Journal: bioRxiv

Article Title: The Pdgfd-Pdgfrb axis orchestrates tumor-nerve crosstalk in pancreatic cancer

doi: 10.1101/2025.08.26.672505

Figure Lengend Snippet: ( A ) Schematic of spatial PNI screen with WT-DSP and 6K-SMI applied to custom PDAC TMAs. ( B ) WT-DSP volcano plot of differentially expr ssed genes in malignant cells <300 µm versus >300 µm from nearest nerve. ( C ) GSEA analysis of enriched genes expressed by malignant cells in N+ AOIs. ( D ) GSEA plot of PDGF family signaling enrichment correlated with PNI. ( E ) PDGFD expression in malignant cells located >300Lµm (no nerve, n = 126 ROIs) versus <300Lµm from the nearest nerve (n = 410 ROIs) in WT-DSP data. ( F ) UMAP of annotated cells from 6K-SMI. ( G ) SCOTIA results from 6K-SMI. ( H ) PDGFD expression in malignant cells located >300Lµm (no nerve; n = 6472 cells) versus <300Lµm from the nearest nerve (n = 6925 cells) in 6K-SMI data. ( I ) Mean fluorescence intensity (MFI) of PDGFD in PDGFD⁺ PanCK⁺ malignant cells (top left) and mean proportion of PanCK+ malignant cells that are PDGFD+ (top right) located >300Lµm (Nerve⁻) or <300Lµm (Nerve⁺) from the nearest nerve. Each dot pair represents the average of all Nerve+ and Nerve-cells analyzed in a single patient (n = 10 patients). Image (bottom left) depicts PDGFD labeling in nerve proximal (top inset) versus distal (bottom inset) PanCK+ malignant cells. Scale bar, 100 µm. **P < 0.01, ****P < 0.0001 [Mann-Whitney test, mean SEM (E, H); paired Student’s t test, MFI and mean proportion (I)].

Article Snippet: DRG-containing domes were placed into the incubator for 15 minutes at 37°C to solidify the Matrigel, after which 100 μL of prewarmed DMEM 10% FBS containing 12,000 cancer cells with or without recombinant Pdgfd protein (R&D Systems, 9738-SB-050) and SU16f (MCE, HY-108628) was added into the well.

Techniques: Expressing, Fluorescence, Labeling, MANN-WHITNEY

Journal: bioRxiv

Article Title: The Pdgfd-Pdgfrb axis orchestrates tumor-nerve crosstalk in pancreatic cancer

doi: 10.1101/2025.08.26.672505

Figure Lengend Snippet: ( A ) IF images of an example N+ (left) and N-(right) field of view of human PDAC with cell objects of interest, including PanCK+ malignant cells (green) and PDGFD+ cells (purple) defined using QuPath for quantitative IF analysis. Scale bars, 100 µm. ( B ) Plots of PDGFD MFI expression values from individual PDAC patients corresponding to in Nerve-(> 300 µm from the nearest nerve) and Nerve+ (< 300 µm from the nearest nerve) regions (each dot corresponds to one cell). ( C ) Mean values of PDGFD MFI in PanCK-PDGFD+ cells (each dot corresponds to a single patient). ( D ) Plots of individual PanCK expression values (each dot corresponds to one cell) between Nerve+ (< 300 um) and Nerve-regions corresponding to panel e. ( E ) Mean values of PanCK MFI in PanCK+ PDGFD+ cells (each dot corresponds to a single patient). *P < 0.05, *** P < 0.001, ****P < 0.0001 [Mann-Whitney test, Mean SD (B-D); Wilcoxon test (E)].

Article Snippet: DRG-containing domes were placed into the incubator for 15 minutes at 37°C to solidify the Matrigel, after which 100 μL of prewarmed DMEM 10% FBS containing 12,000 cancer cells with or without recombinant Pdgfd protein (R&D Systems, 9738-SB-050) and SU16f (MCE, HY-108628) was added into the well.

Techniques: Expressing, MANN-WHITNEY

Journal: bioRxiv

Article Title: The Pdgfd-Pdgfrb axis orchestrates tumor-nerve crosstalk in pancreatic cancer

doi: 10.1101/2025.08.26.672505

Figure Lengend Snippet: ( A, B ) MFI of Pdgfd (A) and Pdgfrb (B) in mouse PDAC cell lines expressing dCas9-VPR for CRISPR activation (n = 7-8 cells). Scale bar, 30 µm. ( C ) Whole DRG invasion assay projection image with trajectories of tdTomato+ cancer spheroids moving towards centrally located DRG over six days. Scale bar, 800 µm. ( D ) Confocal image of DRG from (C) stained with beta-3 tubulin (gray) with invaded tdTomato+ (red) cancer cells. Scale bar, 100 µm. ( E ) Quantification of neuroinvasion index, average invasion speed, and distance invaded by cancer cells upregulating candidate genes (n = 8). ( F ) Neuroinvasion index, average invasion speed, and distance traveled by Pdgfd cancer cells in co-cultures treated with varying concentrations of SU16f (n = 7-8). ( G ) Neuroinvasion index, average invasion speed, and distance traveled by Pdgfrb cells treated with vehicle, 20 nM rPdgfd, or a combination of 20 nM rP and 20nM SU16f (n = 8). *P < 0.05, **P < 0.01, *** P < 0.001, ****P < 0.0001 [Mann-Whitney test, mean + SD (A, B, E-G)]. Abbreviations: Scram = Scramble, rP/rPdgfd = recombinant Pdgfd.

Article Snippet: DRG-containing domes were placed into the incubator for 15 minutes at 37°C to solidify the Matrigel, after which 100 μL of prewarmed DMEM 10% FBS containing 12,000 cancer cells with or without recombinant Pdgfd protein (R&D Systems, 9738-SB-050) and SU16f (MCE, HY-108628) was added into the well.

Techniques: Expressing, CRISPR, Activation Assay, Invasion Assay, Staining, MANN-WHITNEY, Recombinant

Journal: bioRxiv

Article Title: The Pdgfd-Pdgfrb axis orchestrates tumor-nerve crosstalk in pancreatic cancer

doi: 10.1101/2025.08.26.672505

Figure Lengend Snippet: ( A ) Pdgfd (left) and Pdgfrb (middle) mRNA expression from bulk RNAseq of CRISPRa and scramble gRNA control lines (n = 2). **P < 0.01 (Unpaired t test). Heat map representation of CRISPRa and scramble control line expression of Pdgfd and Pdgfrb. ( B ) Volcano plot of genes enriched in Pdgfd-overexpressing cell line (left) and corresponding GSEA analysis (right). ( C ) Volcano plot of genes enriched in Pdgfrb-overexpressing cell line (left) and corresponding GSEA analysis (right).

Article Snippet: DRG-containing domes were placed into the incubator for 15 minutes at 37°C to solidify the Matrigel, after which 100 μL of prewarmed DMEM 10% FBS containing 12,000 cancer cells with or without recombinant Pdgfd protein (R&D Systems, 9738-SB-050) and SU16f (MCE, HY-108628) was added into the well.

Techniques: Expressing, Control

Journal: bioRxiv

Article Title: The Pdgfd-Pdgfrb axis orchestrates tumor-nerve crosstalk in pancreatic cancer

doi: 10.1101/2025.08.26.672505

Figure Lengend Snippet: ( A ) Nerve subtype staining (left) and quantification (right) for Na v 1.8 (cyan) and TH (magenta) in human PDAC (n = 6 patients). **P < 0.01 (Mann-Whitney test, Mean SD). ( B ) Schematic of whole DRG invasion assay. (C) Still frame from live cell imaging of central DRG explant and whole DRG invasion assay at day 0. Cancer cells are visualized by mNeon reen expression. Scale bar, 1 mm. ( D ) End point (day 6) image of whole DRG invasion from (b, left) and DRG-negative control (right). ( E ) Compiled replicates for speed and distance analyses of Pdgfd, Pdgfrb, and control cancer cell invasion of DRGs over 6 days. ( F ) Compiled replicates for speed and distance analyses of Pdgfd cancer cell invasion of DRGs with or without SU16f treatment over 6 days. ( G ) Compiled replicates for speed and distance analyses of Pdgfrb cancer cell invasion of DRGs with or without exogenous recombinant Pdgfd over 6 days. Abbreviations: Scram = Scramble, rP/rPdgfd = recombinant Pdgfd.

Article Snippet: DRG-containing domes were placed into the incubator for 15 minutes at 37°C to solidify the Matrigel, after which 100 μL of prewarmed DMEM 10% FBS containing 12,000 cancer cells with or without recombinant Pdgfd protein (R&D Systems, 9738-SB-050) and SU16f (MCE, HY-108628) was added into the well.

Techniques: Staining, MANN-WHITNEY, Invasion Assay, Live Cell Imaging, Expressing, Negative Control, Control, Recombinant

Journal: bioRxiv

Article Title: The Pdgfd-Pdgfrb axis orchestrates tumor-nerve crosstalk in pancreatic cancer

doi: 10.1101/2025.08.26.672505

Figure Lengend Snippet: ( A ) Transwell invasion assay with scramble gRNA control and Pdgfd cells (n = 6). Scale bar, 200 µm. ( B ) Confocal imaging of 5-week orthotopically transplanted tumors (green) with scramble gRNA control and Pdgfd malignant cells (n = 5 mice). Scale bar, 800 µm. ( C ) Radial invasion assay across malignant (green) cell lines and conditions. Images show Pdgfrb (Ctrl) and Pdgfrb + 20 nM rPdgfd invasion assays at 4 days (left). Scale bar, 1 mm. Graph of invasion area over time (middle) for Pdgfrb, Pdgfrb + 20 nM rPdgfd, Pdgfrb + 20nM rPdgfd and 200nM SU16f, Pdgfd, and Scramble. Quantifi ation of AUC for invasion area (right) after 120 hours (n = 7-9). ( D ) Representative confocal image depicting invading Pdgfrb (Ctrl) and Pdgfrb + 20 nM rPdgfd cancer cells (green) stained with nuclei (blue) and Ki67 (magenta) in radial invasion assay at 5 days. Scale bar, 1 mm. Graph (right) shows Ki67+ invasion area for Pdgfrb line (Ctrl), Pdgfrb + 20 nM rPdgfd, and Pdgfrb + 20nM rPdgfd and 200nM SU16f (n = 6). *P < 0.05, **P < 0.01, ****P < 0.0001 [Mann-Whitney test, Mean SD (A-D)]. Abbreviations: Scram = Scramble, rP/rPdgfd = recombinant Pdgfd.

Article Snippet: DRG-containing domes were placed into the incubator for 15 minutes at 37°C to solidify the Matrigel, after which 100 μL of prewarmed DMEM 10% FBS containing 12,000 cancer cells with or without recombinant Pdgfd protein (R&D Systems, 9738-SB-050) and SU16f (MCE, HY-108628) was added into the well.

Techniques: Transwell Invasion Assay, Control, Imaging, Invasion Assay, Staining, MANN-WHITNEY, Recombinant

Journal: bioRxiv

Article Title: The Pdgfd-Pdgfrb axis orchestrates tumor-nerve crosstalk in pancreatic cancer

doi: 10.1101/2025.08.26.672505

Figure Lengend Snippet: ( A ) Pancreas weight from mice 5 weeks after receiving Pdgfd-overexpressing and control orthotopic tumors. Corresponds to (n = 5 mice). ( B ) Transwell invasion assay with Scramble control, Pdgfrb line with or without recombinant 20 nM Pdgfd, and Pdgfd line (n = 6). ( C ) Schematic of radial invasion assay. ( D ) Incucyte images (day 4) and graph of invasion area over time for Scramble, Pdgfd, and Pdgfrb lines (left and middle). Scale bar, 1 mm. Quantification of AUC for invasion area from 0-72 hours and from 72-120 hours (n = 7-9). *P < 0.05, **P < 0.01, *** P < 0.001, ****P < 0.0001 [Unpaired t test, Mean SD (A); Mann-Whitney test, Mean SD (B), (D)]. Abbreviations: Scram = Scramble, rPdgfd = recombinant Pdgfd.

Article Snippet: DRG-containing domes were placed into the incubator for 15 minutes at 37°C to solidify the Matrigel, after which 100 μL of prewarmed DMEM 10% FBS containing 12,000 cancer cells with or without recombinant Pdgfd protein (R&D Systems, 9738-SB-050) and SU16f (MCE, HY-108628) was added into the well.

Techniques: Control, Transwell Invasion Assay, Recombinant, Invasion Assay, MANN-WHITNEY

Journal: bioRxiv

Article Title: The Pdgfd-Pdgfrb axis orchestrates tumor-nerve crosstalk in pancreatic cancer

doi: 10.1101/2025.08.26.672505

Figure Lengend Snippet: ( A ) Representative images and growth curves of nerves from Na v 1.8-Cre tdTomato+ mice co-cultured with Pdgfd, Pdgfrb, or scramble gRNA control cancer cells (left). Scale bar, 200 µm. Quantification (right) of area under the curve (AUC) for neurite growth curves after 48 hours (n = 10-11). ( B) Images and growth curves of nerves grown in control media, treated with conditioned media (CM) from Pdgfd-overexpressing malignant cells, and treated with a combination of CM and 200 nM of Su16f (left). Scale bar, 200 µm. Quantification (right) of AUC for neurite growth curves after 48 hours (n = 4). ( C ) Images and growth curves of nerves treated with control vehicle, 2 nM, 20 nM, and 200 nM of rPdgfd (left). Scale bar, 200 µm. Quantification (right) of AUC for neurite growth curves after 48 hours. ( D ) Images and quantification of axonal area in DRGs treated with vehicle (Ctrl), 20 nM rPdgfd, 20 nM rPdgfd and 200 nM SU16f, and 200 nM SU16f (n = 10-12). Scale bar, 1 mm. *P < 0.05, **P < 0.01, ****P < 0.0001 [Mann-Whitney test, Mean SD (A-D)]. Abbreviations: Scram = Scramble, rP/rPdgfd = recombinant Pdgfd.

Article Snippet: DRG-containing domes were placed into the incubator for 15 minutes at 37°C to solidify the Matrigel, after which 100 μL of prewarmed DMEM 10% FBS containing 12,000 cancer cells with or without recombinant Pdgfd protein (R&D Systems, 9738-SB-050) and SU16f (MCE, HY-108628) was added into the well.

Techniques: Cell Culture, Control, MANN-WHITNEY, Recombinant

Journal: bioRxiv

Article Title: The Pdgfd-Pdgfrb axis orchestrates tumor-nerve crosstalk in pancreatic cancer

doi: 10.1101/2025.08.26.672505

Figure Lengend Snippet: ( A ) Flow plot and histogram showing Pdgfrb expression in EGFP+ glial cells cultured for 4 days. ( B ) Radial invasion assay with dissociated EGFP+ glial cells (left). Cultures were treated with vehicle (Ctrl), 20 nM rPdgfd, or 20 nM rPdgfd and 20 nM SU16f. Scale bar, 1 mm. Quantification (right) of invasion area at 96 hours (n=4). ( C ) Live confocal image of DRG invasion with Plp-EGFP+ DRG (cyan) and KPT cancer cells (yellow; left). Scale bar, 500 µm. Still frames with elapsed time in hours and minutes of an EGFP+ glial cell (cyan) pulling a cancer spheroid (yellow) towards the DRG (middle). Scale bar, 100 µm. Analysis of distance tdTomato+ cancer spheroids were pulled by EGFP+ glia over 24 hours (n = 37-51 spheroids per group). ( D ) Images of sciatic nerves injected with KPT cancer cells from mice treated daily with vehicle (Ctrl) or SU16f daily for 14 days (left). Scale bar, 2 mm. Quantification of sciatic invasion distance (right) at days 1 and 14 (n = 4-6 mice). ( E ) Sciatic nerve cross-section from Plp-EGFP mouse injected with KPT cancer cells. Pdgfrb (magenta) is absent in glial cells distal to invading cancer cells (left) and present in glial cells proximal to tdTomato+ cancer cells (right). Scale bar, 40 µm. ( F ) Schematic of proposed Pdgfd-Pdgfrb signaling model. *P < 0.05, **P < 0.01, ****P < 0.0001 [Unpaired t test, Mean SD (B); Mann-Whitney test, Mean SD (C, D)]. Abbreviations: rP/rPdgfd = recombinant Pdgfd.

Article Snippet: DRG-containing domes were placed into the incubator for 15 minutes at 37°C to solidify the Matrigel, after which 100 μL of prewarmed DMEM 10% FBS containing 12,000 cancer cells with or without recombinant Pdgfd protein (R&D Systems, 9738-SB-050) and SU16f (MCE, HY-108628) was added into the well.

Techniques: Expressing, Cell Culture, Invasion Assay, Injection, MANN-WHITNEY, Recombinant