Spatial and single-cell transcriptional landscape of human cerebellar development

ABSTRACTCerebellar development and function require precise regulation of molecular and cellular programs to coordinate motor functions and integrate network signals required for cognition and emotional regulation. However, molecular understanding of human cerebellar development is limited. Here, we combined spatially resolved and single-cell transcriptomics to systematically map the molecular, cellular, and spatial composition of early and mid-gestational human cerebellum. This enabled us to transcriptionally profile major cell types and examine the dynamics of gene expression within cell types and lineages across development. The resulting ‘Developmental Cell Atlas of the Human Cerebellum’ demonstrates that the molecular organization of the cerebellar anlage reflects cytoarchitecturally distinct regions and developmentally transient cell types that are insufficiently captured in bulk transcriptional profiles. By mapping disease genes onto cell types, we implicate the dysregulation of specific cerebellar cell types, especially Purkinje cells, in pediatric and adult neurological disorders. These data provide a critical resource for understanding human cerebellar development with implications for the cellular basis of cerebellar diseases.

Download Full-text

Cell Atlas technologies and insights into tissue architecture

Biochemical Journal ◽

10.1042/bcj20190341 ◽

2020 ◽

Vol 477 (8) ◽

pp. 1427-1442 ◽

Cited By ~ 4

Author(s):

Anna Wilbrey-Clark ◽

Kenny Roberts ◽

Sarah A. Teichmann

Keyword(s):

Single Cell ◽

Molecular Level ◽

Cell Types ◽

Tissue Architecture ◽

Robert Hooke ◽

Spatially Resolved ◽

Gene And Protein Expression ◽

Basic Biology ◽

And Function ◽

Fundamental Units

Since Robert Hooke first described the existence of ‘cells’ in 1665, scientists have sought to identify and further characterise these fundamental units of life. While our understanding of cell location, morphology and function has expanded greatly; our understanding of cell types and states at the molecular level, and how these function within tissue architecture, is still limited. A greater understanding of our cells could revolutionise basic biology and medicine. Atlasing initiatives like the Human Cell Atlas aim to identify all cell types at the molecular level, including their physical locations, and to make this reference data openly available to the scientific community. This is made possible by a recent technology revolution: both in single-cell molecular profiling, particularly single-cell RNA sequencing, and in spatially resolved methods for assessing gene and protein expression. Here, we review available and upcoming atlasing technologies, the biological insights gained to date and the promise of this field for the future.

Download Full-text

Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region

Science ◽

10.1126/science.aau5324 ◽

2018 ◽

Vol 362 (6416) ◽

pp. eaau5324 ◽

Cited By ~ 213

Author(s):

Jeffrey R. Moffitt ◽

Dhananjay Bambah-Mukku ◽

Stephen W. Eichhorn ◽

Eric Vaughn ◽

Karthik Shekhar ◽

...

Keyword(s):

Single Cell ◽

Spatial Organization ◽

Social Behaviors ◽

Cell Types ◽

Mapping Method ◽

Preoptic Region ◽

Neuronal Populations ◽

Spatially Resolved ◽

Mechanistic Investigation ◽

And Function

The hypothalamus controls essential social behaviors and homeostatic functions. However, the cellular architecture of hypothalamic nuclei—including the molecular identity, spatial organization, and function of distinct cell types—is poorly understood. Here, we developed an imaging-based in situ cell-type identification and mapping method and combined it with single-cell RNA-sequencing to create a molecularly annotated and spatially resolved cell atlas of the mouse hypothalamic preoptic region. We profiled ~1 million cells, identified ~70 neuronal populations characterized by distinct neuromodulatory signatures and spatial organizations, and defined specific neuronal populations activated during social behaviors in male and female mice, providing a high-resolution framework for mechanistic investigation of behavior circuits. The approach described opens a new avenue for the construction of cell atlases in diverse tissues and organisms.

Download Full-text

Single-cell transcriptomic analysis of mIHC images via antigen mapping

Science Advances ◽

10.1126/sciadv.abc5464 ◽

2021 ◽

Vol 7 (10) ◽

pp. eabc5464

Author(s):

Kiya W. Govek ◽

Emma C. Troisi ◽

Zhen Miao ◽

Rachael G. Aubin ◽

Steven Woodhouse ◽

...

Keyword(s):

Single Cell ◽

Spatial Patterns ◽

Cell Types ◽

Level Of Detail ◽

Cell Populations ◽

Sequencing Data ◽

Spatially Resolved ◽

Murine Spleen ◽

Single Cell Rna Sequencing ◽

Antibody Panel

Highly multiplexed immunohistochemistry (mIHC) enables the staining and quantification of dozens of antigens in a tissue section with single-cell resolution. However, annotating cell populations that differ little in the profiled antigens or for which the antibody panel does not include specific markers is challenging. To overcome this obstacle, we have developed an approach for enriching mIHC images with single-cell RNA sequencing data, building upon recent experimental procedures for augmenting single-cell transcriptomes with concurrent antigen measurements. Spatially-resolved Transcriptomics via Epitope Anchoring (STvEA) performs transcriptome-guided annotation of highly multiplexed cytometry datasets. It increases the level of detail in histological analyses by enabling the systematic annotation of nuanced cell populations, spatial patterns of transcription, and interactions between cell types. We demonstrate the utility of STvEA by uncovering the architecture of poorly characterized cell types in the murine spleen using published cytometry and mIHC data of this organ.

Download Full-text

Single cell analysis reveals immune cell–adipocyte crosstalk regulating the transcription of thermogenic adipocytes

eLife ◽

10.7554/elife.49501 ◽

2019 ◽

Vol 8 ◽

Cited By ~ 17

Author(s):

Prashant Rajbhandari ◽

Douglas Arneson ◽

Sydney K Hart ◽

In Sook Ahn ◽

Graciel Diamante ◽

...

Keyword(s):

Single Cell ◽

Immune Cells ◽

Immune Cell ◽

Single Cell Analysis ◽

Metabolic Response ◽

Cell Types ◽

Specific Cell ◽

Beneficial Effects ◽

Thermogenic Adipocytes ◽

And Function

Immune cells are vital constituents of the adipose microenvironment that influence both local and systemic lipid metabolism. Mice lacking IL10 have enhanced thermogenesis, but the roles of specific cell types in the metabolic response to IL10 remain to be defined. We demonstrate here that selective loss of IL10 receptor α in adipocytes recapitulates the beneficial effects of global IL10 deletion, and that local crosstalk between IL10-producing immune cells and adipocytes is a determinant of thermogenesis and systemic energy balance. Single Nuclei Adipocyte RNA-sequencing (SNAP-seq) of subcutaneous adipose tissue defined a metabolically-active mature adipocyte subtype characterized by robust expression of genes involved in thermogenesis whose transcriptome was selectively responsive to IL10Rα deletion. Furthermore, single-cell transcriptomic analysis of adipose stromal populations identified lymphocytes as a key source of IL10 production in response to thermogenic stimuli. These findings implicate adaptive immune cell-adipocyte communication in the maintenance of adipose subtype identity and function.

Download Full-text

A harmonized atlas of mouse spinal cord cell types and their spatial organization

Nature Communications ◽

10.1038/s41467-021-25125-1 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Daniel E. Russ ◽

Ryan B. Patterson Cross ◽

Li Li ◽

Stephanie C. Koch ◽

Kaya J. E. Matson ◽

...

Keyword(s):

Spinal Cord ◽

Single Cell ◽

Spatial Organization ◽

Neuronal Cell ◽

Cell Types ◽

Molecular Organization ◽

Cell Type ◽

Sequencing Data ◽

Mouse Spinal Cord ◽

Common Reference

AbstractSingle-cell RNA sequencing data can unveil the molecular diversity of cell types. Cell type atlases of the mouse spinal cord have been published in recent years but have not been integrated together. Here, we generate an atlas of spinal cell types based on single-cell transcriptomic data, unifying the available datasets into a common reference framework. We report a hierarchical structure of postnatal cell type relationships, with location providing the highest level of organization, then neurotransmitter status, family, and finally, dozens of refined populations. We validate a combinatorial marker code for each neuronal cell type and map their spatial distributions in the adult spinal cord. We also show complex lineage relationships among postnatal cell types. Additionally, we develop an open-source cell type classifier, SeqSeek, to facilitate the standardization of cell type identification. This work provides an integrated view of spinal cell types, their gene expression signatures, and their molecular organization.

Download Full-text

A multimodal cell census and atlas of the mammalian primary motor cortex

10.1101/2020.10.19.343129 ◽

2020 ◽

Cited By ~ 5

Author(s):

◽

Ricky S. Adkins ◽

Andrew I. Aldridge ◽

Shona Allen ◽

Seth A. Ament ◽

...

Keyword(s):

Motor Cortex ◽

Single Cell ◽

Primary Motor Cortex ◽

Spatial Information ◽

Molecular Genetic ◽

Cell Types ◽

Developmental Trajectory ◽

Open Chromatin ◽

Cell Type ◽

Spatially Resolved

ABSTRACTWe report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex (MOp or M1) as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties, and cellular resolution input-output mapping, integrated through cross-modal computational analysis. Together, our results advance the collective knowledge and understanding of brain cell type organization: First, our study reveals a unified molecular genetic landscape of cortical cell types that congruently integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a unified taxonomy of transcriptomic types and their hierarchical organization that are conserved from mouse to marmoset and human. Third, cross-modal analysis provides compelling evidence for the epigenomic, transcriptomic, and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types and subtypes. Fourth, in situ single-cell transcriptomics provides a spatially-resolved cell type atlas of the motor cortex. Fifth, integrated transcriptomic, epigenomic and anatomical analyses reveal the correspondence between neural circuits and transcriptomic cell types. We further present an extensive genetic toolset for targeting and fate mapping glutamatergic projection neuron types toward linking their developmental trajectory to their circuit function. Together, our results establish a unified and mechanistic framework of neuronal cell type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties.

Download Full-text

High Resolution Single Cell Maps Reveals Distinct Cell Organization and Function Across Different Regions of the Human Intestine

10.1101/2021.11.25.469203 ◽

2021 ◽

Author(s):

John W Hickey ◽

Winston R Becker ◽

Stephanie A Nevins ◽

Aaron M Horning ◽

Almudena Espin Perez ◽

...

Keyword(s):

Single Cell ◽

Immune Surveillance ◽

Cell Types ◽

Open Chromatin ◽

Specific Cell ◽

Symbiotic Relationships ◽

Distinct Cell ◽

Cell Organization ◽

Reference Map ◽

And Function

The colon is a complex organ that promotes digestion, extracts nutrients, participates in immune surveillance, maintains critical symbiotic relationships with microbiota, and affects overall health. To better understand its organization, functions, and its regulation at a single cell level, we performed CODEX multiplexed imaging, as well as single nuclear RNA and open chromatin assays across eight different intestinal sites of four donors. Through systematic analyses we find cell compositions differ dramatically across regions of the intestine, demonstrate the complexity of epithelial subtypes, and find that the same cell types are organized into distinct neighborhoods and communities highlighting distinct immunological niches present in the intestine. We also map gene regulatory differences in these cells suggestive of a regulatory differentiation cascade, and associate intestinal disease heritability with specific cell types. These results describe the complexity of the cell composition, regulation, and organization for this organ, and serve as an important reference map for understanding human biology and disease.

Download Full-text

Combined single-cell and spatial transcriptomics reveals the molecular, cellular and spatial bone marrow niche organization

10.1101/718395 ◽

2019 ◽

Cited By ~ 2

Author(s):

Chiara Baccin ◽

Jude Al-Sabah ◽

Lars Velten ◽

Patrick M. Helbling ◽

Florian Grünschläger ◽

...

Keyword(s):

Bone Marrow ◽

Single Cell ◽

Spatial Organization ◽

Cell Types ◽

Bone Marrow Niche ◽

Cellular Composition ◽

Spatially Resolved ◽

Resident Cell ◽

Cell Gene Expression ◽

Novel Strategy

SUMMARYThe bone marrow (BM) constitutes the primary site for life-long blood production and skeletal regeneration. However, its cellular composition and the spatial organization into distinct ‘niches’ remains controversial. Here, we combine single-cell and spatially resolved transcriptomics to systematically map the molecular and cellular composition of the endosteal, sinusoidal, and arteriolar BM niches. This allowed us to transcriptionally profile all major BM resident cell types, determine their localization, and clarify the cellular and spatial sources of key growth factors and cytokines. Our data demonstrate that previously unrecognized Cxcl12-abundant reticular (CAR) cell subsets (i.e. Adipo- and Osteo-CAR cells) differentially localize to sinusoidal or arteriolar surfaces, locally act as ‘professional cytokine secreting cells’, and thereby establish distinct peri-vascular micro-niches. Importantly, we also demonstrate that the 3-dimensional organization of the BM can be accurately inferred from single-cell gene expression data using the newly developed RNA-Magnet algorithm. Together, our study reveals the cellular and spatial organization of BM niches, and offers a novel strategy to dissect the complex organization of whole organs in a systematic manner.One Sentence SummaryIntegration of single-cell and spatial transcriptomics reveals the molecular, cellular and spatial organization of bone marrow niches

Download Full-text

The spatio-temporal landscape of lung pathology in SARS-CoV-2 infection

10.1101/2020.10.26.20219584 ◽

2020 ◽

Author(s):

André Figueiredo Rendeiro ◽

Hiranmayi Ravichandran ◽

Yaron Bram ◽

Steven Salvatore ◽

Alain Borczuk ◽

...

Keyword(s):

Single Cell ◽

Cell Types ◽

Alveolar Epithelial Cells ◽

Lung Damage ◽

Lung Pathology ◽

Alveolar Epithelial ◽

Spatially Resolved ◽

Injured Lung ◽

Spatio Temporal ◽

Cell Data

SummaryRecent studies have provided insights into the pathology and immune response to coronavirus disease 2019 (COVID-19)1–8. However thorough interrogation of the interplay between infected cells and the immune system at sites of infection is lacking. We use high parameter imaging mass cytometry9 targeting the expression of 36 proteins, to investigate at single cell resolution, the cellular composition and spatial architecture of human acute lung injury including SARS-CoV-2. This spatially resolved, single-cell data unravels the disordered structure of the infected and injured lung alongside the distribution of extensive immune infiltration. Neutrophil and macrophage infiltration are hallmarks of bacterial pneumonia and COVID-19, respectively. We provide evidence that SARS-CoV-2 infects predominantly alveolar epithelial cells and induces a localized hyper-inflammatory cell state associated with lung damage. By leveraging the temporal range of COVID-19 severe fatal disease in relation to the time of symptom onset, we observe increased macrophage extravasation, mesenchymal cells, and fibroblasts abundance concomitant with increased proximity between these cell types as the disease progresses, possibly as an attempt to repair the damaged lung tissue. This spatially resolved single-cell data allowed us to develop a biologically interpretable landscape of lung pathology from a structural, immunological and clinical standpoint. This spatial single-cell landscape enabled the pathophysiological characterization of the human lung from its macroscopic presentation to the single-cell, providing an important basis for the understanding of COVID-19, and lung pathology in general.

Download Full-text

Metabolic Imaging at the Single-Cell Scale: Recent Advances in Mass Spectrometry Imaging

Annual Review of Analytical Chemistry ◽

10.1146/annurev-anchem-061318-115516 ◽

2019 ◽

Vol 12 (1) ◽

pp. 201-224 ◽

Cited By ~ 43

Author(s):

Ian S. Gilmore ◽

Sven Heiles ◽

Cornelius L. Pieterse

Keyword(s):

Mass Spectrometry ◽

Single Cell ◽

Mass Spectrometry Imaging ◽

Secondary Ion Mass Spectrometry ◽

Cell Types ◽

Metabolic Imaging ◽

Spatially Resolved ◽

Recent Advances ◽

Challenges And Opportunities ◽

Future Challenges

There is an increasing appreciation that every cell, even of the same type, is different. This complexity, when additionally combined with the variety of different cell types in tissue, is driving the need for spatially resolved omics at the single-cell scale. Rapid advances are being made in genomics and transcriptomics, but progress in metabolomics lags. This is partly because amplification and tagging strategies are not suited to dynamically created metabolite molecules. Mass spectrometry imaging has excellent potential for metabolic imaging. This review summarizes the recent advances in two of these techniques: matrix-assisted laser desorption ionization (MALDI) and secondary ion mass spectrometry (SIMS) and their convergence in subcellular spatial resolution and molecular information. The barriers that have held back progress such as lack of sensitivity and the breakthroughs that have been made including laser-postionization are highlighted as well as the future challenges and opportunities for metabolic imaging at the single-cell scale.

Download Full-text