Journal: Oncology Letters

Article Title: Exploring multiple biomarkers and constructing ferroptosis-associated competing endogenous RNA networks as dual targets in retinoblastoma

doi: 10.3892/ol.2026.15582

Figure Lengend Snippet: ceRNA networks, drug-gene interactions and PCR validation. (A) The ceRNA-regulating networks illustrate protein-coding genes (red circles), miRNAs (blue diamonds) and lncRNAs (green hexagons), with black lines indicating interactions among lncRNA, miRNA and mRNA, where ceRNA refers to ceRNAs. (B) Validation through reverse transcription-quantitative PCR analysis confirms that CDKN2A and IDH2 expression levels are significantly higher in Y79 cells compared to ARPE-19 cells. Data were normalized to GAPDH expression using the 2 −ΔΔCq method, with each experiment performed in triplicate. ***P<0.001 and ****P<0.0001. (C) The drug-gene interaction analysis shows the linkage map of two hub genes, CDKN2A and IDH2 , along with their potential target drugs, including bisphenol A (code: C006780), sodium arsenite (code: C017947), docetaxel (code: D000077143) and hexabromocyclododecane (code: C089796). ceRNA, competing endogenous RNAs; miRNA, microRNA; lncRNA, long non-coding RNA; RB, retinoblastoma.

Article Snippet: The human retinal pigment epithelium cell line ARPE-19 and the human RB cell line Y79 were sourced from the American Type Culture Collection.

Techniques: Biomarker Discovery, Reverse Transcription, Real-time Polymerase Chain Reaction, Expressing

Journal: bioRxiv

Article Title: Clinically relevant AAV8- PEX1 gene therapy preserves retinal integrity and function long-term in a murine model of Zellweger spectrum disorder

doi: 10.64898/2026.05.11.723906

Figure Lengend Snippet: (A) Schematic of the PEX1 gene therapy vector featuring the human PEX1 transgene driven by a chicken β-actin promoter / cytomegalovirus enhancer (CBh) and a synthetic polyadenylation signal within an AAV proviral plasmid backbone. (B) Immunoblot analysis of c ontrol (WT) and PEX1 - null ARPE-19 cell lysates to assess PEX1 and PEX5 protein levels following transduction with AAV8. PEX1 or AAV8. GFP. (C) Protein levels quantified by band densitometry and normalized to the β-tubulin loading control; 15ug of protein was loaded per lane. (D, E) Immunofluorescence analysis of WT, PEX1-null (untreated), and AAV8. PEX1 -treated ARPE-19 cells co-labeled for PTS1 and ABCD3 (D) or PEX5 and ABCD3 (E), with quantification shown to the right of each panel. White arrows indicate co-localization of PTS1 with the peroxisomal marker ABCD3 in AAV8. PEX1 -treated cells (phenotypic recovery). (F) Immunofluorescence analysis of WT and PEX1-G843D ARPE-19 cells co-labeled for catalase and ABCD3, with quantification shown at right. Images were acquired by fluorescence microscopy at 60x magnification. PTS1, PEX5, or catalase (green) and peroxisome membrane protein ABCD3 (red); colocalization (yellow); DAPI nuclear staining (blue); scale bar, 20µm. n=3 independent experiments with ≥100 cells from ≥6 fields of view quantified per experiment. (G-H) LC-MS/MS quantification of peroxisomal metabolites, C26:0-lysophosphatidylcholine (LPC) and phosphatidylethanolamine (PE) plasmalogens, in WT (untreated), (G) PEX1-null (untreated and AAV8. PEX1 -treated) ARPE-19 cells, and (H) PEX1-G843D (untreated and AAV8. HsPEX1 -treated) ARPE-19 cells, 14 days after transduction. N=3 independent experiments for all; Kruskal–Wallis test with Dunn’s multiple comparison post hoc test; P<0.05 indicated; Mean (SD) shown. Viral dose is expressed as multiplicity of infection (MOI; vg/cell).

Article Snippet: PEX1 -null ARPE-19 cells were generated using CRISPR-Cas9-mediated gene editing at The Jackson Laboratory (Bar Harbor, ME).

Techniques: Plasmid Preparation, Western Blot, Transduction, Control, Immunofluorescence, Labeling, Marker, Fluorescence, Microscopy, Membrane, Staining, Liquid Chromatography with Mass Spectroscopy, Comparison, Infection

Journal: bioRxiv

Article Title: Clinically relevant AAV8- PEX1 gene therapy preserves retinal integrity and function long-term in a murine model of Zellweger spectrum disorder

doi: 10.64898/2026.05.11.723906

Figure Lengend Snippet: (A) Immunofluorescence analysis of WT and PEX1-G844D primary mouse RPE cells treated with various doses of AAV8. PEX1 , co-labelled for PEX5 (green), ABCD3 (red), and DAPI (blue), with quantification shown at right. Images were acquired by fluorescence microscopy at 60x magnification; Scale bar, 20µm. N=3 independent experiments with ≥100 cells from ≥ 6 fields of view quantified per experiment. Viral dose is expressed as multiplicity of infection (MOI; vg/cell). (B) LC-MS/MS quantification of the peroxisomal metabolite C26:0-lysophosphatidylcholine (LPC) in PEX1-G844D primary RPE cells (untreated and AAV8. GFP- or AAV8. PEX1 -treated), 14 days post-transduction. The untreated WT average is shown for reference. (C) Representative confocal z-stack images of WT and PEX1-G844D retinal cryosections 2 months after a single subretinal injection of 6.2 x 10 9 vg AAV8. PEX1 or AAV8. GFP , immunolabelled with PEX1 (green or red) and DAPI (blue); GFP signal is shown in green. PRS, Photoreceptor segments; ONL, outer nuclear layer; INL, inner nuclear layer; GCL, ganglion cell layer. Scale bar, 20 µm. Data are presented as mean and SD, n = 3 mice per group. (D) Immunoblot analysis of whole neural retina or whole RPE lysates to assess PEX1 protein levels 2 months post single subretinal injection of 6.2 x 10 9 vg AAV8. PEX1 or AAV8. GFP. (E, F) Immunoblot analysis of PEX1-G844D whole neural retina ( E ) or whole RPE (F) lysates to assess PEX1 protein levels 2 month after a single subretinal injection of serial dilutions of AAV8. PEX1 . Doses tested (vg/eye): 6.2 x 10 9 (1/1), 1.24 x 10 9 (1/5), 6.2 x 10 8 (1/10), 3.1 x 10 8 (1/20), and 6.2 x 10 7 (1/100). Protein levels were quantified by band densitometry and normalized to the β-tubulin loading control; 15ug of protein was loaded per lane. N=3 independent experiments; Statistical analysis was performed using a Kruskal–Wallis test with Dunn’s multiple-comparisons post hoc test; P < 0.05 indicated. Data are presented as mean (SD).

Article Snippet: PEX1 -null ARPE-19 cells were generated using CRISPR-Cas9-mediated gene editing at The Jackson Laboratory (Bar Harbor, ME).

Techniques: Immunofluorescence, Fluorescence, Microscopy, Infection, Liquid Chromatography with Mass Spectroscopy, Transduction, Injection, Western Blot, Control

Journal: bioRxiv

Article Title: Clinically relevant AAV8- PEX1 gene therapy preserves retinal integrity and function long-term in a murine model of Zellweger spectrum disorder

doi: 10.64898/2026.05.11.723906

Figure Lengend Snippet: AAV8. PEX1 was administered by subretinal injection to 1-month-old PEX1-G844D mice, and assessments were performed 2 months post-treatment (age 3 months). Doses tested (vg/eye): 6.2 x 10 7 (1/100), 6.2 x 10 8 (1/10), 1.24 x 10 9 (1/5), and 6.2 x 10 9 (1/1). Average values from untreated WT littermates are shown as a reference (dotted line). (A) Optomotor reflex testing of functional vision, including full contrast spatial acuity under ambient and scotopic conditions (reported as the highest spatial frequency perceived) and contrast sensitivity under ambient light (reported as the lowest contrast perceived). (B) Full-field flash electroretinography (ffERG) responses were quantified as amplitudes of scotopic a-wave, scotopic b-wave, and photopic b-wave at increasing stimulus intensities. The area under the curve (AUC) is shown below each plot. Data represent 4–8 mice per group (8–12 eyes). Statistical analysis was performed using a Kruskal–Wallis test with Dunn’s multiple-comparisons post hoc test; P < 0.05 indicated; Data are presented as mean (SD).

Article Snippet: PEX1 -null ARPE-19 cells were generated using CRISPR-Cas9-mediated gene editing at The Jackson Laboratory (Bar Harbor, ME).

Techniques: Injection, Functional Assay

Journal: bioRxiv

Article Title: Clinically relevant AAV8- PEX1 gene therapy preserves retinal integrity and function long-term in a murine model of Zellweger spectrum disorder

doi: 10.64898/2026.05.11.723906

Figure Lengend Snippet: AAV8. PEX1 was administered by subretinal injection to 1-month-old PEX1-G844D mice, and assessments were performed 2 months post-treatment (age 3 months). Doses tested (vg/eye) were: 6.2 x 10 7 (1/100), 6.2 x 10 8 (1/10), 1.24 x 10 9 (1/5), and 6.2 x 10 9 (1/1). (A, B) Representative confocal z-stack images from untreated littermate controls (WT) and PEX1-G844D mice across treatment groups. (A) Neural retina flatmounts (photoreceptor side up) stained with peanut agglutinin (PNA), a lectin that labels the extracellular matrix surrounding cone photoreceptors. Scale bar, 100 µm. (B) Retinal cryosections from the same groups stained with peanut agglutinin (PNA) to visualize cone-associated extracellular matrix across retinal layers. Scale bar, 20 µm. (C) Spider plot representation of ONL thickness across the entire retinal circumference. (D) Area under the curve (AUC) analysis of ONL thickness. Data are presented as mean ± SD; n = 3 mice per group. PRS, Photoreceptor segments; ONL, outer nuclear layer; INL, inner nuclear layer; GCL, ganglion cell layer. (E) Representative immunofluorescence images of RPE flatmounts (apical side up) from untreated littermate controls (WT), and PEX1-G844D mice across treatment groups. Subretinal immune cells are labeled with IBA1 (green) and F4/80 (white), and RPE morphology is visualized with TRITC-phalloidin staining of F-actin (red). Scale bar, 100 µm. (F) Quantification of RPE cell density (cells/mm²). (G) Quantification of subretinal immune cell density (IBA1 /F4/80 cells/mm²). n = 4–5 mice per group; Statistical analysis was performed using a Kruskal–Wallis test with Dunn’s multiple-comparisons post hoc test; P < 0.05 indicated. Data are presented as mean (SD).

Article Snippet: PEX1 -null ARPE-19 cells were generated using CRISPR-Cas9-mediated gene editing at The Jackson Laboratory (Bar Harbor, ME).

Techniques: Injection, Staining, Immunofluorescence, Labeling

Journal: bioRxiv

Article Title: Clinically relevant AAV8- PEX1 gene therapy preserves retinal integrity and function long-term in a murine model of Zellweger spectrum disorder

doi: 10.64898/2026.05.11.723906

Figure Lengend Snippet: 1.24 x 10 9 vg/eye AAV8. PEX1 or AAV8. GFP was administered by subretinal injection to 5-week-old PEX1-G844D mice, and assessments were performed 6 months post-treatment (age 7 months). Optomotor reflex testing of functional vision included: (A) full contrast spatial acuity under ambient and scotopic conditions (reported at the highest spatial frequency perceived) and (B) contrast sensitivity at ambient light and scotopic conditions (reported as the lowest contrast perceived). (C-E) Full-field flash electroretinography (ffERG) responses were quantified as amplitudes of (C) scotopic a-wave, (D) , scotopic b-wave, and (E) photopic b-wave at increasing stimulus intensities. Average values from untreated WT littermates are shown as a reference (dotted line). The corresponding area under the curve (AUC) is shown below each plot. Data represent 6–15 mice per group (12–30 eyes). Statistical analysis was performed using a Kruskal–Wallis test with Dunn’s multiple-comparisons post hoc test; P < 0.05 indicated. Data are presented as mean (SD).

Article Snippet: PEX1 -null ARPE-19 cells were generated using CRISPR-Cas9-mediated gene editing at The Jackson Laboratory (Bar Harbor, ME).

Techniques: Injection, Functional Assay

Journal: bioRxiv

Article Title: Clinically relevant AAV8- PEX1 gene therapy preserves retinal integrity and function long-term in a murine model of Zellweger spectrum disorder

doi: 10.64898/2026.05.11.723906

Figure Lengend Snippet: AAV8. PEX1 (1.24 x 10 9 vg/eye) or AAV8.GFP was administered by subretinal injection to 5-week-old PEX1-G844D mice, and assessments were performed 6 months post - treatment (age 7 months). (A) DAPI-stained retinal cryosections spanning both sides of the optic nerve head (ONH), from peripheral ventral to peripheral dorsal retina, illustrating regional variation in ONL thickness. (B) Quantification of ONL thickness across the retinal circumference displayed as a spider plot (n = 3 mice per group). The dorsal pole, the most affected region in untreated mutant mice, remained moderately thinned in treated eyes, whereas ventral ONL was better preserved. The area under curve (AUC) is shown below. Statistical analysis was performed using a Kruskal–Wallis test with Dunn’s multiple-comparisons post hoc test; P < 0.05 indicated. Data are presented as mean ± SD. (C) Representative retinal cryosections stained with peanut agglutinin (PNA) to label cone outer segments. (D) Representative retinal cryosections labeled for glial fibrillary acidic protein (GFAP, red). Robust Müller glial activation was observed in all mutant groups except AAV8. PEX1 -treated eyes, which showed reduced GFAP immunoreactivity. Scale bar, 20µm. PRS, Photoreceptor segments; ONL, outer nuclear layer; INL, inner nuclear layer; GCL, ganglion cell layer.

Article Snippet: PEX1 -null ARPE-19 cells were generated using CRISPR-Cas9-mediated gene editing at The Jackson Laboratory (Bar Harbor, ME).

Techniques: Injection, Staining, Mutagenesis, Labeling, Activation Assay

Journal: bioRxiv

Article Title: Clinically relevant AAV8- PEX1 gene therapy preserves retinal integrity and function long-term in a murine model of Zellweger spectrum disorder

doi: 10.64898/2026.05.11.723906

Figure Lengend Snippet: AAV8. PEX1 (1.24 x 10 9 vg/eye) or AAV8.GFP was administered by subretinal injection to 5-week-old PEX1-G844D mice, and assessments performed 6 months post treatment (age 7 months). Representative confocal z-stack immunofluorescence images are shown. (A) RPE flatmounts (four-petal preparations) stained with TRITC-phalloidin (red) to visualize F-actin. GFP fluorescence (green) is present only in the AAV8. GFP group, indicating sustained transgene expression. Insets highlight the dorsal pole (asterisk), where focal RPE loss appears as holes consistent with geographic atrophy. (B) Representative confocal z-stack images from each group showing triple staining of F-actin (red), IBA1 (green), and F4/80 (white) in the top row, and corresponding IBA1/F4/80 dual staining in the bottom row to visualize subretinal mononuclear phagocyte infiltration. (C) Quantification of RPE cell density (cells/mm²) n = 3–4 mice per group, 6-8 eyes. (D) Quantification of geographic atrophy (GA) area (mm²;n = 3–4 mice per group). (E) Quantification of subretinal mononuclear phagocyte density (cells/mm²) n=3–6 mice per group (6–12 eyes); Scale bar, 100 μm. Statistical analysis was performed using a Kruskal–Wallis test with Dunn’s multiple-comparisons post hoc test; P < 0.05 indicated. Data are presented as mean (SD).

Article Snippet: PEX1 -null ARPE-19 cells were generated using CRISPR-Cas9-mediated gene editing at The Jackson Laboratory (Bar Harbor, ME).

Techniques: Injection, Immunofluorescence, Staining, Fluorescence, Expressing

Journal: bioRxiv

Article Title: Clinically relevant AAV8- PEX1 gene therapy preserves retinal integrity and function long-term in a murine model of Zellweger spectrum disorder

doi: 10.64898/2026.05.11.723906

Figure Lengend Snippet: Levels of total C26:0-lysophosphatidylcholine (LPC), plasmalogens, and subclasses of phosphatidylethanolamine (PE) plasmalogens, were measured in (A) whole neural retina and (B) whole RPE from WT and PEX1-G844D mice 6 months after subretinal injection with vehicle, AAV8. PEX1 (1.24 x 10 9 vg/eye) or AAV8. GFP (age 7 months); N= 5-7 tissues per group. Statistical analysis was performed using a Kruskal–Wallis test with Dunn’s multiple-comparisons post hoc test; P < 0.05 indicated. Data are presented as mean (SD).

Article Snippet: PEX1 -null ARPE-19 cells were generated using CRISPR-Cas9-mediated gene editing at The Jackson Laboratory (Bar Harbor, ME).

Techniques: Injection

Journal: bioRxiv

Article Title: Targeting cancer-associated cell surface RNAs with oligonucleotide-drug conjugates enables broad antitumor activity

doi: 10.64898/2026.05.08.723688

Figure Lengend Snippet: a , Schematic diagram of ODC manufacturing and its mechanism of action. The ODC is generated by conjugating DBCO-PEG4-VC-PAB-MMAE with 5’ azide modified oligonucleotide via click chemistry. The resulting ODC selectively binds the csRNA target, enabling endocytosis-mediated internalization and subsequent lysosomal release of the drug payload. b , Electropherogram (left) and mass spectrum (right) of unconjugated and conjugated U1-targeted oligonucleotides obtained by capillary electrophoresis and LC-MS, respectively. The intensity in the mass spectrum was normalized to the maximum intensity. The standard lower marker (LM) and upper marker (UP) are shown. The purity is defined as the ratio of the product peak area to the total peak area. c , Representative immunofluorescence image of HeLa cells treated with U1-MMAE and stained with 9D5 (red) and MMAE antibody (green). The yellow arrows indicate the M-phase cell. The scale bars are 10µm. d , The intensity plot of the fluorescence channels across the green dashed line indicated in ( c ). e , Representative fluorescent images of HeLa cells under conditions treated with U1-MMAE, polyA-MMAE, random-MMAE or solvent (blank control), followed by fixation and DAPI staining. f , Quantification of cell counts per field of view under conditions shown in ( e ). One-way ANOVA, ****P < 0.0001. g , Cytotoxicity of U1-MMAE, scrambled U1-MMAE, polyA-MMAE and DBCO-MMAE in HeLa cells after a 72-h incubation. Error bars, standard deviation. n = 3. h , Volcano plot for differential analysis of csRNA levels between MDA-MB-231 and MCF-10A cell lines. Differentially detected csRNAs are identified using the Wilcoxon rank-sum test (p value < 0.05 and absolute value of log₂FC > 0.5), and the color of these csRNA dots represents the difference in percentage of cells expressing the csRNA. i , Cytotoxicity of SNORA70F-MMAE in MCF-10A and MDA-MB-231 cells after a 72-h incubation. Error bars, standard deviation. n = 3. j , Cytotoxicity of snoU2_19-MMAE in the ten CIRCmap-profiled cancer and non-tumorigenic cells after a 72-h incubation. Error bars, standard deviation. n = 3. k , Cytotoxicity of snoU2_19-MMAE in additional unprofiled cancer and non-tumorigenic cells after a 72-h incubation. Error bars, standard deviation. n = 2 for ARPE-19, n = 3 for other groups. l , Tumor growth curves in HeLa xenograft-bearing mice with intravenous administration of snoU2_19-MMAE, polyA-MMAE, scrambled snoU2_19-MMAE, and vehicle control. Error bars, standard error of the mean. n = 6, unpaired one-tail t-test (day 42), *P < 0.05, **P < 0.01. m , Body weight change in HeLa xenograft-bearing mice with intravenous administration of snoU2_19-MMAE, polyA-MMAE, scramble-MMAE, and vehicle control. Error bars, standard error of the mean. n = 6, unpaired one-tail t-test, ns, not significant.

Article Snippet: HepG2 (HB-8065, ATCC) and GL261 (CVCL_Y003) cells were cultured in DMEM supplemented with 10% FBS and 1% PS. hTERT-HPNE (CRL-4023, ATCC), ARPE-19 (CRL-2302, ATCC), NCI-H82 (HTB-175, ATCC), HCC827 (CRL-2868, ATCC) cells were cultured in RPMI-1640 medium supplemented with 10% FBS and 1% PS.

Techniques: Generated, Modification, Electrophoresis, Liquid Chromatography with Mass Spectroscopy, Marker, Immunofluorescence, Staining, Fluorescence, Solvent, Control, Incubation, Standard Deviation, Expressing