Journal: International Journal of Molecular Medicine

Article Title: Altered expression of mir-222 and mir-25 influences diverse gene expression changes in transformed normal and anaplastic thyroid cells, and impacts on MEK and TRAIL protein expression

doi: 10.3892/ijmm.2016.2653

Figure Lengend Snippet: All significantly downregulated genes in pre-miR-222 treated cells compared to cells treated with negative control pre-miRs.

Article Snippet: The assays used were as follows: MAL2; Hs00294541_m1, MAL; Hs00242748_m1, TLR3; Hs01551078_m1, ADM; Hs00181605_m1, RAB19; Hs01397748_m1, PDCD1LG2; Hs00228839_m1, RAD51; Hs00947968_m1, ADAM21; Hs01652548_s1, HYOU1; Hs01026180_m1, THBS1; Hs00962908_m1, ETS1; Hs00428287_m1, FGFR2; Hs03466165_gH, CYR61; Hs00609994_m1, PHLDB2; Hs01083801_m1, BIRC3; Hs00154109_m1, PRKAA2; Hs00178903_m1, CYP24A1; Hs00989011_g1, AOX1; Hs00154079_m1, MYO5C; Hs00218921_m1, GPR126; Hs01097890_m1, CDK6; Hs00608037_m1, PPME1; Hs00211693_m1, RBM24; Hs00290607_m1, TNFSF10/TRAIL; Hs00921974_m1, ITGA6; Hs01041012_m1, MPP1; Hs00609971_m1, TIMP2; Hs00234278_m1, ITGA3; Hs01076876_m1, ADAMTS1; Hs00199608_m1, ITGA5; Hs00233732_m1, TRIP13; Hs01020073_m1, MAP2K4; Hs00387426_m1, RAB23; Hs00212407_m1, ADAM10; Hs00153853_m1, TRHDE; Hs00183821_m1, RAB14; Hs00249440_m1, RARB; Hs00233405_m1, MAN2A1; Hs00159007_m1, RGS4; Hs00194501_m1, PTGS2; Hs00153133_m1, EPGN; Hs02385425_m1, SNAP23; Hs01047498_m1, LHFPL2; Hs00299613_m1, MYO1B; Hs01031676_m1, NFIA; Hs00906448_m1, RNF38; Hs01014398_m1 (all from Applied Biosystems).

Techniques: Negative Control, Cell Differentiation, Virus, RNA Binding Assay, Binding Assay, Sequencing, Variant Assay, Expressing

Journal: International Journal of Molecular Medicine

Article Title: Altered expression of mir-222 and mir-25 influences diverse gene expression changes in transformed normal and anaplastic thyroid cells, and impacts on MEK and TRAIL protein expression

doi: 10.3892/ijmm.2016.2653

Figure Lengend Snippet: Downregulated genes following expression of pre-miR-222 in Nthy-ori 3-1.

Article Snippet: The assays used were as follows: MAL2; Hs00294541_m1, MAL; Hs00242748_m1, TLR3; Hs01551078_m1, ADM; Hs00181605_m1, RAB19; Hs01397748_m1, PDCD1LG2; Hs00228839_m1, RAD51; Hs00947968_m1, ADAM21; Hs01652548_s1, HYOU1; Hs01026180_m1, THBS1; Hs00962908_m1, ETS1; Hs00428287_m1, FGFR2; Hs03466165_gH, CYR61; Hs00609994_m1, PHLDB2; Hs01083801_m1, BIRC3; Hs00154109_m1, PRKAA2; Hs00178903_m1, CYP24A1; Hs00989011_g1, AOX1; Hs00154079_m1, MYO5C; Hs00218921_m1, GPR126; Hs01097890_m1, CDK6; Hs00608037_m1, PPME1; Hs00211693_m1, RBM24; Hs00290607_m1, TNFSF10/TRAIL; Hs00921974_m1, ITGA6; Hs01041012_m1, MPP1; Hs00609971_m1, TIMP2; Hs00234278_m1, ITGA3; Hs01076876_m1, ADAMTS1; Hs00199608_m1, ITGA5; Hs00233732_m1, TRIP13; Hs01020073_m1, MAP2K4; Hs00387426_m1, RAB23; Hs00212407_m1, ADAM10; Hs00153853_m1, TRHDE; Hs00183821_m1, RAB14; Hs00249440_m1, RARB; Hs00233405_m1, MAN2A1; Hs00159007_m1, RGS4; Hs00194501_m1, PTGS2; Hs00153133_m1, EPGN; Hs02385425_m1, SNAP23; Hs01047498_m1, LHFPL2; Hs00299613_m1, MYO1B; Hs01031676_m1, NFIA; Hs00906448_m1, RNF38; Hs01014398_m1 (all from Applied Biosystems).

Techniques: Expressing, Microarray

Journal: EMBO Molecular Medicine

Article Title: LILRB1-HLA-G axis defines a checkpoint driving natural killer cell exhaustion in tuberculosis

doi: 10.1038/s44321-024-00106-1

Figure Lengend Snippet: Reagents and tools table

Article Snippet: Rabbit anti-phospho-ETS1 (Thr38) , Bioss , bs-13113R.

Techniques: Recombinant, Western Blot, Sequencing, Modification, Cell Isolation, Enzyme-linked Immunosorbent Assay, Isolation, Antibody Labeling, Transfection, Lysis, Protease Inhibitor, Blocking Assay, Software, Flow Cytometry, Cytometry

Journal: bioRxiv

Article Title: A targeted CRISPR screen identifies ETS1 as a regulator of HIV latency

doi: 10.1101/2024.08.03.606477

Figure Lengend Snippet: (A) Schematic overview of experimental design for CRISPR-Cas9 targeting of host genes in HIV-GFP infected primary CD4 T cells. Activated CD4 T cells were infected with HIV-GFP . At 3 days post infection, infected (GFP+) cells were enriched by magnetic sorting and cultured for 4 days before nucleofection of Cas9/sgRNA complexes targeting AAVS1, SMC3, CDK6, ZIC5, FOXE3, SAMD12, ZNF740, ETS1, and TNFAIP3 or a non-targeting sgRNA (NT). Pools of 3 different gRNAs were used for each target. HIV infected cells are denoted in green color. Differential intensity of green color represents latent and active infection. (B) Relative level of HIV expression measured as GFP using flow cytometry. GFP expression was measured at two weeks post nucleofection (wpN). Data are displayed as GFP expression in fold change normalized to cells nucleofected with NT gRNA. Each condition represents three biological replicates/donors (Yellow, Blue and Purple) and three technical replicates for each donor. (C) Dot plots representing viral GFP expression at two weeks post knockout. Statistical analysis was conducted for cumulative data. Error bars represent standard deviations, and P values displayed were determined by two-way ANOVA Tukey’s multiple comparisons test. WT, wildtype; NT, non-target; CRISPR, clustered regularly interspaced short palindromic repeats; Cas9, CRISPR-associated protein 9.

Article Snippet: Immunoblotting was performed using the primary antibodies, ETS1 (Cell signaling Technology; 14069) at 1:1000, and Beta actin (abcam; ab49900) at 1:10000.

Techniques: CRISPR, Infection, Cell Culture, Expressing, Flow Cytometry, Knock-Out

Journal: bioRxiv

Article Title: A targeted CRISPR screen identifies ETS1 as a regulator of HIV latency

doi: 10.1101/2024.08.03.606477

Figure Lengend Snippet: Primary CD4 T cells were activated, infected with HIV-GFP, enriched and nucleofected as in . (A) Western blot of the ETS1-targeting or a control non-targeting (NT) Cas9/gRNA nucleofected primary cells for beta actin and ETS1 expression at one and two weeks post nucleofection (pKO). (B-E) Flow cytometry of infected cells without stimulation or after 24 h of stimulation with four different LRAs (vorinostat, prostratin, iBET151, and AZD5582 at one (B) and two (D) week post nucleofection. (C and E) Dot plots representing viral GFP expression at one and two weeks post knockout respectively. Data are represented as fold change in percent GFP expression, normalized to cells nucleofected with NT gRNA. Error bars represent standard deviation, and P values displayed were determined by two-way ANOVA Tukey’s multiple comparisons test.

Article Snippet: Immunoblotting was performed using the primary antibodies, ETS1 (Cell signaling Technology; 14069) at 1:1000, and Beta actin (abcam; ab49900) at 1:10000.

Techniques: Infection, Western Blot, Control, Expressing, Flow Cytometry, Knock-Out, Standard Deviation

Journal: bioRxiv

Article Title: A targeted CRISPR screen identifies ETS1 as a regulator of HIV latency

doi: 10.1101/2024.08.03.606477

Figure Lengend Snippet: (A) Schematic of ex vivo CRISPR nucleofection experiment in resting CD4 T cells isolated from PWH on ART. CRISPR nucleofection of ETS1-targeting or non-targeting (NT) Cas9/gRNAs was performed after a 24 hr culture of PWH CD4 T cells followed by quantification of Gag RNA expression at 3 days post nucleofection by quantitative PCR. (B) Depletion of ETS1 in nucleofected resting CD4 T cells was analyzed by western blot. (C) Relative abundance of Gag viral RNA expression in CD4 T cells nucleofected with ETS1-targeting or NT control Cas9/gRNA complexes. Gag viral RNA expression was normalized to cells nucleofected with no gRNA and presented as fold change. Experiment was conducted in three biological replicates/donors with three technical replicates for each condition. Error bars represent standard deviation, and P values displayed were determined by two-way ANOVA Tukey’s multiple comparisons test.

Article Snippet: Immunoblotting was performed using the primary antibodies, ETS1 (Cell signaling Technology; 14069) at 1:1000, and Beta actin (abcam; ab49900) at 1:10000.

Techniques: Ex Vivo, CRISPR, Isolation, RNA Expression, Real-time Polymerase Chain Reaction, Western Blot, Control, Standard Deviation

Journal: bioRxiv

Article Title: A targeted CRISPR screen identifies ETS1 as a regulator of HIV latency

doi: 10.1101/2024.08.03.606477

Figure Lengend Snippet: (A). Western blot of the ETS1-targeting or a control non-targeting (NT) gRNA nucleofected Jurkat latent cells (JLat10.6) for beta actin and ETS1 expression at one-week post nucleofection. (B) Relative abundance of Gag viral RNA expression in latently infected Jurkat cells nucleofected with RNPs including ETS1-targeting or NT control gRNA/Cas9 complexes. Gag viral RNA expression was normalized to input RNA. Error bars represent standard deviation, and P values displayed were determined by two-way ANOVA Tukey’s multiple comparisons test.

Article Snippet: Immunoblotting was performed using the primary antibodies, ETS1 (Cell signaling Technology; 14069) at 1:1000, and Beta actin (abcam; ab49900) at 1:10000.

Techniques: Western Blot, Control, Expressing, RNA Expression, Infection, Standard Deviation

Journal: bioRxiv

Article Title: A targeted CRISPR screen identifies ETS1 as a regulator of HIV latency

doi: 10.1101/2024.08.03.606477

Figure Lengend Snippet: CD4 T cells from three PWH on ART were nucleofected with Cas9/gRNA complexes targeting ETS1 or non-targeting control (NT) as described in , followed by bulk RNAseq. (A) Principal component analysis (PCA) plot of samples based on gene expression data for each sample. ETS1-targeted samples shown by blue dots, non-targeting gRNA samples by red dots. Each data point represents an individual sample. The y-axis and x-axis represent the first and second principal components, respectively. (B) Volcano plot of overall differentially expressed genes (DEGs) between HIV infected CD4 T cells nucleofected with ETS1 targeting sgRNA/Ca9 complexes vs non-targeting. (C) Database for Annotation, Visualization and Integrated Discovery (DAVID) analysis of upregulated and downregulated genes of the RNA-sequencing analysis of ETS1 vs control cells. The 10 most significant KEGG pathways are shown. (D) Number of unique HIV-mapping reads identified in each sample after alignment to an HXB2 reference genome.

Article Snippet: Immunoblotting was performed using the primary antibodies, ETS1 (Cell signaling Technology; 14069) at 1:1000, and Beta actin (abcam; ab49900) at 1:10000.

Techniques: Control, Gene Expression, Infection, RNA Sequencing

Journal: bioRxiv

Article Title: A targeted CRISPR screen identifies ETS1 as a regulator of HIV latency

doi: 10.1101/2024.08.03.606477

Figure Lengend Snippet: (A) ETS1 mapping reads for each of the two conditions (ETS1 and NT control) are visualized using the Integrative Genomics Viewer (IGV). The sudden change in read depth between sgRNA targeting sites is the characteristic of indels that cause larger disruption of ETS1 transcript due to CRISPR nucleofection. The read disruption is present in all the three of the ETS1 nucleofected cells, approximately half the reads and none of the reads in the NT control. Position, strand and sequence of the gRNAs for the ETS1 target is provided at the bottom. ( B ) Spliced HIV reads in ETS1 and NT control. HIV reads were undetected in sample (Donor 1).

Article Snippet: Immunoblotting was performed using the primary antibodies, ETS1 (Cell signaling Technology; 14069) at 1:1000, and Beta actin (abcam; ab49900) at 1:10000.

Techniques: Control, Disruption, CRISPR, Sequencing

Journal: bioRxiv

Article Title: A targeted CRISPR screen identifies ETS1 as a regulator of HIV latency

doi: 10.1101/2024.08.03.606477

Figure Lengend Snippet: In vitro generated primary latent CD4 cells were nucleofected with Cas9/gRNA ribonucleoprotein complexes targeting ETS1, MALAT1, or a combination of ETS1 and MALAT1 as described in , followed by immunoblotting, flow cytometry and RT-PCR. ( A ) Depletion of ETS1 in nucleofected CD4 T cells was analyzed by western blot. ( B-C ) Relative abundance of MALAT1 expression ( B ), and Gag RNA ( C ) in CD4 T cells nucleofected with Cas9/sgRNAs targeting ETS1, MALAT1, or a combination of ETS1 and MALAT1. ( D ) Flow cytometry of infected cells at two-week post nucleofection. MALAT1 and Gag viral RNA expression was normalized to cells nucleofected with NT control. Experiment was conducted in three biological replicates/donors with three technical replicates for each condition. Error bars represent standard deviations, and P values displayed were determined by two-way ANOVA Tukey’s multiple comparisons test.

Article Snippet: Immunoblotting was performed using the primary antibodies, ETS1 (Cell signaling Technology; 14069) at 1:1000, and Beta actin (abcam; ab49900) at 1:10000.

Techniques: In Vitro, Generated, Western Blot, Flow Cytometry, Reverse Transcription Polymerase Chain Reaction, Expressing, Infection, RNA Expression, Control

Journal: Nucleic Acids Research

Article Title: Adenovirus VA RNA-derived miRNAs target cellular genes involved in cell growth, gene expression and DNA repair

doi: 10.1093/nar/gkp1028

Figure Lengend Snippet: Expression analysis in cells expressing mivaRNAs

Article Snippet: Hs00901425_m1 , ETS1 , I-138(TS); I-137 , 2.19 , 2.96 , 9.55 , 5.46 , 1.52 , 2.72 , 1.95 , Transcription, growth.

Techniques: Expressing, Modification