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bioRxiv · 10.1101/2023.04.06.535937

Data driven and cell specific determination of nuclei-associated actin structure

Nikitina, N.·Bursa, N.·Goelzer, M.·Goldfeldt, M.·Crandall, C.·Howard, S.·Rubin, J.·Satici, A.·Uzer, G.
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Abstract

Quantitative and volumetric assessment of filamentous actin fibers (F-actin) remains challenging due to their interconnected nature, leading researchers to utilize threshold based or qualitative measurement methods with poor reproducibility. Here we introduce a novel machine learning based methodology for accurate quantification and reconstruction of nuclei-associated F-actin. Utilizing a Convolutional Neural Network (CNN), we segment actin filaments and nuclei from 3D confocal microscopy images and then reconstruct each fiber by connecting intersecting contours on cross-sectional slices. This allowed measurement of the total number of actin filaments and individual actin filament length and volume in a reproducible fashion. Focusing on the role of F-actin in supporting nucleocytoskeletal connectivity, we quantified apical F-actin, basal F-actin, and nuclear architecture in mesenchymal stem cells (MSCs) following the disruption of the Linker of Nucleoskeleton and Cytoskeleton (LINC) Complexes. Disabling LINC in mesenchymal stem cells (MSCs) generated F-actin disorganization at the nuclear envelope characterized by shorter length and volume of actin fibers contributing a less elongated nuclear shape. Our findings not only present a new tool for mechanobiology but introduce a novel pipeline for developing realistic computational models based on quantitative measures of F- actin.

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Nikitina, N., Bursa, N., Goelzer, M., Goldfeldt, M., Crandall, C., Howard, S., Rubin, J., Satici, A., Uzer, G.. 2023-04-06. Data driven and cell specific determination of nuclei-associated actin structure. https://doi.org/10.1101/2023.04.06.535937

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