Brain-wide projections and differential encoding of prefrontal neuronal classes underlying learned and innate threat avoidance

Abstract

Long-range axonal projections provide the foundation for functional connectivity between brain regions and are critical in the modulation of behavior. Descending projections from medial prefrontal cortex (mPFC) to various target regions regulate critical behavioral functions including decision making, social behavior and mood. While specific mPFC projections have distinct behavioral roles, individual mPFC projection neurons can also innervate multiple target regions. Yet how mPFC projection neurons divide their axons across the brain is poorly understood. In this study, we mapped the axon collaterals of mPFC neurons that project to nucleus accumbens (NAc), ventral tegmental area (VTA), or contralateral mPFC (cmPFC) in mice. We used tissue clearing and light sheet fluorescence microscopy to visualize the 3-D structure of axonal arbors across the intact brain. While machine learning can automate analysis of axons in images of cleared tissue, it is challenging to train a model that generalizes to all axonal structures because the appearance of axons varies by target region. In this study, we present DeepTraCE (Deep learning-based image Tracing with Combined-model Enhancement), a new strategy for axon segmentation and quantification in images of cleared tissue. DeepTraCE is based on the deep-learning framework TRAILMAP; it achieves highly accurate axon detection by combining multiple machine learning models that are each applied to different brain regions. Using DeepTraCE, we find that cmPFC, NAc, and VTA-projecting mPFC neurons represent largely separable classes with unique axon collaterals in cortical, olfactory, and thalamic regions, respectively.

Functional imaging of nine distinct neuronal populations under a miniscope in freely behaving animals

“…5e). The distribution of co-expression, however, did not match previously published descriptions of projection specific neurons and their projection patterns 24 . This is most likely due to differential expression of fluorophores and the differential ability to discern these fluorophores when co-expressed with one another.…”

Prefrontal Cortical Regulation of REM Sleep

“…A key question for future research is whether there exists a clear hierarchy in the REM sleep circuitry with speci c rst-order neurons initiating REM sleep, or whether multiple neural populations, distributed across various areas, form a brain-wide network, in which each node can trigger REM sleep independently. Of note, we cannot exclude that collaterals of the mPFC→LH neurons projecting to other areas besides the LH 17 may also contribute to the observed effects on REM sleep and that other mPFC subpopulations with different postsynaptic targets also play a role in sleep-wake regulation. For instance, prefrontal projections to the dorsomedial hypothalamus have been reported to promote wakefulness 51 .…”

“…The mPFC sends long-range projections to multiple brain regions including cortical and subcortical areas [15][16][17] , but the projections relevant to REM sleep regulation are unknown. To label axonal projections for anterograde tracing, we expressed tdTomato in mPFC Pyr neurons (Extended Data Fig.…”

“…The medial prefrontal cortex (mPFC) is known to interact with multiple brain regions through its longrange connections, allowing it to coordinate various behaviors ranging from emotional processing to the regulation of the autonomic nervous system [14][15][16][17] and to control brain-wide activity dynamics 18 . Downstream regions innervated by the mPFC include subcortical areas in brainstem and hypothalamus involved in sleep-wake regulation.…”