Current Methods and Pipelines for Image-Based Quantitation of Nuclear Shape and Nuclear Envelope Abnormalities

Abstract

Any given cell type has an associated “normal” nuclear morphology, which is important to maintain proper cellular functioning and safeguard genomic integrity. Deviations from this can be indicative of diseases such as cancer or premature aging syndrome. To accurately assess nuclear abnormalities, it is important to use quantitative measures of nuclear morphology. Here, we give an overview of several nuclear abnormalities, including micronuclei, nuclear envelope invaginations, blebs and ruptures, and review the current methods used for image-based quantification of these abnormalities. We discuss several parameters that can be used to quantify nuclear shape and compare their outputs using example images. In addition, we present new pipelines for quantitative analysis of nuclear blebs and invaginations. Quantitative analyses of nuclear aberrations and shape will be important in a wide range of applications, from assessments of cancer cell anomalies to studies of nucleus deformability under mechanical or other types of stress.

The BAF A12T mutation associated with premature aging impedes lamin A/C recruitment to sites of nuclear rupture, contributing to nuclear envelope fragility

“…NGPS cells on the other hand didn’t show lamin A/C recruitment to blebs (Figure 5a, magenta arrowheads). Automated quantification using a CellProfiler based pipeline (Janssen et al, 2022) of either lamin A/C intensity at blebs or enrichment of lamin A/C at blebs when compared to the lamin A/C staining intensity in the rest of the nucleus, confirmed a lack of lamin A/C recruitment in NGPS cells (Figure 5b). Reversion of the A12T mutation in NGPS2 cells was able to rescue the lamin A/C recruitment defect (Figure 5a (green arrowheads) and 5b, Figure S6a-b), demonstrating that this is a specific phenotype caused by the BAF mutation.…”

“…NGPS cells on the other hand didn’t show lamin A/C recruitment to blebs (Figure 5a, magenta arrowheads). Automated quantification using a CellProfiler based pipeline (Janssen et al , 2022) of either lamin A/C intensity at blebs or enrichment of lamin A/C at blebs when compared to the lamin A/C staining intensity in the rest of the nucleus, confirmed a lack of lamin A/C recruitment in NGPS cells (Figure 5b).…”

“…Bleb analysis (Janssen et al , 2022): Chromatin object was identified based on DAPI staining. A lamin B1 object was identified and subtraction of both areas identifies the bleb object as it is devoid of lamin B1.…”

Nuclear morphology predicts cell survival to cisplatin chemotherapy

“…Abnormal nuclear morphology has been regarded as a distinct phenotype of malignant cancer cells that facilitates invasion, migration, and metastasis 55,59,62,64 . Nuclear circularity is a representative 2D feature that allows for the evaluation of morphological abnormalities and it is used as a diagnostic parameter by pathologists 57,59,128,129 . Sphericity is a 3D version of circularity that may provide identical diagnostic potential or even better specificity due to the additional dimensional information 59,130,131 .…”

“…Nuclear circularity is a representative 2D feature that allows for the evaluation of morphological abnormalities and it is used as a diagnostic parameter by pathologists 57,59,128,129 . Sphericity is a 3D version of circularity that may provide identical diagnostic potential or even better specificity due to the additional dimensional information 59,130,131 . Treated cells exhibited a decreasing nuclear volume as a function of recovery time, with the lowest sphericity values occurring in the population of cells in the PACC state at day 15.…”