Sequencing-Based High-Throughput Neuroanatomy: From Mapseq to Bricseq and Beyond

Neural circuit research using molecular barcode technology

In neuroscience research, the primary goal is to understand the complex morphological and anatomical structures of the brain and their physiological and behavioral functional relationships or to understand the causality of diseases that manifest as dysfunction of the brain, and various technologies have been developed to achieve this goal. These include imaging techniques such as magnetic resonance imaging (MRI), functional magnetic resonance imaging (fMRI), and positron emission tomography (PET), which noninvasively visualize brain structure and activity; electrophysiological techniques that measure intracellular potentials and currents and analyze cell electrical properties to understand brain activity; techniques to explore how gene expression affects brain function; genetic methods such as gene knockout/knock-in to study how brain cells function; and computational neuroscience methods such as mathematical modeling and simulation to understand the principles of how brain networks operate. Among these, recent advances, particularly the development of 'single-cell omics analysis,' have led to a paradigm shift in neuroscience research. This technique allows the comprehensive study of the unique genetic and molecular characteristics of individual brain cells at the single-cell level. In this paper, I review the application of single-cell omics analysis, which has advanced dramatically in recent years, to various neuroscience problems, mainly how it contributes to the structure and function of neural circuits, a modality unique to the cranial nervous system.

Populations of Hindbrain Glucagon-Like Peptide 1 (GLP1) Neurons That Innervate the Hypothalamic PVH, Thalamic PVT, or Limbic Forebrain BST Have Axon Collaterals That Reach All Central Regions Innervated by GLP1 Neurons

Neurons in the caudal nucleus of the solitary tract (cNTS) and intermediate reticular nucleus (IRt) that express the glucagon gene (Gcg) give rise to glucagon-like peptide 1 (GLP1)-immunopositive axons in the spinal cord and many subcortical brain regions. Central GLP1 receptor signaling contributes to motivated behavior and stress responses in rats and mice, in which hindbrain GLP1 neurons are activated to express c-Fos in a metabolic state-dependent manner. The present study examined whether GLP1 inputs to distinct brain regions arise from distinct subsets of Gcg-expressing neurons, and mapped the distribution of axon collaterals arising from projection-defined GLP1 neural populations. Using our Gcg-Cre knock-in rat model, Cre-dependent adeno-associated virus (AAV) tracing was conducted in adult male and female rats to compare axonal projections of IRt versus cNTS GLP1 neurons. Overlapping projections were observed in all brain regions that receive GLP1 input, with the caveat that cNTS injections produced Cre-dependent labeling of some IRt neurons, and vice versa. In additional experiments, specific diencephalic or limbic forebrain nuclei were microinjected with Cre-dependent retrograde AAVs (AAVrg) that expressed reporters to fully label the axon collaterals of transduced GLP1 neurons. AAVrg injected into each forebrain site labeled Gcg-expressing neurons in both the cNTS and IRt. The collective axon collaterals of labeled neurons entered the spinal cord and every brain region previously reported to contain GLP1-positive axons. These results indicate that the axons of GLP1 neural populations that innervate the thalamic paraventricular nucleus, paraventricular nucleus of the hypothalamus, and/or bed nucleus of the stria terminalis collectively innervate all central regions that receive GLP1 axonal input.

Emerging strategies for the genetic dissection of gene functions, cell types, and neural circuits in the mammalian brain

The mammalian brain is composed of a large number of highly diverse cell types with different molecular, anatomical, and functional features. Distinct cellular identities are generated during development under the regulation of intricate genetic programs and manifested through unique combinations of gene expression. Recent advancements in our understanding of the molecular and cellular mechanisms underlying the assembly, function, and pathology of the brain circuitry depend on the invention and application of genetic strategies that engage intrinsic gene regulatory mechanisms. Here we review the strategies for gene regulation on DNA, RNA, and protein levels and their applications in cell type targeting and neural circuit dissection. We highlight newly emerged strategies and emphasize the importance of combinatorial approaches. We also discuss the potential caveats and pitfalls in current methods and suggest future prospects to improve their comprehensiveness and versatility.