Fig 2: Heterogeneity of RCC biomarkers on cells in circulation. Flow cytometric evaluation of the frequency of expression of different biomarkers on CTCs from n = 3 different patients (A, B, or C). The first row of pie graphs represents the distribution of CK-positive CTCs (gray) vs. CK-negative / exclusion channel negative cells (purple). The second row of Euler diagrams portrays the frequency of expression of other markers of renal cancer origin (CAIX, CAXII, and EpCAM) within the CK-positive vs. CK-negative / exclusion negative cell fractions. Overlapping circles indicate the co-expression of different biomarkers on the same cells. Subpopulation frequencies are rounded to the nearest whole percent, with percentages < 0.5% excluded. Exact percentages are provided in Supplementary Table 2.

Fig 3: Binding of the two selected anti-human EpCAM antibodies (SB EpCAM, R&D EpCAM) to human breast carcinoma cell lines, MCF-7 and MDA-MB-231, by flow cytometry. Representative frequency distribution curves of logarithmic fluorescent intensity for each cell line are shown (n = 3 independent experiments) (EpCAM antibodies: pink solid curves; rabbit serum or goat gamma globulin controls: gray solid curves with dotted line).

Fig 4: Decreased biliary differentiation and increased fibrosis of biliary atresia (BA) patient iPSCs. A, A schematic diagram of 2D and 3D biliary differentiation procedure. B, C, In a 3D culture, ductal cells from all BA patient induced pluripotent stem cells (iPSCs) formed significantly decreased amount of ductal cysts/tubes at d20 post-differentiation (n = 5, **P < 0.01). Representative data are shown with iBA1, iBA3, and iBA5. D, E, Flow cytometry (FACS)-based protein analysis after 2D ductal differentiation at d20. Compared to controls, all BA patient iPSCs showed decreased CK7, CK19, and EpCAM (cholangiocyte markers) positive cells and increased alpha smooth muscle actin (SMA) (a fibrosis marker) positive cells. Representative data are shown with iBA3, iBA5, and iBA8. E, FACS based quantification of CK7, CK19, EpCAM protein positive, or SMA protein positive cell populations in biliary differentiation culture. BAs represent data obtained from multiple BA iPSCs (n = 5, *P < 0.05). F, Secretin stimulated cholangiocyte functional assays showed increased cAMP in control iPSC-derived cholangiocytes but it was significantly lower in the cholangiocytes derived from patient iPSCs (*P < 0.05). G, Immunofluorescence based protein analysis of CK7 (green), and another fibrosis marker collagen type 1 (Col1, red). Compared to controls, all BA patient iPSCs expressed lower CK7 protein and higher Col1 protein after biliary differentiation. H, Quantitative real time RT-PCR analysis of biliary and fibrosis markers in multiple BA patient iPSCs after biliary differentiation. Compared to controls, all BA iPSC lines express lower biliary markers and higher fibrosis markers after biliary differentiation. *P < 0.05, **P < 0.01. Controls reflect the combined results were from the combination of all control cell lines listed in Table 1 and iBAs represent the combined results from all BA iPSC lines including iBA1, 3, 5, 6, and 8.

Fig 5: Single-Cell Proteomic Analysis of Cellular Subpopulations in EME6/7t EECs and Primary Tumors(A and B) tSNE plots of mass cytometry (CyTOF) analysis visualizing 74,048 epithelial cells, which were divided into clusters (n = 27) based on their proteomic profiles (A). These cells included immortalized EEC line EME6/7t (exposed to ASC-CM ± Tip) and primary endometrial tumors of patients with known BMIs (B).(C) tSNE-based phenographs showing abundance and cellular distributions of JAC proteins.(D) tSNE-based phenographs showing EpCAM and CK8/18 as epithelial cell markers and TGFR-2, SMAD2, and SMAD4 as TGF-ß factors.See also Figure S6 and Tables S2 and S3.