Cell type census in normal colon and CRC. A UMAPs of epithelial, immune and stromal cells, separated by tissue of origin. Color code for cell type assignment. B Relative fractions of epithelial, immune and stromal cell types across all patient-derived libraries. For fractions per patient, see Supplementary Figure 3. C Single cell gene activities of stem cell marker OLFM4, proliferative marker MKI67, differentiated absorptive cell marker FABP1, and secretory cell marker TFF3. D Immunofluorescence analysis for OLFM4, MKI67, FABP1, and TFF3 in normal and tumor tissue. All sections are from patient P009, except the EPCAM/OLFM4 co-staining that was done on tumor tissue of P016. Scale bars indicate 100µm. E Relative fraction of TC1-5 in the tumor tissues of the patients. F Transcriptome-inferred cell-cycle distribution in the tumor cell fractions TC1-TC5 (bar graph), and in the UMAPs of normal and tumor epithelium.

Cell type census in normal colon and CRC. A UMAPs of epithelial, immune and stromal cells, separated by tissue of origin. Color code for cell type assignment. B Relative fractions of epithelial, immune and stromal cell types across all patient-derived libraries. For fractions per patient, see Supplementary Figure 3. C Single cell gene activities of stem cell marker OLFM4, proliferative marker MKI67, differentiated absorptive cell marker FABP1, and secretory cell marker TFF3. D Immunofluorescence analysis for OLFM4, MKI67, FABP1, and TFF3 in normal and tumor tissue. All sections are from patient P009, except the EPCAM/OLFM4 co-staining that was done on tumor tissue of P016. Scale bars indicate 100µm. E Relative fraction of TC1-5 in the tumor tissues of the patients. F Transcriptome-inferred cell-cycle distribution in the tumor cell fractions TC1-TC5 (bar graph), and in the UMAPs of normal and tumor epithelium.

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In colorectal cancer, oncogenic mutations transform a hierarchically organized and homeostatic epithelium into invasive cancer tissue lacking visible organization. We sought to identify differences in cellular composition between normal colon and colorectal cancer, and to define signals controlling cancer cell development. We used single cell RNA a...

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... type census in CRC versus normal colon We next clustered the single-cell profiles of the epithelial, immune and stromal compartments, and used cell-type-specific signatures and marker genes to annotate cell types 14 ( Fig. 2A; Supplementary . CC-BY-NC-ND 4.0 International license It is made available under a perpetuity. this preprint (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for . http://dx.doi.org/10.1101/2020.01.10.901579 doi: bioRxiv preprint first posted online ...
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... . CC-BY-NC-ND 4.0 International license It is made available under a perpetuity. this preprint (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for . http://dx.doi.org/10.1101/2020.01.10.901579 doi: bioRxiv preprint first posted online Jan. 11, 2020; Fig. 2 for genes over-or underrepresented between tumor and normal samples). In the normal epithelium, we identified a zone populated by profiles of undifferentiated cells with high activity of stem cell markers such as OLFM4 and transiently-amplifying proliferative markers. This region bordered on transcriptome clusters annotated as ...
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... activity of stem cell markers such as OLFM4 and transiently-amplifying proliferative markers. This region bordered on transcriptome clusters annotated as enterocyte progenitors, and, ultimately, mature absorptive enterocytes with high expression of markers such as KRT20 and FABP1. BEST4-and OTOP2-expressing enterocytes formed a discrete cluster ( Fig. 2A, identified by the lightest shade of green) 15 ...
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... the tumor samples, the zone of undifferentiated epithelial cells was expanded by five largely tumorspecific clusters (TC1-5, Fig We used immunofluorescence to verify the spatial distributions of epithelial cell types, using marker genes identified in the single-cell data (Fig. 2C, D). We detected the stem cell marker OLFM4 exclusively at the base of normal crypts. However, in tumor sections, OLFM4, as well as the proliferation marker MKI67, stained cells scattered throughout the epithelium, as validated by co-staining with the epithelial marker EPCAM. The goblet cell and enterocyte differentiation markers TFF3 and ...
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... five tumor-specific epithelial cell clusters TC1 to TC5 were represented in different proportions in all eight CRCs under investigation (Fig. 2E). TC1 and TC2 were assigned as highly stem cell-like using prior classifiers 14 , while TC3-4 showed the strongest similarity to transiently-amplifying cell types and TC5 shared similarity with both, transient-amplifying and stem cells. Transcriptome-based cell cycle analysis revealed that TC1 is highly proliferative (Fig. 2F). ...
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... under investigation (Fig. 2E). TC1 and TC2 were assigned as highly stem cell-like using prior classifiers 14 , while TC3-4 showed the strongest similarity to transiently-amplifying cell types and TC5 shared similarity with both, transient-amplifying and stem cells. Transcriptome-based cell cycle analysis revealed that TC1 is highly proliferative (Fig. 2F). Furthermore, TC clusters shared a couple of defining genes that have previously been linked to oncogenic processes in CRC (Supplementary Fig. ...
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... a perpetuity. this preprint (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for . http://dx.doi.org/10.1101/2020.01.10.901579 doi: bioRxiv preprint first posted online Jan. 11, 2020; We annotated immune transcriptome clusters by lineage-specific marker genes ( Fig. 2A, Supplementary Fig. 5). Two main clusters of myeloid cells were assigned as monocytes and macrophages by expression of CD14 and CD68. ITGAX (encoding CD11c) was also expressed in this domain of the UMAP, indicating that these clusters, in addition, also encompass dendritic cells. expressing ACTA2 and DES and pericytes marked by MCAM ...
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... the resulting integrated data set, organoid cell transcriptomes of the two patients and the different passage numbers intermingled (Fig. 5B). Next, we re-clustered the transcriptomes and assigned cell identities per cluster by matching cell types with the previous annotation ( Fig. 5C, D; for the previous annotation, see Fig. 2A, B). We found that profiles corresponding to TA cells, differentiated cells, and the tumor-specific TC1-TC5 cell types were present in the organoids. Stem cells, tuft cells and BEST4/OTOP2-positive enterocytes, which are all cell types that were present only in small numbers in the original primary tumor samples, were not called in any ...

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