Browsing by Author "Slater, John H."
Now showing 1 - 3 of 3
Results Per Page
Sort Options
Item Progeny Clustering: A Method to Identify Biological Phenotypes(Nature Publishing Group, 2015-08-12) Hu, Chenyue W.; Kornblau, Steven M.; Slater, John H.; Qutub, Amina A.; Chenyue W. Hu, Steven M. Kornblau, John H. Slater & Amina A. Qutub; Slater, John H.Estimating the optimal number of clusters is a major challenge in applying cluster analysis to any type of dataset, especially to biomedical datasets, which are high-dimensional and complex. Here, we introduce an improved method, Progeny Clustering, which is stability-based and exceptionally efficient in computing, to find the ideal number of clusters. The algorithm employs a novel Progeny Sampling method to reconstruct cluster identity, a co-occurrence probability matrix to assess the clustering stability, and a set of reference datasets to overcome inherent biases in the algorithm and data space. Our method was shown successful and robust when applied to two synthetic datasets (datasets of two-dimensions and ten-dimensions containing eight dimensions of pure noise), two standard biological datasets (the Iris dataset and Rat CNS dataset) and two biological datasets (a cell phenotype dataset and an acute myeloid leukemia (AML) reverse phase protein array (RPPA) dataset). Progeny Clustering outperformed some popular clustering evaluation methods in the tendimensional synthetic dataset as well as in the cell phenotype dataset, and it was the only method that successfully discovered clinically meaningful patient groupings in the AML RPPA dataset.Item Secretion of the disulphide bond generating catalyst QSOX1 from pancreatic tumour cells into the extracellular matrix: Association with extracellular vesicles and matrix proteins(Journal of Extracellular Biology, 2022-07-02) Millar-Haskell, Catherine S.; Sperduto, John L.; Slater, John H.; Thorpe, Colin; Gleghorn, Jason P.Quiescin sulfhydryl oxidase 1 (QSOX1) is a disulphide bond generating catalyst that is overexpressed in solid tumours. Expression of QSOX1 is linked to cancer cell invasion, tumour grade, and aberrant extracellular matrix (ECM) protein deposition. While the secreted version of QSOX1 is known to be present in various fluids and secretory tissues, its presence in the ECM of cancer is less understood. To characterize secreted QSOX1, we isolated extracellular vesicles (and particles) (EV(P)s) from conditioned media using ultracentrifugation and separated the supernatant using tangential flow filtration. We discovered that most of the secreted QSOX1 resides in the EVP-depleted supernatant and in the soluble protein fraction. Very little QSOX1 could be detected in the EVP fraction. We used immunofluorescence to image subpopulations of EVs and found QSOX1 in Golgi-derived vesicles and medium/large vesicles, but in general, most extracellular QSOX1 was not attributed to these vesicles. Next, we quantified QSOX1 co-localization with the EV marker Alix. For the medium/large EVs, ∼98% contained QSOX1 when fibronectin was used as a coating. However, on collagen coatings, only ∼60% of these vesicles contained QSOX1, suggesting differences in EV cargo based on ECM coated surfaces. About 10% of small EVs co-localized with QSOX1 on every ECM protein surface except for collagen (0.64%). We next investigated adhesion of QSOX1 to ECM proteins in vitro and in situ and found that QSOX1 preferentially adheres to fibronectin, laminins, and Matrigel compared to gelatin and collagen. This mechanism was found to be, in part, mediated by the formation of mixed disulphides between QSOX1 and cysteine-rich ECM proteins. In summary, we found that QSOX1 (1) is in subpopulations of medium/large EVs, (2) seems to interact with small Alix+ EVs, and (3) adheres to cysteine-rich ECM proteins, potentially through the formation of intermediate disulphides. These observations offer significant insight into how enzymes, such as QSOX1, can facilitate matrix remodelling events in solid tumour progression.Item Tuning Hydrogel Adhesivity and Degradability to Model the Influence of Premetastatic Niche Matrix Properties on Breast Cancer Dormancy and Reactivation(Advanced Biology, 2022-03-11) Farino Reyes, Cindy J.; Slater, John H.Dormant, disseminated tumor cells (DTCs) can persist for decades in secondary tissues before being reactivated to form tumors. The properties of the premetastatic niche can influence the DTC phenotype. To better understand how matrix properties of premetastatic niches influence DTC behavior, three hydrogel formulations are implemented to model a permissive niche and two nonpermissive niches. Poly(ethylene glycol) (PEG)-based hydrogels with varying adhesivity ([RGDS]) and degradability ([N-vinyl pyrrolidinone]) are implemented to mimic a permissive niche with high adhesivity and degradability and two nonpermissive niches, one with moderate adhesivity and degradability and one with no adhesivity and high degradability. The influence of matrix properties on estrogen receptor positive (ER+) breast cancer cells (MCF7s) is determined via a multimetric analysis. MCF7s cultured in the permissive niche adopted a growth state, while those in the nonpermissive niche with reduced adhesivity and degradability underwent tumor mass dormancy. Complete removal of adhesivity while maintaining high degradability induced single cell dormancy. The ability to mimic reactivation of dormant cells through a dynamic increase in [RGDS] is also demonstrated. This platform provides the capability of inducing growth, dormancy, and reactivation of ER+ breast cancer and can be useful in understanding how premetastatic niche properties influence cancer cell fate.