Welcome to the IBRO 2023 Interactive Programme

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The human brain directs many key biological processes, from autonomic processes like body temperature, hunger, and sleep, to primary sensorimotor processes such as vision and fine motor control, to language and other human-specialized cognitive functions. It is also the target of multiple developmental and degenerative disorders that are often poorly recapitulated in animal models. However, due to the complex anatomy and sheer size of the human brain, along with practical and ethical limitations, many approaches for studying brain are only possible in other species. Here, I describe the approaches that the Allen Institute has taken to characterize cell types in the cortex of multiple mammalian species and then link these cell types across species to transfer knowledge about long-range projections, developmental origin, and other cellular properties difficult to measure in human. In our initial study we used gene expression signatures of individual cells to define and comprehensively characterize cell types in human middle temporal gyrus and show how these relate to mouse neocortical cell types whose genetic profiles and projection targets were exquisitely profiled. Through this and more recent studies with additional species and better matched experimental conditions, we identify a broadly conserved set of molecularly defined neuronal and non-neuronal cell types in mammalian cortex that allow us to infer properties of cell types across species. For example, we show that morphologically distinct excitatory neurons in layer 5 of frontoinsula (Von Economo neurons) and primary motor cortex (Betz cells) correspond to extratelencephalic-projecting pyramidal neurons in mouse. Despite the overall conservation of homologous types, many differences exist in cell-type proportions, gene expression, and chromatin state in a manner generally mirroring evolutionary distance. These studies lay the groundwork for in-process efforts at integrating cell types across the entire mouse, human, and non-human primate brain and provide unique insights into human brain evolution.

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Although single-cell RNA sequencing has revolutionized our understanding of the mammalian brain, the diversity of cell types that contribute to the human brain remains poorly understood. We therefore used high-throughput single-nucleus RNA sequencing to survey the entire adult human brain. We sampled tissue from approximately 100 dissections across the forebrain, midbrain, and hindbrain in three postmortem donors. Fluorescence-activated nuclei sorting enriched for neurons. The final dataset contained over three million nuclei, among which our analysis identified 461 clusters and 3313 subclusters organized largely according to developmental origins. Non-cortical regions like the hypothalamus, midbrain, and hindbrain comprised a remarkably high diversity of neurons. Glial cells also exhibited regional diversity at multiple scales: astrocytes and oligodendrocyte precursors clustered into subtypes specific to the telencephalon -- the developmental compartment that gives rise to the cortex, hippocampus, and cerebral nuclei -- and non-telencephalic regions of the brain; astrocytes exhibited finer-scale regional diversity. Our findings therefore suggest a unique cellular composition of the telencephalon with respect to all major brain cell types. As the first single-cell transcriptomic census of the entire human brain, these data provide a novel resource for understanding the molecular diversity of the human brain in health and disease.

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In the mammalian brain, tens of millions to billions of cells form complex interaction networks to enable a wide range of functions. The enormous diversity and intricate organization of cells in the brain have so far hindered our understanding of the molecular and cellular basis of its functions. We developed a single-cell transcriptome and genome imaging method, multiplexed error-robust fluorescence in situ hybridization (MERFISH), which allows RNA, DNA, and epigenetic marks to be imaged at the genome scale. This approach enabled spatially resolved transcriptomic profiling, epigenomic profiling, and 3D-genome organization mapping in single cells. The ability to perform single-cell gene expression profiling in intact tissues further enabled the identification, spatial mapping, and functional annotation of distinct cell types in intact tissues. We applied MERFISH to generate molecularly defined and spatially resolved cell alases of both mouse and human brains. In our recent whole mouse brain study, we imaged a panel of >1,100 genes in ~8 million cells across the entire adult mouse brain using MERFISH and performed spatially resolved, single-cell expression profiling at the whole-transcriptome scale by integrating MERFISH and scRNA-seq data. Using this approach, we generated a cell atlas of >5,000 transcriptionally distinct cell clusters, belonging to ~300 major cell types, across the whole mouse brain with high molecular and spatial resolution. We also applied MERFISH to generate a cell alas of the human cortex by imaging 4,000 genes, revealing the spatial organization of >100 transcriptionally distinct cell population in the human middle and superior temporal gyrus. Our results provide rich insights into the molecular and cellular architecture of the brain and a valuable resource for future functional investigations of neural circuits and their dysfunction in diseases. Our human-mouse comparative analyses further provide insights into the evolution of the cerebral cortex.

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Individual neurodevelopmental, behavioral, or intellectual disorders are rare, but collectively pose significant socioeconomic burden to industrialized countries. In some cases, these disorders take severe forms that are caused by genetic mutations. While many pathogenic mutations have been identified, their impact on normal brain development is not well understood. Studies of animal models have provided us with foundational understanding of mammalian neurodevelopment, and emerging technologies now enable us to extend these studies to humans. For example, high-throughput single cell transcriptomics has begun to systematically define the astonishing diversity of the human cerebral cortex at the molecular level1. However, these classifications are divorced from the developmental processes through which specialized cells emerge. They therefore fail to capture the functional interdependencies between differentiated cells that may become vulnerable to genetic or environmental insults.

Our mission is to advance the understanding of human brain development and its relationship to neurodevelopmental, behavioral, and intellectual disorders through basic science research. Our goal is to create a comprehensive blueprint of normal human brain development that will serve as a foundation for studying the consequences of genetic and environmental perturbations on neurodevelopmental processes.

We will focus on addressing two fundamental questions: 1) How do neural stem cells generate the diversity of cell types in the human cerebral cortex? 2) How do the cellular and molecular processes underlying human neurodevelopment compare and contrast across the brain? Answering these questions will reveal genetic, cellular, and tissue level mechanisms that give rise to the functionally- and anatomically defined brain regions in humans.