Journal: Cerebellum (London, England)

Article Title: Innovative 3D-Image Analysis of Cerebellar Vascularization Highlights Angiogenic Gene Dysregulations in a Murine Model of Apnea of Prematurity

doi: 10.1007/s12311-026-02006-1

Figure Lengend Snippet: Images illustrating the Imaris workflow developed for the vascular network modeling. A–I: Sequential workflow steps allowing the analysis of the cerebellar vascular network of a P4 mouse cerebellum on the Imaris software. From a 3D lightsheet acquisition (A) , the cerebellum is delineated (B) and a mask is created (C) . Within that selected volume, the cerebellar vascularization is segmented (D) , which allows the network visualization (E) and the separation of a deep and a superficial network (F) . Then the threshold of seedpoints is defined (G) , and thanks to the artificial intelligence module (AI), Imaris is able to discriminate “true” (blue) and “false” (red) seedpoints (H) , and “true” (blue) and “false” (red) segments (I) . AI: artificial intelligence; Px: postnatal day x

Article Snippet: Then the threshold of seedpoints is defined (G) , and thanks to the artificial intelligence module (AI), Imaris is able to discriminate “true” (blue) and “false” (red) seedpoints (H) , and “true” (blue) and “false” (red) segments (I) .

Techniques: Software

Journal: Science Advances

Article Title: Inhibition of focal adhesion kinase impairs tumor formation and preserves hearing in a murine model of NF2-related schwannomatosis

doi: 10.1126/sciadv.ady8382

Figure Lengend Snippet: ( A and B ) Dose-response curves comparing the effects of defactinib and a FAK-targeting PROTAC on the viability in human (A) and murine (B) NF2-deficient SCs. Cells were treated with increasing concentrations (0 to 20 μM) of either defactinib or PROTAC for 48 hours, at which time viability was determined via CellTiter-Glo assay, and luminescent values were normalized to untreated control (100%). The dotted line indicates 50% viability. Data points represent mean values ± SEM of n = 12 (02.3 NF2 −/− KO3) or n = 4 (MSO3) replicates. ( C ) Colony formation assays stained with methylene blue and showing the effect of increasing concentrations of defactinib (1 to 5 μM) compared to dimethyl sulfoxide (DMSO) control on three NF2-deficient SC lines: 02.3 NF2 −/− K03, HEI-193, and MS03. ( D ) Volcano plot showing changes in MIB binding of kinases following 24-hour treatment with 1 μM defactinib compared to DMSO control in MS03 cells. X axis represents log 2 fold change (FC) in binding, and the y axis shows the negative log 10 of the P value. Dotted lines indicate significance thresholds for FC and P value. ( E ) Scatter plot depicting DRG volumes (in cubic millimeters) from mice treated with VS-4718 ( n = 14) or vehicle control ( n = 11). Dots represent individual DRG ( n = 4 per mouse). P value represents unpaired, two-tailed t test. Error bars reflect the SEM. ( F ) Representative photomicrographs of H&E-stained DRG obtained from Nf2 and DKO mice. HALO AI DenseNet mask is shown in the bottom panel and depicts abnormal tissue (red), neuron cell bodies (blue), and nerve (lavender). ( G and H ) Plots comparing the percentage of abnormal tissue (G) and neuron cell bodies (H) in Nf2 and DKO DRG. Dots represent individual DRG. Error bars reflect the SEM. P values represent unpaired, two-tailed t test. *** P ≤ 0.001 and n.s., not significant.

Article Snippet: Abnormal tissue and nuclear quantifications were performed using H&E-stained slides and a custom or pretrained HALO AI DenseNet module, respectively (Indica Labs, version 4.0, RRID:SCR_018350).

Techniques: Glo Assay, Control, Staining, Binding Assay, Two Tailed Test

Journal: Science Advances

Article Title: Inhibition of focal adhesion kinase impairs tumor formation and preserves hearing in a murine model of NF2-related schwannomatosis

doi: 10.1126/sciadv.ady8382

Figure Lengend Snippet: ( A ) Scatter plot depicting DRG volumes (in cubic millimeters) from mice treated with VS-4718 ( n = 14) and selumetinib ( n = 14), alone or in combination ( n = 15) and compared to two cohorts (V1 and V2) of age- and sex-matched vehicle controls (V1: n = 11; V2: n = 15). Dots represent individual DRG ( n = 4 per mouse). P values represent one-way ANOVA with Tukey’s multiple-comparison test. Error bars reflect SEM. DRG volumes (in cubic millimeters) for vehicles (V1: n = 11) and VS-4718 ( n = 14) were initially presented in and were included in this graph for the purpose of comparison. ( B ) Representative photomicrographs of H&E-stained DRG obtained from mice of the indicated treatment groups. Mask generated using Indica Lab’s HALO AI DenseNet module is shown in the bottom panel and depicts abnormal tissue (red), neuron cell bodies (blue), and nerve (lavender). ( C ) Scatter plot comparing the percentage of abnormal tissue in DRG of mice treated with VS-4718 ( n = 12) and selumetinib ( n = 14), alone or in combination ( n = 12) and compared to age- and sex-matched vehicle controls ( n = 7). Dots represent individual DRG. Error bars reflect the SEM. P values represent one-way ANOVA with Tukey’s multiple-comparison test.( D ) Representative photomicrographs of Masson’s trichrome–stained DRG obtained from mice treated with VS-4718 ( n = 6) and selumetinib ( n = 14), alone or in combination ( n = 11) compared to age- and sex-matched vehicle controls ( n = 6). Mask generated using Indica Lab’s HALO tissue area module is shown in the bottom panel and depicts collagen staining in purple. ( E ) Plot comparing the amount of collagen within the DRG, reflected as percentage of the total tissue area analyzed. Dots represent individual DRGs. Error bars reflect the SEM. P values represent one-way ANOVA with Tukey’s multiple-comparison test. * P ≤ 0.05, ** P ≤ 0.01, *** P ≤ 0.001, **** P ≤ 0.0001, and n.s., not significant.

Article Snippet: Abnormal tissue and nuclear quantifications were performed using H&E-stained slides and a custom or pretrained HALO AI DenseNet module, respectively (Indica Labs, version 4.0, RRID:SCR_018350).

Techniques: Comparison, Staining, Generated

Journal: Science Advances

Article Title: Inhibition of focal adhesion kinase impairs tumor formation and preserves hearing in a murine model of NF2-related schwannomatosis

doi: 10.1126/sciadv.ady8382

Figure Lengend Snippet: ( A and B ) Dose-response curves comparing the effects of defactinib and a FAK-targeting PROTAC on the viability in human (A) and murine (B) NF2-deficient SCs. Cells were treated with increasing concentrations (0 to 20 μM) of either defactinib or PROTAC for 48 hours, at which time viability was determined via CellTiter-Glo assay, and luminescent values were normalized to untreated control (100%). The dotted line indicates 50% viability. Data points represent mean values ± SEM of n = 12 (02.3 NF2 −/− KO3) or n = 4 (MSO3) replicates. ( C ) Colony formation assays stained with methylene blue and showing the effect of increasing concentrations of defactinib (1 to 5 μM) compared to dimethyl sulfoxide (DMSO) control on three NF2-deficient SC lines: 02.3 NF2 −/− K03, HEI-193, and MS03. ( D ) Volcano plot showing changes in MIB binding of kinases following 24-hour treatment with 1 μM defactinib compared to DMSO control in MS03 cells. X axis represents log 2 fold change (FC) in binding, and the y axis shows the negative log 10 of the P value. Dotted lines indicate significance thresholds for FC and P value. ( E ) Scatter plot depicting DRG volumes (in cubic millimeters) from mice treated with VS-4718 ( n = 14) or vehicle control ( n = 11). Dots represent individual DRG ( n = 4 per mouse). P value represents unpaired, two-tailed t test. Error bars reflect the SEM. ( F ) Representative photomicrographs of H&E-stained DRG obtained from Nf2 and DKO mice. HALO AI DenseNet mask is shown in the bottom panel and depicts abnormal tissue (red), neuron cell bodies (blue), and nerve (lavender). ( G and H ) Plots comparing the percentage of abnormal tissue (G) and neuron cell bodies (H) in Nf2 and DKO DRG. Dots represent individual DRG. Error bars reflect the SEM. P values represent unpaired, two-tailed t test. *** P ≤ 0.001 and n.s., not significant.

Article Snippet: Analysis of H&E-stained tissues using the Indica Labs HALO DenseNet AI module ( ) revealed a significant decrease in the percentage of abnormal tissue within the DRG of VS-4718- and combination-, but not selumetinib-, treated mice.

Techniques: Glo Assay, Control, Staining, Binding Assay, Two Tailed Test

Journal: Science Advances

Article Title: Inhibition of focal adhesion kinase impairs tumor formation and preserves hearing in a murine model of NF2-related schwannomatosis

doi: 10.1126/sciadv.ady8382

Figure Lengend Snippet: ( A ) Scatter plot depicting DRG volumes (in cubic millimeters) from mice treated with VS-4718 ( n = 14) and selumetinib ( n = 14), alone or in combination ( n = 15) and compared to two cohorts (V1 and V2) of age- and sex-matched vehicle controls (V1: n = 11; V2: n = 15). Dots represent individual DRG ( n = 4 per mouse). P values represent one-way ANOVA with Tukey’s multiple-comparison test. Error bars reflect SEM. DRG volumes (in cubic millimeters) for vehicles (V1: n = 11) and VS-4718 ( n = 14) were initially presented in and were included in this graph for the purpose of comparison. ( B ) Representative photomicrographs of H&E-stained DRG obtained from mice of the indicated treatment groups. Mask generated using Indica Lab’s HALO AI DenseNet module is shown in the bottom panel and depicts abnormal tissue (red), neuron cell bodies (blue), and nerve (lavender). ( C ) Scatter plot comparing the percentage of abnormal tissue in DRG of mice treated with VS-4718 ( n = 12) and selumetinib ( n = 14), alone or in combination ( n = 12) and compared to age- and sex-matched vehicle controls ( n = 7). Dots represent individual DRG. Error bars reflect the SEM. P values represent one-way ANOVA with Tukey’s multiple-comparison test.( D ) Representative photomicrographs of Masson’s trichrome–stained DRG obtained from mice treated with VS-4718 ( n = 6) and selumetinib ( n = 14), alone or in combination ( n = 11) compared to age- and sex-matched vehicle controls ( n = 6). Mask generated using Indica Lab’s HALO tissue area module is shown in the bottom panel and depicts collagen staining in purple. ( E ) Plot comparing the amount of collagen within the DRG, reflected as percentage of the total tissue area analyzed. Dots represent individual DRGs. Error bars reflect the SEM. P values represent one-way ANOVA with Tukey’s multiple-comparison test. * P ≤ 0.05, ** P ≤ 0.01, *** P ≤ 0.001, **** P ≤ 0.0001, and n.s., not significant.

Article Snippet: Analysis of H&E-stained tissues using the Indica Labs HALO DenseNet AI module ( ) revealed a significant decrease in the percentage of abnormal tissue within the DRG of VS-4718- and combination-, but not selumetinib-, treated mice.

Techniques: Comparison, Staining, Generated

Journal: bioRxiv

Article Title: TMPO promotes cellular dissemination and metastasis in circulating tumor cells

doi: 10.64898/2025.12.27.696673

Figure Lengend Snippet: Panels A and B: Analyses of mouse prostate tumors and CTCs : (A) Diffusion Component (DC) projection of scRNA-seq data from mouse prostate tumors (see ) showing expression levels of Tmpo alone (left) or Tmpo together with Vimentin (right). (B) Immunofluorescence staining of CTCs obtained from NPK end-stage mice. DAPI; YFP, Tmpo and Lamin (Lamin A/C). Scale bars, 20 μm. Panels C-G: Transcriptomic analyses of human prostate cancer patient cohorts : (C) Box plot showing the distribution of TMPO activity depicted by enrichment scores plotted against Gleason score in the TCGA dataset. P values were computed by Pearson correlation of TMPO activity NES versus Pearson score. (D-F) Violin plots depicting distribution of the NES (y axis), which reflect activity levels of TMPO comparing: in panel D , bulk seq data of primary tumors from TCGA ( n = 558) versus metastases from SU2C cohort ( n = 270); in panel E , scRNA-seq data from primary tumors ( n = 7, NeoRED cohort) versus metastases ( n = 8, PRIME-CUT cohort); and in panel F, scRNA-seq data from primary tumors ( n = 12) versus CTCs ( n = 77) from the Myamoto et al. dataset. In panels D-F , P values for each comparison of enrichment scores were computed by Wilcoxon rank-sum test, with Benjamini-Hochberg multiple-testing correction. (G) Kaplan-Meier survival curves showing the association of TMPO activity with Recurrence-free survival (TCGA cohort, left), and Overall survival (SU2C and Glinsky cohorts, middle and right, respectively). P values were calculated using a two-tailed log-rank test. Panels H-J: Protein expression analysis of human prostate cancer patient cohorts : (H-I) Immunostaining of TMPO on tissue microarrays (TMA) of human prostate tumors and metastases. Analysis of TMPO expression was performed on digitized whole-slide images using HALO and HALO AI module (see Methods ). (H) (Left) Violin plot showing the percentage of TMPO positive cells across tumor categories: benign prostate ( n = 74), adenocarcinoma (Adeno, n = 98), castration-resistant prostate cancer (CRPC, n = 8), neuroendocrine prostate cancer (NEPC, n = 7). (Right) Violin plot showing the percentage of TMPO positive cells across benign tissues ( n = 74), primary tumors ( n = 113), and metastases ( n = 20). For comparisons between more than two groups, P values were calculated using the Kruskal-Wallis test with Dunn’s multiple comparison correction. (I) Representative images from the TMAs in panel H showing TMPO immunostaining of benign prostate, adenocarcinoma (Adeno), CRPC, NEPC, and bone metastases (Bone met). Low power, scale bar: 100 μm; high power, scale bar: 20 μm). (J) Representative high-resolution confocal images of pan-CK + CTCs enriched from patients with mCRPC and co-stained for Lamin A/C (Lamin) and TMPO expression (top). CTCs were identified as DAPI⁺/pan-CK⁺/CD45⁻ cells (bottom). Scale bar; 5 μm See also , , , Datasets 8 and 9.

Article Snippet: Image analysis was conducted with HALO (Indica Labs, v4.0) and HALO AI module.

Techniques: Diffusion-based Assay, Expressing, Immunofluorescence, Staining, Activity Assay, Comparison, Two Tailed Test, Immunostaining