A cellular and spatial map of the choroid plexus across brain ventricles and ages

AbstractThe choroid plexus (ChP), located in each brain ventricle, produces cerebrospinal fluid (CSF) and forms the blood-CSF barrier, but is under-characterized. Here, we combine single cell RNA-Seq and spatial mapping of RNA and proteins to construct an atlas of each ChP in the developing and adult mouse brain. Each ChP comprises of epithelial, endothelial, mesenchymal, immune, neuronal, and glial cells, with distinct subtypes, differentiation states and anatomical locations. Epithelial, fibroblast, and macrophage populations had ventricle-specific, regionalized gene expression programs across the developing brain. Key cell types are retained in adult, with loss of developmental signatures and maturation of ventricle-specific regionalization in the epithelial cells. Expression of cognate ligand-receptor pairs across cell subtypes suggests substantial cell-cell interactions within the ChP. Our atlas sheds new light on the development and function of the ChP brain barrier system, and will facilitate future studies on its role in brain development, homeostasis and disease.

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Plasma IL-6 levels following corticosteroid therapy as an indicator of ICU length of stay in critically ill COVID-19 patients

Cell Death Discovery ◽

10.1038/s41420-021-00429-9 ◽

2021 ◽

Vol 7 (1) ◽

Author(s):

Samir Awasthi ◽

Tyler Wagner ◽

A. J. Venkatakrishnan ◽

Arjun Puranik ◽

Matthew Hurchik ◽

...

Keyword(s):

Distress Syndrome ◽

Cell Types ◽

Specific Cell ◽

Cytokine Release ◽

Cytokine Release Syndrome ◽

Rna Seq ◽

Future Studies ◽

Icu Length Of Stay ◽

Potential Association ◽

Clinical Trial Results

AbstractIntensive care unit (ICU) admissions and mortality in severe COVID-19 patients are driven by “cytokine storms” and acute respiratory distress syndrome (ARDS). Interim clinical trial results suggest that the corticosteroid dexamethasone displays better 28-day survival in severe COVID-19 patients requiring ventilation or oxygen. In this study, 10 out of 16 patients (62.5%) that had an average plasma IL-6 value over 10 pg/mL post administration of corticosteroids also had worse outcomes (i.e., ICU stay >15 days or death), compared to 8 out of 41 patients (19.5%) who did not receive corticosteroids (p-value = 0.0024). Given this potential association between post-corticosteroid IL-6 levels and COVID-19 severity, we hypothesized that the glucocorticoid receptor (GR or NR3C1) may be coupled to IL-6 expression in specific cell types that govern cytokine release syndrome (CRS). Examining single-cell RNA-seq data from BALF of severe COVID-19 patients and nearly 2 million cells from a pan-tissue scan shows that alveolar macrophages, smooth muscle cells, and endothelial cells co-express NR3C1 and IL-6, motivating future studies on the links between the regulation of NR3C1 function and IL-6 levels.

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Characterization of rare spindle and root cell transcriptional profiles in the stria vascularis of the adult mouse cochlea

Scientific Reports ◽

10.1038/s41598-020-75238-8 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Shoujun Gu ◽

Rafal Olszewski ◽

Ian Taukulis ◽

Zheng Wei ◽

Daniel Martin ◽

...

Keyword(s):

Hearing Loss ◽

Gene Regulatory Networks ◽

Regulatory Networks ◽

Adult Mouse ◽

Stria Vascularis ◽

Cell Types ◽

Rna Seq ◽

Root Cells ◽

Transcriptional Profiles ◽

Gene Regulatory

Abstract The stria vascularis (SV) in the cochlea generates and maintains the endocochlear potential, thereby playing a pivotal role in normal hearing. Knowing transcriptional profiles and gene regulatory networks of SV cell types establishes a basis for studying the mechanism underlying SV-related hearing loss. While we have previously characterized the expression profiles of major SV cell types in the adult mouse, transcriptional profiles of rare SV cell types remained elusive due to the limitation of cell capture in single-cell RNA-Seq. The role of these rare cell types in the homeostatic function of the adult SV remain largely undefined. In this study, we performed single-nucleus RNA-Seq on the adult mouse SV in conjunction with sample preservation treatments during the isolation steps. We distinguish rare SV cell types, including spindle cells and root cells, from other cell types, and characterize their transcriptional profiles. Furthermore, we also identify and validate novel specific markers for these rare SV cell types. Finally, we identify homeostatic gene regulatory networks within spindle and root cells, establishing a basis for understanding the functional roles of these cells in hearing. These novel findings will provide new insights for future work in SV-related hearing loss and hearing fluctuation.

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Expression of the Na+/K+-ATPase Subunits in Adult Mouse Brain Analyzed by Single-Cell RNA-Seq Profiling

Biophysical Journal ◽

10.1016/j.bpj.2018.11.716 ◽

2019 ◽

Vol 116 (3) ◽

pp. 129a

Author(s):

Song Jiao ◽

Cristina Moreno Vadillo ◽

Miguel Holmgren

Keyword(s):

Single Cell ◽

Mouse Brain ◽

Adult Mouse ◽

Rna Seq ◽

Adult Mouse Brain ◽

Atpase Subunits

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Astrocytes: News about Brain Health and Diseases

Biomedicines ◽

10.3390/biomedicines8100394 ◽

2020 ◽

Vol 8 (10) ◽

pp. 394

Author(s):

Jacopo Meldolesi

Keyword(s):

Glial Cells ◽

Present State ◽

Cell Types ◽

Present Review ◽

Brain Health ◽

Traumatic Injuries ◽

Future Studies ◽

Brain Physiology ◽

And Function

Astrocytes, the most numerous glial cells in the brains of humans and other mammalian animals, have been studied since their discovery over 100 years ago. For many decades, however, astrocytes were believed to operate as a glue, providing only mechanical and metabolic support to adjacent neurons. Starting from a “revolution” initiated about 25 years ago, numerous astrocyte functions have been reconsidered, some previously unknown, others attributed to neurons or other cell types. The knowledge of astrocytes has been continuously growing during the last few years. Based on these considerations, in the present review, different from single or general overviews, focused on six astrocyte functions, chosen due in their relevance in both brain physiology and pathology. Astrocytes, previously believed to be homogeneous, are now recognized to be heterogeneous, composed by types distinct in structure, distribution, and function; their cooperation with microglia is known to govern local neuroinflammation and brain restoration upon traumatic injuries; and astrocyte senescence is relevant for the development of both health and diseases. Knowledge regarding the role of astrocytes in tauopathies and Alzheimer’s disease has grow considerably. The multiple properties emphasized here, relevant for the present state of astrocytes, will be further developed by ongoing and future studies.

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MiR&moRe2: A Bioinformatics Tool to Characterize microRNAs and microRNA-Offset RNAs from Small RNA-Seq Data

International Journal of Molecular Sciences ◽

10.3390/ijms21051754 ◽

2020 ◽

Vol 21 (5) ◽

pp. 1754 ◽

Cited By ~ 3

Author(s):

Enrico Gaffo ◽

Michele Bortolomeazzi ◽

Andrea Bisognin ◽

Piero Di Battista ◽

Federica Lovisa ◽

...

Keyword(s):

Small Rna ◽

Small Rnas ◽

Cell Types ◽

Small Rna Sequencing ◽

Rna Seq ◽

Sequencing Data ◽

Research Findings ◽

Human Blood Cell ◽

And Function ◽

Comprehensive Study

MicroRNA-offset RNAs (moRNAs) are microRNA-like small RNAs generated by microRNA precursors. To date, little is known about moRNAs and bioinformatics tools to inspect their expression are still missing. We developed miR&moRe2, the first bioinformatics method to consistently characterize microRNAs, moRNAs, and their isoforms from small RNA sequencing data. To illustrate miR&moRe2 discovery power, we applied it to several published datasets. MoRNAs identified by miR&moRe2 were in agreement with previous research findings. Moreover, we observed that moRNAs and new microRNAs predicted by miR&moRe2 were downregulated upon the silencing of the microRNA-biogenesis pathway. Further, in a sizeable dataset of human blood cell populations, tens of novel miRNAs and moRNAs were discovered, some of them with significantly varied expression levels among the cell types. Results demonstrate that miR&moRe2 is a valid tool for a comprehensive study of small RNAs generated from microRNA precursors and could help to investigate their biogenesis and function.

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Beyond “Big Eaters”: The Versatile Role of Alveolar Macrophages in Health and Disease

International Journal of Molecular Sciences ◽

10.3390/ijms22073308 ◽

2021 ◽

Vol 22 (7) ◽

pp. 3308

Author(s):

Miriam Hetzel ◽

Mania Ackermann ◽

Nico Lachmann

Keyword(s):

Alveolar Macrophages ◽

Cell Types ◽

Multiple Roles ◽

Pulmonary Diseases ◽

Congenital Diseases ◽

Organ Specific ◽

Macrophage Dysfunction ◽

Macrophage Populations ◽

And Function

Macrophages act as immune scavengers and are important cell types in the homeostasis of various tissues. Given the multiple roles of macrophages, these cells can also be found as tissue resident macrophages tightly integrated into a variety of tissues in which they fulfill crucial and organ-specific functions. The lung harbors at least two macrophage populations: interstitial and alveolar macrophages, which occupy different niches and functions. In this review, we provide the latest insights into the multiple roles of alveolar macrophages while unraveling the distinct factors which can influence the ontogeny and function of these cells. Furthermore, we will highlight pulmonary diseases, which are associated with dysfunctional macrophages, concentrating on congenital diseases as well as pulmonary infections and impairment of immunological pathways. Moreover, we will provide an overview about different treatment approaches targeting macrophage dysfunction. Improved knowledge of the role of macrophages in the onset of pulmonary diseases may provide the basis for new pharmacological and/or cell-based immunotherapies and will extend our understanding to other macrophage-related disorders.

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Whole Animal Multiplexed Single-Cell RNA-Seq Reveals Plasticity of Clytia Medusa Cell Types

10.1101/2021.01.22.427844 ◽

2021 ◽

Author(s):

Tara Chari ◽

Brandon Weissbourd ◽

Jase Gehring ◽

Anna Ferraioli ◽

Lucas Leclère ◽

...

Keyword(s):

High Resolution ◽

Single Cell ◽

Cell Types ◽

Model Organisms ◽

Traditional Model ◽

Rna Seq ◽

Batch Effects ◽

Future Studies ◽

Component Cell ◽

Jellyfish Species

AbstractWe present an organism-wide, transcriptomic cell atlas of the hydrozoan medusa Clytia hemisphaerica, and determine how its component cell types respond to starvation. Utilizing multiplexed scRNA-seq, in which individual animals were indexed and pooled from control and perturbation conditions into a single sequencing run, we avoid artifacts from batch effects and are able to discern shifts in cell state in response to organismal perturbations. This work serves as a foundation for future studies of development, function, and plasticity in a genetically tractable jellyfish species. Moreover, we introduce a powerful workflow for high-resolution, whole animal, multiplexed single-cell genomics (WHAM-seq) that is readily adaptable to other traditional or non-traditional model organisms.

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Cross-species Transcriptomic Comparison of In Vitro and In Vivo Mammalian Neural Cells

Bioinformatics and Biology Insights ◽

10.4137/bbi.s33124 ◽

2015 ◽

Vol 9 ◽

pp. BBI.S33124 ◽

Cited By ~ 5

Author(s):

Peter R. LoVerso ◽

Christopher M. Wachter ◽

Feng Cui

Keyword(s):

Gene Expression ◽

Transcript Abundance ◽

Cell Types ◽

Mammalian Brain ◽

Neural Cells ◽

Rna Seq ◽

Commercial Sources ◽

And Function

The mammalian brain is characterized by distinct classes of cells that differ in morphology, structure, signaling, and function. Dysregulation of gene expression in these cell populations leads to various neurological disorders. Neural cells often need to be acutely purified from animal brains for research, which requires complicated procedure and specific expertise. Primary culture of these cells in vitro is a viable alternative, but the differences in gene expression of cells grown in vitro and in vivo remain unclear. Here, we cultured three major neural cell classes of rat brain (ie, neurons, astrocytes, and oligodendrocyte precursor cells [OPCs]) obtained from commercial sources. We measured transcript abundance of these cell types by RNA sequencing (RNA-seq) and compared with their counterparts acutely purified from mouse brains. Cross-species RNA-seq data analysis revealed hundreds of genes that are differentially expressed between the cultured and acutely purified cells. Astrocytes have more such genes compared to neurons and OPCs, indicating that signaling pathways are greatly perturbed in cultured astrocytes. This dataset provides a powerful resource to demonstrate the similarities and differences of biological processes in mammalian neural cells grown in vitro and in vivo at the molecular level.

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Time- and Stimulus-Dependent Characteristics of Innate Immune Cells in Organ-Cultured Human Corneal Tissue

Journal of Innate Immunity ◽

10.1159/000516669 ◽

2021 ◽

pp. 1-14

Author(s):

Xinyu Zhuang ◽

Günther Schlunck ◽

Julian Wolf ◽

Dennis-Dominik Rosmus ◽

Tim Bleul ◽

...

Keyword(s):

Organ Culture ◽

Immune Cells ◽

Immune Cell ◽

Cell Types ◽

Corneal Tissue ◽

M2 Macrophages ◽

Rna Seq ◽

Culture Time ◽

Macrophage Populations ◽

Macrophage Subtypes

Purpose: The pattern of immune cells infiltrating the corneal stroma has been extensively studied in mice, but data on human tissue have been far less elaborate. To further characterize the number and differentiation state of resident immune cells in organ-cultured human corneal tissue, we employed a comprehensive bioinformatic deconvolution (xCell) of bulk RNA-sequencing (RNA-seq) data, immunohistochemistry (IHC), and flow cytometry (FC). Methods: A transcriptome-based analysis of immune cell types in human corneal samples was performed. The results were validated by IHC, focusing on the identification of pro-inflammatory (M1) and regulatory (M2) macrophages. A protocol was established to identify these 2 different macrophage populations in human corneal tissue by means of FC. Subsequently, corneal samples in organ culture were differentially stimulated by IL-10, IL-4 & IL-13, or LPS and macrophage populations were evaluated regarding their response to these stimuli. Furthermore, cell survival was analyzed in correlation with time in organ culture. Results: xCell-based mathematical deconvolution of bulk RNA-seq data revealed the presence of CD8 T cells, Th17 cells, dendritic cells, and macrophages as the predominant immune cell types in organ-cultured human corneal tissue. Furthermore, RNA-seq allowed the detection of different macrophage marker genes in corneal samples, including PTPRC (CD45), ITGAM (CD11b), CD14, and CD74. Our RNA-seq data showed no evidence of a relevant presence of monocytes in human corneal tissue. The presence of different macrophage subtypes was confirmed by IHC. The disintegration and subsequent FC analysis of human corneal samples showed the presence of both M1 (HLA-DR+, CD282+, CD86+, and CD284+) and M2 (CD163+ and CD206+) macrophage subtypes. Furthermore, we found that the total number of macrophages in corneal samples decreased more than the total cell count with increasing tissue culture time. Treatment with IL-10 led to higher total cell counts per cornea and to an increased expression of the M2 marker CD163 (p < 0.05) while expression levels of various M1 macrophage markers were not significantly reduced by interleukin treatment. Conclusions: Regarding different macrophage populations, untreated human corneas showed more M1 than M2 macrophages. With increasing organ culture time, these macrophages decreased. In terms of cell dynamics, adding interleukins to the organ culture medium influenced the phenotype of macrophages within the cornea as detected by FC. Modifying the immunomodulatory properties of human grafts appears a promising approach to further reduce the risk of graft rejection in patients. In this context, treatment with interleukins was more effective in upregulating M2 macrophages than in suppressing M1 macrophages in corneal tissue.

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Nuclear transcriptomes of the seven neuronal cell types that constitute the Drosophila mushroom bodies

10.1101/412569 ◽

2018 ◽

Author(s):

Meng-Fu Maxwell Shih ◽

Fred P. Davis ◽

Gilbert Lee Henry ◽

Josh Dubnau

Keyword(s):

Neuronal Cell ◽

Cell Types ◽

Mushroom Bodies ◽

Rna Seq ◽

Memory Processing ◽

Neuropeptide Receptors ◽

Invertebrate Model ◽

And Function ◽

And Storage ◽

Neuroscience Community

ABSTRACTThe insect mushroom body (MB) is a conserved brain structure that plays key roles in a diverse array of behaviors. The Drosophila melanogaster MB is the primary invertebrate model of neural circuits related to memory formation and storage, and its development, morphology, wiring, and function has been extensively studied. MBs consist of intrinsic Kenyon Cells that are divided into three major neuron classes (γ, α’/β’ and α/β) and 7 cell subtypes (γd, γm, α’/β’ap, α’/β’m, α/βp, α/βs and α/βc) based on their birth order, morphology, and connectivity. These subtypes play distinct roles in memory processing, however the underlying transcriptional differences are unknown. Here, we used RNA sequencing (RNA-seq) to profile the nuclear transcriptomes of each MB neuronal cell subtypes. We identified 350 MB class- or subtype-specific genes, including the widely used α/β class marker Fas2 and the α’/β’ class marker trio. Immunostaining corroborates the RNA-seq measurements at the protein level for several cases. Importantly, our data provide a full accounting of the neurotransmitter receptors, transporters, neurotransmitter biosynthetic enzymes, neuropeptides, and neuropeptide receptors expressed within each of these cell types. This high-quality, cell type-level transcriptome catalog for the Drosophila MB provides a valuable resource for the fly neuroscience community.

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