Journal: Nature Communications

Article Title: Tuft cells shape airway remodeling by eliciting OXGR1- and SOX9-dependent stem cell programs

doi: 10.1038/s41467-026-70763-y

Figure Lengend Snippet: a Representative Masson’s Trichrome staining in tracheal sections at day 14. Scale bars: 200 μm. Cartilage rings are labelled C1–C6. b – e Quantification of collagen deposition over WT PBS d14 (b) or over WT ALT d14 (d), and gland numbers from C1-C7 cartilages ( c , e ). Group sizes: n = 7, 7, 5, 4, 7 ( b , c ) and n = 4, 5, 3 ( d , e ) mice, from left to right. f Experimental schema. g Representative images of lineage-labelled Sox9-tdT + cells among BCAM + BCs on the SAE at day 14. Scale bar: 200 μm. Areas outlined (a, b) are shown below (Scale bars: 50 μm). Cartilage rings are labelled C1–C7. CC Cricoid cartilage. h , i Quantification of Sox9-tdT + BCAM + cells in the SAE per high power field (HPF) ( h ) and as a percentage of total BCAM + cells ( i ) in ALT-injured trachea at day 14. Group sizes: n = 7, 15, 6 mice, from left to right. j , k Quantification of Sox9-tdT + BCAM + cells in the SAE per HPF ( j ) and as a percentage of total BCAM + cells ( k ) in influenza-injured trachea at 7 days post infection. Group sizes: n = 3, 6, 8 mice, from left to right. l , m Representative images ( l ) and quantification ( m ) of BCAM and SOX9 staining in tracheal sections at day 14. Scale bars: 20 μm. Group sizes: n = 5, 6, 4 mice, from left to right. Two-tailed unpaired Mann-Whitney U test ( b – e , m ). Kruskal–Wallis test followed by Dunn’s multiple-comparisons test with Holm–Bonferroni correction ( h – k ). The dashed outline ( g , i ) marks the border between SAE and SM. Box plots ( b – e , h – k , m ) show median (center line), 25th–75th percentiles (box), and min–max values (whiskers). Each data point represents the average of 3–4 images from one mouse, except for the glandular number ( c , e ), which represents the total glands per trachea measured by tiled imaging. See “Methods”. Panel f was created in BioRender. Lee, M. ( https://BioRender.com/dg3i7rm ). Source data are provided as a Source Data file.

Article Snippet: Female (12 weeks- to 14 weeks) and male (10 weeks- to 12 weeks) mice of the following genotypes and strains were used: C57BL/6 (Charles River Laboratories, CRL# 027), Oxgr1 -/- (KOMP, stock number 048933-UCD), Pou2f3 -/- (The Jackson Laboratory, stock number 037040), Cysltr1 -/- (kindly provided by Dr. Lora Bankova, BWH, Boston), Cysltr2 -/- (kindly provided by Dr. Joshua Boyce, BWH, Boston), Krt5 CreERT2 (The Jackson Laboratory, stock number 029155), Pou2f3 CreERT2 (The Jackson Laboratory, stock number 037511), Sox9 CreERT2 (The Jackson Laboratory, stock number 035092), Sox9 fl/fl (The Jackson Laboratory, stock number 013106), Oxgr1 fl/fl (Barrett Lab), Ltc4s fl/fl (kindly provided by Dr. Lora Bankova, BWH, Boston), and Ai9 (RCL-tdT) (The Jackson Laboratory, stock number 007909).

Techniques: Staining, Infection, Two Tailed Test, MANN-WHITNEY, Imaging

Journal: Nature Communications

Article Title: Tuft cells shape airway remodeling by eliciting OXGR1- and SOX9-dependent stem cell programs

doi: 10.1038/s41467-026-70763-y

Figure Lengend Snippet: a Representative images of DCLK1 and BCAM staining in tracheal sections from the indicated Sox9-tdT reporter strains at day 14. Sox9-tdT + BCAM + cells (white arrow). Scale bars: 50 µm. b Quantification of Sox9-tdT + BCAM + cells in the SAE from the indicated strains at day 14. Group sizes: n = 5, 6, 12, 5 mice, from left to right. Two-tailed unpaired Mann-Whitney U test. c , d Combined in situ hybridization (ISH) for Oxgr1, Krt5 and Krt8 , and immunofluorescence for SOX9 and α-SMA in tracheal sections from WT mice with or without ALT treatment ( Krt5 for BCs, Krt8 for differentiated cells, SOX9 for SMG progenitor cells, and α-SMA for SMG myoepithelial cells). Oxgr1 + SOX9 + cells (green arrows). Scale bars: 20 μm. SMG Submucosal gland. ( e ) Quantification of Oxgr1 + cells in the specified EpC subsets. Group sizes: n = 7, 16, 8, 13, 6, 10, 7, 8 mice, from left to right. Kruskal–Wallis test followed by Dunn’s multiple-comparisons test with Holm–Bonferroni correction. f Quantification of Oxgr1 + cells among the Krt5 + or Krt8 + cells. Group sizes: n = 12, 11, 12, 7 mice, from left to right. Two-tailed unpaired Mann-Whitney U test. g Experimental schema. h , i Representative images ( h ) and quantification ( i ) of BCAM and SOX9 staining in tracheal sections from the indicated strains at day 14. Scale bars: 20 μm. Group sizes: n = 5, 8, 7, 5 mice, from left to right. Kruskal–Wallis test followed by Dunn’s multiple-comparisons test with Holm–Bonferroni correction. The dashed line marks the border between SAE and SM. Box plots ( b , e , f , i ) show median (center line), 25th–75th percentiles (box), and min–max values (whiskers). Each data point represents the average of 3–4 images from one mouse. See “Methods”. Panel g was created in BioRender. Lee, M. ( https://BioRender.com/dg3i7rm ). Source data are provided as a Source Data file.

Article Snippet: Female (12 weeks- to 14 weeks) and male (10 weeks- to 12 weeks) mice of the following genotypes and strains were used: C57BL/6 (Charles River Laboratories, CRL# 027), Oxgr1 -/- (KOMP, stock number 048933-UCD), Pou2f3 -/- (The Jackson Laboratory, stock number 037040), Cysltr1 -/- (kindly provided by Dr. Lora Bankova, BWH, Boston), Cysltr2 -/- (kindly provided by Dr. Joshua Boyce, BWH, Boston), Krt5 CreERT2 (The Jackson Laboratory, stock number 029155), Pou2f3 CreERT2 (The Jackson Laboratory, stock number 037511), Sox9 CreERT2 (The Jackson Laboratory, stock number 035092), Sox9 fl/fl (The Jackson Laboratory, stock number 013106), Oxgr1 fl/fl (Barrett Lab), Ltc4s fl/fl (kindly provided by Dr. Lora Bankova, BWH, Boston), and Ai9 (RCL-tdT) (The Jackson Laboratory, stock number 007909).

Techniques: Staining, Two Tailed Test, MANN-WHITNEY, In Situ Hybridization, Immunofluorescence

Journal: Nature Communications

Article Title: Tuft cells shape airway remodeling by eliciting OXGR1- and SOX9-dependent stem cell programs

doi: 10.1038/s41467-026-70763-y

Figure Lengend Snippet: a Experimental schema. b Principal-component analysis (PCA) of the top 500 most variable genes expressed in the two groups. Numbers in parentheses indicate the percent variance captured by each PC. c Relative expression of Sox9 and canonical BC genes. d Heatmap of 1443 differentially expressed genes (DEGs) following unsupervised hierarchical clustering, defined by |log2FoldChange | > 0.58 and adjusted p-values < 0.05 with multiple testing correction using the Benjamini–Hochberg method ( e ) GSEA enrichment plots for two of the most overrepresented gene sets. Gene set enrichment analysis (GSEA) was performed using a weighted Kolmogorov–Smirnov–like statistic to calculate enrichment scores. Statistical significance was assessed by permutation testing, and nominal P values were derived from the permutation-based null distribution. Normalized enrichment scores (NES) were calculated to account for differences in gene set size, and multiple hypothesis testing was controlled using the Benjamini–Hochberg false discovery rate (FDR) correction. f – h Heatmaps of DEGs related to alarmins and inflammatory genes ( f ), collagen component genes ( g ), and ciliogenesis and cilia assembly genes ( h ). i , j Representative images ( i ) and quantification ( j ) of acetylated tubulin (Ac-tub) staining on tracheal sections from the indicated strains at day 14. Scale bars: 20 μm. The dashed line marks the border between SAE and SM. Group sizes: n = 7, 8 mice, from left to right. Two-tailed unpaired Mann-Whitney U test. Box plots ( j ) show median (center line), 25th–75th percentiles (box), and min–max values (whiskers). Each data point represents the average of 3–4 images from one mouse. See Methods. Panel a was created in BioRender. Lee, M. ( https://BioRender.com/dg3i7rm ). Source data are provided as a Source Data file.

Article Snippet: Female (12 weeks- to 14 weeks) and male (10 weeks- to 12 weeks) mice of the following genotypes and strains were used: C57BL/6 (Charles River Laboratories, CRL# 027), Oxgr1 -/- (KOMP, stock number 048933-UCD), Pou2f3 -/- (The Jackson Laboratory, stock number 037040), Cysltr1 -/- (kindly provided by Dr. Lora Bankova, BWH, Boston), Cysltr2 -/- (kindly provided by Dr. Joshua Boyce, BWH, Boston), Krt5 CreERT2 (The Jackson Laboratory, stock number 029155), Pou2f3 CreERT2 (The Jackson Laboratory, stock number 037511), Sox9 CreERT2 (The Jackson Laboratory, stock number 035092), Sox9 fl/fl (The Jackson Laboratory, stock number 013106), Oxgr1 fl/fl (Barrett Lab), Ltc4s fl/fl (kindly provided by Dr. Lora Bankova, BWH, Boston), and Ai9 (RCL-tdT) (The Jackson Laboratory, stock number 007909).

Techniques: Expressing, Derivative Assay, Staining, Two Tailed Test, MANN-WHITNEY

Journal: Nature Communications

Article Title: Tuft cells shape airway remodeling by eliciting OXGR1- and SOX9-dependent stem cell programs

doi: 10.1038/s41467-026-70763-y

Figure Lengend Snippet: a Combined ISH for Pou2f3 , and immunofluorescence for E-Cadherin in human sinonasal tissue from healthy control (HC) and CRSwNP. Pou2f3 + cells (yellow arrow). Scale bars: 20 µm. b , c Quantification of Pou2f3 + tuft cells ( b ) and E-Cadherin staining ( c ) in the SAE across human sinonasal tissues. Group sizes: n = 6, 11, 27 independent patients, from left to right. Two-tailed unpaired Mann-Whitney U test ( b ). Kruskal–Wallis test followed by Dunn’s multiple-comparisons test with Holm–Bonferroni correction ( c ). d Spearman’s correlation analysis (two-sided) between E-Cadherin levels and Pou2f3 + tuft cell numbers in patients with CRSwNP ( n = 27, independent patients). No multiple comparison adjustment was applied. e Representative images of E-Cadherin, α-SMA, and SOX9 staining in human sinonasal mucosa from CRS patients and healthy control (HC). SOX9 + α-SMA + cells (yellow arrow). Scale bars: 20 µm. f Quantification of SOX9 + and/or α-SMA + cells in the SAE from the indicated groups. Group sizes: n = 6, 11, 27 independent patients, from left to right. Kruskal–Wallis test followed by Dunn’s multiple-comparisons test with Holm–Bonferroni correction. g , h Spearman’s correlation analysis (two-sided) between SOX9 + cell numbers and E-Cadherin intensity ( g ) and α-SMA + cell numbers ( h ) in patients with CRSwNP ( n = 27 independent patients). No multiple comparison adjustment was applied. i Spearman’s correlation analysis (two-sided) between E-Cadherin levels and SOX9 + α-SMA + cell numbers in patients with CRSwNP ( n = 27 independent patients). No multiple comparison adjustment was applied. The Spearman r values and the corresponding P values were calculated ( g – i ). j SOX9 progenitor cell signature module score in basal EpCs from the Wang scRNA-seq dataset (HRA000772) across the patients. One-sided Wilcoxon rank sum test was used. No multiple comparison adjustment was applied. The dashed line marks the border between SAE and SM. Box plots ( b , c , f ) show median (center line), 25th–75th percentiles (box), and min–max values (whiskers). Each data point represents the average of 3–4 images from one patient. See “Methods”. Source data are provided as a Source Data file.

Article Snippet: Female (12 weeks- to 14 weeks) and male (10 weeks- to 12 weeks) mice of the following genotypes and strains were used: C57BL/6 (Charles River Laboratories, CRL# 027), Oxgr1 -/- (KOMP, stock number 048933-UCD), Pou2f3 -/- (The Jackson Laboratory, stock number 037040), Cysltr1 -/- (kindly provided by Dr. Lora Bankova, BWH, Boston), Cysltr2 -/- (kindly provided by Dr. Joshua Boyce, BWH, Boston), Krt5 CreERT2 (The Jackson Laboratory, stock number 029155), Pou2f3 CreERT2 (The Jackson Laboratory, stock number 037511), Sox9 CreERT2 (The Jackson Laboratory, stock number 035092), Sox9 fl/fl (The Jackson Laboratory, stock number 013106), Oxgr1 fl/fl (Barrett Lab), Ltc4s fl/fl (kindly provided by Dr. Lora Bankova, BWH, Boston), and Ai9 (RCL-tdT) (The Jackson Laboratory, stock number 007909).

Techniques: Immunofluorescence, Control, Staining, Two Tailed Test, MANN-WHITNEY, Comparison

Journal: Nature Communications

Article Title: Tuft cells shape airway remodeling by eliciting OXGR1- and SOX9-dependent stem cell programs

doi: 10.1038/s41467-026-70763-y

Figure Lengend Snippet: (Left) In homeostasis, basal cells are the dominant progenitor of all ciliated and secretory epithelial cells on the SAE. (Right) In the setting of tissue damage elicited by allergens or by influenza ( 1 ), tuft cells generate CysLTs (2). Leukotriene E 4 (LTE 4 ) activates OXGR1 (also known as CysLTR3 and GPR99) on SOX9 + SMG progenitors ( 3 ). This results in airway remodeling including SMG hyperplasia ( 4 ) and submucosal collagen deposition ( 5 ). SOX9 + progenitors regenerate the SAE but allow persistent barrier leak ( 6 ), bringing a program that is rich in mesenchymal genes and deficient in ciliogenesis genes. This leads to an SAE with reduced ciliated cells, reduced E-Cadherin, and increased α-SMA ( 7 ). This figure was created in BioRender. Barrett, N. ( https://BioRender.com/d9cr3ur ).

Article Snippet: Female (12 weeks- to 14 weeks) and male (10 weeks- to 12 weeks) mice of the following genotypes and strains were used: C57BL/6 (Charles River Laboratories, CRL# 027), Oxgr1 -/- (KOMP, stock number 048933-UCD), Pou2f3 -/- (The Jackson Laboratory, stock number 037040), Cysltr1 -/- (kindly provided by Dr. Lora Bankova, BWH, Boston), Cysltr2 -/- (kindly provided by Dr. Joshua Boyce, BWH, Boston), Krt5 CreERT2 (The Jackson Laboratory, stock number 029155), Pou2f3 CreERT2 (The Jackson Laboratory, stock number 037511), Sox9 CreERT2 (The Jackson Laboratory, stock number 035092), Sox9 fl/fl (The Jackson Laboratory, stock number 013106), Oxgr1 fl/fl (Barrett Lab), Ltc4s fl/fl (kindly provided by Dr. Lora Bankova, BWH, Boston), and Ai9 (RCL-tdT) (The Jackson Laboratory, stock number 007909).

Techniques:

Journal: Molecular Therapy. Nucleic Acids

Article Title: Smart exosomes with lymph node homing and immune-amplifying capacities for enhanced immunotherapy of metastatic breast cancer

doi: 10.1016/j.omtn.2021.10.009

Figure Lengend Snippet: Construction and characterization of Exo OX40L (A) Schematic representation of the experimental procedure. OX40L-overexpressing lentivirus was packaged. DC2.4 cells as exosome donor cells were then infected with the lentivirus, followed by exosome isolation and characterization. (B) Western blot analysis of the expression of OX40L and inclusive and exclusive exosomal markers in both the parental cells and derived exosomes. Representative data of three different experiments. (C) Transmission electron microscopy (TEM) analysis of Exo OX40L . (D) Size distribution of the indicated exosomes was analyzed by NanoSight. (E) Nanoparticle tracking analysis of the captured exosomes by anti-OX40L antibody. ∗∗P<0.01 by one-way ANOVA. ns, no significance.

Article Snippet: After blocking with 3% bovine serum albumin (BSA), the membranes were subsequently incubated with first antibodies anti-OX40L (ab229021, Abcam), anti-CD62L (ab253241, Abcam), anti-GM130 (11308-1-AP, ProteinTech), anti-TSG101 (ab83, Abcam), anti-CD9 (ab92726, Abcam), and anti-GAPDH (D110016-0100, BBI Life Sciences) at 4°C for 12 h. After being washed three times in TBST (Tris buffered saline with tween-20), the membranes were incubated with the secondary antibodies (anti-mouse [7076, CST] or anti-rabbit [7074, CST]) in Tris-buffered saline at room temperature for 1 h. The images were developed by chemiluminescence (GE Healthcare, Chalfont St. Giles, UK) in a dark room.

Techniques: Infection, Isolation, Western Blot, Expressing, Derivative Assay, Transmission Assay, Electron Microscopy

Journal: Molecular Therapy. Nucleic Acids

Article Title: Smart exosomes with lymph node homing and immune-amplifying capacities for enhanced immunotherapy of metastatic breast cancer

doi: 10.1016/j.omtn.2021.10.009

Figure Lengend Snippet: Exo Smart promotes effector T cell activation and inhibits Tregs in lymph nodes simultaneously (A) Experimental procedure for Exo Smart . Donor cells were forced expressed with CD62L and OX40L by infection of the overexpressing lentivirus. (B) Schematic representation of the exosome treatment. 4T1 breast tumor-bearing mice were injected with the exosomes at the indicated time. (C) Representative images of immunostaining of Ki67 (red) and CD3 (green) in lymph nodes from mice with indicated treatments. n = 3. (D) Representative images of immunostaining of Ki67 (red) and Foxp3 (green) in lymph nodes from mice with indicated treatments. n = 3. (E) Representative flow cytometric analysis of CTL (CD3 + CD8 + T cells) in lymph nodes from mice with indicated treatments. (F) Representative flow cytometric analysis of CD4 + helper cells (CD3 + CD4 + T cells) in lymph nodes from mice with indicated treatments. (G) Representative flow cytometric analysis of Tregs (CD3 + CD4 + Foxp3 + T cells) in lymph nodes from mice with indicated treatments. (H) qPCR analysis of the expression of IL-2 and IFN-γ in lymph nodes from mice with indicated treatments. (I) qPCR analysis of the expression of IL-10, Foxp3, and TGF-β detected in lymph nodes from mice with indicated treatments. Data are representative of three different experiments and expressed as mean ± SEM. ∗p < 0.05, ∗∗p < 0.01 by one-way ANOVA.

Article Snippet: After blocking with 3% bovine serum albumin (BSA), the membranes were subsequently incubated with first antibodies anti-OX40L (ab229021, Abcam), anti-CD62L (ab253241, Abcam), anti-GM130 (11308-1-AP, ProteinTech), anti-TSG101 (ab83, Abcam), anti-CD9 (ab92726, Abcam), and anti-GAPDH (D110016-0100, BBI Life Sciences) at 4°C for 12 h. After being washed three times in TBST (Tris buffered saline with tween-20), the membranes were incubated with the secondary antibodies (anti-mouse [7076, CST] or anti-rabbit [7074, CST]) in Tris-buffered saline at room temperature for 1 h. The images were developed by chemiluminescence (GE Healthcare, Chalfont St. Giles, UK) in a dark room.

Techniques: Activation Assay, Infection, Injection, Immunostaining, Expressing

Journal: The International journal of developmental biology

Article Title: Gonadal defects in Cited2-mutant mice indicate a role for SF1 in both testis and ovary differentiation.

doi: 10.1387/ijdb.092920ac

Figure Lengend Snippet: Fig. 1. Abnormal testis morphology in Cited2 -/- mice. (A-C) Represen- tative images of gonadal morphology from 12.5 - 14.5 dpc Cited2+/+ and Cited2+/- embryos. Asterisks indicate testis cords and an arrow indicates the coelomic vessel. (D-F) Abnormal morphology in Cited2 -/- gonads demonstrates that testis development is defective in embryos lacking this gene. Arrows indicate the coelomic vessel, brackets highlight re- gions where Sertoli and germ cells are not organised into testis cords, asterisks mark testis cords. A-F, Sertoli cells are marked by an anti-SOX9 antibody (green). A, B, D, E are confocal images of wholemount gonads; germ cells and vasculature are marked by an anti PECAM-1 antibody (red). C and F are confocal images of paraffin sections; germ cells are marked by an anti-OCT4 antibody (red). n ≥ 3 for each knockout stage analysed. Scale bar, 100 μm.

Article Snippet: The following antibodies were used: Rabbit anti-SOX9 antibody (Wilhelm et al., 2005), Rat anti-platelet endothelial cell adhesion molecule-1/CD31 (PECAM-1, 1:200, BD Biosciences), Mouse antiOCT4 (1:50, Santa Cruz Biotechnology).

Techniques: Knock-Out

Journal: International journal of molecular sciences

Article Title: Metabolic Reconfiguration Activates Stemness and Immunomodulation of PDLSCs.

doi: 10.3390/ijms23074038

Figure Lengend Snippet: Figure 3. Curcumin increased the capabilities of osteogenic and chondrogenic differentiation in PDLSCs. (A) Heat map of RNA-seq analysis data showing the PDLSC function-related genes that were differentially regulated by curcumin treatment. (B,C) qPCR assay showed the significantly elevated levels of osteoprogenitor markers (B) and chondroprogenitor markers (C) in curcumin treated PDLSCs. (D) Alizarin red staining showed that curcumin treated PDLSCs has increased capacity to form mineralized nodules under osteoinductive conditions. (E) Western blot analysis showed the expression levels of the osteogenic genes RUNX2 and ALP were greatly increased in curcumin treated PDLSCs under osteoinductive conditions. β-actin was used as a loading control. (F) Histological analysis showed chondrogenic differentiation of vehicle and curcumin treated PDLSCs. Scale bar, 25 µm. IF staining showed increased ACAN+ and SOX9+ cells after curcumin treatment in PDLSCs. Scale bar, 25 µm. * p < 0.005. Error bars represent the s.d. from the mean values.

Article Snippet: Anti-ACAN antibody was purchased from Abcam, Cambridge, UK, and anti-SOX9 antibody was purchased from Novus Biologicals, Littleton, CO, USA.

Techniques: RNA Sequencing, Staining, Western Blot, Expressing, Control

Journal: BMC developmental biology

Article Title: Sonic hedgehog promotes chondrogenesis of rabbit bone marrow stem cells in a rotary cell culture system.

doi: 10.1186/s12861-019-0198-4

Figure Lengend Snippet: Fig. 5 The effect of Shh on cartilage related markers during differentiation induction in the RCCS environment. a-h RT-PCR analysis of Sox9, ACAN, collagen II, collagen X, RUNX2, ALP, PPAR-γ and leptin on days 7,14 and 21 during differentiation induction. i, j Expression of Sox 9, collagen II, ACAN, collagen X, RUNX2, ALP and PPAR-γ in the RCCS dimensional environment on days 10 and 21 of chondrogenesis. The representative results were from three independent experiments. Significant differences between the control group are indicated by * p < 0.05, **p < 0.01; differences between Shh and TGF-β transfection groups are indicated by # p < 0.05 or ## p < 0.01

Article Snippet: Antibodies recognising Ptc (Aviva Systems Biology, San Diego, CA, USA; 1:500), Smo (Aviva Systems Biology; 1:1,600), Gli1 (Biorbyt, Cambridgeshire, UK; 1:1,000), Sox9 (OriGene, Rockville, MD, USA; 1:500), collagen II (Novus Biologicals, Littleton, CO, USA; 1:200), ACAN (Novus Biologicals; 1:100), collagen X (Abcam; 1:500), RUNX2 (Abcam; 1:500), ALP (Abcam; 1:500), PPAR-γ (Santa Cruz Biotechnology; 1:1000) and GAPDH (Novus Biologicals; 1:2000) were used as primary antibodies.

Techniques: Reverse Transcription Polymerase Chain Reaction, Expressing, Control, Transfection