Fibronectin induces a transition from amoeboid to a fan morphology and modifies migration in Entamoeba histolytica.

Cell migration modes can vary, depending on a number of environmental and intracellular factors. The high motility of the pathogenic amoeba Entamoeba histolytica is a decisive factor in its ability to cross the human colonic barrier. We used quantitative live imaging techniques to study the migration of this parasite on fibronectin, a key tissue component. Entamoeba histolytica amoebae on fibronectin contain abundant podosome-like structures. By using a laminar flow chamber, we determined that the adhesion forces generated on fibronectin were twice those on non-coated glass. When migrating on fibronectin, elongated amoeboid cells converted into fan-shaped cells characterized by the presence of a dorsal column of F-actin and a broad cytoplasmic extension at the front. The fan shape depended on the Arp2/3 complex, and the amoebae moved laterally and more slowly. Intracellular measurements of physical variables related to fluid dynamics revealed that cytoplasmic pressure gradients were weaker within fan-shaped cells; hence, actomyosin motors might be less involved in driving the cell body forward. We also found that the Rho-associated coiled-coil containing protein kinase regulated podosome dynamics. We conclude that E. histolytica spontaneously changes its migration mode as a function of the substrate composition. This adaptive ability might favour E. histolytica's invasion of human colonic tissue. By combining microfluidic experiments, mechanical modelling, and image analysis, our work also introduces a computational pipeline for the study of cell migration.

Genomic loci influence patterns of structural covariance in the human brain.

Normal and pathologic neurobiological processes influence brain morphology in coordinated ways that give rise to patterns of structural covariance (PSC) across brain regions and individuals during brain aging and diseases. The genetic underpinnings of these patterns remain largely unknown. We apply a stochastic multivariate factorization method to a diverse population of 50,699 individuals (12 studies and 130 sites) and derive data-driven, multi-scale PSCs of regional brain size. PSCs were significantly correlated with 915 genomic loci in the discovery set, 617 of which are newly identified, and 72% were independently replicated. Key pathways influencing PSCs involve reelin signaling, apoptosis, neurogenesis, and appendage development, while pathways of breast cancer indicate potential interplays between brain metastasis and PSCs associated with neurodegeneration and dementia. Using support vector machines, multi-scale PSCs effectively derive imaging signatures of several brain diseases. Our results elucidate genetic and biological underpinnings that influence structural covariance patterns in the human brain.

Chemokine-biased robust self-organizing polarization of migrating cells in vivo.

To study the mechanisms controlling front-rear polarity in migrating cells, we used zebrafish primordial germ cells (PGCs) as an in vivo model. We find that polarity of bleb-driven migrating cells can be initiated at the cell front, as manifested by actin accumulation at the future leading edge and myosin-dependent retrograde actin flow toward the other side of the cell. In such cases, the definition of the cell front, from which bleb-inhibiting proteins such as Ezrin are depleted, precedes the establishment of the cell rear, where those proteins accumulate. Conversely, following cell division, the accumulation of Ezrin at the cleavage plane is the first sign for cell polarity and this aspect of the cell becomes the cell back. Together, the antagonistic interactions between the cell front and back lead to a robust polarization of the cell. Furthermore, we show that chemokine signaling can bias the establishment of the front-rear axis of the cell, thereby guiding the migrating cells toward sites of higher levels of the attractant. We compare these results to a theoretical model according to which a critical value of actin treadmilling flow can initiate a positive feedback loop that leads to the generation of the front-rear axis and to stable cell polarization. Together, our in vivo findings and the mathematical model, provide an explanation for the observed nonoriented migration of primordial germ cells in the absence of the guidance cue, as well as for the directed migration toward the region where the gonad develops.

Artifacts in optical projection tomography due to refractive-index mismatch: model and correction.

Optical projection tomography (OPT) is a powerful tool for three-dimensional (3D) imaging of mesoscopic samples. While it is able to achieve resolution of a few tens of microns over a sample volume of several cubic centimeters, the reconstructed images often suffer from artifacts caused by inaccurate calibration. In this work, we focus on the refractive-index mismatch between the sample and the surrounding medium. We derive a 3D cone-beam forward model of OPT that approximates the effect of refractive-index mismatch. We then implement a fast and efficient reconstruction method to correct for the induced seagull-shaped artifacts on experimental images of fluorescent beads.

Sensitivity-Aware Density Estimation in Multiple Dimensions.

We formulate an optimization problem to estimate probability densities in the context of multidimensional problems that are sampled with uneven probability. It considers detector sensitivity as an heterogeneous density and takes advantage of the computational speed and flexible boundary conditions offered by splines on a grid. We choose to regularize the Hessian of the spline via the nuclear norm to promote sparsity. As a result, the method is spatially adaptive and stable against the choice of the regularization parameter, which plays the role of the bandwidth. We test our computational pipeline on standard densities and provide software. We also present a new approach to PET rebinning as an application of our framework.

Deep-prior ODEs augment fluorescence imaging with chemical sensors.

To study biological signalling, great effort goes into designing sensors whose fluorescence follows the concentration of chemical messengers as closely as possible. However, the binding kinetics of the sensors are often overlooked when interpreting cell signals from the resulting fluorescence measurements. We propose a method to reconstruct the spatiotemporal concentration of the underlying chemical messengers in consideration of the binding process. Our method fits fluorescence data under the constraint of the corresponding chemical reactions and with the help of a deep-neural-network prior. We test it on several GCaMP calcium sensors. The recovered concentrations concur in a common temporal waveform regardless of the sensor kinetics, whereas assuming equilibrium introduces artifacts. We also show that our method can reveal distinct spatiotemporal events in the calcium distribution of single neurons. Our work augments current chemical sensors and highlights the importance of incorporating physical constraints in computational imaging.

Three-dimensional cell culture conditions promoted the Mesenchymal-Amoeboid Transition in the Triple-Negative Breast Cancer cell line MDA-MB-231.

Introduction: Breast cancer (BC) is the leading cause of death among women, primarily due to its potential for metastasis. As BC progresses, the extracellular matrix (ECM) produces more type-I collagen, resulting in increased stiffness. This alteration influences cellular behaviors such as migration, invasion, and metastasis. Specifically, cancer cells undergo changes in gene expression that initially promote an epithelial-to-mesenchymal transition (EMT) and subsequently, a transition from a mesenchymal to an amoeboid (MAT) migration mode. In this way, cancer cells can migrate more easily through the stiffer microenvironment. Despite their importance, understanding MATs remains challenging due to the difficulty of replicating in vitro the conditions for cell migration that are observed in vivo. Methods: To address this challenge, we developed a three-dimensional (3D) growth system that replicates the different matrix properties observed during the progression of a breast tumor. We used this model to study the migration and invasion of the Triple-Negative BC (TNBC) cell line MDA-MB-231, which is particularly subject to metastasis. Results: Our results indicate that denser collagen matrices present a reduction in porosity, collagen fiber size, and collagen fiber orientation, which are associated with the transition of cells to a rounder morphology with bleb-like protrusions. We quantified how this transition is associated with a more persistent migration, an enhanced invasion capacity, and a reduced secretion of matrix metalloproteinases. Discussion: Our findings suggest that the proposed 3D growth conditions (especially those with high collagen concentrations) mimic key features of MATs, providing a new platform to study the physiology of migratory transitions and their role in BC progression.

The genetic architecture of multimodal human brain age.

The complex biological mechanisms underlying human brain aging remain incompletely understood. This study investigated the genetic architecture of three brain age gaps (BAG) derived from gray matter volume (GM-BAG), white matter microstructure (WM-BAG), and functional connectivity (FC-BAG). We identified sixteen genomic loci that reached genome-wide significance (P-value < 5×10-8). A gene-drug-disease network highlighted genes linked to GM-BAG for treating neurodegenerative and neuropsychiatric disorders and WM-BAG genes for cancer therapy. GM-BAG displayed the most pronounced heritability enrichment in genetic variants within conserved regions. Oligodendrocytes and astrocytes, but not neurons, exhibited notable heritability enrichment in WM and FC-BAG, respectively. Mendelian randomization identified potential causal effects of several chronic diseases on brain aging, such as type 2 diabetes on GM-BAG and AD on WM-BAG. Our results provide insights into the genetics of human brain aging, with clinical implications for potential lifestyle and therapeutic interventions. All results are publicly available at https://labs.loni.usc.edu/medicine .

Genetic and clinical correlates of two neuroanatomical AI dimensions in the Alzheimer's disease continuum.

Alzheimer's disease (AD) is associated with heterogeneous atrophy patterns. We employed a semi-supervised representation learning technique known as Surreal-GAN, through which we identified two latent dimensional representations of brain atrophy in symptomatic mild cognitive impairment (MCI) and AD patients: the "diffuse-AD" (R1) dimension shows widespread brain atrophy, and the "MTL-AD" (R2) dimension displays focal medial temporal lobe (MTL) atrophy. Critically, only R2 was associated with widely known sporadic AD genetic risk factors (e.g., APOE ε4) in MCI and AD patients at baseline. We then independently detected the presence of the two dimensions in the early stages by deploying the trained model in the general population and two cognitively unimpaired cohorts of asymptomatic participants. In the general population, genome-wide association studies found 77 genes unrelated to APOE differentially associated with R1 and R2. Functional analyses revealed that these genes were overrepresented in differentially expressed gene sets in organs beyond the brain (R1 and R2), including the heart (R1) and the pituitary gland, muscle, and kidney (R2). These genes were enriched in biological pathways implicated in dendritic cells (R2), macrophage functions (R1), and cancer (R1 and R2). Several of them were "druggable genes" for cancer (R1), inflammation (R1), cardiovascular diseases (R1), and diseases of the nervous system (R2). The longitudinal progression showed that APOE ε4, amyloid, and tau were associated with R2 at early asymptomatic stages, but this longitudinal association occurs only at late symptomatic stages in R1. Our findings deepen our understanding of the multifaceted pathogenesis of AD beyond the brain. In early asymptomatic stages, the two dimensions are associated with diverse pathological mechanisms, including cardiovascular diseases, inflammation, and hormonal dysfunction-driven by genes different from APOE-which may collectively contribute to the early pathogenesis of AD. All results are publicly available at https://labs-laboratory.com/medicine/ .

Reformulating Optical Flow to Solve Image-Based Inverse Problems and Quantify Uncertainty.

From meteorology to medical imaging and cell mechanics, many scientific domains use inverse problems (IPs) to extract physical measurements from image movement. To this end, motion estimation methods such as optical flow (OF) pre-process images into motion data to feed the IP, which then inverts for the measurements through a physical model. However, this combined OFIP pipeline exacerbates the ill-posedness inherent to each technique, propagating errors and preventing uncertainty quantification. We introduce a Bayesian PDE-constrained framework that transforms visual information directly into physical measurements in the context of probability distributions. The posterior mean is a constrained IP that tracks brightness while satisfying the physical model, thereby translating the aperture problem from the motion to the underlying physics; whereas the posterior covariance derives measurement error out of image noise. As we illustrate with traction force microscopy, our approach offers several advantages: more accurate reconstructions; unprecedented flexibility in experiment design (e.g., arbitrary boundary conditions); and the exclusivity of measurement error, central to empirical science, yet still unavailable under the OFIP strategy.

Neuroimaging-AI Endophenotypes of Brain Diseases in the General Population: Towards a Dimensional System of Vulnerability.

Disease heterogeneity poses a significant challenge for precision diagnostics in both clinical and sub-clinical stages. Recent work leveraging artificial intelligence (AI) has offered promise to dissect this heterogeneity by identifying complex intermediate phenotypes - herein called dimensional neuroimaging endophenotypes (DNEs) - which subtype various neurologic and neuropsychiatric diseases. We investigate the presence of nine such DNEs derived from independent yet harmonized studies on Alzheimer's disease (AD1-2)1, autism spectrum disorder (ASD1-3)2, late-life depression (LLD1-2)3, and schizophrenia (SCZ1-2)4, in the general population of 39,178 participants in the UK Biobank study. Phenome-wide associations revealed prominent associations between the nine DNEs and phenotypes related to the brain and other human organ systems. This phenotypic landscape aligns with the SNP-phenotype genome-wide associations, revealing 31 genomic loci associated with the nine DNEs (Bonferroni corrected P-value < 5×10-8/9). The DNEs exhibited significant genetic correlations, colocalization, and causal relationships with multiple human organ systems and chronic diseases. A causal effect (odds ratio=1.25 [1.11, 1.40], P-value=8.72×1-4) was established from AD2, characterized by focal medial temporal lobe atrophy, to AD. The nine DNEs and their polygenic risk scores significantly improved the prediction accuracy for 14 systemic disease categories and mortality. These findings underscore the potential of the nine DNEs to identify individuals at a high risk of developing the four brain diseases during preclinical stages for precision diagnostics. All results are publicly available at: http://labs.loni.usc.edu/medicine/.

The Genetic Architecture of Multimodal Human Brain Age.

The complex biological mechanisms underlying human brain aging remain incompletely understood, involving multiple body organs and chronic diseases. In this study, we used multimodal magnetic resonance imaging and artificial intelligence to examine the genetic architecture of the brain age gap (BAG) derived from gray matter volume (GM-BAG, N=31,557 European ancestry), white matter microstructure (WM-BAG, N=31,674), and functional connectivity (FC-BAG, N=32,017). We identified sixteen genomic loci that reached genome-wide significance (P-value<5×10-8). A gene-drug-disease network highlighted genes linked to GM-BAG for treating neurodegenerative and neuropsychiatric disorders and WM-BAG genes for cancer therapy. GM-BAG showed the highest heritability enrichment for genetic variants in conserved regions, whereas WM-BAG exhibited the highest heritability enrichment in the 5' untranslated regions; oligodendrocytes and astrocytes, but not neurons, showed significant heritability enrichment in WM and FC-BAG, respectively. Mendelian randomization identified potential causal effects of several exposure variables on brain aging, such as type 2 diabetes on GM-BAG (odds ratio=1.05 [1.01, 1.09], P-value=1.96×10-2) and AD on WM-BAG (odds ratio=1.04 [1.02, 1.05], P-value=7.18×10-5). Overall, our results provide valuable insights into the genetics of human brain aging, with clinical implications for potential lifestyle and therapeutic interventions. All results are publicly available at the MEDICINE knowledge portal: https://labs.loni.usc.edu/medicine.

4D live imaging and computational modeling of a functional gut-on-a-chip evaluate how peristalsis facilitates enteric pathogen invasion.

Physical forces are essential to biological function, but their impact at the tissue level is not fully understood. The gut is under continuous mechanical stress because of peristalsis. To assess the influence of mechanical cues on enteropathogen invasion, we combine computational imaging with a mechanically active gut-on-a-chip. After infecting the device with either of two microbes, we image their behavior in real time while mapping the mechanical stress within the tissue. This is achieved by reconstructing three-dimensional videos of the ongoing invasion and leveraging on-manifold inverse problems together with viscoelastic rheology. Our results show that peristalsis accelerates the destruction and invasion of intestinal tissue by Entamoeba histolytica and colonization by Shigella flexneri. Local tension facilitates parasite penetration and activates virulence genes in the bacteria. Overall, our work highlights the fundamental role of physical cues during host-pathogen interactions and introduces a framework that opens the door to study mechanobiology on deformable tissues.

Bioimage Analysis and Cell Motility.

Bioimage analysis (BIA) has historically helped study how and why cells move; biological experiments evolved in intimate feedback with the most classical image processing techniques because they contribute objectivity and reproducibility to an eminently qualitative science. Cell segmentation, tracking, and morphology descriptors are all discussed here. Using ameboid motility as a case study, these methods help us illustrate how proper quantification can augment biological data, for example, by choosing mathematical representations that amplify initially subtle differences, by statistically uncovering general laws or by integrating physical insight. More recently, the non-invasive nature of quantitative imaging is fertilizing two blooming fields: mechanobiology, where many biophysical measurements remain inaccessible, and microenvironments, where the quest for physiological relevance has exploded data size. From relief to remedy, this trend indicates that BIA is to become a main vector of biological discovery as human visual analysis struggles against ever more complex data.

E-cadherin focuses protrusion formation at the front of migrating cells by impeding actin flow.

The migration of many cell types relies on the formation of actomyosin-dependent protrusions called blebs, but the mechanisms responsible for focusing this kind of protrusive activity to the cell front are largely unknown. Here, we employ zebrafish primordial germ cells (PGCs) as a model to study the role of cell-cell adhesion in bleb-driven single-cell migration in vivo. Utilizing a range of genetic, reverse genetic and mathematical tools, we define a previously unknown role for E-cadherin in confining bleb-type protrusions to the leading edge of the cell. We show that E-cadherin-mediated frictional forces impede the backwards flow of actomyosin-rich structures that define the domain where protrusions are preferentially generated. In this way, E-cadherin confines the bleb-forming region to a restricted area at the cell front and reinforces the front-rear axis of migrating cells. Accordingly, when E-cadherin activity is reduced, the bleb-forming area expands, thus compromising the directional persistence of the cells.

Fluid dynamics during bleb formation in migrating cells in vivo.

Blebs are cellular protrusions observed in migrating cells and in cells undergoing spreading, cytokinesis, and apoptosis. Here we investigate the flow of cytoplasm during bleb formation and the concurrent changes in cell volume using zebrafish primordial germ cells (PGCs) as an in vivo model. We show that bleb inflation occurs concomitantly with cytoplasmic inflow into it and that during this process the total cell volume does not change. We thus show that bleb formation in primordial germ cells results primarily from redistribution of material within the cell rather than being driven by flow of water from an external source.

Tracking and line integration of diffuse cellular subdomains by mesh advection.

Active molecular transport ensures a purposeful spatiotemporal distribution of cellular proteins and is therefore key to a wide range of processes such as morphogenesis, homeostasis or migration. However, redistributions of molecules in bulk are seldom quantified because the regions involved are too diffuse to be segmented consistently. To bridge this gap, we propose a Laplace-corrected Runge-Kutta advection that is based on mesh triangulation. Our framework can follow the movement and deformation of multiple parts of a diffuse region at once and offers a seamless combination with spatiotemporal line integration in Lagrangian coordinates. This allows the flexibility to taylor specific measures to the question at hand, e.g. mechanical work, bringing long-established physics concepts into biology grounds. We exemplify our approach by quantifying how the isotropy of intracellular protein distributions changes during cargo transport.

BioFlow: a non-invasive, image-based method to measure speed, pressure and forces inside living cells.

Cell motility is governed by a complex molecular machinery that converts physico-chemical cues into whole-cell movement. Understanding the underlying biophysical mechanisms requires the ability to measure physical quantities inside the cell in a simple, reproducible and preferably non-invasive manner. To this end, we developed BioFlow, a computational mechano-imaging method and associated software able to extract intracellular measurements including pressure, forces and velocity everywhere inside freely moving cells in two and three dimensions with high spatial resolution in a non-invasive manner. This is achieved by extracting the motion of intracellular material observed using fluorescence microscopy, while simultaneously inferring the parameters of a given theoretical model of the cell interior. We illustrate the power of BioFlow in the context of amoeboid cell migration, by modelling the intracellular actin bulk flow of the parasite Entamoeba histolytica using fluid dynamics, and report unique experimental measures that complement and extend both theoretical estimations and invasive experimental measures. Thanks to its flexibility, BioFlow is easily adaptable to other theoretical models of the cell, and alleviates the need for complex or invasive experimental conditions, thus constituting a powerful tool-kit for mechano-biology studies. BioFlow is open-source and freely available via the Icy software.