title: Loss of the integral nuclear envelope protein SUN1 induces alteration of nucleoli.
abstract: A supervised machine learning algorithm, which is qualified for image classification and analyzing similarities, is based on multiple discriminative morphological features that are automatically assembled during the learning processes. The algorithm is suitable for population-based analysis of images of biological materials that are generally complex and heterogeneous. Here we used the algorithm wndchrm to quantify the effects on nucleolar morphology of the loss of the components of nuclear envelope in a human mammary epithelial cell line. The linker of nucleoskeleton and cytoskeleton (LINC) complex, an assembly of nuclear envelope proteins comprising mainly members of the SUN and nesprin families, connects the nuclear lamina and cytoskeletal filaments. The components of the LINC complex are markedly deficient in breast cancer tissues. We found that a reduction in the levels of SUN1, SUN2, and lamin A/C led to significant changes in morphologies that were computationally classified using wndchrm with approximately 100% accuracy. In particular, depletion of SUN1 caused nucleolar hypertrophy and reduced rRNA synthesis. Further, wndchrm revealed a consistent negative correlation between SUN1 expression and the size of nucleoli in human breast cancer tissues. Our unbiased morphological quantitation strategies using wndchrm revealed an unexpected link between the components of the LINC complex and the morphologies of nucleoli that serves as an indicator of the malignant phenotype of breast cancer cells.
authors.affiliation: a Osaka University , Graduate School of Medicine and Health Science , Suita City , Osaka , Japan.
authors.forename: Ayaka
authors.initials: A
authors.lastname: Matsumoto
authors.affiliation: b Department of Medical Cell Biology , Institute of Molecular Embryology and Genetics, Kumamoto University , Kumamoto , Japan.
authors.forename: Chiyomi
authors.initials: C
authors.lastname: Sakamoto
authors.affiliation: b Department of Medical Cell Biology , Institute of Molecular Embryology and Genetics, Kumamoto University , Kumamoto , Japan.
authors.forename: Haruka
authors.initials: H
authors.lastname: Matsumori
authors.affiliation: c Osaka University , Graduate School of Frontier Bioscience , Suita City , Osaka , Japan.
authors.forename: Jun
authors.initials: J
authors.lastname: Katahira
authors.affiliation: b Department of Medical Cell Biology , Institute of Molecular Embryology and Genetics, Kumamoto University , Kumamoto , Japan.
authors.forename: Yoko
authors.initials: Y
authors.lastname: Yasuda
authors.affiliation: d Department of Breast Surgery , Osaka Police Hospital , Tennoji-ku , Osaka , Japan.
authors.forename: Katsuhide
authors.initials: K
authors.lastname: Yoshidome
authors.affiliation: e Department of Pathology , Osaka Police Hospital , Tennoji-ku , Osaka , Japan.
authors.forename: Masahiko
authors.initials: M
authors.lastname: Tsujimoto
authors.affiliation: f Image Informatics and Computational Biology Unit, Laboratory of Genetics , National Institute on Aging, National Institutes of Health , Baltimore , MD USA.
authors.forename: Ilya G
authors.initials: IG
authors.lastname: Goldberg
authors.affiliation: a Osaka University , Graduate School of Medicine and Health Science , Suita City , Osaka , Japan.
authors.forename: Nariaki
authors.initials: N
authors.lastname: Matsuura
authors.affiliation: b Department of Medical Cell Biology , Institute of Molecular Embryology and Genetics, Kumamoto University , Kumamoto , Japan.|g Core Research for Evolutional Science and Technology (CREST) , Japan Agency for Medical Research and Development , Tokyo , Japan.
authors.forename: Mitsuyoshi
authors.initials: M
authors.lastname: Nakao
authors.affiliation: b Department of Medical Cell Biology , Institute of Molecular Embryology and Genetics, Kumamoto University , Kumamoto , Japan.
authors.forename: Noriko
authors.initials: N
authors.lastname: Saitoh
authors.affiliation: a Osaka University , Graduate School of Medicine and Health Science , Suita City , Osaka , Japan.
authors.forename: Miki
authors.initials: M
authors.lastname: Hieda
mesh_terms: D000465:Algorithms; D001943:Breast Neoplasms / Q000235:genetics / Q000378:metabolism* / Q000648:ultrastructure; D045744:Cell Line, Tumor; D002466:Cell Nucleolus / Q000235:genetics / Q000378:metabolism* / Q000648:ultrastructure; D005260:Female; D006801:Humans; D000069550:Machine Learning; D008565:Membrane Proteins / Q000235:genetics / Q000378:metabolism*; D008869:Microtubule-Associated Proteins / Q000235:genetics / Q000378:metabolism*; D009363:Neoplasm Proteins / Q000235:genetics / Q000378:metabolism*; D009685:Nuclear Envelope / Q000235:genetics / Q000378:metabolism* / Q000648:ultrastructure; D009687:Nuclear Proteins / Q000235:genetics / Q000378:metabolism*; D012334:RNA, Neoplasm / Q000096:biosynthesis / Q000235:genetics; D012335:RNA, Ribosomal / Q000096:biosynthesis / Q000235:genetics
chemical_list: D008565:Membrane Proteins; D008869:Microtubule-Associated Proteins; D009363:Neoplasm Proteins; D009687:Nuclear Proteins; D012334:RNA, Neoplasm; D012335:RNA, Ribosomal; C506117:SUN1 protein, human
keywords: LINC complex; SUN1; SUN2; breast cancer; lamin A/C; nuclear envelope; nuclear morphology; wndchrm