primary cd3 cd56 nk cells  (Miltenyi Biotec)

Journal: iScience

Article Title: SpaHE-Infil: A spatial heterogeneity framework for decoding TME infiltration from H&E-stained slides

doi: 10.1016/j.isci.2026.115155

Figure Lengend Snippet: Microscopy-optimized spatial reconstruction with mIHC benchmarking (A) Algorithm validation and optimization using colon cancer H&E sections. Scale bars, 100 μm. (B and C) Enhanced immune cell detection sensitivity after TME_ADJ calibration. (D) Reproducibility of sensitivity improvement in pancreatic cancer. Scale bars, 100 μm. (E and F) Spatial signals of tumor and microenvironmental cells identified by the algorithm. (G) Immunomarker expression detected by mIHC on consecutive sections. Scale bars, 100 μm. (H) mIHC signal distribution. Each dot represents a cell, colored by its mIHC marker (DAPI: gray; CD8: red; CD68: green; Vimentin: cyan; Vimentin: yellow; CD56: purple) and signal intensity (gradient: 2×10 4 to 10×10 4 ), showing spatial heterogeneity of marker expression across the tissue section. (I) Cell type proportion comparison. Bar chart showing relative proportions of NK cells, macrophages, CD8 + T cells, fibroblasts, and tumor cells, quantified by SpaHE-Infil and validated by mIHC, demonstrating consistency between computational inference and experimental staining. (J and K) Spatial signals in ovarian cancer H&E sections. Scale bars, 100 μm. (L and M) Spatial signals in gastric cancer H&E sections. Scale bars, 100 μm.

Article Snippet: CD56 primary antibody , Cell Signaling Technology , #99746; RRID: AB_2868490.

Techniques: Microscopy, Biomarker Discovery, Expressing, Marker, Comparison, Staining

Journal: iScience

Article Title: Epigenetic control of myogenic identity of human muscle stem cells in Duchenne muscular dystrophy

doi: 10.1016/j.isci.2024.111350

Figure Lengend Snippet: In vitro behavior of DMD-MuSCs (A–C) CD56 pos MuSCs isolated from healthy control (HC) and Duchenne (DMD) muscles were analyzed for their capacity to implement in vitro myogenesis. (A) Proliferation was assessed in growth medium (GM) as the number of EdU pos cells (red). (B) Differentiation was quantified after 5 days in differentiation medium (DM) as the number of myogenin pos cells (green) among desmin pos cells (red). (C) Fusion index was quantified in differentiated cells grown at high density, as the number of nuclei in desmin expressing myotubes (red) related to the total number of nuclei. Hoechst labels nuclei (blue). Bar: 100 μm. (D) Expression of CD56 was evaluated by flow cytometry during the culture of initially pure CD56 pos HC- and DMD-MuSCs in growth medium. (E) Calculation of the loss of CD56 per cell division from (D). (F) Experimental procedure of the clonal culture of Myf5-transduced CD56 pos MuSCs. (G) Immunostaining of clones for CD56 (red), GFP(Myf5) (green) and TCF7L2 (cyan). Hoechst labels nuclei (blue). Red arrowheads show myogenic CD56 pos Myf5 pos cells, blue arrowheads show fibrogenic TCF7L2 pos cells and yellow arrowheads show cells harboring both myogenic and fibrogenic markers. Bar: 50 μm. (H) Quantification of cells according to the immunostaining shown in (G). Each shape symbol represents one clone. Results are means ± SEM of 3–9 samples in (A–E) and of 6 clones issued from 3 HC donors and of 5 clones issued from 3 DMD donors in (H). ns: non significant, ∗ p < 0.05 using unpaired (A–E) or paired (H) t test.

Article Snippet: CD56 primary antibody , Miltenyi , #130-050-401 RRID: AB_3076236.

Techniques: In Vitro, Isolation, Control, Muscles, Expressing, Flow Cytometry, Immunostaining, Clone Assay

Journal: iScience

Article Title: Epigenetic control of myogenic identity of human muscle stem cells in Duchenne muscular dystrophy

doi: 10.1016/j.isci.2024.111350

Figure Lengend Snippet: Gene expression in CD56 pos and CD56 neg cells from HC- and DMD-MuSC cultures (A) Experimental procedure for CD56 pos and CD56 neg cell purification originating from pure healthy control (HC)- and Duchenne (DMD) CD56 pos population. Cells were cultured in growth medium. (B and C) Normalized relative quantity (NRQ) expression by CD56 pos and CD56 neg cells from HC- and DMD-samples evaluated by RT-qPCR of (B) the myogenic related genes PAX7 , ACTA1 , MYF5 , and MYOD and (C) the fibrogenic related genes COL1A1 , CTGF , LOX , and SPP1 . Results are means ± SEM of 3–6 samples. Each shape symbol represents cells issued from one initial culture. (D) Gene ontology ( DAVID software) of differentially expressed genes (DEG) after microarray analysis of CD56 pos and CD56 neg cell s issues from healthy control (HC)- and Duchenne (DMD) CD56 pos MuSC cultures. (E) Microarray fold change of the 11 genes found down expressed in both HC-CD56 neg vs. HC-CD56 pos and DMD-CD56 pos vs. HC-CD56 pos cells. (F) NRQ expression by RT-qPCR of CBX3 , H2AZ2 , H3F3B , and SMC3 genes in HC- and DMD-CD56 pos cells. Results from 3 HC and 3 DMD samples. Each shape symbol represents the same culture. ∗ p < 0.05, ∗∗ p < 0.001 using paired t test.

Article Snippet: CD56 primary antibody , Miltenyi , #130-050-401 RRID: AB_3076236.

Techniques: Gene Expression, Purification, Control, Cell Culture, Expressing, Quantitative RT-PCR, Software, Microarray

Journal: iScience

Article Title: Epigenetic control of myogenic identity of human muscle stem cells in Duchenne muscular dystrophy

doi: 10.1016/j.isci.2024.111350

Figure Lengend Snippet: Transduction of DMD-CD56 pos cells with CBX3, H2AZ2, H3F3B, and SMC3 coding lentiviruses (A) Experimental procedure for DMD-CD56 pos cell transduction with lentiviruses. Cells were cultured in growth medium. (B) Flow cytometry quantification of the number of CD56 pos cells in each condition. Results are from 4 to 5 DMD samples. Results are means ± SEM of 3 DMD samples (each shape symbol is used for cells issued from the same initial culture). ∗ p < 0.05, ∗∗ p < 0.001 using paired t test. (C) Experimental design of ATAC-seq analysis of DMD-CD56 pos and DMD-CD56 neg cells initially non-transduced (day0-CD56 pos ) or transduced with either empty (empty-CD56 pos/neg ) or CBX3, H2AZ2, H3F3B, and SMC3 lentiviruses together (4V-CD56 pos/neg ). (D) UpSet plot of the comparison between the samples to identify genes differentially expressed in cells transduced with the 4 epigenetic regulators and non-transduced (red arrows) versus the 3 other conditions (red rectangle). (E) Expression by RT-qPCR of the MEF2B gene in DMD-CD56 pos cells transduced with CBX3 , H2AZ2 , H3F3B , and/or SMC3 lentiviruses. (F) Screenshot of MEF2B locus. From top to bottom: chromosome scale, gene and regulatory sequences, ATAC-seq tracks in CD56 pos DMD-MuSCs initially non-transduced (red), DMD-CD56 pos (blue) and DMD-CD56 neg (brown) cells from CD56 pos DMD-MuSCs initially transduced with an empty vector, and DMD-CD56 pos cells from CD56 pos DMD-MuSCs initially transduced with the 4 epigenetic regulators (green). Results are means ± SEM of 4 samples.

Article Snippet: CD56 primary antibody , Miltenyi , #130-050-401 RRID: AB_3076236.

Techniques: Transduction, Cell Culture, Flow Cytometry, Comparison, Expressing, Quantitative RT-PCR, Plasmid Preparation

Journal: iScience

Article Title: Epigenetic control of myogenic identity of human muscle stem cells in Duchenne muscular dystrophy

doi: 10.1016/j.isci.2024.111350

Figure Lengend Snippet: MEF2B and the maintenance of MuSC myogenicity (A) Normalized relative quantity (NRQ) expression of MEF2B promoter and enhancer sequences by RT-qPCR after Cut&Tag library preparation with transduced DMD-CD56 pos cells using anti-HA antibodies to target the 4 epigenetic regulators. Dotted lines correspond to the expression after using control IgGs. (B) Loss of function experiments where HC-CD56 pos were transduced with shRNA MEF2B lentiviruses (and shLuciferase as a control) and were analyzed for their CD56 expression by flow cytometry (far left) in growing medium, their expression of myogenin (left), the number of cells expressing MHC (right) and the fusion index (far right) after cultured in differentiation medium. Representative pictures of 2 cultures are shown for myogenin expression (green) and MHC expression (red) (blue = Hoechst). (C) Gain of function experiments where DMD-CD56 pos cells were transduced with a lentivirus encoding for MEF2B and were analyzed for their CD56 expression by flow cytometry (left panel) in growing medium and for their myogenic capacity, assessed by their fusion index when cultured in differentiation medium. Representative pictures are shown for desmin (red) (blue = Hoechst). Data are shown for 4 DMD donors. ∗ p < 0.05, using paired t test. Data are means ± SEM of 3 experiments. Each shape symbol represents the same culture. ∗ p < 0.05 using paired t test. Bars: 100 μm.

Article Snippet: CD56 primary antibody , Miltenyi , #130-050-401 RRID: AB_3076236.

Techniques: Expressing, Quantitative RT-PCR, Control, Transduction, shRNA, Flow Cytometry, Cell Culture

Journal: iScience

Article Title: Epigenetic control of myogenic identity of human muscle stem cells in Duchenne muscular dystrophy

doi: 10.1016/j.isci.2024.111350

Figure Lengend Snippet:

Article Snippet: CD56 primary antibody , Miltenyi , #130-050-401 RRID: AB_3076236.

Techniques: Control, Recombinant, Magnetic Beads, Reverse Transcription, Imaging, TUNEL Assay, PCR Cloning, SYBR Green Assay, Purification, Plasmid Preparation, Software