Rotational 3D mechanogenomic Turing patterns of human colon Caco-2 cells during differentiation

Abstract

Recent reports suggest that actomyosin meshwork act in a mechanobiological manner alter cell/nucleus/tissue morphology, including human colon epithelial Caco-2 cancer cells that form polarized 2D epithelium or 3D sphere/tube when placed in different culture conditions. We observed the rotational motion of the nucleus in Caco-2 cells in vitro that appears to be driven by actomyosin network prior to the formation of a differentiated confluent epithelium. Caco-2 cell monolayer preparations demonstrated 2D patterns consistent with Allan Turing’s “gene morphogen” hypothesis based on live cell imaging analysis of apical tight junctions indicating the actomyosin meshwork. Caco-2 cells in 3D culture are frequently used as a model to study 3D epithelial morphogenesis involving symmetric and asymmetric cell divisions. Differentiation of Caco-2 cells in vitro demonstrated similarity to intestinal enterocyte differentiation along the human colon crypt axis. We observed rotational 3D patterns consistent with gene morphogens during Caco-2 cell differentiation. Single- to multi-cell ring/torus-shaped genomes were observed that were similar to complex fractal Turing patterns extending from a rotating torus centre in a spiral pattern consistent with gene morphogen motif. Rotational features of the epithelial cells may contribute to well-described differentiation from stem cells to the luminal colon epithelium along the crypt axis. This dataset may be useful to study the role of mechanobiological processes and the underlying molecular mechanisms as determinants of cellular and tissue architecture in space and time, which is the focal point of the 4D nucleome initiative.

Deep Learning in Pharmacogenomics: From Gene Regulation to Patient Stratification

“…13 Results from the 4D Nucleome program, funded by the U.S. National Institutes of Health, have led to the realization that significant molecular variation, which accounts for human differences in medication response and adverse events are likely based on the intricate organization of the spatial genome [18,56]. Spatial and temporal morphological changes in the nucleus and nucleoli are associated with the underlying reorganization of the chromatin architecture in 3D and 4D (time dimension added) [57,58].…”

3D Cell Nuclear Morphology: Microscopy Imaging Dataset and Voxel-Based Morphometry Classification Results

“…Conversely, studies in mechanobiology show that external geometric constraints and mechanical forces that deform the cell nucleus affect chromatin dynamics and gene and pathway activation [32]. Thus, nuclear morphological quantification becomes of major relevance as the studies of the reorganization of the chromatin and DNA architecture in the spatial and temporal framework, known as the 4D nucleome, emerge [11,36]. Cellular structures of interest in the context of the 4D nucleome include not only the nucleus itself, but also the nucleolus and nucleolar-associating domains, chromosome territories, topologically associating domains, lamina-associating domains, and loop domains in transcription factories [10].…”

Evaluation of Methods for Cell Nuclear Structure Analysis from Microscopy Data

“…Cell nuclear architecture is regulated by complex biological mechanisms related to cell differentiation, development, proliferation, and disease [3,10,11]. Changes in nuclear architecture are related to altered functional properties such as gene regulation and expression.…”