Journal: Cell

Article Title: Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches

doi: 10.1016/j.cell.2021.12.018

Figure Lengend Snippet: Combination of CITE-seq, scRNA-seq, snRNA-seq, and spatial analyses enables identification of all hepatic cell types including bona fide cell doublets, related to Figure 1 (A and B) Top DEGs (A) and DEPs (B) for cell types from Figure 1 B. (C) Distinct profiles of cells or nuclei within the UMAP depending on isolation protocols; 71,162 cells from ex vivo digestions, 96,066 cells from in vivo digestions, and 18,666 nuclei. Numbers on plots represent numbers of cells/nuclei per population. (D) Correlation plots showing genes captured within the KC, B cell and neutrophil populations with and without addition of CITE-seq antibodies. (E) Expression of VSIG4, CD206, and ESAM (protein, top) and Vsig4 , Mrc1 , and Esam (mRNA, bottom). (F) UMAP showing clusters of cells when only minimal QC for gene number and % mitochondrial genes is performed; 17,669 cells pooled from 3 samples. Expression of Cd5l, Cd19 , and Kdr by the clusters facilitating identification of cell types per annotation. (G) CITE-seq data from (F) in Flow-Jo showing expression of CD206 and ESAM in total KCs (left) and total B cells (middle). Numbers represent % of entire KC or B cell population. Identified populations were then mapped back onto the original UMAP (right). (H) Expression of CD31, CD26, and CD38 by indicated populations. (I) Heatmaps showing expression of top DEGs between KC1s and LSECs (left), KC2s and KC1s + LSECs (middle) and B cell2s and B cell1s + LSECs (right). (J) 3D reconstruction of murine liver following perfusion with antigen fix to inflate endothelial cells and staining with antibodies against CD31, CD206, and F4/80. (K) UMAP showing clusters generated from Visium analysis of liver tissue (4 samples) and liver capsule (1 sample). (L) Top unbiased genes defining zonation trajectory from portal to central vein in Visium. (M) Expression of Glul and Epcam by confocal microscopy (left), annotation of portal, periportal, mid, and central regions on same tissue section (middle) and overlay of both datasets (right). (N) Identification of cholangiocyte (left) and cDC (right) signatures on zonated Visium spots. (P) Molecular Cartography showing expression of indicated zonated hepatocyte mRNAs in liver tissue. Data are representative of 2 mice. (O) Expression of Itgae (encoding CD103) in the UMAP of the total liver (left) and flow cytometric analysis of total cDC1s for CD103 and MHCII expression in the healthy murine liver (right).

Article Snippet: Anti-Mouse CD26 (REA1196) PE , Miltenyi Biotec , 130-122-775; RRID: AB_2801934.

Techniques: Isolation, Ex Vivo, In Vivo, Expressing, Staining, Generated, Confocal Microscopy

Journal: Cell

Article Title: Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches

doi: 10.1016/j.cell.2021.12.018

Figure Lengend Snippet:

Article Snippet: Anti-Mouse CD26 (REA1196) PE , Miltenyi Biotec , 130-122-775; RRID: AB_2801934.

Techniques: Purification, Recombinant, Staining, cDNA Synthesis, Gene Expression, Software, Microscopy

Journal: Emerging Infectious Diseases

Article Title: Domestic Pig Unlikely Reservoir for MERS-CoV

doi: 10.3201/eid2306.170096

Figure Lengend Snippet: Comparison of the amino acid residues shown to be essential in binding of Middle East respiratory syndrome coronavirus spike protein to DPP4 of human, dromedary camel, and domestic pig*

Article Snippet: We investigated whether DPP4 is expressed in the pig respiratory tract by performing immunohistochemical staining on the nasal mucosa and lung tissue obtained from healthy pigs using an antibody against DPP4 (mouse monoclonal anti-DPP4 [CD26], clone OTI11D7, 1:2,500; Origene Technologies, Inc., Rockville, MD, USA).

Techniques: Comparison, Binding Assay

Journal: Emerging Infectious Diseases

Article Title: Domestic Pig Unlikely Reservoir for MERS-CoV

doi: 10.3201/eid2306.170096

Figure Lengend Snippet: Dipeptidyl peptidase (DPP) 4 expression in the domestic pig respiratory tract. Tissues were stained by using a cross-reactive mouse monoclonal antibody against DPP4 (CD26, clone OTI11D7, 1:2,500; Origene Technologies, Inc., Rockville, MD, USA). DPP4 expression was absent in the nasal mucosa (A) but present in lung tissue (B) of healthy domestic pigs. Original magnification: nasal mucosa ×40; lung ×200.

Article Snippet: We investigated whether DPP4 is expressed in the pig respiratory tract by performing immunohistochemical staining on the nasal mucosa and lung tissue obtained from healthy pigs using an antibody against DPP4 (mouse monoclonal anti-DPP4 [CD26], clone OTI11D7, 1:2,500; Origene Technologies, Inc., Rockville, MD, USA).

Techniques: Expressing, Staining

Journal: The American Journal of Pathology

Article Title: Clinicopathologic, Immunohistochemical, and Ultrastructural Findings of a Fatal Case of Middle East Respiratory Syndrome Coronavirus Infection in the United Arab Emirates, April 2014

doi: 10.1016/j.ajpath.2015.10.024

Figure Lengend Snippet: Primary Antibodies Used for IHC

Article Snippet: 1547 , DPP4 (clone OTI11D7) , MAB , 1:100 , PK , Origene Technologies , (no. 1371) Envision Doublestain , .

Techniques:

Journal: The American Journal of Pathology

Article Title: Clinicopathologic, Immunohistochemical, and Ultrastructural Findings of a Fatal Case of Middle East Respiratory Syndrome Coronavirus Infection in the United Arab Emirates, April 2014

doi: 10.1016/j.ajpath.2015.10.024

Figure Lengend Snippet: Immunohistochemical and ultrastructural localization of MERS-CoV and associated histologic findings. A: MERS-CoV and cytokeratin antigens in pneumocytes ( arrow ); red stain, MERS-CoV; brown stain, cytokeratin. B: MERS-CoV antigens in pneumocytes ( arrowhead ) and CD68 antigens in macrophages ( arrow ); red stain, CD68; brown stain, MERS-CoV. C: MERS-CoV and surfactant antigens in type 2 pneumocytes ( arrow ); red stain, surfactant; brown stain, MERS-CoV. D: MERS-CoV and DPP4 in pneumocytes ( arrow ); red stain, DPP4; brown stain, MERS-CoV. E: Fragmented pneumocyte infected with MERS-CoV, hyaline membrane ( arrowhead ) present. F: Magnified from the boxed area in E . MERS-CoV virions dispersed as single particles ( arrow ) or in clusters within membrane-bound vesicles ( arrowhead ). Spherical and pleomorphic particles ranged in size from 50 to 150 nm diameter. Scale bars: 2 μm ( E ); 500 nm ( F ). Original magnification: ×100 ( A and C ); ×63 ( B ); ×75 ( D ). DPP4, dipeptidyl peptidase 4; MERS-CoV, Middle East respiratory syndrome coronavirus.

Article Snippet: 1547 , DPP4 (clone OTI11D7) , MAB , 1:100 , PK , Origene Technologies , (no. 1371) Envision Doublestain , .

Techniques: Immunohistochemical staining, Staining, Infection, Membrane

Journal: Biomedicines

Article Title: Is Spheroid a Relevant Model to Address Fibrogenesis in Keloid Research?

doi: 10.3390/biomedicines11092350

Figure Lengend Snippet: Figure 4. Three-Dimensional culture and TGF-β1 activation converge to downregulate CD26 and TGFβRII expression. TGFβRII (A) and DPP4 (B) mRNA synthesis were evaluated by RT-qPCR in monolayers and spheroids performed either with NDFs or KFs in the presence of TGF-β1 vs. control [n = 4 per condition]. After 7 days of treatment, spheroids thus treated were immunostained for CD26 (green) and TGFβRII (red) observation (C) and semi quantification (D,E). Nuclei were counterstained with DAPI (Blue). [n = 10 spheroid and n= 2–6 images per spheroid]. Statistical analyses were performed using two-way ANOVA * for p < 0.05; ** for p < 0.005; *** for p < 0.001; **** for p < 0.0001.

Article Snippet: Appropriate dilutions of primary antibodies targeting αSMA (A2547, Sigma Aldrich, Saint-Louis, MO, USA), CD26 (OTI11D7, OriGene, Rockville, MD, USA), and TGFβRII (PA5-35076, Invitrogen, Carlsbad, CA, USA) were added on glass slides before incubation (overnight, 4 ◦C in a wet chamber).

Techniques: Activation Assay, Expressing, Quantitative RT-PCR, Control

Journal: Journal of Virology

Article Title: Species-Specific Colocalization of Middle East Respiratory Syndrome Coronavirus Attachment and Entry Receptors

doi: 10.1128/JVI.00107-19

Figure Lengend Snippet: MERS-CoV S1 A binds specifically to the nasal epithelium of dromedary camels. (A) Nanoparticles displaying a multivalent MERS-CoV S1 A domain (np-S1 A ) bind to the apical surface of camel nasal ciliated epithelial cells, as revealed by red staining. np-S1 A binding is inhibited by prior neuraminidase treatment of these nasal tissues. Blank nanoparticles also do not bind to these tissues. (B) Goblet cells (arrows), visualized in purple by periodic acid-Schiff stain, are DPP4 negative, unlike nasal ciliated columnar epithelial cells (arrowheads). DPP4 expression is indicated in red. MERS-CoV S1 A binding to these goblet cells (red) can be abrogated by neuraminidase treatment. In MERS-CoV-infected camels, MERS-CoV S1 A (green) binds to both nasal ciliated columnar epithelial cells and goblet cells, while MERS-CoV N protein (red) is detected only in nasal ciliated columnar epithelial cells. np-S1 A binding is abrogated by a nanobody against the S1 A domain (Nb anti-S1 A ) but not by one against the S1 B domain (Nb anti-S1 B ). The tissues used in these experiments were sequentially cut. All pictures were taken at a ×400 magnification. (C) Nb anti-S1 A and Nb anti-S1 B bind specifically to S1 A and S1 B domains, respectively, and both bind to S1 protein, as revealed by an ELISA. The control nanobody does not bind to S1, S1 A , and S1 B . Nanobody binding is expressed as optical density at 450 nm (OD 450 ) values determined by an ELISA.

Article Snippet: MERS-CoV nucleoprotein was detected with 5 μg/ml mouse anti-MERS nucleoprotein (Sino-Biological, Beijing, China), while DPP4 expression was detected with either 5 μg/ml goat anti-human DPP4 (R&D, Minneapolis, MN, USA) or 10 μg/ml mouse anti-human DPP4 (clone 11D7; Origene, Rockville, MD, USA).

Techniques: Staining, Binding Assay, Expressing, Infection, Enzyme-linked Immunosorbent Assay

Journal: Journal of Virology

Article Title: Species-Specific Colocalization of Middle East Respiratory Syndrome Coronavirus Attachment and Entry Receptors

doi: 10.1128/JVI.00107-19

Figure Lengend Snippet: Detection of MERS-CoV N protein, DPP4, α2,3-sialic acids, and MERS-CoV S1 A binding in the nasal epithelium of dromedary camels, pigs, and rabbits. MERS-CoV N protein, DPP4, α2,3-sialic acid, and MERS-CoV S1 A binding are all indicated in red. MERS-CoV N protein is detected in the nasal epithelium tissues of MERS-CoV-infected dromedary camels, pigs, and rabbits. DPP4, α2,3-sialic acid, and MERS-CoV S1 A binding were evaluated on the tissues of noninfected animals. MERS-CoV N protein and DPP4 are detected in the nasal epithelium of dromedary camel, pig, and rabbit. α2,3-Sialic acids are detected in the nasal epithelium of dromedary camel and rabbit but not in that of pig. Meanwhile, MERS-CoV S1 A binds merely to the nasal epithelium of dromedary camel. Magnification, ×400.

Article Snippet: MERS-CoV nucleoprotein was detected with 5 μg/ml mouse anti-MERS nucleoprotein (Sino-Biological, Beijing, China), while DPP4 expression was detected with either 5 μg/ml goat anti-human DPP4 (R&D, Minneapolis, MN, USA) or 10 μg/ml mouse anti-human DPP4 (clone 11D7; Origene, Rockville, MD, USA).

Techniques: Binding Assay, Infection

Journal: Journal of Virology

Article Title: Species-Specific Colocalization of Middle East Respiratory Syndrome Coronavirus Attachment and Entry Receptors

doi: 10.1128/JVI.00107-19

Figure Lengend Snippet: DPP4 expression and MERS-CoV S1 A binding in intestinal tissues of common pipistrelle bat, serotine bat, Gambian epauletted fruit bat, and Egyptian fruit bat. DPP4 expression and MERS-CoV S1 A binding are indicated in red. DPP4 is expressed at the apical surface of the intestinal epithelial cells of these four bat species. MERS-CoV S1 A binds to the apical surface of the intestinal epithelial cells of common pipistrelle bats in both villi and crypts, while in other bat species, it mostly binds to intestinal epithelial cells within the crypts. Magnification, ×400.

Article Snippet: MERS-CoV nucleoprotein was detected with 5 μg/ml mouse anti-MERS nucleoprotein (Sino-Biological, Beijing, China), while DPP4 expression was detected with either 5 μg/ml goat anti-human DPP4 (R&D, Minneapolis, MN, USA) or 10 μg/ml mouse anti-human DPP4 (clone 11D7; Origene, Rockville, MD, USA).

Techniques: Expressing, Binding Assay

Journal: Journal of Virology

Article Title: Species-Specific Colocalization of Middle East Respiratory Syndrome Coronavirus Attachment and Entry Receptors

doi: 10.1128/JVI.00107-19

Figure Lengend Snippet: MERS-CoV receptor and attachment factor in the human lower respiratory tract epithelium. (A) The MERS-CoV receptor, DPP4, is expressed in the nasal epithelium of dromedary camels, while in the lungs, it is mainly expressed in endothelial cells. In the human respiratory tract, DPP4 is expressed in bronchiolar epithelial cells (arrowhead) and type II pneumocytes (arrow) in the lungs but not in the nasal epithelium. (B) α2,3-Sialic acid expression and MERS-CoV S1 A binding are also detected in human bronchiolar epithelial cells (arrowheads) and type II pneumocytes (arrows). DPP4 expression, α2,3-sialic acids, and MERS-CoV S1 A binding are indicated in red. (C) In human alveoli, DPP4 expression (red) colocalizes in the same cells where MERS-CoV S1 A binds (green). Pictures of the nasal epithelium were taken at a ×400 magnification, and those of the alveoli were taken at a ×1,000 magnification.

Article Snippet: MERS-CoV nucleoprotein was detected with 5 μg/ml mouse anti-MERS nucleoprotein (Sino-Biological, Beijing, China), while DPP4 expression was detected with either 5 μg/ml goat anti-human DPP4 (R&D, Minneapolis, MN, USA) or 10 μg/ml mouse anti-human DPP4 (clone 11D7; Origene, Rockville, MD, USA).

Techniques: Expressing, Binding Assay

Journal: Journal of Virology

Article Title: Species-Specific Colocalization of Middle East Respiratory Syndrome Coronavirus Attachment and Entry Receptors

doi: 10.1128/JVI.00107-19

Figure Lengend Snippet: Binding of the MERS-CoV S1 A domain and MERS-CoV infection in primary normal human bronchial epithelial cells are inhibited upon prior neuraminidase treatment. (A) Removal of sialic acids using neuraminidase (NA) treatment diminishes MERS-CoV S1 A binding to primary normal human bronchial epithelial cells but not DPP4 expression in these cells. (B) The same treatment also significantly inhibits MERS-CoV infection in these cells up to 50%. Immunofluorescence images in panel A were taken at a ×400 magnification, and those in panel B were taken at a ×100 magnification. ***, P value of <0.0001 by a t test.

Article Snippet: MERS-CoV nucleoprotein was detected with 5 μg/ml mouse anti-MERS nucleoprotein (Sino-Biological, Beijing, China), while DPP4 expression was detected with either 5 μg/ml goat anti-human DPP4 (R&D, Minneapolis, MN, USA) or 10 μg/ml mouse anti-human DPP4 (clone 11D7; Origene, Rockville, MD, USA).

Techniques: Binding Assay, Infection, Expressing, Immunofluorescence