Journal: bioRxiv

Article Title: NK cell immunotherapy administered at the time of HIV recrudescence is associated with viral control

doi: 10.1101/2025.11.19.688897

Figure Lengend Snippet: A) Schematic figure showing the overview of NK cell production and the overview of the mouse study timeline. Red circles on the timeline indicate blood collection, black dots indicate scheduled necropsies. Schematic of transgene design: MND promoter, CAR (CD4-MBL-CD8TM-4-1BB-CD3z), CXCR5, IL-15, the BgH PolyA tail, with separation mediated by P2A and T2A sites, and inverted terminal repeats (ITRs). Schematic showing expression of all transgene components as well as base editor-mediated knock out of PD-1 on the NK cell surface. Figure made using Biorender.com. B) Expression of CAR (MBL) and CXCR5 molecules was confirmed in the cell product using flow cytometry. Cells were pre-gated sequentially on lymphocytes, singlets, live cells, CD56+, and CD3-. C) PD-1 knockout was detected at the RNA level by RT-PCR, CAR NK (blue) relative to control NK cells (black). D) IL-15 expression in CAR NK (blue) and control NK (black) cells via IL-15 ELISA of cell culture supernatant. E) CAR (blue) and control (black) cell proliferation over one week post-thaw. F) The specific lysis of HIV Envelope P815s by CAR (blue) or control (black) NK cells via DELFIA cytotoxicity assay. 5:1, 10:1, and 20:1 E:T ratios were tested. All assays were performed in duplicate or triplicate. Data are represented as mean + standard deviation (error bars).

Article Snippet: After a 2-day recovery, CAR NK cells were sorted on CD56+ CD4+ using the MACSQuant Tyto Cell Sorter (Miltenyi Biotec) and expanded for an additional 7 days following the procedure described above.

Techniques: Expressing, Knock-Out, Flow Cytometry, Reverse Transcription Polymerase Chain Reaction, Control, Enzyme-linked Immunosorbent Assay, Cell Culture, Lysis, Cytotoxicity Assay, Standard Deviation

Journal: bioRxiv

Article Title: NK cell immunotherapy administered at the time of HIV recrudescence is associated with viral control

doi: 10.1101/2025.11.19.688897

Figure Lengend Snippet: NK (CD56+) cells in CAR (blue), control (black), or PBS (red) treated groups from A) Peripheral Blood, B) Lymph node (at necropsies), and C) Spleen (at necropsies). CAR+CXCR5+ NK cells over time in D) Peripheral Blood, E) Lymph node (at necropsies), and F) Spleen (at necropsies). Flow was pre-gated on Lymphocytes, Singlets, Live Cells, human CD45+, mouse CD45-, CD3+, and then through CD56+ MBL+ CXCR5+ (see Fig. S4 for gating strategy). Median viral loads (green), NK cell levels (orange), post-treatment in G) controllers or H) non-controllers. I) Median human hematopoietic cell counts (CD45+)/ ul blood of controllers (gray) or non-controllers (pink).

Article Snippet: After a 2-day recovery, CAR NK cells were sorted on CD56+ CD4+ using the MACSQuant Tyto Cell Sorter (Miltenyi Biotec) and expanded for an additional 7 days following the procedure described above.

Techniques: Control

Journal: bioRxiv

Article Title: NK cell immunotherapy administered at the time of HIV recrudescence is associated with viral control

doi: 10.1101/2025.11.19.688897

Figure Lengend Snippet: CD4:CD8 ratios over time in A) CAR NK-treated animals (blue), B) control NK-treated animals (black), and C) PBS-treated animals (red). CD4:CD8 ratios in CAR (blue), control NK (black), and PBS (red) treated groups at D) -6 DPT, E) 6 DPT, F) 14 DPT, G) 28 DPT, H) 42 DPT, and I) 56 DPT. Lines represent median values. CD4:CD8 ratios were determined by flow cytometry and pre-gated on Lymphocytes, Singlets, Live Cells, Human CD45+, Mouse CD45-, CD3+ (see gating strategy in Fig. S4 ).

Article Snippet: After a 2-day recovery, CAR NK cells were sorted on CD56+ CD4+ using the MACSQuant Tyto Cell Sorter (Miltenyi Biotec) and expanded for an additional 7 days following the procedure described above.

Techniques: Control, Flow Cytometry

Journal: Cell Genomics

Article Title: Single-cell profiling of bone metastasis ecosystems from multiple cancer types reveals convergent and divergent mechanisms of bone colonization

doi: 10.1016/j.xgen.2025.100888

Figure Lengend Snippet: Immunofluorescence staining verifies distinct immune archetypes (A) Representative fields selected from tissue section immunofluorescence (IF) staining of patients classified by archetypes (columns), highlighting three major cell types (rows). CTSK marks the OC population, CD4 and FOXP3 double-positive signals indicate CD4 Treg populations, and CD8A and TIM3 double-positive signals represent CD8 Tex populations. (B) Cell counting from IF staining of tissue sections from 21 patients, grouped by archetypes: Mφ-OC ( N = 6 patients), Treg-Tex ( N = 8 patients), and Mono ( N = 7 patients). Three major cell types were analyzed: OC cells were manually counted from entire tissue sections. Treg and Tex populations were quantified from selected fields (regions of interest based on CD4 or CD8A positivity, shown in ). Left: Proportion of OC cells out of total cells; Middle: Proportion of CD4 Tregs out of total CD4 T cells; Right: Proportion of CD8 Tex cells out of total CD8 T cells. (Significance test: One-way ANOVA, ∗ p < 0.05; ∗∗ p < 0.01).

Article Snippet: Mouse anti-Human CD4, 1:100 , ThermoFisher scientific , Cat#14-2444-82; RRID: AB_2572868.

Techniques: Immunofluorescence, Staining, Cell Counting

Journal: Cell Genomics

Article Title: Single-cell profiling of bone metastasis ecosystems from multiple cancer types reveals convergent and divergent mechanisms of bone colonization

doi: 10.1016/j.xgen.2025.100888

Figure Lengend Snippet: Immune archetypes in published dataset (A) Schematic of the workflow for cell type identification and frequency estimation. (Illustration created with BioRender.) (B) Hierarchical clustering of 957 patients (columns) based on estimated cell types and their frequencies (rows). (C) Subset analysis of 158 patients (from B) with cancer metastasis to the bones. Patients were clustered into three groups based on the frequencies of selected cell types: Monocytes, Mφ, OC, CD4 Treg, CD8 pTex, and CD8 Tex. (D) Confusion matrix displaying the correlation clustering of matched patients based on the cell frequencies of selected cell types (from C), comparing the primary breast tumor microenvironment (TME) with their bone metastasis TME. (E) Confusion matrix displaying patient clustering based on the frequencies of selected cell types, annotated with patients' progression-free survival (PFS). (F) Correlation analysis of patients from (E), examining the relationship between PFS probability and the expression of Treg and Tex cell signatures (Treg/Tex infiltration). The analysis was conducted across different metastatic tissues ( p values reported from Log Rank Test).

Article Snippet: Mouse anti-Human CD4, 1:100 , ThermoFisher scientific , Cat#14-2444-82; RRID: AB_2572868.

Techniques: Expressing

Journal: Cell Genomics

Article Title: Single-cell profiling of bone metastasis ecosystems from multiple cancer types reveals convergent and divergent mechanisms of bone colonization

doi: 10.1016/j.xgen.2025.100888

Figure Lengend Snippet: Distinct differentiation routes of myeloid populations and T lymphocytes (A) Trajectory inferences of myeloid and T cells (columns) across archetypes (rows). Streamlines in the background UMAP represent unbiased, calculated cell state transitions, while arrows and gradient-colored dots depict supervised least action paths (LAPs), directed from designated initiating cell populations to terminal cell populations: CD14hi Mono to Mϕ/OC (Myeloid), naive CD4 T to CD4 Treg (CD4 T), and CD8 Teff to CD8 Tex (CD8 T). (B) Gene expression kinetics (RNA velocity). Clear and visible kinetic shifts indicate committed differentiation events. (C) Gene expression accelerations (a derivative of RNA velocity). Distinct and visible acceleration shifts indicate committed differentiation potential.

Article Snippet: Mouse anti-Human CD4, 1:100 , ThermoFisher scientific , Cat#14-2444-82; RRID: AB_2572868.

Techniques: Gene Expression

Journal: Biosensors

Article Title: White Light Spectroscopy Characteristics and Expansion Dynamic Behavior of Primary T-Cells: A Possibility of Online, Real-Time, and Sampling-Less CAR T-Cell Production Monitoring

doi: 10.3390/bios15040251

Figure Lengend Snippet: List of reagents and equipment.

Article Snippet: PE Mouse anti human CD4 , Becton Dickinson (Franklin Lakes, NJ, USA, supplier France) , 555347.

Techniques: Staining, Cytometry, Flow Cytometry, Software

Journal: eLife

Article Title: Sex-dependent gastrointestinal colonization resistance to MRSA is microbiota and Th17 dependent

doi: 10.7554/eLife.101606

Figure Lengend Snippet: ( A ) Nlrp3 gene counts from bulk RNA sequencing (RNA-seq) analysis from cells isolated from the colon lamina propria (LP) or colon epithelial cells (EC). ( B ) Il-1β gene counts from bulk RNA-seq analysis from cells isolated from the colon lamina propria (LP) or colon epithelial cells (EC). ( C ) MRSA colony forming units (CFU) in stool following oral inoculation of Nlrp3 −/− and Nlrp3 +/− mice bred at NYU. Nlrp3 −/− n=6, Nlrp3 +/− n=6. ( D ) Representative flow gating to confirm depletion of CD4+ T cells in colon lamina propria 3 days post injection. Data points represent mean ± SEM from at least two independent experiments. Statistical analysis: area under the curve followed by a two-tailed t-test. ns: not significant.

Article Snippet: C57BL/6J mice bred at NYU were injected intraperitoneally with either 200 μg rat anti-mouse Ly6G or rat IgG2a isotype control antibody to deplete neutrophils and 250 μg rat anti-mouse CD4 or rat IgG2a isotype control antibody to deplete CD4+ T cells (Bio-X-Cell, West Lebanon, NH, USA).

Techniques: RNA Sequencing, Isolation, Injection, Two Tailed Test

Journal: eLife

Article Title: Sex-dependent gastrointestinal colonization resistance to MRSA is microbiota and Th17 dependent

doi: 10.7554/eLife.101606

Figure Lengend Snippet: ( A ) Methicillin-resistant S. aureus (MRSA) colony forming units (CFU) in stool following oral inoculation of Rag2 −/− and Rag2 +/− mice bred at NYU. Male Rag2 −/− n=12, male Rag2 +/− n=12, female Rag2 −/− n=12, female Rag2 +/− n=11. ( B ) MRSA CFU in stool following oral inoculation of Ighm −/− and Ighm +/− mice bred at NYU. Male Ighm −/− n=6, male Ighm +/− n=6, female Ighm −/− n=8, female Ighm +/− n=5. ( C ) MRSA CFU in stool following oral inoculation of female NYU B6 mice injected intraperitoneally (IP) with 250 μg of anti-CD4 depleting antibody or anti-IgG control. Anti-IgG n=8, anti-CD4 n=10. Data points represent mean ± SEM from at least two independent experiments. Statistical analysis: area under the curve analyzed by a one-way ANOVA with Sidak’s multiple comparison test for ( A ) and ( B ) and a two-tailed t-test for ( C ). ns: not significant.

Article Snippet: C57BL/6J mice bred at NYU were injected intraperitoneally with either 200 μg rat anti-mouse Ly6G or rat IgG2a isotype control antibody to deplete neutrophils and 250 μg rat anti-mouse CD4 or rat IgG2a isotype control antibody to deplete CD4+ T cells (Bio-X-Cell, West Lebanon, NH, USA).

Techniques: Injection, Control, Comparison, Two Tailed Test

Journal: eLife

Article Title: Sex-dependent gastrointestinal colonization resistance to MRSA is microbiota and Th17 dependent

doi: 10.7554/eLife.101606

Figure Lengend Snippet: ( A ) Flow cytometry of cecal-colonic lamina propria CD4+ T cells as a percentage of CD45+ cells in male and female NYU mice treated with phosphate-buffered saline (PBS) or MRSA 2 days post inoculation (dpi). ( B ) Flow cytometry of cecal-colonic lamina propria IL17A+ CD4+ T cells as a percentage of total CD4+ T cells in male and female NYU mice treated with PBS or MRSA 2 dpi. ( C ) Flow cytometry of cecal-colonic lamina propria γδ T cells as a percentage of CD45+ cells in male and female NYU mice treated with PBS or MRSA 2 dpi. ( D ) Flow cytometry of cecal-colonic lamina propria IL17A+ γδ T cells as a percentage of total CD4+ T cells in male and female NYU mice treated with PBS or MRSA 2 dpi. ( E ) MRSA colony forming units (CFU) in stool following oral inoculation of Rorc −/− and Rorc +/− mice bred at NYU. Male Rorc +/− n = 5, male Rorc −/− n=7, female Rorc +/− n = 9, female Rorc −/− n=9. ( F ) MRSA CFU in stool following oral inoculation of female Il17ra +/- and Il17ra -/- mice bred at NYU. Il17ra +/- n = 6, Il17ra -/- n=6. ( G ) MRSA CFU in stool following oral inoculation of Tcrd +/− and Tcrd −/− mice bred at NYU. Male Tcrd +/− n = 6, male Tcrd −/− n=6, female Tcrd +/− n=8, and female Tcrd −/− n=12. ( H ) Flow cytometry of cecal-colonic lamina propria Ly6G+CD11b+ neutrophils as a percentage of CD45+ cells in male and female NYU mice treated with PBS or MRSA 2 dpi. ( I ) Quantification of mean fluorescence intensity (MFI) of surface CD11b on neutrophils by flow cytometry normalized to mock-treated controls. ( J ) MRSA CFU in stool following oral inoculation of NYU B6 mice treated with anti-Ly6G neutrophil depleting antibody or anti-IgG control. Male anti-IgG n=6, male anti-Ly6G n=8, female anti-IgG n = 12, and female anti-CD4+ n = 15. Data points represent mean ± SEM from at least two independent experiments. Statistical analysis: two-way ANOVA+Sidak’s multiple comparisons test for ( A – D ) and ( H ), area under the curve followed by a one-way ANOVA+Sidak’s multiple comparisons test for ( E ), ( G ), ( J ) or a two-tailed t-test for ( F ) and a two-tailed t-test for ( I ). ns: not significant.

Article Snippet: C57BL/6J mice bred at NYU were injected intraperitoneally with either 200 μg rat anti-mouse Ly6G or rat IgG2a isotype control antibody to deplete neutrophils and 250 μg rat anti-mouse CD4 or rat IgG2a isotype control antibody to deplete CD4+ T cells (Bio-X-Cell, West Lebanon, NH, USA).

Techniques: Flow Cytometry, Saline, Fluorescence, Control, Two Tailed Test

Journal: eLife

Article Title: Sex-dependent gastrointestinal colonization resistance to MRSA is microbiota and Th17 dependent

doi: 10.7554/eLife.101606

Figure Lengend Snippet: ( A ) Flow cytometry gating scheme for innate lymphoid cells (ILCs), CD4+ and γδ T cell populations. ( B ) Representative sample gating of IL17A+ CD4+ populations in unstimulated, mock and 2 days post inoculation (dpi) methicillin-resistant S. aureus (MRSA)-treated samples.

Article Snippet: C57BL/6J mice bred at NYU were injected intraperitoneally with either 200 μg rat anti-mouse Ly6G or rat IgG2a isotype control antibody to deplete neutrophils and 250 μg rat anti-mouse CD4 or rat IgG2a isotype control antibody to deplete CD4+ T cells (Bio-X-Cell, West Lebanon, NH, USA).

Techniques: Flow Cytometry

Journal: eLife

Article Title: Sex-dependent gastrointestinal colonization resistance to MRSA is microbiota and Th17 dependent

doi: 10.7554/eLife.101606

Figure Lengend Snippet: ( A ) Flow cytometry of small intestinal (SI) lamina propria CD4+ T cells as a percentage of CD45+ cells in male and female NYU mice treated with phosphate-buffered saline (PBS) or methicillin-resistant S. aureus (MRSA) 2 days post inoculation (dpi). ( B ) Flow cytometry of SI lamina propria IL-17A+ CD4+ T cells as a percentage of total CD4+ T cells in male and female NYU mice treated with PBS or MRSA 2 dpi. ( C ) Flow cytometry of cecal-colonic lamina propria CD127+ innate lymphoid cells (ILCs) as a percentage of CD45+ in male and female NYU mice treated with PBS or MRSA 2 dpi. ( D ) Flow cytometry of cecal-colonic lamina propria IL17A+ ILCs as a percentage of total ILCs in male and female NYU mice treated with PBS or MRSA 2 dpi. ( E ) Representative flow gating of CD45+ Ly6G+ cells isolated from the spleens of B6 NYU mice treated with anti-Ly6G neutrophil depleting antibody or anti-IgG control. ( F ) Representative flow cytometry gating plot of CD45+Ly6G+CD11b+ neutrophils isolated from the cecal-colonic tissue of B6 NYU mice treated with a PBS mock control or MRSA. Representative flow cytometry gating plot of CD11b mean fluorescent intensity (MFI) of Ly6G+CD11b+ neutrophils. Data points represent mean ± SEM from at least two independent experiments. Statistical analysis: two-way ANOVA+Sidak’s multiple comparisons test for ( A – D ). ns: not significant.

Article Snippet: C57BL/6J mice bred at NYU were injected intraperitoneally with either 200 μg rat anti-mouse Ly6G or rat IgG2a isotype control antibody to deplete neutrophils and 250 μg rat anti-mouse CD4 or rat IgG2a isotype control antibody to deplete CD4+ T cells (Bio-X-Cell, West Lebanon, NH, USA).

Techniques: Flow Cytometry, Saline, Isolation, Control

Journal: eLife

Article Title: Sex-dependent gastrointestinal colonization resistance to MRSA is microbiota and Th17 dependent

doi: 10.7554/eLife.101606

Figure Lengend Snippet: ( A ) MRSA colony forming units (CFU) in stool following oral inoculation of male or female mice that were irradiated and reconstituted with bone marrow (BM) from donor male or female mice. Female BM into female recipients (F→F) n=8, male BM into male recipients (M→M) n=7, female BM into male recipients (F→M) n=8. ( B ) MRSA CFU in stool following oral inoculation of ovariectomized female mice or sham operated littermate controls. Ovariectomized (OVX) n=10, sham n=10. ( C ) MRSA CFU in stool following oral inoculation of Esr1 +/- and Esr1 -/- female mice bred at NYU. Esr1 +/ - n = 6, Esr1 -/- n=6. ( D ) MRSA CFU in stool following oral inoculation of four core genotype mice. XX n=5, XY( -Sry ) n=5. XY n=5, XX( +Sry ) n=4. ( E ) CD4+ T cells from cecal-colonic lamina propria of XX females and XX( +Sry ) males 2 days post inoculation (dpi) inoculation with MRSA or mock control. ( F ) Percentage of IL-17A+CD4+ T cells in cecal-colonic lamina propria of XX females and XX(+ Sry ) males 2 dpi inoculation with MRSA or mock control. Data points represent mean ± SEM from at least two independent experiments. Statistical analysis: area under the curve followed by a one-way ANOVA with Sidak’s multiple comparisons for ( A , C ) and two-tailed t-test for ( B , F ) and two-way ANOVA+Sidak’s multiple comparisons test for ( D – E ). ns: not significant.

Article Snippet: C57BL/6J mice bred at NYU were injected intraperitoneally with either 200 μg rat anti-mouse Ly6G or rat IgG2a isotype control antibody to deplete neutrophils and 250 μg rat anti-mouse CD4 or rat IgG2a isotype control antibody to deplete CD4+ T cells (Bio-X-Cell, West Lebanon, NH, USA).

Techniques: Irradiation, Control, Two Tailed Test