Paralysis occurring in amyotrophic lateral sclerosis (ALS) results from denervation of skeletal muscle as a consequence of motor neuron degeneration. Interactions between motor neurons and glia ...contribute to motor neuron loss, but the spatiotemporal ordering of molecular events that drive these processes in intact spinal tissue remains poorly understood. Here, we use spatial transcriptomics to obtain gene expression measurements of mouse spinal cords over the course of disease, as well as of postmortem tissue from ALS patients, to characterize the underlying molecular mechanisms in ALS. We identify pathway dynamics, distinguish regional differences between microglia and astrocyte populations at early time points, and discern perturbations in several transcriptional pathways shared between murine models of ALS and human postmortem spinal cords.
Capture array-based spatial transcriptomics methods have been widely used to resolve gene expression in tissues; however, their spatial resolution is limited by the density of the array. Here we ...present expansion spatial transcriptomics to overcome this limitation by clearing and expanding tissue prior to capturing the entire polyadenylated transcriptome with an enhanced protocol. This approach enables us to achieve higher spatial resolution while retaining high library quality, which we demonstrate using mouse brain samples.
The lung contains numerous specialized cell types with distinct roles in tissue function and integrity. To clarify the origins and mechanisms generating cell heterogeneity, we created a comprehensive ...topographic atlas of early human lung development. Here we report 83 cell states and several spatially resolved developmental trajectories and predict cell interactions within defined tissue niches. We integrated single-cell RNA sequencing and spatially resolved transcriptomics into a web-based, open platform for interactive exploration. We show distinct gene expression programmes, accompanying sequential events of cell differentiation and maturation of the secretory and neuroendocrine cell types in proximal epithelium. We define the origin of airway fibroblasts associated with airway smooth muscle in bronchovascular bundles and describe a trajectory of Schwann cell progenitors to intrinsic parasympathetic neurons controlling bronchoconstriction. Our atlas provides a rich resource for further research and a reference for defining deviations from homeostatic and repair mechanisms leading to pulmonary diseases.
The adult human brain comprises more than a thousand distinct neuronal and glial cell types, a diversity that emerges during early brain development. To reveal the precise sequence of events during ...early brain development, we used single-cell RNA sequencing and spatial transcriptomics and uncovered cell states and trajectories in human brains at 5 to 14 postconceptional weeks (pcw). We identified 12 major classes that are organized as ~600 distinct cell states, which map to precise spatial anatomical domains at 5 pcw. We described detailed differentiation trajectories of the human forebrain and midbrain and found a large number of region-specific glioblasts that mature into distinct pre-astrocytes and pre–oligodendrocyte precursor cells. Our findings reveal the establishment of cell types during the first trimester of human brain development.
INTRODUCTION
The adult human brain is divided into hundreds of spatial domains, each comprising tens or hundreds of distinct neuronal, glial, and other cell types. This complex arrangement of cells is initially established during the first trimester of development, yet the difficulty of accessing such early embryos has hindered detailed molecular analysis. Dissecting the spatial, temporal, and transcriptional changes that occur in the whole brain during the first trimester promises to reveal the fundamental blueprint of the human brain.
RATIONALE
To comprehensively map brain cell types and gene expression trajectories during the first trimester, we collected 26 brain specimens spanning 5 to 14 postconceptional weeks (pcw) that were dissected into 111 distinct biological samples. Each of these samples was subjected to single-cell RNA sequencing, resulting in a collection of 1,665,937 high-quality single-cell transcriptomes. These data were complemented by a spatial transcriptomic analysis at 5 pcw using highly multiplexed RNA fluorescence in situ hybridization (FISH) and spatial transcriptomics. We identified 616 clusters, which we annotated with metadata, including class and subclass, spatial location, embryonic age distribution, and specific gene expression markers.
RESULTS
The detailed resolution of the dataset allowed us to characterize general principles of brain development as well as delineate the differentiation trajectories of several brain regions. The developing excitatory neuron lineages in the neocortex revealed three different ongoing molecular programs: differentiation from radial glia to neurons, cell cycle, and maturation. We found a delicate balance between progenitor and differentiation factors in intermediate progenitor cells (IPCs), with the induction of neurogenic transcription factors visible after the G
1
cell cycle phase. Our findings support a conserved progressive transcriptional maturation in older specimens. Many genes were induced in late radial glia and glioblasts, making up a program that drives progenitors toward neurogenesis as well as gliogenesis. In the forebrain γ-aminobutyric acid–mediated (GABAergic) neuronal lineage, we found evidence of migration of
CRABP
-expressing cells from the medial ganglionic eminence into the thalamus, which are predicted to give rise to thalamic
PVALB
+
neurons in the adult. Examining ventral midbrain development, we found a diverse set of progenitors already arising at 8 pcw, defining broad
TH
class identity, although adult
TH
subtype identities must arise after 14 pcw. Focusing on developing glia, we found a large set of region-specific glioblasts, of which most showed evidence of maturation into astrocytes. This provides a plausible mechanism for the specification of adult region-specific astrocyte types. We further identified oligodendrocyte precursor cells (OPCs) specific to the forebrain, midbrain, and hindbrain that expressed large numbers of functionally conserved genes.
CONCLUSION
Although previous studies have explored specific regions of the brain during development, this is the first known comprehensive study of the whole human brain during the crucial first trimester. We found that although neurons were the most diverse, both pre-astrocytes and OPCs were regionally distinct, and their gene expression suggests region- and cell type–specific supportive functions. These findings highlight the importance of early patterning events and provide a rich resource for the interpretation of the many brain disorders that show region-specific patterns of occurrence or severity and for identifying therapeutic targets for human disorders that affect specific brain cell populations.
Atlas of the developing human brain.
We studied the human brain using single-cell RNA sequencing from 5 to 14 pcw and multiplexed in situ
RNA detection at 5 pcw. Our findings reveal how early patterning events establish the organization of the future brain and how maturation and differentiation trajectories are superimposed on this basic plan to generate the extraordinary complexity of the adult nervous system.
Spatially resolved transcriptomics has enabled precise genome-wide mRNA expression profiling within tissue sections. The performance of methods targeting the polyA tails of mRNA relies on the ...availability of specimens with high RNA quality. Moreover, the high cost of currently available spatial resolved transcriptomics assays requires a careful sample screening process to increase the chance of obtaining high-quality data. Indeed, the upfront analysis of RNA quality can show considerable variability due to sample handling, storage, and/or intrinsic factors. We present RNA-Rescue Spatial Transcriptomics (RRST), a workflow designed to improve mRNA recovery from fresh frozen specimens with moderate to low RNA quality. First, we provide a benchmark of RRST against the standard Visium spatial gene expression protocol on high RNA quality samples represented by mouse brain and prostate cancer samples. Then, we test the RRST protocol on tissue sections collected from five challenging tissue types, including human lung, colon, small intestine, pediatric brain tumor, and mouse bone/cartilage. In total, we analyze 52 tissue sections and demonstrate that RRST is a versatile, powerful, and reproducible protocol for fresh frozen specimens of different qualities and origins.
Abstract Impairment of the central nervous system (CNS) poses a significant health risk for astronauts during long-duration space missions. In this study, we employed an innovative approach by ...integrating single-cell multiomics (transcriptomics and chromatin accessibility) with spatial transcriptomics to elucidate the impact of spaceflight on the mouse brain in female mice. Our comparative analysis between ground control and spaceflight-exposed animals revealed significant alterations in essential brain processes including neurogenesis, synaptogenesis and synaptic transmission, particularly affecting the cortex, hippocampus, striatum and neuroendocrine structures. Additionally, we observed astrocyte activation and signs of immune dysfunction. At the pathway level, some spaceflight-induced changes in the brain exhibit similarities with neurodegenerative disorders, marked by oxidative stress and protein misfolding. Our integrated spatial multiomics approach serves as a stepping stone towards understanding spaceflight-induced CNS impairments at the level of individual brain regions and cell types, and provides a basis for comparison in future spaceflight studies. For broader scientific impact, all datasets from this study are available through an interactive data portal, as well as the National Aeronautics and Space Administration (NASA) Open Science Data Repository (OSDR).
Alzheimer disease (AD) is a devastating neurological disease associated with progressive loss of mental skills and cognitive and physical functions whose etiology is not completely understood. Here, ...our goal was to simultaneously uncover novel and known molecular targets in the structured layers of the hippocampus and olfactory bulbs that may contribute to early hippocampal synaptic deficits and olfactory dysfunction in AD mice. Spatially resolved transcriptomics was used to identify high-confidence genes that were differentially regulated in AD mice relative to controls. A diverse set of genes that modulate stress responses and transcription were predominant in both hippocampi and olfactory bulbs. Notably, we identify Bok, implicated in mitochondrial physiology and cell death, as a spatially downregulated gene in the hippocampus of mouse and human AD brains. In summary, we provide a rich resource of spatially differentially expressed genes, which may contribute to understanding AD pathology.
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•Spatial transcriptomics identifies differentially expressed genes with spatial patterns•Early application of spatial transcriptomics to olfactory bulbs from AD models•Bok gene is spatially differentially expressed in AD mouse and patient brains•Paip1 and Homer1 genes are regulated in a PolB-dependent manner
Cellular Neuroscience; Omics; Transcriptomics
Spatially resolved transcriptomics methodologies using RNA sequencing principles have and will continue to contribute to decode the molecular landscape of tissues. Linking quantitative sequencing ...data with tissue morphology empowers profiling of cellular morphology and transcription over time and space in health and disease. To view this SnapShot, open or download the PDF.
Spatially resolved transcriptomics methodologies using RNA sequencing principles have and will continue to contribute to decode the molecular landscape of tissues. Linking quantitative sequencing data with tissue morphology empowers profiling of cellular morphology and transcription over time and space in health and disease. To view this SnapShot, open or download the PDF.
Spatially resolved transcriptomics methodologies using RNA sequencing principles have and will continue to contribute to decode the molecular landscape of tissues. Linking quantitative sequencing ...data with tissue morphology empowers profiling of cellular morphology and transcription over time and space in health and disease. To view this SnapShot, open or download the PDF.
Angiotensin-converting enzyme 2 (ACE2) and accessory proteases (TMPRSS2 and CTSL) are needed for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cellular entry, and their expression may ...shed light on viral tropism and impact across the body. We assessed the cell-type-specific expression of ACE2, TMPRSS2 and CTSL across 107 single-cell RNA-sequencing studies from different tissues. ACE2, TMPRSS2 and CTSL are coexpressed in specific subsets of respiratory epithelial cells in the nasal passages, airways and alveoli, and in cells from other organs associated with coronavirus disease 2019 (COVID-19) transmission or pathology. We performed a meta-analysis of 31 lung single-cell RNA-sequencing studies with 1,320,896 cells from 377 nasal, airway and lung parenchyma samples from 228 individuals. This revealed cell-type-specific associations of age, sex and smoking with expression levels of ACE2, TMPRSS2 and CTSL. Expression of entry factors increased with age and in males, including in airway secretory cells and alveolar type 2 cells. Expression programs shared by ACE2
TMPRSS2
cells in nasal, lung and gut tissues included genes that may mediate viral entry, key immune functions and epithelial-macrophage cross-talk, such as genes involved in the interleukin-6, interleukin-1, tumor necrosis factor and complement pathways. Cell-type-specific expression patterns may contribute to the pathogenesis of COVID-19, and our work highlights putative molecular pathways for therapeutic intervention.
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