CellPhoneDB: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes

Efremova, Mirjana; Vento-Tormo, Miquel; Teichmann, Sarah A.; Vento‐Tormo, Roser

doi:10.1038/s41596-020-0292-x

Cited by 2,304 publications

(2,242 citation statements)

References 38 publications

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“…To evaluate potential cell-cell communication, we used CellPhoneDB (v2.0.6; Vento-Tormo et al, 2018, Efremova et al, 2020) to examine the expression of ligand-receptor pairs between different scRNA-seq clusters. Briefly, we exported raw gene count matrices from Seurat, converted gene IDs to Ensembl IDs using bioMart (v2.38.0; Durinck et al, 2005).…”

Section: Methodsmentioning

confidence: 99%

Antibody repertoire and gene expression dynamics of diverse human B cell states during affinity maturation

King

Orban

Riches

et al. 2020

Preprint

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15In response to antigen challenge, B cells clonally expand, undergo selection and differentiate to produce 16 mature B cell subsets and high affinity antibodies. However, the interplay between dynamic B cell states 17 and their antibody-based selection is challenging to decipher in primary human tissue. We have applied 18 an integrated analysis of bulk and single-cell antibody repertoires paired with single-cell transcriptomics 19 of human B cells undergoing affinity maturation. We define unique gene expression and antibody 20 repertoires of known and novel B cell states, including a pre-germinal centre state primed to undergo 21 class switch recombination. We dissect antibody class-dependent gene expression of germinal centre 22 and memory B cells to find that class switching prior to germinal centre entry dictates the capacity of B 23 cells to undergo antibody-based selection and differentiate. Together, our analyses provide 24 unprecedented resolution into the gene expression and selection dynamics that shape B cell-mediated 25 immunity. 26 27 121 122 157 sampling of IgH sequences from bulk repertoires to enhance genotype correction, identification of 158

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Section: Methodsmentioning

confidence: 99%

Antibody repertoire and gene expression dynamics of diverse human B cell states during affinity maturation

King

Orban

Riches

et al. 2020

Preprint

Self Cite

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“…We conducted cell-cell interaction analysis utilizing cellphonedb function curated by CellPhoneDB database [21]. The significant cell-cell interactions were selected with p-value < 0.01.…”

Section: Cell-cell Interaction Analysismentioning

confidence: 99%

“…We sought to identify potential immune cells crosstalking with CoVs-targeted cells. The cell-cell interaction analysis was conducted by CellPho-neDB [21]. The interactions with p-value < 0.01 were adopted to construct the interaction relationship between cell types in each tissue.…”

Section: Macrophages Are Frequently Interacted With the Ace2expressinmentioning

confidence: 99%

Single cell RNA sequencing of 13 human tissues identify cell types and receptors of human coronaviruses

Shen

Zhang

et al. 2020

Biochemical and Biophysical Research Communications

838

774

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a b s t r a c tThe new coronavirus (SARS-CoV-2) outbreak from December 2019 in Wuhan, Hubei, China, has been declared a global public health emergency. Angiotensin I converting enzyme 2 (ACE2), is the host receptor by SARS-CoV-2 to infect human cells. Although ACE2 is reported to be expressed in lung, liver, stomach, ileum, kidney and colon, its expressing levels are rather low, especially in the lung. SARS-CoV-2 may use co-receptors/auxiliary proteins as ACE2 partner to facilitate the virus entry. To identify the potential candidates, we explored the single cell gene expression atlas including 119 cell types of 13 human tissues and analyzed the single cell co-expression spectrum of 51 reported RNA virus receptors and 400 other membrane proteins. Consistent with other recent reports, we confirmed that ACE2 was mainly expressed in lung AT2, liver cholangiocyte, colon colonocytes, esophagus keratinocytes, ileum ECs, rectum ECs, stomach epithelial cells, and kidney proximal tubules. Intriguingly, we found that the candidate co-receptors, manifesting the most similar expression patterns with ACE2 across 13 human tissues, are all peptidases, including ANPEP, DPP4 and ENPEP. Among them, ANPEP and DPP4 are the known receptors for human CoVs, suggesting ENPEP as another potential receptor for human CoVs. We also conducted "CellPhoneDB" analysis to understand the cell crosstalk between CoV-targets and their surrounding cells across different tissues. We found that macrophages frequently communicate with the CoVs targets through chemokine and phagocytosis signaling, highlighting the importance of tissue macrophages in immune defense and immune pathogenesis.

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“…To evaluate cell -cell interactions of the immune cells in cardiac homeostasis and remodelling we used cellphonedb 66 . Thus we predicted putative cross-talk among myeloid and lymphoid cells, CM, and FB ( Figure 4C and Supplementary Table E3 ) 64 .…”

Section: ( Supplementarymentioning

confidence: 99%

Cells and gene expression programs in the adult human heart

Litviňuková

Talavera-López

Maatz

et al. 2020

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SummaryCardiovascular disease is the leading cause of death worldwide. Advanced insights into disease mechanisms and strategies to improve therapeutic opportunities require deeper understanding of the molecular processes of the normal heart. Knowledge of the full repertoire of cardiac cells and their gene expression profiles is a fundamental first step in this endeavor. Here, using large-scale single cell and nuclei transcriptomic profiling together with state-of-the-art analytical techniques, we characterise the adult human heart cellular landscape covering six anatomical cardiac regions (left and right atria and ventricles, apex and interventricular septum). Our results highlight the cellular heterogeneity of cardiomyocytes, pericytes and fibroblasts, revealing distinct subsets in the atria and ventricles indicative of diverse developmental origins and specialized properties. Further we define the complexity of the cardiac vascular network which includes clusters of arterial, capillary, venous, lymphatic endothelial cells and an atrial-enriched population. By comparing cardiac cells to skeletal muscle and kidney, we identify cardiac tissue resident macrophage subsets with transcriptional signatures indicative of both inflammatory and reparative phenotypes. Further, inference of cell-cell interactions highlight a macrophage-fibroblast-cardiomyocyte network that differs between atria and ventricles, and compared to skeletal muscle. We expect this reference human cardiac cell atlas to advance mechanistic studies of heart homeostasis and disease.

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CellPhoneDB: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes

Abstract: CellPhoneDB combines an interactive database and a statistical framework for the exploration of ligand-receptor interactions inferred from single cell transcriptomics measurements.

Cited by 2,304 publications

References 38 publications

Antibody repertoire and gene expression dynamics of diverse human B cell states during affinity maturation

Antibody repertoire and gene expression dynamics of diverse human B cell states during affinity maturation

Single cell RNA sequencing of 13 human tissues identify cell types and receptors of human coronaviruses

Cells and gene expression programs in the adult human heart

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