Journal: Nature Biotechnology

Article Title: Deep Visual Proteomics defines single-cell identity and heterogeneity

doi: 10.1038/s41587-022-01302-5

Figure Lengend Snippet: a , AI-driven nucleus and cytoplasm segmentation of normal-appearing and cancer cells and tissue using BIAS. b , We benchmarked the accuracy of its segmentation approach using the F1 metric and compared results to three additional methods—M 1 is unet4nuclei , M 2 is CellProfiler and M is Cellpose —while OUR refers to nucleAIzer . Bars show mean F1 scores with s.e.m.; n = 10 independent images for melanoma tissue and (U2OS) cells, and n = 20 for salivary gland tissue. Visual representation of the segmentation results: green areas correspond to true positive, blue to false positive and red to false negative. c , BIAS serves as the interface between the scanning and an LMD microscope, allowing high-accuracy transfers of cell contours between the microscopes. Illustration of cutting offset with respect to the object of interest and optimal path finding. d , Practical illustration of the functions in the upper panel. e , Immunofluorescence staining of the human fallopian tube epithelium with FOXJ1 and EpCAM antibodies, detecting ciliated and epithelial cells, respectively. Left panel: Ciliated (FOXJ1-positive) and secretory (FOXJ1-negative) cells. Right panel: Cell classification based on FOXJ1 intensity. Class 1 (FOXJ1-positive) and class 2 (FOXJ1-negative); magnification factor = ×387. f , PCA of FOXJ1-positive and FOXJ1-negative cell proteomes. g , Heat map of known protein markers for secretory and ciliated cells. Protein levels are z-scored. Asterisks represent imputed data. The marker list was derived from the Human Protein Atlas project and based on literature mining. h , Volcano plot of the pairwise proteomic comparison between FOXJ1-positive and FOXJ1-negative cells. Cell-type-specific marker proteins are highlighted in green and turquoise, and black represents potential novel marker proteins. Significant enriched cell-type-specific proteins are displayed above the black lines (two-sided t -test, FDR < 0.05, s 0 = 0.1, n = 4 biological replicates).

Article Snippet: Primary antibodies targeting FOXJ1 (mouse, dilution 1:200, 14-9965-80, Invitrogen) and EpCAM (rabbit, dilution 1:200, 14452, Cell Signaling Technology) were diluted in 10% goat serum and incubated overnight at 4 °C in a humidified chamber.

Techniques: Microscopy, Immunofluorescence, Staining, Marker, Derivative Assay

Journal: British Journal of Cancer

Article Title: Fibroblast activation protein identifies Consensus Molecular Subtype 4 in colorectal cancer and allows its detection by 68 Ga-FAPI-PET imaging

doi: 10.1038/s41416-022-01748-z

Figure Lengend Snippet: a Dot plot showing relative FAP expression levels in primary CRC tumours in the TCGA cohort ( n = 592) versus primary tumours with peritoneal involvement ( n = 35) and the peritoneal metastases derived from them ( n = 59). b Dot plot showing FAP expression levels in peritoneal metastases and their matched primary tumours. CMS subtypes are colour-coded. Tissue type is annotated by shape. c Scatter plot showing the correlation of FAP mRNA levels with CMS4 probabilities of all tumours in the primary tumour/peritoneal metastasis cohort. d Immunohistochemistry for FAP expression in peritoneal metastasis. See Supplementary Fig. for a comprehensive overview of FAP protein expression in peritoneal metastases. e Boxplot of FAP expression quantification on IHC slides of colorectal liver metastasis (CRLM, n = 21) and peritoneal metastasis (PM, n = 19). FAP expression is measured as the number of FAP-positive cells and corrected for tumour size using an EpCAM staining of the sequential slide. f Boxplot of the percentage of FAP-positive stromal cells of colorectal liver metastasis (CRLM, n = 21) and peritoneal metastasis (PM, n = 19). g Boxplot of the percentage of FAP-positive tumour cells of colorectal liver metastasis (CRLM, n = 21) and peritoneal metastasis (PM, n = 19).

Article Snippet: Sections were incubated overnight at 4 C with one of the following primary antibodies: anti-FAP (ab207178 Abcam, dilution 1:400), anti-EpCAM (CS 14452 Cell Signaling, dilution 1:200), anti-ZEB1 (HPA027524 Sigma, 1:500) or anti-HTR2B (HPA012867 Sigma, 1:75).

Techniques: Expressing, Derivative Assay, Immunohistochemistry, Staining

Journal: British Journal of Cancer

Article Title: Fibroblast activation protein identifies Consensus Molecular Subtype 4 in colorectal cancer and allows its detection by 68 Ga-FAPI-PET imaging

doi: 10.1038/s41416-022-01748-z

Figure Lengend Snippet: a Immunohistochemistry for FAP on peritoneal metastases tissue that was resected one year prior to FAPI-PET imaging. b Immunohistochemistry of EpCAM-positive tumour cells in the peritoneum show a strong ZEB1 and HTR2B staining. c FAPI-PET image shows tracer accumulation in pelvic peritoneal depositions and along the abdominal peritoneal lining (white arrows). See also Supplementary Fig. . d FAPI-PET image (same coronal section, same scaling)) after 2 months of chemotherapy shows a reduction of FAPI tracer uptake in the pelvic lesion and the serosal lesion and a complete loss of diffuse FAPI tracer uptake along the peritoneum.

Article Snippet: Sections were incubated overnight at 4 C with one of the following primary antibodies: anti-FAP (ab207178 Abcam, dilution 1:400), anti-EpCAM (CS 14452 Cell Signaling, dilution 1:200), anti-ZEB1 (HPA027524 Sigma, 1:500) or anti-HTR2B (HPA012867 Sigma, 1:75).

Techniques: Immunohistochemistry, Imaging, Staining