Journal: iScience

Article Title: Immune hub genes and a proof-of-concept prognostic signature in EBV-associated gastric carcinoma

doi: 10.1016/j.isci.2026.115243

Figure Lengend Snippet: Expression and immune correlation of hub genes (A) Violin plots show the expression levels of PTPRC and ITGB2 in EBVaGC (blue) and EBVnGC (red) from the TCGA-STAD cohort. Statistical significance is indicated (∗ p < 0.05 and ∗∗ p < 0.01). (B) Correlation heatmap illustrates the relationships between hub genes (PTPRC and ITGB2) and 22 tumor-infiltrating immune cell subsets. Circle size and color intensity represent the strength of correlation, with orange indicating positive correlations and teal indicating negative correlations. (C) Scatterplots demonstrates correlations between PTPRC expression and infiltration levels of five immune cell types: B cells memory, CD4 + memory activated T cells, CD8 + T cells, M1 macrophages, and M2 macrophages. Pearson’s correlation coefficients (R) and p values are shown for each comparison. (D) Scatterplots show correlations between ITGB2 expression and infiltration levels of the same five immune cell types as in (C). Pearson’s correlation coefficients (R) and p values are indicated.

Article Snippet: Anti-CD45 (PTPRC), mouse monoclonal, clone PD7/26+2B11 , Zhongshan Golden Bridge Biotechnology (ZSGB-BIO) , Cat# Kit-0024.

Techniques: Expressing, Comparison

Journal: iScience

Article Title: Immune hub genes and a proof-of-concept prognostic signature in EBV-associated gastric carcinoma

doi: 10.1016/j.isci.2026.115243

Figure Lengend Snippet: Increased CD18+, CD45+, and CD68 + immune-cell infiltration in EBVaGC (A) Representative immunohistochemistry (IHC) micrographs for CD18, CD45, and CD68 in EBVaGC (top) and EBVnGC (bottom). Brown DAB indicates positive staining; hematoxylin counterstain. Images were acquired at 40× objective; scale bars, 50 μm. (B) Dot-and-box plots showing quantitative cell densities (cells/mm 2 ) of CD18 + , CD45 + , and CD68 + cells in EBVaGC versus EBVnGC. Each dot represents one case (EBVaGC n = 20; EBVnGC n = 20; per case, the mean of ≥3 non-necrotic high-power fields was used). Boxes show IQR, center line the median, whiskers the range. p values are from two-sided exact Wilcoxon rank-sum tests (CD18: ∗∗∗ p < 0.0001; CD45: ∗∗∗ p < 0.0001; and CD68: ∗∗∗ p < 0.0001). Units and statistics are indicated on the plots.

Article Snippet: Anti-CD45 (PTPRC), mouse monoclonal, clone PD7/26+2B11 , Zhongshan Golden Bridge Biotechnology (ZSGB-BIO) , Cat# Kit-0024.

Techniques: Immunohistochemistry, Staining

Journal: iScience

Article Title: Immune hub genes and a proof-of-concept prognostic signature in EBV-associated gastric carcinoma

doi: 10.1016/j.isci.2026.115243

Figure Lengend Snippet: Construction and characterization of the four-gene immune score model in EBVaGC (A) Co-expression analysis of PTPRC and ITGB2 in EBVaGC samples. High-high expression pairs are highlighted in red. (B) GO biological process enrichment of immune genes co-expressed with PTPRC and ITGB2, highlighting terms such as leukocyte-mediated immunity and T cell activation. (C) KEGG pathway enrichment showing cytokine-cytokine receptor interaction, chemokine signaling, and other immune-related pathways. (D) LASSO Cox regression coefficients (lambda.min) for the selected prognostic genes GMPR and TIMD4. (E) Heatmap of GMPR and TIMD4 expression across risk groups. (F) Forest plot of multivariate Cox regression showing hazard ratios (HRs) and 95% confidence intervals for the four model genes. (G) GO enrichment of the final model genes, revealing involvement in phagocytosis, glial cell activation, and inflammatory response. (H) KEGG enrichment of model genes, with pathways such as cell adhesion molecules and primary immunodeficiency.

Article Snippet: Anti-CD45 (PTPRC), mouse monoclonal, clone PD7/26+2B11 , Zhongshan Golden Bridge Biotechnology (ZSGB-BIO) , Cat# Kit-0024.

Techniques: Expressing, Activation Assay

Journal: bioRxiv

Article Title: The Protein Tyrosine Phosphatase CD45 promotes PMN Transepithelial Migration, Antimicrobial Function and Colonic Mucosal Repair

doi: 10.64898/2026.03.25.714205

Figure Lengend Snippet: (A,B) 1 x 10 6 Human PMNs were incubated with 500nM CD45 inhibitor VI or vehicle control or 10ug/ml anti CD45 mAb (MEM-28) or isotype matched control IgG mAb before being added to the basolateral surface of confluent inverted T84 monolayers. PMNs were allowed to migrate in the physiologically relevant basolateral to apical direction for 1 hour in response to a 100nM gradient of n-formyl-methionyl-leucyl-phenylalanine (fMLF). The number of migrated PMNs were quantified by myeloperoxidase assay. Data are means ± SEM (n=5 donors per group, **** p<0.0001). (C,D) 1 x 10 6 Human PMNs were incubated with 500nM CD45 inhibitor VI or vehicle control or 10ug/ml anti CD45 mAb MEM-28 or isotype matched control IgG mAb before being added to the basolateral surface of confluent inverted human colonoid derived monolayers of primary IECs. PMNs were allowed to migrate in the physiologically relevant basolateral to apical direction for 1 hour in response to a 100nM gradient of fMLF. Data are means ± SEM (n=3 donors per group, ** p<0.01; *** p<0.001). (E, F) Quantification of absolute number of PMNs recruited into the lumen of proximal colon loops following intraluminal injection of 1nM LTB4 ± 500nM CD45 inhibitor VI or intraperitoneal injection of 3mg/kg body weight CD45 inhibitor VI. Data are mean ± SEM (n=3-4 mice per group, ** p<0.01).

Article Snippet: Primers for murine Cd45 (Origene MP222432), primers for human CD45 (Origene HP206460).

Techniques: Incubation, Control, Myeloperoxidase Assay, Derivative Assay, Injection

Journal: bioRxiv

Article Title: The Protein Tyrosine Phosphatase CD45 promotes PMN Transepithelial Migration, Antimicrobial Function and Colonic Mucosal Repair

doi: 10.64898/2026.03.25.714205

Figure Lengend Snippet: (A-D) Human PMN were exposed to 500nM CD45 inhibitor VI, vehicle control (Vehicle) or HBSS+ (Ctrl) for 30 minutes at 37°C followed by stimulation with 1.25μM LaB and 5μM fMLF to induce degranulation before assessment of surface expression of CD66b and CD63 by flow cytometry. Data shown are fold-change in mean fluorescence intensity (MFI) compared to PMN not stimulated with 1.25μM LaB and 5μM fMLF (Ctrl) and are expressed as mean ± SEM (n=3 PMN donors, * p<0.05; ** p<0.01). (E-H) Murine PMN were exposed to 500nM CD45 inhibitor VI, vehicle control (Vehicle) or HBSS+ (Ctrl) for 30 minutes at 37°C followed by stimulation with 1.25μM LaB and 5μM fMLF to induce degranulation before assessment of surface expression of CD66b and CD15 by flow cytometry. Data shown are fold-change in mean fluorescence intensity (MFI) compared to PMN not stimulated with 1.25μM LaB and 5μM fMLF (Ctrl) and are expressed as mean ± SEM (n=3 mice per group; * p<0.05; ** p<0.01; *** p<0.001; **** p<0.0001).

Article Snippet: Primers for murine Cd45 (Origene MP222432), primers for human CD45 (Origene HP206460).

Techniques: Control, Expressing, Flow Cytometry, Fluorescence

Journal: bioRxiv

Article Title: The Protein Tyrosine Phosphatase CD45 promotes PMN Transepithelial Migration, Antimicrobial Function and Colonic Mucosal Repair

doi: 10.64898/2026.03.25.714205

Figure Lengend Snippet: (A,B,C) Human PMN were incubated with 500nM CD45 inhibitor VI, vehicle control (Vehicle) or HBSS+ (Ctrl) in conjunction with 100nM fMLF for 60 minutes at 37°C before fluorescent microsphere phagocytosis/uptake was quantified by measuring changes in fluorescence by flow cytometry. Data is mean fluorescence intensity normalized to Ctrl PMN and is expressed as mean ± SEM (n = 3 donors per group *** p<0.001; **** p<0.0001). (D,E,F) Murine PMN were incubated with 500nM CD45 inhibitor VI, vehicle control or HBSS+ (Ctrl PMN) in conjunction with 200nM fMLF for 60 minutes at 37°C before fluorescent microsphere phagocytosis/uptake was quantified by measuring changes in fluorescence by flow cytometry. Data is mean fluorescence intensity normalized to Ctrl PMN and is expressed as mean ± SEM (n = 5 mice per group, ** p<0.01).

Article Snippet: Primers for murine Cd45 (Origene MP222432), primers for human CD45 (Origene HP206460).

Techniques: Incubation, Control, Fluorescence, Flow Cytometry

Journal: bioRxiv

Article Title: The Protein Tyrosine Phosphatase CD45 promotes PMN Transepithelial Migration, Antimicrobial Function and Colonic Mucosal Repair

doi: 10.64898/2026.03.25.714205

Figure Lengend Snippet: CD45 was knocked down by CRISPR/Cas9 in the human promyelocytic cell line HL60 (CD45KO). (A) Lysates from HL60, SCR HL60 or CD45KO HL60 cells differentiated into a neutrophil like state were immunoblotted for CD45 or Gapdh. (B) Densitometry analysis revealed a <98% reduction in CD45 expression (normalized to Gapdh) in CD45KO HL60s relative to non-transduced HL60 cells or SCR HL60 cells. Data is expressed as mean ± SEM normalized to Gapdh and relative to non-transduced HL60 cells (n = 3, **** p<0.0001). (C) Flow cytometry analysis using a PerCP labeled anti-CD45 mAb (30-F11), and a PerCP labeled IgG matched control mAb to show non-specific background fluorescence, revealed a <98% reduction in CD45 surface expression in differentiated CD45KO HL60 cells relative to SCR HL60 cells. Data is mean fluorescence intensity normalized to HL60 Scr IgG control and is expressed as mean ± SEM (n =3, ****, p<0.0001). (E,F) Differentiated SCR HL60 cells and CD45KO HL60 cells were stimulated with 1.25μM LaB and 5μM fMLF to induce degranulation before assessment of surface expression of CD63 by flow cytometry. Data shown are fold-change in mean fluorescence intensity (MFI) normalized to SCR HL60 IgG and are expressed as mean ± SEM (n=3, ** p<0.01). (G,H) Differentiated SCR HL60 and CD45KO HL60 cells were stimulated with 100nM fMLF for 60 minutes at 37°C before fluorescent microsphere phagocytosis/uptake was quantified by measuring changes in fluorescence by flow cytometry. Data is mean fluorescence intensity normalized to SCR HL60 and is expressed as mean ± SEM (n=5, ** p<0.01).

Article Snippet: Primers for murine Cd45 (Origene MP222432), primers for human CD45 (Origene HP206460).

Techniques: CRISPR, Expressing, Flow Cytometry, Labeling, Control, Fluorescence

Journal: bioRxiv

Article Title: The Protein Tyrosine Phosphatase CD45 promotes PMN Transepithelial Migration, Antimicrobial Function and Colonic Mucosal Repair

doi: 10.64898/2026.03.25.714205

Figure Lengend Snippet: (A)) PCR analysis on bone marrow PMN revealed a 90% reduction in Cd45 expression in PMN from MRP8-Cre;Cd45 fl/fl mice compared to PMN from Cd45 fl/fl control mice. Data is mean ± SEM (n=3, **** p<0.00001). (B,C) Western blot showing knockdown of CD45 in bone marrow PMN isolated from MRP8-Cre;Cd45 fl/fl compared to PMN from Cd45 fl/fl control mice. Blot is representative of PMN isolated from 3 independent mice per genotype. Densitometry revealed a 90% reduction in CD45 protein expression in PMN from MRP8-Cre;Cd45 fl/fl compared to PMN from Cd45 fl/fl control mice. Data ± SEM is mean band intensity normalized to Gapdh relative to Cd45 fl/fl (n=3, **** p<0.0001). (D) Gating strategy for bone marrow derived immune cells showing CD11b +ve , Siglec F -ve Ly6gG +ve , Ly6C +ve cells (PMN) and CD11b +ve , Siglec F -ve , Ly6G -ve , Ly6C +ve cells (monocytes). (E) Flow cytometry analysis of Ly6gG +ve , Ly6C +ve PMNs shows a 90% reduction in Cd45 surface expression in bone marrow PMN (Ly6gG +ve , Ly6C +ve ) from MRP8-Cre;Cd45 fl/fl mice compared to PMN from Cd45 fl/fl control mice. Data is mean fluorescence intensity and is expressed as mean ± SEM (n=3, * p<0.05) (G,H) Flow cytometry analysis shows no reduction in CD45 surface expression in monocytes (Ly6G -ve , Ly6C +ve ) isolated from bone marrow of MRP8-Cre;Cd45 fl/fl mice compared to monocytes isolated from Cd45 fl/fl control mice. Data is mean fluorescence intensity and is expressed as mean ± SEM (n=3). (I) Gating strategy for blood derived immune cells showing CD11b +ve , Siglec F -ve Ly6gG +ve , Ly6C +ve cells (PMN) and CD11b +ve , Siglec F -ve Ly6G -ve , Ly6C +ve cells (monocytes). (J,K) Flow cytometry analysis of Ly6gG +ve , Ly6C +ve PMNs shows a 90% reduction in Cd45 surface expression in circulating PMN (Ly6gG +ve , Ly6C +ve ) from MRP8-Cre;Cd45 fl/fl mice compared to PMN from Cd45 fl/fl control mice. Data is mean fluorescence intensity and is expressed as mean ± SEM (n = 3, ** p<0.01) (L,M) Flow cytometry analysis shows no reduction in CD45 surface expression in monocytes (Ly6G -ve , Ly6C +ve ) isolated from blood of MRP8-Cre;Cd45 fl/fl mice compared to monocytes isolated from Cd45 fl/fl control mice. Data is mean fluorescence intensity and is expressed as mean ± SEM (n=3).

Article Snippet: Primers for murine Cd45 (Origene MP222432), primers for human CD45 (Origene HP206460).

Techniques: Expressing, Control, Western Blot, Knockdown, Isolation, Derivative Assay, Flow Cytometry, Fluorescence

Journal: bioRxiv

Article Title: The Protein Tyrosine Phosphatase CD45 promotes PMN Transepithelial Migration, Antimicrobial Function and Colonic Mucosal Repair

doi: 10.64898/2026.03.25.714205

Figure Lengend Snippet: (A,B) PMN isolated from MRP8-Cre;Cd45 fl/fl mice and control Cd45 fl/fl mice were stimulated with 100nM fMLF for 60 minutes at 37°C before fluorescent microsphere phagocytosis/uptake was quantified by flow cytometry. Data is fold changes in mean fluorescence intensity normalized to Cd45 fl/fl PMN and is expressed as mean ± SEM (n = 3 **, p<0.01). (C,D) PMN isolated from MRP8-Cre;Cd45 fl/fl mice and control Cd45 fl/fl mice were stimulated with 1.25μM LaB and 5μM fMLF to induce degranulation before assessment of surface expression of CD63 by flow cytometry. Data shown are fold-change in mean fluorescence intensity (MFI) normalized to Cd45 fl/fl PMN and are expressed as mean ± SEM (n=4, *** p<0.001).

Article Snippet: Primers for murine Cd45 (Origene MP222432), primers for human CD45 (Origene HP206460).

Techniques: Isolation, Control, Flow Cytometry, Fluorescence, Expressing

Journal: bioRxiv

Article Title: The Protein Tyrosine Phosphatase CD45 promotes PMN Transepithelial Migration, Antimicrobial Function and Colonic Mucosal Repair

doi: 10.64898/2026.03.25.714205

Figure Lengend Snippet: (A) Disease Activity Index (DAI) score consisting of body weight changes, stool consistency, and presence of occult blood in MRP8-Cre;Cd45 fl/fl mice and Cd45 fl/fl mice administered water containing 3% DSS for 5 days followed by regular water for 5 days (n=3 independent experiments with 5-10 mice per group). (B) At day 10 mice were euthanized and tissues harvested for histological analysis. Representative histological images of Swiss rolls of whole colons with magnifications of the rectum to assess levels of DSS-induced colitis. Left image is from a Cd45 fl/fl mouse, right image is from an MRP8-Cre;Cd45 fl/fl mouse. (C,D) Histological scoring of colonic tissue on day 10 scored by 2 independent investigators. Data are shown as means ± SEM and were analyzed by 1-way ANOVA followed by Tukey’s post hoc testing, * p<0.05; ** p < 0.01; **** p < 0.0001 (each dot represents data from an individual mouse across 2 independent experiments, 13 mice per group).

Article Snippet: Primers for murine Cd45 (Origene MP222432), primers for human CD45 (Origene HP206460).

Techniques: Activity Assay

Journal: bioRxiv

Article Title: The Protein Tyrosine Phosphatase CD45 promotes PMN Transepithelial Migration, Antimicrobial Function and Colonic Mucosal Repair

doi: 10.64898/2026.03.25.714205

Figure Lengend Snippet: (A) Representative images of wounds from MRP8-Cre;Cd45 fl/fl and Cd45 fl/fl mice at 24h and 72h post biopsy wounding. (B) Quantification of % wound healing in MRP8-Cre;Cd45 fl/fl and Cd45 fl/fl mice at 72h post biopsy wounding (Data is mean ± SEM, each dot represents data from one mouse with an average of 4-6 wounds per mouse, n=2, **p<0.001).

Article Snippet: Primers for murine Cd45 (Origene MP222432), primers for human CD45 (Origene HP206460).

Techniques:

Journal: bioRxiv

Article Title: The Protein Tyrosine Phosphatase CD45 promotes PMN Transepithelial Migration, Antimicrobial Function and Colonic Mucosal Repair

doi: 10.64898/2026.03.25.714205

Figure Lengend Snippet: (A,B) Human PMN exposed to 500nM CD45 inhibitor VI or vehicle control were incubated with a FITC conjugated anti-CD11b mAb or a FITC conjugated isotype matched IgG control mAb and assessed by flow cytometry. Inhibition of CD45 phosphatase activity resulted in a significant decrease in levels of CD11b surface expression relative to vehicle control (Vehicle). Data ± SEM represent fold change in mean fluorescence intensity for CD11b normalized to Ctrl (n=3, * p<0.05, ** p<0.01). (C,D) Human PMN exposed to 500nM CD45 inhibitor VI or vehicle control were assessed for CD11b activation by flow cytometry using the activation reporter antibody CBRM1/5. Inhibition of CD45 phosphatase activity resulted in a significant decrease in levels of active CD11b on the surface of PMNs. Data ± SEM represent fold change in mean fluorescence intensity of CBRM1/5 normalized to Ctrl (n=3, ** p<0.01). (E,F) Decreased surface expression of CD11b was detected by flow cytometry of CD45KO HL60 cells relative to SCR HL60s or non-transduced HL60 cells. Data ± SEM represent fold change in mean fluorescence intensity of CD11b normalized to non-transduced HL60 cells (n=3, * p<0.05). (G,H) Decreased surface expression of active CD11b in CD45KO HL60 cells relative to SCR HL60s or non-transduced HL60 cells was detected by flow cytometry. Data ± SEM represent fold change in mean fluorescence intensity of CBRM1/5 normalized to non-transduced HL60 cells (n=3, * p<0.05). (I,J) PMN isolated from WT mice were exposed to 500nM CD45 inhibitor VI or vehicle control and incubated with an APC conjugated anti-CD11b mAb or an APC conjugated isotype matched control mAb before analysis of CD11b surface expression by flow cytometry. Inhibition of CD45 phosphatase activity resulted in a significant decrease in levels of CD11b surface expression. Data ± SEM represent fold change in mean fluorescence intensity for CD11b normalized to vehicle control (n=4, * p<0.05). (K,L) PMN isolated from MRP8-Cre;Cd45 fl/fl mice or Cd45 fl/fl mice were incubated with an APC conjugated anti-CD11b mAb or an APC conjugated isotype matched control mAb before analysis of CD11b surface expression by flow cytometry. Data ± SEM represent fold change in mean fluorescence intensity of CD11b normalized to Cd45 fl/fl PMN (n=4, ** p<0.01).

Article Snippet: Primers for murine Cd45 (Origene MP222432), primers for human CD45 (Origene HP206460).

Techniques: Control, Incubation, Flow Cytometry, Inhibition, Activity Assay, Expressing, Fluorescence, Activation Assay, Isolation

Journal: bioRxiv

Article Title: The Protein Tyrosine Phosphatase CD45 promotes PMN Transepithelial Migration, Antimicrobial Function and Colonic Mucosal Repair

doi: 10.64898/2026.03.25.714205

Figure Lengend Snippet: (A) CD45KO HL60 cells or SCR control HL60 cells differentiated to a PMN like state were stimulated with 100nM fMLF over 60 minutes. Representative blots are shown for indicated proteins or phosphoproteins. Blots are representative of n=3 independent experiments. (B) Densitometry showing statistically significant decreases in Lyn dephosphorylation at Tyr 507 but no changes in Hck or Lyn phosphorylation upon CD45 knockdown. Data ± SEM represent phosphorylated protein levels normalized to GAPDH relative to total protein levels normalized to GAPDH (n=3, ** p<0.01; *** p<0.001; **** p<0.0001). (C) PMN from MRP8-Cre; Cd45 fl/fl mice and Cd45 fl/fl mice were stimulated with 100nM fMLF over a 1-hour time course. Representative blots are shown for indicated proteins. Blots are representative of n=3 independent experiments. (D) Densitometry showing statistically significant decreases in Lyn dephosphorylation at Tyr 507 but no changes in Hck or Lyn phosphorylation in PMN from MRP8-Cre; Cd45 fl/fl mice relative to PMN from Cd45 fl/fl mice. Data ± SEM represent phosphorylated protein levels normalized to GAPDH relative to total protein levels normalized to GAPDH (n=3, * p<0.05; ** p<0.01; *** p<0.001).

Article Snippet: Primers for murine Cd45 (Origene MP222432), primers for human CD45 (Origene HP206460).

Techniques: Control, De-Phosphorylation Assay, Phospho-proteomics, Knockdown

Journal: bioRxiv

Article Title: The Protein Tyrosine Phosphatase CD45 promotes PMN Transepithelial Migration, Antimicrobial Function and Colonic Mucosal Repair

doi: 10.64898/2026.03.25.714205

Figure Lengend Snippet: Model figure showing how CD11b recruits Lyn Kinase which is activated by CD45 phosphatase in turn stabilizing CD11b/CD18 surface expression and activation and promoting PMN anti-microbial effector functions.

Article Snippet: Primers for murine Cd45 (Origene MP222432), primers for human CD45 (Origene HP206460).

Techniques: Expressing, Activation Assay

Journal: bioRxiv

Article Title: Retrotransposons Promote Clonal Hematopoiesis Through Aging-Related Stromal Inflammation

doi: 10.64898/2026.02.23.707588

Figure Lengend Snippet: (A) Schematic of Lx8 overexpression vector (top) and ex vivo competitive co-culture model (below). LT-HSCs (SLAM⁺ CD34⁻ LSKs) were sorted from WT CD45.2 mice and Vav-iCre Dnmt3a fl-R878H/+ CD45.1/CD45.2 mice. WT (CD45.2) and Dnmt3a -mutant (CD45.1/CD45.2) LT-HSCs were mixed at a 2:1 ratio and co-cultured with MS5 cells transfected with an empty vector or the Lx8 construct. After 11 days of co-culture, HSCs were analyzed by flow cytometry. (B) Representative flow cytometry gating to determine LSK counts from co-culture experiment described in (A). CD86 was used in place of Sca-1 staining for LSK cells due to IFNα-induced Sca1 upregulation. Absolute cell numbers are shown in bottom right of each plot. (C) Flow cytometry analysis of mutant chimerism in total cells, restricted progenitors (LK), and LSKs after ex vivo co-culture (n=5-6). Mutant chimerism was calculated as the ratio of Dnmt3a -mutant CD45.1/CD45.2 cells to total CD45 cells within the defined compartment. Statistical significance was determined by multiple t-tests. (D) Quantification of absolute LSK numbers after mixed HSCs were co-cultured with MS5-EV and MS5-Lx8 (n=5-6). Statistical significance was determined by multiple t-tests. (E) Flow cytometry gating scheme (left) and representative flow plots (right) for determining early and late apoptosis frequency in LSK cells. Analysis was conducted by flow cytometry using DAPI and Annexin-V. (F) Overall cell viability in WT and mutant LSK populations co-cultured with MS5-EV and MS5-Lx8 (G) Cell frequency of early/late apoptosis and naked nuclei in WT and mutant LSK populations co-cultured with MS5-EV (left) and MS5-Lx8 (right). (H) Pie charts depicting the cell cycle distribution of Dnmt3a -mutant and WT LSKs co-cultured with MS5-EV and MS5-Lx8. Analysis conducted by flow cytometry using DNA content and nuclear Ki-67 staining. (I) Bar chart quantification of the pie chart data in (H), comparing cell cycle phase frequencies of LSKs co-cultured with MS5-EV and MS5-Lx8 (n=5-6). Statistical significance was determined by multiple t-tests.

Article Snippet: CD45.2 mice (JAX#000664) and Ptprc em6Lutzy /J CD45.1 mice (JAX#033076) were obtained from The Jackson Laboratory and maintained in the Animal Resource Center at UTSW under pathogen-free conditions.

Techniques: Over Expression, Plasmid Preparation, Ex Vivo, Co-Culture Assay, Mutagenesis, Cell Culture, Transfection, Construct, Flow Cytometry, Staining

Journal: bioRxiv

Article Title: Retrotransposons Promote Clonal Hematopoiesis Through Aging-Related Stromal Inflammation

doi: 10.64898/2026.02.23.707588

Figure Lengend Snippet: (A) Diagram of how retrotransposons can invoke a viral mimicry response to induce IFN-I. (B) Schematic of the ex vivo competitive co-culture model with or without recombinant IFNα treatment. LT-HSCs (SLAM⁺ CD34⁻ LSKs) were sorted from WT CD45.2 mice and Vav-iCre ; Dnmt3a fl-R878H /+ CD45.1/CD45.2 mice. WT and Dnmt3a -mutant LT-HSCs were mixed at a 2:1 ratio. After 11 days of co-culture, HSCs were analyzed by flow cytometry. (C) Flow cytometry analysis of mutant chimerism in total cells, restricted progenitors (LKs), and LSKs after ex vivo co-culture with or without 5ng/mL recombinant IFNα treatment (n=5-6). Mutant chimerism was calculated as the ratio of Dnmt3a -mutant CD45.1/CD45.2 cells to total cells within population. (D) Quantification of absolute LSK counts for mixed HSCs co-cultured with MS5 cells with or without 5ng/mL recombinant IFNα (n=5-6). Statistical significance for (C) and (D) was determined by multiple t-tests. (E) Immunofluorescent imaging of MAVS aggregation in parental MS5 cells and MS5 cells transfected with pIpC, EV, or Lx8. DAPI stained in blue. MAVS stained in green. White arrows identifying MAVS aggregated cells. (F) Quantification of the frequency of cells containing cytoplasmic MAVS aggregation. Statistical significance was determined by multiple t-tests. (G) Western blot analysis of STING and IRF3 phosphorylation in MS5 cells transfected with EV or retrotransposon constructs. (H) Schematic of the ex vivo competitive co-culture model using MS5 cells expressing shLuciferase (shLuc) control or shIrf3. (I-K) Flow cytometry analysis of mutant chimerism in total cells (I), restricted progenitors (J), or LSK cells (K) after ex vivo co-culture with MS5 cells expressing shLuciferase (shLuc) control or shIrf3 (n=5-6). Mutant chimerism was calculated as the ratio of Dnmt3a -mutant CD45.1/CD45.2 cells to total cells within population. Statistical significance was determined by multiple t-tests. (L-M) Quantification of absolute LSK counts for mixed HSCs co-cultured with MS5-EV or MS5-Lx8 cells expressing shLuc control (L) or shSting (M). (N) Schematic of the ex vivo competitive co-culture model in which WT HSCs are competed with Dnmt3a -mutant HSCs containing either an intact or deleted interferon alpha receptor ( Ifnar1). MS5 cells are treated with vehicle or 5ng/mL recombinant IFNα. (O) Flow cytometry analysis of mutant chimerism in LSKs after ex vivo co-culture as described in (N). (P) Schematic of the ex vivo competitive co-culture model in which Dnmt3a -mutant HSCs are competed either with WT HSCs or HSCs containing a deleted interferon alpha receptor ( Ifnar1). MS5 cells are treated with vehicle or 5ng/mL recombinant IFNα. (Q) Flow cytometry analysis of mutant chimerism in LSKs after ex vivo co-culture as described in (P). Statistical significance for (O) and (Q) was determined by multiple t-tests. (R) Heatmap of interferon alpha response genes in young and old MSCs. (S) Differential activation of IFN gene sets defined in (R) for WT and Dnmt3a -mutant HSC with or without IFNα treatment. (T) Proposed model for retrotransposon-driven clonal hematopoiesis during aging. Figures (A), (B), (H), (J), (L), and (P) created with the aid of Biorender.

Article Snippet: CD45.2 mice (JAX#000664) and Ptprc em6Lutzy /J CD45.1 mice (JAX#033076) were obtained from The Jackson Laboratory and maintained in the Animal Resource Center at UTSW under pathogen-free conditions.

Techniques: Ex Vivo, Co-Culture Assay, Recombinant, Mutagenesis, Flow Cytometry, Cell Culture, Imaging, Transfection, Staining, Western Blot, Phospho-proteomics, Construct, Expressing, Control, Activation Assay

Journal: International Journal of Molecular Sciences

Article Title: Cytosine Deaminase-TRAIL Expressing Human Adipose Stem Cells Inhibit Tumor Growth in Castration Resistant Prostate Cancer Bearing Mice with Less Toxicity

doi: 10.3390/ijms27031563

Figure Lengend Snippet: Flow cytometric characterization of parental hTERT-ADSC and ADSC.CD.sTRAIL cells. Representative flow histograms for surface markers. Blue peaks = specific antibody staining; gray peaks = isotype control. Both cell types were strongly positive for MSC markers CD90 and CD105, and negative for hematopoietic markers CD34 and CD45. These results confirm maintenance of the MSC phenotype after immortalization and genetic modification. Abbreviations: ADSC—adipose-derived stem cell.

Article Snippet: Cells were stained with antibodies against canonical MSC surface markers CD29, CD90, and CD105, as well as hematopoietic lineage markers CD34 and CD45 (all antibodies 1:50 dilution; Origene or Invitrogen, Rockville, MD, USA).

Techniques: Staining, Control, Modification, Derivative Assay

Journal: bioRxiv

Article Title: Strong sustained type I IFN signaling acts cell intrinsically to impair IFNγ responses and cause tuberculosis susceptibility

doi: 10.64898/2026.01.19.700487

Figure Lengend Snippet: (A) Quantification of Viperin-expressing cells of Non-Target Control (NTC) or Ifnar2 −/− BMMs upon IFN β or IFN γ . UT = Untreated. (B) Representative flow cytometry plots and (C) quantification of CXCL9 and/or Viperin expressing cells from pure WT (left), Ifnar1 −/− (right) or mixed WT Ifnar1 −/− (middle) BMM culture upon exposure to both IFN β and IFN γ . (D) MFI of Viperin staining in IMs from Mtb -infected B6 and B6. Ifnar1 −/− mice at day 25-26 pi. (E) MFI of Viperin staining in IMs and (F) quantification of CXCL9 and/or Viperin expressing IMs from Mtb -infected B6, Sp140 −/− and Sp140 −/− Ifnar1 −/− mice at day 28-29 pi. (G) Flow cytometry-based comparison of Viperin-positive and -negative IMs from Mtb -infected Sp140 −/− mice at day 28-29 pi showing CXCL9 MFI (H) percentage infected IMs and (I) Mtb -mWasabi MFI. (J-M) Analysis of Mtb -infected mixed Sp140 −/− bone marrow chimeras containing IFNAR-proficient (CD45.1) and -deficient cells (CD45.2) at day 25-26 pi. (J) MFI of Viperin staining in Ifnar1 +/+ and Ifnar −/− IMs. (K) Comparison of Ifnar1 +/+ IMs (negative or positive for Viperin) and Ifnar −/− IMs (negative for Viperin, see (J)) in terms of CXCL9 MFI, (L) percentage infected IMs and (M) Mtb -mWasabi MFI. Statistical significance was calculated in (A, E) with Brown-Forsythe/Welch ANOVA test and in (D) with Welch’s t-test, both with Dunnett’s T3 multiple comparisons test, in (G-J) Paired t-test, in (K-M) RM one-way ANOVA with Sidak’s multiple comparison test. *p < 0.05, **p < 0.01, ***p < 0.001, ns = not significant.

Article Snippet: Mouse lines used are C57BL/6J (B6), B6.129S2- Ifnar1 tm1Agt/ Mmjax ( Ifnar1 −/− ), B6.129S7- Ifngr1 tm1Agt/J ( Ifngr1 −/− ), C57BL/6J- Ptprc em6Lutzy/J (CD45.1) and B6.Cg- Mx1 tm1.1Agsa/J ( Mx1-g fp ) that were purchased from Jackson Laboratories.

Techniques: Expressing, Control, Flow Cytometry, Staining, Infection, Comparison

Journal: bioRxiv

Article Title: Strong sustained type I IFN signaling acts cell intrinsically to impair IFNγ responses and cause tuberculosis susceptibility

doi: 10.64898/2026.01.19.700487

Figure Lengend Snippet: (A) Quantification of percentage of CXCL9 expressing cells from pure WT or mixed WT Ifnar1 −/− BMM culture upon exposure to IFN γ alone. (B) Representative flow cytometry plots of IMs for CXCL9 and Viperin expression from Mtb -infected B6, Sp140 −/− and Sp140 −/− If-nar1 −/− mice at day 28-29 pi. (C) Analysis of Mtb-infected mixed Sp140 −/− bone marrow chimeras containing CD45.1- and CD45.2-positive cells, either both IFNAR-proficient (control) or IFNAR-proficient and IFNAR-deficient, respectively, at day 25-26 pi, showing cells stained for Viperin, (D) CXCL9, (E) percentage infected IMs and (F) Mtb -mWasabi MFI. Statistical significance was calculated in (A) with Welch’s test, in (C-F) with paired t-test. *p < 0.05, **p < 0.01, ***p < 0.001, ns = not significant.

Article Snippet: Mouse lines used are C57BL/6J (B6), B6.129S2- Ifnar1 tm1Agt/ Mmjax ( Ifnar1 −/− ), B6.129S7- Ifngr1 tm1Agt/J ( Ifngr1 −/− ), C57BL/6J- Ptprc em6Lutzy/J (CD45.1) and B6.Cg- Mx1 tm1.1Agsa/J ( Mx1-g fp ) that were purchased from Jackson Laboratories.

Techniques: Expressing, Flow Cytometry, Infection, Control, Staining