Journal: Molecules

Article Title: Preparation and Preclinical Evaluation of 18 F-Labeled Olutasidenib Derivatives for Non-Invasive Detection of Mutated Isocitrate Dehydrogenase 1 (mIDH1)

doi: 10.3390/molecules29163939

Figure Lengend Snippet: mIDH1-selective quinolinone-based inhibitors selected as lead structures (left) and radiolabeled analogs prepared in the present study (right). IC 50 values indicated below the lead structures correspond to the reported potency for inhibition of the most frequent mIDH1 R132H mutation in biochemical assays, while the selectivity factors correspond to the ratio of the biochemical IC 50 values for mIDH1 R132H and the wildtype enzyme.

Article Snippet: Human glioblastoma cells with a c.395G>A knock-in mutation encoding mIDH1 R132H (HTB-14IGTM) and the corresponding wildtype cells (HTB-14TM) were purchased from the American Type Culture Collection (ATCC).

Techniques: Inhibition, Mutagenesis

Journal: Molecules

Article Title: Preparation and Preclinical Evaluation of 18 F-Labeled Olutasidenib Derivatives for Non-Invasive Detection of Mutated Isocitrate Dehydrogenase 1 (mIDH1)

doi: 10.3390/molecules29163939

Figure Lengend Snippet: Dose-response curves and half-maximal inhibitory concentrations (IC 50 ) for suppression of mIDH1 R132H by the fluorinated olutasidenib derivatives. Data are shown as mean ± standard deviation (n = 3). For additional fit parameters and 95% confidence intervals, see .

Article Snippet: Human glioblastoma cells with a c.395G>A knock-in mutation encoding mIDH1 R132H (HTB-14IGTM) and the corresponding wildtype cells (HTB-14TM) were purchased from the American Type Culture Collection (ATCC).

Techniques: Standard Deviation

Journal: PLoS Biology

Article Title: The endoplasmic reticulum proteostasis network profoundly shapes the protein sequence space accessible to HIV envelope

doi: 10.1371/journal.pbio.3001569

Figure Lengend Snippet: (A) Chemical genetic strategy to orthogonally regulate XBP1s and ATF6 in SupT1 DAX cells. (B–D) RNA sequencing (RNA-Seq) analysis of the transcriptomic consequences of (B) XBP1s, (C) ATF6, and (D) XBP1s/ATF6 induction. Transcripts that were differentially expressed under each condition based on a >1.5-fold change in expression level (for dox-, TMP-, or dox- and TMP-treated versus vehicle-treated cells) and a non-adjusted p -value < 10 −10 are separated by dashed lines and plotted in red, with select transcripts labeled. The lowest nonzero p -value recorded was 10 −291 ; therefore, p -values equal to 0 were replaced with p -value = 1.00 × 10 −300 for plotting purposes. Transcripts for which p -values could not be calculated owing to extremely low expression or noisy count distributions were excluded from plotting. (E–G) Comparison of transcript fold change upon (E) +XBP1s versus +ATF6, (F) +ATF6 versus +XBP1s/+ATF6, and (G) +XBP1s versus +XBP1s/+ATF6 remodeling of the endoplasmic reticulum proteostasis network. Only transcripts with false-discovery-rate-adjusted p -value < 0.05 and fold increase > 1 in both of the indicated conditions are plotted. Dashed lines indicate a 1.5-fold filter to assign genes as selectively induced by the proteostasis condition on the x -axis (red), y -axis (blue), or lacking selectivity (purple). Transcripts with fold increase < 1.2 in either proteostasis environment are colored in grey to indicate low differential expression. The complete RNA-Seq differential expression analysis is provided in . dox, doxycycline; TMP, trimethoprim.

Article Snippet: The selected SupT1 single colony cell line encoding tetracycline-inducible XBP1s was then transduced with lentivirus encoding DHFR.ATF6(1–373) via the spinoculation protocol described above, and stable cells were selected using 400 μg/mL hygromycin B (Gibco).

Techniques: RNA Sequencing, Expressing, Labeling, Comparison, Quantitative Proteomics

Journal: PLoS Biology

Article Title: The endoplasmic reticulum proteostasis network profoundly shapes the protein sequence space accessible to HIV envelope

doi: 10.1371/journal.pbio.3001569

Figure Lengend Snippet: (A) Scheme for deep mutational scanning of Env in 4 distinct ER proteostasis environments (basal, +XBP1s, +ATF6, and +XBP1s/+ATF6). SupT1 DAX cells were pretreated with DMSO (basal), dox (+XBP1s), TMP (+ATF6), or both dox and TMP (+XBP1s/+ATF6) 18 h prior to infection with biological triplicate Env viral libraries. 4 d post-infection, cells were harvested, and non-integrated viral DNA was sequenced to quantify the diffsel of Env variants. (B) Diffsel for each amino acid variant can be visualized in a sequence logo plot. The black horizontal lines at the center represent the diffsel for the wild-type amino acid at that site, and the height of the amino acid letter abbreviations is proportional to the diffsel of that variant in the remodeled ER proteostasis environment relative to the basal environment. Variants that are relatively enriched in the indicated ER proteostasis environment (positive diffsel) are located above the black horizontal line. Variants that are relatively depleted in the indicated ER proteostasis environment (negative diffsel) are located below the black horizontal line. (C) Net site diffsel for all Env sites in 3 perturbed ER proteostasis environments, averaged over biological triplicates. The black horizontal lines on the violin plots indicate the median (solid line) and the first and the third quartiles (dashed lines) of the distribution. The significance of deviation from null (net site diffsel = 0, no selection) was tested using a 1-sample t test, with 2-tailed p -values shown. The mean of the distribution and the number of sites with net site diffsel >0 or <0 are listed below the distribution. (D and E) Correlation for net site diffsel values for (D) +XBP1s/+ATF6 versus +XBP1s and (E) +XBP1s/+ATF6 versus +ATF6, normalized to the basal proteostasis environment. Pearson correlation coefficients ( r ) and corresponding p -values are shown. Select sites with highly positive or highly negative net site diffsel values in both proteostasis environments are marked in red and labeled with site numbers. (F) Diffsel for individual Env variants in 3 perturbed ER proteostasis environments, averaged over biological triplicates. The black horizontal lines on the violin plots indicate the median (solid line) and the first and the third quartiles (dashed lines) of the distribution. The significance of deviation from null (diffsel = 0, no selection) was tested using a 1-sample t test, with 2-tailed p -values shown. The mean of the distribution and the number of sites with diffsel >0 and <0 are listed below the distribution. Diffsel values (C–F) are provided at https://github.com/yoon-jimin/2021_HIV_Env_DMS . diffsel, differential selection; dox, doxycycline; ER, endoplasmic reticulum; TMP, trimethoprim; WT, wild-type.

Article Snippet: The selected SupT1 single colony cell line encoding tetracycline-inducible XBP1s was then transduced with lentivirus encoding DHFR.ATF6(1–373) via the spinoculation protocol described above, and stable cells were selected using 400 μg/mL hygromycin B (Gibco).

Techniques: Infection, Variant Assay, Sequencing, Selection, Labeling