Biology subjects

Balcioglu, H. E.

Publications and source records attributed to Balcioglu, H. E..

3 recordsLinked to original sources

bioRxiv2024

CLEAR-IT: Contrastive Learning Enabled Accurate Registration of Immune and Tumor cells from multiplexed images with limited labels in a platform-independent manner

Accurate phenotyping of cells in the tumor microenvironment is crucial for understanding cancer biology and developing effective therapies. However, current methods require precise cell segmentations and struggle to generalize across different imaging modalities, limiting their utility in digital pathology. Here, we show that Contrastive Learning Enabled Accurate Registration of Immune and Tumor Cells (CLEAR-IT) overcomes these limitations, providing a robust and versatile tool for cell phenotyping. CLEAR-IT accurately phenotypes cells comparable to state-of-the-art methods, generalizes across multiplex imaging modalities, maintains high performance even with limited number of labels, and enables the extraction of prognostic markers. Additionally, CLEAR-IT can be combined with existing methods to boost their performance, whereas its lack of need for precise cell segmentations significantly reduces training efforts. This method enhances the robustness and efficiency of digital pathology workflows, making it a valuable tool for cancer research and diagnostics.

bioinformatics↗

bioRxiv2021

Substrate rigidity modulates traction forces and stoichiometry of cell matrix adhesions.

In cell matrix adhesions, integrin receptors and associated proteins provide a dynamic coupling of the extracellular matrix (ECM) to the cytoskeleton. This allows bidirectional transmission of forces between the ECM and the cytoskeleton, which tunes intracellular signaling cascades that control survival, proliferation, differentiation, and motility. The quantitative relationships between recruitment of distinct cell matrix adhesion proteins and local cellular traction forces are not known. Here, we applied quantitative superresolution microscopy to cell matrix adhesions formed on fibronectin-stamped elastomeric pillars and developed an approach to relate the number of talin, vinculin, paxillin, and focal adhesion kinase (FAK) molecules to the local cellular traction force. We find that FAK recruitment does not show an association with traction-force application whereas a ~60 pN force increase is associated with the recruitment of one talin, two vinculin, and two paxillin molecules on a substrate of effective stiffness of 47 kPa. On a substrate with a four-fold lower effective stiffness the stoichiometry of talin:vinculin:paxillin changes to 2:12:6 for the same ~60 pN traction force. The relative change in force-related vinculin recruitment indicates a stiffness-dependent switch in vinculin function in cell matrix adhesions. Our results reveal a substrate-stiffness-dependent modulation of the relation between cellular traction-force and the molecular stoichiometry of cell-matrix adhesions.

biophysics↗

bioRxiv2018

p130Cas contributes to cellular mechanosensing and force exertion.

Cell survival, differentiation, and migration are all dependent on the cells interaction with its external environment. In addition to chemical cues, cells react to their physical environment, particularly the stiffness of the substrate. In order for cells to react to these elements, they must make use of cellular machinery to signal changes in their microenvironment. One such proposed machinery is the protein p130Cas, which has been shown to regulate focal adhesion turnover, actin dynamics, and cell migration. Here we show that p130Cas localizes to focal adhesions depending on substrate stiffness and subsequently modulates cellular force exertion. We compared on substrates of tunable stiffness knock-out CAS-/-cells to cells re-expressing either the full-length p130Cas or a mutant lacking the focal adhesion targeting domains. On polyacrylamide gels, we observed that p130Cas prevented focal adhesion formation at low stiffness. On structured micro-pillar arrays, p130Cas preferentially localized to sites of force exertion when the apparent Youngs modulus of the substrate was higher than E = 47 kPa. Stiffness-dependent localization of p130Cas coincided with slower, but increased force exertion for the full-length p130Cas. Cas localization to focal adhesions preceded force build-up by three minutes, suggesting a coordinating role for p130Cas in the cellular mechanoresponse. Thus, p130Cas appears to relay mechanosensory information in the cell through its ability to tune force exertion at the focal adhesion.

biophysics↗