Biology subjects

Pals, S. T.

Publications and source records attributed to Pals, S. T..

3 recordsLinked to original sources

bioRxiv2022

GOAT: Deep learning-enhanced Generalized Organoid Annotation Tool

Organoids have emerged as a powerful technology to investigate human development, model diseases and for drug discovery. However, analysis tools to rapidly and reproducibly quantify organoid parameters from microscopy images are lacking. We developed a deep-learning based generalized organoid annotation tool (GOAT) using instance segmentation with pixel-level identification of organoids to quantify advanced organoid features. Using a multicentric dataset, including multiple organoid systems (e.g. liver, intestine, tumor, lung), we demonstrate generalization of the tool to annotate a diverse range of organoids generated in different laboratories and high performance in comparison to previously published methods. In sum, GOAT provides fast and unbiased quantification of organoid experiments to accelerate organoid research and facilitates novel high-throughput applications.

bioinformatics↗

bioRxiv2020

The CXCL12gamma chemokine immobilized by heparan sulfate on stromal niche cells controls adhesion and mediates drug resistance in multiple myeloma

The homing/retention, survival and proliferation of multiple myeloma (MM) cells critically depends on interaction with CXCL12 expressing stromal cells in the bone marrow (BM) niche. Here, we report a unique role in this interaction for the recently characterized CXCL12gamma isoform, which contains an extended C-terminal domain that binds heparan-sulfate proteoglycans (HSPGs) with an extraordinary high affinity. We observed that CXCL12{gamma} is expressed in situ by reticular stromal cells in both normal and MM BM, as well as by primary BM stromal-cell (BMSC) isolates and BMSC lines. Importantly, upon secretion, CXCL12{gamma}, unlike the CXCL12 isoform, was retained on the surface of these BMSCs. This membrane retention of CXCL12{gamma} is HSPG-mediated, since it was completely annulated by CRISPR-Cas9 mediated deletion of the heparan-sulfate (HS) co-polymerase EXT1. Recombinant CXCL12{gamma} was found to induce strong adhesion of MM cells to vascular cell-adhesion molecule 1 (VCAM-1) coated plates. Furthermore, CXCL12{gamma} expressed by BMSCs and membrane-retained by HSPGs, supported robust adhesion of MM cells to the BMSCs. Specific genetic deletion of either CXCL12{gamma} or of EXT1 significantly attenuated the ability of BMSCs to support MM cell adhesion and, in addition, impaired their capacity to protect MM cells from bortezomib-induced cell death. Our data indicate that CXCL12{gamma} functions as a membrane-bound niche chemokine, which plays a unique role in the interaction of MM cells with the stromal niche by controlling adhesion/retention as well as cell adhesion-mediated drug resistance (CAM-DR). These findings designate CXCL12{gamma} and associated HSPGs as potential therapeutic targets in MM.

cancer biology↗

bioRxiv2019

Targeting AKT elicits tumor suppressive functions of FOXO transcription factors and GSK3 kinase in Multiple Myeloma

The phosphatidylinositide-3 kinases (PI3K) and the downstream mediator AKT drive survival and proliferation of multiple myeloma (MM) cells and several AKT inhibitors are currently being tested in clinical trials for MM patients. AKT inhibition has pleiotropic effects, and the key aspects that determine therapeutic efficacy are not fully clear. Therefore, we investigated the antimyeloma mechanism(s) of AKT inhibition. Among the various downstream AKT targets are Forkhead box O (FOXO) transcription factors, and we demonstrate that they are crucial for changes in gene expression upon AKT inhibition. Based on gene expression profiling we defined an AKT-induced FOXO-dependent gene set that has prognostic significance in a large cohort of MM patients, where low FOXO activity correlates with inferior survival. We show that cell cycle exit and cell death of MM cells after AKT inhibition required FOXO. In addition, glycogen synthase kinase 3 (GSK3), a negatively regulated AKT substrate, proved to be pivotal to induce cell death and to inhibit cell cycle progression after AKT inhibition. Finally, we demonstrate that FOXO and GSK3 induced cell death by increasing the turnover of the myeloid cell leukemia 1 (MCL1) protein. In concordance, the AKT inhibitor MK2206 greatly sensitized MM cells for the MCL1 inhibitor S63845. Thus, our results indicate that FOXO and GSK3 are crucial mediators of the antimyeloma effects of AKT inhibition, and suggest combination therapies that may have therapeutic potential in MM.\n\nKEYPOINTSO_LIFOXO transcription factors and the GSK3 kinase are pivotal tumor suppressors downstream of AKT inhibition in MM cells.\nC_LIO_LIFOXO and GSK3 activation after AKT inhibition leads to a decrease in MCL1 levels in MM cells resulting in cell death.\nC_LI

cancer biology↗