Journal: bioRxiv

Article Title: A DNA foundation model predicts osteoporosis risk genes without proximity bias

doi: 10.64898/2026.03.09.707383

Figure Lengend Snippet: a. All variant–gene pairs within a receptive field of 256kbp are scored by Rosalind. Genes above the elbow threshold are kept as candidate causal genes. b. The distribution of protein-coding genes around the 1103 lead variants from the eBMD GWAS (Morris et al. ) when using a window of 256kbp. c. Overlap of Rosalind-predicted genes with nearest genes is shown, with genes known to regulate eBMD highlighted. d. Mineralization assay experimental workflow: arrayed CRISPR/Cas9 knock-out screen of hFOB1.19 human osteoblasts. e. Plot shows SNP RSID-gene pairs, where at least one hit was observed in the osteoblast mineralisation assay. Hit calling was performed using Region of Practical Equivalence (ROPE) analysis and results show hits at ROPE 0.5 or greater (‘moderate’ effect size) f. Experimental validation summary, with assay “hits” represented in blue and “no effect” represented in red.

Article Snippet: hFOB1.19 (ATCC) were cultured in flasks in DMEM/F-12, 10% FBS (Sigma F7524 lot.0001663052), antibiotic/antimycotic (Gibco 15240-062) and G418 sulfate (ab144261) at 34oC until 80-90% confluent.

Techniques: Variant Assay, Mineralization Assay, CRISPR, Knock-Out, Biomarker Discovery

Journal: Cell Death Discovery

Article Title: Unveiling the toxic effects of perfluorooctanoic acid on osteoblast function and extracellular matrix deposition using 2D and 3D models

doi: 10.1038/s41420-025-02863-5

Figure Lengend Snippet: a , c Representative brightfield images of hFOB1.19 spheroids after 2 and 5 days of exposure to PFOA, respectively. Spheroids exposed to 0.02% of vehicle (DMSO) were used as the control. Images were obtained using the Light Lionheart FX Microscope. Scale bar = 200 μm (magnification 10×). b , d Morphological parameters of hFOB1.19 spheroids after 2 and 5 days of exposure to PFOA, respectively. ImageJ software determined area, solidity, circularity, and roundness after 2 and 5 days of exposure to different PFOA concentrations ( n = 31–40), individual biological replicates. P values indicate the results of comparisons between each PFOA-treated group and the control group. Values of p < 0.05 are considered statistically significant.

Article Snippet: The human osteoblast cell line hFOB1.19 (ATCC CRL-11372) was obtained from the American Type Culture Collection (ATCC, USA) in March 2021.

Techniques: Control, Microscopy, Software

Journal: Cell Death Discovery

Article Title: Unveiling the toxic effects of perfluorooctanoic acid on osteoblast function and extracellular matrix deposition using 2D and 3D models

doi: 10.1038/s41420-025-02863-5

Figure Lengend Snippet: Western blot analysis of oxidative stress marker expression, a (60 kDa) CAT and b (96 kDa) NRF2 for 2D ( n = 5 biological replicates). c – e CAT levels in hFOB1.19 spheroids exposed to different PFOA concentrations for 2 days ( c ) and 5 days ( e ). NRF2 levels in hFOB1.19 spheroids exposed to different PFOA concentrations for 2 days ( d ) and 5 days ( f ) ( n = 3–4 individual biological replicates). P values indicate the results of comparisons between each PFOA-treated group and the control group. Values of p < 0.05 are considered statistically significant.

Article Snippet: The human osteoblast cell line hFOB1.19 (ATCC CRL-11372) was obtained from the American Type Culture Collection (ATCC, USA) in March 2021.

Techniques: Western Blot, Marker, Expressing, Control

Journal: Cell Death Discovery

Article Title: Unveiling the toxic effects of perfluorooctanoic acid on osteoblast function and extracellular matrix deposition using 2D and 3D models

doi: 10.1038/s41420-025-02863-5

Figure Lengend Snippet: Western blot analysis of COL1A2 and CB1 levels. a , b (120 kDa) COL1A2 and (53 kDa) CB1 respectively for 2D ( n = 5 individual biological replicates). c – e Degraded COL1A2 (60 kDa) levels in hFOB1.19 spheroids exposed to different PFOA concentrations for 2 and 5 days, respectively. d , f CB1 levels in hFOB1.19 spheroids exposed to different PFOA concentrations for 2 and 5 days, respectively ( n = 3–4 individual biological replicates). P values indicate the results of comparisons between each PFOA-treated group and the control group. Values of p < 0.05 are considered statistically significant. g Localization of CB1 on the osteoblast membrane on the spheroid surface. Scale bar: 20 μm. Image captured using confocal microscope LSM 800 (Zeiss) (40×).

Article Snippet: The human osteoblast cell line hFOB1.19 (ATCC CRL-11372) was obtained from the American Type Culture Collection (ATCC, USA) in March 2021.

Techniques: Western Blot, Control, Membrane, Microscopy