Journal: bioRxiv

Article Title: Site-Specific Entry Factors Define Cellular Susceptibility to SARS-CoV-2 in Human Tissues

doi: 10.64898/2026.05.07.723425

Figure Lengend Snippet: SARS-CoV-2 pseudovirus ex vivo infected nasal epithelial cells (n=3 pools). (E-H) SARS-CoV-2 pseudovirus ex vivo infected lung epithelial cells (n= 9). (I-L) SARS-CoV-2 pseudovirus ex vivo infected renal cortex cells (n=7). Flow cytometry plots showing the phenotypic comparison between GFP⁺ (infected, green) and GFP⁻ (uninfected) cells of CD45 - CD31 - EpCAM + cells from the (A) pool #NAL02 (n= 7) or (E) #HLTE197, which includes a paired sample exposed to a spike-empty pseudovirus (background). (B and F) Violin plots depicting the frequency (%) of different epithelial marker expressions within total nasal ( B ) or pulmonary ( F ) EpCAM + (grey) and EpCAM + GFP + cells (green). (C-D and G-H) Boolean pie charts displaying the proportion of nasal ( C-D ) or pulmonary ( G-H ) EpCAM + ( C-G ) and EpCAM + GFP + ( D-H ) cells expressing combinations of color code molecules according to the legend and indicated as surrounding arcs around the pie chart. (I) Flow cytometry plots showing the phenotypic comparison of CD45 - CD31 - cells from #RINN22, either infected (GFP⁺; green) or exposed to a ‘background’ pseudovirus. (J) Violin plots depicting the frequency (%) of various molecules within total CD31 - (grey) and CD31 - GFP + cells (green). (K-L) Boolean pie charts displaying the proportion of CD31 - ( K ) and CD31 - GFP + ( L ) cells expressing combinations of color code molecules according to the legend and indicated as surrounding arcs around the pie chart. For all violin plots, data are represented as median ± IQR. Statistical analyses were performed using two-sided nonparametric Wilcoxon matched-pairs signed-rank test.

Article Snippet: Nasal epithelial cells were obtained with an ASI Rhino-Pro® nasal curette (Arlington, IL, USA) into Bronchial Epithelial Cell Medium (BEpiCM) (Innoprot) washed with PBS with 5 mM EDTA, incubated on a shaker (15 min. 30 rpm, 4°C) centrifuged, filtered and counted.

Techniques: Ex Vivo, Infection, Flow Cytometry, Comparison, Marker, Expressing

Journal: bioRxiv

Article Title: Site-Specific Entry Factors Define Cellular Susceptibility to SARS-CoV-2 in Human Tissues

doi: 10.64898/2026.05.07.723425

Figure Lengend Snippet: (A) UMAP projection of high-dimension single-cell flow cytometry nasal data of EpCAM + cells from ex vivo SARS-CoV-2 pseudovirus infected samples, depicting the differentiation of 8 clusters (MC) and relative abundance of each cluster across the three pools of nasal samples. (B) UMAP visualization highlighting the EpCAM + GFP + infected population (green). Adjacent heatmap displays normalized mean fluorescence intensity of epithelial markers across the 8 identified clusters as indicated in (A) . (C) UMAP-based visualization of the spatial expression of six molecules (top) and density histograms comparing EpCAM⁺ and EpCAM⁺GFP⁺ populations (bottom).

Article Snippet: Nasal epithelial cells were obtained with an ASI Rhino-Pro® nasal curette (Arlington, IL, USA) into Bronchial Epithelial Cell Medium (BEpiCM) (Innoprot) washed with PBS with 5 mM EDTA, incubated on a shaker (15 min. 30 rpm, 4°C) centrifuged, filtered and counted.

Techniques: Single Cell, Flow Cytometry, Ex Vivo, Infection, Fluorescence, Expressing

Journal: bioRxiv

Article Title: Site-Specific Entry Factors Define Cellular Susceptibility to SARS-CoV-2 in Human Tissues

doi: 10.64898/2026.05.07.723425

Figure Lengend Snippet: (A) UMAP projection of high-dimension single-cell flow cytometry data of pulmonary EpCAM + cells from uninfected or ex vivo SARS-CoV-2 pseudovirus infected samples, depicting the differentiation of 8 clusters (MC) and relative abundance of each cluster across uninfected versus infected samples (bars on top). Bars below show the percentage of less represented clusters (MC03-MC08). (B) UMAP visualization highlighting the EpCAM + GFP + infected population (green). Adjacent heatmap (bottom) displays normalized mean fluorescence intensity of epithelial markers across the 8 identified clusters as indicated in (A) highlighting the cluster representing GFP + cells (MC07). (C) Volcano plot displaying the differential cluster abundance comparing uninfected and infected samples, the green dot corresponds to MC07. (D) UMAP-based visualization of the spatial expression of six molecules (top) and density histograms comparing EpCAM⁺ and EpCAM⁺GFP⁺ populations (bottom).

Article Snippet: Nasal epithelial cells were obtained with an ASI Rhino-Pro® nasal curette (Arlington, IL, USA) into Bronchial Epithelial Cell Medium (BEpiCM) (Innoprot) washed with PBS with 5 mM EDTA, incubated on a shaker (15 min. 30 rpm, 4°C) centrifuged, filtered and counted.

Techniques: Single Cell, Flow Cytometry, Ex Vivo, Infection, Fluorescence, Expressing

Journal: bioRxiv

Article Title: Site-Specific Entry Factors Define Cellular Susceptibility to SARS-CoV-2 in Human Tissues

doi: 10.64898/2026.05.07.723425

Figure Lengend Snippet: (A) UMAP projection of high-dimension single-cell flow cytometry data of renal CD31 - cells from uninfected or ex vivo SARS-CoV-2 pseudovirus infected samples, depicting the differentiation of 17 clusters (MC) and relative abundance of each cluster across uninfected versus infected samples. (B) UMAP visualization highlighting the CD31 - GFP + infected population (green). Adjacent heatmap displays normalized mean fluorescence intensity of epithelial markers across the 17 identified clusters as indicated in ( A ) highlighting the cluster representing GFP + cells (MC05). (C) Volcano plot displaying the differential cluster abundance comparing uninfected and infected samples, the green dot corresponds to MC05. (D) UMAP-based visualization of the spatial expression of six molecules (top) and density histograms comparing CD31 - and CD31 - GFP + populations (bottom).

Article Snippet: Nasal epithelial cells were obtained with an ASI Rhino-Pro® nasal curette (Arlington, IL, USA) into Bronchial Epithelial Cell Medium (BEpiCM) (Innoprot) washed with PBS with 5 mM EDTA, incubated on a shaker (15 min. 30 rpm, 4°C) centrifuged, filtered and counted.

Techniques: Single Cell, Flow Cytometry, Ex Vivo, Infection, Fluorescence, Expressing

Journal: bioRxiv

Article Title: Site-Specific Entry Factors Define Cellular Susceptibility to SARS-CoV-2 in Human Tissues

doi: 10.64898/2026.05.07.723425

Figure Lengend Snippet: (A) Schematic overview of the experimental workflow. Epithelial cells were isolated from nasal, lung, and kidney tissues and infected ex vivo with SARS-CoV-2 pseudovirus. GFP⁺ (infected) and GFP⁻ (uninfected) cells were sorted and processed using Smart-seq2. After quality control, cells were clustered and analyzed by tissue. (B–D) Nasal epithelial cells. (B) UMAP embedding of five transcriptionally distinct clusters. (C) Cluster distribution across all nasal epithelial cells. (D) Cluster proportions stratified by GFP⁺ and GFP⁻ conditions. (E–G) Lung epithelial cells. (E) UMAP embedding of lung-derived cells showing the separation of three epithelial and one stromal population. (F) Cluster distribution across epithelial and stromal populations. (G) Cluster proportions by infection status. (H–J) Renal cortex epithelial cells. (H) UMAP embedding of two epithelial clusters. (I) Cluster distribution across all renal epithelial cells. (J) Cluster proportions stratified by GFP⁺ and GFP⁻ conditions.

Article Snippet: Nasal epithelial cells were obtained with an ASI Rhino-Pro® nasal curette (Arlington, IL, USA) into Bronchial Epithelial Cell Medium (BEpiCM) (Innoprot) washed with PBS with 5 mM EDTA, incubated on a shaker (15 min. 30 rpm, 4°C) centrifuged, filtered and counted.

Techniques: Isolation, Infection, Ex Vivo, Control, Derivative Assay

Journal: bioRxiv

Article Title: Site-Specific Entry Factors Define Cellular Susceptibility to SARS-CoV-2 in Human Tissues

doi: 10.64898/2026.05.07.723425

Figure Lengend Snippet: (A) Violin plots showing distributions of standard single-cell RNA-seq quality control metrics across all cells, including the number of detected genes (nFeature_RNA), total UMI counts (nCount_RNA), and the percentage of mitochondrial transcripts (percent.mt). ( B ) Heatmap of the top 10 differentially expressed genes for each identified cluster. Genes are ranked by average log-normalized expression within each cluster relative to others. Color scale indicates scaled expression levels. ( C ) Violin plots depicting normalized expression levels of selected epithelial marker genes ( EPCAM, ELF3, CLDN4 , and CDH1 ) across the indicated clusters, highlighting cluster-specific expression patterns. ( D ) Dot plot summarizing the expression of representative marker genes across clusters, based on Ahn, J.H., et al. (2021. J. Clin. Invest). Dot size reflects the percentage of cells expressing each gene, and color intensity represents the average expression level within each cluster

Article Snippet: Nasal epithelial cells were obtained with an ASI Rhino-Pro® nasal curette (Arlington, IL, USA) into Bronchial Epithelial Cell Medium (BEpiCM) (Innoprot) washed with PBS with 5 mM EDTA, incubated on a shaker (15 min. 30 rpm, 4°C) centrifuged, filtered and counted.

Techniques: Single Cell, RNA Sequencing, Control, Expressing, Marker

Journal: bioRxiv

Article Title: Site-Specific Entry Factors Define Cellular Susceptibility to SARS-CoV-2 in Human Tissues

doi: 10.64898/2026.05.07.723425

Figure Lengend Snippet: (A) Violin plots showing distributions of standard single-cell RNA-seq quality control metrics across all cells, including the number of detected genes (nFeature_RNA), total UMI counts (nCount_RNA), and the percentage of mitochondrial transcripts (percent.mt). (B) Heatmap of the top 10 differentially expressed genes per cluster, highlighting transcriptionally distinct epithelial and stromal compartments. Genes are ranked by average log-normalized expression within each cluster relative to others. Color scale indicates scaled expression levels. (C) Violin plots depicting normalized expression levels of representative markers: epithelial markers EPCAM and ELF3 enriched in epithelial groups, and stromal/extracellular matrix markers DCN and MFAP4 enriched in fibroblasts.

Article Snippet: Nasal epithelial cells were obtained with an ASI Rhino-Pro® nasal curette (Arlington, IL, USA) into Bronchial Epithelial Cell Medium (BEpiCM) (Innoprot) washed with PBS with 5 mM EDTA, incubated on a shaker (15 min. 30 rpm, 4°C) centrifuged, filtered and counted.

Techniques: Single Cell, RNA Sequencing, Control, Expressing

Journal: bioRxiv

Article Title: Site-Specific Entry Factors Define Cellular Susceptibility to SARS-CoV-2 in Human Tissues

doi: 10.64898/2026.05.07.723425

Figure Lengend Snippet: (A) Violin plots showing distributions of standard single-cell RNA-seq quality control metrics across all cells, including the number of detected genes (nFeature_RNA), total UMI counts (nCount_RNA), and the percentage of mitochondrial transcripts (percent.mt). (B) Heatmap of the top 10 differentially expressed genes per cluster, separating proximal tubular epithelial cells from broader epithelial populations. Genes are ranked by average log-normalized expression within each cluster relative to others. Color scale indicates scaled expression levels. (C) Violin plots depicting normalized expression levels of representative markers: epithelial marker EPCAM enriched in epithelial cells, proximal-tubule markers AQP1 and CUBN enriched in the proximal tubular epithelial cluster and SLC12A3 , expressed in the distal convoluted tubule.

Article Snippet: Nasal epithelial cells were obtained with an ASI Rhino-Pro® nasal curette (Arlington, IL, USA) into Bronchial Epithelial Cell Medium (BEpiCM) (Innoprot) washed with PBS with 5 mM EDTA, incubated on a shaker (15 min. 30 rpm, 4°C) centrifuged, filtered and counted.

Techniques: Single Cell, RNA Sequencing, Control, Expressing, Marker

Journal: bioRxiv

Article Title: Site-Specific Entry Factors Define Cellular Susceptibility to SARS-CoV-2 in Human Tissues

doi: 10.64898/2026.05.07.723425

Figure Lengend Snippet: Volcano plots showing differentially expressed genes between GFP⁺ and GFP⁻ in overall epithelial cells from the (A) nasal mucosa, (B) lung parenchyma and (C) renal cortex; or in individual clusters from a given tissue: (D) epithelial cluster 0 from the nasal mucosa; (F) alveolar type 2 (AT2) cells from the lung; and (G) general epithelial cluster from renal cortex. The horizontal axis shows log₂ fold change, and the vertical axis shows –log₁₀ adjusted p values. Selected significantly upregulated genes (in red) are highlighted in bigger dots.

Article Snippet: Nasal epithelial cells were obtained with an ASI Rhino-Pro® nasal curette (Arlington, IL, USA) into Bronchial Epithelial Cell Medium (BEpiCM) (Innoprot) washed with PBS with 5 mM EDTA, incubated on a shaker (15 min. 30 rpm, 4°C) centrifuged, filtered and counted.

Techniques:

Journal: bioRxiv

Article Title: Site-Specific Entry Factors Define Cellular Susceptibility to SARS-CoV-2 in Human Tissues

doi: 10.64898/2026.05.07.723425

Figure Lengend Snippet: ( A–B ) SARS-CoV-2 pseudovirus entry in lung ( A ) and kidney ( B ) epithelial cells following treatment with inhibitors. Lung or renal cortex-derived cells were exposed to pseudovirus in the presence of anti-ACE2 (25 µg/ml), Camostat (100 µM), KP-457 (ADAM17 inhibitor, 100 µM), anti-IL1R1 (100 µM), Ruxolitinib (JAK1/2 inhibitor, 100 µM), anti-ADAMTSL3 (250 ng/ml), anti-CADM1 (625 ng/ml), anti-GULP1 (625 ng/ml), anti-MDGA2 (62.5 ng/ml), anti-PILRα (1.25 µg/ml) or anti-PTPRK (1.25 µg/ml). Infection levels, quantified by luciferase activity, are expressed relative to untreated controls (100% infection). Each color-coded dot indicates an individual tissue with median and interquartile range indicated for each treatment with dotted lines. Statistical significance was assessed using a Kruskal–Wallis test for multiple comparisons (****P < 0.0001, ***P < 0.001, **P < 0.01, *P < 0.05). ( C ) Plots showing Spearman correlation coefficients and associated significant P values comparing inhibitor effects across lung and kidney tissues.

Article Snippet: Nasal epithelial cells were obtained with an ASI Rhino-Pro® nasal curette (Arlington, IL, USA) into Bronchial Epithelial Cell Medium (BEpiCM) (Innoprot) washed with PBS with 5 mM EDTA, incubated on a shaker (15 min. 30 rpm, 4°C) centrifuged, filtered and counted.

Techniques: Derivative Assay, Infection, Luciferase, Activity Assay

Journal: bioRxiv

Article Title: Kinetic proofreading as a mechanism for transcriptional specificity in living human cells

doi: 10.64898/2026.03.17.711757

Figure Lengend Snippet: (A) Schematic for transcriptional regulation by ligand-inducible nuclear receptors. (B) Experimental designs for either 2 or 4h activation of GR, RXR, RARa, and PPARy nuclear receptors using synthetic ligands in human bronchial epithelial cells. (C) Volcano plots showing differentially expressed genes by RNA-seq after activation of nuclear receptors 2h post-treatment (dashed lines indicate adj p-val threshold of 0.05). (D-E) RNA-seq genome browser tracks (D) and read count values (E) at the ERRFI1 and MYH9 loci at the indicated ligand treatments. (F) GR-ChIP and H3K27ac-ChIP genome browser tracks at ERRFI1 in the absence and presence of Dex. (G) Summary of GR transcription factor acting as a specific transcription factor for ERRFI1 and non-specific transcription factor for MYH9 gene.

Article Snippet: Cells were cultured in Airway Epithelial Cell Basal Medium (ATCC, PCS-300-030) supplemented with 1% penicillin/streptomycin and Bronchial Epithelial Cell Growth Kit (ATCC, PCS-300-040) containing HLL Supplement, L-glutamine, Extract P, and Airway Epithelial Cell Supplement (“complete medium”).

Techniques: Activation Assay, RNA Sequencing

Journal: Cell Death Discovery

Article Title: Trifluoperazine causes mast cell apoptosis through a secretory granule-mediated pathway

doi: 10.1038/s41420-026-03122-x

Figure Lengend Snippet: A Human lung smooth muscle cells (HLSMCs), lung fibroblasts (HLFs), and small airway epithelial cells (HSAECs) were treated with TFP at the indicated concentrations for 24 h. Human peripheral blood eosinophils and neutrophils were treated with TFP for 2 h. Cell viability was assessed by staining the cells with Annexin V (AnnV) and DRAQ7. Viable cells, AnnV − DRAQ7 − ; apoptotic cells, AnnV + DRAQ7 − ; necrotic/late apoptotic cells, AnnV + DRAQ7 + . HSAECs, n = 6 from three independent experiments; HLSMCs, eosinophils, neutrophils, n = 4 from four independent experiments; HLFs, n = 3 from one individual experiment representative of three independent experiments (One-way ANOVA for HLSMCs, HLFs; Kruskal-Wallis for HSAECs; Friedman test for eosinophils, neutrophils). B – C Bone marrow-derived MCs (BMMCs) and peritoneal cell-derived MCs (PCMCs) treated under the same conditions as in ( A ) for 24 h. BMMCs, n = 5 from two independent experiments; PCMCs, n = 3 from one individual experiment representative of three independent experiments (One-way ANOVA). Untreated (control) cells were used for statistical comparisons to all other groups in all figures. The bar charts show mean values + SEM or median + interquartile range. * P < 0.05; ** P < 0 .01; **** P < 0.0001. D Effect of TFP on DNA degradation. MCs were preincubated with bafilomycin A1 (Baf A1) (20 nM) for 2 h followed by treatment with TFP (10 μΜ) for 2 h. DNA was extracted from MCs and fragmentation was assessed by agarose gel electrophoresis. St standard marker.

Article Snippet: Primary human small airway epithelial cells (HSAECs) (PCS-301-010) were obtained from ATCC and cultured in Airway Epithelial Cell Basal Medium (ATCC) containing a Bronchial Epithelial Cell Growth Kit (ATCC) and penicillin-streptomycin (100 U/mL, 100 μg/mL).

Techniques: Staining, Derivative Assay, Control, Agarose Gel Electrophoresis, Marker