Cell migration, but not proliferation, is dysregulated in <i>donut^s908</i> mutants.

<p>(A–D) EdU incorporation assay in WT (A,C) and <i>donut^s908</i> mutant (B,D) animals at 56 (A,B) and 75 (C,D) hpf. (E) Quantification of proliferation assay data shows no significant change in acinar cell proliferation at early or late stages of pancreatic tail formation. (F–I) Morphology of exocrine tissues at 84 hpf in WT (F,H) and <i>metMO-</i>injected (G,I) larvae revealed by <i>Tg(ptf1a:</i>GFP) (acinar; F,G) or <i>Tg(nkx2.2a(-3.5 kb):</i>GFP) (duct; H,I) expression. In <i>metMO-</i>injected embryos, acinar and ductal cells fail to migrate caudally, and remain near the principal islet (β). In <i>metMO</i> larvae, ductal cells exhibit a more rounded morphology in the exocrine pancreas (insets) and are also observed in the liver region (asterisk). (J,K) 84 hpf WT (J) and <i>metMO</i>-injected (K) <i>Tg(duct:GFP)</i> larvae stained with Prox1 (blue) and Alcam (red). Pancreatic ductal cells are ectopically localized in the liver (li) along tracts of biliary ducts. (L) Quantification of pancreatic tail defects in small molecule treated larvae; inhibitors of the MAPK pathway (UO126, SB203580) and furin function (CMK) had little effect on pancreatic tail outgrowth, while inhibitors of PI3K (LY294002) and STAT3 (SU6656) function mimicked the type 1 and type 2 <i>donut</i> phenotypes. epd, extrapancreatic duct.</p

S6 Fig -

(A) Heatmaps indicating the group specific cell-cell interaction between different cell types in healthy controls (left panel), moderate patients (middle panel) and severe patients (right panel) for the PBMC dataset collection. Rows indicate the sender cell types and columns indicate the receiver cell types. (B) Heatmaps indicate the difference in group specific cell-cell interaction between different cell types in moderate patients and healthy controls (left panel), severe patients and healthy controls (middle panel) and severe patients and moderate patients (right panel) for the PBMC dataset collection. Red color indicates a higher interaction in severe patients and blue color indicates a higher interaction in moderate patients. Rows indicate the sender cell types and columns indicate the receiver cell types. (DOCX)</p

<i>donut^s908</i> is a hypomorphic allele of <i>met</i>.

<p>(A–E) Exocrine pancreas (xp) structure marked by <i>ptf1a:</i>GFP expression in 3 dpf WT (A,D), and in type 1 (B) and type 2 (C,E) <i>donut</i> mutants. The pectoral fins (arrowheads) of <i>donut</i> mutants lack muscle tone, often asymmetrically, leading to their “open wing” appearance (right arrow, E). (F) Penetrance (pen) and expressivity (ex) of the <i>donut</i> phenotype. A small fraction of WT embryos shows <i>donut</i>-like pancreatic phenotypes, while 22% of clutchmates from heterozygous intercrosses exhibited either a spherical (55%) or an intermediately shortened (45%) pancreas. <i>n</i> below bars represents the number of embryos examined from WT clutches (right), heterozygote in-crossed clutches (center), and embryos exhibiting donut-like pancreatic phenotypes (right). (G–I) <i>donut</i> mutants have a lesion in <i>met. donut</i> was mapped to a critical interval on Chr. 25 containing 14 annotated genes (G); <i>met</i> showed a T2324G variant (H) causing an L775R amino acid substitution (I). (J,K) Model structures of the human MET IPT3 domain with isoleucine 777 (analogous to zebrafish residue L775) marked green (J) or substituted arginine marked red (K). (L) Diagram of Met showing the I777R substitution localized to the high affinity HGF binding site in IPT3, and the furin cleavage site in the semaphorin-like domain. (M–P) Morpholino-mediated knockdown of <i>met</i> (M,N) or <i>hgfa/b</i> (O,P) resulted in phenocopy of the <i>donut</i> mutation. (Q) Dose dependence of morpholino-induced phenotypes. At 8 ng, metMO exhibited some non-specific developmental delay, suggesting toxicity. pen, penetrance; ex, expressivity; li, liver; pm, plasma membrane.</p

S7 Fig -

(A) tSNE plot of monocytes in the Chua dataset, colored by the five cellular subtypes of monocytes. (B) Stacked bar plots representing the number of cells for healthy, moderate and severe groups. The x-axis represents the five cellular subtypes of monocytes for the Chua dataset. (C) Heatmap indicates the scaled average marker expression of the five cellular subtypes of monocytes. (D) Gene ontology analysis for the cellular subtypes of monocytes. (DOCX)</p

Monocyte and neutrophil interaction in COVID-19 patients.

A. Heatmap of the pathway-specific cell-cell interaction (pCCI) contribution in monocytes as ligands and neutrophils as receptors in the Chua dataset, where the rows indicate the signaling pathways and columns indicate the samples. The signaling pathways are clustered into 6 groups. B. Dot plot indicating the cell-cell interaction contribution (pathway-cluster cell-cell interaction) in monocyte subgroups as ligands and neutrophils as receptors of the pathway-cluster 2 (upper panel) and pathway-cluster 4 (lower panel) as defined in (A). The columns indicate the 5 cellular subtypes of monocytes as ligands and the rows indicate the signaling pathways. A larger dot represents a higher level of cell-cell interaction. C. Bar plot indicating the log-ratio of cell-cell interaction contributions between two time points (y-axis) for longitudinal samples of 4 patients (2 moderate: BIH-CoV-12, BIH-CoV-15; 2 severe: BIH-CoV-06, BIH-CoV-07) in monocytes as ligands and neutrophils as receptors. The x-axis represents the signaling pathways. D. Heatmap of the cell-cell interaction contribution in monocytes as ligands and neutrophils as receptors for two patients (C143 and C146) in the Liao dataset that have more than 20 neutrophils, where the rows indicate the signaling pathways and columns indicate the samples. The signaling pathways are highlighted by the 6 signaling pathway clusters from (A).</p

Hepatocyte Growth Factor Signaling in Intrapancreatic Ductal Cells Drives Pancreatic Morphogenesis

<div><p>In a forward genetic screen for regulators of pancreas development in zebrafish, we identified <i>donut^s908</i>, a mutant which exhibits failed outgrowth of the exocrine pancreas. The <i>s908</i> mutation leads to a leucine to arginine substitution in the ectodomain of the hepatocyte growth factor (HGF) tyrosine kinase receptor, Met. This missense mutation impedes the proteolytic maturation of the receptor, its trafficking to the plasma membrane, and diminishes the phospho-activation of its kinase domain. Interestingly, during pancreatogenesis, <i>met</i> and its <i>hgf</i> ligands are expressed in pancreatic epithelia and mesenchyme, respectively. Although Met signaling elicits mitogenic and migratory responses in varied contexts, normal proliferation rates in <i>donut</i> mutant pancreata together with dysmorphic, mislocalized ductal cells suggest that <i>met</i> primarily functions motogenically in pancreatic tail formation. Treatment with PI3K and STAT3 inhibitors, but not with MAPK inhibitors, phenocopies the <i>donut</i> pancreatic defect, further indicating that Met signals through migratory pathways during pancreas development. Chimera analyses showed that Met-deficient cells were excluded from the duct, but not acinar, compartment in the pancreatic tail. Conversely, wild-type intrapancreatic duct and “tip cells” at the leading edge of the growing pancreas rescued the <i>donut</i> phenotype. Altogether, these results reveal a novel and essential role for HGF signaling in the intrapancreatic ducts during exocrine morphogenesis.</p></div

Goblet and immune cell interaction in COVID-19 patients.

A. Heatmap of the pathway-specific cell-cell interaction contribution in goblets as ligands and immune cells (macrophages, monocytes and T cells) as receptors in the Chua dataset, where the rows indicate the signaling pathways and columns indicate the samples. The signaling pathways are clustered into 6 groups. B. Bar plot indicates the log-ratio of cell-cell interaction contributions between two time points (y-axis) for longitude samples of 4 patients (2 moderate: BIH-CoV-12, BIH-CoV-15; 2 severe: BIH-CoV-06, BIH-CoV-07) in goblets as ligands and immune cells (macrophages, monocytes and T cells) as receptors. The x-axis represents the signaling pathways. C. PCA for samples using the selected pathway-specific cell-cell interaction features, colored by disease severity (Healthy, Moderate, Severe, Convalescence): the Chua dataset (top left panel), the Wilk dataset (bottom left panel), the Arunachalam dataset (top right panel) and the Zhang dataset (bottom right panel) with the corresponding LOOCV accuracy rate for four datasets presented in S1 Table.</p

S2 Fig -

(A) tSNE plot of scRNA-seq data from BALF (the Liao dataset), colored by the reannotation from scClassify. (B) Cell type composition of each sample in the Liao dataset. (C) Heatmap indicating the difference of group specific cell-cell interaction between different cell types in severe patients and moderate patients in the Liao dataset. Red color indicates a higher interaction in severe patients and blue color indicates a higher interaction in moderate patients. Rows indicate the sender cell types and columns indicate the receiver cell types. (DOCX)</p

Breakdown of rescued embryos by WT tissue contribution.

<p>Breakdown of rescued embryos by WT tissue contribution.</p

Cell type composition of each individual sample in the six PBMC datasets.

(DOCX)</p