Journal: Nature Communications

Article Title: Skin basal cell carcinomas assemble a pro-tumorigenic spatially organized and self-propagating Trem2+ myeloid niche

doi: 10.1038/s41467-023-37993-w

Figure Lengend Snippet: a CODEX study design for human BCCs. b BCC sample overview with the tumor labeled with Pan-Keratin (white) and CD31 (red). Cell fluoresce metadata for each marker was extracted and integrated with Seurat. c Feature plots of markers used to identify key populations. d Quantification of cell types in c . e Immune Swarm (IS), Upper Tumor (UT), and Lower Tumor (LT) in the CODEX sample. The tumor epithelium and epidermis labeled with Pan-Keratin (white), KI67 (yellow), CD3 (cyan), and HLA-DR (magenta). f Cell fluoresce metadata for each marker was extracted from each distinct neighborhood defined in e and integrated with Seurat. g Quantification of cell types by neighborhood region. h Quantification of the proliferative tumor by neighborhood region. i Representative images of CD3 + cells (cyan)/HLA-DR + cells (magenta) and FoxP3 + (red) cells/CD3 + (cyan) cells within neighborhood regions. Red arrows point to CD3 + FoxP3 + cells. j Cellular ratios between CD3 + cells and HLA-DR + cells globally and within the neighborhood regions. Chi-Square analysis ( X 2 = 23.04, p = 0.0008, two-tailed) show neighborhoods do not follow a normal distribution. Fisher Exact analysis (two-tailed) between the LT and UT for the HLA-DR + to CD3 + FoxP3 − ( p = 0.003) and CD3 + FoxP3 + to CD3 + FoxP3 − ratios indicate nonrandom associations. k Spatial localization and quantification of LY6D (yellow) clones within different regions of K14 + tumor epithelium (white). White dotted lines indicate LY6D + clones. l Spatial localization of HLA-DR + cells (magenta) relative to the proliferative Ki67 + (green) LY6D - tumor epithelium ( n = 4 independent tumors). Tumor is labeled with K14 (white), Ki67 (green), HLA-DR (magenta), and LY6D (yellow). Green arrows show KI67 + cells. Magenta arrows show HLA-DR + cells. Dotted yellow line indicates LY6D + region. Length of each scale bar is noted in figure. For d , g , h , j , k , n = 3 independent tumors. For b , e , f , i , representative data from a single biological replicate ( n = 3 biological replicates collected). Error bars represent mean +/− SD. p values unless specified otherwise were calculated using an unpaired, two-tailed t test. Source data are provided as a Source data file.

Article Snippet: The antibodies used from the Maxpar Human Mono/Macro Phenotyping Panel Kit (Fluidigm; 201317) were: CD19-142Nd, Cd11b-144Nd, CD7-147Sm, CD66-149Sm, CD36-152Sm, CD163-154Sm, CD11c-159Tb, CD14-160Gd, CD16-165Ho, CD38-167Er, CD206-168Er, CD33-169Tm, CD3-170Er, HLA-DR-174Yb.

Techniques: Labeling, Marker, Two Tailed Test, Clone Assay

Journal: Nature Communications

Article Title: Skin basal cell carcinomas assemble a pro-tumorigenic spatially organized and self-propagating Trem2+ myeloid niche

doi: 10.1038/s41467-023-37993-w

Figure Lengend Snippet: a Merged UMAP plot of scRNA-Seq data of HLA-DRA + cells ( n = 4 independent tumors). b Feature plots for CD207, ITGAM , CD68 , and TREM2 from the UMAP that is shown in a . c UMAP plot of scRNA-Seq data of HLA-DRA + cells from an individual sample. d Feature plots for CD207 , ITGAM , CD68 , and TREM2 from the UMAP that is shown in c . e CyTOF study design for examining human BCC tumor single-cell suspensions. f TSNE plot of the merged CD45 + cells from BCC samples. g Feature plots for the key CD3 + and HLA-DR + clusters within the CD45 + fraction. h Quantification of the proportions of CD3 + , HLA-DR + , and other cell types by sample. i Feature plots for CD11b, CD206, and TREM2 from the subset of HLA-DR + cells. j Quantification of the percentages of cells that are HLA-DR + CD11b + , HLA-DR + CD11b + TREM2 + , and HLA-DR + CD11b + TREM2 + Ki67 + . For f , h , i , j , n = 13 independent tumors. Source data are provided as a Source data file.

Article Snippet: The antibodies used from the Maxpar Human Mono/Macro Phenotyping Panel Kit (Fluidigm; 201317) were: CD19-142Nd, Cd11b-144Nd, CD7-147Sm, CD66-149Sm, CD36-152Sm, CD163-154Sm, CD11c-159Tb, CD14-160Gd, CD16-165Ho, CD38-167Er, CD206-168Er, CD33-169Tm, CD3-170Er, HLA-DR-174Yb.

Techniques:

Journal: Nature Communications

Article Title: Skin basal cell carcinomas assemble a pro-tumorigenic spatially organized and self-propagating Trem2+ myeloid niche

doi: 10.1038/s41467-023-37993-w

Figure Lengend Snippet: a Sorting strategies for RFP + and RFP − cells and downstream allograft and organoid models. b Tumor volumes from allografts ( n = 3 independent tumors). c Images of tumors from transplants in b . d Representative images of organoid experiments. e Diagram of Cd11b + and Cd11c + column depletion strategies. f Flow cytometry analysis confirming depletion of Cd11b + and Cd11c + from tumor fractions before transplanting. g Tumor volumes from transplants into NOD SCID mice of control, Cd11b-depleted, and Cd11c-depleted tumor fractions ( n = 4 independent tumors from 4 mice). h Trem2 neutralization strategies to target SCAMs in actively growing tumors. i Tumor volumes after Trem2 neutralizations ( n = 5 independent tumors from 5 mice). j RNAScope analysis of Trem2 (green), Vcam1 (magenta), and K14-protein (white) in allografted tumors from mice treated with anti-IgG or anti-Trem2 antibodies. Boxes are indicating Trem2 + and/or Vcam1 + cells with two examples further zoomed in showing only the Trem2 signal. k Quantification of the Trem2/Vcam1 signal in cells in allografted tumors from mice treated with anti-IgG or anti-Trem2 antibodies. l Average number of Trem2 + and/or Vcam1 + cells in allografted tumors from mice treated with anti-IgG or anti-Trem2 antibodies. m PDO treatment strategies with anti-TREM2 and aPD1. n Flow cytometry analysis showing the levels of Apotracker Green in the EPCAM + cells. o Fold change in ApoGreen percentage between anti-IgG and anti-TREM2 treated PDOs ( n = 4 independent tumors). p Flow cytometry analysis of TREM2 on TREM2 + cells from Patient 1 and Patient 3. q Sorting strategies for SCAMs, Ly6d − , and Ly6d + cells for organoid models. r The number of organoids from control and then experimental combinations of the Ly6d - or Ly6d + tumor epithelial fractions with or without SCAMs ( n = 3 independent sorts/cultures from 3 independent tumors). s Represented images of organoids. Length of each scale bar is noted in figure. For k , l , n = 2 independent tumors. Error bars represent mean +/− SD. p values were calculated using paired, two-tailed t test. Source data are provided as a Source data file.

Article Snippet: The antibodies used from the Maxpar Human Mono/Macro Phenotyping Panel Kit (Fluidigm; 201317) were: CD19-142Nd, Cd11b-144Nd, CD7-147Sm, CD66-149Sm, CD36-152Sm, CD163-154Sm, CD11c-159Tb, CD14-160Gd, CD16-165Ho, CD38-167Er, CD206-168Er, CD33-169Tm, CD3-170Er, HLA-DR-174Yb.

Techniques: Flow Cytometry, Control, Neutralization, RNAscope, Two Tailed Test

Journal: Nature Communications

Article Title: Skin basal cell carcinomas assemble a pro-tumorigenic spatially organized and self-propagating Trem2+ myeloid niche

doi: 10.1038/s41467-023-37993-w

Figure Lengend Snippet: a CODEX study design for human BCCs. b BCC sample overview with the tumor labeled with Pan-Keratin (white) and CD31 (red). Cell fluoresce metadata for each marker was extracted and integrated with Seurat. c Feature plots of markers used to identify key populations. d Quantification of cell types in c . e Immune Swarm (IS), Upper Tumor (UT), and Lower Tumor (LT) in the CODEX sample. The tumor epithelium and epidermis labeled with Pan-Keratin (white), KI67 (yellow), CD3 (cyan), and HLA-DR (magenta). f Cell fluoresce metadata for each marker was extracted from each distinct neighborhood defined in e and integrated with Seurat. g Quantification of cell types by neighborhood region. h Quantification of the proliferative tumor by neighborhood region. i Representative images of CD3 + cells (cyan)/HLA-DR + cells (magenta) and FoxP3 + (red) cells/CD3 + (cyan) cells within neighborhood regions. Red arrows point to CD3 + FoxP3 + cells. j Cellular ratios between CD3 + cells and HLA-DR + cells globally and within the neighborhood regions. Chi-Square analysis ( X 2 = 23.04, p = 0.0008, two-tailed) show neighborhoods do not follow a normal distribution. Fisher Exact analysis (two-tailed) between the LT and UT for the HLA-DR + to CD3 + FoxP3 − ( p = 0.003) and CD3 + FoxP3 + to CD3 + FoxP3 − ratios indicate nonrandom associations. k Spatial localization and quantification of LY6D (yellow) clones within different regions of K14 + tumor epithelium (white). White dotted lines indicate LY6D + clones. l Spatial localization of HLA-DR + cells (magenta) relative to the proliferative Ki67 + (green) LY6D - tumor epithelium ( n = 4 independent tumors). Tumor is labeled with K14 (white), Ki67 (green), HLA-DR (magenta), and LY6D (yellow). Green arrows show KI67 + cells. Magenta arrows show HLA-DR + cells. Dotted yellow line indicates LY6D + region. Length of each scale bar is noted in figure. For d , g , h , j , k , n = 3 independent tumors. For b , e , f , i , representative data from a single biological replicate ( n = 3 biological replicates collected). Error bars represent mean +/− SD. p values unless specified otherwise were calculated using an unpaired, two-tailed t test. Source data are provided as a Source data file.

Article Snippet: The antibodies used from the Maxpar Human Mono/Macro Phenotyping Panel Kit (Fluidigm; 201317) were: CD19-142Nd, Cd11b-144Nd, CD7-147Sm, CD66-149Sm, CD36-152Sm, CD163-154Sm, CD11c-159Tb, CD14-160Gd, CD16-165Ho, CD38-167Er, CD206-168Er, CD33-169Tm, CD3-170Er, HLA-DR-174Yb.

Techniques: Labeling, Marker, Two Tailed Test, Clone Assay

Journal: Nature Communications

Article Title: Skin basal cell carcinomas assemble a pro-tumorigenic spatially organized and self-propagating Trem2+ myeloid niche

doi: 10.1038/s41467-023-37993-w

Figure Lengend Snippet: a Merged UMAP plot of scRNA-Seq data of HLA-DRA + cells ( n = 4 independent tumors). b Feature plots for CD207, ITGAM , CD68 , and TREM2 from the UMAP that is shown in a . c UMAP plot of scRNA-Seq data of HLA-DRA + cells from an individual sample. d Feature plots for CD207 , ITGAM , CD68 , and TREM2 from the UMAP that is shown in c . e CyTOF study design for examining human BCC tumor single-cell suspensions. f TSNE plot of the merged CD45 + cells from BCC samples. g Feature plots for the key CD3 + and HLA-DR + clusters within the CD45 + fraction. h Quantification of the proportions of CD3 + , HLA-DR + , and other cell types by sample. i Feature plots for CD11b, CD206, and TREM2 from the subset of HLA-DR + cells. j Quantification of the percentages of cells that are HLA-DR + CD11b + , HLA-DR + CD11b + TREM2 + , and HLA-DR + CD11b + TREM2 + Ki67 + . For f , h , i , j , n = 13 independent tumors. Source data are provided as a Source data file.

Article Snippet: The antibodies used from the Maxpar Human Mono/Macro Phenotyping Panel Kit (Fluidigm; 201317) were: CD19-142Nd, Cd11b-144Nd, CD7-147Sm, CD66-149Sm, CD36-152Sm, CD163-154Sm, CD11c-159Tb, CD14-160Gd, CD16-165Ho, CD38-167Er, CD206-168Er, CD33-169Tm, CD3-170Er, HLA-DR-174Yb.

Techniques: