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 CD8a, 1:500 , ThermoFisher scientific , Cat#14-0008-82; RRID: AB_2572848.

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 CD8a, 1:500 , ThermoFisher scientific , Cat#14-0008-82; RRID: AB_2572848.

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 CD8a, 1:500 , ThermoFisher scientific , Cat#14-0008-82; RRID: AB_2572848.

Techniques: Gene Expression

Journal: eLife

Article Title: JAK inhibition decreases the autoimmune burden in Down syndrome

doi: 10.7554/eLife.99323

Figure Lengend Snippet:

Article Snippet: Antibody , Mouse monoclonal anti-human CD8a (clone RPA-T8) , Fluidigm , Cat # 3162015; RRID: AB_2661802 , Lot 0171813, 1:100.

Techniques: Isolation, Biomarker Discovery, Staining, Antibody Labeling, Software, Sequencing

Journal: The Journal of Clinical Investigation

Article Title: Viral infection induces inflammatory signals that coordinate YAP regulation of dysplastic cells in lung alveoli

doi: 10.1172/JCI176828

Figure Lengend Snippet: ( A and B ) Illustration of IAV- and bleomycin-induced lung injury models. Sac, sacrifice. ( C and D ) Immunofluorescence staining for KRT5 and SCGB1A1 in IAV- and bleomycin-injured lungs. Data are representative of sections from 3 mice. Scale bars: 500 μm (top row); 50 μm (bottom row). ( E and F ) Immunofluorescence images of dysplastic cells (KRT5 + PDPN + ) and AT1 (PDPN + ) cells. Scale bars: 500 μm (top row); 50 μm (bottom row). ( G ) Quantification of percentages of KRT5 + lung areas in total damaged alveolar areas (PDPN – and KRT5 + ) in IAV- and bleomycin-injured lungs ( n ≥ 4 mice per group). ( H ) Krt5 expression was assayed by qRT-PCR in IAV- and bleomycin-injured lungs ( n = 3 mice per group). ( I and J ) PAS staining and quantification of goblet cells in IAV- and bleomycin-injured lungs ( n = 5 mice per group). Scale bar: 50 μm. ( K ) Inflammatory factor mRNA expression was assayed by qRT-PCR in IAV- and bleomycin-injured lungs at indicated time points ( n = 3 mice per group). ( L ) Flow cytometry analysis of immune cells from PBS-, repetitive bleomycin–, or IAV-treated lungs at indicated time points ( n = 4 mice per group). ( M ) Immunofluorescence staining for CD4, CD8a, F4/80, CCR2, or NK1.1 with KRT5 in IAV- and bleomycin-injured lungs at 14 dpi. Data are representative of sections from 3 mice. Scale bar: 50 μm. * P < 0.05; ** P < 0.01; *** P < 0.001. Error bars represent means ± SEM. Multiple t tests ( H , K , and L ); 2-tailed Mann-Whitney U test ( G and J ).

Article Snippet: The following primary antibodies were used at the indicated concentrations for immunofluorescence staining: goat anti-SCGB3A2 polyclonal antibody (5 μg/mL) (R&D Systems, AF3465), rat anti-ITGB4 monoclonal antibody (5 μg/mL) (BioLegend, 123615), rat anti-F4/80 monoclonal antibody (5 μg/mL) (BioLegend, 111603), rabbit anti-CCR2 monoclonal antibody (5 μg/mL) (Abcam, ab216863), rabbit anti-KRT5 polyclonal antibody (5 μg/mL) (BioLegend, 905504), chicken anti-KRT5 polyclonal antibody (5 μg/mL) (BioLegend, 905903), mouse anti-SCGB1A1 monoclonal antibody (5 μg/mL) (Santa Cruz Biotechnology Inc., sc-365992), rabbit anti-CCSP polyclonal antibody (5 μg/mL) (Seven Hills, WRAB-3950), mouse anti-FOXJ1 monoclonal antibody (5 μg/mL) (Invitrogen, 14-9965-82), hamster anti-PDPN monoclonal antibody (5 μg/mL) (Invitrogen, 14-5381-82), rat anti-CD4 monoclonal antibody (5 μg/mL) (BioLegend, 100427), rat anti-CD8a monoclonal antibody (5 μg/mL) (BioLegend, 100707), mouse anti-NK1.1 monoclonal antibody (5 μg/mL) (BioLegend, 108729), rabbit anti-DCAMKL1 polyclonal antibody (5 μg/mL) (Abcam, ab31704), rabbit anti-proSPC polyclonal antibody (5 μg/mL) (MilliporeSigma, AB3786), rabbit anti-phospho-Src(Tyr416) polyclonal antibody (5 μg/mL) (Cell Signaling Technology, 2101S), rabbit anti-YAP polyclonal antibody (5 μg/mL) (Cell Signaling Technology, 4912S), mouse anti-KI67 monoclonal antibody(5 μg/mL) (BioLegend, 151204), rabbit anti-KI67 monoclonal antibody (5 μg/mL) (Cell Signaling Technology, 9129S), mouse anti-P63 monoclonal antibody (5 μg/mL) (Abcam, ab735), mouse anti-KRT17 monoclonal antibody (5 μg/mL) (Santa Cruz Biotechnology Inc., sc-393002), rat anti-KRT8 polyclonal antibody (5 μg/mL) (DSHB, Troma-1), mouse anti-human HTII-280 (5 μg/mL) (Terrace Biotech, TB-27AHT2-280), and mouse anti-human CD8a monoclonal antibody (5 μg/mL) (Invitrogen, 12-0088-42).

Techniques: Immunofluorescence, Staining, Expressing, Quantitative RT-PCR, Flow Cytometry, MANN-WHITNEY

Journal: The Journal of Clinical Investigation

Article Title: Viral infection induces inflammatory signals that coordinate YAP regulation of dysplastic cells in lung alveoli

doi: 10.1172/JCI176828

Figure Lengend Snippet: ( A ) H&E staining and immunofluorescence staining for CD8a, p-SRC, YAP, and KRT5 on lung sections from COVID-19 patients. Scale bar: 50 μm. ( B ) Illustration of human AT2 organoid culture experiment. ( C – F ) Bright-field and immunofluorescence images of human AT2 organoids treated with PBS, IFN-γ, IFN-γ and Src inhibitor (dasatinib), or IFN-γ and FAK inhibitor (PF-573228). Scale bar: 25 μm. ( G – L ) Quantification of percentages of HTII-280–, SFTPC-, KRT8-, KRT17-, and KRT5-expressing organoids in total human AT2 organoids treated with PBS, IFN-γ, IFN-γ and Src inhibitor (dasatinib), or IFN-γ and FAK inhibitor (PF-573228) ( n = 3 technical replicates, experiment repeated twice). * P < 0.05; ** P < 0.01; *** P < 0.001. Error bars represent means ± SEM. One-way ANOVA ( G – L ).

Article Snippet: The following primary antibodies were used at the indicated concentrations for immunofluorescence staining: goat anti-SCGB3A2 polyclonal antibody (5 μg/mL) (R&D Systems, AF3465), rat anti-ITGB4 monoclonal antibody (5 μg/mL) (BioLegend, 123615), rat anti-F4/80 monoclonal antibody (5 μg/mL) (BioLegend, 111603), rabbit anti-CCR2 monoclonal antibody (5 μg/mL) (Abcam, ab216863), rabbit anti-KRT5 polyclonal antibody (5 μg/mL) (BioLegend, 905504), chicken anti-KRT5 polyclonal antibody (5 μg/mL) (BioLegend, 905903), mouse anti-SCGB1A1 monoclonal antibody (5 μg/mL) (Santa Cruz Biotechnology Inc., sc-365992), rabbit anti-CCSP polyclonal antibody (5 μg/mL) (Seven Hills, WRAB-3950), mouse anti-FOXJ1 monoclonal antibody (5 μg/mL) (Invitrogen, 14-9965-82), hamster anti-PDPN monoclonal antibody (5 μg/mL) (Invitrogen, 14-5381-82), rat anti-CD4 monoclonal antibody (5 μg/mL) (BioLegend, 100427), rat anti-CD8a monoclonal antibody (5 μg/mL) (BioLegend, 100707), mouse anti-NK1.1 monoclonal antibody (5 μg/mL) (BioLegend, 108729), rabbit anti-DCAMKL1 polyclonal antibody (5 μg/mL) (Abcam, ab31704), rabbit anti-proSPC polyclonal antibody (5 μg/mL) (MilliporeSigma, AB3786), rabbit anti-phospho-Src(Tyr416) polyclonal antibody (5 μg/mL) (Cell Signaling Technology, 2101S), rabbit anti-YAP polyclonal antibody (5 μg/mL) (Cell Signaling Technology, 4912S), mouse anti-KI67 monoclonal antibody(5 μg/mL) (BioLegend, 151204), rabbit anti-KI67 monoclonal antibody (5 μg/mL) (Cell Signaling Technology, 9129S), mouse anti-P63 monoclonal antibody (5 μg/mL) (Abcam, ab735), mouse anti-KRT17 monoclonal antibody (5 μg/mL) (Santa Cruz Biotechnology Inc., sc-393002), rat anti-KRT8 polyclonal antibody (5 μg/mL) (DSHB, Troma-1), mouse anti-human HTII-280 (5 μg/mL) (Terrace Biotech, TB-27AHT2-280), and mouse anti-human CD8a monoclonal antibody (5 μg/mL) (Invitrogen, 12-0088-42).

Techniques: Staining, Immunofluorescence, Expressing