Exploration of the brain at single-cell resolution
The brain contains hundreds of cell types, each with a different biological mission. Each expresses different genes in the pursuit of its own specialized biological functions. A longstanding scientific need is to understand how each cell type contributes to brain function and where each gene acts; this is also critical for understanding how genes shape risk of illness. The Macosko lab develops new genomic technologies to identify these novel populations, characterize their roles within normal circuitry, and understand how they contribute to disease states in pathological contexts.
The McCarroll and Macosko labs recently developed a technology for profiling RNA expression genome-wide in thousands of individual cells at once. The method involves separating cells into millions of nanoliter-sized droplets, lysing the cells in droplets, and barcoding the contents of each droplet to mark the cell-of-origin of each RNA molecule. In a single sequencing reaction, they routinely profile gene expression genome-wide in thousands of individual cells. This technology is called Drop-Seq.
The teams are using Drop-Seq to ascertain:
The cell types that populate the brain;
The pathophysiology involved in schizophrenia, autism, and other illnesses; and
The ways in which genetic variation acts at the level of specific cell populations within complex tissues.
The field now needs new kinds of algorithms and computational strategies to recognize all of the biologically meaningful information that is present in these vast novel data sets.
Furthermore, the Macosko team is developing and deploying cutting-edge molecular techniques to more deeply understand the function of cellular specialization in the nervous system. In particular, the team seeks clear, actionable explanations for how the cells of the brain go awry in major mental illness.
Single Cell Genomics
The Levin lab is dedicated to bringing the most appropriate genomics technology solutions to answer important questions in biology. Over the past 14 years, the lab has pioneered new RNA-seq methods and made definitive and comprehensive comparisons of available methods to guide this highly dynamic field. In addition to performing experiments, the group has a strong computational capability in place to understand the genetic and biochemical mechanisms underlying psychiatric disorders such as schizophrenia and autism in the mammalian brain. By deploying the most powerful and appropriate technology to study these biological systems, and by collaborating with other Stanley Center scientists, the group aims to shed light on devastating — and in many cases currently incurable — brain disorders.
Brain Interaction Network
Advances in human genetics have nominated many genes and specific cell types implicated in psychiatric illnesses but linking these findings with biochemical processes remains challenging. The Lage lab works with collaborators at the Stanley Center to overcome these challenges by combining recent genetic discoveries with proteomics to determine the brain networks of physically interacting proteins that are perturbed in neuropsychiatric disorders. By using neurons derived from human pluripotent stem cells, the Lage team targets proteins linked to neuropsychiatric disorders for immunoprecipitation and mass spectrometry analysis. The resulting protein networks are then analyzed for disease risk enrichment and provide a rich reference for other scientists in the field to use in the interpretation of their own datasets.
To analyze proteomic data, the Lage team develops tools, such as Genoppi, which integrates cell-type-specific protein networks with genetic data from public or user-defined gene lists. Follow-up studies consist in elucidating the biochemical relationships of relevant protein interactions in human neurons and further connecting these results with growing genetic datasets from diverse patient populations. These combined investigations result in a map of protein networks that inform about neuronal pathways that are perturbed in neuropsychiatric disorders.
The vector engineering team at the Stanley Center for Psychiatric Research, led by Ben Deverman, is interested in creating viral tools that enable more efficient and selective expression of genes in defined cell types in the brain. The group focuses mostly on adeno-associated viruses (AAVs), which have become a widely used and versatile platform for gene delivery to the brain due to their low immunogenicity and ability to provide long-term gene expression. AAVs allow researchers to test hypotheses about gene and cell function by expressing, knocking down, or editing genes of interest in vivo and by monitoring or modulating the state of specific cell populations using a rapidly expanding collection of genetically encoded sensors and actuators. In addition, AAVs are also being developed and used as gene therapy vehicles.
The group applies a variety of high-throughput selection and screening techniques to customize AAV capsids and recombinant genomes for targeting specific cell types and circuits. In particular, Deverman and his colleagues recently developed CREATE, a Cre recombinase-based method for selecting AAV capsids that target specific cell types in vivo, and which has allowed them to identify AAV variants that can cross the blood-brain barrier.
Through internal technology development and collaborations with fellow Stanley Center scientists, the vector engineering team supports disease model studies aimed at identifying new effective treatments for psychiatric disorders.
Adam Cohen's research focuses on developing and applying new physical tools to probe molecules, cells, and organisms. Projects in the lab range from quantum mechanics to pure biology. The Cohen Lab discovered that a light-driven proton pump called Archaerhodopsin 3, derived from a Dead Sea microorganism, could be run `in reverse’ to convert changes in membrane voltage into flashes of fluorescence. His lab engineered variants of this protein called QuasAr1 and QuasAr2 which, when expressed in mammalian neurons, enable optical monitoring of neuro-electrical activity. By co-expressing the voltage indicators with channelrhodopsin optogenetic actuators, the Cohen Lab developed a bidirectional neuro-optical interface.
The optical electrophysiology team and their collaborators are now applying these techniques to study function of neurons, cardiomyocytes, and other electrically active cells in health and disease. Optical electrophysiology measurements in human stem cell-derived neurons can be used to identify characteristic signatures of genetically based disease, and to test the response to candidate therapeutics. Recent work in the Cohen Lab has transitioned these tools to measurements in awake behaving mice and zebrafish. These measurements are beginning to reveal the details of neuronal function in the context of sensory inputs and behavior.