Journal: bioRxiv

Article Title: Biomarker-driven and gene-enhanced viral therapy for malignant peripheral nerve sheath tumor

doi: 10.64898/2026.10.12.758653

Figure Lengend Snippet: A) Schematic representation of the proposed viral silencing mechanism, wherein the host Polycomb Repressive Complex 2 (PRC2) deposits H3K27me3 on host histones associated with viral DNA, reducing RNA polymerase II (RNAPII) transcription. B) Excess total cell H3K27me3 immunoblotting is observed in doxycycline-induced TY5005 (TY/Dox) at 24 hours post-infection (left). Similarly, excess H3K27me3 is observed in the infected PRC2-proficient N0(32.1) at both 12 and 24 hours post-infection (right). C-D) CUT&RUN analysis of H3K27me3 occupancy on the human genome (C) and HSV-1 episome (D) in TY5005 with or without SUZ12 genetic rescue. Y-axes represent total H3K27me3 genomic occupancy, normalized to an E. coli spike-in control and mathematically background-subtracted against matched IgG negative controls (H3K27me3 - IgG). Statistical significance was determined using a Two-Way ANOVA followed by post-hoc pairwise comparisons via estimated marginal means [***: p ≤0.001; ns: not significant]. C) Quantification of H3K27me3 on the human genome confirms successful doxycycline induction of global H3K27me3, with no significant difference observed in host genome deposition between uninfected and infected TY5005/Dox biological replicates. D) H3K27me3 accumulation on the HSV-1 genome was detected specifically after PRC2 rescue, consistent with PRC2-dependent chromatinization of viral DNA. E) Representative track plot visualizing H3K27me3 occupancy across the HSV-1 genome (GU734771.1) for the conditions evaluated in panel D. Robust, widespread H3K27me3 deposition is visible across the viral episome strictly in the TY5005 + Dox + HSV condition. Regions lacking signal correspond to HSV-1 repeat regions that are excluded in multimapping alignment filtering.

Article Snippet: Chromatin cleavage was performed with pAG-MNase (EpiCypher #15-1016), with 0.5 ng E. coli DNA (EpiCypher #18-1401k) per 500,000 nuclei added for spike-in normalization.

Techniques: Western Blot, Infection, Analysis, Control

Journal: bioRxiv

Article Title: Escape from replicative crisis and immortalization precedes complex genome evolution

doi: 10.64898/2026.10.09.758087

Figure Lengend Snippet: ( A ) Telomerase Repeat Amplification Protocol (TRAP) of parental IMR90 E6E7 and postcrisis clones. RNaseI treated or untreated extracts of IMR90 cells ectopically overexpressing hTERT are used as negative and positive control, respectively. Representative of two independent experiments. ( B ) Hi-C sequencing analysis of IMR90 E6E7 and postcrisis clones. The surrounding of the TERT locus (chr5:500000-2100000, GRCh38/hg38) is shown as contact map with Virtual4C (chr5:900000-925000, GRCh38/hg38). The detected loop anchor is marked with an arrow and if statistically significant (FDR < 0.05) with an asterisk in Virtual4C. Differential CTCF contacts are color coded according to fold change. Two replicates per sample. ( C ) H3K27me3, H3K27ac and DNA methylation in IMR90 E6E7 (PD64-72) and PC7 (PD76-82) were measured by Cut&Run, ChIP-seq and Oxford nanopore technologies (ONT) sequencing, respectively. Differential peaks (FDR < 0.01) and differentially methylated regions (DMR) are shown in red and blue for increased and reduced signal in PC7 relative to IMR90 E6E7 . Two replicates for Cut&Run and ChIP-seq, and one replicate for ONT sequencing. ( D ) Relative hTERT expression levels by RT-qPCR in PC7 (PD82-91) cells transfected with control and Rad21 siRNA pool. The means of three independent experiments with three technical replicates are shown. Two-tailed paired t test. ( E ) Hi-C sequencing analysis of B-cell Acute Lymphoblastic Leukemia (B-ALL) samples reported in . The surrounding of the TERT locus (chr5:500000-2100000, GRCh38/hg38) is shown as contact map with the loop anchor marked by an arrow. ( F ) TERT promoter DNA methylation in IMR90 E6E7 and PC7. Methylation of individual CpG sites are shown as points and the average methylation of a 100 base pairs (bp) window are shown as a line. ATG and THOR are the TERT start codon and the TERT hypermethylated oncological region (chr5:1,295,206-1,295,638, GRCh38/hg38), respectively. The DMR that partially overlaps with THOR and is hypermethylated in PC7 relative to IMR90 E6E7 is shown in red.

Article Snippet: CUT&RUN was performed using the CUTANA CUT&RUN Kit (EpiCypher, 14-1048) according to manufacturer’s instructions.

Techniques: Amplification, Clone Assay, Positive Control, Hi-C, Sequencing, Analysis, DNA Methylation Assay, ChIP-sequencing, Methylation, Expressing, Quantitative RT-PCR, Transfection, Control, Two Tailed Test