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Lowengrub, J. S.

Publications and source records attributed to Lowengrub, J. S..

5 recordsLinked to original sources

BiLO: Bilevel Local Operator Learning for PDE Inverse Problems

We propose a new neural network based method for solving inverse problems for partial differential equations (PDEs) by formulating the PDE inverse problem as a bilevel optimization problem. At the upper level, we minimize the data loss with respect to the PDE parameters. At the lower level, we train a neural network to locally approximate the PDE solution operator in the neighborhood of a given set of PDE parameters, which enables an accurate approximation of the descent direction for the upper level optimization problem. The lower level loss function includes the least-square penalty of both the residual and its derivative with respect to the PDE parameters. We apply gradient descent simultaneously on both the upper and lower level optimization problems, leading to an effective and fast algorithm. The method, which we refer to as BiLO (Bilevel Local Operator learning), is also able to efficiently infer unknown functions in the PDEs through the introduction of an auxiliary variable. We provide a theoretical analysis that justifies our approach. Through extensive experiments over multiple PDE systems, we demonstrate that our method enforces strong PDE constraints, is robust to sparse and noisy data, and eliminates the need to balance the residual and the data loss, which is inherent to the soft PDE constraints in many existing methods.

systems biology↗

Integrating Mathematical and Mouse Models Identifies T regulatory Cell Influx as a Key Determinant of Acquired Resistance to PD-1 Immunotherapy

The immune system can eradicate cancer, but various immunosuppressive mechanisms active within a tumor curb this beneficial response. However, unraveling the effects of multimodal interactions between tumor and immune cells and their contributions to tumor control using an experimental approach alone is time- and resource-intensive. To identify the critical immunological features associated with tumor control and escape, we built a mechanistic mathematical model of the interactions between CD8+ T cells, Tregs, DCs, and tumor cells deeply rooted in current biological concepts. A distinguishing feature of our model is that it captures Treg accrual occurring after checkpoint blockade immunotherapy. After successfully fitting the model to experimental data of a mouse model of immunogenic melanoma, we generated hundreds of parameter sets, each representing a unique virtual mouse, that fit the data equally as well to capture variability across individuals. Our model indicates that the tumor and immune states before therapy are a key limiting factor of the immune response. Increasing the initial number of tumor-killing CD8+ T cells alone doesnt always result in a better outcome; instead, the model implies that there exist optimal initial ratios of immune cells that will result in improved tumor control. The model further predicts that the Treg influx into the tumor is a key determinant of resistance to PD-1 immunotherapy. We validated this predictions experimentally. Overall, this integrated approach of modeling and experimental validation identified crucial determinants of resistance to immunotherapy and can be used to guide the development of more effective therapeutic strategies.

immunology↗

Cahn-Hilliard dynamical models for condensed biomolecular systems

Biomolecular condensates create dynamic subcellular compartments that alter systems-level properties of the networks surrounding them. One model combining soluble and condensed states is the Cahn-Hilliard equation, which specifies a diffuse interface between the two phases. Customized approaches required to solve this equation are largely inaccessible. Using two complementary numerical strategies, we built stable, self-consistent Cahn-Hilliard solvers in Python, MATLAB, and Julia. The algorithms simulated the complete time evolution of condensed droplets as they dissolved or persisted, relating critical droplet size to a coefficient for the diffuse interface in the Cahn-Hilliard equation. We applied this universal relationship to the chromosomal passenger complex, a multi-protein assembly that reportedly condenses on mitotic chromosomes. The fully constrained Cahn-Hilliard simulations yielded dewetting and coarsening behaviors that closely mirrored experiments in different cell types. The Cahn-Hilliard equation tests whether condensate dynamics behave as a phase-separated liquid, and its numerical solutions advance generalized modeling of biomolecular systems.

systems biology↗

PIEZO1 regulates leader cell formation and cellular coordination during collective keratinocyte migration

The collective migration of keratinocytes during wound healing requires both the generation and transmission of mechanical forces for individual cellular locomotion and the coordination of movement across cells. Leader cells along the wound edge transmit mechanical and biochemical cues to ensuing follower cells, ensuring their coordinated direction of migration across multiple cells. Despite the observed importance of mechanical cues in leader cell formation and in controlling coordinated directionality of cell migration, the underlying biophysical mechanisms remain elusive. The mechanically-activated ion channel PIEZO1 was recently identified to play an inhibitory role during the reepithelialization of wounds. Here, through an integrative experimental and mathematical modeling approach, we elucidate PIEZO1s contributions to collective migration. Time-lapse microscopy reveals that PIEZO1 activity inhibits leader cell formation at the wound edge. To probe the relationship between PIEZO1 activity, leader cell formation and inhibition of reepithelialization, we developed an integrative 2D continuum model of wound closure that links observations at the single cell and collective cell migration scales. Through numerical simulations and subsequent experimental validation, we found that coordinated directionality plays a key role during wound closure and is inhibited by upregulated PIEZO1 activity. We propose that PIEZO1-mediated retraction suppresses leader cell formation which inhibits coordinated directionality between cells during collective migration. Author summaryDuring the healing of a wound, cells called keratinocytes that make up the outer layer of the skin migrate collectively to close the wound gap. The mechanically activated ion channel PIEZO1 was previously found to inhibit wound closure. Here, through a combined modeling and experimental approach, we investigate the role of PIEZO1 in regulating collective migration. Specialized cells called leader cells, which typically form along the wound edge, are important for guiding the migration of neighboring cells. These leader cells dictate the coordinated directionality, or the cohesiveness of the migration direction between neighboring cells, through the transmission of mechanical and biochemical cues. We find that PIEZO1 activity inhibits the formation of these leader cells and, as a result, inhibits cell coordinated directionality causing the collective movement of cells to become disorganized and less effective in closing the wound. Our findings shed light on the complex mechanisms underlying collective migration, providing valuable insight into how mechanical cues affect the movement of cells during wound closure.

biophysics↗

Determinants of stem cell enrichment in healthy tissues and tumors: implications for non-genetic drug resistance

Drug resistance is a major challenge for cancer therapy. While resistance mutations are often the focus of investigation, non-genetic resistance mechanisms are also important. One such mechanism is the presence of relatively high fractions of cancer stem cells (CSCs), which have reduced susceptibility to chemotherapy, radiation, and targeted treatments compared to more differentiated cells. The reasons for high CSC fractions (CSC enrichment) are not well understood. Previous experimental and mathematical modeling work identified a particular feedback loop in tumors that can promote CSC enrichment. Here, we use mathematical models of hierarchically structured cell populations to build on this work and to provide a comprehensive analysis of how different feedback regulatory processes that might partially operate in tumors can influence the stem cell fractions during somatic evolution of healthy tissue or during tumor growth. We find that depending on the particular feedback loops that are present, CSC fractions can increase or decrease. We define characteristics of the feedback mechanisms that are required for CSC enrichment to occur, and show how the magnitude of enrichment is determined by parameters. In particular, enrichment requires a reduction in division rates or an increase in death rates with higher population sizes, and the feedback mediators that achieve this can be secreted by either CSCs or by more differentiated cells. The extent of enrichment is determined by the death rate of CSCs, the probability of CSC self-renewal, and by the strength of feedback on cell divisions. Defining these characteristics can guide experimental approaches that aim to screen for and identify feedback mediators that can promote CSC enrichment in specific cancers, which in turn can help understand and overcome the phenomenon of CSC-based therapy resistance.

evolutionary biology↗