Fig 1.
The morphological spectrum of different cell types (representative example using HE staining of a human colon).
Regions of interest with different cell types are highlighted with coloured boxes, i.e., inflammatory cells (lymphocytes, macrophages, eosinophils, neutrophils, and plasma cells), epithelial cells (here, an enterocyte forming the cellular unit of crypts), endothelium, and stromal fibroblasts. Prominent cytoplasm (asterisk) in a representative macrophage. See Table 1 and section “The hematoxylin and eosin (HE) stain” for further description. Overview scanned on a Hamamatsu Nanozoomer whole slide scanner (Hamamatsu Photonics, Hamamatsu, Japan), magnification: 40×; individual cell types captured on a Zeiss Axio Imager Z2 microscope platform (Carl Zeiss AG, Oberkochen, Germany), magnification: 63×. Arrow: Blood vessel lined with endothelial cells (grey box). Asterisks: Cytoplasm. Crosses: nucleus. Partly created with BioRender.com.
Table 1.
Cell types, their morphology (Fig 1), detection, and disease association.
CD, Cluster of Differentiation; HE, hematoxylin and eosin; MUM1, Multiple Myeloma Oncogene 1; SMA, smooth muscle antigen; TME, tumour microenvironment.
Fig 2.
The morphology of “cancer,” HE.
(A) Nonneoplastic epithelium (left) versus adenocarcinoma glands/cells (right, separated by dotted line) in a The Cancer Genome Atlas (TCGA) sample of colorectal adenocarcinoma (COAD, TCGA-A6-2678). Dashed inset (corresponding to the dashed rectangle): Higher magnification showing malignant COAD glands with malignant nuclear features and a focus of “dirty” necrosis within the cancer gland (asterisk). Insets: On the one hand, enterocytes (e, colonic epithelium) with regular contours, polarised towards the lumen with a goblet (mucus-containing) cell (G) on top. On the other hand, cancer cell (c) with a prominent nucleolus (cross), large size and irregular contours. Arrow: Regular colonic crypts, rich in goblet cells (arrow on goblet cell). Arrowhead: High-grade dysplasia at the surface mucosa. (B) Tumour parenchyma (red) and tumour stroma (blue, green) in pancreatic adenocarcinoma (PAAD, TCGA-2J-AAB6). PAAD glands are surrounded by dense “desmoplasia” (blue, inset) with pinkish collagen deposition (black arrowhead) and immune cell infiltrate (green, inset), mainly lymphocytes (white arrowheads) among microvessels (arrows). (C) Phenotype of invasion. From left to right: Invasive breast cancer (BRCA) clusters (BRCA, TCGA-3C-AALJ), prostatic adenocarcinoma (PRAD, TCGA-EJ-7792) glands with loss of basal cell layer (arrows: benign prostatic parenchyma), invasive squamous cell carcinoma of the cervix (CESC, TCGA-C5-A7XC) with adjacent high-grade squamous intraepithelial lesion (HSIL, white asterisk) and of the head and neck region (HNSC, TCGA-BA-4076). See Table 2 and section “The hematoxylin and eosin (HE) stain” for further description. Asterisks: Surface squamous epithelium, arrowheads: invasive SC. Crosses: Extracellular matrix/stroma between BRCA clusters.
Fig 3.
Example of computational modelling of an oncologic precursor lesion (low-grade dysplasia (LGD), human colon) with feature extraction.
(A) Conventional features of (sporadic) colonic LGD, i.e., hyperchromasia, next to normal colonic mucosa (separated by black line) with inconspicuous enterocytes and crypts (representative example of an inflammatory bowel disease cohort, HE stain). Arrows: Hyperchromatic, pseudostratified (pencillate) nuclei in LGD. (B) Nuclei detection, produced using a deep neural network [77]. Inset: High magnification. (C) Nuclei intensity mapping. Computed from the segmentation mask in B by normalising the nuclei intensities across the whole slide image. LGD shows higher intensities, histologically corresponding to hyperchromasia (darker staining in HE).
Table 2.
Features of epithelial tumours and strategies of incorporating them into modelling systems.
Fig 4.
Immunohistochemistry (IHC) and multiplexing.
(A) Singleplex IHC and tissue microarrays (TMAs). Left: Preserved nuclear expression of the mismatch repair protein MSH6 in a colorectal adenocarcinoma sample (asterisks). Arrow: Preserved expression in stromal fibroblasts. On the right, the principle of TMA construction: Tissue cores, usually 6 to 10 mm in diameter, are punched and transferred to a new FFPE block, which is composed of multiple patients and tissues. Inset: Overview of colorectal cancer tissue and illustrative punches. (B) Basic multiplex immunofluorescence (mIF) panel on colorectal mucosa consisting of 2 markers and DAPI (blue) as a standard nuclear stain. CD20 (light blue) labels B-cells and a lymphoid follicle (arrowheads). Beta-catenin stains colonic crypts (red, arrows). (C) Extended mIF panel with 6 markers and DAPI. Beta-catenin (red) highlights colorectal adenocarcinoma glands (asterisks), while the space between malignant glands is composed of immune cells, such as B-cells (CD20, light blue), and macrophages (CD68, green, black arrowheads). CD31 (orange) highlights blood vessels (grey arrowheads, intermixed with SMA, yellow) and might suggest vascular invasion. The stroma is represented by Vimentin (purple, grey arrowheads)-positive fibroblasts and smooth muscle (SMA, yellow. arrow). CD, Cluster of Differentiation; SMA, smooth muscle actin.
Table 3.
Representative markers for multiplexing panels (Fig 4).
ALK, anaplastic lymphoma kinase; AR, androgen receptor; ARID1A, AT-rich interactive domain-containing protein 1A; Bax, Bcl-2-associated X protein; CA, carboanhydrase; CD, Cluster of Differentiation; CK, cytokeratin; EGFR: Epidermal Growth Factor Receptor; ER, oestrogen receptor; ERG, ETS-Related Gene; FOXP3, forkhead box P3; GLUT1, glucose transporter member 1; INSM1, insulinoma-associated protein 1; LCA, leukocyte common antigen; LDH, lactate dehydrogenase; MCT, moncarboxylate transporter; mdm2, mouse double minute 2 homolog; MMR, mismatch repair; MEK, mitogen-activated protein kinase kinase enzyme; MPO, myeloperoxidase; MUM1 (IRF4), multiple myeloma 1 (interferon regulatory factor 4); PD-1/PD-L1, programmed death/ligand-1; PHH3, phospho-histone H3; PgR, progesterone receptor; PTEN, phosphatase and tensin homolog; Rb1, retinoblastoma protein; SMA, smooth muscle antigen; SOX10, SRY related HMG box 10.