Journal: PloS one

Article Title: HMGB1 accelerates alveolar epithelial repair via an IL-1β- and αvβ6 integrin-dependent activation of TGF-β1.

doi: 10.1371/journal.pone.0063907

Figure Lengend Snippet: Figure 1. Endogenous HMGB1 released by damaged primary rat ATII cells increases alveolar epithelial wound closure. (A) HMGB1 was elevated in cell supernatant from rat ATII monolayers that underwent scratch wounds (MS Cell Sup) compared to cell supernatant from rat ATII monolayers that did not undergo scratch wounds (condition media). (B) MS Cell Sup increases the rate of wound closure of primary rat ATII cell monolayers compared to cell supernatant from rat ATII monolayers that did not undergo scratch wounds. HMGB1 was depleted from MS Cell Sup by immunoprecipitation using 30 mg/ml of HMGB1 specific Ab (MS Cell Sup IP w/HMGB1 Ab). Controls were MS Cell Sup immunoprecipitated with a control IgG (MS Cell Sup IP w/Cont Ab). (C) HMGB1 is secreted by primary rat ATII cell monolayers after scratch wounds. Multiple scratches (MS) were performed on primary rat ATII cell monolayers. Fresh cell media were added for 6 hours to the monolayers after extensive washes. Cell supernatants were then centrifuged to remove dead cells and cell debris, then analyzed by western blot (40 ml loaded per lanes from a 1 ml MS Cell Sup sample). (D) MS Cell Sup increases the rate of wound closure of a primary rat ATII cell monolayers via RAGE- and TLR4-dependent pathways, but not via a CXCR4-dependent mechanism. MS Cell Sup, and either 30 mg/ml of blocking RAGE or TLR4 antibodies or their isotype control IgG, or 1 mM of AMD3100, a CXCR4 inhibitor, were added to the monolayers after the scratch. Rate of wound closure is expressed as percent of control 16 h after wounding. *p,0.05 from monolayers exposed to control cell media; **p,0.05 from monolayers exposed to MS Cell Sup. For western blot experiments, one representative experiment is shown, three additional experiments gave comparable results; *p,0.05 from monolayers exposed to condition media. doi:10.1371/journal.pone.0063907.g001

Article Snippet: Rat RAGE blocking antibody was obtained from R&D Systems (Minneapolis, MN).

Techniques: Immunoprecipitation, Control, Western Blot, Blocking Assay

Journal: bioRxiv

Article Title: Aerosolized ApoA1 Nanoparticles Synthesized by Microfluidics Cross the Lung Barrier and Modulate Inflammation

doi: 10.1101/2025.07.09.663869

Figure Lengend Snippet: Cellular localization of A1NPs after aerosolization. Immunofluorescence of lung sections from mice 6 hours after A1NP administration. ApoA1 appears in green and cell nuclei are stained with DAPI (blue). (A) AGER (red), specific to type I pneumocytes. (B) SFTPC (orange), marker for type II pneumocytes. (C) EMCN (red), characteristic of pulmonary endothelial cells. Representative illustration of 10 mice with A1NPs-DilC18.

Article Snippet: In parallel, specific antibodies were applied: a mouse anti-AGER rat antibody diluted 1:100 for type I pneumocytes (MAB 1179-500; R&D Systems), a mouse anti-SFTPC rabbit antibody diluted 1:200 for type II pneumocytes (10774-1AP; Proteintech), and a mouse anti-EMCN goat antibody diluted 1:100 for endothelial cells (AF4666-SP; R&D Systems).

Techniques: Immunofluorescence, Staining, Marker

Journal: Nature Communications

Article Title: Human iPSC-based Modeling of Pulmonary Fibrosis Reveals p300/CBP Inhibition Suppresses Alveolar Transitional Cell State

doi: 10.1038/s41467-026-68909-z

Figure Lengend Snippet: a Gene expression of ATCS markers in the micro-patterned culture. Each well was treated with either DMSO or p300/CBP inhibitors (10 μM) from days 11 to 14. Data are presented as mean ± SEM (n = 3 biologically independent experiments). One-way ANOVA followed by Tukey’s multiple comparisons test; ** p < 0.01, *** p < 0.001, **** p < 0.0001. b Dot plots displaying the gene expression of iATCs-specific markers in representative cell populations from the micro-patterned culture, corresponding to those shown in Fig. . c Immunostaining of CD54 (ICAM1), lineage markers for ATCS (KRT19), AT1 cells (HT1-56), AT2 cells (NaPi2b), and nuclei (Hoechst) in micro-patterned cultures. Representative images from three biologically independent experiments with similar results are shown. Scale bar: 100 μm. d, e Flow cytometry analysis assessing the CD54 + cell ratio in the micro-patterned culture. Each well was treated with either DMSO or p300/CBP inhibitors (10 μM) from days 11 to 14. Data are presented as mean ± SEM (n = 3 biologically independent experiments). One-way ANOVA followed by Tukey’s multiple comparisons test; ** p < 0.01. f Schematic outline for sorting CD54 + iATCs from day 14 of the micro-patterned culture. Created in BioRender. Tsutsui, Y. (2026) https://BioRender.com/v51i925 g Gene expression data of ATCS markers in the micro-patterned culture. Data are presented as mean ± SEM ( n = 3 biologically independent experiments). One-way ANOVA followed by Tukey’s multiple comparisons test; ** p < 0.01, *** p < 0.001, **** p < 0.0001. h Schematic outline of the co-culture experiment involving isolated CD54 + iATCs and NHLFs. Created in BioRender. Tsutsui, Y. (2026) https://BioRender.com/nbi6c0b i Gene expression analysis of ATCS markers in isolated CD54 + iATCs. Data are presented as mean ± SEM ( n = 3 biologically independent experiments). One-way ANOVA followed by Tukey’s multiple comparisons test; ** p < 0.01. ns; not significant ( p > 0.05). j Gene expression analysis of fibroblast activation markers in NHLFs cocultured with or without iATCs. Data are presented as mean ± SEM ( n = 3 biologically independent experiments). Unpaired two-tailed Student’s t test: ∗ p < 0.05.

Article Snippet: Primary antibodies used in this study included GFP (1:500, Aves Labs, GFP-1020), SFN (1:200, Abcam, ab77187), act-p300 (1:200, biorbyt, ORB6262), EpCAM (1:200, Santa Cruz Biotechnology, sc-66020), KRT19 (1:200, Merck, MABT913), KRT17 (1:100, Abcam, ab109725), COL1A1 (1:200, Abcam, ab138492), CD54 (1:200, BioLegend, 353102), CD54 (1:200, Atlas, HPA002126), HT1-56 (1:200, Terrace Biotech, TB29AHT1-56), NaPi2b (1:200, kindly provided by Dr. Gerd Ritter (MX35)), AGER (R&D systems, AF1145), H3K27ac (1:200, Cell Signaling technology, 8173), FLAG (1:500, Cell Signaling technology, 14793), alpha smooth muscle Actin (1:100, Abcam ab5694), and Fluorescin (1:1000, Vector Laboratories, FL-1171).

Techniques: Gene Expression, Immunostaining, Flow Cytometry, Co-Culture Assay, Isolation, Activation Assay, Two Tailed Test

Journal: iScience

Article Title: Host biomarker-based quantitative rapid tests for detection and treatment monitoring of tuberculosis and COVID-19.

doi: 10.1016/j.isci.2022.105873

Figure Lengend Snippet: Figure 1. Evaluation of host biomarkers for TB and LTBI in a European cohort Levels of IL-6, IP-10, ferritin, SAA1/A2, CRP, ApoA1, and S100A12 were measured by UCP-LFA in serum samples of TB patients (n = 30; green dots) and LTBI (n = 29; gray dots) from Europe. Median values for each group are indicated by horizontal bars. Mann-Whitney U tests were performed to determine the statistical significance between groups (pvalues: *p%0 $ 05, **p%0 $ 01, ***p%0 $ 001, ****p%0 $ 0001). Green dots: TB cohort 1; gray dots: LTBI cohort 1. AUC: area under the curve; Fc: flow control line; LTBI: latent tuberculosis infection; T: test line; TB: tuberculosis.

Article Snippet: 4 mm width UCP-LF strips specific for a single host protein – ApoA1, CRP, ferritin, IL-6, IP-10, SAA1/A2, and S100A12 - were produced as described earlier.24,28,29 For ApoA1, CRP, ferritin, IL-6, IP-10, SAA1/A2, and S100A12 LF strips, each Test (T) line comprised 200 ng of the following antibodies: goat-anti-human ApoA1 pAb (AF3664; R&D systems, Minneapolis, MN, USA), mouse-anti-human CRP mAb (C5; Labned.com, Amstelveen, the Netherlands), mouse-anti-human ferritin mAb (F31; Novus Biologicals, Littleton, CO, USA), rat-anti-human IL-6 mAb (MQ2-39C3; Biolegend, San Diego, CA, USA), mouse-anti-human IP-10 mAb (B-C55; Diaclone Research, Besancon, France), mouse-anti-human SAA1/A2 mAb (865504; R&D systems, Minneapolis, MN, USA), and goat-anti-human S100A12 pAb (AF1052; R&D systems, Minneapolis, MN, USA), respectively.

Techniques: MANN-WHITNEY, Control, Infection

Journal: iScience

Article Title: Host biomarker-based quantitative rapid tests for detection and treatment monitoring of tuberculosis and COVID-19.

doi: 10.1016/j.isci.2022.105873

Figure Lengend Snippet: Figure 2. Evaluation of host biomarkers for Dutch COVID-19 patients and healthy controls Levels of IL-6, IP-10, ferritin, SAA1/A2, CRP, ApoA1, and S100A12 were measured by UCP-LFA in serum samples of COVID-19 patients (n = 102) and healthy controls (n = 39; n = 27 from before (May) 2019 (n = 12 from after 2019 (June/July 2020)) from the Netherlands. Median values for each group are indicated by horizontal bars. Mann-Whitney U tests were performed to determine the statistical significance between groups (pvalues: *p%0 $ 05, **p%0 $ 01, ***p%0 $ 001, ****p %0 $ 0001). Orange dots: healthy controls from before 2019; purple dots: healthy controls from after 2019; black dots: COVID-19 patients with a fatal outcome; yellow dots: COVID-19 patients with severe disease; turquoise dots: COVID-19 patients with moderate disease. AUC: area under the curve; COVID-19: coronavirus disease 2019; Fc: flow control line; T: test line.

Article Snippet: 4 mm width UCP-LF strips specific for a single host protein – ApoA1, CRP, ferritin, IL-6, IP-10, SAA1/A2, and S100A12 - were produced as described earlier.24,28,29 For ApoA1, CRP, ferritin, IL-6, IP-10, SAA1/A2, and S100A12 LF strips, each Test (T) line comprised 200 ng of the following antibodies: goat-anti-human ApoA1 pAb (AF3664; R&D systems, Minneapolis, MN, USA), mouse-anti-human CRP mAb (C5; Labned.com, Amstelveen, the Netherlands), mouse-anti-human ferritin mAb (F31; Novus Biologicals, Littleton, CO, USA), rat-anti-human IL-6 mAb (MQ2-39C3; Biolegend, San Diego, CA, USA), mouse-anti-human IP-10 mAb (B-C55; Diaclone Research, Besancon, France), mouse-anti-human SAA1/A2 mAb (865504; R&D systems, Minneapolis, MN, USA), and goat-anti-human S100A12 pAb (AF1052; R&D systems, Minneapolis, MN, USA), respectively.

Techniques: MANN-WHITNEY, Control

Journal: iScience

Article Title: Host biomarker-based quantitative rapid tests for detection and treatment monitoring of tuberculosis and COVID-19.

doi: 10.1016/j.isci.2022.105873

Figure Lengend Snippet: Figure 3. Evaluation of host biomarkers for TB and COVID-19 patients Levels of IL-6, IP-10, ferritin, SAA1/A2, CRP, ApoA1, and S100A12 were measured by UCP-LFA in serum samples of TB patients (n = 46) and COVID-19 patients (n = 102) collected in European hospitals. Median values for each group are indicated by horizontal bars. Mann-Whitney U tests were performed to determine the statistical significance between groups (pvalues: *p%0 $ 05, **p%0 $ 01, ***p%0 $ 001, ****p%0 $ 0001). Green dots: TB cohort 1; blue dots: TB cohort 2; black dots: COVID-19 patients. AUC: area under the curve; COVID-19: coronavirus disease 2019; Fc: flow control line; T: test line; TB: tuberculosis.

Article Snippet: 4 mm width UCP-LF strips specific for a single host protein – ApoA1, CRP, ferritin, IL-6, IP-10, SAA1/A2, and S100A12 - were produced as described earlier.24,28,29 For ApoA1, CRP, ferritin, IL-6, IP-10, SAA1/A2, and S100A12 LF strips, each Test (T) line comprised 200 ng of the following antibodies: goat-anti-human ApoA1 pAb (AF3664; R&D systems, Minneapolis, MN, USA), mouse-anti-human CRP mAb (C5; Labned.com, Amstelveen, the Netherlands), mouse-anti-human ferritin mAb (F31; Novus Biologicals, Littleton, CO, USA), rat-anti-human IL-6 mAb (MQ2-39C3; Biolegend, San Diego, CA, USA), mouse-anti-human IP-10 mAb (B-C55; Diaclone Research, Besancon, France), mouse-anti-human SAA1/A2 mAb (865504; R&D systems, Minneapolis, MN, USA), and goat-anti-human S100A12 pAb (AF1052; R&D systems, Minneapolis, MN, USA), respectively.

Techniques: MANN-WHITNEY, Control

Journal: iScience

Article Title: Host biomarker-based quantitative rapid tests for detection and treatment monitoring of tuberculosis and COVID-19.

doi: 10.1016/j.isci.2022.105873

Figure Lengend Snippet: Figure 4. Treatment monitoring for TB Levels of IL-6, IP-10, ferritin, SAA1/A2, CRP, ApoA1, and S100A12 were measured by UCP-LFA in serum samples of pulmonary TB patients (n = 22) before treatment (t0), at months 2–4 (t1), and months 5–9 (t2) of treatment. Median values for each group are indicated by horizontal bars. The gray dotted lines represent the median value of the corresponding marker measured for 39 healthy controls. S100A12 data were missing for one patient. Friedman test with Dunn’s correction for multiple testing was performed to determine the statistical significance between timepoints (pvalues: *p%0 $ 05, **p%0 $ 01, ***p%0 $ 001, ****p%0 $ 0001). Fc: flow control line; T: test line; TB: tuberculosis; t0: first timepoints; t1: 2–4 months after the beginning of treatment; t2: 5–9 months after the beginning of treatment.

Article Snippet: 4 mm width UCP-LF strips specific for a single host protein – ApoA1, CRP, ferritin, IL-6, IP-10, SAA1/A2, and S100A12 - were produced as described earlier.24,28,29 For ApoA1, CRP, ferritin, IL-6, IP-10, SAA1/A2, and S100A12 LF strips, each Test (T) line comprised 200 ng of the following antibodies: goat-anti-human ApoA1 pAb (AF3664; R&D systems, Minneapolis, MN, USA), mouse-anti-human CRP mAb (C5; Labned.com, Amstelveen, the Netherlands), mouse-anti-human ferritin mAb (F31; Novus Biologicals, Littleton, CO, USA), rat-anti-human IL-6 mAb (MQ2-39C3; Biolegend, San Diego, CA, USA), mouse-anti-human IP-10 mAb (B-C55; Diaclone Research, Besancon, France), mouse-anti-human SAA1/A2 mAb (865504; R&D systems, Minneapolis, MN, USA), and goat-anti-human S100A12 pAb (AF1052; R&D systems, Minneapolis, MN, USA), respectively.

Techniques: Marker, Control

Journal: iScience

Article Title: Host biomarker-based quantitative rapid tests for detection and treatment monitoring of tuberculosis and COVID-19.

doi: 10.1016/j.isci.2022.105873

Figure Lengend Snippet: Figure 5. Treatment monitoring for COVID-19 Levels of IL-6, IP-10, ferritin, SAA1/A2, CRP, ApoA1, and S100A12 were measured by UCP-LFA in serum samples from COVID-19 patients (n = 25) at hospital admission (t0) and follow-up (t2). Median values for each group are indicated by horizontal bars. The gray dotted lines represent the median value of the corresponding marker measured for 39 healthy controls. Wilcoxon matched pairs signed rank tests were performed to determine the statistical significances between timepoints (pvalues: *p%0 $ 05, **p%0 $ 01, ***p%0 $ 001, ****p%0 $ 0001). COVID-19: coronavirus disease 2019; Fc: flow control line; T: test line; t0: timepoint of hospital admission; t2: follow-up around 6 weeks after hospital discharge.

Article Snippet: 4 mm width UCP-LF strips specific for a single host protein – ApoA1, CRP, ferritin, IL-6, IP-10, SAA1/A2, and S100A12 - were produced as described earlier.24,28,29 For ApoA1, CRP, ferritin, IL-6, IP-10, SAA1/A2, and S100A12 LF strips, each Test (T) line comprised 200 ng of the following antibodies: goat-anti-human ApoA1 pAb (AF3664; R&D systems, Minneapolis, MN, USA), mouse-anti-human CRP mAb (C5; Labned.com, Amstelveen, the Netherlands), mouse-anti-human ferritin mAb (F31; Novus Biologicals, Littleton, CO, USA), rat-anti-human IL-6 mAb (MQ2-39C3; Biolegend, San Diego, CA, USA), mouse-anti-human IP-10 mAb (B-C55; Diaclone Research, Besancon, France), mouse-anti-human SAA1/A2 mAb (865504; R&D systems, Minneapolis, MN, USA), and goat-anti-human S100A12 pAb (AF1052; R&D systems, Minneapolis, MN, USA), respectively.

Techniques: Marker, Control