Cell state transitions: catch them if you can

The Company of Biologists' 2022 workshop on 'Cell State Transitions: Approaches, Experimental Systems and Models' brought together an international and interdisciplinary team of investigators spanning the fields of cell and developmental biology, stem cell biology, physics, mathematics and engineering to tackle the question of how cells precisely navigate between distinct identities and do so in a dynamic manner. This second edition of the workshop was organized after a successful virtual workshop on the same topic that took place in 2021.

Interplay between mechanics and signalling in regulating cell fate

Mechanical signalling affects multiple biological processes during development and in adult organisms, including cell fate transitions, cell migration, morphogenesis and immune responses. Here, we review recent insights into the mechanisms and functions of two main routes of mechanical signalling: outside-in mechanical signalling, such as mechanosensing of substrate properties or shear stresses; and mechanical signalling regulated by the physical properties of the cell surface itself. We discuss examples of how these two classes of mechanical signalling regulate stem cell function, as well as developmental processes in vivo. We also discuss how cell surface mechanics affects intracellular signalling and, in turn, how intracellular signalling controls cell surface mechanics, generating feedback into the regulation of mechanosensing. The cooperation between mechanosensing, intracellular signalling and cell surface mechanics has a profound impact on biological processes. We discuss here our understanding of how these three elements interact to regulate stem cell fate and development.

Cell surface fluctuations regulate early embryonic lineage sorting

In development, lineage segregation is coordinated in time and space. An important example is the mammalian inner cell mass, in which the primitive endoderm (PrE, founder of the yolk sac) physically segregates from the epiblast (EPI, founder of the fetus). While the molecular requirements have been well studied, the physical mechanisms determining spatial segregation between EPI and PrE remain elusive. Here, we investigate the mechanical basis of EPI and PrE sorting. We find that rather than the differences in static cell surface mechanical parameters as in classical sorting models, it is the differences in surface fluctuations that robustly ensure physical lineage sorting. These differential surface fluctuations systematically correlate with differential cellular fluidity, which we propose together constitute a non-equilibrium sorting mechanism for EPI and PrE lineages. By combining experiments and modeling, we identify cell surface dynamics as a key factor orchestrating the correct spatial segregation of the founder embryonic lineages.

StemBond hydrogels control the mechanical microenvironment for pluripotent stem cells

Studies of mechanical signalling are typically performed by comparing cells cultured on soft and stiff hydrogel-based substrates. However, it is challenging to independently and robustly control both substrate stiffness and extracellular matrix tethering to substrates, making matrix tethering a potentially confounding variable in mechanical signalling investigations. Moreover, unstable matrix tethering can lead to poor cell attachment and weak engagement of cell adhesions. To address this, we developed StemBond hydrogels, a hydrogel in which matrix tethering is robust and can be varied independently of stiffness. We validate StemBond hydrogels by showing that they provide an optimal system for culturing mouse and human pluripotent stem cells. We further show how soft StemBond hydrogels modulate stem cell function, partly through stiffness-sensitive ERK signalling. Our findings underline how substrate mechanics impact mechanosensitive signalling pathways regulating self-renewal and differentiation, indicating that optimising the complete mechanical microenvironment will offer greater control over stem cell fate specification.

Cell state transitions: definitions and challenges

A fundamental challenge when studying biological systems is the description of cell state dynamics. During transitions between cell states, a multitude of parameters may change - from the promoters that are active, to the RNAs and proteins that are expressed and modified. Cells can also adopt different shapes, alter their motility and change their reliance on cell-cell junctions or adhesion. These parameters are integral to how a cell behaves and collectively define the state a cell is in. Yet, technical challenges prevent us from measuring all of these parameters simultaneously and dynamically. How, then, can we comprehend cell state transitions using finite descriptions? The recent virtual workshop organised by The Company of Biologists entitled 'Cell State Transitions: Approaches, Experimental Systems and Models' attempted to address this question. Here, we summarise some of the main points that emerged during the workshop's themed discussions. We also present examples of cell state transitions and describe models and systems that are pushing forward our understanding of how cells rewire their state.

Three-dimensional geometry controls division symmetry in stem cell colonies

Proper control of division orientation and symmetry, largely determined by spindle positioning, is essential to development and homeostasis. Spindle positioning has been extensively studied in cells dividing in two-dimensional (2D) environments and in epithelial tissues, where proteins such as NuMA (also known as NUMA1) orient division along the interphase long axis of the cell. However, little is known about how cells control spindle positioning in three-dimensional (3D) environments, such as early mammalian embryos and a variety of adult tissues. Here, we use mouse embryonic stem cells (ESCs), which grow in 3D colonies, as a model to investigate division in 3D. We observe that, at the periphery of 3D colonies, ESCs display high spindle mobility and divide asymmetrically. Our data suggest that enhanced spindle movements are due to unequal distribution of the cell-cell junction protein E-cadherin between future daughter cells. Interestingly, when cells progress towards differentiation, division becomes more symmetric, with more elongated shapes in metaphase and enhanced cortical NuMA recruitment in anaphase. Altogether, this study suggests that in 3D contexts, the geometry of the cell and its contacts with neighbors control division orientation and symmetry. This article has an associated First Person interview with the first author of the paper.

Membrane Tension Gates ERK-Mediated Regulation of Pluripotent Cell Fate

Cell fate transitions are frequently accompanied by changes in cell shape and mechanics. However, how cellular mechanics affects the instructive signaling pathways controlling cell fate is poorly understood. To probe the interplay between shape, mechanics, and fate, we use mouse embryonic stem cells (ESCs), which change shape as they undergo early differentiation. We find that shape change is regulated by a β-catenin-mediated decrease in RhoA activity and subsequent decrease in the plasma membrane tension. Strikingly, preventing a decrease in membrane tension results in early differentiation defects in ESCs and gastruloids. Decreased membrane tension facilitates the endocytosis of FGF signaling components, which activate ERK signaling and direct the exit from the ESC state. Increasing Rab5a-facilitated endocytosis rescues defective early differentiation. Thus, we show that a mechanically triggered increase in endocytosis regulates early differentiation. Our findings are of fundamental importance for understanding how cell mechanics regulates biochemical signaling and therefore cell fate.

Abscission Couples Cell Division to Embryonic Stem Cell Fate

Cell fate transitions are key to development and homeostasis. It is thus essential to understand the cellular mechanisms controlling fate transitions. Cell division has been implicated in fate decisions in many stem cell types, including neuronal and epithelial progenitors. In other stem cells, such as embryonic stem (ES) cells, the role of division remains unclear. Here, we show that exit from naive pluripotency in mouse ES cells generally occurs after a division. We further show that exit timing is strongly correlated between sister cells, which remain connected by cytoplasmic bridges long after division, and that bridge abscission progressively accelerates as cells exit naive pluripotency. Finally, interfering with abscission impairs naive pluripotency exit, and artificially inducing abscission accelerates it. Altogether, our data indicate that a switch in the division machinery leading to faster abscission regulates pluripotency exit. Our study identifies abscission as a key cellular process coupling cell division to fate transitions.

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Mouse embryonic stem cells exit naive pluripotency after mitosis

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Naive embryonic stem cells display slow abscission and remain connected by bridges

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Cells exiting naive pluripotency display faster abscission

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Accelerating abscission facilitates exit from naive pluripotency

Cortical cell stiffness is independent of substrate mechanics

Cortical stiffness is an important cellular property that changes during migration, adhesion and growth. Previous atomic force microscopy (AFM) indentation measurements of cells cultured on deformable substrates have suggested that cells adapt their stiffness to that of their surroundings. Here we show that the force applied by AFM to a cell results in a significant deformation of the underlying substrate if this substrate is softer than the cell. This 'soft substrate effect' leads to an underestimation of a cell's elastic modulus when analysing data using a standard Hertz model, as confirmed by finite element modelling and AFM measurements of calibrated polyacrylamide beads, microglial cells and fibroblasts. To account for this substrate deformation, we developed a 'composite cell-substrate model'. Correcting for the substrate indentation revealed that cortical cell stiffness is largely independent of substrate mechanics, which has major implications for our interpretation of many physiological and pathological processes.

Microfluidic platform for 3D cell culture with live imaging and clone retrieval

Combining live imaging with the ability to retrieve individual cells of interest remains a technical challenge. Combining imaging with precise cell retrieval is of particular interest when studying highly dynamic or transient, asynchronous, or heterogeneous cell biological and developmental processes. Here, we present a method to encapsulate live cells in a 3D hydrogel matrix, via hydrogel bead compartmentalisation. Using a small-scale screen, we optimised matrix conditions for the culture and multilineage differentiation of mouse embryonic stem cells. Moreover, we designed a custom microfluidic platform that is compatible with live imaging. With this platform we can long-term culture and subsequently extract individual cells-in-beads by media flow only, obviating the need for enzymatic cell removal from the platform. Specific beads may be extracted from the platform in isolation, without disrupting the adjacent beads. We show that we can differentiate mouse embryonic stem cells, monitor reporter expression by live imaging, and retrieve individual beads for functional assays, correlating reporter expression with functional response. Overall, we present a highly flexible 3D cell encapsulation and microfluidic platform that enables both monitoring of cellular dynamics and retrieval for molecular and functional assays.

Embryonic stem cells become mechanoresponsive upon exit from ground state of pluripotency

Stem cell fate decisions are driven by a broad array of signals, both chemical and mechanical. Although much progress has been made in our understanding of the impact of chemical signals on cell fate choice, much less is known about the role and influence of mechanical signalling, particularly in embryonic stem (ES) cells. Many studies use substrates with different stiffness to study mechanical signalling, but changing substrate stiffness can induce secondary effects which are difficult to disentangle from the direct effects of forces/mechanical signals. To probe the direct impact of mechanical stress on cells, we developed an adaptable cell substrate stretcher to exert specific, reproducible forces on cells. Using this device to test the response of ES cells to tensile strain, we found that cells experienced a transient influx of calcium followed by an upregulation of the so-called immediate and early genes. On longer time scales, however, ES cells in ground state conditions were largely insensitive to mechanical stress. Nonetheless, as ES cells exited the ground state, their susceptibility to mechanical signals increased, resulting in broad transcriptional changes. Our findings suggest that exit from ground state of pluripotency is unaffected by mechanical signals, but that these signals could become important during the next stage of lineage specification. A better understanding of this process could improve our understanding of cell fate choice in early development and improve protocols for differentiation guided by mechanical cues.

Remyelination and ageing: Reversing the ravages of time

Remyelination is a neuroprotective regenerative response to demyelination that restores saltatory conduction and decreases the vulnerability of axons to irreversible degeneration. It is a highly efficient process: however, as with all regenerative processes, its efficiency declines with ageing. Here we argue that this age-related decline in remyelination has a major impact on the natural history of multiple sclerosis (MS), a disease often of several decades' duration. We describe recent work on (1) how ageing changes the function of oligodendrocyte progenitor cells (OPCs), the cells primarily responsible for generating new myelin-forming oligodendrocytes in remyelination, (2) how these changes are induced by age-related changes in the OPC niche and (3) how these changes can be reversed, thereby opening up the possibility of therapeutically maintaining remyelination efficiency throughout the disease, preserving axonal health and treating the progressive phase of MS.

Niche stiffness underlies the ageing of central nervous system progenitor cells

Ageing causes a decline in tissue regeneration owing to a loss of function of adult stem cell and progenitor cell populations1. One example is the deterioration of the regenerative capacity of the widespread and abundant population of central nervous system (CNS) multipotent stem cells known as oligodendrocyte progenitor cells (OPCs)2. A relatively overlooked potential source of this loss of function is the stem cell 'niche'-a set of cell-extrinsic cues that include chemical and mechanical signals3,4. Here we show that the OPC microenvironment stiffens with age, and that this mechanical change is sufficient to cause age-related loss of function of OPCs. Using biological and synthetic scaffolds to mimic the stiffness of young brains, we find that isolated aged OPCs cultured on these scaffolds are molecularly and functionally rejuvenated. When we disrupt mechanical signalling, the proliferation and differentiation rates of OPCs are increased. We identify the mechanoresponsive ion channel PIEZO1 as a key mediator of OPC mechanical signalling. Inhibiting PIEZO1 overrides mechanical signals in vivo and allows OPCs to maintain activity in the ageing CNS. We also show that PIEZO1 is important in regulating cell number during CNS development. Thus we show that tissue stiffness is a crucial regulator of ageing in OPCs, and provide insights into how the function of adult stem and progenitor cells changes with age. Our findings could be important not only for the development of regenerative therapies, but also for understanding the ageing process itself.

Transforming growth factor-beta renders ageing microglia inhibitory to oligodendrocyte generation by CNS progenitors

It is now well-established that the macrophage and microglial response to CNS demyelination influences remyelination by removing myelin debris and secreting a variety of signaling molecules that influence the behaviour of oligodendrocyte progenitor cells (OPCs). Previous studies have shown that changes in microglia contribute to the age-related decline in the efficiency of remyelination. In this study, we show that microglia increase their expression of the proteoglycan NG2 with age, and that this is associated with an altered micro-niche generated by aged, but not young, microglia that can divert the differentiation OPCs from oligodendrocytes into astrocytes in vitro. We further show that these changes in ageing microglia are generated by exposure to high levels of TGFβ. Thus, our findings suggest that the rising levels of circulating TGFβ known to occur with ageing contribute to the age-related decline in remyelination by impairing the ability of microglia to promote oligodendrocyte differentiation from OPCs, and therefore could be a potential therapeutic target to promote remyelination.

Force-based three-dimensional model predicts mechanical drivers of cell sorting

Many biological processes, including tissue morphogenesis, are driven by cell sorting. However, the primary mechanical drivers of sorting in multicellular aggregates (MCAs) remain controversial, in part because there is no appropriate computational model to probe mechanical interactions between cells. To address this important issue, we developed a three-dimensional, local force-based simulation based on the subcellular element method. In our method, cells are modelled as collections of locally interacting force-bearing elements. We use the method to investigate the effects of tension and cell-cell adhesion on MCA sorting. We predict a minimum level of adhesion to produce inside-out sorting of two cell types, which is in excellent agreement with observations in several developmental systems. We also predict the level of tension asymmetry needed for robust sorting. The generality and flexibility of the method make it applicable to tissue self-organization in a myriad of other biological processes, such as tumorigenesis and embryogenesis.

Equally probable positive and negative Poisson's ratios in disordered planar systems

Auxetic materials, characterised by a negative Poisson's ratio, have properties that are different from most conventional materials. These are a result of the constraints on the kinematics of the material's basic structural components, and have important technological implications. Models of these materials have been studied extensively, but theoretical descriptions have remained largely limited to materials with an ordered microstructure. Here we investigate whether negative Poisson's ratios can arise spontaneously in disordered systems. To this end, we develop a quantitative description of the structure in systems of connected basic elements, which enables us to analyse the local and global responses to small external tensile forces. We find that the Poisson's ratios in these disordered systems are equally likely to be positive or negative on both the element and system scales. Separating the strain into translational, rotational and expansive components, we find that the translational strains of neighbouring basic structural elements are positively correlated, while their rotations are negatively correlated. There is no correlation in this type of system between the local auxeticity and local structural characteristics. Our results suggest that auxeticity is more common in disordered structures than the ubiquity of positive Poisson's ratios in macroscopic materials would suggest.

A microfluidic device for characterizing nuclear deformations

Cell nuclei experience and respond to a wide range of forces, both in vivo and in vitro. In order to characterize the nuclear response to physical stress, we developed a microfluidic chip and used it to apply mechanical stress to live cells and measure their nuclear deformability. The device design is optimized for the detection of both nucleus and cytoplasm, which can then be conveniently quantified using a custom-written Matlab program. We measured nuclear sizes and strains of embryonic stem cells, for which we observed negative Poisson ratios in the nuclei. In addition, we were able to detect changes in the nuclear response after treatment with actin depolymerizing and chromatin decondensing agents. Finally, we showed that the device can be used for biologically relevant high-resolution confocal imaging of cells under compression. Thus, the device presented here allows for accurate physical phenotyping at high throughput and has the potential to be applied to a range of cell types.

Myosin II Activity Softens Cells in Suspension

The cellular cytoskeleton is crucial for many cellular functions such as cell motility and wound healing, as well as other processes that require shape change or force generation. Actin is one cytoskeleton component that regulates cell mechanics. Important properties driving this regulation include the amount of actin, its level of cross-linking, and its coordination with the activity of specific molecular motors like myosin. While studies investigating the contribution of myosin activity to cell mechanics have been performed on cells attached to a substrate, we investigated mechanical properties of cells in suspension. To do this, we used multiple probes for cell mechanics including a microfluidic optical stretcher, a microfluidic microcirculation mimetic, and real-time deformability cytometry. We found that nonadherent blood cells, cells arrested in mitosis, and naturally adherent cells brought into suspension, stiffen and become more solidlike upon myosin inhibition across multiple timescales (milliseconds to minutes). Our results hold across several pharmacological and genetic perturbations targeting myosin. Our findings suggest that myosin II activity contributes to increased whole-cell compliance and fluidity. This finding is contrary to what has been reported for cells attached to a substrate, which stiffen via active myosin driven prestress. Our results establish the importance of myosin II as an active component in modulating suspended cell mechanics, with a functional role distinctly different from that for substrate-adhered cells.

Refractive index measurements of single, spherical cells using digital holographic microscopy

In this chapter, we introduce digital holographic microscopy (DHM) as a marker-free method to determine the refractive index of single, spherical cells in suspension. The refractive index is a conclusive measure in a biological context. Cell conditions, such as differentiation or infection, are known to yield significant changes in the refractive index. Furthermore, the refractive index of biological tissue determines the way it interacts with light. Besides the biological relevance of this interaction in the retina, a lot of methods used in biology, including microscopy, rely on light-tissue or light-cell interactions. Hence, determining the refractive index of cells using DHM is valuable in many biological applications. This chapter covers the main topics that are important for the implementation of DHM: setup, sample preparation, and analysis. First, the optical setup is described in detail including notes and suggestions for the implementation. Following that, a protocol for the sample and measurement preparation is explained. In the analysis section, an algorithm for the determination of quantitative phase maps is described. Subsequently, all intermediate steps for the calculation of the refractive index of suspended cells are presented, exploiting their spherical shape. In the last section, a discussion of possible extensions to the setup, further measurement configurations, and additional analysis methods are given. Throughout this chapter, we describe a simple, robust, and thus easily reproducible implementation of DHM. The different possibilities for extensions show the diverse fields of application for this technique.

Auxetic nuclei in embryonic stem cells exiting pluripotency

Embryonic stem cells (ESCs) self-renew in a state of naïve pluripotency in which they are competent to generate all somatic cells. It has been hypothesized that, before irreversibly committing, ESCs pass through at least one metastable transition state. This transition would represent a gateway for differentiation and reprogramming of somatic cells. Here, we show that during the transition, the nuclei of ESCs are auxetic: they exhibit a cross-sectional expansion when stretched and a cross-sectional contraction when compressed, and their stiffness increases under compression. We also show that the auxetic phenotype of transition ESC nuclei is driven at least in part by global chromatin decondensation. Through the regulation of molecular turnover in the differentiating nucleus by external forces, auxeticity could be a key element in mechanotransduction. Our findings highlight the importance of nuclear structure in the regulation of differentiation and reprogramming.

Bacterial infection of macrophages induces decrease in refractive index

Infection of cells by pathogens leads to both biochemical and structural modifications of the host cell. To study the structural modifications in a label-free manner, we use digital holographic microscopy, DHM, to obtain the integral refractive index distribution of cells. Primary murine bone marrow derived macrophages (BMDM) infected with Salmonella enterica serovar Typhimurium, undergo highly significant reduction in refractive index, RI, compared to uninfected cells. Infected BMDM cells from genetically modified mice lacking an inflammatory protein that causes cell death, caspase 1, also exhibit similar decrease in RI. These data suggest that any reduction in RI of Salmonella-infected BMDMs is pathogen induced and independent of caspase 1-induced inflammation or cell death. This finding suggests DHM may be useful for general real time monitoring of host cell interactions with infectious pathogens.

Nuclear morphology measurements with angle-resolved low coherence interferometry for application to cell biology and early cancer detection

The study of intact, living cells using non-invasive optical spectroscopic methods offers the opportunity to assess cellular structure and organization in a way that is not possible with commonly used cell biology imaging techniques. We have developed a novel spectroscopic technique for diagnosing disease at the cellular level based on using low-coherence interferometry (LCI) to detect the angular distribution of scattered light. Angle-resolved LCI (a/LCI) combines the ability of LCI to isolate scattering from sub-surface tissue layers with the ability of light scattering spectroscopy to obtain structural information on sub-wavelength scales. In application to examining cellular structure, a/LCI enables quantitative measurements of changes in the size and texture of cell nuclei. These quantitative measurements are characteristic of different pathological states. The capabilities of a/LCI were demonstrated using a clinical system that can be applied in endoscopic surveillance of esophageal tissue, producing high sensitivity and specificity for detecting dysplastic tissues in vivo. Experiments with in vitro cell samples also show the utility of a/LCI in observing structural changes due to environmental stimuli as well as detecting apoptosis due to chemotherapeutic agents.

Chromatin decondensation and nuclear softening accompany Nanog downregulation in embryonic stem cells

The interplay between epigenetic modification and chromatin compaction is implicated in the regulation of gene expression, and it comprises one of the most fascinating frontiers in cell biology. Although a complete picture is still lacking, it is generally accepted that the differentiation of embryonic stem (ES) cells is accompanied by a selective condensation into heterochromatin with concomitant gene silencing, leaving access only to lineage-specific genes in the euchromatin. ES cells have been reported to have less condensed chromatin, as they are capable of differentiating into any cell type. However, pluripotency itself-even prior to differentiation-is a split state comprising a naïve state and a state in which ES cells prime for differentiation. Here, we show that naïve ES cells decondense their chromatin in the course of downregulating the pluripotency marker Nanog before they initiate lineage commitment. We used fluorescence recovery after photobleaching, and histone modification analysis paired with a novel, to our knowledge, optical stretching method, to show that ES cells in the naïve state have a significantly stiffer nucleus that is coupled to a globally more condensed chromatin state. We link this biophysical phenotype to coinciding epigenetic differences, including histone methylation, and show a strong correlation of chromatin condensation and nuclear stiffness with the expression of Nanog. Besides having implications for transcriptional regulation and embryonic cell sorting and suggesting a putative mechanosensing mechanism, the physical differences point to a system-level regulatory role of chromatin in maintaining pluripotency in embryonic development.

Stem cell differentiation indicated by noninvasive photonic characterization and fractal analysis of subcellular architecture

We hypothesised that global structural changes in stem cells would manifest with differentiation, and that these changes would be observable with light scattering microscopy. Analysed with a fractal dimension formalism, we observed significant structural changes in differentiating human mesenchymal stem cells within one day after induction, earlier than could be detected by gene expression profiling. Moreover, light scattering microscopy is entirely non-perturbative, so the same sample could be monitored throughout the differentiation process. We explored one possible mechanism, chromatin remodelling, to account for the changes we observed. Correlating with the staining of HP1α, a heterochromatin protein, we applied novel microscopy methods and fractal analysis to monitor the plastic dynamics of chromatin within stem cell nuclei. We showed that the level of chromatin condensation changed during differentiation, and provide one possible explanation for the changes seen with the light scattering method. These results lend physical insight into stem cell differentiation while providing physics-based methods for non-invasive detection of the differentiation process.

Exact analytical expansion of an off-axis Gaussian laser beam using the translation theorems for the vector spherical harmonics

The interaction of a Gaussian laser beam with a particle that is located off axis is a fundamental problem encountered across many scientific fields, including biological physics, chemistry, and medicine. For spherical geometries, generalized Lorenz-Mie theory affords a solution of Maxwell's equations for the scattering from such a particle. The solution can be obtained by expanding the laser fields in terms of vector spherical harmonics (VSHs). However, the computation of the VSH expansion coefficients for off-axis beams has proven challenging. In the present study, we provide a very viable, theoretical framework to efficiently compute the sought-after expansion coefficients with high numerical accuracy. We use the existing theory for the expansion of an on-axis laser beam and employ Cruzan's translation theorems [Q. Appl. Math.20, 33 (1962)] for the VSHs to obtain a description for more general off-axis beams. The expansion coefficients for the off-axis laser beam are presented in an analytical form in terms of an infinite series over the underlying translation coefficients. A direct comparison of the electromagnetic fields of such a beam expansion with the original laser fields and with results obtained using numerical quadratures shows excellent agreement (relative errors are on the order of ≲10(-3). In practice, the analytical approach presented in this study has numerous applications, reaching from multiparticle scattering problems in atmospheric physics and climatology to optical trapping, sorting, and sizing techniques.

Near- and far-field scattering from arbitrary three-dimensional aggregates of coated spheres using parallel computing

Many scientific fields--including astronomy, climatology, and biology, among others--require the calculation of the scattered optical fields from multiparticle distributions. In the present study, we combine the established results for the scattering from clusters of homogeneous spheres and from single core-shell particles into a computationally tractable solution that is valid for irregular configurations of nonidentical, coated particles. The presented multiparticle scattering (MPS) model is based on a generalized Lorenz-Mie theory framework and the vector translation theorems for the vector spherical harmonics. We provide the MPS model in both the near and far fields, and for plane-wave and Gaussian beam illumination. A message-passing-interface protocol is used for the computational implementation of the model in a parallel computer program. The computer model is validated by verifying the accuracy of the vector translation theorems utilized in our theoretical methods and by qualitative comparison to existing multiparticle scattering data. We conclude by presenting the scattering profiles from several examples of particle distributions. This MPS model is a practicable method of calculating the optical fields arising in the scattering from particle aggregates and is straightforwardly extensible to arbitrary illumination and to more complex internal-particle structures, such as stratified spheres. Vital applications of this model include the exact computation of forces exerted on irregular objects in optical traps and the simulation of light propagation through biological tissues.

Nuclear morphology measurements with angle-resolved low coherence interferometry for application to cell biology and early cancer detection

The study of intact, living cells using non-invasive optical spectroscopic methods offers the opportunity to assess cellular structure and organization in a way that is not possible with commonly used cell biology imaging techniques. We have developed a novel spectroscopic technique for diagnosing disease at the cellular level based on using low-coherence interferometry (LCI) to detect the angular distribution of scattered light. Angle-resolved LCI (a/LCI) combines the ability of LCI to isolate scattering from sub-surface tissue layers with the ability of light scattering spectroscopy to obtain structural information on sub-wavelength scales. In application to examining cellular structure, a/LCI enables quantitative measurements of changes in the size and texture of cell nuclei. These quantitative measurements are characteristic of different pathological states. The capabilities of a/LCI were demonstrated using a clinical system that can be applied in endoscopic surveillance of esophageal tissue, producing high sensitivity and specificity for detecting dysplastic tissues in vivo. Experiments with in vitro cell samples also show the utility of a/LCI in observing structural changes due to environmental stimuli as well as detecting apoptosis due to chemotherapeutic agents.

Physical insight into light scattering by photoreceptor cell nuclei

A recent study showed that the rod photoreceptor cell nuclei in the retina of nocturnal and diurnal mammals differ considerably in architecture: the location of euchromatin and heterochromatin in the nucleus is interchanged. This inversion has significant implications for the refractive index distribution and the light scattering properties of the nucleus. Here, we extend previous two-dimensional analysis to three dimensions (3D) by using both a numerical finite-difference time-domain and an analytic Mie theory approach. We find that the specific arrangement of the chromatin phases in the nuclear core-shell models employed have little impact on the far-field scattering cross section. However, scattering in the near field, which is the relevant regime inside the retina, shows a significant difference between the two architectures. The "inverted" photoreceptor cell nuclei of nocturnal mammals act as collection lenses, with the lensing effect being much more pronounced in 3D than in two dimensions. This lensing helps to deliver light efficiently to the light-sensing outer segments of the rod photoreceptor cells and thereby improve night vision.

Deformation of stem cell nuclei by nanotopographical cues

Cells sense cues in their surrounding microenvironment. These cues are converted into intracellular signals and transduced to the nucleus in order for the cell to respond and adapt its function. Within the nucleus, structural changes occur that ultimately lead to changes in the gene expression. In this study, we explore the structural changes of the nucleus of human mesenchymal stem cells as an effect of topographical cues. We use a controlled nanotopography to drive shape changes to the cell nucleus, and measure the changes with both fluorescence microscopy and a novel light scattering technique. The nucleus changes shape dramatically in response to the nanotopography, and in a manner dependent on the mechanical properties of the substrate. The kinetics of the nuclear deformation follows an unexpected trajectory. As opposed to a gradual shape change in response to the topography, once the cytoskeleton attains an aligned and elongation morphology on the time scale of several hours, the nucleus changes shape rapidly and intensely.

Interaction of Gaussian beam with near-spherical particle: an analytic-numerical approach for assessing scattering and stresses

We derive a straightforward theoretical method to determine the electromagnetic fields for the incidence of a monochromatic laser beam on a near-spherical dielectric particle. The beam-shape coefficients are obtained from the radial laser fields and expressed as a finite series in a form that has, to our knowledge, not been published before. Our perturbation approach to solve Maxwell's equations in spherical coordinates employs two alternative techniques to match the boundary conditions: an analytic approach for small particles with low eccentricity and an adapted point-matching method for larger spheroids with higher aspect ratios. We present results for the internal and external fields, scattering intensities, and stresses exerted on the particle. While similarly accurate as others, our approach is easily implemented numerically and thus particularly useful in praxis, e.g., for analyzing optical traps, such as the optical stretcher.

Experimental verification of T-matrix-based inverse light scattering analysis for assessing structure of spheroids as models of cell nuclei

Inverse light scattering analysis (ILSA) seeks to associate measured scattering properties with the most probable theoretical scattering distribution, making it a useful tool for assessing structure in biological materials. The accuracy of ILSA depends on the compatibility of the light scattering geometry with the light scattering model. In this study, we compare the accuracy obtained when analyzing light scattering data from spheroids using a numerical implementation of Mie theory, and the T matrix, a numerical method of solving light scattering from spheroids. Our experimental data are acquired using novel optical phantoms containing spheroidal scatterers and angle-resolved low-coherence interferometry, a depth- and angle-resolved light scattering measurement modality. The results show that Mie theory can accurately assess spheroidal structure despite the geometric incompatibility provided measurements are taken in multiple orientations of the sample relative to the incident polarization and the measured scattering angle. In comparison, analysis using the T-matrix method is highly accurate and more reliable yet requires measurements from only a single orientation.

Light scattering measurements of subcellular structure provide noninvasive early detection of chemotherapy-induced apoptosis

We present a light scattering study using angle-resolved low coherence interferometry (a/LCI) to assess nuclear morphology and subcellular structure within MCF-7 cells at several time points after treatment with chemotherapeutic agents. Although the nuclear diameter and eccentricity are not observed to change, the light scattering signal reveals a change in the organization of subcellular structures that we interpret using fractal dimension (FD). The FD of subcellular structures in cells treated with paclitaxel and doxorubicin is observed to increase significantly compared with that of control cells as early as 1.5 and 3 hours after application, respectively. The FD is then found to decrease slightly at 6 hours postapplication for both agents only to increase again from 12 to 24 hours posttreatment when the observations ceased. The changes in structure appear over two time scales, suggesting that multiple mechanisms are evident in these early apoptotic stages. Indeed, quantitative image analysis of fluorescence micrographs of cells undergoing apoptosis verifies that the FD of 4',6-diamidino-2-phenylindole-stained nuclear structures does not change significantly in cells until 12 hours after treatment, whereas that of MitoTracker stained mitochondria is seen to modulate as early as 3 hours after treatment. In contrast, cells receiving an increased dose of paclitaxel that induced G(2)-M arrest, but not apoptosis, only exhibited the early change in subcellular structure but did not show the later change associated with changes in nuclear substructure. These results suggest that a/LCI may have utility in detecting early apoptotic events for both clinical and basic science applications.

Nonlinear osmotic properties of the cell nucleus

In the absence of active volume regulation processes, cell volume is inversely proportional to osmolarity, as predicted by the Boyle Van't Hoff relation. In this study, we tested the hypothesis that nuclear volume has a similar relationship with extracellular osmolarity in articular chondrocytes, cells that are exposed to changes in the osmotic environment in vivo. Furthermore, we explored the mechanism of the relationships between osmolarity and nuclear size and shape. Nuclear size was quantified using two independent techniques, confocal laser scanning microscopy and angle-resolved low coherence interferometry. Nuclear volume was osmotically sensitive but this relationship was not linear, showing a decline in the osmotic sensitivity in the hypo-osmotic range. Nuclear shape was also influenced by extracellular osmolarity, becoming smoother as the osmolarity decreased. The osmotically induced changes in nuclear size paralleled the changes in nuclear shape, suggesting that shape and volume are interdependent. The osmotic sensitivity of shape and volume persisted after disruption of the actin cytoskeleton. Isolated nuclei contracted in response to physiologic changes in macromolecule concentration but not in response to physiologic changes in ion concentration, suggesting solute size has an important influence on the osmotic pressurization of the nucleus. This finding in turn implies that the diffusion barrier that causes osmotic effects is not a semi-permeable membrane, but rather due to size constraints that prevent large solute molecules from entering small spaces in the nucleus. As nuclear morphology has been associated previously with cell phenotype, these findings may provide new insight into the role of mechanical and osmotic signals in regulating cell physiology.

Application of the T-matrix method to determine the structure of spheroidal cell nuclei with angle-resolved light scattering

We demonstrate an inverse light-scattering analysis procedure based on using the T-matrix method as a light-scattering model. We measure light scattered by in vitro cell monolayers using angle-resolved low-coherence interferometry (a/LCI) and compare the data to predictions of the T-matrix theory. The comparison yields measurements of the equal volume diameter and aspect ratio of the spheroid cell nuclei with accuracy comparable to quantitative image analysis of fixed and stained samples. These improvements represent a significant upgrade for the a/LCI technique, expanding both the range of tissue in which it is applicable and potentially increasing its value as a diagnostic tool.

Application of Mie theory to assess structure of spheroidal scattering in backscattering geometries

Inverse light scattering analysis seeks to associate measured scattering properties with the most probable theoretical scattering distribution. Although Mie theory is a spherical scattering model, it has been used successfully for discerning the geometry of spheroidal scatterers. The goal of this study was an in-depth evaluation of the consequences of analyzing the structure of spheroidal geometries, which are relevant to cell and tissue studies in biology, by employing Mie-theory-based inverse light scattering analysis. As a basis for this study, the scattering from spheroidal geometries was modeled using T-matrix theory and used as test data. In a previous study, we used this technique to investigate the case of spheroidal scatterers aligned with the optical axis. In the present study, we look at a broader scope which includes the effects of aspect ratio, orientation, refractive index, and incident light polarization. Over this wide range of parameters, our results indicate that this method provides a good estimate of spheroidal structure.

Application of Mie theory to determine the structure of spheroidal scatterers in biological materials

We present here the results of a numerical study on light scattering from nonspherical particles with relevance to detecting precancerous states in epithelial tissues. In previous studies of epithelial cell nuclei, the experimental light scattering data have been analyzed by comparison with Mie theory. However, given the spheroidal shape of many cell nuclei, the validity of this assumption demands a thorough investigation. We investigate this assumption by using the T-matrix method to model light scattered from spheroids with parameters relevant to epithelial cell nuclei. In our previous studies, we have developed a data analysis procedure that extracts the oscillatory component of the angular-scattering distribution for an ensemble of epithelial cell nuclei for comparison with Mie theory. We demonstrate that application of our analysis procedure to the predictions of the T-matrix method for spheroids, oriented such that their axis of symmetry is aligned with the incident light propagation direction, generally yields the spheroid dimension that is transverse to the incident light propagation direction with subwavelength accuracy.

In situ assessment of intraepithelial neoplasia in hamster trachea epithelium using angle-resolved low-coherence interferometry

Optical spectroscopy was used to evaluate the transformation of nuclear morphology associated with intraepithelial neoplasia in an animal model of carcinogenesis. In this pilot study, we have assessed the capability of angle-resolved low-coherence interferometry (a/LCI) to monitor in situ the neoplastic progression of hamster trachea epithelial tissue. By using the depth resolution made possible by coherence gating, the a/LCI system has been adapted to the unique geometry of the hamster trachea to allow us to extract useful nuclear morphometric information from cells in the epithelial layer without the need for exogenous staining or tissue fixation. Analysis of a/LCI nuclear morphology measurements has identified two important biomarkers of neoplastic transformation in hamster trachea epithelium, the size and the refractive index of epithelial cell nuclei. By comparing the a/LCI measurements of these two biomarkers to pathologic classification, we distinguished nuclear morphology changes for normal tissue, low-grade dysplasia, and high-grade dysplasia. Given its previous usefulness for tracking neoplastic change through nuclear morphometry measurements, the a/LCI technique may prove to be a useful tool in evaluating chemopreventive agents in future studies of hamster trachea epithelium.

Quantitative phase microscopy with asynchronous digital holography

We demonstrate a new method of measuring quantitative phase in imaging of biological materials. This method, asynchronous digital holography, employs knowledge of a moving fringe created by acousto-optic modulators to execute phase-shifting interferometry using two near-simultaneous interferograms. The method can be used to obtain quantitative phase images of dynamic biological samples on millisecond time scales. We present results on a standard sample, and on live cell samples.

In situ detection of nuclear atypia in Barrett's esophagus by using angle-resolved low-coherence interferometry

BACKGROUND

Monitoring of patients with Barrett's esophagus (BE) for dysplasia, currently done by systematic biopsy, can be improved through increasing the proportion of at-risk tissue examined.

OBJECTIVE

Optical biopsy techniques, which do not remove the tissue but interrogate the tissue with light, offer a potential method to improve the monitoring of BE. Frequency-domain angle resolved low-coherence interferometry (fa/LCI) is an optical spectroscopic technique applied through an endoscopic fiber bundle and measures the depth-resolved nuclear morphology of tissue, a key biomarker for identifying dysplasia. The aim of the study was to assess the diagnostic capability of fa/LCI for differentiating healthy and dysplastic tissue in patients with BE.

METHODS

Depth-resolved angular scattering data are acquired by using fa/LCI from tissue excised from 3 patients who had esophagogastrectomy. The data are processed to determine the average nuclear size and density as a function of depth beneath the tissue surface. These data are compared with the pathologic classification of the tissue.

MAIN OUTCOME MEASUREMENTS

Average of depth-resolved nuclear diameter and nuclear density measurements in tissue samples.

RESULTS

Upon comparison to pathologic diagnosis, the fa/LCI data results report the nuclear atypia characteristic of dysplasia in the epithelial tissue. Examination of the average nuclear morphology over the superficial 150 mum results in complete separation between healthy columnar and BE dysplastic tissues.

LIMITATIONS

Lack of in vivo data; lack of nondysplastic BE data because of limited sample size.

CONCLUSIONS

In complicated tissue structures, such as BE, depth-resolved nuclear morphology measurements provided an excellent means to identify dysplasia. The preliminary results demonstrate the great potential for the in vivo application of fa/LCI as a targeting mechanism for physical biopsy in patients with BE.

Fourier-domain angle-resolved low coherence interferometry through an endoscopic fiber bundle for light-scattering spectroscopy

We present a novel endoscopic fiber bundle probe incorporated in a Fourier-domain angle-resolved low coherence interferometry system for the measurement of depth-resolved angular scattering distributions to permit the determination of scatterer size via elastic scattering properties. Depth resolution is achieved with a superluminescent diode via a Mach-Zehnder interferometer. The sample is illuminated with a collimated beam, and a Fourier plane image of the backscattered light is collected by a coherent fiber bundle. The angular scattering distribution relayed by the fiber bundle is mixed with the reference field and made to coincide with the input slit of an imaging spectrograph. The data collected are processed in real time, producing a depth-resolved angular scattering distribution in 0.37 s. The data are used to determine the sizes of polystyrene microspheres with subwavelength precision and accuracy.