High-throughput mapping of single-neuron projection and molecular features by retrograde barcoded labeling
- Chinese Academy of Sciences, China
- ShanghaiTech University, China
Abstract
Deciphering patterns of connectivity between neurons in the brain is a critical step toward understanding brain function. Imaging-based neuroanatomical tracing identifies area-to-area or sparse neuron-to-neuron connectivity patterns, but with limited throughput. Barcode-based connectomics maps large numbers of single-neuron projections, but remains a challenge for jointly analyzing single-cell transcriptomics. Here, we established a rAAV2-retro barcode-based multiplexed tracing method that simultaneously characterizes the projectome and transcriptome at the single neuron level. We uncovered dedicated and collateral projection patterns of ventromedial prefrontal cortex (vmPFC) neurons to five downstream targets and found that projection-defined vmPFC neurons are molecularly heterogeneous. We identified transcriptional signatures of projection-specific vmPFC neurons, and verified Pou3f1 as a marker gene enriched in neurons projecting to the lateral hypothalamus, denoting a distinct subset with collateral projections to both dorsomedial striatum and lateral hypothalamus. In summary, we have developed a new multiplexed technique whose paired connectome and gene expression data can help reveal organizational principles that form neural circuits and process information.
Data availability
Raw gene expression, barcode count matrices and metadata were available from the Gene Expression Omnibus (GSE210174). The computational code used in the study is available at GitHub (https://github.com/MichaelPeibo/MERGE-seq-analysis). The data needed to evaluate the conclusions in the paper can be downloaded at https://figshare.com/projects/High-throughput_mapping_of_single-neuron_projection_and_molecular_features_by_retrograde_barcoded_labeling/150207. All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials and source data files.
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High-throughput mapping of single-neuron projection and molecular features by retrograde barcoded labelingNCBI Gene Expression Omnibus, GSE210174.
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Cell type-specific transcriptional programs in mouse prefrontal cortex during adolescence and addictionNCBI Gene Expression Omnibus, GSE124952.
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Differential encoding in prefrontal cortex projection neuron classes across cognitive tasksNCBI Gene Expression Omnibus, GSE161936.
Article and author information
Author details
Funding
National Key Research and Development Program of China (2018YFA0108000)
- Yuejun Chen
National Natural Science Foundation of China (32170806)
- Yuejun Chen
National Natural Science Foundation of China (32130035)
- Zhen-Ge Luo
Thousand Young Talents Program of China
- Yuejun Chen
National Key Research and Development Program of China (2021ZD0202500)
- Zhen-Ge Luo
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Ethics
Animal experimentation: All animal experiments were conducted according to a protocol approved by the IACUC at the Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technol- ogy of the Chinese Academy of Sciences (Shanghai, China). (reference number for approval: NA-034-2022).
Copyright
© 2024, Xu et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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High-throughput mapping of single-neuron projection and molecular features by retrograde barcoded labeling
eLife 13:e85419.
https://doi.org/10.7554/eLife.85419
Further reading
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