Cell Identity Determination in Human Brain: Somatic Mutation and Cell Lineage

Boston Children'S Hospital, Boston MA

Investigators

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Abstract

Project Summary Deciphering the cell lineage of the human brain is vital for understanding the expansion of brain size and cognitive capabilities in humans and for elucidating the causes of, and finding treatments for, a growing number of human neurological disorders. Somatic mutations are the drivers of brain cancer and are the most common cause of intractable pediatric epilepsy resulting in brain surgery. They have also been implicated in adult temporal lobe epilepsy, autism spectrum disorders, and schizophrenia, and may contribute to neurodegeneration. Work from our lab and others have shown that somatic mutations occurring during fetal development represent clonal marks that can be used to trace the lineage of the cells. Each cell division is associated with ≈2-4 somatic single nucleotide variants, so that every brain cell carries a unique DNA “barcode” that can be exploited to reconstruct lineage relationships between cell types. Recent technical developments in single-cell RNA sequencing allow analysis of cell types in postmortem human brain at a level of detail previously thought impossible, allowing description of the many transcriptional patterns that characterize distinct neuronal and glial cell types in human brain. The proposed experiments will integrate DNA lineage marks with RNA analysis of cell types, and describe additional new methods that can outline the major features of clonal dynamics that generate neuronal and glial types in human brain and clonal dispersion that underlies the architecture of the functional subdivision of the human cerebral cortex. Our research will advance three specific aims: Lineage Analysis of Neurons: We will investigate the late divergence of excitatory and inhibitory neuron lineages in the human frontal lobe, using deep whole genome sequencing (WGS) of sorted neuronal populations. By understanding these lineages, we hope to clarify how distinct neuronal types emerge and interconnect, which is critical for grasping the functional organization of the brain. Oligodendrocyte Lineage Dynamics: Oligodendrocytes exhibit unique mutational patterns. We will analyze their lineage and proliferation through WGS and single-cell RNA sequencing. This aim seeks to reveal how oligodendrocyte precursor cells (OPCs) contribute to brain health and disease. High-Throughput cell type-specific lineage and aging: Utilizing the innovative Duplex Multiome technology, we will explore the accumulation of age-related somatic mutations across different cell types. This approach will enable us to identify patterns of mutation and lineage in a single experiment. These data provide three major discoveries not obtainable by any other means: 1] direct cell lineage data from the adult human brain, which is essential for understanding how our brain develops and how developmental somatic mutations cause disease, 2] preliminary lineage maps connecting neuronal and glial cell classes, and 3] cell type-informed understanding of the age-related process of mutation accumulation.