Biology subjects

Hinck, L.

Publications and source records attributed to Hinck, L..

4 recordsLinked to original sources

bioRxiv2025

Defects in the DNA Damage Response of Patient-derived Endometriosis Stromal Cells

With each menstrual cycle, endometrial cells rapidly proliferate and decidualize in preparation for pregnancy. Such rapid proliferation generates replication stress and results in DNA damage with irreparable cells undergoing senescence. Here, we examine the DNA damage response (DDR) of patient-derived stromal cell lines from menstrual effluent (MenSC) of healthy donors and donors with endometriosis. We found that proliferating MenSCs from endometriosis patients (Endo) have a defective DDR that is also present when these cells reach confluence. In G1, these cells contain more 53BP1-nuclear bodies (NBs) and are less senescent than healthy samples. We also treated with hydroxyurea (Hu) to generate replication stress and found that Endo MenSCs responded to this treatment by activating the DDR and generating more 53BP1-NBs. We examined the MRN complex, upstream of the ATM-dependent DDR. Hu treatment of our cell lines resulted in downregulation of all genes encoding the MRN complex, and RAD50 and NBS1 proteins. In a scRNA-seq dataset of endometriosis stromal tissue, we also identified downregulation of RAD50 and NBS1. To evaluate the growth potential of MenSCs, we decidualized cells after Hu treatment and then replated them in growing medium. Untreated endometriosis MenSCs formed more colonies than healthy MenSCs; neither sample type formed colonies after Hu treatment. Together, our studies suggest that endometriosis MenSCs have a defective DDR that may be exploited therapeutically.

cell biology↗

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↗

bioRxiv2022

Subfunctionalized expression drives evolutionary retention of ribosomal protein paralogs in vertebrates

The formation of paralogs through gene duplication is a core evolutionary process. For paralogs that encode components of protein complexes such as the ribosome, a central question is whether they encode functionally distinct proteins, or whether they exist to maintain appropriate total expression of equivalent proteins. Here, we systematically tested evolutionary models of paralog function using the mammalian ribosomal protein paralogs eS27 (Rps27) and eS27L (Rps27l) as a case study. We first showed that eS27 and eS27L have inversely correlated mRNA abundance across cell types, with the highest eS27 in lymphocytes and the highest eS27L in mammary alveolar cells and hepatocytes. By endogenously tagging the eS27 and eS27L proteins, we demonstrated that eS27- and eS27L- ribosomes associate preferentially with different transcripts. Furthermore, we generated murine eS27 and eS27L loss-of-function alleles that are homozygous lethal at different developmental stages. However, strikingly, we found that expressing eS27 protein from the endogenous eS27L locus, or vice versa, completely rescues loss-of-function lethality and yields mice with no detectable deficits. Together, these findings suggest that eS27 and eS27L are evolutionarily retained because their subfunctionalized expression patterns render both genes necessary to achieve the requisite total expression of two equivalent proteins across cell types. Our work represents the most in-depth characterization of a mammalian ribosomal protein paralog to date and highlights the importance of considering both protein function and expression when investigating paralogs.

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↗