Biology subjects

Levine, H.

Publications and source records attributed to Levine, H..

24 records · Page 2Linked to original sources

bioRxiv2017

EMT and MET: necessary or permissive for metastasis?

Epithelial-to-mesenchymal transition (EMT) and its reverse mesenchymal-to-epithelial transition (MET) have been often suggested to play crucial roles in metastatic dissemination of carcinomas. Recent studies have revealed that neither of these processes is binary. Instead, carcinoma cells often exhibit a spectrum of epithelial/mesenchymal phenotype(s). While epithelial-mesenchymal plasticity has been observed pre-clinically and clinically, whether any of these phenotypic transitions are indispensable for metastatic outgrowth remains an unanswered question. Here, we focus on epithelial-mesenchymal plasticity in metastatic dissemination and propose alternative mechanisms for successful dissemination and metastases beyond the traditional EMT-MET view. We highlight multiple hypotheses that can help reconcile conflicting observations, and outline the next set of key questions that can offer valuable insights into mechanisms of metastasis in multiple tumor models.

cancer biology↗

bioRxiv2017

On the mechanism of long-range alignment order of fibroblasts

Long-range alignment ordering of fibroblasts have been observed in the vicinity of cancerous tumors and can be recapitulated with in vitro experiments. However, the mechanisms driving their ordering are not understood. Here we show that local collision-driven nematic alignment interactions among fibroblasts are insufficient to explain observed long-range alignment. One possibility is that there exists another orientation field co-evolving with the cells and reinforcing their alignment. We propose that this field reflects the mechanical cross-talk between the fibroblasts and the underlying fibrous material on which they move. We demonstrate that this new long-range interaction can give rise to high nematic order and to the observed patterning of the cancer microenvironment.\n\nSignificance StatementLong-range alignment patterns of fibroblasts have been observed both in vivo and in vitro. However, there has not been much understanding of the underlying mechanism. In this work, we demonstrate that these patterns cannot be simply explained by their steric interaction with one another during collisions. Instead, we propose that fibroblasts may collectively align through non-local interactions arising from their modification of an underlying extracellular matrix. The proposed mechanism explains the observed co-alignment between fibroblasts and collagen fibers around tumors and can be be tested in future experiments that can image the dynamics of this pattern formation in vivo or in vitro

biophysics↗

bioRxiv2017

Inflammatory Breast Cancer: a model for investigating cluster-based dissemination

Metastases claim more than 90% of cancer-related patient deaths and are usually seeded by a subset of circulating tumor cells (CTCs) shed off from the primary tumor. In circulation, CTCs are found both as single cells and as clusters of cells. The clusters of CTCs, although many fewer in number, possess much higher metastatic potential as compared to that of individual CTCs. In this review, we highlight recent insights into molecular mechanisms that can enable the formation of these clusters - (a) hybrid epithelial/mesenchymal (E/M) phenotype of cells that couples their ability to migrate and adhere, and (b) intercellular communication that can spatially coordinate the cluster formation and provide survival signals to cancer cells. Building upon these molecular mechanisms, we also offer a possible mechanistic understanding of why clusters are endowed with a higher metastatic potential. Finally, we discuss the highly aggressive Inflammatory Breast Cancer (IBC) as an example of a carcinoma that can metastasize via clusters and corroborates the proposed molecular mechanisms.

cancer biology↗

bioRxiv2017

Guiding the design of bacterial signaling interactions using a coevolutionary landscape

The selection of amino acid identities that encode new interactions between two-component signaling (TCS) proteins remains a significant challenge. Recent work constructed a co-evolutionary landscape that can be used to select mutations to maintain signal transfer interactions between partner TCS proteins without introducing signal transfer between non-partners (crosstalk). A bigger challenge is to introduce mutations between non-natural partner TCS proteins using the landscape to enhance, suppress, or have a neutral effect on their basal signal transfer rates. This study focuses on the selection of mutations to a response regulator (RR) from Bacilus subtilis and its effect on phosphotransfer with a histidine kinase (HK) from Escherichia Coli. Twelve single-point mutations of the RR protein are selected from the landscape and experimentally expressed to directly test the theoretical predictions on the effect of signal transfer. Differential Scanning Calorimetry is used to monitor any protein stability effects caused by the mutations, which could be detrimental to proper protein function. Of these proteins, seven mutants successfully perturb phosphoryl transfer activity in the computationally predicted manner between the TCS proteins. Furthermore, brute-force exhaustive mutagenesis approaches indicate that only 1% of mutations result in enhanced activity. In comparison, of the six mutations predicted to enhance phosphotransfer, two mutations exhibit a significant enhancement while two mutations are comparable to the wild-type. Thus co-evolutionary landscape theory offers significant improvement over traditional large-scale mutational studies in the efficiency of selecting mutations for protein engineering and design.

bioinformatics↗

bioRxiv2017

Distinguishing Mechanisms Underlying EMT Tristability

BackgroundThe Epithelial-Mesenchymal Transition (EMT) endows epithelial-looking cells with enhanced migratory ability during embryonic development and tissue repair. EMT can also be co-opted by cancer cells to acquire metastatic potential and drug-resistance. Recent research has argued that epithelial (E) cells can undergo either a partial EMT to attain a hybrid epithelial/mesenchymal (E/M) phenotype that typically displays collective migration, or a complete EMT to adopt a mesenchymal (M) phenotype that shows individual migration. The core EMT regulatory network - miR-34/SNAIL/miR-200/ZEB1 - has been identified by various studies, but how this network regulates the transitions among the E, E/M, and M phenotypes remains controversial. Two major mathematical models - ternary chimera switch (TCS) and cascading bistable switches (CBS) - that both focus on the miR-34/SNAIL/miR-200/ZEB1 network, have been proposed to elucidate the EMT dynamics, but a detailed analysis of how well either or both of these two models can capture recent experimental observations about EMT dynamics remains to be done.\n\nResultsHere, via an integrated experimental and theoretical approach, we first show that both these two models can be used to understand the two-step transition of EMT - E[->]E/M[->]M, the different responses of SNAIL and ZEB1 to exogenous TGF-{beta} and the irreversibility of complete EMT. Next, we present new experimental results that tend to discriminate between these two models. We show that ZEB1 is present at intermediate levels in the hybrid E/M H1975 cells, and that in HMLE cells, overexpression of SNAIL is not sufficient to initiate EMT in the absence of ZEB1 and FOXC2.\n\nConclusionsThese experimental results argue in favor of the TCS model proposing that miR-200/ZEB1 behaves as a three-way decision-making switch enabling transitions among the E, hybrid E/M and M phenotypes.

cancer biology↗

bioRxiv2016

Interrogating the Topological Robustness of Gene Regulatory Circuits

One of the most important roles of cells is performing their cellular tasks properly for survival. Cells usually achieve robust functionality, for example cell-fate decision-making and signal transduction, through multiple layers of regulation involving many genes. Despite the combinatorial complexity of gene regulation, its quantitative behavior has been typically studied on the basis of experimentally-verified core gene regulatory circuitry, composed of a small set of important elements. It is still unclear how such a core circuit operates in the presence of many other regulatory molecules and in a crowded and noisy cellular environment. Here we report a new computational method, named random circuit perturbation (RACIPE), for interrogating the robust dynamical behavior of a gene regulatory circuit even without accurate measurements of circuit kinetic parameters. RACIPE generates an ensemble of random kinetic models corresponding to a fixed circuit topology, and utilizes statistical tools to identify generic properties of the circuit. By applying RACIPE to simple toggle-switch-like motifs, we observed that the stable states of all models converge to experimentally observed gene state clusters even when the parameters are strongly perturbed. RACIPE was further applied to a proposed 22-gene network of the Epithelial-to-Mesenchymal transition (EMT), from which we identified four experimentally observed gene states, including the states that are associated with two different types of hybrid Epithelial/Mesenchymal phenotypes. Our results suggest that dynamics of a gene circuit is mainly determined by its topology, not by detailed circuit parameters. Our work provides a theoretical foundation for circuit-based systems biology modeling. We anticipate RACIPE to be a powerful tool to predict and decode circuit design principles in an unbiased manner, and to quantitatively evaluate the robustness and heterogeneity of gene expression.

systems biology↗