Biology subjects

Stevens, H. Y.

Publications and source records attributed to Stevens, H. Y..

3 recordsLinked to original sources

bioRxiv2025

Multi-omics integration at cell type resolution uncovers gene-metabolite mechanisms underlying osteoarthritis heterogeneity

Metabolic dysregulation is an important factor for osteoarthritis pathogenesis, but comprehensive studies of underlying mechanisms and pathways are rare. We analyzed newly generated metabolomics data on bone marrow from 119 osteoarthritis patients, along with single-cell transcriptomics data to reconstruct networks of gene-metabolite associations at cell type resolution. Hubs of these networks - cell type-specific as well as pan-cell type hubs - revealed key molecular factors of osteoarthritis heterogeneity. Systems-level analysis of hubs revealed major roles for glycerophospholipid, glycerolipid and sphingolipid metabolism pathways, along with lipid signaling. We used Machine Learning models of gene-metabolite relationships to discover cell types most relevant to each metabolite. Integrative analysis of disease severity scores along with multi-omics data revealed a shift in specific immune cell subtypes in low versus high grade disease. We conclude that leveraging gene-metabolite covariation in a patient cohort can uncover underlying molecular mechanisms, overcoming the challenges posed by high dimensionality of multi-omics data.

bioinformatics↗

bioRxiv2020

Single-Cell Transcriptomic Attributes and Unbiased Computational Modeling for the Prediction of Immunomodulatory Potency of Mesenchymal Stromal Cells

Mesenchymal stromal cells (MSCs) are currently being tested in numerous clinical trials as potential cell therapies for the treatment of various diseases and due to their potential immunomodulatory, pro-angiogenic, and regenerative properties. However, variabilities in tissue sources, donors, and manufacturing processes and the lack of defined critical quality attributes (CQAs) and clinically relevant mechanism of action (MoA) pose significant challenges to identify MSC cell therapy products with a predictable therapeutic outcome. This also hinders regulatory considerations and broad clinical translation of MSCs. MSC products are often administered to the patient immediately after thawing from cryopreserved vials (out-of-thaw). However, the qualifying quality-control assays are either performed before cryopreservation, or after culturing the post-thaw cells for 24-48 hours (culture-rescued), none of which represent the out-of-thaw product administered to patients. In this study, we performed a broad functional characterization of out-of-thaw and culture-rescue MSCs from bone marrow (BM-MSCs) and cord tissue (CT-MSCs) using macrophage activation and T cell proliferation-based in vitro potency assays and deep phenotypic characterization using single-cell RNA-sequencing. Using this data, we developed unbiased computational models, specifically symbolic regression (SR) and canonical correlation analysis (CCA) models to predict the immunomodulatory potency of MSCs. Overall, our results suggest that manufacturing conditions (OOT vs. CR) have a strong effect on MSC-function on MSC interactions with macrophages and T cells. Furthermore, single-cell RNA-seq analyses of out-of-thaw BM and CT-MSCs indicate a tissue of origin-dependent variability and heterogeneity in the transcriptome profile. Using symbolic regression modeling we identified specific single-cell transcriptomic attributes of MSCs that predict their immunomodulatory potency. In addition, CCA modeling predicted MSC donors with high or low immunomodulatory potency from their transcriptome profiles. Taken together, our results provide a broad framework for identifying predictive CQAs of MSCs that could ultimately help in better understanding of their MOAs and improved reproducibility and manufacturing control of MSCs.

immunology↗

bioRxiv2018

Effects of BMP-2 dose and delivery of microvascular fragments on healing of bone defects with concomitant volumetric muscle loss

Traumatic composite bone-muscle injuries, such as open fractures, often require multiple surgical interventions and still typically result in long-term disability. Clinically, a critical indicator of composite injury severity is vascular integrity; vascular damage alone is sufficient to assign an open fracture to the most severe category. Challenging bone injuries are often treated with bone morphogenetic protein 2 (BMP-2), an osteoinductive growth factor, delivered on collagen sponge. Previous studies in a composite defect model found that a minimally bridging dose in the segmental defect model was unable to overcome concomitant muscle damage, but the effect of BMP dose on composite injuries has not yet been studied. Here, we test the hypotheses that BMP-2-mediated functional regeneration of composite extremity injuries is dose dependent and can be further enhanced via co-delivery of adipose-derived microvascular fragments (MVF), which have been previously shown to increase tissue vascular volume. Although MVF treatment did not improve healing outcomes, we observed a significant BMP-2 dose-dependent increase in regenerated bone volume and biomechanical properties. While high dose BMP-2 delivery can induce heterotopic ossification (HO) and increased inflammation, the maximum 10 g dose used in this study did not result in HO and was associated with a lower circulating inflammatory cytokine profile than the low dose (2.5 g) group. These data support the potential benefits of an increased, though still moderate, BMP-2 dose for treatment of bone defects with concomitant muscle damage. Future work to improve vascularization may further improve healing.

bioengineering↗