weissman genome wide crispr activation crispra library  (Addgene inc)

Journal: eLife

Article Title: Ex vivo and in vivo CRISPR/Cas9 screenings identify the roles of protein N-glycosylation in regulating T-cell activation and functions

doi: 10.7554/eLife.108724

Figure Lengend Snippet: ( a ) Schematic view of ex vivo CRISPR/Cas9 screening in mouse primary CD8 + T-cells. ( b ) Volcano plot showing results of ex vivo CRISPR/Cas9 genome-wide screenings. The screenings were repeated independently once. The p-values were calculated using the α-robust rank aggregation (α-RRA) algorithm in MAGeCK. ( c ) Verification of candidate genes by individual single gRNAs. The relative expression levels of surface PD-1 protein and PD-1 mRNA were measured by FACS as mean fluorescent intensity (MFI) and RT-qPCR, respectively. The verification assays were biologically replicated twice. ( d ) GSEA of significantly enriched KEGG pathways in genome-wide screening. The enrichment score (ES) and statistical significance were calculated using the clusterProfiler (version 3.12.0) R package.

Article Snippet: A whole-genome CRISPR knockout gRNA library (1000000096) was purchased from Addgene.

Techniques: Ex Vivo, CRISPR, Genome Wide, Expressing, Quantitative RT-PCR

Journal: eLife

Article Title: Ex vivo and in vivo CRISPR/Cas9 screenings identify the roles of protein N-glycosylation in regulating T-cell activation and functions

doi: 10.7554/eLife.108724

Figure Lengend Snippet: ( a ) Schematic view of in vivo CRISPR/Cas9 screening in mouse primary CD8 + T-cells. ( b ) Volcano plot showing results of ex vivo CRISPR/Cas9 screening. The screenings were repeated independently once. The p-values were calculated using the α-RRA algorithm in MAGeCK. ( c ) Volcano plot showing results of in vivo CRISPR/Cas9 screenings. The screenings were repeated independently once. The p-values were calculated using the α-RRA algorithm in MAGeCK.

Article Snippet: A whole-genome CRISPR knockout gRNA library (1000000096) was purchased from Addgene.

Techniques: In Vivo, CRISPR, Ex Vivo

Journal: eLife

Article Title: Ex vivo and in vivo CRISPR/Cas9 screenings identify the roles of protein N-glycosylation in regulating T-cell activation and functions

doi: 10.7554/eLife.108724

Figure Lengend Snippet: ( a ) CRISPR/Cas9 knockout of B4galt1 (sgB4galt1) (sg2) in CD8 + T-cells increases expression of PD-1 before and after co-culture with B16F10-OVA cells. The MFIs of PD-1 were measured by FACS (n=6). The relative mRNA levels of PD-1 were measured by quantitative RT-qPCR (n=6). The p-values were calculated using a two-tailed Student’s t -test. ( b ) The effect of B4galt1 knockout on PD-1 surface expression could be rescued by overexpression of either long- or short-isoform B4galt1 (n=3). The p-values were calculated using a two-tailed Student’s t -test. ( c ) CRISPR/Cas9 knockout of B4galt1 in CD8 + T-cells increases expression of TNFα and IFNγ after co-culture with B16F10-OVA cells. The relative mRNA levels were measured by quantitative RT-qPCR (n=3). The secreted TNFα and IFNγ in medium were measured by ELISA (n=6). The p-values were calculated using a two-tailed Student’s t -test. ( d ) CRISPR/Cas9 knockout of B4galt1 in OT-I CD8 + T-cells increases in vitro specific killing activities on B16F10-OVA cells (n=3). The p-values were calculated using a two-tailed Student’s t -test. ( e ) Schematic view of B4GALT1 knockdown in human NY-ESO-1 TCR-T-cells. ( f ) Knockdown of B4GALT1 in human NY-ESO-1 TCR-T-cells by shRNA increases in vitro killing activities on A375 cells (n=5). The p-values were calculated using a two-tailed Student’s t -test. ( g ) Knockdown of B4GALT1 in human NY-ESO-1 TCR-T-cells increases expression of TNFα and IFNγ after co-culture with A375 cells. The secreted TNFα and IFNγ in medium were measured by ELISA (n=3). The p-values were calculated using a two-tailed Student’s t -test. ( h ) Heatmap demonstrating differentially expressed genes (DEGs) between B4galt1 knockout and control mouse OT-I CD8 + T-cells after co-culture. The genes in TCR signaling pathway are labeled on the left side. ( i ) Volcano plot showing upregulated and downregulated genes (p-value <0.01) in B4galt1 knockout mouse OT-I CD8 + T-cells after co-culture. The genes in TCR signaling pathway are labeled with dark blue and dark red. Top genes and some genes in TCR signaling pathway are annotated. The p-value was calculated using the Wald test, and p.adjust was calculated using Benjamini–Hochberg with the R package DESeq2 (version 1.22.2). ( j ) Bar graph showing KEGG pathways significantly changed in B4galt1 knockout mouse OT-I CD8 + T-cells after co-culture. The p-value was calculated using the clusterProfiler (version 3.12.0) R package. All of these functional effects were biologically replicated at least twice. Data are shown as the mean ± SEM. *p<0.05; **p<0.01; ***p<0.001.

Article Snippet: A whole-genome CRISPR knockout gRNA library (1000000096) was purchased from Addgene.

Techniques: CRISPR, Knock-Out, Expressing, Co-Culture Assay, Quantitative RT-PCR, Two Tailed Test, Over Expression, Enzyme-linked Immunosorbent Assay, In Vitro, Knockdown, shRNA, Control, Labeling, Functional Assay

Journal: eLife

Article Title: Ex vivo and in vivo CRISPR/Cas9 screenings identify the roles of protein N-glycosylation in regulating T-cell activation and functions

doi: 10.7554/eLife.108724

Figure Lengend Snippet: CRISPR/Cas9 knockout of B4GALT1 in hCD19-CAR-T-cells does not affect in vitro killing of Nalm6 target cells (n=3). The killing assays were biologically replicated three times. Data are shown as the mean ± SEM. NS, not significant.

Article Snippet: A whole-genome CRISPR knockout gRNA library (1000000096) was purchased from Addgene.

Techniques: CRISPR, Knock-Out, In Vitro

Journal: eLife

Article Title: Ex vivo and in vivo CRISPR/Cas9 screenings identify the roles of protein N-glycosylation in regulating T-cell activation and functions

doi: 10.7554/eLife.108724

Figure Lengend Snippet: ( a ) Schematic view of B4galt1 functional test in tumor microenvironment. ( b ) CRISPR/Cas9 knockout of B4galt1 in OT-I T-cells enhances growth control of B16F10-OVA tumors in vivo. The p-value was calculated using two-way ANOVA. ( c ) Compared with control OT-I T-cells, the tumors were significantly smaller when B4galt1 knockout OT-I T-cells were transplanted (n=5 for control, n=7 for sgB4galt1). The p-value was calculated using a two-tailed Student’s t -test. ( d ) CRISPR/Cas9 knockout of B4galt1 increases numbers of OT-I T-cells in B16F10-OVA tumors (n=5 for control, n=7 for sgB4galt1). The p-value was calculated using a two-tailed Student’s t -test. The in vivo functional effects were biologically replicated at least twice. Data are shown as the mean ± SEM. *p<0.05; **p<0.01.

Article Snippet: A whole-genome CRISPR knockout gRNA library (1000000096) was purchased from Addgene.

Techniques: Functional Assay, CRISPR, Knock-Out, Control, In Vivo, Two Tailed Test

Journal: bioRxiv

Article Title: Systematic Evaluation Defines the Limits of Ferroptosis in Cancer Therapy

doi: 10.64898/2026.03.11.711115

Figure Lengend Snippet: A , Immunoblot from lysates of A549 cells or HT-1080 cells for indicated proteins in the presence or absence of CySS or βMe (50μM). Inferred MW of band indicated. B , Viability (ATP) of HT-1080 or KYSE30 cells expressing the indicated GPX4 cDNAs and selenocysteine (U46C) or SEICS (Δ3’UTR) mutants, cultured in indicated CySS conditions, 3 days. Data report mean ± SEM of n=3 biological replicates. C , Model-based Analysis of Genome-scale CRISPR-Cas9 Knockout (MAGeCK) score from genome-wide CRISPR screens of A549 SLC7A11 knockout cells or A549 cells cultured in the absence of cystine comparing culture in the absence or presence of βMe (50μM). LPCAT3 (red dot, indicated) is the top ranked gene in both conditions for promoting survival in the absence of βMe. Data are from a single screen. D , Viability (ATP) of indicated cell lines cultured in indicated CySS conditions or RSL-3 dose, in combination with inhibitors of ACSL4 (ROSI, 25μM) or LPCAT3 (HTS-3, 10μM), 3 days. Data report mean ± SEM of n=3 biological replicates.

Article Snippet: Genome-wide resistance screens were performed using the Human Activity-Optimized CRISPR Knockout Library (Addgene pooled library #1000000100).

Techniques: Western Blot, Expressing, Cell Culture, CRISPR, Knock-Out, Genome Wide

Journal: Cell Death & Disease

Article Title: PGC-1α protects against MASH via Tim23-dependent inhibition of DRP1-mediated ferroptosis

doi: 10.1038/s41419-026-08493-8

Figure Lengend Snippet: Primary hepatocytes were transfected with negative control (NC) or PGC-1α CRISPR activation plasmid (PGC-1α CRISPR ACT) and treated with PA, leading to four groups of the Act-NC, Act-NC + PA, Act-PGC-1α and Act-PGC-1α + PA. A Oil Red O, Perls’ Blue staining and Tim23 Immunohistochemistry. B , B ’ Western blot analyses of the relative levels of hepatic PGC-1α, Tim23, Drp1, P-Drp1 Ser616 , ACSL4, GPX4 and FTH1 to GAPDH. C RT-qPCR analyses of the relative levels of PGC-1α, Drp1, ACSL4, GPX4, TFR1 and FTH1 mRNA transcripts. D The GSH levels. E Images of MitoTracker and MitoSOX staining. F Images of C11-BODIPY 581/591 staining. Data are representative images or expressed as the mean ± SD of each group ( n = 3) from at least three independent treatments. * P < 0.05, ** P < 0.01, *** P < 0.001.

Article Snippet: Special reagents included primary antibodies against Drp1, Nrf1, P-Drp1ser616, alpha-smooth muscle actin (α-SMA), collagen I, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), cytochrome c oxidase subunit 4 (COXIV) and cleaved caspase-3 (Cell Signaling Technology, Beverly, USA); PGC-1α, ACSL4, tumor necrosis factor (TNF)α, Hepatocyte nuclear factor 4-alpha (HNF-4α), Desmin and interleukin (IL)-6 (Abcam, Cambridge, USA); Tim23 (Santa, TX, USA); glutathione peroxidase 4 (GPX4), Ferroton heavy chain 1 (FTH1), transferrin receptor 1 (TFR1) and F4/80 (Proteintech, Wuhan, China); Lymphatic Vessel Endothelial Receptor-1(Lyve-1) (ABclonal, Wuhan, China); Nrf2, P-MLKL, GSDMD-N (HUABIO, Hangzhou, China); special kits for hematoxylin and eosin (H&E), Sirius Red, and Oil Red staining (Solarbio, Beijing, China); immunohistochemical staining kit (Maixin Biological Technology, Fujian, China); the kits for measurements of alanine aminotransferase (ALT), triglyceride (TG), total cholesterol (T-CHO), low-density lipoprotein cholesterol (LDL-C), glucose, glutathione (GSH), malondialdehyde (MDA), and iron contents (Jiancheng Biological Engineering Institute, Nanjing, China); enzyme-linked immunosorbent assay (ELISA) kits for measurements of insulin (Crystal Chem, Chicago, USA); Tissue mitochondria isolation kit (Beyotime, Shanghai, China); Perls’ blue (Sbjbio, Nanjing, China); PGC-1α clustered regularly interspaced short palindromic repeats (CRISPR) activation plasmid (sc-400070-ACT) and Protein A/G plus-agarose (Santa Cruz Biotechnology, CA, USA); PGC-1α and Drp1 small interfering RNAs (siRNAs) (LIKELI, Beijing, China); dual luciferase assay kits and TnT® quick coupled transcription/ translation systems (Promega, Wisconsin, USA); Lipofectamine 2000, C-11 BODIPY 581/591, MitoSOX and Mitotracker (Invitrogen, CA, USA); JC-1 (Chemodex, SG, SUI); Ferrostatin-1 (Fer-1) (MedChemExpress, NJ, USA).

Techniques: Transfection, Negative Control, CRISPR, Activation Assay, Plasmid Preparation, Staining, Immunohistochemistry, Western Blot, Quantitative RT-PCR