Journal: Cell reports

Article Title: Uncovering genetic interactions in the DNA repair network in response to endogenous damage and ionizing radiation

doi: 10.1016/j.celrep.2025.116850

Figure Lengend Snippet: (A) Distribution of the observed phenotypes depleted in the basal screen results, indicating where the MRE11A-UBR5 gene pair falls relative to other depleted interactions. (B) Ranked observed phenotypes from the basal screen for both UBR5 and MRE11A . Blue/red regions highlight significantly enriched/depleted UBR5 -gene and MRE11A -gene interactions, respectively. Blue and red regions highlight gene combinations that are enriched above (blue) or depleted below (red) one standard deviation (+0.6981 and −0.7791) of the mean of all basal interactions and possess a Fisher-combined p < 0.05. (C) Time-lapse images of growth from Dox-induced dual-guide vectors with NT-1 x UBR5 -g2 or NT-1 x NT-2 in nuclear-EGFP-expressing cells co-cultured with nuclear-RFP-expressing cells grown in DMSO or 6.25 μM mirin (+mirin). Images are from one well per condition over the first 72 h of growth. Scale bar: 100 μM. (D) Measurements are calculated as the log 2 fold change (log 2 FC) of Dox induced over uninduced growth for the labeled condition, relative to the growth of co-cultured RFP+ cells, as seen in (C). Data represent mean ± SEM of 3 biological repliactes. The gray bar indicates the 72 h of growth shown in (C), though imaging continued. (E) Comparative growth differences at 96 h of two separate, inducible UBR5 guides from experiments performed similarly to those shown in (C) and (D). Bars are only shown for Dox-treated conditions but are normalized to uninduced, DMSO-treated control wells for each genotype and replicate. Mirin: 5 μM. Blue prediction bars are calculated from an additive model assuming no interaction, with the average effect of mirin on NT cells plus the average effect of UBR5 depletion for each guide and replicate. Data represent mean ± SEM of 2 biological replicates, and statistics represent a two-way ANOVA with Dunnett multiple comparisons test; p = 0.0277. (F) Western blot depicting robust UBR5 KO in two selected HT1080-6TG clones. (G) Dose curve of HT1080-6TG clones shown in (F) grown in increasing doses of mirin in a colony formation assay. IC50 was calculated from a sigmoidal interpolation of all datasets. Error bars: ± SEM from three biological replicates. Statistics match in color the clone they reference, relative to NT cells. Statistics: a two-way ANOVA with Dunnett’s multiple comparisons test between NT-treated cells and UBR5 -KO clones at each concentration; * p < 0.01 and **** p < 0.0001. (H) Western blot showing UBR5 depletion in U2-OS cells electroporated with either an sgNT-RNP or an sg UBR5 -RNP. (I) Log 2 of the relative confluence over time (relative to DMSO) for sgNT-RNP- or sg UBR5 -RNP-treated U2-OS cells from (H), grown with 25 μM mirin over 120 h. The shaded area around each solid line indicates the SEM from three biological replicates. Statistics: a two-way ANOVA at 120 h with Šídák’s multiple comparisons test; p = 0.0317. See also .

Article Snippet: U2-OS , ATCC , HTB-96.

Techniques: Standard Deviation, Expressing, Cell Culture, Labeling, Imaging, Control, Western Blot, Clone Assay, Colony Assay, Concentration Assay

Journal: bioRxiv

Article Title: C9ORF72-derived polyGR polypeptides disrupt passive nucleocytoplasmic transport by tuning protein affinity for the nuclear pore barrier

doi: 10.64898/2026.03.16.711670

Figure Lengend Snippet: a, Schematic of the experimental design for assessing polyGR association with nuclear pores using two-colour STORM microscopy in U2OS-CRISPR–NUP96–mEGFP cells. Angled beam imaging was used to selectively excite single molecules of ATTO655-labelled GR 20 or ATTO655 dye alone and Nup96-mEGFP labelled with anti-GFP nanobodies by DNA-PAINT at the basal nuclear envelope. b, Averaged NPC localisations from STORM imaging of fixed cells showing that ATTO655 dye alone does not localize to NPCs (upper panel), whereas ATTO655–GR 20 exhibits localisation in close proximity to NPCs, not co-localising with the structural component Nup96, but instead in surrounding regions including within the central channel. Scale bars = 50 nm.

Article Snippet: U2OS-CRISPR-NUP96-mEGFP cells (Cytion, #300174) were cultured in McCoy’s 5A (Modified) Medium (Thermo Fisher Scientific, 26600023) supplemented with 10% fetal bovine serum (Pan Biotech, P30-3031), 1% non-essential amino acids (Thermo Fisher Scientific, 11140035), 1% penicillin/streptomycin (Thermo Fisher Scientific, 15140122), and 1% sodium pyruvate (Thermo Fisher Scientific, 11360039).

Techniques: Microscopy, CRISPR, Imaging

Journal: Bone Research

Article Title: Chemotherapeutic drug-triggered AEP-cleaved G3BP1 orchestrates stress granules/nucleoli/mitochondria in osteosarcoma

doi: 10.1038/s41413-025-00453-w

Figure Lengend Snippet: Chemotherapeutic drugs induced SG assembly and triggered AEP to specifically cleave G3BP1 at N258/N309. a Representative immunofluorescences (IF) images of SG assembly in U2OS, 143B, U87-MG and A549 cells exposed to cisplatin (5 and 50 μmol/L) or vehicle for 6 h. Scale Bar = 10 μm. b Quantification of the counts of SGs per cell ( n = 50) and SG + cell ratio ( n = 6) in cells of ( a ). c WB analysis of G3BP1 and AEP in U2OS and 143B with NC or AEP-knockdown (KD) exposed to different chemotherapeutic drugs for 6 h. The arrows point out the truncated fragments of G3BP1 cleaved by AEP. d In vitro cleavage experiment of AEP and G3BP1 (WT and point mutants) purified recombinant proteins. Data are expressed as mean ± SD. *** P < 0.001, **** P < 0. 0001. Comparisons were conducted using one-way ANOVA

Article Snippet: Stable cell lines of U2OS, 143B, and U87-MG were seeded in 96-well cell culture plates and treated with cisplatin (50 μmol/L) or appropriate vehicle solution for 6 h. OCR Fluorometric Assay Kit (Cat# E-BC-F068, Elabscience, Wuhan, China) was used according to manufacturer’s protocol.

Techniques: Knockdown, In Vitro, Purification, Recombinant

Journal: Bone Research

Article Title: Chemotherapeutic drug-triggered AEP-cleaved G3BP1 orchestrates stress granules/nucleoli/mitochondria in osteosarcoma

doi: 10.1038/s41413-025-00453-w

Figure Lengend Snippet: tG3BP1-Ns competitively bind to full-length G3BP1 and negatively modulate SG. a Representative images of SGs in U2OS cells with or without AEP-KD exposed to cisplatin (50 μmol/L), doxorubicin (50 μmol/L) for 6 h. Scale bar = 10 μm. b Quantification of the SG counts per cell ( n = 50) and SG + cell ratio ( n = 6) in cells of ( a ). c Representative images of G3BP1-FL colocalized with tG3BP1-Ns or tG3BP1-Cs in Hela cells. Scale bar = 5 μm. d Co-IP and WB assays of mCherry-tagged tG3BP1-Ns or Cs cotransfected with flag-tagged full-length G3BP1 in HEK293T. e Representative images of SGs in tG3BP1-Ns overexpressed U2OS cells exposed to cisplatin (5 μmol/L), doxorubicin (5 μmol/L) for 6 h. Scale bar = 10 μm. f Quantification of SG counts per cell ( n = 50) and SG + cell ratio ( n = 6) of ( e ). Data are expressed as mean ± SD. * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.000 1. ns no significance. One-way ANOVA

Article Snippet: Stable cell lines of U2OS, 143B, and U87-MG were seeded in 96-well cell culture plates and treated with cisplatin (50 μmol/L) or appropriate vehicle solution for 6 h. OCR Fluorometric Assay Kit (Cat# E-BC-F068, Elabscience, Wuhan, China) was used according to manufacturer’s protocol.

Techniques: Co-Immunoprecipitation Assay

Journal: Bone Research

Article Title: Chemotherapeutic drug-triggered AEP-cleaved G3BP1 orchestrates stress granules/nucleoli/mitochondria in osteosarcoma

doi: 10.1038/s41413-025-00453-w

Figure Lengend Snippet: tG3BP1-Cs translocate into the nucleolus and sequester mRNAs of ribosomal proteins in the nucleolus to inhibit cellular translation. a Representative images of the sub-nucleolar localization of tG3BP1-Cs and sub-nucleolar markers in Hela cells. Scale bar = 5 μm. b Representative images of FISH and IF assays present the nucleolar colocalization of tG3BP1-Cs with FAM-conjugated probes of ribosomal mRNAs, RPS4X, RPL11, and RP27A. c SUnSET experiments analyzed the protein synthesis in U2OS, 143B, and U87-MG cells treated with cisplatin (50 μmol/L) or vehicle for 6 h. d Quantification of protein synthesis of the aforementioned cell lines exposed to cisplatin (50 μmol/L) or vehicle for 6 h were detected with the Click-iT HPG system ( n = 3). Data are expressed as mean ± SD. ** P < 0.01, **** P < 0.000 1. ns no significance. One-way ANOVA

Article Snippet: Stable cell lines of U2OS, 143B, and U87-MG were seeded in 96-well cell culture plates and treated with cisplatin (50 μmol/L) or appropriate vehicle solution for 6 h. OCR Fluorometric Assay Kit (Cat# E-BC-F068, Elabscience, Wuhan, China) was used according to manufacturer’s protocol.

Techniques:

Journal: Bone Research

Article Title: Chemotherapeutic drug-triggered AEP-cleaved G3BP1 orchestrates stress granules/nucleoli/mitochondria in osteosarcoma

doi: 10.1038/s41413-025-00453-w

Figure Lengend Snippet: tG3BP1-Cs bind to mitochondrial mRNA targets and suppress their translation to alleviate mitochondrial stress. a Representative images of the colocalization of tG3BP1-Cs with the mitochondrial marker TOMM20 in Hela cells. Scale bar = 10 μm. b RNP-IP analysis of the mRNA target encoding ribosomal proteins and oxidative phosphorylation binding to tG3BP1-Cs ( n = 3) in tG3BP1-Cs overexpressed U2OS cells. c Ribosome profiling-qPCR analysis demonstrated that tG3BP1 overexpression in U2OS cells significantly downregulates mitochondrial genes translation. d WB analysis of mitochondrial genes expression in cell lines exposed to cisplatin (50 μmol/L) or vehicle for 6 h. e Cisplatin-induced mitochondrial damage was detected by JC-1 probe staining in cells of ( d ). Data are expressed as mean ± SD. *** P < 0.001, **** P < 0.000 1. One-way ANOVA

Article Snippet: Stable cell lines of U2OS, 143B, and U87-MG were seeded in 96-well cell culture plates and treated with cisplatin (50 μmol/L) or appropriate vehicle solution for 6 h. OCR Fluorometric Assay Kit (Cat# E-BC-F068, Elabscience, Wuhan, China) was used according to manufacturer’s protocol.

Techniques: Marker, Phospho-proteomics, Binding Assay, Over Expression, Expressing, Staining

Journal: Nature Methods

Article Title: Optimal precision and accuracy in 4Pi-STORM using dynamic spline PSF models

doi: 10.1038/s41592-022-01465-8

Figure Lengend Snippet: Mic60 is a component of the MICOS complex, and is involved in the formation and maintenance of crista junctions that connect the crista membrane with the inner boundary membrane. a , Mic60 in a U-2 OS cell, labeled with primary and secondary antibodies. The Mic60 signals appear as structured, punctate clusters. The localizations are color coded according to their z coordinate (identical color scales in a – d ). Scale bar, 200 nm. b , Magnified view of the boxed region in a . Scale bar, 50 nm. c , Mic60 in a COS-7 cell, in which the crista junctions exhibit a linear organization over segments of the inner boundary membrane. Scale bar, 200 nm. d , Magnified view of the boxed region in c . Scale bar, 50 nm. e , f , Unwrapped views of the Mic60 localization density around the surface of the mitochondria, showing the nanoscale distribution of Mic60. In U-2 OS cells, Mic60 appears predominantly punctate, with pairs or clusters of signal density separated by 20–40 nm (Extended Data Fig. and Supplementary Fig. ). In COS-7 cells, Mic60 appears to have a zigzag or double-line arrangement, with a typical width of approximately 25 nm (Extended Data Fig. and Supplementary Fig. ). Dashed lines indicate the extent of the data in f . g , Two-color image of Mic60 (blue) and mitochondrial nucleoids (yellow) in a COS-7 cell, stained with antibodies labeled with Alexa Fluor 647 and Cy5.5, respectively. Scale bar, 1 µm. h , Detailed view of the boxed region in g . Lower density of Mic60 close to the DNA signal, suggesting fewer crista junctions in these regions. i , Cross-section ( x – z ) through the region indicated by the dashed lines in h , showing Mic60 at the inner boundary membrane, and a DNA cluster in the center of the mitochondrion. j , A 3D perspective view of the mitochondrion shown in h and i , where the Mic60 and DNA signals have been rendered as isosurfaces. Scale bars, 250 nm ( h – j ).

Article Snippet: Experiments were performed using either standard COS-7 cells or U-2 OS cells obtained from American Type Culture Collection (ATCC), or gene-edited U-2 OS cells expressing a SNAP-tagged version of the nucleoporin Nup107 (CLS Cell Lines Service, U-2OS-ZFN-SNAP-Nup107 clone 294) or Nup96 (CLS Cell Lines Service, U-2OS-CRISPR-NUP96-SNAP clone 33) .

Techniques: Labeling, Staining