Comparative transcriptomics of retinal cell types
Cell-type specific genomics and transcriptomics of HIV in the brain
Exploration of genome organization and function in the HIV infected brain is critical to aid in the understanding and development of treatments for HIV-associated neurocognitive disorder (HAND). Here, we applied a multiomic approach, including single nuclei transcriptomics, cell-type specific Hi-C 3D genome mapping, and viral integration site sequencing (IS-seq) to frontal lobe tissue from HIV-infected individuals with encephalitis (HIVE) and without encephalitis (HIV+). We observed reorganization of open/repressive (A/B) compartment structures in HIVE microglia encompassing 6.4% of the genome with enrichment for regions containing interferon (IFN) pathway genes. 3D genome remodeling was associated with transcriptomic reprogramming, including down-regulation of cell adhesion and synapse-related functions and robust activation of IFN signaling and cell migratory pathways, and was recapitulated by IFN-g stimulation of cultured microglial cells. Microglia from HIV+ brains showed, to a lesser extent, similar transcriptional alterations. IS-seq recovered 1,221 integration sites in the brain that were enriched for chromosomal domains newly mobilized into a permissive chromatin environment in HIVE microglia. Viral transcription, which was detected in 0.003% of all nuclei in HIVE brain, occurred in a subset of highly activated microglia that drove differential expression in HIVE. Thus, we observed a dynamic interrelationship of interferon-associated 3D genome and transcriptome remodeling with HIV integration and transcription in the brain.
Brain and behavioural impacts of early life adversity
Abuse, neglect, and other forms of uncontrollable stress during childhood and early adolescence can lead to adverse outcomes later in life, including especially perturbations in the regulation of mood and emotional states, and specifically anxiety disorders and depression. However, stress experiences vary from one individual to the next, meaning that causal relationships and mechanistic accounts are often difficult to establish in humans. This interdisciplinary talk considers the value of research in experimental animals where stressor experiences can be tightly controlled and detailed investigations of molecular, cellular, and circuit-level mechanisms can be carried out. The talk will focus on the widely used repeated maternal separation procedure in rats where rat offspring are repeatedly separated from maternal care during early postnatal life. This early life stress has remarkably persistent effects on behaviour with a general recognition that maternally-deprived animals are susceptible to depressive-like phenotypes. The validity of this conclusion will be critically appraised with convergent insights from a recent longitudinal study in maternally separated rats involving translational brain imaging, transcriptomics, and behavioural assessment.
What transcriptomics tells us about retinal development, disease and evolution
Classification of neurons, long viewed as a fairly boring enterprise, has emerged as a major bottleneck in analysis of neural circuits. High throughput single cell RNA-seq has provided a new way to improve the situation. We initially applied this method to mouse retina, showing that its five neuronal classes (photoreceptors, three groups of interneurons, and retinal ganglion cells) can be divided into 130 discrete types. We then applied the method to other species including human, macaque, zebrafish and chick. With the atlases in hand, we are now using them to address questions about how retinal cell types diversify, how they differ in their responses to injury and disease, and the extent to which cell classes and types are conserved among vertebrates.
The Fabric of the Neocortex
Toward a Comprehensive Classification of Mouse Retinal Ganglion Cells: Morphology, Function, Gene Expression, and Central Projections
I will introduce a web portal for the retinal neuroscience community to explore the catalog of mouse retinal ganglion cell (RGC) types, including data on light responses, correspondences with morphological types in EyeWire, and gene expression data from single-cell transcriptomics. Our current classification includes 43 types, accounting for 90% of the cells in EyeWire. Many of these cell types have new stories to tell, and I will cover two of them that represent opposite ends of the spectrum of levels of analysis in my lab. First, I will introduce the “Bursty Suppressed-by-Contrast” RGC and show how its intrinsic properties rather than its synaptic inputs differentiate its function from that of a different well-known RGC type. Second, I will present the histogram of cell types that project to the Olivary Pretectal Nucleus, focusing on the recently discovered M6 ipRGC.
The evolutionary origins of cortical cell types
In the last 500 million years, the dorsal telencephalon changed like no other region of the vertebrate brain. Differences range from the six-layered neocortex of mammals, to the small three-layered cortex of reptiles, and the complete absence of lamination in birds. These anatomical differences have prompted endless discussions on the origins and evolution of the cerebral cortex. We have approached this problem from a cell type and transcriptomics perspective. This reveals a more granular picture, where different cell types and classes have followed independent trajectories of evolutionary change. In this presentation, I will discuss how the molecular analysis of cell types in the brains of turtles, lizards and amphibians is updating our views on the evolution of the cerebral cortex, and the new questions emerging from these results.