Journal: bioRxiv

Article Title: Context-specific genetic interaction mapping reveals combinatorial KRAS/FGFR dependence in pancreatic cancer

doi: 10.64898/2026.09.24.754062

Figure Lengend Snippet: (A) LFC plot in KRAS mut PDAC versus all other lines. (B) Volcano plot of differential LFC in KRAS mut PDAC versus all other lines. Y-axis shows statistical significance (-log 10 p value). Horizontal dashed line marks p = 0.001. (C) Differential synergy map showing all gene pairs with differential Combinatory score ≤ -1 in KRAS mut PDAC versus all other lines. (D-E) Boxplots display LFC scores for KRAS_FRS2 (D) and KRAS_EGFR (E) and corresponding single genes, separated into KRAS mut PDAC, KRAS mut CRC, and KRAS WT lines. (F) siRNA dual knockdown of KRAS and FGFR-pathway genes leads to significantly reduced growth versus single knockdown in SNU410 cells. Cell growth was assayed using Incucyte and normalized to timepoint 0. Data represent mean ± SD. P values calculated by extra sum-of-squares F test comparing growth rate constants of exponential growth curve fits. Single gene knockdowns were compared versus siNT/siNT, and dual gene knockdowns were compared versus siKRAS/siNT. ***: P < 0.001, NS: P > 0.05. (G) Zoldonrasib dose-response curve of PANC0203 cells with or without doxycycline induction of an shRNA targeting FRS2. Viability measured by CellTiter-Glo. Data represent mean ± SD.

Article Snippet: The next day, Incucyte Annexin V Red Dye (Sartorius, #4641) was reconstituted in PBS and diluted 1:200 into all wells.

Techniques: Knockdown, shRNA

Journal: bioRxiv

Article Title: Context-specific genetic interaction mapping reveals combinatorial KRAS/FGFR dependence in pancreatic cancer

doi: 10.64898/2026.09.24.754062

Figure Lengend Snippet: (A) Zoldonrasib x futibatinib Bliss synergy matrices for the KRAS G12D PDAC 2D cell lines SNU410 (left) and PANC0203 (right). Viability was measured by CellTiter-Glo, and Bliss synergy scores were calculated across the full dose-response matrix. (B) Zoldonrasib x futibatinib Bliss synergy matrices for the PDAC organoids PANFR0418 (KRAS G12D ; left) and PANFR0305 (KRAS WT ; right). Viability was measured by CellTiter-Glo 3D, and Bliss synergy scores were calculated across the full dose-response matrix. (C) Large scale, longitudinal drug treatment experiments in SNU410 (left) and PANC0203 (right), treated with zoldonrasib 1000nM, futibatinib 300nM, combination, or vehicle. Cell counts are plotted over time on a log10-scaled y-axis. The dotted line indicates the starting cell number of 20*10 6 cells; values at the bottom of the y-axis indicate no remaining cells. (D) Annexin V staining of SNU410 cells treated with zoldonrasib 1000nM, futibatinib 300nM, combination, or vehicle. Annexin V staining was assayed using Incucyte and normalized to confluence. (E) Measurements of SNU410 (left; vehicle/zoldonrasib/combination: n = 5, futibatinib: n = 3) and PANC0203 (right; all cohorts: n = 6-10) subcutaneous tumors in mice treated with zoldonrasib (100mg/kg PO ǪD), futibatinib (25mg/kg PO ǪD), combination, or vehicle. Mice were treated continuously for 3-4 weeks, followed by treatment cessation with continued tumor monitoring; the gray area on each plot represents treatment period. Dotted line indicates average tumor size for each cohort at start of treatment. (F) Tumor shrinkage of zoldonrasib versus combination treatment cohorts at 2 weeks of treatment (SNU410: left, day 15; PANC0203: right, day 14), normalized to tumor shrinkage in zoldonrasib cohorts. P value calculated by two-tailed unpaired Student’s t test. (G) Representative sections showing on-treatment PANC0203 subcutaneous tumors after staining with hematoxylin and eosin (Scale bars: 400µm). (H) Necrotic area and tumor cell count analysis on pathologist-annotated tumor bed regions in zoldonrasib- or combination-treated tumors. (I) Representative sections showing on-treatment PANC0203 subcutaneous tumors after staining with anti-phospho-ERK (brown) and counter-stained with hematoxylin (Scale bars: 200µm).

Article Snippet: The next day, Incucyte Annexin V Red Dye (Sartorius, #4641) was reconstituted in PBS and diluted 1:200 into all wells.

Techniques: Organoids, Staining, Two Tailed Test, Cell Characterization, Analysis

Journal: Nature Communications

Article Title: Cell-autonomous restoration of splicing homeostasis and RP11 phenotype in patient-derived RPE and retinal organoids by PRPF31 .AAV gene therapy

doi: 10.1038/s41467-026-78065-z

Figure Lengend Snippet: A Restoration of RPE phagocytosis. RP11-RPE cells exhibit increased phagocytic capacity following PRPF31 .AAV treatment. Internalised Photoreceptor Outer Segments (POSs) were labelled with pHrodo dye (red), which fluoresces upon acidification within the phagolysosome. Quantification displays the percentage of positive area and mean fluorescence intensity after 4 h of incubation. Scale bars: 200 µm. B , C Spatiotemporal RGC firing patterns. Raster plots (top) and firing rate histograms (bottom; 5 s bins) for 25 representative RGCs demonstrating either a 25% increase ( B ) or decrease ( C ) in spiking activity during pulsed light stimulation. In raster plots, vertical bars represent individual spikes; in histograms, the y axis represents the mean spike rate across the population. The red line indicates the onset of pulsed light stimulation. D Light-evoked RGC response distribution. (Left) Heatmaps showing the population-wide distribution of RGC activity shifts in GFP.AAV (control) vs. PRPF31 .AAV-treated ROs. Colour coding: yellow (no change), purple (≥50% increase), and pink (≥50% decrease). (Right) Quantitative analysis of responsive RGC subpopulations. PRPF31 .AAV treatment significantly increased the proportion of RGCs exhibiting “ON” (increased) responses compared to controls. No significant difference was observed in the “OFF” (decreased) subpopulation. Statistical analysis: data are presented as mean ± SD. For ( A ), significance was determined by one-way ANOVA with Tukey’s test (*** p < 0.001, **** p < 0.0001), n = 3 images per condition for % of area and n = 10 images per condition for mean intensity analysis. D An unpaired t test was used to compare increased vs. decreased activity proportions (*** p < 0.001). No significant difference was observed in decreased activity, n = GFP.AAV increased (21), PRPF31 .AAV increased (40); GFP.AAV decreased (84), PRPF31 .AAV decreased (81). Box plots in ( A , D ) show the median (centre line) with the box representing the 25th−75th percentiles, and the whiskers extend from the minimum to the maximum values. Source data are provided in the Source Data file.

Article Snippet: Bovine rod photoreceptor outer segments (POSs) were labelled with IncuCyte pHrodo red cell labelling dye (Sartorius, 4649) for 1 h at room temperature in the dark with shaking, as per manufacturer’s protocol.

Techniques: Fluorescence, Incubation, Activity Assay, Control, Analysis

Journal: Nature Communications

Article Title: Cell-autonomous restoration of splicing homeostasis and RP11 phenotype in patient-derived RPE and retinal organoids by PRPF31 .AAV gene therapy

doi: 10.1038/s41467-026-78065-z

Figure Lengend Snippet: A Restoration of nuclear homeostasis. Mature RP11-RPE cells (treated post-maturation) show restored nuclear localisation of PRPF31 (red) and reorganised SC35+ nuclear speckles (red). Quantitative analysis confirms significant increases in SC35+ area, fluorescence intensity, and the percentage of SC35+ cells following PRPF31 .AAV treatment. Nuclei are counterstained with DAPI (blue). Scale bars: 25 µm. B Clearance of established proteotoxic aggregates. Immunostaining reveals a significant reduction in the volume of HSPB1 (red) and RLBP1 (red) cytoplasmic aggregates in mature RPE cells upon treatment. Aggregate burden is expressed as the total aggregate volume per cell. Nuclei are counterstained with DAPI (blue). Scale bars: 25 µm. C Rescue of ciliary architecture. Immunofluorescence analysis using the ciliary marker ARL13B (red) demonstrates that PRPF31 augmentation restores both cilia length and cilia incidence (percentage of ciliated cells) in mature RP11-RPE, reversing the stunted ciliary phenotype observed in controls. Nuclei are counterstained with DAPI (blue). Scale bar: 25 µm. D Recovery of functional phagocytosis. Phagocytic capacity in mature RPE is significantly improved following treatment, as evidenced by the internalisation of pHRodo-labeled Photoreceptor Outer Segments (POS; red). Data are quantified by positive area percentage and mean fluorescence intensity after 4 h of incubation. Scale bar: 400 µm. E Brightfield image of mature RP11-RPE cells demonstrating characteristic RPE morphology, including hexagonal shape and pigmentation. Scale bars: 200 µm and 100 µm. Statistical analysis: data are presented as mean ± SD. Statistical significance was determined by one-way ANOVA with Tukey’s test, except for cilia length ( C ), which was assessed via Kruskal-Wallis with Dunn’s multiple comparisons test (* p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001). B , D Box plots show the median (centre line) with the box representing the 25th−75th percentiles, and the whiskers extend from the minimum to the maximum values. Sample sizes: A n = 5, B n = 6, C n = 7 representative images per marker/condition; D n = 10 and n = 15 representative images per condition for % of area and for Orange Image Mean analysis, respectively; E Representative image from n = 3 independent experiments. Source data are provided in the Source Data file.

Article Snippet: Bovine rod photoreceptor outer segments (POSs) were labelled with IncuCyte pHrodo red cell labelling dye (Sartorius, 4649) for 1 h at room temperature in the dark with shaking, as per manufacturer’s protocol.

Techniques: Analysis, Fluorescence, Immunostaining, Immunofluorescence, Marker, Functional Assay, Labeling, Incubation, Brightfield, Morphology

Journal: bioRxiv

Article Title: Synergism of TNF-α and IFN-γ triggers inflammatory cell death, tissue damage, and mortality in SARS-CoV-2 infection and cytokine shock syndromes

doi: 10.1101/2020.10.29.361048

Figure Lengend Snippet: (A) Heatmap depicting the levels of pro-inflammatory cytokines in serum of patients with COVID-19 and healthy people . (B) Pro-inflammatory cytokines released from PBMCs infected with SARS-CoV-2. (C) Percent of BMDMs that are dead 48 h after cytokine treatment using the IncuCyte imaging system and propidium iodide (PI) staining. “Cocktail-1” contained all 8 cytokines (IL-6, IL-18, IFN-γ, IL-15, TNF-α, IL-1α, IL-1β, and IL-2). (D) Percent of BMDMs that are dead 48 h after treatment with the indicated combination of cytokines. (E) Real-time analysis of cell death in BMDMs treated with the indicated cytokines. (F, G) Representative images of cell death in BMDMs (F) and THP-1 cells (G) after 48 h of the indicated treatments. Scale bar, 50 μm. Data are representative of at least three independent experiments. ** P < 0.01; **** P < 0.0001. Analysis was performed using the one-way ANOVA (B–D) or the two-way ANOVA (E). Significance asterisks in C and D indicate the comparison to the media-treated control. Data are shown as mean ± SEM (B–E). See also Figure S1.

Article Snippet: The kinetics of cell death were determined using the IncuCyte S3 (Essen BioScience) live-cell automated system.

Techniques: Infection, Imaging, Staining, Comparison