Neural Coding of Fear: From Genes to Brain-Wide Dynamics

Fear is essential for survival. Predator threats, aggressive conspecifics, and environmental dangers elicit innate defensive responses that do not require learning. Although these responses are hardwired, animals display remarkable flexibility in selecting the most adaptive behaviors. The neural circuits that enable such dynamic representations of internal fear states remain poorly understood. The dorsomedial and central subdivisions of the ventromedial hypothalamus (VMHdm) integrate multisensory threat-related inputs and are both necessary and sufficient to drive defensive responses. In this thesis, I investigate how VMHdm neurons encode internal states associated with predator fear, across multiple biological scales—from transcriptomic profile, single-cell neural dynamics to brain-wide activity patterns. First, I characterized the transcriptomic profile of VMH neurons activated by predator exposure using activity-dependent single-cell RNA sequencing (act-seq). I then combined optogenetic perturbation of VMHdm with act-seq to identify state-dependent transcriptomic correlates in a downstream output, the periaqueductal gray (PAG). To investigate the real-time dynamics of these neurons during naturalistic predator encounters, I developed a novel behavioral paradigm and performed microendoscopic single-cell calcium imaging. Contrary to the long-held view of VMHdm as a uniformly threat-activated population, my analyses revealed functionally distinct clusters that encode not only threat, but also safety, arousal or novelty or neophobia, predator imminence, and anxiety. Moreover, I found that individual variation in behavioral defensiveness was correlated with VMHdm neural dynamics. Finally, to assess how local hypothalamic activation influences global brain states, I combined VMHdm optogenetic stimulation with functional ultrasound imaging (fUSI), which permits high-resolution recording of brain-wide hemodynamics. This approach revealed the spatiotemporal propagation of neural activity from the hypothalamus to distributed brain regions. These findings demonstrate how a genetically defined hypothalamic subpopulation can engage a dynamic, brain-wide ensemble to orchestrate defensive responses. Together, these studies provide a multi-modal, multi-scale analysis of the innate fear state and its flexible representation via the hypothalamus, embedded within a dynamic global network of interacting regions. These findings offer insight into how internal states are encoded and broadcast, with potential implications for understanding the neural basis of human psychiatric disorders and the distributed computation of affective states.