Characterizing cell-cell interactions induced spatial organization of cell phenotypes: application to density-dependent protein nucleocytoplasmic distribution

Identification of cell-to-cell interactions by ligand-receptor pairs in human fetal heart

The heart is the first organ to form during embryogenesis and its development is a complex process. In this study, we identified 120 ligand-receptor pairs including 65 ligands and 58 receptors specifically expressed in one of the nine cell types. The correlation analysis of the cell proportions revealed that the cell-to-cell contact exhibited spatial patterns in human fetal heart. Specifically, the cardiomyocytes (CMs) proportion might have negative correlation with proportion of endothelial cell in left atrium and ventricle during the heart development. In contrast, fibroblast-like cells and macrophages were jointly increased with the gestation. Furthermore, the ligand in CM, NPPA (Natriuretic Peptide A), and receptor in endothelial cell (EC), NPR3 (Natriuretic Peptide Receptor 3), were specifically expressed in atrial CM and endocardial cells, respectively, indicating that the atrial CM might communicate with endocardial cells via NPPA-NRP3 interaction. Moreover, the interplay between fibroblast-like cell and macrophage was observed in both left and right atriums via the ligand-receptor interactions of COL1A1/COL1A2 (Collagen Type I Alpha 1/2 Chain)-CD36 and CTGF (connective tissue growth factor)-ITGB2 (Integrin Subunit Beta 2). Functional enrichment analysis revealed that the ligand-receptor interactions might be associated with the intracellular activation of cGMP-PKG signaling pathway in ECs, PDGF-beta signaling pathway in fibroblast-like cell, and Toll-like receptor signaling in macrophage, respectively. Collectively, the present study unveiled the potential cell-cell communication and underlying mechanism involved in cardiac development, which broadened our insights into developmental biology of heart.

Association between NF-κB Activation in Peripheral Blood Mononuclear Cells and Late Skin and Subcutaneous Fibrosis following Radiotherapy

Background

This study aimed at evaluating the association between the speed of nuclear factor-kappa B (NF-κB) activation in peripheral blood mononuclear cells (PBMCs) and late skin and subcutaneous fibrosis in patients with head and neck squamous cell carcinoma (HNSCC) after radiotherapy.

Methods

The speed of NF-κB activation was represented by the nuclear p65 expression ratio before and after irradiation. The optimal time point to measure the ratio was determined by Western blot in the PBMCs from healthy outpatients ranging from 0 to 12 hours after ex vivo irradiation. We recruited patients with HNSCC who had received ratiotherapy and who were under regular follow-up care. We assessed the association between the risk of developing ≥grade 2 late fibrosis and the nuclear p65 expression ratio in the PBMCs after ex vivo irradiation in these patients.

Results

The maximum nuclear p65 ratio was observed at 1 hour after ex vivo irradiation in the PBMCs from the healthy outpatients. The speed of NF-κB activation was then represented by the nuclear p65 ratio in the PBMCs before and 1 hour after ex vivo irradiation. A total of 200 patients with HNSCC were recruited, 32.50% (n = 65) of which presented with ≥grade 2 late fibrosis. There was a significant association between the speed of NF-κB activation in the PBMCs and an increased risk of developing ≥grade 2 late fibrosis in these patients (P = 0.004). Subgroup analysis suggested that this finding was independent of the known clinical characteristics.

Conclusions

The speed of NF-κB activation might be a potential predictor of late toxicity in cancer patients after radiotherapy. Prospective studies are needed for validation.

Cell Type Classification and Unsupervised Morphological Phenotyping From Low-Resolution Images Using Deep Learning

Convolutional neural networks (ConvNets) have proven to be successful in both the classification and semantic segmentation of cell images. Here we establish a method for cell type classification utilizing images taken with a benchtop microscope directly from cell culture flasks, eliminating the need for a dedicated imaging platform. Significant flask-to-flask morphological heterogeneity was discovered and overcome to support network generalization to novel data. Cell density was found to be a prominent source of heterogeneity even when cells are not in contact. For the same cell types, expert classification was poor for single-cell images and better for multi-cell images, suggesting experts rely on the identification of characteristic phenotypes within subsets of each population. We also introduce Self-Label Clustering (SLC), an unsupervised clustering method relying on feature extraction from the hidden layers of a ConvNet, capable of cellular morphological phenotyping. This clustering approach is able to identify distinct morphological phenotypes within a cell type, some of which are observed to be cell density dependent. Finally, our cell classification algorithm was able to accurately identify cells in mixed populations, showing that ConvNet cell type classification can be a label-free alternative to traditional cell sorting and identification.

Intensity calibration and flat-field correction for fluorescence microscopes

Standardization in fluorescence microscopy involves calibration of intensity in reproducible units and correction for spatial nonuniformity of illumination (flat-field or shading correction). Both goals can be achieved using concentrated solutions of fluorescent dyes. When a drop of a highly concentrated fluorescent dye is placed between a slide and a coverslip it produces a spatially uniform field, resistant to photobleaching and with reproducible quantum yield; it can be used as a brightness standard for wide-field and confocal microscopes. For wide-field microscopes, calibration can be further extended to absolute molecular units. This can be done by imaging a solution of known concentration and known depth; the latter can be prepared by placing a small spherical lens in a diluted solution of the same fluorophore that is used in the biological specimen.