Jason Reed

Rapid, massively parallel single-cell drug response measurements via live cell interferometry

A central question in cancer therapy is how individual cells within a population of tumor cells respond to drugs designed to arrest their growth. However, the absolute growth of cells, their change in physical mass, whether cancerous or physiologic, is difficult to measure directly with traditional techniques. Here, we develop live cell interferometry for rapid, real-time quantification of cell mass in cells exposed to a changing environment. We used tunicamycin induction of the unfolded protein stress response in multiple myeloma cells to generate a mass response that was temporally profiled for hundreds of cells simultaneously. Within 2 h, the treated cells were growth suppressed compared to controls, with a few cells in both populations showing a robust increase (+15%) or little change (<5%) in mass accumulation. Overall, live cell interferometry provides a conceptual advance for assessing cell populations to identify, monitor, and measure single cell responses, such as to therapeutic drugs.

Characterization of Ocular Tissues Using Microindentation and Hertzian Viscoelastic Models

PURPOSEnThe authors applied a novel microindentation technique to characterize biomechanical properties of small ocular and orbital tissue specimens using the hertzian viscoelastic formulation, which defines material viscoelasticity in terms of the contact pressure required to maintain deformation by a harder body.nnnMETHODSnThey used a hard spherical indenter having 100 nm displacement and 100 μg force precision to impose small deformations on fresh bovine sclera, iris, crystalline lens, kidney fat, orbital pulley tissue, and orbital fatty tissue; normal human orbital fat, eyelid fat, and dermal fat; and orbital fat associated with thyroid eye disease. For each tissue, stress relaxation testing was performed using a range of ramp displacements. Results for single displacements were used to build quantitative hertzian models that were, in turn, compared with behavior for other displacements. Findings in orbital tissues were correlated with quantitative histology.nnnRESULTSnViscoelastic properties of small specimens of orbital and ocular tissues were reliably characterized over a wide range of rates and displacements by microindentation using the hertzian formulation. Bovine and human orbital fatty tissues exhibited highly similar elastic and viscous behaviors, but all other orbital tissues exhibited a wide range of biomechanical properties. Stiffness of fatty tissues tissue depended strongly on the connective tissue content.nnnCONCLUSIONSnRelaxation testing by microindentation is a powerful method for characterization of time-dependent behaviors of a wide range of ocular and orbital tissues using small specimens, and provides data suitable to define finite element models of a wide range of tissue interactions.

Mechanical Interferometry Imaging for Creep Modeling of the Cornea

PURPOSEnA novel nanoindentation technique was used to biomechanically characterize each of three main layers of the cornea by using Hertzian viscoelastic formulation of creep, the deformation resulting from sustained-force application.nnnMETHODSnThe nanoindentation method known as mechanical interferometry imaging (MII) with <1-nm displacement precision was used to observe indentation of bovine corneal epithelium, endothelium, and stroma by a spherical ferrous probe in a calibrated magnetic field. For each specimen, creep testing was performed using two different forces for 200 seconds. Measurements for single force were used to build a quantitative Hertzian model that was then used to predict creep behavior for another imposed force.nnnRESULTSnFor all three layers, displacement measurements were highly repeatable and were well predicted by Hertzian models. Although short- and long-term stiffnesses of the endothelium were highest of the three layers at 339.2 and 20.2 kPa, respectively, both stromal stiffnesses were lowest at 100.4 and 3.6 kPa, respectively. Stiffnesses for the epithelium were intermediate at 264.6 and 12.2 kPa, respectively.nnnCONCLUSIONSnPrecise, repeatable measurements of corneal creep behavior can be conveniently obtained using MII at mechanical scale as small as one cell thickness. When interpreted in analytical context of Hertzian viscoelasticity, MII technique proved to be a powerful tool for biomechanical characterization of time-dependent biomechanics of corneal regions.

Atomic force microscopy determination of Young׳s modulus of bovine extra-ocular tendon fiber bundles

Extra-ocular tendons (EOTs) transmit the oculorotary force of the muscles to the eyeball to generate dynamic eye movements and align the eyes, yet the mechanical properties of the EOTs remain undefined. The EOTs are known to be composed of parallel bundles of small fibers whose mechanical properties must be determined in order to characterize the overall behavior of EOTs. The current study aimed to investigate the transverse Young׳s modulus of EOT fiber bundles using atomic force microscopy (AFM). Fresh bovine EOT fiber bundle specimens were maintained under temperature and humidity control, and indented 100nm by the inverted pyramid tip of an AFM (Veeco Digital Instruments, NY). Ten indentations were conducted for each of 3 different locations of 10 different specimens from each of 6 EOTs, comprising a total of 1800 indentations. Young׳s modulus for each EOT was determined using a Hertzian contact model. Young׳s moduli for fiber bundles from all six EOTs were determined. Mean Young׳s moduli for fiber bundles were similar for the six anatomical EOTs: lateral rectus 60.12±2.69 (±SD)MPa, inferior rectus 59.69±5.34MPa, medial rectus 56.92±1.91MPa, superior rectus 59.66±2.64MPa, inferior oblique 57.7±1.36MPa, and superior oblique 59.15±2.03. Variation in Young׳s moduli among the six EOTs was not significant (P>0.25). The Young׳s modulus of bovine EOT fibers is highly uniform among the six extraocular muscles, suggesting that each EOT is assembled from fiber bundles representing the same biomechanical elements. This uniformity will simplify overall modeling.

Rapidly quantifying drug sensitivity of dispersed and clumped breast cancer cells by mass profiling

Live cell mass profiling is a promising new approach for rapidly quantifying responses to therapeutic agents through picogram-scale changes in cell mass over time. A significant barrier in mass profiling is the inability of existing methods to handle pleomorphic cellular clusters and clumps, which are more commonly present in patient-derived samples or tissue cultures than are isolated single cells. Here we demonstrate automated Live Cell Interferometry (LCI) as a rapid and accurate quantifier of the sensitivity of single cell and colony-forming human breast cancer cell lines to the HER2-directed monoclonal antibody, trastuzumab (Herceptin). The relative sensitivities of small samples (<500 cells) of four breast cancer cell lines were determined tens-to-hundreds of times faster than is possible with traditional proliferation assays. These LCI advances in clustered sample assessment and speed open up the possibility for therapeutic response testing of patient-derived solid tumor samples, which are viable only for short periods ex vivo and likely to be in the form of cell aggregates and clusters.

Live cell interferometry quantifies dynamics of biomass partitioning during cytokinesis.

The equal partitioning of cell mass between daughters is the usual and expected outcome of cytokinesis for self-renewing cells. However, most studies of partitioning during cell division have focused on daughter cell shape symmetry or segregation of chromosomes. Here, we use live cell interferometry (LCI) to quantify the partitioning of daughter cell mass during and following cytokinesis. We use adherent and non-adherent mouse fibroblast and mouse and human lymphocyte cell lines as models and show that, on average, mass asymmetries present at the time of cleavage furrow formation persist through cytokinesis. The addition of multiple cytoskeleton-disrupting agents leads to increased asymmetry in mass partitioning which suggests the absence of active mass partitioning mechanisms after cleavage furrow positioning.

Dynamical system modeling to simulate donor T cell response to whole exome sequencing-derived recipient peptides: Understanding randomness in alloreactivity incidence following stem cell transplantation

Quantitative relationship between the magnitude of variation in minor histocompatibility antigens (mHA) and graft versus host disease (GVHD) pathophysiology in stem cell transplant (SCT) donor-recipient pairs (DRP) is not established. In order to elucidate this relationship, whole exome sequencing (WES) was performed on 27 HLA matched related (MRD), & 50 unrelated donors (URD), to identify nonsynonymous single nucleotide polymorphisms (SNPs). An average 2,463 SNPs were identified in MRD, and 4,287 in URD DRP (p<0.01); resulting peptide antigens that may be presented on HLA class I molecules in each DRP were derived in silico (NetMHCpan ver2.0) and the tissue expression of proteins these were derived from determined (GTex). MRD DRP had an average 3,670 HLA-binding-alloreactive peptides, putative mHA (pmHA) with an IC50 of <500 nM, and URD, had 5,386 (p<0.01). To simulate an alloreactive donor cytotoxic T cell response, the array of pmHA in each patient was considered as an operator matrix modifying a hypothetical cytotoxic T cell clonal vector matrix; each responding T cell clone’s proliferation was determined by the logistic equation of growth, accounting for HLA binding affinity and tissue expression of each alloreactive peptide. The resulting simulated organ-specific alloreactive T cell clonal growth revealed marked variability, with the T cell count differences spanning orders of magnitude between different DRP. Despite an estimated, uniform set of constants used in the model for all DRP, and a heterogeneously treated group of patients, higher total and organ-specific T cell counts were associated with cumulative incidence of moderate to severe GVHD in recipients. In conclusion, exome wide sequence differences and the variable alloreactive peptide binding to HLA in each DRP yields a large range of possible alloreactive donor T cell responses. Our findings also help understand the apparent randomness observed in the development of alloimmune responses.

Atomic force microscopic detection enabling multiplexed low-cycle-number quantitative polymerase chain reaction for biomarker assays.

Quantitative polymerase chain reaction is the current “golden standard” for quantification of nucleic acids; however, its utility is constrained by an inability to easily and reliably detect multiple targets in a single reaction. We have successfully overcome this problem with a novel combination of two widely used approaches: target-specific multiplex amplification with 15 cycles of polymerase chain reaction (PCR), followed by single-molecule detection of amplicons with atomic force microscopy (AFM). In test experiments comparing the relative expression of ten transcripts in two different human total RNA samples, we find good agreement between our single reaction, multiplexed PCR/AFM data, and data from 20 individual singleplex quantitative PCR reactions. This technique can be applied to virtually any analytical problem requiring sensitive measurement concentrations of multiple nucleic acid targets.

High-Speed Atomic Force Microscopy Revealing Contamination in DNA Purification Systems

Motivated by reports of low-level DNA contamination in popular commercial DNA purification kits, we employed a novel high-speed atomic force microscopy (HS-AFM) method to detect and characterize particulate and polymeric contaminants in four such systems: Qiagen MinElute PCR Purification, Zymo Research DNA Clean and Concentrator-5, Invitrogen ChargeSwitch-Pro PCR Purification, and Beckman Coulter AMPure XP. HS-AFM avoids amplification artifacts present in PCR or in the sequencing of amplified products, and it requires no chemical labels and easily achieves near-single-molecule sensitivity. Using this technique, we found trace levels of filamentous contamination, similar in appearance to dsDNA, in eluates from the Zymo, Qiagen, and ChargeSwitch kits. Conversely, we detected no contaminants in magnetic bead-based AMPure XP solutions. Eluates from the Zymo kits also tested positive for DNA in fluorescent intercalator dye and whole genome amplification (WGA) assays. Qiagen kits tested positive in the fluorescence assay but negative in the WGA assay. Both ChargeSwitch and AMPure XP tested negative in the fluorescence assay while the WGA results for these two kits were ambiguous. Taken together, our findings suggest AMPure XP would be the best choice for analyses requiring very high analytical stringency. While HS-AFM alone does not provide chemical specificity, it is a potentially valuable tool for characterizing and quantifying trace contaminants in molecular biology reagents and instruments in cases where conventional techniques fail.

High-Speed Live-Cell Interferometry: A New Method for Quantifying Tumor Drug Resistance and Heterogeneity

We report the development of high-speed live-cell interferometry (HSLCI), a new multisample, multidrug testing platform for directly measuring tumor therapy response via real-time optical cell biomass measurements. As a proof of concept, we show that HSLCI rapidly profiles changes in biomass in BRAF inhibitor (BRAFi)-sensitive parental melanoma cell lines and in their isogenic BRAFi-resistant sublines. We show reproducible results from two different HSLCI platforms at two institutions that generate biomass kinetic signatures capable of discriminating between BRAFi-sensitive and -resistant melanoma cells within 24 h. Like other quantitative phase imaging (QPI) modalities, HSLCI is well-suited to noninvasive measurements of single cells and cell clusters, requiring no fluorescence or dye labeling. HSLCI is substantially faster and more sensitive than field-standard growth inhibition assays, and in terms of the number of cells measured simultaneously, the number of drugs tested in parallel, and temporal measurement range, it exceeds the state of the art by more than 10-fold. The accuracy and speed of HSLCI in profiling tumor cell heterogeneity and therapy resistance are promising features of potential tools to guide patient therapeutic selections.