A modular microfluidic platform to study how fluid shear stress alters estrogen receptor phenotype in ER+ breast cancer cells

Metastatic breast cancer leads to poor prognoses and worse outcomes in patients due to its invasive behavior and poor response to therapy. It is still unclear what biophysical and biochemical factors drive this more aggressive phenotype in metastatic cancer; however recent studies have suggested that exposure to fluid shear stress in the vasculature could cause this. In this study a modular microfluidic platform capable of mimicking the magnitude of fluid shear stress (FSS) found in human vasculature was designed and fabricated. This device provides a platform to evaluate the effects of FSS on MCF-7 cell line, an estrogen receptor positive (ER+) breast cancer cell line, during circulation in the vessels. Elucidation of the effects of FSS on MCF-7 cells was carried out utilizing two approaches: single cell analysis and bulk analysis. For single cell analysis, cells were trapped in a microarray after exiting the serpentine channel and followed by immunostaining on the device (on-chip). Bulk analysis was performed after cells were collected in a microtube at the outlet of the microfluidic serpentine channel for western blotting (off-chip). It was found that cells exposed to an FSS magnitude of 10 dyn/cm2 with a residence time of 60 s enhanced expression of the proliferation marker Ki67 in the MCF-7 cell line at a single cell level. To understand possible mechanisms for enhanced Ki67 expression, on-chip and off-chip analyses were performed for pro-growth and survival pathways ERK, AKT, and JAK/STAT. Results demonstrated that after shearing the cells phosphorylation of p-AKT, p-mTOR, and p-STAT3 were observed. However, there was no change in p-ERK1/2. AKT is a mediator of ER rapid signaling, analysis of phosphorylated ERα was carried out and no significant differences between sheared and non-sheared populations were observed. Taken together these results demonstrate that FSS can increase phosphorylation of proteins associated with a more aggressive phenotype in circulating cancer cells. These findings provide additional information that may help inform why cancer cells located at metastatic sites are usually more aggressive than primary breast cancer cells.

A modular microfluidic platform to study how fluid shear stress alters estrogen receptor phenotype in ER+ breast cancer cells

Metastatic breast cancer leads to poor prognoses and worse outcomes in patients due to its invasive behavior and poor response to therapy. It is still unclear what biophysical and biochemical factors drive this more aggressive phenotype in metastatic cancer; however recent studies have suggested that exposure to fluid shear stress in the vasculature could cause this. In this study a modular microfluidic platform capable of mimicking the magnitude of fluid shear stress (FSS) found in human vasculature was designed and fabricated. This device provides a platform to evaluate the effects of FSS on MCF-7 cell line, a receptor positive (ER+) breast cancer cell line, during circulation in the vessels. Elucidation of the effects of FSS on MCF-7 cells was carried out utilizing two approaches: single cell analysis and bulk analysis. For single cell analysis, cells were trapped in a microarray after exiting the serpentine channel and followed by immunostaining on the device (on-chip). Bulk analysis was performed after cells were collected in a microtube at the outlet of the microfluidic serpentine channel for western blotting (off-chip). It was found that cells exposed to an FSS magnitude of 10 dyn/cm2 with a residence time of 60 seconds enhanced expression of the proliferation marker Ki67 in the MCF-7 cell line at a single cell level. To understand possible mechanisms for enhanced Ki67 expression, on-chip and off-chip analyses were performed for pro-growth and survival pathways ERK, AKT, and JAK/STAT. Results demonstrated that after shearing the cells phosphorylation of p-AKT, p-mTOR, and p-STAT3 were observed. However, there was no change in p-ERK1/2. AKT is a mediator of ER rapid signaling, analysis of phosphorylated ERα was carried out and no significant differences between sheared and non-sheared populations were observed. Taken together these results demonstrate that FSS can increase phosphorylation of proteins associated with a more aggressive phenotype in circulating cancer cells. These findings provide additional information that may help inform why cancer cells located at metastatic sites are usually more aggressive than primary breast cancer cells.

Incorporating a β-hairpin sequence motif to increase intracellular stability of a peptide-based PROTAC

Proteolysis targeting chimeras (PROTACs) have emerged as a new class of therapeutics that utilize the ubiquitin-proteasome system (UPS) to facilitate proteasomal degradation of "undruggable" targets. Peptide-based PROTACs contain three essential components: a binding motif for the target protein, a short amino acid sequence recognized by an E3 ligase called a degron, and a cell penetrating peptide to facilitate uptake into intact cells. While peptide-based PROTACs have been shown to successfully degrade numerous targets, they have often been found to exhibit low cell permeability and high protease susceptibility. Prior work identified peptides containing a β-hairpin sequence motif that function not only as protecting elements, but also as CPPs and degrons. The goal of this study was to investigate if a β-hairpin sequence could replace commonly used unstructured peptides sequences as the degron and the CPP needed for PROTAC uptake and function. The degradation of the protein Tau was selected as a model system as several published works have identified a Tau binding element that could easily be conjugated to the β-hairpin sequence. A series of time- and concentration-dependent studies confirmed that the βhairpin sequence was an adequate alternative CPP and degron to facilitate the proteasomemediated degradation of Tau. Microscopy studies confirmed the time-dependent uptake of the PROTAC and a degradation assay confirmed that the β-hairpin conjugated PROTAC had a greater lifetime in cells.

Cells collectively migrate during ammonium chemotaxis in Chlamydomonas reinhardtii

The mechanisms governing chemotaxis in Chlamydomonas reinhardtii are largely unknown compared to those regulating phototaxis despite equal importance on the migratory response in the ciliated microalga. To study chemotaxis, we made a simple modification to a conventional Petri dish assay. Using the assay, a novel mechanism governing Chlamydomonas ammonium chemotaxis was revealed. First, we found that light exposure enhances the chemotactic response of wild-type Chlamydomonas strains, yet phototaxis-incompetent mutant strains, eye3-2 and ptx1, exhibit normal chemotaxis. This suggests that Chlamydomonas transduces the light signal pathway in chemotaxis differently from that in phototaxis. Second, we found that Chlamydomonas collectively migrate during chemotaxis but not phototaxis. Collective migration during chemotaxis is not clearly observed when the assay is conducted in the dark. Third, the Chlamydomonas strain CC-124 carrying agg1^-, the AGGREGATE1 gene (AGG1) null mutation, exhibited a more robust collective migratory response than strains carrying the wild-type AGG1 gene. The expression of a recombinant AGG1 protein in the CC-124 strain suppressed this collective migration during chemotaxis. Altogether, these findings suggest a unique mechanism; ammonium chemotaxis in Chlamydomonas is mainly driven by collective cell migration. Furthermore, it is proposed that collective migration is enhanced by light and suppressed by the AGG1 protein.

Fluorometric Characterization of DUB Activity: From Single-Enzyme Reactions to Live Intact Cells

Fluorescently tagged molecular probes capable of time- and concentration-dependent quantification of deubiquitinating enzyme (DUB) activity allow for precise characterization of both enzyme and DUB inhibitor. These probes are compatible with most plate readers allowing for rapid, facile fluorometric analysis of DUB activity. DUB activity can be measured in purified enzyme reactions, in cell lysates, or in intact cells depending upon the choice of the fluorometric probe. This chapter describes protocols and potential analysis tools to investigate DUB activity in these three scenarios.

Generation of 3D Spheroids Using a Thiol-Acrylate Hydrogel Scaffold to Study Endocrine Response in ER+ Breast Cancer

Culturing cancer cells in a three-dimensional (3D) environment better recapitulates in vivo conditions by mimicking cell-to-cell interactions and mass transfer limitations of metabolites, oxygen, and drugs. Recent drug studies have suggested that a high rate of preclinical and clinical failures results from mass transfer limitations associated with drug entry into solid tumors that 2D model systems cannot predict. Droplet microfluidic devices offer a promising alternative to grow 3D spheroids from a small number of cells to reduce intratumor heterogeneity, which is lacking in other approaches. Spheroids were generated by encapsulating cells in novel thiol–acrylate (TA) hydrogel scaffold droplets followed by on-chip isolation of single droplets in a 990- or 450-member trapping array. The TA hydrogel rapidly (∼35 min) polymerized on-chip to provide an initial scaffold to support spheroid development followed by a time-dependent degradation. Two trapping arrays were fabricated with 150 or 300 μm diameter traps to investigate the effect of droplet size and cell seeding density on spheroid formation and growth. Both trapping arrays were capable of ∼99% droplet trapping efficiency with ∼90% and 55% cellular encapsulation in trapping arrays containing 300 and 150 μm traps, respectively. The oil phase was replaced with media ∼1 h after droplet trapping to initiate long-term spheroid culturing. The growth and viability of MCF-7 3D spheroids were confirmed for 7 days under continuous media flow using a customized gravity-driven system to eliminate the need for syringe pumps. It was found that a minimum of 10 or more encapsulated cells are needed to generate a growing spheroid while fewer than 10 parent cells produced stagnant 3D spheroids. As a proof of concept, a drug susceptibility study was performed treating the spheroids with fulvestrant followed by interrogating the spheroids for proliferation in the presence of estrogen. Following fulvestrant exposure, the spheroids showed significantly less proliferation in the presence of estrogen, confirming drug efficacy.

How Cargo Identity Alters the Uptake of Cell-Penetrating Peptide (CPP)/Cargo Complexes: A Study on the Effect of Net Cargo Charge and Length

Cell-penetrating peptides (CPPs) have emerged as a powerful tool for the delivery of otherwise impermeable cargoes into intact cells. Recent efforts to improve the delivery capability of peptides have mainly focused on the identity of the CPP; however, there is evidence that the identity of the cargo itself affects the uptake. The goal of this work was to investigate how the characteristics of a peptide cargo, including net charge and length, either enhance or diminish the internalization efficiency of the CPP/cargo complex. A small library of CPP/cargo complexes were synthesized consisting of structured and unstructured CPPs with cargoes of net positive, negative, or neutral charge and lengths of 4 or 8 amino acids. Cargoes with a net positive charge were found to enhance the overall uptake of the complexes while net neutral and negatively charged cargoes diminished uptake. Conversely, the net length of the cargo had no significant effect on uptake of the CPP/cargo complexes. Microcopy images confirmed the increased uptake of the positively charged cargoes; however, an increase in punctate regions with the addition of a cargo was also observed. The effects of the net positively charged cargoes were confirmed with both structured and unstructured CPPs, which demonstrated similar trends of an increase in uptake with the addition of positively charged residues. These findings demonstrate that the net charge of cargoes impacts the uptake of the complex, which can be considered in the future when designing peptide-based reporters or therapeutics.

Co-culture of Two Different Cell Lines in a Two-Layer Microfluidic Device

Microfluidic devices have become a promising alternative approach for cellular co-culture. Many approaches incorporate a semipermeable barrier to physically separate, yet chemically connect, two cell types; however, the majority of these approaches utilize batch culture conditions which can result in nutrient depletion and waste accumulation. This chapter describes an alternative approach that allows for the continuous infusion of media, relieving the constraints of batch culture. The microfluidic device consists of two separate layers: a bottom layer of 3% (w/v) agarose to facilitate chemical diffusion and a top polydimethylsiloxane (PDMS) layer into which four parallel fluidic channels were imprinted. The microfluidic approach allows for facile visualization of cells with light microscopy and the ability to add (or subtract) drugs or biomolecules to interrogate the system or modulate the cellular response. Finally, the approach allows for terminal immunostaining of either (or both) cell types.

Fluorescent visualization of oil displacement in a microfluidic device for enhanced oil recovery applications

A microfluidic device was developed to mimic the reservoir pore-scale and track the oil/water phases during air flooding. The chip was generated by combining soft-lithography and NOA81 replication. A unique feature of this approach is the inclusion of fluorescent dyes into the oil/water phases, allowing for real-time visualization of oil recovery without altering the phases' surface properties. As a proof of concept, the air was injected into the water/oil-flooded device for enhanced oil recovery applications.

Simultaneous Droplet Generation with In-Series Droplet T-Junctions Induced by Gravity-Induced Flow

Droplet microfluidics offers a wide range of applications, including high-throughput drug screening and single-cell DNA amplification. However, these platforms are often limited to single-input conditions that prevent them from analyzing multiple input parameters (e.g., combined cellular treatments) in a single experiment. Droplet multiplexing will result in higher overall throughput, lowering cost of fabrication, and cutting down the hands-on time in number of applications such as single-cell analysis. Additionally, while lab-on-a-chip fabrication costs have decreased in recent years, the syringe pumps required for generating droplets of uniform shape and size remain cost-prohibitive for researchers interested in utilizing droplet microfluidics. This work investigates the potential of simultaneously generating droplets from a series of three in-line T-junctions utilizing gravity-driven flow to produce consistent, well-defined droplets. Implementing reservoirs with equal heights produced inconsistent flow rates that increased as a function of the distance between the aqueous inlets and the oil inlet. Optimizing the three reservoir heights identified that taller reservoirs were needed for aqueous inlets closer to the oil inlet. Studying the relationship between the ratio of oil-to-water flow rates (Φ) found that increasing Φ resulted in smaller droplets and an enhanced droplet generation rate. An ANOVA was performed on droplet diameter to confirm no significant difference in droplet size from the three different aqueous inlets. The work described here offers an alternative approach to multiplexed droplet microfluidic devices allowing for the high-throughput interrogation of three sample conditions in a single device. It also has provided an alternative method to induce droplet formation that does not require multiple syringe pumps.

Development of a Flow-free Gradient Generator Using a Self-Adhesive Thiol-acrylate Microfluidic Resin/Hydrogel (TAMR/H) Hybrid System

Microfluidic gradient generators have been used to study cellular migration, growth, and drug response in numerous biological systems. One type of device combines a hydrogel and polydimethylsiloxane (PDMS) to generate "flow-free" gradients; however, their requirements for either negative flow or external clamps to maintain fluid-tight seals between the two layers have restricted their utility among broader applications. In this work, a two-layer, flow-free microfluidic gradient generator was developed using thiol-ene chemistry. Both rigid thiol-acrylate microfluidic resin (TAMR) and diffusive thiol-acrylate hydrogel (H) layers were synthesized from commercially available monomers at room temperature and pressure using a base-catalyzed Michael addition. The device consisted of three parallel microfluidic channels negatively imprinted in TAMR layered on top of the thiol-acrylate hydrogel to facilitate orthogonal diffusion of chemicals to the direction of flow. Upon contact, these two layers formed fluid-tight channels without any external pressure due to a strong adhesive interaction between the two layers. The diffusion of molecules through the TAMR/H system was confirmed both experimentally (using fluorescent microscopy) and computationally (using COMSOL). The performance of the TAMR/H system was compared to a conventional PDMS/agarose device with a similar geometry by studying the chemorepulsive response of a motile strain of GFP-expressing Escherichia coli. Population-based analysis confirmed a similar migratory response of both wild-type and mutant E. coli in both of the microfluidic devices. This confirmed that the TAMR/H hybrid system is a viable alternative to traditional PDMS-based microfluidic gradient generators and can be used for several different applications.

Catalytic Enhancement of Inductively Heated Fe3 O4 Nanoparticles by Removal of Surface Ligands

Heat management in catalysis is limited by each material's heat transfer efficiencies, resulting in energy losses despite current thermal engineering strategies. In contrast, induction heating of magnetic nanoparticles (NPs) generates heat at the surface of the catalyst where the reaction occurs, reducing waste heat via dissipation. However, the synthesis of magnetic NPs with optimal heat generation requires interfacial ligands, such as oleic acid, which act as heat sinks. Surface treatments using tetramethylammonium hydroxide (TMAOH) or pyridine are used to remove these ligands before applications in hydrophilic media. In this study, Fe₃ O₄ NPs are surface treated to study the effect of induction heating on the catalytic oxidation of 1-octanol. Whereas TMAOH was unsuccessful in removing oleic acid, pyridine treatment resulted in a roughly 2.5-fold increase in heat generation and product yield. Therefore, efficient surfactant removal has profound implications in induction heating catalysis by increasing the heat transfer and available surface sites.

Evaluation of intercellular communication between breast cancer cells and adipose-derived stem cells via passive diffusion in a two-layer microfluidic device

Breast cancer tumorigenesis and response to therapy is regulated by cancer cell interactions with the tumor microenvironment (TME). Breast cancer signaling to the surrounding TME results in a heterogeneous and diverse tumor microenvironment, which includes the production of cancer-associated fibroblasts, macrophages, adipocytes, and stem cells. The secretory profile of these cancer-associated cell types results in elevated chemokines and growth factors that promote cell survival and proliferation within the tumor. Current co-culture approaches mostly rely on transwell chambers to study intercellular signaling between adipose-derived stem cells (ASCs) and cancer cells; however, these methods are limited to endpoint measurements and lack dynamic control. In this study, a 4-channel, "flow-free" microfluidic device was developed to co-culture triple-negative MDA-MB-231 breast cancer cells and ASCs to study intercellular communication between two distinct cell types found in the TME. The device consists of two layers: a top PDMS layer with four imprinted channels coupled with a bottom agarose slab enclosed in a Plexiglas chamber. For dynamic co-culture, the device geometry contained two centered, flow-free channels, which were supplied with media from two outer flow channels via orthogonal diffusion through the agarose. Continuous fresh media was provided to the cell culture channel via passive diffusion without creating any shearing effect on the cells. The device geometry also allowed for the passive diffusion of cytokines and growth factors between the two cell types cultured in parallel channels to initiate cell-to-cell crosstalk. The device was used to show that MDA-MB-231 cells co-cultured with ASCs exhibited enhanced growth, a more aggressive morphology, and polarization toward the ASCs. The MDA-MB-231 cells were found to exhibit a greater degree of resistance to the drug paclitaxel when co-cultured with ASCs when compared to single culture studies. This microfluidic device is an ideal platform to study intercellular communication for many types of cells during co-culture experiments and allows for new investigations into stromal cell-mediated drug resistance in the tumor microenvironment.

Lignin-graft-PLGA drug-delivery system improves efficacy of MEK1/2 inhibitors in triple-negative breast cancer cell line

Aim: Few targeted therapies are available for triple-negative breast cancer (TNBC) patients. Here, we propose a novel alkaline-lignin-conjugated-poly(lactic- co-glycolic acid) (L-PLGA) nanoparticle drug delivery system to improve the efficacy of targeted therapies. Materials & methods: L-PLGA nanoparticles (NPs) loaded with the MEK1/2 inhibitor GDC-0623 were characterized, tested in vitro on MDA-MB-231 TNBC cell line and compared with loaded PLGA NPs. Results: Loaded L-PLGA NPs were less than half the size of PLGA NPs, had slower drug release and improved the efficacy of GDC-0623 when tested in vitro. We demonstrated that GDC-0623 reversed epithelial-to-mesenchymal transition in TNBC. Conclusion: Our findings indicate that L-PLGA NPs are superior to PLGA NPs in delivering GDC-0623 to cancer cells for improved efficacy in vitro.

Dipole-Modulated Downconversion Nanoparticles as Label-Free Biological Sensors

Ultrasensitive detection of proteins and biomolecules has been previously achieved by optical nanoparticles (NPs) using the principles of Förster resonance energy transfer (FRET). However, the inherent need for labeling the target analyte in these assays hinders their applicability in point-of-use (POU) diagnostics. In this work, a label-free NP-based sensor has been developed that utilizes downconversion luminescence and surface electric dipoles as a novel approach for the detection of avidin. The long-lived luminescence of Eu³⁺-doped biotinylated NPs was effectively quenched in the presence of avidin in a concentration-dependent manner. The NPs exhibited high avidin selectivity and sensitivity with a limit of detection (LOD) of 7.8 nM and a wide dynamic range spanning 1 nM to 10 μM in deionized (DI) water. The application of the assay in a complex biological matrix consisting of cell growth medium supplemented with 10% v/v serum was verified with minor effects on avidin sensitivity exhibited by an LOD of 34.7 nM. The performance of the system was evaluated by comparing the photoluminescence (PL) intensities of known avidin concentration and the values predicted by the generated calibration curve. The new biosensing strategy has the potential to be extended to the detection of other disease biomarkers or pathogens with LOD and limited matrix effects in POU settings.

Abstract A105: Novel lignin-conjugated PLGA drug delivery system improves efficacy of MEK1/2 inhibitor in triple negative breast cancer

In 2019, it is predicted that more than a quarter of a million women in the U.S. will be diagnosed with breast cancer (BC). Nearly 15% of those cases will be classified as triple negative breast cancer (TNBC). Patients with TNBC typically have a worse prognosis due to its lack of classically targeted hormone receptors associated with other BC subtypes. Because the more well tolerated targeted endocrine therapies cannot be used to treat TNBC, novel targeted therapies and drug delivery systems must be created. They are needed to assist physicians in battling TNBC while minimizing deleterious effects and comorbidities for the patients associated with chemotherapies that are used as adjuvant therapies. Here we propose a novel lignin-conjugated-PLGA (L-PLGA) biopolymer for a nanoparticle drug delivery system (NPDDS) to improve the efficacy of the targeted therapy GDC-0623, a MEK1/2 inhibitor, to treat the TNBC cell line, MDA-MB-231. We compared our NPDDS to the commonly used PLGA. Our L-PLGA-GDC NPs had an average size of 78 ± 4 nm while PLGA-GDC NPs were 201 ± 2.5 nm making L-PLGA-GDC better suited for passive targeting based on the enhanced permeability and retention effect. Despite having a greater surface-to-volume ratio which favors diffusion, the L-PLGA NPs loaded with drug exhibited a more sustained release over 48 hours than the larger PLGA NPs. QCM-D modeling predicted the ability of our L-PLGA NPs to interact with the lipid bilayer of cells. Cells treated with L-PLGA-GDC NPs had a significant reduction in cell numbers (nearly 50%) compared to free GDC-0623 and PLGA-GDC NPs. Western blot confirmed L-PLGA-GDC was better at inhibiting phosphorylation of GDC-0623 target protein ERK1/2 than free GDC-0623 or PLGA-GDC NPs. We hypothesize that the increase in efficacy was due to the NPs interacting with the cell membrane, being taken up by the cell, and increasing the local drug concentration. This mechanism was predicted by QCM-D and confirmed by fluorescent microscopy of TRITC-conjugated NPs. Cells treated with GDC-0623 presented a different morphology than untreated cells and qPCR confirmed that GDC-0623 reverses EMT in MDA-MB-231 cells. L-PLGA-GDC was more effective at reversing EMT than free GDC-0623 and PLGA-GDC NPs. Our findings indicate that lignin conjugation improves characteristics of PLGA NPDDSs and improves efficacy of GDC-0623 in multiple assays.

Citation Format: Ethan Byrne, Carlos E. Astete, Manibarathi Vaithiyanathan, Adam T Melvin, Mahsa Moradipour, Stephen E. Rankin, Barbara L. Knutson, Elizabeth C. Martin, Cristina Sabliov. Novel lignin-conjugated PLGA drug delivery system improves efficacy of MEK1/2 inhibitor in triple negative breast cancer [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr A105. doi:10.1158/1535-7163.TARG-19-A105

Static microdroplet array generated by spraying and analyzed with automated microscopy and image processing

Microdroplets have received increasing interest as practical platforms for high-throughput biochemical analysis. Typically, numerous discrete aqueous microdroplets containing biochemical targets are generated in a continuous oil phase and characterized using a flow-through configuration. Although this approach is capable of extremely high throughput, it is challenging to provide dynamic characterization of time-dependent reaction kinetics. In this paper, we present a practical and affordable method to create and analyze a massive array of static aqueous microdroplets immersed in oil for biochemical analysis. The discrete microdroplets were produced by an air-spray gun, imaged by automated microscopy, and then characterized by image processing. The location, area, and fluorescence intensity of randomly generated individual microdroplets were automatically registered for high-throughput characterization. With this approach, we rapidly produced and characterized a static microdroplet array of over 0.7 million microdroplets with an average volume of 300 fL and a mean population density of 1.5*10⁵ microdroplets/cm². Using the developed setup, we demonstrated the dependency of the microdroplets' fluorescence intensity on their volume, as well as characterized the time-dependent enzyme reaction kinetics of β-galactosidase-mediated cleavage of the substrate fluorescein di-β-d-galactopyranoside (FDG). The new approach described herein provides an inexpensive alternative solution for high-throughput analysis of dynamic biochemical processes.

Direct measurement of deubiquitinating enzyme activity in intact cells using a protease-resistant, cell-permeable, peptide-based reporter

Deubiquitinating enzymes (DUBs) regulate the removal of the polyubiquitin chain from proteins targeted for degradation. Current approaches to quantify DUB activity are limited to test tube-based assays that incorporate enzymes or cell lysates, but not intact cells. The goal of this work was to develop a novel peptide-based biosensor of DUB activity that is cell permeable, protease-resilient, fluorescent, and specific to DUBs. The biosensor consists of an N-terminal β-hairpin motif that acts as both a 'protectide' to increase intracellular stability and a cell penetrating peptide (CPP) to facilitate the uptake into intact cells. The β-hairpin was conjugated to a C-terminal substrate consisting of the last four amino acids in ubiquitin (LRGG) to facilitate DUB mediated cleavage of a C-terminal fluorophore (AFC). The kinetics of the peptide reporter were characterized in cell lysates by dose response and inhibition enzymology studies. Inhibition studies with an established DUB inhibitor (PR-619) confirmed the specificity of both reporters to DUBs. Fluorometry and fluorescent microscopy experiments followed by mathematical modeling established the capability of the biosensor to measure DUB activity in intact cells while maintaining cellular integrity. The novel reporter introduced here is compatible with high-throughput single cell analysis platforms such as FACS and droplet microfluidics facilitating direct quantification of DUB activity in single intact cells with direct application in point-of-care cancer diagnostics and drug discovery.

CPProtectides: Rapid uptake of well-folded β-hairpin peptides with enhanced resistance to intracellular degradation

Cell penetrating peptides (CPPs) have emerged as powerful tools for delivering bioactive cargoes, such as biosensors or drugs to intact cells. One limitation of CPPs is their rapid degradation by intracellular proteases. β-hairpin "protectides" have previously been demonstrated to be long-lived under cytosolic conditions due to their secondary structure. The goal of this work was to demonstrate that arginine-rich β-hairpin peptides function as both protectides and as CPPs. Peptides exhibiting a β-hairpin motif were found to be rapidly internalized into cells with their uptake efficiency dependent on the number of arginine residues in the sequence. Cellular internalization of the β-hairpin peptides was compared to unstructured, scrambled sequences and to commercially available, arginine-rich CPPs. The unstructured peptides displayed greater uptake kinetics compared to the structured β-hairpin sequences; however, intracellular stability studies revealed that the β-hairpin peptides exhibited superior stability under cytosolic conditions with a 16-fold increase in peptide half-life. This study identifies a new class of long-lived CPPs that can overcome the stability limitations of peptide-based reporters or bioactive delivery mechanisms in intact cells.

Population-based analysis of cell-penetrating peptide uptake using a microfluidic droplet trapping array

Cell-penetrating peptides (CPPs) have garnered significant attention as a method to introduce reporters and therapeutics into intact cells. While numerous studies have been performed identifying new CPP sequences, relatively little is known about their uptake efficiency at the single-cell level. Here, a droplet microfluidic trapping array was used to characterize CPP uptake across a population of single intact cells. The microfluidic device allowed for facile and rapid isolation and analysis of single-cell fluorescence in a 787-member overhead trapping array with > 99% droplet trapping efficiency. The permeability efficiencies of four different CPPs were studied and compared in HeLa cells. Population analysis was performed using linkage hierarchical cluster analysis by R programming to bin cells into subpopulations expressing very low to very high peptide uptake efficiencies. CPP uptake was observed to be heterogeneous across the population of cells with peptide concentration and sequence both playing important roles in the diversity of CPP uptake, the overall peptide uptake efficiency, and the intracellular homogeneity of peptide distribution. This microfluidic-based analytical approach finds application in personalized medicine and provides new insight in the heterogeneity of CPP uptake which has the potential to affect both biosensor and drug internalization in intact cells. Graphical abstract .

FluoroCellTrack: An algorithm for automated analysis of high-throughput droplet microfluidic data

High-throughput droplet microfluidic devices with fluorescence detection systems provide several advantages over conventional end-point cytometric techniques due to their ability to isolate single cells and investigate complex intracellular dynamics. While there have been significant advances in the field of experimental droplet microfluidics, the development of complementary software tools has lagged. Existing quantification tools have limitations including interdependent hardware platforms or challenges analyzing a wide range of high-throughput droplet microfluidic data using a single algorithm. To address these issues, an all-in-one Python algorithm called FluoroCellTrack was developed and its wide-range utility was tested on three different applications including quantification of cellular response to drugs, droplet tracking, and intracellular fluorescence. The algorithm imports all images collected using bright field and fluorescence microscopy and analyzes them to extract useful information. Two parallel steps are performed where droplets are detected using a mathematical Circular Hough Transform (CHT) while single cells (or other contours) are detected by a series of steps defining respective color boundaries involving edge detection, dilation, and erosion. These feature detection steps are strengthened by segmentation and radius/area thresholding for precise detection and removal of false positives. Individually detected droplet and contour center maps are overlaid to obtain encapsulation information for further analyses. FluoroCellTrack demonstrates an average of a ~92-99% similarity with manual analysis and exhibits a significant reduction in analysis time of 30 min to analyze an entire cohort compared to 20 h required for manual quantification.

Microfluidic and Paper-Based Devices for Disease Detection and Diagnostic Research

Recent developments in microfluidic devices, nanoparticle chemistry, fluorescent microscopy, and biochemical techniques such as genetic identification and antibody capture have provided easier and more sensitive platforms for detecting and diagnosing diseases as well as providing new fundamental insight into disease progression. These advancements have led to the development of new technology and assays capable of easy and early detection of pathogenicity as well as the enhancement of the drug discovery and development pipeline. While some studies have focused on treatment, many of these technologies have found initial success in laboratories as a precursor for clinical applications. This review highlights the current and future progress of microfluidic techniques geared toward the timely and inexpensive diagnosis of disease including technologies aimed at high-throughput single cell analysis for drug development. It also summarizes novel microfluidic approaches to characterize fundamental cellular behavior and heterogeneity.

Biophysical analysis of fluid shear stress induced cellular deformation in a microfluidic device

Even though the majority of breast cancers respond well to primary therapy, a large percentage of patients relapse with metastatic disease, for which there is no treatment. In metastasis, a tumor sheds a small number of cancerous cells, termed circulating tumor cells (CTCs), into the local vasculature, from where they spread throughout the body to form new tumors. As CTCs move through the circulatory system, they experience physiological forces not present in the initial tumor environment, namely, fluid shear stress (FSS). Evidence suggests that CTCs respond to FSS by adopting a more aggressive phenotype; however, to date single-cell morphological changes have not been quantified to support this observation. Furthermore, the methodology of previous studies involves inducing FSS by flowing cells through the tubing, which lacks a precise and tunable control of FSS. Here, a microfluidic approach is used for isolating and characterizing the biophysical response of single breast cancer cells to conditions experienced in the circulatory system during metastasis. To evaluate the single-cell response of multiple breast cancer types, two model circulating tumor cell lines, MDA-MB-231 and MCF7, were challenged with FSS at precise magnitudes and durations. As expected, both MDA-MB-231 and MCF7 cells exhibited greater deformability due to increasing duration and magnitudes of FSS. However, wide variations in single-cell responses were observed. MCF7 cells were found to rapidly deform but reach a threshold value after 5 min of FSS, while MDA-MB-231 cells were observed to deform at a slower rate but with a larger threshold of deformation. This behavioral diversity suggests the presence of distinct cell subpopulations with different phenotypes.

Development of β-Hairpin Peptides for the Measurement of SCF-Family E3 Ligase Activity in Vitro via Ornithine Ubiquitination

Regulation of the ubiquitin-proteasome system (UPS) to treat select types of cancer has become a popular area of drug discovery research. The FDA approval of proteasome inhibitors Bortezomib and Carfilzomib in the treatment of multiple myeloma has led to an increased need for chemical reporters capable of detecting and quantifying protein ubiquitination and the activity of members of the UPS including E3 ubiquitin ligases and the proteasome in the tumor cells of the patients. One limitation of peptide-based reporters is their rapid degradation in the cellular environment by cytosolic peptidases. Conversely, β-hairpin "protectides" exhibit a pronounced secondary structure that significantly increases their lifetime under cellular conditions. The goal of this work was to develop a family of novel, ornithine-rich protectides that could act as primary degrons serving as substrates for in vitro ubiquitination. The fluorescent peptide-based reporters were demonstrated to be highly resistant to degradation in multiple myeloma cell lysates. The most stable β-hairpin primary degron, containing a single ornithine residue at the N-terminus, OWRWR [Ac-OWVRVpGO(FAM)WIRQ-NH2], demonstrated rapid ubiquitination kinetics and a 20-fold increase in stability when compared with an unstructured primary degron. A screen of E1 and E3 enzyme inhibitors in cell lysates showed that ubiquitination of OWRWR was significantly impaired by inhibitors of the SCF family of E3 ligases. Furthermore, this is the first report demonstrating the use of an ornithine residue on a primary degron as a ubiquitination site. This study serves as a strong foundation for the development of stable, fluorescent, peptide-based reporters capable of quantifying protein ubiquitination and the enzymatic activity of members of the UPS.

Identification of a p53-based portable degron based on the MDM2-p53 binding region

In recent years the ubiquitin proteasome system (UPS) has garnered increasing interest as a target for chemotherapeutics. Due to the success of the proteasome inhibitors Bortezomib and Carfilzomib in the treatment of multiple myeloma, several new compounds have been developed to target E3 ubiquitin ligases and the proteasome in numerous human cancers. This has increased the need for new analytical methods to precisely measure intracellular enzyme activity in cells. A key component of a desired analytical method is a substrate that is capable of rapid intracellular ubiquitination yet easily incorporated into the next generation of more sophisticated UPS reporters. Portable degradation sequences, or degrons, have the ability to bind to E3 ligases and promote substrate ubiquitination when the sequence is presented in isolation or appended to other entities such as fluorescent peptide-based reporters. Previous work identified an E3 ligase (MDM2)-binding element at p53 amino acids 92-112, which was later demonstrated to be rapidly ubiquitinated in cytosolic lysates effectively functioning as a transportable degron. In this work, a shortened p53 sequence within amino acids 92-112 that displayed rapid ubiquitination kinetics was identified. A nine-member peptide library was synthesized using sequence elements of various sizes and lengths, all based on the initial 22 amino acid long sequence, containing a single ubiquitination site lysine. The ubiquitination kinetics were determined using a combination of gel electrophoresis and analytical high performance liquid chromatography (HPLC) to rank the members of the library and identify the optimal ubiquitination sequence. This analysis identified the five amino acid sequence, KGSYG, corresponding to residues 105-108 with an added N-terminal lysine, as a portable degron since this sequence demonstrated the most rapid ubiquitination kinetics.

Oil-material fractionation in Gulf deep water horizontal intrusion layer: Field data analysis with chemodynamic fate model for Macondo 252 oil spill

Among the discoveries of the Deepwater Horizon blowout was the so-called "sub-surface plume"; herein termed the "oil-trapping layer". Hydrocarbons were found positioned at ~1100-1300m with thickness ~100-150m and moving horizontally to the SW in a vertically stratified layer at the junction of the cold abyssal water and the permanent thermocline. This study focuses on its formation process and fate of the hydrocarbons within. The originality of this work to the field is two-fold, first it provides a conceptual framework which places layer origin in the context of a horizontal "intrusion" from the near-field, vertical, blow-out plume and second, it offers a theoretical model for the hydrocarbon chemicals within the horizontal layer as it moves far-afield. The model quantifies the oil-material fractionation process for the soluble and fine particle. The classical Box model, retrofitted with an internal gradient, the "G-Box", allows an approach that includes turbulent eddy diffusion coupled with droplet rise velocity and reactive decay to produce a simple, explicit, transparent, algebraic model with few parameters for the fate of the individual fractions. Computations show the soluble and smallest liquid droplets moving very slowly vertically through the layer appearing within the trapping layer at low concentration with high persistence. The larger droplets move-through this trapping zone quickly, attain high concentrations, and eventually form the sea surface slick. It impacts the field of oil spill engineering science by providing the conceptual idea and the algorithms for projecting the quantities and fractions of oil-material in a deep water, horizontal marine current being dispersed and moving far afield. In the field of oil spill modeling this work extends the current generation near-field plume source models to the far-field. The theory portrays the layer as an efficient oil-material trap. The model-forecasted concentration profiles for alkanes and aromatics against the available field data support the proposed theory and the resulting model.

Fibroblast Migration Is Regulated by Myristoylated Alanine-Rich C-Kinase Substrate (MARCKS) Protein

Myristoylated alanine-rich C-kinase substrate (MARCKS) is a ubiquitously expressed substrate of protein kinase C (PKC) that is involved in reorganization of the actin cytoskeleton. We hypothesized that MARCKS is involved in regulation of fibroblast migration and addressed this hypothesis by utilizing a unique reagent developed in this laboratory, the MANS peptide. The MANS peptide is a myristoylated cell permeable peptide corresponding to the first 24-amino acids of MARCKS that inhibits MARCKS function. Treatment of NIH-3T3 fibroblasts with the MANS peptide attenuated cell migration in scratch wounding assays, while a myristoylated, missense control peptide (RNS) had no effect. Neither MANS nor RNS peptide treatment altered NIH-3T3 cell proliferation within the parameters of the scratch assay. MANS peptide treatment also resulted in inhibited NIH-3T3 chemotaxis towards the chemoattractant platelet-derived growth factor-BB (PDGF-BB), with no effect observed with RNS treatment. Live cell imaging of PDGF-BB induced chemotaxis demonstrated that MANS peptide treatment resulted in weak chemotactic fidelity compared to RNS treated cells. MANS and RNS peptides did not affect PDGF-BB induced phosphorylation of MARCKS or phosphoinositide 3-kinase (PI3K) signaling, as measured by Akt phosphorylation. Further, no difference in cell migration was observed in NIH-3T3 fibroblasts that were transfected with MARCKS siRNAs with or without MANS peptide treatment. Genetic structure-function analysis revealed that MANS peptide-mediated attenuation of NIH-3T3 cell migration does not require the presence of the myristic acid moiety on the amino-terminus. Expression of either MANS or unmyristoylated MANS (UMANS) C-terminal EGFP fusion proteins resulted in similar levels of attenuated cell migration as observed with MANS peptide treatment. These data demonstrate that MARCKS regulates cell migration and suggests that MARCKS-mediated regulation of fibroblast migration involves the MARCKS amino-terminus. Further, this data demonstrates that MANS peptide treatment inhibits MARCKS function during fibroblast migration and that MANS mediated inhibition occurs independent of myristoylation.

Migrating fibroblasts reorient directionality by a metastable, PI3K-dependent mechanism

Mesenchymal cell migration as exhibited by fibroblasts is distinct from amoeboid cell migration and is characterized by dynamic competition among multiple protrusions, which determines directional persistence and responses to spatial cues. Localization of phosphoinositide 3-kinase (PI3K) signaling is thought to play a broadly important role in cell motility, yet the context-dependent functions of this pathway have not been adequately elucidated. By mapping the spatiotemporal dynamics of cell protrusion/retraction and PI3K signaling monitored by total internal reflection fluorescence microscopy, we show that randomly migrating fibroblasts reorient polarity through PI3K-dependent branching and pivoting of protrusions. PI3K inhibition did not affect the initiation of newly branched protrusions, nor did it prevent protrusion induced by photoactivation of Rac. Rather, PI3K signaling increased after, not before, the onset of local protrusion and was required for the lateral spreading and stabilization of nascent branches. During chemotaxis, the branch experiencing the higher chemoattractant concentration was favored, and, thus, the cell reoriented so as to align with the external gradient.

In chemotaxing fibroblasts, both high-fidelity and weakly biased cell movements track the localization of PI3K signaling

Cell movement biased by a chemical gradient, or chemotaxis, coordinates the recruitment of cells and collective migration of cell populations. During wound healing, chemotaxis of fibroblasts is stimulated by platelet-derived growth factor (PDGF) and certain other chemoattractants. Whereas the immediate PDGF gradient sensing response has been characterized previously at the level of phosphoinositide 3-kinase (PI3K) signaling, the sensitivity of the response at the level of cell migration bias has not yet been studied quantitatively. In this work, we used live-cell total internal reflection fluorescence microscopy to monitor PI3K signaling dynamics and cell movements for extended periods. We show that persistent and properly aligned (i.e., high-fidelity) fibroblast migration does indeed correlate with polarized PI3K signaling; accordingly, this behavior is seen only under conditions of high gradient steepness (>10% across a typical cell length of 50 μm) and a certain range of PDGF concentrations. Under suboptimal conditions, cells execute a random or biased random walk, but nonetheless move in a predictable fashion according to the changing pattern of PI3K signaling. Inhibition of PI3K during chemotaxis is accompanied by loss of both cell-substratum contact and morphological polarity, but after a recovery period, PI3K-inhibited fibroblasts often regain the ability to orient toward the PDGF gradient.

Spontaneous phosphoinositide 3-kinase signaling dynamics drive spreading and random migration of fibroblasts

During directed cell migration (chemotaxis), cytoskeletal dynamics are stimulated and spatially biased by phosphoinositide 3-kinase (PI3K) and other signal transduction pathways. Live-cell imaging using total internal reflection fluorescence (TIRF) microscopy revealed that, in the absence of soluble cues, 3'-phosphoinositides are enriched in a localized and dynamic fashion during active spreading and random migration of mouse fibroblasts on adhesive surfaces. Surprisingly, we found that PI3K activation is uncoupled from classical integrin-mediated pathways and feedback from the actin cytoskeleton. Inhibiting PI3K significantly impairs cell motility, both in the context of normal spreading and when microtubules are dissociated, which induces a dynamic protrusion phenotype as seen by TIRF in our cells. Accordingly, during random migration, 3'-phosphoinositides are frequently localized to regions of membrane protrusion and correlate quantitatively with the direction and persistence of cell movement. These results underscore the importance of localized PI3K signaling not only in chemotaxis but also in basal motility/migration of fibroblasts.