Search bioRxiv⌕ Search

bioRxiv · 10.1101/2024.03.18.585466

Consequences of neuronal morphology for spatially precise optogenetic stimulation

Abstract

Single-photon optogenetic stimulation is a crucial tool in neuroscience, enabling precise, cell-type-specific modulation of neuronal circuits. Miniaturization of this technique in the form of fully implantable wide-field stimulator arrays enables interrogation of cortical circuits in long-term experiments and promises to enhance Brain-Machine Interfaces for restoring sensory and motor functions. However, for both basic science and clinical applications, it is essential that this technique achieves the precision needed for selective activation of sensory and motor representations at the single-column level. Yet studies report differing and sometimes conflicting neuronal responses within the stimulated cortical areas. While recurrent network mechanisms contribute to complex responses, here we demonstrate that complexity starts already at the level of neuronal morphology. Simulating optogenetic responses in detailed models of layer-2/3 and layer-5 pyramidal neurons, we accounted for realistic physiological dynamics across different stimulation intensities, including threshold, sustained, and depolarization-block responses. Our findings suggest that the spatial distribution of activated neurons from a single stimulator location at the cortical surface can be inhomogeneous and varies with stimulation intensity and neuronal morphology across layers, potentially explaining the observed response heterogeneity in earlier experiments. We found that activation spreads laterally up to several hundred micrometers from the light source due to neuronal morphology. To enhance precision, we explored two strategies: preferentially somatic expression of channelrhodopsin, which was effective only in layer-5 neurons, and narrowing the stimulating light beam, which improved precision in both layers. Our results indicate that, under the right optical setup, single-column precision of stimulation is achievable, and that optical enhancements to the stimulator may offer more significant precision improvements than genetic modifications targeting the soma.

Source connections

Explore related subjects

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Berling, D., Baroni, L., Chaffiol, A., Gauvain, G., Picaud, S., Antolik, J.. 2024-03-18. Consequences of neuronal morphology for spatially precise optogenetic stimulation. https://doi.org/10.1101/2024.03.18.585466

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

The Unreasonable Effectiveness of Cell Types in Describing Neuronal Physiological Features

Single-cell RNA sequencing (scRNA-seq) captures detailed gene expression profiles at scale, while patch-clamp recordings measure intrinsic neuronal electrophysiological properties. Modeling the relations between these two modalities remains a challenge. Here, we compare how well electrophysiological features can be predicted by traditional transcriptomic cell type classification, representations derived from a foundational model (scGPT) pretrained on large-scale scRNA-seq datasets, ion channel-coding genes, and highly variable genes. Using paired transcriptomic and electrophysiological patch-sequencing data from 495 human neurons from neurosurgical tissue, we find that cluster-level cell type representations consistently outperform highly variable gene selection, ion channel gene selection, and context-enriched scGPT embeddings. Notably, performance varies across model architectures and initializations, and the best results are obtained by combining the outputs of separate cell type and scGPT-based models. Together, these findings suggest that traditional discrete cellular classification is highly effective in predicting physiological features. For maximum performance it can be complemented by pretrained transformer models.

neuroscience↗

A nonlinear inhibition pathway underlying cortical responses to tuned holographic optogenetic perturbations

Optogenetics enables causal manipulation of cortical activity. Perturbation responses can be counterintuitive due to network interactions, making theory essential for predicting them. Existing approaches often rely on linear approximations, which fail for many biologically relevant perturbations. Here we develop a nonlinear theory of responses to holographic perturbations in cell-type-specific recurrent networks with structured connectivity. We fit a nonlinear model to mouse V1 data, which shows cotuned-ensemble suppression: perturbing spatially clustered neurons with similar preferred orientations yields markedly stronger short-range suppression than perturbing untuned ensembles. We show that cotuned-ensemble suppression arises from a feature-tuned, nonlinear inhibition pathway implicating somatostatin-positive (SST) interneurons. The theory predicts that cotuned ensembles suppress parvalbumin-positive (PV) neurons but facilitate SST neurons, and links the degree of cotuned-ensemble suppression or facilitation to the variance of the SST response. This framework identifies mechanisms by which nonlinear inhibition sculpts cortical dynamics and establishes a predictive basis for targeted optogenetic interventions.

neuroscience↗

Proteomic signatures of APOE ε4 across human tissues and cell types in Alzheimers disease

The apolipoprotein E {varepsilon}4 (APOE {varepsilon}4) allele is the strongest genetic risk factor for late-onset Alzheimers disease (AD). However, the underlying molecular mechanisms remain unclear. This study included 1691 participants from the Religious Orders Study and Rush Memory and Aging Project (ROSMAP), 1226 participants from the Accelerating Medicines Partnership - Alzheimers Disease (AMP-AD) Diverse Cohorts Study, and 735 participants from the Alzheimers Disease Neuroimaging Initiative (ADNI). To characterise APOE {varepsilon}4 molecular effects, we analysed proteomic data from plasma, cerebrospinal fluid (CSF), and induced pluripotent stem cell (iPSC)-derived astrocytes and neurons, as well as transcriptomic and proteomic data from multiple brain regions. The association of APOE {varepsilon}4 with AD neuropathology was also examined. APOE {varepsilon}4 carriers shared a plasma proteomic signature enriched for immune processes, irrespective of AD diagnosis. A machine learning classifier trained on this signature discriminated APOE {varepsilon}4 carriers from non-carriers in an independent cohort using CSF proteomics. APOE {varepsilon}4 carriage was associated with higher Braak stages and Consortium to Establish a Registry for Alzheimers Disease (CERAD) score. However, only limited APOE {varepsilon}4-associated transcriptomic and proteomic changes were observed in bulk brain tissue, with poor cross-layer concordance. Proteomic analyses of iPSC-derived astrocytes and neurons further revealed cell-type-specific APOE {varepsilon}4-associated changes. APOE {varepsilon}4 is associated with a consistent proteomic signature across plasma and CSF. Its molecular effects in the brain differ across cell types, brain regions and molecular layers. These findings support the need for cell-type-resolved multi-omic studies to elucidate how APOE {varepsilon}4 confers AD risk.

neuroscience↗