# Publications by Year: 2017

2017
Kalinich, M. ; Bhan, I. ; Kwan, T. T. ; Miyamoto, D. T. ; Javaid, S. ; LiCausi, J. A. ; Milner, J. D. ; Hong, X. ; Goyal, L. ; Sil, S. ; et al. Absolute quantification of circulating tumor cell RNA enables high specificity detection of hepatocellular carcinoma. Cancer Res. 2017, 77, 1734. Publisher's VersionAbstract

Background: Although liver cancer has the second-highest mortality rate among cancers internationally, accurate and scalable assays for the early detection and longitudinal monitoring of hepatocellular carcinoma are lacking. Circulating tumor cells are released from invasive cancers into the blood stream, but the difficulty inherent in isolating, identifying, and characterizing these ultra-rare cells has precluded their widespread implementation as a biomarker. By combining a high-throughput microfluidic negative depletion CTC isolation strategy with the absolute quantification of lineage-specific RNAs, we report the highly specific detection of hepatocellular carcinoma CTCs from patient blood draws.

Methods: Blood draws from 48 hepatocellular carcinoma patients, 31 chronic liver disease patients, 25 healthy donors, and 44 patients with primary cancers other than hepatocellular carcinoma were processed through the microfluidic device (CTC-iChip). RNA was extracted, whole-transcriptome amplified, and quantified using droplet digital PCR. Transcript counts were used to fit a logistic regression model to integrate distinct transcript levels into a single CTC-score. The technical feasibility of utilizing RNA sequencing for identification of novel CTC transcripts of interest was also demonstrated with a liver cancer cell line spike-in study.

Results: 9 of the 16 untreated HCC patients were successfully detected, while only 1/31 chronic liver disease patients were incorrectly classified. HCC patients undergoing treatment showed a significant decrease in their CTC-score; only 9/32 patients actively receiving treatment were positive. The CTC-score was not correlated with the HCC serum biomarker alpha-fetoprotein, and combining these two orthogonal measures led to estimated positive and negative predictive values of 80% and 86%, respectively, in a high-risk cohort. RNAseq analysis of cell line spike-in data revealed the potential of RNA sequencing for uncovering novel transcripts of interest.

Conclusion: Coupling microfluidic depletion with droplet digital PCR allows for the highly specific detection of hepatocellular carcinoma. The CTC-score generated from these data tracks with clinical intervention and is orthogonal to the existing biomarker AFP; combining these two assays has the potential to provide superior detection compared to either individual approach.

Liber, S. R. ; Indech, G. ; van der Wee, E. B. ; Butenko, A. V. ; Kodger, T. E. ; Lu, P. J. ; Schofield, A. B. ; Weitz, D. A. ; van Blaaderen, A. ; Sloutskin, E. Axial Confocal Tomography of Capillary-Contained Colloidal Structures. Langmuir 2017, 33, 13343–13349. Publisher's VersionAbstract
Confocal microscopy is widely used for three-dimensional (3D) sample reconstructions. Arguably, the most significant challenge in such reconstructions is posed by the resolution along the optical axis being significantly lower than in the lateral directions. In addition, the imaging rate is lower along the optical axis in most confocal architectures, prohibiting reliable 3D reconstruction of dynamic samples. Here, we demonstrate a very simple, cheap, and generic method of multiangle microscopy, allowing high-resolution high-rate confocal slice collection to be carried out with capillary-contained colloidal samples in a wide range of slice orientations. This method, realizable with any common confocal architecture and recently implemented with macroscopic specimens enclosed in rotatable cylindrical capillaries, allows 3D reconstructions of colloidal structures to be verified by direct experiments and provides a solid testing ground for complex reconstruction algorithms. In this paper, we focus on the implementation of this method for dense nonrotatable colloidal samples, contained in complex-shaped capillaries. Additionally, we discuss strategies to minimize potential pitfalls of this method, such as the artificial appearance of chain-like particle structures.
Chen, D. ; Amstad, E. ; Zhao, C. - X. ; Cai, L. ; Fan, J. ; Chen, Q. ; Hai, M. ; Koehler, S. ; Zhang, H. ; Liang, F. ; et al. Biocompatible Amphiphilic Hydrogel–Solid Dimer Particles as Colloidal Surfactants. ACS Nano 2017, 11, 11978–11985. Publisher's VersionAbstract
Emulsions of two immiscible liquids can slowly coalesce over time when stabilized by surfactant molecules. Pickering emulsions stabilized by colloidal particles can be much more stable. Here, we fabricate biocompatible amphiphilic dimer particles using a hydrogel, a strongly hydrophilic material, and achieve large contrast in the wetting properties of the two bulbs, resulting in enhanced stabilization of emulsions. We generate monodisperse single emulsions of alginate and shellac solution in oil using a flow-focusing microfluidics device. Shellac precipitates from water and forms a solid bulb at the periphery of the droplet when the emulsion is exposed to acid. Molecular interactions result in amphiphilic dimer particles that consist of two joined bulbs: one hydrogel bulb of alginate in water and the other hydrophobic bulb of shellac. Alginate in the hydrogel compartment can be cross-linked using calcium cations to obtain stable particles. Analogous to surfactant molecules at the interface, the resultant amphiphilic particles stand at the water/oil interface with the hydrogel bulb submerged in water and the hydrophobic bulb in oil and are thus able to stabilize both water-in-oil and oil-in-water emulsions, making these amphiphilic hydrogel–solid particles ideal colloidal surfactants for various applications.
Liu, J. ; Wang, N. \ddotu\elseü\fi}; Yu, L. - J. ; Karton, A. ; Li, W. ; Zhang, W. ; Guo, F. ; Hou, L. ; Cheng, Q. ; Jiang, L. ; et al. Bioinspired graphene membrane with temperature tunable channels for water gating and molecular separation. Nat. Commun. 2017, 8 2011. Publisher's VersionAbstract
Smart regulation of substance permeability through porous membranes is highly desirable for membrane applications. Inspired by the stomatal closure feature of plant leaves at relatively high temperature, here we report a nano-gating membrane with a negative temperature-response coefficient that is capable of tunable water gating and precise small molecule separation. The membrane is composed of poly(N-isopropylacrylamide) covalently bound to graphene oxide via free-radical polymerization. By virtue of the temperature tunable lamellar spaces of the graphene oxide nanosheets, the water permeance of the membrane could be reversibly regulated with a high gating ratio. Moreover, the space tunability endows the membrane with the capability of gradually separating multiple molecules of different sizes. This nano-gating membrane expands the scope of temperature-responsive membranes and has great potential applications in smart gating systems and molecular separation.
Guo, M. ; Pegoraro, A. F. ; Mao, A. ; Zhou, E. H. ; Arany, P. R. ; Han, Y. ; Burnette, D. T. ; Jensen, M. H. ; Kasza, K. E. ; Moore, J. R. ; et al. Cell volume change through water efflux impacts cell stiffness and stem cell fate. Proc. Natl. Acad. Sci. U.S.A. 2017, 201705179. Publisher's VersionAbstract
Cell volume is thought to be a well-controlled cellular characteristic, increasing as a cell grows, while macromolecular density is maintained. We report that cell volume can also change in response to external physical cues, leading to water influx/efflux, which causes significant changes in subcellular macromolecular density. This is observed when cells spread out on a substrate: Cells reduce their volume and increase their molecular crowding due to an accompanying water efflux. Exploring this phenomenon further, we removed water from mesenchymal stem cells through osmotic pressure and found this was sufficient to alter their differentiation pathway. Based on these results, we suggest cells chart different differentiation and behavioral pathways by sensing/altering their cytoplasmic volume and density through changes in water influx/efflux.
Hu, Y. ; Mao, A. S. ; Desai, R. M. ; Wang, H. ; Weitz, D. A. ; Mooney, D. J. Controlled self-assembly of alginate microgels by rapidly binding molecule pairs. Lab Chip 2017, 17, 2481–2490. Publisher's VersionAbstract
Controlled self-assembly of cell-encapsulating microscale polymeric hydrogels (microgels) could be advantageous in a variety of tissue engineering and regenerative medicine applications. Here, a method of assembly by chemical modification of alginate polymer with binding pair molecules (BPM) was explored. Alginate was modified with several types of BPM, specifically biotin and streptavidin and click chemistry compounds, and fabricated into 25–30 μm microgels using a microfluidic platform. These microgels were demonstrated to self-assemble under physiological conditions. By combining complementary microgels at a high ratio, size-defined assemblages were created, and the effects of BPM type and assembly method on the number of microgels per assemblage and packing density were determined. Furthermore, a magnetic process was developed to separate assemblages from single microgels, and allow formation of multilayer spheroids. Finally, cells were singly encapsulated into alginate microgels and assembled using BPM-modified alginate, suggesting potential applications in regenerative medicine.
Prodanovic, R. ; Ostafe, R. ; Kovacevic, G. ; Weitz, D. ; Fisher, R. Development of ultrahigh-throughput screening platforms for directed evolution of glucose oxidase. New Front. Chem. 2017, 26, S4\_OP2. Publisher's Version
Chen, D. ; Zhao, C. - X. ; Lagoin, C. ; Hai, M. ; Arriaga, L. R. ; Koehler, S. ; Abbaspourrad, A. ; Weitz, D. A. Dispersing hydrophobic natural colourant $\beta$-carotene in shellac particles for enhanced stability and tunable colour. R. Soc. Open Sci. 2017, 4 170919. Publisher's VersionAbstract
Colour is one of the most important visual attributes of food and is directly related to the perception of food quality. The interest in natural colourants, especially β-carotene that not only imparts colour but also has well-documented health benefits, has triggered the research and development of different protocols designed to entrap these hydrophobic natural molecules to improve their stability against oxidation. Here, we report a versatile microfluidic approach that uses single emulsion droplets as templates to prepare microparticles loaded with natural colourants. The solution of β-carotene and shellac in the solvent is emulsified by microfluidics into droplets. Upon solvent diffusion, β-carotene and shellac co-precipitates, forming solid microparticles of β-carotene dispersed in the shellac polymer matrix. We substantially improve the stability of β-carotene that is protected from oxidation by the polymer matrix and achieve different colour appearances by loading particles with different β-carotene concentrations. These particles demonstrate great promise for practical use in natural food colouring.
Thiery, J. ; Rodts, S. ; Weitz, D. A. ; Coussot, P. Drying regimes in homogeneous porous media from macro- to nanoscale. Phys. Rev. Fluids 2017, 2 074201. Publisher's VersionAbstract
Magnetic resonance imaging visualization down to nanometric liquid films in model porous media with pore sizes from micro- to nanometers enables one to fully characterize the physical mechanisms of drying. For pore size larger than a few tens of nanometers, we identify an initial constant drying rate period, probing homogeneous desaturation, followed by a falling drying rate period. This second period is associated with the development of a gradient in saturation underneath the sample free surface that initiates the inward recession of the contact line. During this latter stage, the drying rate varies in accordance with vapor diffusion through the dry porous region, possibly affected by the Knudsen effect for small pore size. However, we show that for sufficiently small pore size and/or saturation the drying rate is increasingly reduced by the Kelvin effect. Subsequently, we demonstrate that this effect governs the kinetics of evaporation in nanopores as a homogeneous desaturation occurs. Eventually, under our experimental conditions, we show that the saturation unceasingly decreases in a homogeneous manner throughout the wet regions of the medium regardless of pore size or drying regime considered. This finding suggests the existence of continuous liquid flow towards the interface of higher evaporation, down to very low saturation or very small pore size. Paradoxically, even if this net flow is unidirectional and capillary driven, it corresponds to a series of diffused local capillary equilibrations over the full height of the sample, which might explain that a simple Darcy's law model does not predict the effect of scaling of the net flow rate on the pore size observed in our tests.
Ung, W. L. ; Mutafopulos, K. ; Spink, P. ; Rambach, R. W. ; Franke, T. ; Weitz, D. A. Enhanced surface acoustic wave cell sorting by 3D microfluidic-chip design. Lab Chip 2017, 17, 4059–4069. Publisher's VersionAbstract
We demonstrate an acoustic wave driven microfluidic cell sorter that combines advantages of multilayer device fabrication with planar surface acoustic wave excitation. We harness the strong vertical component of the refracted acoustic wave to enhance cell actuation by using an asymmetric flow field to increase cell deflection. Precise control of the 3-dimensional flow is realized by topographical structures implemented on the top of the microchannel. We experimentally quantify the effect of the structure dimensions and acoustic parameter. The design attains cell sorting rates and purities approaching those of state of the art fluorescence-activated cell sorters with all the advantages of microfluidic cell sorting.
Habib, N. ; Avraham-Davidi, I. ; Basu, A. ; Burks, T. ; Shekhar, K. ; Hofree, M. ; Choudhury, S. R. ; Aguet, F. \mboxç\elseç\fi}ois; Gelfand, E. ; Ardlie, K. ; et al. Massively parallel single-nucleus RNA-seq with DroNc-seq. Nat. Methods 2017, 14, 955. Publisher's VersionAbstract
Single-nucleus RNA sequencing (sNuc-seq) profiles RNA from tissues that are preserved or cannot be dissociated, but it does not provide high throughput. Here, we develop DroNc-seq: massively parallel sNuc-seq with droplet technology. We profile 39,111 nuclei from mouse and human archived brain samples to demonstrate sensitive, efficient, and unbiased classification of cell types, paving the way for systematic charting of cell atlases.
Du, J. S. ; Park, J. ; Kim, Q. H. ; Jhe, W. ; Dravid, V. P. ; Yang, D. ; Weitz, D. A. Multistage Transformation and Lattice Fluctuation at AgCl–Ag Interface. J. Phys. Chem. Lett. 2017, 8 5853–5860. Publisher's VersionAbstract
Solid-state transformation between different materials is often accompanied by mechanical expansion and compression due to their volume change and structural evolution at interfaces. However, these two types of dynamics are usually difficult to monitor in the same time. In this work, we use in situ transmission electron microscopy to directly study the reduction transformation at the AgCl–Ag interface. Three stages of lattice fluctuations were identified and correlated to the structural evolution. During the steady state, a quasi-layered growth mode of Ag in both vertical and lateral directions were observed due to the confinement of AgCl lattices. The development of planar defects and depletion of AgCl are respectively associated with lattice compression and relaxation. Topography and structure of decomposing AgCl was further monitored by in situ scanning transmission electron microscopy. Silver species are suggested to originate from both the surface and the interior of AgCl, and be transported to the interface. Such mass transport may have enabled the steady state and lattice compression in this volume-shrinking transformation.
Wang, L. ; Chen, D. ; Gutierrez-Cuevas, K. G. ; Bisoyi, H. K. ; Fan, J. ; Zola, R. S. ; Li, G. ; Urbas, A. M. ; Bunning, T. J. ; Weitz, D. A. ; et al. Optically reconfigurable chiral microspheres of self-organized helical superstructures with handedness inversion. Mater. Horiz. 2017, 4 1190–1195. Publisher's VersionAbstract
Optically reconfigurable monodisperse chiral microspheres of self-organized helical superstructures with dynamic chirality were fabricated via a capillary-based microfluidic technique. Light-driven handedness-invertible transformations between different configurations of microspheres were vividly observed and optically tunable RGB photonic cross-communications among the microspheres were demonstrated.
Weitz, D. A. Perspective on droplet-based single-cell sequencing. Lab Chip 2017, 17, 2539.
Shi, W. ; Weitz, D. A. Polymer Phase Separation in a Microcapsule Shell. Macromolecules 2017, 50, 7681–7686. Publisher's VersionAbstract
Phase separation has been used for engineering microscale fluids and particles with designed structures. But it is challenging to use phase separation to create complicated microcapsules because phase separation in the shell correlates with applied osmotic pressure and affects capsule stability significantly. Here we employ two biodegradable polymers to study the phase separation in microcapsule shells and its effect on the mechanical stability. The dynamic process reveals that phase separation creates a patchy shell with distinct regions transiently, then transports the discrete domains across the shell, and coalesces them at the surface. The equilibrium structure with balanced osmotic pressure is a Janus shell, where one component forms the shell and the other component dewets on the surface. Under slight osmotic pressure to the shell, phase separation reaches a different Janus shape, which consists of two partial shells of each component. We can in further take advantage of phase separation and osmotic pressure to rupture microcapsules at specific locations. Phase separation in the shell provides a facile approach to create versatile capsule structures and affords a reliable strategy to harness the shell mechanics.
Egan, P. F. ; Moore, J. R. ; Ehrlicher, A. J. ; Weitz, D. A. ; Schunn, C. ; Cagan, J. ; LeDuc, P. Robust mechanobiological behavior emerges in heterogeneous myosin systems. Proc. Natl. Acad. Sci. U.S.A. 2017, 201713219. Publisher's VersionAbstract
Biological complexity presents challenges for understanding natural phenomenon and engineering new technologies, particularly in systems with molecular heterogeneity. Such complexity is present in myosin motor protein systems, and computational modeling is essential for determining how collective myosin interactions produce emergent system behavior. We develop a computational approach for altering myosin isoform parameters and their collective organization, and support predictions with in vitro experiments of motility assays with α-actinins as molecular force sensors. The computational approach models variations in single myosin molecular structure, system organization, and force stimuli to predict system behavior for filament velocity, energy consumption, and robustness. Robustness is the range of forces where a filament is expected to have continuous velocity and depends on used myosin system energy. Myosin systems are shown to have highly nonlinear behavior across force conditions that may be exploited at a systems level by combining slow and fast myosin isoforms heterogeneously. Results suggest some heterogeneous systems have lower energy use near stall conditions and greater energy consumption when unloaded, therefore promoting robustness. These heterogeneous system capabilities are unique in comparison with homogenous systems and potentially advantageous for high performance bionanotechnologies. Findings open doors at the intersections of mechanics and biology, particularly for understanding and treating myosin-related diseases and developing approaches for motor molecule-based technologies.
Alim, K. ; Parsa, S. ; Weitz, D. A. ; Brenner, M. P. Local Pore Size Correlations Determine Flow Distributions in Porous Media. Physical Review Letters 2017, 119, 144501. Publisher's Version
Zhang, H. ; Qu, X. ; Chen, H. ; Kong, H. ; Ding, R. ; Chen, D. ; Zhang, X. ; Pei, H. ; Santos, H. A. ; Hai, M. ; et al. Fabrication of Calcium Phosphate-Based Nanocomposites Incorporating DNA Origami, Gold Nanorods, and Anticancer drugs for Biomedical Applications. Advanced Healthcare Materials 2017, 6. Publisher's Version
Wu, J. ; Cai, L. - H. ; Weitz, D. A. Tough Self-Healing Elastomers by Molecular Enforced Integration of Covalent and Reversible Networks. Advanced Materials 2017, 29, 1702616. Publisher's Version
Pegoraro, A. F. ; Janmey, P. ; Weitz, D. A. Mechanical Properties of the Cytoskeleton and Cells. Cold Spring Harbor-Perspectives in Biology 2017, 1-12. Publisher's VersionAbstract

The cytoskeleton is the major mechanical structure of the cell; it is a complex, dynamic
biopolymer network comprising microtubules, actin, and intermediate filaments. Both the
individual filaments and the entire network are not simple elastic solids but are instead highly nonlinear structures. Appreciating the mechanics of biopolymer networks is key to under-
standing the mechanics of cells. Here, we review the mechanical properties of cytoskeletal polymers and discuss the implications for the behavior of cells.