Biology subjects

Rubio, S.

Publications and source records attributed to Rubio, S..

3 recordsLinked to original sources

bioRxiv2023

Nuclear VANGL2 Inhibits Lactogenic Differentiation

Planar cell polarity (PCP) proteins coordinate tissue morphogenesis by governing cell patterning and polarity. Asymmetrically localized on the plasma membrane of cells, PCP proteins are also trafficked by endocytosis, suggesting they may have intracellular functions that are dependent or independent of their extracellular role, but whether these functions extend to transcriptional control remains unknown. Here, we show the nuclear localization of transmembrane, PCP protein, VANGL2, in undifferentiated, but not differentiated, HC11 cells, which serve as a model for mammary lactogenic differentiation. Loss of Vangl2 function results in upregulation of pathways related to STAT5 signaling. We identify DNA binding sites and a nuclear localization signal in VANGL2, and use CUT&RUN to demonstrate direct binding of VANGL2 to specific DNA binding motifs, including one in the Stat5a promoter. Knockdown (KD) of Vangl2 in HC11 cells and primary mammary organoids results in upregulation of Stat5a, Ccnd1 and Csn2, larger acini and organoids, and precocious differentiation; phenotypes rescued by overexpression of Vangl2, but not Vangl2{Delta}NLS. Together, these results advance a paradigm whereby PCP proteins coordinate tissue morphogenesis by keeping transcriptional programs governing differentiation in check.

cell biology↗

bioRxiv2023

An oligodendrocyte silencer element underlies the pathogenic impact of lamin B1 structural variants

The role of non-coding regulatory elements and how they might contribute to tissue type specificity of disease phenotypes is poorly understood. Autosomal Dominant Leukodystrophy (ADLD) is a fatal, adult-onset, neurological disorder that is characterized by extensive CNS demyelination. Most cases of ADLD are caused by tandem genomic duplications involving the lamin B1 gene (LMNB1) while a small subset are caused by genomic deletions upstream of the gene. Utilizing data from recently identified families that carry LMNB1 gene duplications but do not exhibit demyelination, ADLD patient tissues, CRISPR modified cell lines and mouse models, we have identified a novel silencer element that is lost in ADLD patients and that specifically targets overexpression to oligodendrocytes. This element consists of CTCF binding sites that mediate three-dimensional chromatin looping involving the LMNB1 and the recruitment of the PRC2 repressor complex. Loss of the silencer element in ADLD identifies a previously unknown role for silencer elements in tissue specificity and disease causation.

genetics↗

bioRxiv2021

DeepSea: An efficient deep learning model for automated cell segmentation and tracking

Dynamics and non-genetic heterogeneity are two fundamental characteristics of basic processes of life such as cell division or differentiation. Time-lapse microscopy is the only method that can directly capture the dynamics and heterogeneity of fundamental cellular processes at the singlecell level with high temporal resolution. Successful application of single-cell time-lapse microscopy requires automated segmentation and tracking of hundreds of individual cells over several time points. Recently, deep learning models have ushered in a new era in the quantitative analysis of microscopy images. However, integrated segmentation and tracking of single cells remain challenges for the analysis of time-lapse microscopy images. This work presents a versatile and trainable deep-learning software, termed DeepSea, that allows for both segmentation and tracking of single cells in sequences of phase-contrast live microscopy images. Our segmentation model can easily be trained to segment phase-contrast images of different cell types with higher precision than existing models. Our tracking model allows for quantification of dynamics of several cell biological features of individual cells, such as cell division cycle, mitosis, cell morphology, and cell size, with high precision using phase-contrast images. We showcase the application of DeepSea by analyzing cell size regulation in embryonic stem cells. Our findings show that embryonic stem cells exhibit cell size control in the G1 phase of the cell cycle despite their unusual fast division cycle. Our training dataset, user-friendly software, and code are available here https://deepseas.org.

systems biology↗