Journal: bioRxiv

Article Title: Single-Cell Cross-Species Profiling identifies Conserved Transcriptional Networks in Early Pancreatic Tumourigenesis

doi: 10.64898/2026.03.03.708839

Figure Lengend Snippet: (A) Schematic representation of the transgenes used to generate the control (Ac-G) and the acinar-derived pancreatic tumour model (Ac-K). (B-E) 5-day zebrafish larvae expressing the protein GFP ( B,D ) or GFP-KRAS G12D ( C,E ) in the acinar cells of the pancreas. White asterisk indicates gut autofluorescence. White arrows indicate the fluorescent heart, marked by the cmlc2:GFP reporter. Panels D and E show magnified views of the pancreata outlined with white dashed lines in panels B and C. i: principal islet, a: acinar cells. Scale bars : 200 µm. (F-G) Representative photographs of male zebrafish showing a marked abdominal protrusion, indicative of tumour presence ( G, white arrow), compared to a control male ( F ). Scale bars: 2mm. (H-I) Dissected digestive systems of an adult control zebrafish ( H ), showing a healthy pancreas (P, white dashes) or of an Ac-K p53 m/m fish ( I ) with a pancreatic tumour (T, yellow dashes). L: liver, G: gut, S: spleen, P: pancreas, T: tumour. Scale bars: 2mm. (J) Tumour incidence across various TP53 backgrounds. K-L: Hematoxylin and eosin (HE) staining of transversal sections of control pancreas (K) and Ac-K p53 m/m tumour (L) with close-up regions (K’,L’) outlined by black boxes. M-N : Immunofluorescence staining with phospho-histone H3 (pH3) antibody on control (M ) and tumoral tissue sections (N). Control and tumoral pancreatic tissues are surrounded by green dashes. L; Liver, G; gut, d; extrapancreatic duct, i; principal islet, a; acinar cells. Scale bars: 200 µm. O : Quantification of pH3-positive cells in four Ac-K p53 m/m tumours compared to six control pancreas (3 p53 +/+ ; 1 p53 +/m , 2 p53 m/m ). The percentage of pH3 positive cells was calculated as the ratio of the pH3-positive area to the DAPI-positive area, based on the mean of two independent sections per fish. Each point represents an individual fish. Data are presented as mean ± SD; **P = 0.0095, determined using the Mann–Whitney test.

Article Snippet: Immunofluorescence staining was performed with anti-GFP (rabbit, Cell Signalling #2956S 1:200), anti-Caveolin-1(rabbit, Cell Signalling #3238 1:250), anti-α-Amylase (rabbit, Cell Signalling #3796 1:200), anti-Phospho-Histone H3 (pH3) antibodies (rabbit, Cell Signalling #3377T 1:200) overnight at 4°C followed by rabbit HRP SignalStain Boost (Cell Signalling #8114), and Tyramide-FITC, Tyramide-Cy3 (TSA Plus Cyanine 3 System #NEL744001KT Akoya BioSciences) or Tyramide-Cy5 substrate (TSA Plus Cyanine 5 System #NEL745001KT Akoya BioSciences).

Techniques: Control, Derivative Assay, Expressing, Staining, Immunofluorescence, MANN-WHITNEY

Journal: bioRxiv

Article Title: Iro-C/IRX creates anti-cancerized epithelial field against IL-6-dependent malignant tumorigenesis

doi: 10.64898/2026.01.21.700777

Figure Lengend Snippet: (A and B) Pouch+Hinge (P+H) region (A) or Notum (N) region (B) of the wing disc bearing GFP-labeled Ras V12 + scrib.IR clones stained with anti-cleaved PARP antibody, dissected at AEL7. (C) Quantification of the number of dying cells (cPARP-positive cells) in the Ras V12 + scrib.IR clones in the P+H or N region (n=29, p=0.9133). n.s. (not significant); Wilcoxon rank sum test. (D and E) Wing discs bearing GFP-labeled Ras V12 / scrib -/- +LacZ (D) and Ras V12 / scrib -/- +miRHG (E) expressing clones, dissected at AEL7. (F) Quantification of the clone size in the notum region for Ras V12 / scrib -/- +LacZ (n=11) and Ras V12 / scrib -/- +miRHG (n=10, p=0.7564) expressing clones. n.s. (not significant); Wilcoxon rank sum test. (G, H, K, and L) Pouch+Hinge (P+H) region (G and K) or Notum (N) region (H and L) of the wing disc bearing GFP-labeled wild-type or Ras V12 / scrib -/- clones stained with anti-PH3 antibody, dissected at AEL5 (wild-type) or AEL7 (Ras V12 / scrib -/- ). (I, J, M, and N) Pouch+Hinge (P+H) region (I and M) or Notum (N) region (J and N) of the wing disc bearing GFP-labeled wild-type or Ras V12 / scrib -/- clones stained with EdU, dissected at AEL6. (O) Quantification of the PH3-positive cells in wild-type (n=7, p=0.9015) or Ras V12 / scrib -/- (n=7, p=0.0033) clones in the P+H or N region. **p < 0.01; n.s. (not significant); Wilcoxon rank sum test. (P) Quantification of the EdU-positive cells in wild-type (n=9, p=0.6588) or Ras V12 / scrib -/- (n=12, p=0.0020) clones in the P+H or N region. **p < 0.01; n.s. (not significant); Wilcoxon rank sum test. Scale bar, 100 µm.

Article Snippet: Larval tissues were stained with chicken anti-β-galactosidase antibody (Abcam; ab9361, 1:2000), chicken anti-GFP antibody (AVES Labs; GFP-1010, 1:1000), rabbit anti-PH3 antibody (Cell Signaling Technology; 9701, 1:100), rabbit anti-cleaved-PARP antibody (Cell Signaling Technology; 9541, 1:100), rabbit anti-Upd1 antibody (D. Harrison, 1:500), rat anti-Upd3 antibody ( Hirooka et al , 2025 ; Li et al , 2025 ).

Techniques: Labeling, Clone Assay, Staining, Expressing

Journal: bioRxiv

Article Title: Sustained ERK signaling couples the injury response to organizer formation during Hydra head regeneration

doi: 10.64898/2025.12.27.696609

Figure Lengend Snippet: (A) Representative images of H. vulgaris treated with ERK inhibitors (U0126 or BVD-523) or DMSO vehicle control for the first 12 hours of regeneration stained with pH3 antibody to identify mitotic cells and counterstained with Hoechst (nuclei). Scale bar = 100µm. (B) Quantification of pH3-positive nuclei normalized by tissue area for the experiment described in panel A (DMSO n=16, U0126 n=25, BVD-523 n=20). Statistical comparisons were performed using the Wilcoxon rank-sum test.

Article Snippet: Primary antibody incubation was performed overnight at 4°C anti-pH3 antibody (Cell Signaling, #4370) diluted 1:200 in blocking buffer (1% BSA w/v, 10% goat serum v/v; 0.1% Triton X-100 in PBS).

Techniques: Control, Staining

Journal: bioRxiv

Article Title: Sustained ERK signaling couples the injury response to organizer formation during Hydra head regeneration

doi: 10.64898/2025.12.27.696609

Figure Lengend Snippet: (A) Quantification of pH3-positive nuclei normalized to tissue area in animals treated with ERK inhibitors during the first 3 or 8 hpa. Each dot represents an individual animal. For 0–8 hpa treatments, sample sizes were DMSO n = 20, U0126 n = 26, and BVD-523 n = 15. For 0–3 hpa treatments, sample sizes were DMSO n = 18, U0126 n = 12, and BVD-523 n = 22. Statistical comparisons were performed using the Wilcoxon rank-sum test. (B) Representative immunofluorescence images of regenerating animals stained for pH3 and Hoechst following ERK inhibitor treatment during the first 3 or 8 hours of regeneration. Scale bar = 200 µm.

Article Snippet: Primary antibody incubation was performed overnight at 4°C anti-pH3 antibody (Cell Signaling, #4370) diluted 1:200 in blocking buffer (1% BSA w/v, 10% goat serum v/v; 0.1% Triton X-100 in PBS).

Techniques: Immunofluorescence, Staining