by chemogenetic VPPV neuron inhibition. Taken together, our results identify VPPV neurons and their associated PNNs as critical drivers of opioid seeking. Given the key role of PNNs in regulating neural plasticity and memory processes, targeting PNNs in the VP could provide a useful novel therapeutic avenue for treating persistent craving and relapse in opioid use disorder.

neuroscience↗