scholarly journals The Normal and Fibrotic Mouse Lung in Situ Classified by High Dimensional Single Cell Analysis on Routinely Processed Tissue

2021 ◽  
Author(s):  
Roberta Ciccimarra ◽  
Maddalena M. Bolognesi ◽  
Matteo Zoboli ◽  
Giorgio Cattoretti ◽  
Fabio F. Stellari ◽  
...  
Keyword(s):  
Single Cell ◽  
Single Cell Analysis ◽  
Progressive Increase ◽  
Mouse Lung ◽  
Alveolar Type ◽  
Type I ◽  
Alveolar Cells ◽  
Antibody Staining ◽  
Fibrotic Process

Abstract Single cell classification is elucidating homeostasis and pathology in tissues and whole organs. We applied in situ spatial proteomics by multiplex antibody staining to routinely processed mouse lung, healthy and during a fibrosis model. With a limited validated antibody panel (24) we classify the normal constituents (alveolar type I and II, bronchial epithelia, endothelial, muscular, stromal and hematopoietic cells) and by quantitative measurements, we show the progress of lung fibrosis over a 4 weeks course, the changing landscape and the cell-specific quantitative variation of a multidrug transporter. An early decline in AT2 alveolar cells and a progressive increase in stromal cells seems at the core of the fibrotic process.

Development of a platform for single cell genomics using convex lens-induced confinement

Lab on a Chip ◽  
2015 ◽  
Vol 15 (14) ◽  
pp. 3013-3020 ◽  
Author(s):  
Sara Mahshid ◽  
Mohammed Jalal Ahamed ◽  
Daniel Berard ◽  
Susan Amin ◽  
Robert Sladek ◽  
...  
Keyword(s):  
Single Cell ◽  
Base Pair ◽  
Single Cell Analysis ◽  
Lab On A Chip ◽  
Cell Analysis ◽  
Next Generation ◽  
Single Cell Genomics ◽  
Convex Lens ◽  
Genomic Dnas

We present a lab-on-a-chip for the next generation of single-cell genomics, performing full-cycle single-cell analysis by demonstrating mega-base pair genomic DNAs in nanochannels extracted in situ.

scholarly journals Integrated single-cell analysis unveils diverging immune features of COVID-19, influenza, and other community-acquired pneumonia

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Alex R Schuurman ◽  
Tom DY Reijnders ◽  
Anno Saris ◽  
Ivan Ramirez Moral ◽  
Michiel Schinkel ◽  
...  
Keyword(s):  
Single Cell ◽  
Influenza A ◽  
Mononuclear Cells ◽  
Single Cell Analysis ◽  
Community Acquired Pneumonia ◽  
Type I ◽  
Cell Analysis ◽  
Peripheral Blood Mononuclear ◽  
The Common ◽  
Peripheral Immune Response

The exact immunopathophysiology of community-acquired pneumonia (CAP) caused by SARS-CoV-2 (COVID-19) remains clouded by a general lack of relevant disease controls. The scarcity of single-cell investigations in the broader population of patients with CAP renders it difficult to distinguish immune features unique to COVID-19 from the common characteristics of a dysregulated host response to pneumonia. We performed integrated single-cell transcriptomic and proteomic analyses in peripheral blood mononuclear cells from a matched cohort of eight patients with COVID-19, eight patients with CAP caused by Influenza A or other pathogens, and four non-infectious control subjects. Using this balanced, multi-omics approach, we describe shared and diverging transcriptional and phenotypic patterns—including increased levels of type I interferon-stimulated natural killer cells in COVID-19, cytotoxic CD8 T EMRA cells in both COVID-19 and influenza, and distinctive monocyte compositions between all groups—and thereby expand our understanding of the peripheral immune response in different etiologies of pneumonia.

scholarly journals Targeted Disruption of Mouse Dip2B Leads to Abnormal Lung Development and Prenatal Lethality

2020 ◽  
Vol 21 (21) ◽  
pp. 8223
Author(s):  
Rajiv Kumar Sah ◽  
Jun Ma ◽  
Fatoumata Binta Bah ◽  
Zhenkai Xing ◽  
Salah Adlat ◽  
...  
Keyword(s):  
Lung Development ◽  
Cell Types ◽  
Branching Morphogenesis ◽  
Brdu Incorporation ◽  
Mouse Lung ◽  
Alveolar Type ◽  
Type I ◽  
Lung Maturation ◽  
M Phase

Molecular and anatomical functions of mammalian Dip2 family members (Dip2A, Dip2B and Dip2C) during organogenesis are largely unknown. Here, we explored the indispensable role of Dip2B in mouse lung development. Using a LacZ reporter, we explored Dip2B expression during embryogenesis. This study shows that Dip2B expression is widely distributed in various neuronal, myocardial, endothelial, and epithelial cell types during embryogenesis. Target disruption of Dip2b leads to intrauterine growth restriction, defective lung formation and perinatal mortality. Dip2B is crucial for late lung maturation rather than early-branching morphogenesis. The morphological analysis shows that Dip2b loss leads to disrupted air sac formation, interstitium septation and increased cellularity. In BrdU incorporation assay, it is shown that Dip2b loss results in increased cell proliferation at the saccular stage of lung development. RNA-seq analysis reveals that 1431 genes are affected in Dip2b deficient lungs at E18.5 gestation age. Gene ontology analysis indicates cell cycle-related genes are upregulated and immune system related genes are downregulated. KEGG analysis identifies oxidative phosphorylation as the most overrepresented pathways along with the G2/M phase transition pathway. Loss of Dip2b de-represses the expression of alveolar type I and type II molecular markers. Altogether, the study demonstrates an important role of Dip2B in lung maturation and survival.

scholarly journals SpliceRCA: in Situ Single-Cell Analysis of mRNA Splicing Variants

2018 ◽  
Vol 4 (6) ◽  
pp. 680-687 ◽  
Author(s):  
Xiaojun Ren ◽  
Ruijie Deng ◽  
Kaixiang Zhang ◽  
Yupeng Sun ◽  
Xucong Teng ◽  
...  
Keyword(s):  
Single Cell ◽  
Single Cell Analysis ◽  
Mrna Splicing ◽  
Cell Analysis ◽  
Splicing Variants

scholarly journals Integrated Single-Cell RNA-Sequencing Analysis of Aquaporin 5-Expressing Mouse Lung Epithelial Cells Identifies GPRC5A as a Novel Validated Type I Cell Surface Marker

Cells ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 2460 ◽  
Author(s):  
Masafumi Horie ◽  
Alessandra Castaldi ◽  
Mitsuhiro Sunohara ◽  
Hongjun Wang ◽  
Yanbin Ji ◽  
...  
Keyword(s):  
Cell Surface ◽  
Single Cell ◽  
Rna Sequencing ◽  
Surface Marker ◽  
Mouse Lung ◽  
Type I ◽  
Cell Markers ◽  
Lung Epithelial ◽  
Single Cell Rna Sequencing

Molecular and functional characterization of alveolar epithelial type I (AT1) cells has been challenging due to difficulty in isolating sufficient numbers of viable cells. Here we performed single-cell RNA-sequencing (scRNA-seq) of tdTomato+ cells from lungs of AT1 cell-specific Aqp5-Cre-IRES-DsRed (ACID);R26tdTomato reporter mice. Following enzymatic digestion, CD31-CD45-E-cadherin+tdTomato+ cells were subjected to fluorescence-activated cell sorting (FACS) followed by scRNA-seq. Cell identity was confirmed by immunofluorescence using cell type-specific antibodies. After quality control, 92 cells were analyzed. Most cells expressed ‘conventional’ AT1 cell markers (Aqp5, Pdpn, Hopx, Ager), with heterogeneous expression within this population. The remaining cells expressed AT2, club, basal or ciliated cell markers. Integration with public datasets identified three robust AT1 cell- and lung-enriched genes, Ager, Rtkn2 and Gprc5a, that were conserved across species. GPRC5A co-localized with HOPX and was not expressed in AT2 or airway cells in mouse, rat and human lung. GPRC5A co-localized with AQP5 but not pro-SPC or CC10 in mouse lung epithelial cell cytospins. We enriched mouse AT1 cells to perform molecular phenotyping using scRNA-seq. Further characterization of putative AT1 cell-enriched genes revealed GPRC5A as a conserved AT1 cell surface marker that may be useful for AT1 cell isolation.

In vivo exposure to hyperoxia induces DNA damage in a population of alveolar type II epithelial cells

2004 ◽  
Vol 286 (5) ◽  
pp. L1045-L1054 ◽  
Author(s):  
Jason M. Roper ◽  
Dawn J. Mazzatti ◽  
Richard H. Watkins ◽  
William M. Maniscalco ◽  
Peter C. Keng ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Transmembrane Protein ◽  
Dna Integrity ◽  
Alveolar Type ◽  
Type I ◽  
Type Ii Cells ◽  
Type Ii ◽  
Alveolar Cells ◽  
Endogenous Expression

It is well established that hyperoxia injures and kills alveolar endothelial and type I epithelial cells of the lung. Although type II epithelial cells remain morphologically intact, it remains unclear whether they are also damaged. DNA integrity was investigated in adult mice whose type II cells were identified by their endogenous expression of pro-surfactant protein C or transgenic expression of enhanced green fluorescent protein. In mice exposed to room air, punctate perinuclear 8-oxoguanine staining was detected in ∼4% of all alveolar cells and in 30% of type II cells. After 48 or 72 h of hyperoxia, 8-oxoguanine was detected in 11% of all alveolar cells and in >60% of type II cells. 8-Oxoguanine colocalized by confocal microscopy with the mitochondrial transmembrane protein cytochrome oxidase subunit 1. Type II cells isolated from hyperoxic lungs exhibited nuclear DNA strand breaks by comet assay even though they were viable and morphologically indistinguishable from cells isolated from lungs exposed to room air. These data reveal that type II cells exposed to in vivo hyperoxia have oxidized and fragmented DNA. Because type II cells are essential for lung remodeling, our findings raise the possibility that they are proficient in DNA repair.

scholarly journals Simultaneous isolation of endothelial and alveolar epithelial type I and type II cells during mouse lung development in the absence of a transgenic reporter

2020 ◽  
Vol 318 (4) ◽  
pp. L619-L630 ◽  
Author(s):  
Yves Donati ◽  
Sanja Blaskovic ◽  
Isabelle Ruchonnet-Métrailler ◽  
Josefina Lascano Maillard ◽  
Constance Barazzone-Argiroffo
Keyword(s):  
Epithelial Cell ◽  
De Novo ◽  
Morphological Changes ◽  
Alveolar Epithelial Cell ◽  
Mouse Lung ◽  
Cell Populations ◽  
Type I ◽  
Type Ii ◽  
Alveolar Cells ◽  
Alveolar Epithelial

Mouse lung developmental maturation and final alveolarization phase begin at birth. During this dynamic process, alveolar cells modify their morphology and anchorage to the extracellular matrix. In particular, alveolar epithelial cell (AEC) type I undergo cytoplasmic flattening and folding to ensure alveoli lining. We developed FACS conditions for simultaneous isolation of alveolar epithelial and endothelial cells in the absence of specific reporters during the early and middle alveolar phase. We evidenced for the first time a pool of extractable epithelial cell populations expressing high levels of podoplanin at postnatal day (pnd)2, and we confirmed by RT-qPCR that these cells are already differentiated but still immature AEC type I. Maturation causes a decrease in isolation yields, reflecting the morphological changes that these cell populations are undergoing. Moreover, we find that major histocompatibility complex II (MHCII), reported as a good marker of AEC type II, is poorly expressed at pnd2 but highly present at pnd8. Combined experiments using LysoTracker and MHCII demonstrate the de novo acquisition of MCHII in AEC type II during lung alveolarization. The lung endothelial populations exhibit FACS signatures from vascular and lymphatic compartments. They can be concomitantly followed throughout alveolar development and were obtained with a noticeable increased yield at the last studied time point (pnd16). Our results provide new insights into early lung alveolar cell isolation feasibility and represent a valuable tool for pure AEC type I preparation as well as further in vitro two- and three-dimensional studies.

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