title: Blue intensity matters for cell cycle profiling in fluorescence DAPI-stained images.
abstract: In the past decades, there has been an amazing progress in the understanding of the molecular mechanisms of the cell cycle. This has been possible largely due to a better conceptualization of the cycle itself, but also as a consequence of technological advances. Herein, we propose a new fluorescence image-based framework targeted at the identification and segmentation of stained nuclei with the purpose to determine DNA content in distinct cell cycle stages. The method is based on discriminative features, such as total intensity and area, retrieved from in situ stained nuclei by fluorescence microscopy, allowing the determination of the cell cycle phase of both single and sub-population of cells. The analysis framework was built on a modified k-means clustering strategy and refined with a Gaussian mixture model classifier, which enabled the definition of highly accurate classification clusters corresponding to G1, S and G2 phases. Using the information retrieved from area and fluorescence total intensity, the modified k-means (k=3) cluster imaging framework classified 64.7% of the imaged nuclei, as being at G1 phase, 12.0% at G2 phase and 23.2% at S phase. Performance of the imaging framework was ascertained with normal murine mammary gland cells constitutively expressing the Fucci2 technology, exhibiting an overall sensitivity of 94.0%. Further, the results indicate that the imaging framework has a robust capacity to both identify a given DAPI-stained nucleus to its correct cell cycle phase, as well as to determine, with very high probability, true negatives. Importantly, this novel imaging approach is a non-disruptive method that allows an integrative and simultaneous quantitative analysis of molecular and morphological parameters, thus awarding the possibility of cell cycle profiling in cytological and histological samples.
authors.affiliation: i3S - Instituto de Investigação e Inovação em Saúde, Epithelial Interactions in Cancer (EpIC) Group, Universidade do Porto, Porto, Portugal.|IPATIMUP, Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal.
authors.forename: Anabela
authors.initials: A
authors.lastname: Ferro
authors.affiliation: Institute for Systems and Robotics (ISR/IST), LARSyS, Bioengineering Department, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.
authors.forename: Tânia
authors.initials: T
authors.lastname: Mestre
authors.affiliation: i3S - Instituto de Investigação e Inovação em Saúde, Epithelial Interactions in Cancer (EpIC) Group, Universidade do Porto, Porto, Portugal.|IPATIMUP, Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal.
authors.forename: Patrícia
authors.initials: P
authors.lastname: Carneiro
authors.affiliation: Institute for Systems and Robotics (ISR/IST), LARSyS, Bioengineering Department, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.
authors.forename: Ivan
authors.initials: I
authors.lastname: Sahumbaiev
authors.affiliation: i3S - Instituto de Investigação e Inovação em Saúde, Epithelial Interactions in Cancer (EpIC) Group, Universidade do Porto, Porto, Portugal.|IPATIMUP, Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal.|Departamento de Patologia e Oncologia, Faculdade de Medicina da Universidade do Porto, Porto, Portugal.
authors.forename: Raquel
authors.initials: R
authors.lastname: Seruca
authors.affiliation: Institute for Systems and Robotics (ISR/IST), LARSyS, Bioengineering Department, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.
authors.forename: João M
authors.initials: JM
authors.lastname: Sanches
mesh_terms: D000818:Animals; D002453:Cell Cycle / Q000502:physiology*; D002460:Cell Line; D002467:Cell Nucleus / Q000737:chemistry; D005456:Fluorescent Dyes / Q000032:analysis* / Q000737:chemistry; D006651:Histocytochemistry; D007091:Image Processing, Computer-Assisted; D007211:Indoles / Q000032:analysis* / Q000737:chemistry; D051379:Mice; D008856:Microscopy, Fluorescence / Q000379:methods*; D012680:Sensitivity and Specificity; D059010:Single-Cell Analysis / Q000379:methods*
chemical_list: D005456:Fluorescent Dyes; D007211:Indoles; C007293:DAPI