Journal: bioRxiv

Article Title: Spatiotemporal profiling reveals the role of inflammatory niche in driving prostate cancer

doi: 10.64898/2026.04.19.719485

Figure Lengend Snippet: A, Experimental workflow for generating and assaying prostate organoid morphology. B, TKO organoids are more resistant to an AR degrader. Viability (y axis) of control (NTC, left) and TKO (right) organoids at different concentrations (x axis) of an AR degrader. IC50 values are shown at bottom left. C,D, Cell state heterogeneity in TKO organoids. C, UMAP embeddings of scRNA-seq profiles (dots) of NTC and TKO cells (as in ) colored by gene module scores. D, Fraction of cells (right) with top score for each gene module in control (NTC) and TKO organoids (x axis). Right: Enriched top GO terms (FDR<0.05 as in ) in each module. E, Neoantigen and GFP expression in NINJA prostate organoids. Flow cytometry plots of percentage of cells expressing GFP, in-frame with neoantigens, in NINJA prostate organoids without CRE recombinase (CRE), doxycycline, and tamoxifen (left), with CRE but without doxycycline and tamoxifen (middle), and with CRE, doxycycline and tamoxifen for 72 hours (right). F , Experimental mouse model. TKO organoids from NINJA mice treated with doxycycline and tamoxifen pre-transplantation were transplanted into immunocompetent (C57BL/6, n=10) and immunodeficient (NSG, n=10) mice. G,H CD8 T cell infiltration. G, (Left) Workflow. Right: Representative flow cytometry plots from stained (left) and unstained (right) samples, gated for CD8a, MHC class I tetramer (for neoantigen-specific T cells), and PD1 expression. H, Percentage (y axis) of neoantigen-specific (tetramer-positive, left) and PD1-positive CD8+ T cells (right), at 6- and 12-weeks post-transplantation with castration (x axis). Dots: individual mice. I , Prostates from different experimental groups.

Article Snippet: For in vitro delivery of CRE recombinase, Takara’s CRE recombinase gesicles (Takara Bio USA, (Catalog No. 631449) were used according to the manufacturer’s instructions.

Techniques: Control, Expressing, Flow Cytometry, Immunopeptidomics, Transplantation Assay, Staining

Journal: Redox Biology

Article Title: Aryl hydrocarbon receptor in club cells drives Th17-mediated lung injury following inhalation exposure to environmentally persistent free radicals

doi: 10.1016/j.redox.2026.104105

Figure Lengend Snippet: Generation and validation of club cell-specific AHR knockout mice ( Ahr ΔCC). (a) Schematic of breeding strategy to generate Ahr ΔCC mice by crossing Ahr fl/fl mice with Scgb1a1-CreER TM mice, followed by tamoxifen induction. (b) Immunofluorescence staining showing club cell marker CC10 (green), AHR (red) and DAPI (blue) in lung sections of Cre-negative Ahr fl/fl LM control (top panel) and Ahr ΔCC (bottom panel) mice. (c) Representative flow cytometry plots of lung epithelial cells gated as CD45 − CD31 − EpCAM + CC10 + cells isolated from lungs of LM (left) or Ahr ΔCC (center) mice and Fluorescence-minus-one (FMO) control for AHR staining (right). (d) Quantification of the percentage of AHR + CC10 + cells in the lungs of LM (white bar) and Ahr ΔCC (gray bar) mice. Data represent mean ± SEM, n = 3-4 mice per group. Statistical significance was determined using Student's t-test; ∗p < 0.05.

Article Snippet: Male Ahr tm3.1Bra /J mice carrying a floxed exon 2 allele of the Ahr gene (JAX stock #006203) and female B6N.129S6(Cg)- Scgb1a1 tm1(cre/ERT)Blh /J mice expressing tamoxifen-inducible Cre recombinase under the control of the club cell-specific Scgb1a1 promoter (JAX stock #016225) were obtained from Jackson Laboratory.

Techniques: Biomarker Discovery, Knock-Out, Immunofluorescence, Staining, Marker, Control, Flow Cytometry, Isolation, Fluorescence

Journal: bioRxiv

Article Title: Spatiotemporal profiling reveals the role of inflammatory niche in driving prostate cancer

doi: 10.64898/2026.04.19.719485

Figure Lengend Snippet: A, Experimental workflow for generating and assaying prostate organoid morphology. B, TKO organoids are more resistant to an AR degrader. Viability (y axis) of control (NTC, left) and TKO (right) organoids at different concentrations (x axis) of an AR degrader. IC50 values are shown at bottom left. C,D, Cell state heterogeneity in TKO organoids. C, UMAP embeddings of scRNA-seq profiles (dots) of NTC and TKO cells (as in ) colored by gene module scores. D, Fraction of cells (right) with top score for each gene module in control (NTC) and TKO organoids (x axis). Right: Enriched top GO terms (FDR<0.05 as in ) in each module. E, Neoantigen and GFP expression in NINJA prostate organoids. Flow cytometry plots of percentage of cells expressing GFP, in-frame with neoantigens, in NINJA prostate organoids without CRE recombinase (CRE), doxycycline, and tamoxifen (left), with CRE but without doxycycline and tamoxifen (middle), and with CRE, doxycycline and tamoxifen for 72 hours (right). F , Experimental mouse model. TKO organoids from NINJA mice treated with doxycycline and tamoxifen pre-transplantation were transplanted into immunocompetent (C57BL/6, n=10) and immunodeficient (NSG, n=10) mice. G,H CD8 T cell infiltration. G, (Left) Workflow. Right: Representative flow cytometry plots from stained (left) and unstained (right) samples, gated for CD8a, MHC class I tetramer (for neoantigen-specific T cells), and PD1 expression. H, Percentage (y axis) of neoantigen-specific (tetramer-positive, left) and PD1-positive CD8+ T cells (right), at 6- and 12-weeks post-transplantation with castration (x axis). Dots: individual mice. I , Prostates from different experimental groups.

Article Snippet: For in vitro delivery of CRE recombinase, Takara’s CRE recombinase gesicles (Takara Bio USA, (Catalog No. 631449) were used according to the manufacturer’s instructions.

Techniques: Control, Expressing, Flow Cytometry, Immunopeptidomics, Transplantation Assay, Staining

Journal: Journal of Extracellular Vesicles

Article Title: Distinguishing Pseudotransduction and True Transduction Enables Characterization and Bioengineering of Extracellular Vesicle‐Adeno‐Associated Virus Vectors

doi: 10.1002/jev2.70258

Figure Lengend Snippet: A Cre recombinase‐based dual reporter system distinguishes mixed delivery and transduction. (A) Schematic depicting the expected function of the stoplight dual‐reporter system in which Cre expressed in recipient cells acts upon incoming AAV genomes to switch them from expression of a red reporter to a green reporter. Free AAV mediates transduction only (green); EV‐AAV mediates both mixed delivery (red) and transduction (green) and sometimes both (yellow); No Rep/Cap EVs can only mediate mixed delivery (red). (B) Cre‐responsive plasmids were evaluated in this experiment. (C, D) Mixed delivery (C) and transduction (D) conferred by various vector compositions. Note: some mCherry gene expression could occur in recipient cells prior to Cre‐mediated recombination (or in the possible absence of recombination), such that (C) includes both mixed delivery and this ambiguous de novo gene expression. Samples were normalized to include 1e9 vector genomes per well (for AAV crude lysate conditions) or a volume‐equivalent of the AAV2 crude lysate condition for No Rep/Cap crude lysate conditions (10 4 recipient cells). Experiments were performed in biological triplicate. One of two independent experiments is shown (second experiment: Figure S10 ). Error bars indicate the standard error of the mean. Multicomparison statistical analysis was performed using a two‐way ANOVA test, followed by Tukey's multiple comparison test to evaluate specific comparisons (* p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001). NLS, nuclear localization sequence; ns, not significant; PBS, phosphate‐buffered saline.

Article Snippet: RepCap plasmids for AAV2 (pRep2Cap2) and AAV6 (pRep2Cap6) were gifts from the Vector Core at the University of Pennsylvania (Penn Vector Core (RRID: SCR_022432)). pcDNA is plasmid pPD005 (Addgene plasmid # 138749; http://n2t.net/addgene:138749 ; RRID:Addgene_138749) (Donahue et al. ). psPAX2 and pMD2.G plasmids were gifted by William Miller from Northwestern University. pHIE822 was created by introducing point mutations (K47Q, R354A) in the VSV‐G‐encoding gene of pMD2.G using site‐directed mutagenesis by PCR. pCMV‐VSV‐G(P127D)‐Myc (pJB042) was a gift from Wesley Sundquist (Addgene plasmid # 80055; http://n2t.net/addgene:80055 ; RRID:Addgene_80055) (Votteler et al. ). pHIE963 was created using standard restriction enzyme cloning to insert a Cre recombinase gene into a third‐generation lentiviral transfer vector provided by Twist Bioscience (pTwist Lenti SFFV PuroR).

Techniques: Transduction, Expressing, Plasmid Preparation, Gene Expression, Comparison, Sequencing, Saline