Single-Cell Proliferation Microfluidic Device for High Throughput Investigation of Replicative Potential and Drug Resistance of Cancer Cells.

Introduction: Cell proliferation represents a major hallmark of cancer biology, and manifests itself in the assessment of tumor growth, drug resistance and metastasis. Tracking cell proliferation or cell fate at the single-cell level can reveal phenotypic heterogeneity. However, characterization of cell proliferation is typically done in bulk assays which does not inform on cells that can proliferate under given environmental perturbations. Thus, there is a need for single-cell approaches that allow longitudinal tracking of the fate of a large number of individual cells to reveal diverse phenotypes. Methods: We fabricated a new microfluidic architecture for high efficiency capture of single tumor cells, with the capacity to monitor cell divisions across multiple daughter cells. This single-cell proliferation (SCP) device enabled the quantification of the fate of more than 1000 individual cancer cells longitudinally, allowing comprehensive profiling of the phenotypic heterogeneity that would be otherwise masked in standard cell proliferation assays. We characterized the efficiency of single cell capture and demonstrated the utility of the SCP device by exposing MCF-7 breast tumor cells to different doses of the chemotherapeutic agent doxorubicin. Results: The single cell trapping efficiency of the SCP device was found to be ~ 85%. At the low doses of doxorubicin (0.01 µM, 0.001 µM, 0.0001 µM), we observed that 50-80% of the drug-treated cells had undergone proliferation, and less than 10% of the cells do not proliferate. Additionally, we demonstrated the potential of the SCP device in circulating tumor cell applications where minimizing target cell loss is critical. We showed selective capture of breast tumor cells from a binary mixture of cells (tumor cells and white blood cells) that was isolated from blood processing. We successfully characterized the proliferation statistics of these captured cells despite their extremely low counts in the original binary suspension. Conclusions: The SCP device has significant potential for cancer research with the ability to quantify proliferation statistics of individual tumor cells, opening new avenues of investigation ranging from evaluating drug resistance of anti-cancer compounds to monitoring the replicative potential of patient-derived cells. Supplementary Information: The online version contains supplementary material available at 10.1007/s12195-023-00773-z.

Comprehensive Profiling of Cancer-Associated Cells in the Blood of Breast Cancer Patients Undergoing Neoadjuvant Chemotherapy to Predict Pathological Complete Response.

Neoadjuvant chemotherapy (NAC) can affect pathological complete response (pCR) in breast cancers; the resection that follows identifies patients with residual disease who are then offered second-line therapies. Circulating tumor cells (CTCs) and cancer-associated macrophage-like cells (CAMLs) in the blood can be used as potential biomarkers for predicting pCR before resection. CTCs are of epithelial origin that undergo epithelial-to-mesenchymal transition to become more motile and invasive, thereby leading to invasive mesenchymal cells that seed in distant organs, causing metastasis. Additionally, CAMLs in the blood of cancer patients are reported to either engulf or aid the transport of cancer cells to distant organs. To study these rare cancer-associated cells, we conducted a preliminary study where we collected blood from patients treated with NAC after obtaining their written and informed consent. Blood was collected before, during, and after NAC, and Labyrinth microfluidic technology was used to isolate CTCs and CAMLs. Demographic, tumor marker, and treatment response data were collected. Non-parametric tests were used to compare pCR and non-pCR groups. Univariate and multivariate models were used where CTCs and CAMLs were analyzed for predicting pCR. Sixty-three samples from 21 patients were analyzed. The median(IQR) pre-NAC total and mesenchymal CTC count/5 mL was lower in the pCR vs. non-pCR group [1(3.5) vs. 5(5.75); p = 0.096], [0 vs. 2.5(7.5); p = 0.084], respectively. The median(IQR) post-NAC CAML count/5 mL was higher in the pCR vs. non-pCR group [15(6) vs. 6(4.5); p = 0.004]. The pCR group was more likely to have >10 CAMLs post-NAC vs. non-pCR group [7(100%) vs. 3(21.4%); p = 0.001]. In a multivariate logistic regression model predicting pCR, CAML count was positively associated with the log-odds of pCR [OR = 1.49(1.01, 2.18); p = 0.041], while CTCs showed a negative trend [Odds Ratio (OR) = 0.44(0.18, 1.06); p = 0.068]. In conclusion, increased CAMLs in circulation after treatment combined with lowered CTCs was associated with pCR.

Deep learning assisted holography microscopy for in-flow enumeration of tumor cells in blood.

Currently, detection of circulating tumor cells (CTCs) in cancer patient blood samples relies on immunostaining, which does not provide access to live CTCs, limiting the breadth of CTC-based applications. Here, we take the first steps to address this limitation, by demonstrating staining-free enumeration of tumor cells spiked into lysed blood samples using digital holographic microscopy (DHM), microfluidics and machine learning (ML). A 3D-printed module for laser assembly was developed to simplify the optical set up for holographic imaging of cells flowing through a sheath-based microfluidic device. Computational reconstruction of the holograms was performed to localize the cells in 3D and obtain the plane of best focus images to train deep learning models. We developed a custom-designed light-weight shallow Network dubbed s-Net and compared its performance against off-the-shelf CNN models including ResNet-50. The accuracy, sensitivity and specificity of the s-Net model was found to be higher than the off-the-shelf ML models. By applying an optimized decision threshold to mixed samples prepared in silico, the false positive rate was reduced from 1 × 10-2 to 2.77 × 10-4. Finally, the developed DHM-ML framework was successfully applied to enumerate spiked MCF-7 breast cancer cells and SkOV3 ovarian cancer cells from lysed blood samples containing white blood cells (WBCs) at concentrations typical of label-free enrichment techniques. We conclude by discussing the advances that need to be made to translate the DHM-ML approach to staining-free enumeration of actual CTCs in cancer patient blood samples.

Phenotyping of rare circulating cells in the blood of non-metastatic breast cancer patients using microfluidic Labyrinth technology.

Label-free technologies for isolating rare circulating cells in breast cancer patients are widely available; however, they are mostly validated on metastatic patient blood samples. Given the need to use blood-based biomarkers to inform on disease progression and treatment decisions, it is important to validate these technologies in non-metastatic patient blood samples. In this study, we specifically focus on a recently established label-free microfluidic technology Labyrinth and assess its capabilities to phenotype a variety of rare circulating tumor cells indicative of epithelial-to-mesenchymal transition as well as cancer-associated macrophage-like (CAML) cells. We specifically chose a patient cohort that is non-metastatic and selected to undergo neoadjuvant chemotherapy to assess the performance of the Labyrinth technology. We enrolled 21 treatment naïve non-metastatic breast cancer patients of various disease stages. Our results indicate that (i) Labyrinth microfluidic technology is successfully able to isolate different phenotypes of CTCs despite the counts being low. (ii) Invasive phenotypes of CTCs such as transitioning CTCs and mesenchymal CTCs were found to be present in high numbers in stage III patients as compared to stage II patients. (iii) As the total load of CTCs increased, the mesenchymal CTCs were found to be increasing. (iv) Labyrinth was able to isolate CAMLs with the counts being higher in stage III patients as compared to stage II patients. Our study demonstrates the ability of the Labyrinth microfluidic technology to isolate rare cancer-associated cells from the blood of treatment naïve non-metastatic breast cancer patients, laying the foundation for tracking oncogenic spread and immune response in patients undergoing neoadjuvant chemotherapy.

Inertial focusing of particles and cells in the microfluidic labyrinth device: Role of sharp turns.

Inertial, size-based focusing was investigated in the microfluidic labyrinth device consisting of several U-shaped turns along with circular loops. Turns are associated with tight curvature and, therefore, induce strong Dean forces for separating particles; however, systematic studies exploring this possibility do not exist. We characterized the focusing dynamics of different-sized rigid particles, cancer cells, and white blood cells over a range of fluid Reynolds numbers R e f . Streak widths of the focused particle streams at all the turns showed intermittent fluctuations that were substantial for smaller particles and at higher R e f . In contrast, cell streaks were less prone to fluctuations. Computational fluid dynamics simulations revealed the existence of strong turn-induced Dean vortices, which help explain the intermittent fluctuations seen in particle focusing. Next, we developed a measure of pairwise separability to evaluate the quality of separation between focused streams of two different particle sizes. Using this, we assessed the impact of a single sharp turn on separation. In general, the separability was found to vary significantly as particles traversed the tight-curvature U-turn. Comparing the separability at the entry and exit sections, we found that turns either improved or reduced separation between different-sized particles depending on R e f . Finally, we evaluated the separability at the downstream expansion section to quantify the performance of the labyrinth device in terms of achieving size-based enrichment of particles and cells. Overall, our results show that turns are better for cell focusing and separation given that they are more immune to curvature-driven fluctuations in comparison to rigid particles.

Detection of live breast cancer cells in bright-field microscopy images containing white blood cells by image analysis and deep learning.

SIGNIFICANCE: Circulating tumor cells (CTCs) are important biomarkers for cancer management. Isolated CTCs from blood are stained to detect and enumerate CTCs. However, the staining process is laborious and moreover makes CTCs unsuitable for drug testing and molecular characterization. AIM: The goal is to develop and test deep learning (DL) approaches to detect unstained breast cancer cells in bright-field microscopy images that contain white blood cells (WBCs). APPROACH: We tested two convolutional neural network (CNN) approaches. The first approach allows investigation of the prominent features extracted by CNN to discriminate in vitro cancer cells from WBCs. The second approach is based on faster region-based convolutional neural network (Faster R-CNN). RESULTS: Both approaches detected cancer cells with higher than 95% sensitivity and 99% specificity with the Faster R-CNN being more efficient and suitable for deployment presenting an improvement of 4% in sensitivity. The distinctive feature that CNN uses for discrimination is cell size, however, in the absence of size difference, the CNN was found to be capable of learning other features. The Faster R-CNN was found to be robust with respect to intensity and contrast image transformations. CONCLUSIONS: CNN-based DL approaches could be potentially applied to detect patient-derived CTCs from images of blood samples.

A Region of UNC-89 (Obscurin) Lying between Two Protein Kinase Domains Is a Highly Elastic Spring Required for Proper Sarcomere Organization.

In Caenorhabditis elegans, unc-89 encodes a set of giant multi-domain proteins (up 8081 residues) localized to the M-lines of muscle sarcomeres and required for normal sarcomere organization and whole-animal locomotion. Multiple UNC-89 isoforms contain two protein kinase domains. There is conservation in arrangement of domains between UNC-89 and its two mammalian homologs, obscurin and SPEG: kinase, a non-domain region of 647-742 residues, Ig domain, Fn3 domain and a second kinase domain. In all three proteins, this non-domain "interkinase region" has low sequence complexity, has high proline content, and lacks predicted secondary structure. We report that a major portion of this interkinase (571 residues out of 647 residues) when examined by single molecule force spectroscopy in vitro displays the properties of a random coil and acts as an entropic spring. We used CRISPR/Cas9 to create nematodes carrying an in-frame deletion of the same 571-residue portion of the interkinase. These animals display severe disorganization of all portions of the sarcomere in body wall muscle. Super-resolution microscopy reveals extra, short-A-bands lying close to the outer muscle cell membrane and between normally spaced A-bands. Nematodes with this in-frame deletion show defective locomotion and muscle force generation. We designed our CRISPR-generatedin-frame deletion to contain an HA tag at the N terminus of the large UNC-89 isoforms. This HA tag results in normal organization of body wall muscle, but approximately half the normal levels of the giant UNC-89 isoforms, dis-organization of pharyngeal muscle, small body size, and reduced muscle force, likely due to poor nutritional uptake.

A microfluidic device for label-free isolation of tumor cell clusters from unprocessed blood samples.

Primary cancers disseminate both single circulating tumor cells (CTCs) and CTC "clusters," the latter of which have been shown to demonstrate greater metastatic propensity and adverse impact on prognosis. Many devices developed to isolate single CTCs also capture CTC clusters, but there is translational potential for a platform specifically designed to isolate CTC clusters. Herein, we introduce our microfluidic device for isolating CTC clusters ("Microfluidic Isolation of CTC Clusters" or MICC), which is equipped with ∼10 000 trap chambers that isolate tumor cell clusters based on their large sizes and dynamic force balance against a pillar obstacle in the trap chamber. Whole blood is injected, followed by a wash step to remove blood cells and a final backflush to release intact clusters for downstream analysis. Using clusters from tumor cell-line and confocal microscopy, we verified the ability of the MICC platform to specifically capture tumor cell clusters in the trap chambers. Our flow rate optimization experiments identified 25 µl/min for blood injection, 100 µl/min as wash flow rate, and 300 µl/min as the release flow rate - indicating that 1 ml of whole blood can be processed in less than an hour. Under these optimal flow conditions, we assessed the MICC platform's capture and release performance using blood samples spiked with different concentrations of clusters, revealing a capture efficiency of 66%-87% and release efficiency of 76%-90%. The results from our study suggest that the MICC platform has the potential to isolate CTC clusters from cancer patient blood, enabling it for clinical applications in cancer management.

Hydrodynamic mobility of confined polymeric particles, vesicles, and cancer cells in a square microchannel.

The transport of deformable objects, including polymer particles, vesicles, and cells, has been a subject of interest for several decades where the majority of experimental and theoretical studies have been focused on circular tubes. Due to advances in microfluidics, there is a need to study the transport of individual deformable particles in rectangular microchannels where corner flows can be important. In this study, we report measurements of hydrodynamic mobility of confined polymeric particles, vesicles, and cancer cells in a linear microchannel with a square cross-section. Our operating conditions are such that the mobility is measured as a function of geometric confinement over the range 0.3 < λ < 1.5 and at specified particle Reynolds numbers that are within 0.1 < Rep < 2.5. The experimental mobility data of each of these systems is compared with the circular-tube theory of Hestroni, Haber, and Wacholder [J. Fluid Mech. 41, 689-705 (1970)] with modifications made for a square cross-section. For polymeric particles, we find that the mobility data agrees well over a large confinement range with the theory but under predicts for vesicles. The mobility of vesicles is higher in a square channel than in a circular tube, and does not depend significantly on membrane mechanical properties. The mobility of cancer cells is in good agreement with the theory up to λ ≈ 0.8, after which it deviates. Comparison of the mobility data of the three systems reveals that cancer cells have higher mobility than rigid particles but lower than vesicles, suggesting that the cell membrane frictional properties are in between a solid-like interface and a fluid bilayer. We explain further the differences in the mobility of the three systems by considering their shape deformation and surface flow on the interface. The results of this study may find potential applications in drug delivery and biomedical diagnostics.

Multi-sample deformability cytometry of cancer cells.

There is growing recognition that cell deformability can play an important role in cancer metastasis and diagnostics. Advancement of methods to characterize cell deformability in a high throughput manner and the capacity to process numerous samples can impact cancer-related applications ranging from analysis of patient samples to discovery of anti-cancer compounds to screening of oncogenes. In this study, we report a microfluidic technique called multi-sample deformability cytometry (MS-DC) that allows simultaneous measurement of flow-induced deformation of cells in multiple samples at single-cell resolution using a combination of on-chip reservoirs, distributed pressure control, and data analysis system. Cells are introduced at rates of O(100) cells per second with a data processing speed of 10 min per sample. To validate MS-DC, we tested more than 50 cell-samples that include cancer cell lines with different metastatic potential and cells treated with several cytoskeletal-intervention drugs. Results from MS-DC show that (i) the cell deformability correlates with metastatic potential for both breast and prostate cancer cells but not with their molecular histotype, (ii) the strongly metastatic breast cancer cells have higher deformability than the weakly metastatic ones; however, the strongly metastatic prostate cancer cells have lower deformability than the weakly metastatic counterparts, and (iii) drug-induced disruption of the actin network, microtubule network, and actomyosin contractility increased cancer cell deformability, but stabilization of the cytoskeletal proteins does not alter deformability significantly. Our study demonstrates the capacity of MS-DC to mechanically phenotype tumor cells simultaneously in many samples for cancer research.

Label-free, high-throughput holographic screening and enumeration of tumor cells in blood.

We introduce inline digital holographic microscopy (in-line DHM) as a label-free technique for detecting tumor cells in blood. The optimized DHM platform fingerprints every cell flowing through a microchannel at 10 000 cells per second, based on three features - size, maximum intensity and mean intensity. To identify tumor cells in a background of blood cells, we developed robust gating criteria using machine-learning approaches. We established classifiers from the features extracted from 100 000-cell training sets consisting of red blood cells, peripheral blood mononuclear cells and tumor cell lines. The optimized classifier was then applied to targeted features of a single cell in a mixed cell population to make quantitative cell-type predictions. We tested our classification system with tumor cells spiked at different levels into a background of lysed blood that contained predominantly peripheral blood mononuclear cells. Results show that our holographic screening method can readily detect as few as 10 tumor cells per mL, and can identify tumor cells at a false positive rate of at most 0.001%. This purely optical approach obviates the need for antibody labeling and allows large volumes of sample to be quickly processed. Moreover, our in-line DHM approach can be combined with existing circulation tumor cell enrichment strategies, making it a promising tool for label-free analysis of liquid-biopsy samples.

Label-free fingerprinting of tumor cells in bulk flow using inline digital holographic microscopy.

Large-scale and label-free phenotyping of cells holds great promise in medicine, especially in cancer diagnostics and prognosis. Here, we introduce inline digital holography microscopy for volumetric imaging of cells in bulk flow and fingerprinting of flowing tumor cells based on two metrics, in-focus scattered intensity and cell diameter. Using planar distribution of immobilized particles, we identify the optimal recording distance and microscope objective magnification that minimizes the error in measurement of particle position, size and scattered intensity. Using the optimized conditions and the two metrics, we demonstrate the capacity to enumerate and fingerprint more than 100,000 cells. Finally, we highlight the power of our label-free and high throughput technology by characterizing breast tumor cell lines with different metastatic potentials and distinguishing drug resistant ovarian cancer cells from their parental cell line.

Microfluidic cell isolation technology for drug testing of single tumor cells and their clusters.

Drug assays with patient-derived cells such as circulating tumor cells requires manipulating small sample volumes without loss of rare disease-causing cells. Here, we report an effective technology for isolating and analyzing individual tumor cells and their clusters from minute sample volumes using an optimized microfluidic device integrated with pipettes. The method involves using hand pipetting to create an array of cell-laden nanoliter-sized droplets immobilized in a microfluidic device without loss of tumor cells during the pipetting process. Using this technology, we demonstrate single-cell analysis of tumor cell response to the chemotherapy drug doxorubicin. We find that even though individual tumor cells display diverse uptake profiles of the drug, the onset of apoptosis is determined by accumulation of a critical intracellular concentration of doxorubicin. Experiments with clusters of tumor cells compartmentalized in microfluidic drops reveal that cells within a cluster have higher viability than their single-cell counterparts when exposed to doxorubicin. This result suggests that circulating tumor cell clusters might be able to better survive chemotherapy drug treatment. Our technology is a promising tool for understanding tumor cell-drug interactions in patient-derived samples including rare cells.

Flow-Induced Transport of Tumor Cells in a Microfluidic Capillary Network: Role of Friction and Repeated Deformation.

INTRODUCTION: Circulating tumor cells (CTCs) in microcirculation undergo significant deformation and frictional interactions within microcapillaries. To understand the physical parameters governing their flow-induced transport, we studied the pressure-driven flow of cancer cells in a microfluidic model of a capillary network. METHODS: Our microfluidic device contains an array of parallel constrictions separated by regions where cells can repetitively deform and relax. To characterize the transport behavior, we measured the entry time, transit time, and shape deformation of tumor cells as they squeeze through the network. RESULTS: We found that entry and transit times of cells are much lower after repetitive deformation as their elongated shape enables easy transport in subsequent constrictions. Furthermore, upon repetitive deformation, the cells were able to relieve only 25% of their 40% imposed compressional strain, suggesting that tumor cells might have undergone plastic deformation or fatigue. To investigate the influence of surface friction, we characterized the transport behavior in the absence and presence of bovine serum albumin (BSA) coating on the constriction walls. We observed that BSA coating reduces the entry and transit time significantly. Finally, using two breast tumor cell lines, we investigated the effect of metastatic potential on transport properties. We found that the cell lines could be distinguished only upon surface treatment with BSA, thus surface-induced friction is an indicator of metastatic potential. CONCLUSIONS: Our results suggest that pre-deformation can enhance the transport of CTCs in microcirculation and that frictional interactions with capillary walls can play an important role in influencing the transport of metastatic CTCs.

Microfluidic cell fragmentation for mechanical phenotyping of cancer cells.

Circulating tumor cells (CTCs) shed from the primary tumor undergo significant fragmentation in the microvasculature, and very few escape to instigate metastases. Inspired by this in vivo behavior of CTCs, we report a microfluidic method to phenotype cancer cells based on their ability to arrest and fragment at a micropillar-based bifurcation. We find that in addition to cancer cell size, mechanical properties determine fragmentability. We observe that highly metastatic prostate cancer cells are more resistant to fragmentation than weakly metastatic cells, providing the first indication that metastatic CTCs can escape rupture and potentially initiate secondary tumors. Our method may thus be useful in identifying phenotypes that succumb to or escape mechanical trauma in microcirculation.

The integrin-adhesome is required to maintain muscle structure, mitochondrial ATP production, and movement forces in Caenorhabditis elegans.

The integrin-adhesome network, which contains >150 proteins, is mechano-transducing and located at discreet positions along the cell-cell and cell-extracellular matrix interface. A small subset of the integrin-adhesome is known to maintain normal muscle morphology. However, the importance of the entire adhesome for muscle structure and function is unknown. We used RNA interference to knock down 113 putative Caenorhabditis elegans homologs constituting most of the mammalian adhesome and 48 proteins known to localize to attachment sites in C. elegans muscle. In both cases, we found >90% of components were required for normal muscle mitochondrial structure and/or proteostasis vs. empty vector controls. Approximately half of these, mainly proteins that physically interact with each other, were also required for normal sarcomere and/or adhesome structure. Next we confirmed that the dystrophy observed in adhesome mutants associates with impaired maximal mitochondrial ATP production (P < 0.01), as well as reduced probability distribution of muscle movement forces compared with wild-type animals. Our results show that the integrin-adhesome network as a whole is required for maintaining both muscle structure and function and extend the current understanding of the full complexities of the functional adhesome in vivo.

On the origins of the universal dynamics of endogenous granules in mammalian cells.

Endogenous granules (EGs) that consist of lipid droplets and mitochondria have been commonly used to assess intracellular mechanical properties via multiple particle tracking microrheology (MPTM). Despite their widespread use, the nature of interaction of EGs with the cytoskeletal network and the type of forces driving their dynamics--both of which are crucial for the interpretation of the results from MPTM technique--are yet to be resolved. In this report, we study the dynamics of endogenous granules in mammalian cells using particle tracking methods. We find that the ensemble dynamics of EGs is diffusive in three types of mammalian cells (endothelial cells, smooth muscle cells and fibroblasts), thereby suggesting an apparent universality in their dynamical behavior. Moreover, in a given cell, the amplitude of the mean-squared displacement for EGs is an order of magnitude larger than that of injected particles. This observation along with results from ATP depletion and temperature intervention studies suggests that cytoskeletal active forces drive the dynamics of EGs. To elucidate the dynamical origin of the diffusive-like nonthermal motion, we consider three active force generation mechanisms--molecular motor transport, actomyosin contractility and microtubule polymerization forces. We test these mechanisms using pharmacological interventions. Experimental evidence and model calculations suggest that EGs are intimately linked to microtubules and that microtubule polymerization forces drive their dynamics. Thus, endogenous granules could serve as non-invasive probes for microtubule network dynamics in mammalian cells.

Dynamics of ballistically injected latex particles in living human endothelial cells.

We studied the dynamics of ballistically injected latex particles (BIP) inside endothelial cells, using video particle tracking to measure the mean squared displacement (MSD) as a function of lag time. The MSD shows a plateau at short times and a linear behavior at longer times, indicating that the BIP are trapped into a viscoelastic network. To reveal more about the molecular constituents and the dynamics of this actin network, we added a variety of drugs. Latrunculin and Jasplakinolide aimed at intervening with the actin network caused a strong increase in MSD, whereas Taxol aimed at microtubules gave no measurable change in MSD. Additional corroborating information about these drug effects were obtained from MSD amplitude and exponent distributions and from fluorescent staining images of the actin and microtubule networks. Our evidence strongly suggests that BIP are primarily embedded in the actin network. Additional drug interventions aimed at disabling non-thermal forces could not conclusively resolve the nature of the forces driving BIP dynamics.