Correlated Gene Modules Uncovered by Single-Cell Transcriptomics with High Detectability and Accuracy

AbstractSingle cell transcriptome sequencing has become extremely useful for cell typing. However, such differential expression data has shed little light on regulatory relationships among genes. Here, by examining pairwise correlations between mRNA levels of any two genes under steady-state conditions, we uncovered correlated gene modules (CGMs), clusters of intercorrelated genes that carry out certain biological functions together. We report a novel single-cell RNA-seq method called MALBAC-DT with higher detectability and accuracy, allowing determination of the covariance matrix of the expressed mRNAs for a homogenous cell population. We observed a prevalence of positive correlations between pairs of genes, with higher correlations corresponding to higher likelihoods of protein-protein interactions. Some CGMs, such as the p53 module in a cancer cell line, are cell type specific, while others, such as the protein synthesis CGM, are shared by different cell types. CGMs distinguished direct targets of p53 and exposed different modes of regulation of these genes in different cell types. Our covariance analyses of steady-state fluctuations provides a powerful way to advance our functional understanding of gene-to-gene interactions.

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A single cell transcriptome atlas reveals the heterogeneity of the healthy human cornea and identifies novel markers of the corneal limbus and stroma

10.1101/2021.07.07.451489 ◽

2021 ◽

Author(s):

Pere Catala ◽

Nathalie Groen ◽

Jasmin A Dehnen ◽

Eduardo Soares ◽

Arianne JH van Velthoven ◽

...

Keyword(s):

Single Cell ◽

Cell Types ◽

Human Cornea ◽

Corneal Tissue ◽

Healthy Human ◽

Disease States ◽

Cell Niche ◽

Cell Transcriptome ◽

Single Cell Transcriptome ◽

Different Cell Types

The cornea is the clear window that lets light into the eye. It is composed of five layers: epithelium, Bowman layer, stroma, Descemet membrane and endothelium. The maintenance of its structure and transparency are determined by the functions of the different cell types populating each layer. Attempts to regenerate corneal tissue and understand disease conditions requires knowledge of how cell profiles vary across this heterogeneous tissue. We performed a single cell transcriptomic profiling of 19,472 cells isolated from eight healthy donor corneas. Our analysis delineates the heterogeneity of the corneal layers by identifying cell populations and revealing cell states that contribute in preserving corneal homeostasis. We identified that the expression of CAV1, CXCL14, HOMER3 and CPVL were exclusive to the corneal epithelial limbal stem cell niche, CKS2, STMN1 and UBE2C were exclusively expressed in highly proliferative transit amplifying cells, and NNMT was exclusively expressed by stromal keratocytes. Overall, this research provides a basis to improve current primary cell expansion protocols, for future profiling of corneal disease states, to help guide pluripotent stem cells into different corneal lineages, and to understand how engineered substrates affect corneal cells to improve regenerative therapies.

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Single-cell transcriptome analysis of the zebrafish embryonic trunk

10.1101/2021.05.07.443129 ◽

2021 ◽

Author(s):

Sanjeeva S Metikala ◽

Satish Casie Chetty ◽

Saulius Sumanas

Keyword(s):

Single Cell ◽

Molecular Mechanisms ◽

Cell Lineage ◽

Cell Types ◽

Rna Seq ◽

Cell Lineages ◽

Distinct Cell ◽

Cell Transcriptome ◽

Single Cell Transcriptome ◽

Different Cell Types

During embryonic development, cells differentiate into a variety of distinct cell types and subtypes with diverse transcriptional profiles. To date, transcriptomic signatures of different cell lineages that arise during development have been only partially characterized. Here we used single-cell RNA-seq to perform transcriptomic analysis of over 20,000 cells disaggregated from the trunk region of zebrafish embryos at the 30 hpf stage. Transcriptional signatures of 27 different cell types and subtypes were identified and annotated during this analysis. This dataset will be a useful resource for many researchers in the fields of developmental and cellular biology and facilitate the understanding of molecular mechanisms that regulate cell lineage choices during development.

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Single-cell transcriptome analysis of the zebrafish embryonic trunk

PLoS ONE ◽

10.1371/journal.pone.0254024 ◽

2021 ◽

Vol 16 (7) ◽

pp. e0254024

Author(s):

Sanjeeva Metikala ◽

Satish Casie Chetty ◽

Saulius Sumanas

Keyword(s):

Single Cell ◽

Molecular Mechanisms ◽

Cell Lineage ◽

Cell Types ◽

Rna Seq ◽

Cell Lineages ◽

Distinct Cell ◽

Cell Transcriptome ◽

Single Cell Transcriptome ◽

Different Cell Types

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scRNASeqDB: a database for gene expression profiling in human single cell by RNA-seq

10.1101/104810 ◽

2017 ◽

Cited By ~ 7

Author(s):

Yuan Cao ◽

Junjie Zhu ◽

Guangchun Han ◽

Peilin Jia ◽

Zhongming Zhao

Keyword(s):

Single Cell ◽

Expression Profiles ◽

Cell Types ◽

Or Groups ◽

Cell Transcriptome ◽

Almost All ◽

Single Cell Transcriptome ◽

Different Cell Types ◽

Online Web

AbstractSummary: Single-cell RNA sequencing (scRNA-Seq) is quickly becoming a powerful tool for high-throughput transcriptomic analysis of cell states and dynamics. Both the number and quality of scRNA-Seq datasets have dramatically increased recently. So far, there is no database that comprehensively collects and curates scRNA-Seq data in humans. Here, we present scRNASeqDB, a database that includes almost all the currently available human single cell transcriptome datasets (n= 36) covering 71 human cell lines or types and 8910 samples. Our online web interface allows user to query and visualize expression profiles of the gene(s) of interest, search for genes that are expressed in different cell types or groups, or retrieve differentially expressed genes between cell types or groups. The scRNASeqDB is a valuable resource for single cell transcriptional studies.Availability: The database is available at https://bioinfo.uth.edu/scrnaseqdb/.Contact: [email protected]

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Genomic Architecture of Cells in Tissues (GeACT): Study of Human Mid-gestation Fetus

10.1101/2020.04.12.038000 ◽

2020 ◽

Author(s):

Feng Tian ◽

Fan Zhou ◽

Xiang Li ◽

Wenping Ma ◽

Honggui Wu ◽

...

Keyword(s):

Transcription Factors ◽

Single Cell ◽

Human Cell ◽

Expression Profiles ◽

Single Cells ◽

Cell Types ◽

List Type ◽

Cell Type ◽

Genomic Architecture ◽

Gene Modules

SummaryBy circumventing cellular heterogeneity, single cell omics have now been widely utilized for cell typing in human tissues, culminating with the undertaking of human cell atlas aimed at characterizing all human cell types. However, more important are the probing of gene regulatory networks, underlying chromatin architecture and critical transcription factors for each cell type. Here we report the Genomic Architecture of Cells in Tissues (GeACT), a comprehensive genomic data base that collectively address the above needs with the goal of understanding the functional genome in action. GeACT was made possible by our novel single-cell RNA-seq (MALBAC-DT) and ATAC-seq (METATAC) methods of high detectability and precision. We exemplified GeACT by first studying representative organs in human mid-gestation fetus. In particular, correlated gene modules (CGMs) are observed and found to be cell-type-dependent. We linked gene expression profiles to the underlying chromatin states, and found the key transcription factors for representative CGMs.HighlightsGenomic Architecture of Cells in Tissues (GeACT) data for human mid-gestation fetusDetermining correlated gene modules (CGMs) in different cell types by MALBAC-DTMeasuring chromatin open regions in single cells with high detectability by METATACIntegrating transcriptomics and chromatin accessibility to reveal key TFs for a CGM

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SARS-CoV-2 Neurotropism and Single Cell Responses in Brain Organoids Containing Innately Developing Microglia

10.1101/2021.07.07.451463 ◽

2021 ◽

Author(s):

Samudyata ◽

Ana Osorio Oliveira ◽

Susmita Malwade ◽

Nuno Rufino de Sousa ◽

Sravan K Goparaju ◽

...

Keyword(s):

Single Cell ◽

Neuronal Cell Death ◽

Neuronal Cell ◽

Transcriptome Profiling ◽

Cell Types ◽

Cellular Responses ◽

Cellular Respiration ◽

Neuropsychiatric Manifestations ◽

Altered Blood ◽

Cell Transcriptome

Neuropsychiatric manifestations are common in both acute and post-acute phase of SARS-CoV-2 infection, but the mechanism of these effects is unknown. Here, we derive human brain organoids with innately developing microglia to investigate the cellular responses to SARS-CoV-2 infection on a single cell level. We find evidence of limited tropism to SARS-CoV-2 for all major cell types and observe extensive neuronal cell death that also include non-infected cells. Single cell transcriptome profiling reveals distinct responses in microglia and astrocytes that share features with cellular states observed in neurodegenerative diseases, includes upregulation of genes with relevance for synaptic stripping, and suggests altered blood brain barrier integrity. Across all cell types, we observe a global translational shut-down as well as altered carbohydrate metabolism and cellular respiration. Together, our findings provide insights into cellular responses of the resident brain immune cells to SARS-CoV-2 and pinpoint mechanisms that may be of relevance for the neuropathological changes observed in COVID-19 patients.

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Single cell transcriptome profiling of the human developing spinal cord reveals a conserved genetic programme with human specific features

10.1101/2021.04.12.439474 ◽

2021 ◽

Author(s):

Teresa Rayon ◽

Rory J. Maizels ◽

Christopher Barrington ◽

James Briscoe

Keyword(s):

Gene Expression ◽

Spinal Cord ◽

Single Cell ◽

Motor Neurons ◽

Neural Tube ◽

Transcriptome Profiling ◽

Cell Types ◽

Human Embryos ◽

Neuronal Populations ◽

Cell Transcriptome

AbstractThe spinal cord receives input from peripheral sensory neurons and controls motor output by regulating muscle innervating motor neurons. These functions are carried out by neural circuits comprising molecularly and physiologically distinct neuronal subtypes that are generated in a characteristic spatial-temporal arrangement from progenitors in the embryonic neural tube. The systematic mapping of gene expression in mouse embryos has provided insight into the diversity and complexity of cells in the neural tube. For human embryos, however, less information has been available. To address this, we used single cell mRNA sequencing to profile cervical and thoracic regions in four human embryos of Carnegie Stages (CS) CS12, CS14, CS17 and CS19 from Gestational Weeks (W) 4-7. In total we recovered the transcriptomes of 71,219 cells. Analysis of progenitor and neuronal populations from the neural tube, as well as cells of the peripheral nervous system, in dorsal root ganglia adjacent to the neural tube, identified dozens of distinct cell types and facilitated the reconstruction of the differentiation pathways of specific neuronal subtypes. Comparison with existing mouse datasets revealed the overall similarity of mouse and human neural tube development while highlighting specific features that differed between species. These data provide a catalogue of gene expression and cell type identity in the developing neural tube that will support future studies of sensory and motor control systems and can be explored at https://shiny.crick.ac.uk/scviewer/neuraltube/.

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Cytokine-induced changes in chromatin structure and in vivo footprints in the inducible NOS promoter

AJP Lung Cellular and Molecular Physiology ◽

10.1152/ajplung.2001.280.3.l390 ◽

2001 ◽

Vol 280 (3) ◽

pp. L390-L399 ◽

Cited By ~ 25

Author(s):

Jane K. Mellott ◽

Harry S. Nick ◽

Michael F. Waters ◽

Timothy R. Billiar ◽

David A. Geller ◽

...

Keyword(s):

Epithelial Cells ◽

Protein Interactions ◽

Molecular Mechanisms ◽

Cell Types ◽

Specific Pattern ◽

Mrna Levels ◽

Inos Gene ◽

In Vivo Footprinting ◽

Induced Changes

Transcription of the human inducible nitric oxide synthase ( iNOS) gene is regulated by inflammatory cytokines in a tissue-specific manner. To determine whether differences in cytokine-induced mRNA levels between pulmonary epithelial cells (A549) and hepatic biliary epithelial cells (AKN-1) result from different protein or DNA regulatory mechanisms, we identified cytokine-induced changes in DNase I-hypersensitive (HS) sites in 13 kb of the iNOS 5′-flanking region. Data showed both constitutive and inducible HS sites in an overlapping yet cell type-specific pattern. Using in vivo footprinting and ligation-mediated PCR to detect potential DNA or protein interactions, we examined one promoter region near −5 kb containing both constitutive and cytokine-induced HS sites. In both cell types, three in vivo footprints were present in both control and cytokine-treated cells, and each mapped within a constitutive HS site. The remaining footprint appeared only in response to cytokine treatment and mapped to an inducible HS site. These studies, performed on chromatin in situ, identify a portion of the molecular mechanisms regulating transcription of the human iNOS gene in both lung- and liver-derived epithelial cells.

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High-Throughput Single-Cell Transcriptome Profiling of Plant Cell Types

Cell Reports ◽

10.1016/j.celrep.2019.04.054 ◽

2019 ◽

Vol 27 (7) ◽

pp. 2241-2247.e4 ◽

Cited By ~ 57

Author(s):

Christine N. Shulse ◽

Benjamin J. Cole ◽

Doina Ciobanu ◽

Junyan Lin ◽

Yuko Yoshinaga ◽

...

Keyword(s):

Single Cell ◽

Plant Cell ◽

High Throughput ◽

Transcriptome Profiling ◽

Cell Types ◽

Cell Transcriptome ◽

Single Cell Transcriptome

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A fate-mapping approach reveals the composite origin of the connecting tubule and alerts on “single-cell”-specific KO model of the distal nephron

AJP Renal Physiology ◽

10.1152/ajprenal.00286.2016 ◽

2016 ◽

Vol 311 (5) ◽

pp. F901-F906 ◽

Cited By ~ 22

Author(s):

Francesco Trepiccione ◽

Christelle Soukaseum ◽

Anna Iervolino ◽

Federica Petrillo ◽

Miriam Zacchia ◽

...

Keyword(s):

Single Cell ◽

Kidney Development ◽

Fluorescent Protein ◽

Collecting Duct ◽

Yellow Fluorescent Protein ◽

Cell Types ◽

Intercalated Cells ◽

Distal Nephron ◽

Principal Cells ◽

Different Cell Types

The distal nephron is a heterogeneous part of the nephron composed by six different cell types, forming the epithelium of the distal convoluted (DCT), connecting, and collecting duct. To dissect the function of these cells, knockout models specific for their unique cell marker have been created. However, since this part of the nephron develops at the border between the ureteric bud and the metanephric mesenchyme, the specificity of the single cell markers has been recently questioned. Here, by mapping the fate of the aquaporin 2 (AQP2) and Na+-Cl−cotransporter (NCC)-positive cells using transgenic mouse lines expressing the yellow fluorescent protein fluorescent marker, we showed that the origin of the distal nephron is extremely composite. Indeed, AQP2-expressing precursor results give rise not only to the principal cells, but also to some of the A- and B-type intercalated cells and even to cells of the DCT. On the other hand, some principal cells and B-type intercalated cells can develop from NCC-expressing precursors. In conclusion, these results demonstrate that the origin of different cell types in the distal nephron is not as clearly defined as originally thought. Importantly, they highlight the fact that knocking out a gene encoding for a selective functional marker in the adult does not guarantee cell specificity during the overall kidney development. Tools allowing not only cell-specific but also time-controlled recombination will be useful in this sense.

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