murine control mouse embryonic fibroblasts  (ATCC)

Journal: bioRxiv

Article Title: Phosphorylated ubiquitin is a secondary messenger and an epigenetic mark mediating mitochondria to nucleus signaling

doi: 10.64898/2026.04.24.719390

Figure Lengend Snippet: A - Human fibroblasts were treated with mitochondrial toxins (CCCP, 50µM; valinomycin, 1µM; oligomycin 10µM + antimycin, 4µM) or DMSO for 0, 4, 8 and 24 hrs. Top: Representative immunofluorescence images from 24 hr timepoint showing distribution of pS65Ub (green). Bottom: Quantification shows mean +/- SEM pS65Ub intensity in cytoplasm, nucleus and nucleus:cytoplasm relative to 0 hrs timepoint (separated with vertical dashed line) from 1 experiment with 3 technical repeats. The horizontal line shows the 0hr-normalized baseline. B - Fibroblasts were treated with valinomycin (1µM, 24 hrs) before pS65Ub (green) was visualized by immunofluorescence using multiple specific antibodies. Nuclei (blue) are annotated with green asterisks. C - Confocal Z-stack max projections showing human induced dopaminergic neurons treated with oligomycin + antimycin (OA, 1µM, 24 hrs) and stained for pS65Ub (green), the dopaminergic neuron marker tyrosine hydroxylase (TH; magneta), MAP2 (white) and Hoechst (blue). Dashed boxes indicate areas magnified in pS65Ub channel inset and dashed circles delineate nuclei. D - Wild type (WT) and PINK1 knockout (KO) HeLa cells were treated with CCCP (20µM, 4 hrs) as indicated, then subcellular fractionations were analysed by Western blot. E - HeLa were treated with CCCP (20µM, 4 hrs) or OA (1µM, 24 hrs) before immunoblot analysis of whole-cell lysates using two pS65Ub antibodies. F - HeLa, HEK293T, NCI-H226, murine melanoma, murine PDAC or human skin fibroblast cells were treated with OA, then pS65Ub levels were assessed by Western blot. G - NGN2-induced iPSC-derived neurons were treated with OA (1µM, 6 or 24 hrs) before subcellular fractionation and Western blot analysis. H - HeLa were treated with CCCP (20µM, 4 hrs), rotenone (Rot - 20µM, 20 hrs), paraquat (P3/P6 - 3/6mM, 20 hrs) or CCCP+i (PINK1 inhibitor/PRT062607, 2.5µM, 4 hrs). Quantifications show mean +/-SEM from three independent repeats, *** p<0.0001 (CCCP+i treatment performed twice only so excluded from quantification). I - HeLa cells were treated with 10µM Gamitrinib-TPP (GTPP) for 0, 3 or 20hrs before analysis of whole-cell lysates by Western blot. Red asterisks mark the pS65Ub-histone band. Scale bars 10µm (50µM for panel D). Dashed lines in panels E and F indicate where identical samples were run on separate blots.

Article Snippet: Control primary fibroblasts (#106-05A) were from Cell Applications, Inc., PINK1 (Q456X/Q456X, #sc1028) and Parkin (Ex4-7 del / c.203_204 del AG, #sc1064) mutant fibroblasts are available from the NINDS stem cell repository.

Techniques: Immunofluorescence, Staining, Marker, Knock-Out, Western Blot, Derivative Assay, Fractionation

Journal: bioRxiv

Article Title: Phosphorylated ubiquitin is a secondary messenger and an epigenetic mark mediating mitochondria to nucleus signaling

doi: 10.64898/2026.04.24.719390

Figure Lengend Snippet: A - Schematic depiction of subcellular fraction experiment performed in . Detergent buffers used for fractionation are given in italics. CIB and MIB buffers are from Cell Fractionation Kit (Cell Signaling Technologies, #9038), while HNTE was made in house. B - Cells were treated with OA (1µM, 18 hrs), MG132 (20µM, 4 hrs) or DMSO before subcellular fractionation and Western blotting. Protein subcellular localizations are annotated (IMM = inner mitochondrial membrane, OMM = outer mitochondrial membrane) and arrows indicate both full length and cleaved PINK1 bands. For the pS65Ub blot, identical samples were analyzed on a separate gel (separated by dashed lines). C - PINK1-HA was transiently expressed in HeLa cells before treatment with OA, MG132 or DMSO as before. The distributions of pS65Ub (green), HA (red) and DNA (blue) were assessed by immunofluorescence. Magnified regions of interest are indicated by dashed boxes. Red dashed lines indicate regions captured by intensity profile (performed in the red/HA channel), graphed below. D - WT or PINK1 KO HeLa were transiently transfected with empty vector (EV), PINK1-FKBP (P) or FIS1-FRB (F) in combinations indicated before 18 hrs treatment with OA (1μM) or rapalog (500nM). A dashed line reveals where identical samples were analyzed on a separate gel. E - Schematic depiction of experiments performed in Extended Data Figures 4F, G. F - WT or PINK1 KO HeLa cells were transiently transfected with EV, PINK1 WT, PINK1-NES or PINK1-NLS before treatment with CCCP and Western blot analysis. Two plasmid amounts were used for transfection to achieve high and low relative PINK1 expression, captured by high and low exposures (HiExp/LoExp respectively). G - PINK1-myc tagged with NES/NLS signals were transiently expressed in HeLa cells before treatment with CCCP (20µM, 4 hrs) or MG132 (20µM, 4 hrs). Cells were fixed and stained for myc (green), pS65Ub (blue, grayscale in the far right column) or mitochondrial marker HSP60 (red). Nuclear exclusion (NES) and sequestration (NLS) is observed after MG132 treatment. H - Quantification of nuclear vs cytoplasmic pS65Ub signal density (arbitrary units/µm 2 ) in healthy control, PRKN (left) and PINK1 (right) mutant iPSC-derived dopaminergic neurons after treatment with CCCP (10µM, 6 hrs). The horizontal line shows the signal on DMSO-treatment, considered background due to negligible PINK1 activation/pS65Ub levels. Mean +/- SEM from three independent cell lines per genotype. I - iPSC-derived dopaminergic neurons from PD patients with mutations in PINK1 were treated with CCCP (10µM, 6 hrs). Dashed boxes annotate the area magnified in the inset and dashed circles show nuclear borders. Inset zoom in of pS65Ub channel. See for Control and PRKN mutant conditions. J - Skin fibroblasts from PINK1 / PRKN mutant PD donors and healthy controls were treated with valinomycin (1µM, 8 hours) before Western blot analysis. Maximal Parkin activity (revealed by MFN2 ubiquitination, see band shift) and PINK1 activity (substrate pS65Ubiquitination) is only detected in WT cells treated with valinomycin. K - Fibroblasts were treated with valinomycin (1µM, 0-24 hrs) before fixation and immunofluorescence analysis of pS65Ub (green, grayscale in the left hand column), TOM20 (orange) and DNA (blue). Nuclear:cytoplasmic pS65Ub signal intensity from three experiments was quantified, with mean +/-SEM, 2-way ANOVA shown. Red asterisks identify the pS65Ub-histone band *p<0.05, **p<0.01, ***p<0.001. Scale bars 10µm.

Article Snippet: Control primary fibroblasts (#106-05A) were from Cell Applications, Inc., PINK1 (Q456X/Q456X, #sc1028) and Parkin (Ex4-7 del / c.203_204 del AG, #sc1064) mutant fibroblasts are available from the NINDS stem cell repository.

Techniques: Fractionation, Cell Fractionation, Western Blot, Membrane, Immunofluorescence, Transfection, Plasmid Preparation, Expressing, Staining, Marker, Control, Mutagenesis, Derivative Assay, Activation Assay, Activity Assay, Ubiquitin Proteomics, Electrophoretic Mobility Shift Assay

Journal: Journal of Extracellular Vesicles

Article Title: Cholesterol Deficiency Directs Autophagy‐Dependent Secretion of Extracellular Vesicles

doi: 10.1002/jev2.70218

Figure Lengend Snippet: Cholesterol depletion promotes small extracellular vesicle release. (A) Cholesterol metabolic reactions targeted with small molecule inhibitors (red text). Rare diseases of cholesterol biosynthesis (blue text) arise from genetic mutations to indicated enzymes (grey). (B) GC‐MS analysis of human fibroblasts shows Smith–Lemli–Opitz syndrome (SLOS) and lathosterolosis (LATH) are cholesterol‐deficient and accumulate sterol precursors (mean ± SEM; n = 3 biological replicates from 3 independent experiments). (C) Small extracellular vesicle (sEV) release is elevated in SLOS and LATH fibroblasts relative to controls (mean ± SEM; n = 4 biological replicates from 4 independent experiments). One‐way ANOVA (F2,9 = 10.22, p ≤ 0.0048), Dunnett's multiple comparisons (* p ≤ 0.05; ** p ≤ 0.005). (D) Nanoparticle tracking analysis (NTA) of sEV size from HEK293T, HaCaT and HMC3 cells (mean; n = 4 biological replicates from 4 independent experiments). (E) Representative transmission electron microscopy (TEM) image of sEVs isolated from HEK293T cells. Scale bar, 100 nm. (F) CD9 immunoblot in HEK293T‐isolated sEVs following treatment with respective cholesterol biosynthesis inhibition. (G) Inhibition of cholesterol biosynthesis in HEK293T cells results in increased sEV release (mean ± SEM; n = 4 biological replicates from 4 independent experiments). One‐way ANOVA (F5,18 = 20.51, p < 0.0001), Dunnett's multiple comparisons test (** p ≤ 0.005, **** p < 0.0001). (H) Regression analysis of sEVs from HEK293T cells reveals a strong negative correlation between sEV secretion and cellular cholesterol levels. Linear regression (F1,4 = 15.17, R 2 = 0.7913, p ≤ 0.0176).

Article Snippet: Control fibroblasts were purchased commercially (ATCC, CRL‐2522).

Techniques: Gas Chromatography-Mass Spectrometry, Transmission Assay, Electron Microscopy, Isolation, Western Blot, Inhibition

Journal: Antioxidants

Article Title: Bioenergetic Signatures of DLD Deficiency: Dissecting PDHc- and α-KGDHc-Linked Defects

doi: 10.3390/antiox15010019

Figure Lengend Snippet: Mitochondrial respiration is impaired in fibroblasts derived from patients with DLD deficiency. Mitochondrial oxygen consumption was assessed in controls (Ctrl1 and Ctrl2) and patient (Pt1–Pt6) fibroblasts using high-resolution respirometry (Oroboros O2k). ( A ) Routine respiration; ( B ) maximal respiration calculated as the difference between FCCP-stimulated and α-chaconine–permeabilized rates; ( C ) complex I-linked respiration (NADH-linked respiration, N-pathway), calculated as the difference between ADP and α-chaconine; ( D ) complex II-linked respiration (NS-pathway) calculated as the difference between respiration after rotenone and α-chaconine addition; ( E ) effect of complex I inhibition, calculated as the difference between FCCP-stimulated and rotenone-inhibited respiration; and ( F ) complex I/complex II respiration ratio (complex I-linked activity divided by complex II-linked activity). Each open circle represents an independent experimental run (N = 4–8 repeats per sample). All data were normalized to cell number. Statistical analysis was performed using the Mann–Whitney U test. * p < 0.05 vs. Ctrl1; numerical p values (0.05 < p < 0.1) are indicated on the plots. Abbreviations: Ctrl, control; Pt, patient.

Article Snippet: Dermal fibroblast primary cell lines from six genetically confirmed patients with DLD deficiency were obtained from the Pediatric Metabolic Disease Unit, Sheba Medical Center (IRB# SMC-21-8644, Figure 1, Table 1, and ), as well as two control cell lines: a control human dermal fibroblast cell line was purchased from ATCC (PCS-201-012; Ctrl 1, Manassas, VA, USA), and a primary cell line from a 39-year-old healthy male (Ctrl 2).

Techniques: Derivative Assay, Inhibition, Activity Assay, MANN-WHITNEY, Control

Journal: Medicina

Article Title: Evaluation of TAM Receptor Targeting in Pathophysiology of Idiopathic Pulmonary Fibrosis

doi: 10.3390/medicina61101837

Figure Lengend Snippet: Relative mRNA expression levels of Axl, Tyro3, and Gas6 genes in IPF FBs and HPFs quantified by RT-qPCR. No Mer expression was detected in both fibroblast types. TBP gene was used as housekeeping gene. N = 4.

Article Snippet: Control human pulmonary fibroblasts (HPFs, C12360 , PromoCell, St. Louis, MO, USA) were cultured in 25 mM glucose DMEM supplemented with 10% FBS and 1% penicillin/streptomycin solution, and cells were used between passages 7 and 15.

Techniques: Expressing, Quantitative RT-PCR