Journal: Stem Cell Research & Therapy

Article Title: A transgenic mouse embryonic stem cell line for puromycin selection of V0 V interneurons from heterogenous induced cultures

doi: 10.1186/s13287-022-02801-7

Figure Lengend Snippet: Inserting PAC into a single Evx1 locus using CRISPR/Cas9-mediated homology-directed repair. A Schematic showing electroporation of mESCs to incorporate 3 plasmids: SpCas9, Evx1 guide RNA (gRNA), and the pWS-TK3-Evx1-PAC donor vector. The donor vector contains homology arms (5′ and 3′ HAs) against Evx1 genomic sequences flanking the cut site, PAC , floxed PGK- Neo for positive selection, and the negative selection marker TK3. B Schematic showing SpCas9 being guided to the Evx1 genomic locus by Evx1 gRNA. The Cas9 cut site is flanked by homologous sequences to the HAs of the donor vector, which is inserted into the double-stranded break (DSB) through homology-directed repair (HDR). Cre-mediated recombination removes the Neo cassette so that only PAC remains in the Evx1 locus. C jPCR images showing the wildtype RW4 mESCs as a control, with PAC insertion in both Evx1-PAC and Neo -excised (n.e.) Evx1-PAC, as well as presence of Neo in Evx1-PAC and absence in Evx1-PAC n.e. mESCs. D Copy number assay using the previously established Hb9-puro mESC line as a control for one copy of PAC and RW4 mESCs as a control for two copies of GAPDH as a reference. Evx1-PAC and Evx1-PAC n.e. mESCs show one copy of PAC . Error bars show the range of possible copies, not S.E.M

Article Snippet: 1 × 10 7 RW4 mouse embryonic stem cells were dissociated with 0.25% trypsin–EDTA, quenched with CM, and pelleted at 300 × g . Two plasmid mixtures were made, one for each of the guide RNA vectors: 10 µg of pWS-TK3-Evx1-PAC, 1 µg of SpCas9 vector (Addgene, 43945), and 1 µg of either of the MLM3636-guide RNA vectors (guide 21 or 28) were mixed with 800 µL electroporation buffer (20 mM HEPES pH 7.5, 137 mM NaCl, 5 mM KCl, 0.7 mM Na2HPO4, 6 mM dextrose) and used to resuspend the RW4 mESCs.

Techniques: CRISPR, Electroporation, Plasmid Preparation, Genomic Sequencing, Selection, Marker

Journal: Nature

Article Title: DDX3X acts as a live-or-die checkpoint in stressed cells by regulating NLRP3 inflammasome

doi: 10.1038/s41586-019-1551-2

Figure Lengend Snippet: a, Co-immunoprecipitation (IP) of NLRP3 and DDX3X in BMDMs treated with LPS with or without nigericin. Representative blots (n= 3). b, Immunoblot analysis of CASP1 cleavage in wild-type (WT), Ddx3xfl/fl, Ddx3xfl/flLysMcre and Nlrp3−/− BMDMs treated with LPS and nigericin. Representative blots (n > 3). c, Immunoblots of DDX3X expression and CASP1 cleavage after siRNA-mediated knockdown of Ddx3x in BMDMs treated with LPS with or without nigericin. Representative blots (n = 2). d, Confocal microscopy imaging of ASC specks in BMDMs treated with LPS with or without nigericin, to visualize the subcellular localization of DDX3X, NLRP3 and ASC. Scale bars, 10 μm. Representative images (n = 3). e, Schematic of N-terminal Flag-tagged NLRP3 expression constructs: full-length NLRP3 (Flag-NLRP3-FL), the pyrin domain of NLRP3 (Flag-PYD; amino acids 1–90 of NLRP3), the NACHT domain of NLRP3 (Flag-NACHT; amino acids 91–710 of NLRP3) and the LRR domain of NLRP3 (Flag-LRR; amino acids 711–1034 of NLRP3). f, Immunoblot (IB) analysis of input lysates used for co-immunoprecipitation of Flag-tagged NLRP3 constructs and DDX3X-mCherry. Representative blots (n > 3). g, Immunoblot analysis of immunoprecipitation of DDX3X-mCherry and the indicated NLRP3 constructs. Red asterisk indicates the antibody light chain. Representative blots (n > 3).

Article Snippet: NLRP3 expression constructs pCDNA3-N-Flag-NLRP3, pCDNA3-N-Flag-NLRP3 1–90, pCDNA3-N-Flag-NLRP3 91–710 and pCDNA3-N-Flag-NLRP3 711–1034 were purchased from AddGene.

Techniques: Immunoprecipitation, Western Blot, Expressing, Confocal Microscopy, Imaging, Construct

Journal: Nature

Article Title: DDX3X acts as a live-or-die checkpoint in stressed cells by regulating NLRP3 inflammasome

doi: 10.1038/s41586-019-1551-2

Figure Lengend Snippet: a, Immunoblot analysis of lysates fractionated by analytical ultra-centrifugation to test the oligomerization of NLRP3, DDX3X and ASC in BMDMs stimulated with LPS and treated either with nigericin or with arsenite and nigericin. Representative blots (n = 2). MW, molecular weight. b, Immunoblot analysis of ASC from the insoluble fraction of samples from a under non-reducing (without β-mercaptoethanol; – BME) and reducing (+BME) conditions. Representative blots (n = 2). c, STORM imaging of ASC speck assembly and its spatial organization with DDX3X over time. Scale bars, 5 μm (whole-cell images); 1 μm (magnified images). Representative images (n = 2). d, Plot of the r-index to show the extent of colocalization of ASC and DDX3X with the duration of nigericin treatment (n = 2). R2 was calculated using linear regression analysis; P = 0.0125 (for the significance of the slope being non-zero). Data are mean ± s.e.m. e, f, Immunoblot analysis of CASP1 cleavage in LPS-primed BMDMs to which arsenite was added at various time points (30 and 15 min before adding nigericin, simultaneously with nigericin and 15 and 30 min after adding nigericin), without (e) or with (f) pre-treatment with anisomycin. Representative blots (n = 3). g, h, Structured illumination microscopy of BMDMs to visualize the subcellular localization of DDX3X, G3BP1 and ASC in LPS-primed BMDMs treated with nigericin alone (g) or with arsenite and nigericin (h). Scale bars, 3 μm. Representative images (n = 3).

Article Snippet: NLRP3 expression constructs pCDNA3-N-Flag-NLRP3, pCDNA3-N-Flag-NLRP3 1–90, pCDNA3-N-Flag-NLRP3 91–710 and pCDNA3-N-Flag-NLRP3 711–1034 were purchased from AddGene.

Techniques: Western Blot, Centrifugation, Molecular Weight, Imaging, Microscopy

Journal: Nature

Article Title: DDX3X acts as a live-or-die checkpoint in stressed cells by regulating NLRP3 inflammasome

doi: 10.1038/s41586-019-1551-2

Figure Lengend Snippet: a, Confocal microscopy imaging of peritoneal CD45+ cells to visualize in vivo stress granules in Ddx3xfl/fl and Ddx3xfl/flLysMcre mice that were treated with PBS or arsenite. Scale bars, 10 μm. Representative images (n = 2). b, Quantification of CD45+ cells that contain stress granules, from the peritoneal cavity of Ddx3xfl/fl and Ddx3xfl/flLysMcre mice that were injected with arsenite or PBS. ****P < 0.0001 (unpaired two-sided t-test). Data represent two biologically independent experiments (n = 10 frames). c, Quantification of the numbers and percentage of CD11b+ myeloid cells in the peritoneal cavity. P values (from left to right): ***P = 0.0001, ***P = 0.0005 (unpaired two-sided t-test; n = 7). d, e, Levels of IL-1β in the serum (d) and peritoneal fluid (PF) (e) of mice that were injected with LPS with or without prior arsenite injection in the peritoneum. P values: **P = 0.0026 (d), P = 0.09 (e) (unpaired two-sided t-test; n = 7). f, Levels of IL-1β in the serum and peritoneal fluid of Ddx3xfl/fl and Ddx3xfl/flLysMcre mice that were injected with LPS in the peritoneum. P values (from top to bottom): **P = 0.0073, *P = 0.0123 (unpaired two-sided t-test; n ≥ 6). Data are mean ± s.e.m. (b-f). g, Schematic of the interplay between the inflammasome and stress granules that is involved in cell-fate decisions. DDX3X promotes NLRP3 inflammasome activation and the pro-death cell-fate decision probably by interacting with the NLRP3 NACHT domain through its helicase (Heli) domain. Induction of stress granules causes the sequestration of DDX3X (along with 40S ribosomal subunits and translation initiation factors (eIFs)), thus making it unavailable for NLRP3 inflammasome activation and thereby allowing the cells to make a pro-survival cell-fate choice.

Article Snippet: NLRP3 expression constructs pCDNA3-N-Flag-NLRP3, pCDNA3-N-Flag-NLRP3 1–90, pCDNA3-N-Flag-NLRP3 91–710 and pCDNA3-N-Flag-NLRP3 711–1034 were purchased from AddGene.

Techniques: Confocal Microscopy, Imaging, In Vivo, Injection, Activation Assay