Journal: Cells

Article Title: SHIP1 Is Present but Strongly Downregulated in T-ALL, and after Restoration Suppresses Leukemia Growth in a T-ALL Xenotransplantation Mouse Model

doi: 10.3390/cells12131798

Figure Lengend Snippet: Reduced expression of SHIP1 in primary T-ALL samples. ( A ) SHIP1 mRNA expression was analyzed in peripheral blood mononuclear cells (PBMC) from healthy donors, healthy CD3-enriched (CD3+) cells and primary T-ALL patient samples. ( B ) SHIP1 protein expression was analyzed in Jurkat cells containing a Tet-regulated wild-type SHIP1 cDNA, in healthy CD3-positve cells and in primary T-ALL samples. Ponceau S staining of the membrane was performed as a loading and blotting control.

Article Snippet: CD3-positive T cells were isolated from fresh peripheral blood mononuclear cells of healthy donors using EasySep Human CD3 positive selection kit (STEMCELL Technologies) with the associated EasySep magnet (STEMCELL Technologies) for the selection of magnetic particles.

Techniques: Expressing, Staining

Journal: iScience

Article Title: Targeting SRSF2 mutations in leukemia with RKI-1447: A strategy to impair cellular division and nuclear structure

doi: 10.1016/j.isci.2024.109443

Figure Lengend Snippet: in vivo efficacy and toxicity of RKI-1447 (A) CD3-depleted frozen PBMC from three SRSF2 -mutated acute myeloid leukemia (AML) samples were injected into SGM3 (#800667) or NSG mice (#209945 and #830163) intrafemorally (i.f.); after 5 weeks transplantation mice were treated with RKI-1447 (50 mg/kg) or DMSO control for 21 days. (B) NSG mice (n = 5–10/sample) were injected with 80,000 to 150,000 CD34 + cells from three mobilized peripheral blood samples (i.f.). On day 35 the animals were randomized to RKI-1447 or a carrier control. RKI-1447 was administered i.p. at a dose of 50 mg/kg daily for 21 days. On day 56 mice were sacrificed and analyzed for human CD45 + (hCD45) cells engraftment by flow cytometry. Mann-Whitney U test with FDR correction for multiple hypothesis testing, ∗p < 0.05; ∗∗p < 0.005; ∗∗∗p < 0.0005. (C) 5 ∗ 10ˆ6 MOLM14 mutated cells were injected into 225 rad irradiated NSG mice. The mice were treated with RKI-1447 (50 mg/kg/day), starting from day 3 following cell transplantation. The mice were treated every day via intraperitoneal (i.p.) injection for 21 days. The Kaplan-Meier test p = 0.01.

Article Snippet: Frozen primary SRSF2 Mut/WT AML samples were thawed and CD3 + cells were depleted with CD3 positive selection kit (EasySep Human CD3 Positive Selection Kit II, STEMCELL Cat.17851).

Techniques: In Vivo, Injection, Transplantation Assay, Control, Flow Cytometry, MANN-WHITNEY, Irradiation

Journal: iScience

Article Title: Targeting SRSF2 mutations in leukemia with RKI-1447: A strategy to impair cellular division and nuclear structure

doi: 10.1016/j.isci.2024.109443

Figure Lengend Snippet:

Article Snippet: Frozen primary SRSF2 Mut/WT AML samples were thawed and CD3 + cells were depleted with CD3 positive selection kit (EasySep Human CD3 Positive Selection Kit II, STEMCELL Cat.17851).

Techniques: Selection, Sequencing

Journal: Science Advances

Article Title: Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells

doi: 10.1126/sciadv.adg1610

Figure Lengend Snippet: ( A ) Schematic representation describes the experimental procedure. Blood was taken from eight healthy volunteers at five time points: 7 days before DI exposure (day 0, orange); 7 (blue), 14 (teal), and 21 (green) days during DI exposure; and 7 days after DI exposure (day 28, pink). CD3 + T cells were isolated from the blood, and bulk RNA-seq was performed. ( B ) Horizontal bars show the fraction of granulocytes, lymphocytes, and monocytes in blood isolates before CD3 + T cell isolation as determined by flow cytometry. Values are indicated as means + 1.96 × SEM. ( C ) Horizontal bars display the estimated fraction of T cell populations detectable in the bulk RNA-seq data as determined by deconvolution analysis with the quanTIseq algorithm. Values are indicated as means + 1.96 × SEM. ( D ) Factorial map of the PC analysis separates bulk RNA-seq gene expression data of each individual volunteers (small dots) and mean values across all volunteers (large dots). The proportion of variance explained by each PC is indicated in parentheses. Color-coding is according to the different time points. ( E ) The dot plot shows PC1 separation of bulk RNA-seq samples by time point. Individual values (small dots) and mean values (large dots) are shown per time point (color-coded). Error bars indicate means ± 1.96 × SEM. ( F ) Illustration displays differentially expressed genes (DEGs) identified by pairwise time point comparisons using DESeq2. The number of significantly (adjusted P < 0.01) up- [positive log 2 FC (fold change), red] and down-regulated (negative log 2 FC, blue) genes is indicated. ( G ) Line charts show the two k -means clusters and number of differentially expressed genes per cluster detected in at least one time point comparison. Standardized gene expression profiles for individual genes (gray lines) and the cluster center (connected dots) are shown.

Article Snippet: Human T cells were enriched by the positive CD3 cell selection Kit (EasySep Human CD3 Positive Selection Kit II, STEMCELL Technology) with a purity of 90 to 95%.

Techniques: Isolation, RNA Sequencing, Cell Isolation, Flow Cytometry, Gene Expression, Comparison

Journal: Science Advances

Article Title: Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells

doi: 10.1126/sciadv.adg1610

Figure Lengend Snippet: ( A ) Heatmap demonstrates expression of overall down-regulated genes in CD3 + T cells identified upon DI (cluster 3 in fig. S9, n = 148) (left ) that overlap with genes in CD4 + (middle) and CD8 + (right) T cells obtained in the NASA twin study. Gene expression changes are shown as log 2 FC to day 0 for DI and log 2 FC for relevant comparisons in the NASA study (gray if missing). Relevant genes are highlighted. ( B ) Vertical bars display changes in expression for selected genes [ x axis annotated according to (A)]. Log 2 FC values show up- (red) and down-regulation (blue). ( C ) The dot plot denotes mean fluorescence intensity (MFI) ratio of cell surface marker CD25 compared to control as determined by flow cytometry. Values for individual volunteers (small dots) and mean values across all volunteers (large dots) are shown for each time point (color-coded). Error bars indicate means ± 1.96 × SEM.

Article Snippet: Human T cells were enriched by the positive CD3 cell selection Kit (EasySep Human CD3 Positive Selection Kit II, STEMCELL Technology) with a purity of 90 to 95%.

Techniques: Expressing, Gene Expression, Fluorescence, Marker, Control, Flow Cytometry

Journal: Cell Reports Methods

Article Title: Multiscale domain identification for spatial transcriptomics via persistent homology

doi: 10.1016/j.crmeth.2026.101376

Figure Lengend Snippet: PHD-MS analyzes tumor microenvironment morphology (A) Expert annotated tumors from immunofluorescent image, with anti-CD3 intensity in pink and DAPI intensity in green. IDC is outlined in yellow, carcinoma in situ is outlined in blue, benign hyperplasia is outlined in red, and unclassified tumor is in green. (B) Prominent multiscale domains identified by PHD-MS, selected from the most persistent domains. Regions are numbered to correspond with the labels in (A). (C) PHD-MS heterogeneity map highlights highly heterogeneous regions. The heterogeneity score approximates the number of persistent domains that contain each spot. (D) Mean normalized immune expression from a set of immune genes (PTPRC, CD4, CD8A, CD14, CD68, and IGHG3). (E) Normalized expression of key oncogenes APOE, PGK1, and MALAT1 in the lower IDC. From DGE analysis, APOE is overexpressed in region 7 relative to 8 and 9, PGK1 is overexpressed in 8, and MALAT1 is overexpressed in 9.

Article Snippet: Visium Invasive Ductal Carcinoma Stained With Fluorescent CD3 Antibody , Zhao et al. , https://www.10xgenomics.com/datasets/invasive-ductal-carcinoma-stained-with-fluorescent-cd-3-antibody-1-standard-1-2-0.

Techniques: In Situ, Expressing