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Biology subjects

Karabay, E. T.

Publications and source records attributed to Karabay, E. T..

2 recordsLinked to original sources

The impact of patient biology on racial disparities in breast cancer outcome

Hormone receptor positive (HR+) breast cancer is the most common subtype of breast cancer diagnosed globally. Despite effective targeted therapies, HR+ breast cancer remains a leading cause of cancer-related death in women. Long-standing epidemiological research identifies significantly worse outcomes for Black women diagnosed with HR+ breast cancer relative to White women. While structural factors such as access to healthcare and education level contribute to this outcome disparity, it persists even in analyses where these factors are controlled. In-depth analyses of the somatic molecular biology that may underlie these outcome disparities are hampered by a lack of datasets that represent Black patient populations. Here, we generate a HR+ breast cancer patient transcriptomic dataset that overrepresents Black women and controls for access to healthcare and education level. We find that signatures relating to the tumor microenvironment, i.e. collagen deposition and prognostically unfavorable T-cell landscapes are enriched in HR+ tumors from Black women. Importantly, we find, using experimental model systems in vitro and in vivo, that race-aligned collagen deposition patterns are at least partially attributable to tumor cell-intrinsic signaling and critical for Black breast cancer metastasis. We also find that unfavorable T-cell signatures in HR+ tumors from Black women, which have previously been attributed to race and ancestry, are more strongly poverty-aligned. Using multiple independent datasets, we identify STAT4 as a potential master regulator of this poverty-associated tumor immune signature. Together, these findings provide new evidence that somatic molecular biology of breast cancer patients can be modified by multiple structural factors such as self-identified race and poverty burden to promote poor patient outcomes. Integrating an understanding of structural factors into molecular cancer research is critical for implementing truly personalized, and maximally effective, oncology systems.

cancer biology↗

Predicting phenotype to mechanotype relationships in cells based on intra-cellular signaling network

Cells originating from the same tissue can respond differently to external signals depending on the genotypic and phenotypic state of the cell and its local environment. We have developed a semi-quantitative-computational model to analyze the intracellular signaling network and its outcome in the presence of multiple external signals including growth factors, hormones, and extracellular matrix. We use this model to analyze the cells mechanical response to external stimuli and identify the key internal elements of the network that drive specific outcomes within the response space. The model is built upon the Boolean approach to network modeling, where the state of any given node is determined using the state of the connecting nodes and Boolean logic. This allows us to analyze the network behavior without the need to estimate all the various interaction rates between different cellular components. However, such an approach is limited in its ability to predict network dynamics and temporal evolution of the cell state. So, we introduce modularity in the model and incorporate dynamical aspects, mass-action kinetics, and chemo-mechanical effects on only certain transition rates within specific modules as required, creating a Boolean-Hybrid-Modular (BoHyM) signal transduction model. We present this model as a comprehensive, cell-type agnostic, user-modifiable tool to investigate how extra-and intra-cellular signaling can regulate cellular cytoskeletal components and consequently influence cell-substrate interactions, force generation, and migration. Using this tool, we show how slight changes in signaling network architectures due to phenotypic changes can alter cellular response to stress hormone signaling in an environment-dependent manner. The tool also allows isolating effector proteins driving specific cellular mechanical responses. Ultimately, we show the utility of the tool in analyzing transient chemo-mechanical dynamics of cells in response to time-varying chemical stimuli.

systems biology↗