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Journal: bioRxiv
Article Title: TRIM21 is a molecular rheostat for influenza A virus replication
doi: 10.64898/2026.03.16.711963
Figure Lengend Snippet: (A and B) A549 cells were infected with H1N1pdm at varying MOI (0.01, 0.1, 0.5, 1 and 2) and harvested at the indicated timepoints. (A) Total cellular RNA was isolated, and TRIM21 mRNA was analyzed by real-time PCR. The dotted line indicates fold change of 1. (B) Lysates prepared from infected cells were immunoblotted with antibodies against TRIM21. GAPDH was used as a loading control. (C) Viral titer in wild-type (WT) and TRIM21 knockout (TRIM21 −/− ) A549 cells infected with H1N1pdm, H3N2, or H9N2 (MOI = 0.01) at the indicated time points were measured by plaque assay. Data are shown as means of n = 2 or 3 ± standard deviations (SD). Two-way ANOVA was used to analyze data (*p < 0.05, **p < 0.01, ***p < 0.001). (D) Viral entry was assessed by flow cytometric analysis of R18-positive populations for 1 hpi. Data are shown as means of n = 3 ± standard deviations (SD). (E) Influenza polymerase reconstitution assay was performed in WT and TRIM21 −/− HEK293T cells using RNP components from H1N1, H1N1pdm, H3N2, H9N2, or H5N1. Polymerase activity was normalized to Renilla luciferase. Data are shown as means of n = 3 or 4 ± standard deviations (SD). Two-tailed Student’s unpaired t-test was used to analyze data (**p < 0.01, ***p < 0.001, ****p < 0.0001).
Article Snippet: The following cell lines were used in this study:
Techniques: Infection, Isolation, Real-time Polymerase Chain Reaction, Control, Knock-Out, Plaque Assay, Reconstitution Assay, Activity Assay, Luciferase, Two Tailed Test
Journal: bioRxiv
Article Title: TRIM21 is a molecular rheostat for influenza A virus replication
doi: 10.64898/2026.03.16.711963
Figure Lengend Snippet: (A) HEK293T cells were transiently co-transfected with Myc-TRIM21 and Flag-tagged PA, PB1, PB2 or NP from A/Puerto Rico/8/1934 (PR8). Lysates were immunoprecipitated with anti-c-Myc magnetic beads, and immunoprecipitates (IP) were analyzed by immunoblotting with anti-Myc and anti-Flag antibodies. Transfected TRIM21 and viral proteins in cell lysates (CL) were confirmed by immunoblotting. (B) HEK293T cells were transiently co-transfected with Myc-TRIM21 and Flag-tagged NP from PR8, A/California/04/2009 (Ca04) or A/Quail/ Hong Kong/G1/97 (G1). Lysates were immunoprecipitated with anti-c-Myc magnetic beads and analyzed by immunoblotting. (C) Immunofluorescence imaging of TRIM21 and NP was performed in mock and H1N1pdm-infected A549 cells (MOI = 10). (D) HEK293T cells were co-transfected with Myc-TRIM21 and Flag-PR8-NP. Lysates were treated with or without RNAse A (50 mg/mL) for 10 minutes at 37°C prior to immunoprecipitation using anti-Flag M2 affinity beads. IP and CL were then analyzed by immunoblotting. (E) The binding affinities of H1N1-Ca04-NP (blue), H1N1-PR8-NP (purple), H3N2-HK68-NP (pink) and influenza B NP (orange) to TRIM21 were measured by ELISA. PBS was included as a negative control. (F) The schematic diagram of TRIM21 and its truncated mutants. TRIM21 contains a tripartite motif bearing an N-terminal RING domain, a B-box and coiled-coil domain. TRIM21 bears an PRYSPRY domain responsible for substrate interaction. Triad catalytic inactive mutant (C16A/C31A/H33W) is marked with red stalk. (G and H) HEK293T cells were transiently co-transfected with Flag-PR8-TRIM21 and Myc-TRIM21 constructs, including (G) WT, catalytic inactive mutant (Mut), or deletion mutants lacking the RING (ýRING), B-box (ýBbox) or SPRY (ýSPRY) domain, or (H) WT or point mutants within the SPRY domain. Lysates were immunoprecipitated with anti-Flag M2 affinity beads and then analyzed by immunoblotting.
Article Snippet: The following cell lines were used in this study:
Techniques: Transfection, Immunoprecipitation, Magnetic Beads, Western Blot, Immunofluorescence, Imaging, Infection, Binding Assay, Enzyme-linked Immunosorbent Assay, Negative Control, Mutagenesis, Construct
Journal: bioRxiv
Article Title: TRIM21 is a molecular rheostat for influenza A virus replication
doi: 10.64898/2026.03.16.711963
Figure Lengend Snippet: (A) Viral titer in WT, TRIM21 −/− , WT TRIM21-reconstitued (TRIM21 WT ), catalytic inactive mutant of TRIM21-reconstituted (TRIM21 Mut ) and SPRY domain-deficient TRIM21-reconstituted (TRIM21 ýSPRY ) A549 cells infected with H1N1pdm infection (MOI = 0.01) at 24 hpi were measured by TCID 50/ mL. Data are shown as means of n = 3 ± standard deviations (SD). Two-tailed Student’s unpaired t-test was used to analyze data (ns: not significant, **p < 0.01). (B) H1N1pdm influenza polymerase reconstitution assay in the indicated HEK293T cell lines. Polymerase activity was normalized to Renilla luciferase. Data are shown as means of n = 3 ± standard deviations (SD). Two-tailed Student’s unpaired t-test was used to analyze data (ns: not significant, *p < 0.05, **p < 0.01). (C) HEK293T cells were transiently co-transfected with Flag-PR8-NP and increasing amount of WT or Mut Myc-TRIM21. (D) HEK293T cells were transiently co-transfected with Flag-PR8-NP and Myc-TRIM21 and treated with or without 25 μM proteasomal inhibitor MG132 for 6 hours prior to harvest. (C and D) NP and TRIM21 expression were measured by immunoblotting using anti-Flag and anti-Myc antibodies, respectively. Increasing TRIM21 expression is indicated by progressively larger black dots; white dots indicate no TRIM21 transfection. (E and F) HEK293T cells were transiently co-transfected with Flag-PR8-NP, Myc-TRIM21, and HA-ubiquitin (WT versus linkage-specific constructs as indicated). In (F) , Myc-TRIM21 was transfected at increasing amount, denoted by progressively larger black dots. Cells were treated with MG132, followed by immunoprecipitation using anti-Flag M2 affinity beads. IP and CL were then analyzed by immunoblotting. Black and white dots indicate the presence or absence of plasmid transfection, respectively. (G) A549 cells were transiently transfected with empty vector control, WT Myc-TRIM21, or Mut Myc-TRIM21 at increasing amount and subsequently infected with H1N1pdm virus (MOI = 0.01). Viral titers at 24 hpi were determined by TCID 50/ mL. The dotted line indicates the mean viral titer of the empty vector control. Data are shown as means of n = 3 ± standard deviations (SD). Two-tailed Student’s unpaired t-test was used to analyze data (*p < 0.05). (H) H1N1pdm influenza polymerase reconstitution assay in HEK293T cells transiently transfected with empty vector control, WT Myc-TRIM21 or Mut Myc-TRIM21 at increasing amount, together with H1N1pdm RNP components and reporter constructs. Polymerase activity was normalized to Renilla luciferase. The dotted line indicates the mean polymerase activity of the empty vector control. Data are shown as means of n = 3 ± standard deviations (SD). Two-tailed Student’s unpaired t-test was used to analyze data (****p < 0.0001). (I) Viral titer in WT A549 cells, WT cells stably overexpressing TRIM21 (TRIM21 WT+/+ ), or the catalytically inactive mutant (TRIM21 Mut+/+ ) infected with H1N1pdm infection (MOI = 0.01) at 24 hpi were measured by TCID 50/ mL. Data are shown as means of n = 3 ± standard deviations (SD). Two-tailed Student’s unpaired t-test was used to analyze data (ns: not significant, *p < 0.05). (J) WT, TRIM21 WT+/+ , TRIM21 Mut+/+ A549 cells were infected with H1N1pdm (MOI = 0.01). Total cell lysates were collected at 24 hpi and immunoblotted for RIG-I and phosphorylated STAT1 (pSTAT1). Cell lines are indicated by black dots.
Article Snippet: The following cell lines were used in this study:
Techniques: Mutagenesis, Infection, Two Tailed Test, Reconstitution Assay, Activity Assay, Luciferase, Transfection, Expressing, Western Blot, Ubiquitin Proteomics, Construct, Immunoprecipitation, Plasmid Preparation, Control, Virus, Stable Transfection
Journal: bioRxiv
Article Title: TRIM21 is a molecular rheostat for influenza A virus replication
doi: 10.64898/2026.03.16.711963
Figure Lengend Snippet: (A) Heatmap showing the relative abundance of proteins identified as statistically significant (p < 0.05) by two-way ANOVA across genotypes (WT or TRIM21 −/− ), conditions (basal control, mock- or H1N1pdm-infected), and their interaction. Protein abundance was calculated using maximum label-free quantification per protein per sample, normalized with z-score. Only proteins significant in all three comparisons (genotype, infection and interaction) are shown. Colors indicate upregulated (red) or downregulated (blue) proteins. Experiment was performed in four replicates for each condition. The cells were harvested at 48 hpi (MOI 0.01), the time point at which viral production differed most markedly between the cells (B) WT and TRIM21 −/− A549 cells were treated with polyIC for 24 hours, and cell lysates were immunoblotted for RIG-I, pSTAT1, and phosphorylated STAT2 (pSTAT2). (C and D) HEK293T cells were transiently transfected with the indicated (C) plasmids or (D) siRNAs, together with an ISRE-driven firefly luciferase reporter and a Renilla luciferase control. At 24 hours post-transfection, cells were treated with IFN-α for an additional 24 hours prior to measurement of luciferase activities. Data are shown as means of n = 3 ± standard deviations (SD). Two-tailed Student’s unpaired t-test was used to analyze data (ns: not significant, **p < 0.01). The dotted line indicates the mean ISRE activity in empty vector or non-targeting (NT) control. (E) The indicated proteins were depleted by siRNA in both WT and TRIM21 −/− A549 cells, followed by polyIC treatment. Lysates were immunoblotted for RIG-I, pSTAT1, and pSTAT2. (F) HEK293T cells were transiently co-transfected with Myc-TRIM21 and Flag-PRKDC. Lysates were immunoprecipitated with anti-c-Myc magnetic beads and analyzed by immunoblotting. Black and white dots indicate the presence or absence of plasmid transfection, respectively. (G) HEK293T cells were transiently co-transfected with Flag-PRKDC, Myc-TRIM21, and HA-ubiquitin (WT versus linkage specific constructs as indicated). Cells were treated with MG132, followed by immunoprecipitation using anti-Flag M2 affinity beads. IP and CL were then analyzed by immunoblotting. Black and white dots indicate the presence or absence of plasmid transfection, respectively. (H) HEK293T cells were transiently co-transfected with Flag-PRKDC and increasing amount of WT Myc-TRIM21 and treated with or without proteasomal inhibitor MG132. PRKDC and TRIM21 expression were measured by immunoblotting using anti-Flag and anti-Myc antibodies, respectively.
Article Snippet: The following cell lines were used in this study:
Techniques: Control, Infection, Quantitative Proteomics, Transfection, Luciferase, Two Tailed Test, Activity Assay, Plasmid Preparation, Immunoprecipitation, Magnetic Beads, Western Blot, Ubiquitin Proteomics, Construct, Expressing
Journal: bioRxiv
Article Title: TRIM21 is a molecular rheostat for influenza A virus replication
doi: 10.64898/2026.03.16.711963
Figure Lengend Snippet: (A) WT and TRIM21 −/− A549 cells were transfected with non-targeting siRNA (NT) or siRNA targeting the indicated protein of interest, followed by infection with H1N1pdm (MOI = 0.01). Viral titers at 24 hpi were determined by TCID 50/ mL. The dotted line indicates the mean viral titer of NT-treated WT A549 cells. Data are shown as means of n = 3 ± standard deviations (SD). Two-tailed Student’s unpaired t-test was used to analyze data (**p < 0.01). (B) WT and TRIM21 −/− HEK293T cells were transfected with NT or PRKDC-targeting siRNA and subjected to an H1N1pdm influenza polymerase reconstitution assay. Polymerase activity was normalized to Renilla luciferase. The dotted line indicates the mean polymerase activity in NT-treated WT A549 cells. Data are shown as means of n = 3 ± standard deviations (SD). Two-tailed Student’s unpaired t-test was used to analyze data (****p < 0.0001). (C) RNA-FISH analysis in indicated PR8-infected A549 cells (MOI = 10). (D) The indicated proteins were depleted by siRNA in WT and TRIM21 −/− A549 cells, followed by H1N1pdm infection (MOI = 0.01). Lysates were immunoblotted for RIG-I, pSTAT1, and pSTAT2. (E) WT and TRIM21 −/− A549 cells were transfected with NT or PRKDC-targeting siRNA and subsequently infected with H1N1pdm (MOI = 10). Total and surface expression of viral M2 protein were quantified by flow cytometry. The dotted line indicates the mean M2 expression in NT-treated WT A549 cells. Data are shown as means of n = 3 ± SD.
Article Snippet: The following cell lines were used in this study:
Techniques: Transfection, Infection, Two Tailed Test, Reconstitution Assay, Activity Assay, Luciferase, Expressing, Flow Cytometry
Journal: Cell Systems
Article Title: Interdependence between EGFR and Phosphatases Spatially Established by Vesicular Dynamics Generates a Growth Factor Sensing and Responding Network
doi: 10.1016/j.cels.2018.06.006
Figure Lengend Snippet: EGFR Phosphorylation and Vesicular Dynamics (A) Quantifying ectopic EGFR-mTFP expression in MCF7 cells. Average EGF-Alexa647 versus EGFR-mTFP fluorescence in single MCF7 (green) or MCF10A cells without EGFR-mTFP (black). Histograms (left) reflect that levels of EGF-Alexa647 binding to MCF7 with ectopic EGFR-mTFP expression (green) and MCF10A with endogenous EGFR (black) are similar. (B) EGFR Y 1068 phosphorylation (left) and Akt phosphorylation (right) in MCF7 cells ectopically expressing EGFR-mTFP (solid lines) and for endogenous EGFR in MCF10A cells (dashed lines), following 5-min pulsed (5P-EGF, 200 ng/mL, blue) or sustained EGF stimulation (S-EGF, 200 ng/mL, red), determined by in-cell western assay. Data are normalized to the maximum response in each respective condition (means ± SEM, N = 3). (C) Representative fluorescence image series of EGF-Alexa647, EGFR-mTFP, PTB-mCherry, and PTB-mCherry (magenta)/EGFR-mTFP (green) overlay from single-cell dose-response experiment. Cells were stimulated every ∼1.5 min with increasing EGF-Alexa647 doses (2.5–600 ng/mL). Scale bar, 20 μm. (D) Fraction of phosphorylated versus ligand-bound EGFR-mTFP (n = 21, N = 10; B–S1D). Dashed lines: moving averages from single cells; shaded bounds: SDs; dash-dotted lines: estimated contribution of ligandless to the fraction of phosphorylated EGFR. (E) Live cell fluorescence anisotropy microscopy measurements of EGFR-QG-mCitrine dimerization state as a function of the fraction of ligand-bound receptor (mean ± SEM, n = 30, N = 3, F and S1G). (F–H) Average spatial-temporal maps of the estimated fraction of ligand-bound EGFR (F, EGF-Alexa647/EGFR-mCitrine), ligandless EGFR (G, 1 − [EGF-Alexa647/EGFR-mCitrine]), and the fraction of phosphorylated EGFR-mCitrine estimated by PTB-mCherry translocation (H, PTB-mCherry/EGFR-mCitrine). Data were acquired at 1-min intervals in live MCF7 cells following 200 ng/mL S-EGF (top, n = 16, N = 3; I and S1J) or 5P-EGF (n = 14, N = 2; I and S1J) stimulation. White dotted lines: trajectories representing the change in distribution of ligand-bound (F) and ligandless (G) EGFR. PM, plasma membrane; NM, nuclear membrane. (I) The respective plasma membrane fractions of ligand-bound (EGF-Alexa647/EGFR-mCitrine, red) and phosphorylated EGFR (PTB-mCherry/EGFR-mCitrine, blue) derived from (F) and (H) (median ± AMD). Extracellular EGF-Alexa647 fluorescence is shown in gray. (J) Dimerization state measured by anisotropy (black) and the fraction of ligand-bound EGFR-QG-mCitrine (red) at the plasma membrane for live cells following 200 ng/mL S-EGF (top, n = 5, N = 3) or 5P-EGF (bottom, n = 5, N = 3) stimulation (means ± SEM). (K) The dose response of EGFR-mTFP phosphorylation (red, control) is significantly altered upon ectopic Rab11 S25N expression (green; p = 0.02; n = 12, N = 4). Lines are the same as in (D). (L) EGFR trafficking dynamics: ligandless EGFR recycles via early (EE) and recycling endosomes (RE) to the plasma membrane (red arrows) whereas upon EGF binding (thin green arrow), ubiquitinated EGF-EGFR Ub unidirectionally traffics via the early to the late endosomes (LE, green arrow) to be degraded in lysosomes (∅). Causal links are denoted by solid black lines.
Article Snippet:
Techniques: Phospho-proteomics, Expressing, Fluorescence, Binding Assay, In-Cell ELISA, Microscopy, Translocation Assay, Clinical Proteomics, Membrane, Derivative Assay, Control
Journal: Cell Systems
Article Title: Interdependence between EGFR and Phosphatases Spatially Established by Vesicular Dynamics Generates a Growth Factor Sensing and Responding Network
doi: 10.1016/j.cels.2018.06.006
Figure Lengend Snippet:
Article Snippet:
Techniques: Modification, Virus, Recombinant, Blocking Assay, cDNA Synthesis, Sequencing, Plasmid Preparation, Expressing, Construct, Software, Magnetic Beads
Journal: Cell reports
Article Title: Broad and potently neutralizing monoclonal antibodies isolated from human survivors of New World hantavirus infection
doi: 10.1016/j.celrep.2021.109086
Figure Lengend Snippet: (A and B) Neutralization potency of SNV-reactive mAbs (A) or ANDV-reactive mAbs (B) to pseudotyped VSV particles (pVSV/SNV or pVSV/ANDV), SNV strain SN77734 (SNV), or ANDV strain Chile-9717869 (ANDV). Antibodies in a dilution series of decreasing concentrations were incubated with pVSVs or authentic virus, the suspension was used to inoculate cells, and then GFP + cells or plaques were counted to determine relative infectivity. IC 50 or IC 90 values were obtained using non-linear fit analysis, with the top of the curve constrained to 100 and the bottom of the curve constrained to 0, using Prism software version 7 (GraphPad Software). The colors indicate the relative potency of the antibody. The data shown are average values from 2–3 independent experiments. Binding to proteins for each hantavirus species was determined by flow cytometric analysis. Gn and Gc were displayed on the surface of mammalian cells and incubated with decreasing concentrations of mAb. EC 50 binding values were obtained using non-linear fit analysis, with the bottom of the curve constrained to 0, using Prism software. The value for %PE + cells was determined by gating on cells stained only with secondary antibodies. The colors indicate the relative potency of the antibody. > indicates that the neutralization or reactivity was not detected at the highest concentration tested, 20 μg/mL. NT indicates that the mAb was not tested. The data shown are average values from 3 independent experiments. PCDH-1 blocking (%) was determined through a flow cytometric assay, in which mAbs were added at saturating concentration before the addition of the soluble PCDH-1 domain, sEC-1 labeled with Alexa Fluor 647 dye. PCDH-1 blocking was defined by the reduction of the maximal binding score to <50% of un-competed binding (green boxes). The data shown are average values from 3 independent experiments. The fusion index (%) was determined by adding mAbs to Vero cells transfected with cDNAs encoding SNV or ANDV Gn/Gc, and then inducing fusion through exposure to medium with low pH and counting the percentage of multinucleated cells by fluorescent microscopy. The percentage of multinucleated cells in mAb-treated samples then was divided by the percentage of multinucleated cells in a non-mAb-treated sample (representing maximal fusion index). Fusion-inhibiting mAbs were defined by the reduction of the maximal fusion index to <50% of non-mAb-treated cells (yellow boxes). The data shown are the average values from 3 independent experiments. (C) Representative binding curves of neutralizing antibodies mediating complete (top) or incomplete (bottom) neutralization for authentic SNV (left) or ANDV (right). The dotted lines indicate 10% or 50% relative infectivity. The data shown are average values for technical replicates ± SDs. The experiment was performed 2–3 times independently with similar results; one experiment is shown. See also – and and .
Article Snippet: B95.8 cells (ATCC® CRL-1612, female) producing Epstein-Barr virus and the non-secreting myeloma HMMA2.5 heteromyeloma cell line (kindly provided by Lisa Cavacini, female human and female mice elements) used as the fusion partner for human B cell hybridoma formation each were cultured at 37°C in 8% CO 2 in ClonaCell-HY medium A. BHK-21(WI-2) cell lines (Kerafast, golden Syrian hamster, sex unspecified) and
Techniques: Neutralization, Incubation, Virus, Suspension, Infection, Software, Binding Assay, Staining, Concentration Assay, Blocking Assay, Flow Cytometry, Labeling, Transfection, Microscopy
Journal: Cell reports
Article Title: Broad and potently neutralizing monoclonal antibodies isolated from human survivors of New World hantavirus infection
doi: 10.1016/j.celrep.2021.109086
Figure Lengend Snippet: KEY RESOURCES TABLE
Article Snippet: B95.8 cells (ATCC® CRL-1612, female) producing Epstein-Barr virus and the non-secreting myeloma HMMA2.5 heteromyeloma cell line (kindly provided by Lisa Cavacini, female human and female mice elements) used as the fusion partner for human B cell hybridoma formation each were cultured at 37°C in 8% CO 2 in ClonaCell-HY medium A. BHK-21(WI-2) cell lines (Kerafast, golden Syrian hamster, sex unspecified) and
Techniques: Recombinant, Produced, Virus, Infection, Transfection, Expressing, Sterility, Plasmid Preparation, Bicinchoninic Acid Protein Assay, Software, Chromatography
Journal: Cell metabolism
Article Title: PHD3 loss promotes exercise capacity and fat oxidation in skeletal muscle
doi: 10.1016/j.cmet.2020.06.017
Figure Lengend Snippet: KEY RESOURCES TABLE
Article Snippet: Cell Lines HEK293T (human embryonic kidney, female), C2C12 (mouse mesenchymal precursor, sex of cell lines were unknown) and immortalized
Techniques: Recombinant, Western Blot, Plasmid Preparation, shRNA, Cloning, Software
Journal:
Article Title: Scaffold Attachment Region-Mediated Enhancement of Retroviral Vector Expression in Primary T Cells
doi:
Figure Lengend Snippet: Summary of SCID-hu thymus-liver reconstitution experiments for LMiLy- and LMiLyS-transduced HSPC
Article Snippet: CD34 + -selected MPB tissues were phenotyped for
Techniques: Plasmid Preparation, Fluorescence