Weikang Nicholas
Lin‡
a,
Matthew Zirui
Tay‡
b,
Joel Xu En
Wong
b,
Chia Yin
Lee
c,
Siew-Wai
Fong
b,
Cheng-I
Wang
c,
Lisa Fong Poh
Ng
bdef,
Laurent
Renia
bgh,
Chia-Hung
Chen
h and
Lih Feng
Cheow
*aij
aDepartment of Biomedical Engineering, National University of Singapore, Singapore. E-mail: lihfeng.cheow@nus.edu.sg
bA*STAR Infectious Diseases Labs, Agency for Science, Technology and Research (A*STAR), Singapore
cSingapore Immunology Network, A*STAR, Singapore
dDepartment of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
eNational Institute of Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
fInstitute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
gLee Kong Chian School of Medicine, Nanyang Technological University, Singapore
hSchool of Biological Sciences, Nanyang Technological University, Singapore
iDepartment of Biomedical Engineering, City University of Hong Kong, Hong Kong
jInstitute for Health Innovation & Technology (iHealthtech), Singapore
First published on 13th June 2022
As part of the body's immune response, antibodies (Abs) have the ability to neutralize pathogenic viruses to prevent infection. To screen for neutralizing Abs (nAbs) from the immune repertoire, multiple screening techniques have been developed. However, conventional methods have a trade-off between screening throughput and the ability to screen for nAbs via their functional efficacy. Although droplet microfluidic platforms have the ability to bridge this disparity, the majority of such reported platforms still rely on Ab-binding assays as a proxy for function, which results in irrelevant hits. Herein, we report the multi-module Droplet-based Platform for Effective Antibody RetrievaL (DROP-PEARL) platform, which can achieve high-throughput enrichment of Ab-secreting cells (ASCs) based on the neutralizing activity of secreted nAbs against the a target virus. In this study, in-droplet Chikungunya virus (CHIKV) infection of host cells and neutralization was demonstrated via sequential delivery of viruses and host cells via picoinjection. In addition, we demonstrate the ability of the sorting system to accurately discriminate and isolate uninfected droplets from a mixed population of droplets at a rate of 150000 cells per hour. As a proof of concept, a single-cell neutralization assay was performed on two populations of cells (nAb-producing and non-Ab producing cells), and up to 2.75-fold enrichment of ASCs was demonstrated. Finally, we demonstrated that DROP-PEARL is able to achieve similar enrichment for low frequency (∼2%) functional nAb-producing cells in a background of excess cells secreting irrelevant antibodies, highlighting its potential prospect as a first round enrichment platform for functional ASCs. We envision that the DROP-PEARL platform could potentially be used to accelerate the discovery of nAbs against other pathogenic viral targets, and we believe it will be a useful in the ongoing fight against biological threats.
Currently, there are tremendous pressures on nAb discovery efforts to keep up with the rapid mutation of existing virus strains and the emergence of novel viral threats. Although fluorescence-activated sorting (FACS) and display systems can screen a large numbers of antibody-secreting cells (ASCs) for their binding to a particular protein antigen, binding affinity is often not reflective of the true functional efficacy of a nAb candidate.7 Many high affinity mAbs bind to non-neutralizing epitopes on the viral antigen, rendering them unsuitable for therapeutic applications (Fig. 1a). In the worst case, administration of non-neutralizing Abs could contribute to antibody-dependent enhancement (ADE) effects that increase the severity of multiple viral infections.8 Meanwhile, cells producing effective nAbs can be directly screened through hybridoma generation9 and single B cell activation/expansion,10 but the laborious nature of these procedures results in a long workflow. The majority of the immune repertoire11 is overlooked due to the low throughput (102–103 candidates) nature of existing virus neutralization assays. As such, there is an unmet need for an integrated system that can rapidly perform functional Ab neutralization assay on a large population of ASCs, with the ability to not just identify but also to isolate promising candidates.
Droplet microfluidics platforms present several key advantages that make them ideal for the functional screening of ASCs, which include: 1) high operating throughputs at 10–104 droplets per second,12 2) well-established toolkit for droplet manipulation such as merging,13 splitting14 and sorting15 enable complex multi-step assays to be performed, 3) the ability to accommodate a variety of assay reagents type via co-encapsulation,16 particularly reporter or effector cells needed in most Ab functional assays. While droplet-based ASC screening via Ab binding affinity has been well established,17–19 the much more clinically relevant ASC screening via a true virus neutralization assay is still lacking due to the technical challenges of performing the complex multi-step assay. A recent work describes a platform for visualization of virus neutralization by ASCs in microfluidic droplets.20 Nonetheless, this method is limited to evaluating virus neutralizing activities from 100–1000 droplets in the field-of-view and lacks the critical capability of sorting and retrieving potent nAb secreting cells for downstream analysis or expansion.
To address the current research gaps, we established the DROPlet-based Platform for Effective Antibody RetrievaL (DROP-PEARL) platform, a high-throughput droplet microfluidic system capable of selection and retrieval of ASCs based on the neutralizing function of secreted Abs from single cells. As a proof-of-concept, we demonstrated the use of the DROP-PEARL platform to enrich for cells secreting nAbs against Chikungunya virus (CHIKV). High-throughput screening of functional ASCs with droplet microfluidics could be a new paradigm for the rapid discovery of potent and functional biologics.
We reasoned that the most time-consuming step of the current workflow (i.e. cell immortalization and clonal expansion) can be eliminated if secreted Abs from a single ASC can approach concentration levels needed for effective virus neutralization. Confinement of single ASC in small volumes would allow rapid accumulation of Abs as diffusion is prevented. In the DROP-PEARL platform, single ASCs are encapsulated within picoliter droplets to facilitate rapid Ab accumulation (Fig. 1b, bottom). This is followed by delivery of live virus to each droplet to allow for binding, and finally delivery of susceptible host cells into the same droplets for virus infection to occur. Most importantly, our platform allows high throughput interrogation (at a rate of 700000 droplets per hour) of virus infection and integrated sorting and recovery of droplets with low virus infection where neutralization has occurred.
We used a Chikungunya virus (CHIKV) infection model to validate the principles and performance of the DROP-PEARL platform. Chikungunya virus is a re-emerging pathogen that is endemic in Africa and many parts of Asia, with massive outbreaks with case numbers in the millions in recent decades.21,22 There are currently no clinically licensed vaccines or treatments available for Chikungunya infection, but a monoclonal nAb treatment has shown positive results in a phase I clinical trial.23 The ability to rapidly screen for monoclonal nAbs is pertinent to the development of better therapy regimens for Chikungunya infections.
We developed a strategy using picoinjection to deliver virus and host cells into ASC-containing droplets. Since picoinjection delivers only a fraction of the incoming droplet's volume, contents can be delivered successfully without significantly increasing droplet size.28 The self-triggering mechanism of picoinjection also results in robust performance even when droplet periodicity may change over the course of the experiment.29 This ensures that reagents are delivered to all droplets to maximise the proportion of droplets where CHIKV infection occurs. After each round of picoinjection, the droplet diameters were observed to increase by approximately 10 μm, or a corresponding volume increase of 50.9% and 35.8% respectively (ESI† Table S2).
In the DROP-PEARL workflow, a picoinjector chip30 is first used to deliver CHIKV into fully-formed 70 μm diameter droplets containing single ASC. Subsequently, a second picoinjector chip delivers host cells into droplets at a rate of 300 droplets per second. High cell densities ranging from 50 to 200 million cells per mL were used to ensure that multiple host cells can be delivered to each droplet. Fig. 3d showed that the number of host cells delivered into each droplet can be controlled by varying the cell densities. Finally, we investigated the viability of host cells that were delivered via picoinjection. Cell viability remained high at 94.6% at 24 hours (Fig. 3e), indicating that the process was suitable for in-droplet infection to occur. Likewise, the excellent viability of multiple cells (88.4%) over 41 hours of incubation in droplets clearly shows that sufficient nutrients are available to sustain both the ASCs and host cells throughout the DROP-PEARL workflow. The much-enhanced viability of cells in droplet could in part be attributed to the optimized nutrient-rich culture media in droplets (ESI† Fig. S2) and improved gas-exchange of droplets during incubation in 12-well plates (Methods).
To investigate the effect of nAbs on CHIKV infection, droplets containing 20 μg mL−1 of purified 8810 nAbs were injected with 37.5 kPFU μL−1 of CHIKV, and in-droplet infection was compared against a virus-only control (Fig. 4a). The droplet signal intensities (average of 2D image) were analysed via imaging (Fig. 4b) and compared against a continuous-flow PMT detection system (peak fluorescence of each droplet) (Fig. 4c). A significant reduction in the average CHIKV infection signal was observed in the majority of the nAb containing droplets, suggesting partial inhibition of CHIKV infection amongst the infected droplets. Partial suppression of infection is a biological phenomenon and is consistent with observations in bulk virus neutralization assay (Fig. 2b). Furthermore, a broad distribution of infection signals were observed for both nAb-containing droplets and virus-only droplets, reflecting the biological heterogeneity of the CHIKV and 293T cells.
To determine the optimal viral titer to be used in the subsequent single-cell neutralization experiments, two conditions need to be considered. Firstly, the CHIKV viral titer to be used should achieve a sufficiently high infection rate needed to reduce the number of false positives during the downstream droplet sorting step. Secondly, to reduce the probability of false negatives which stem from infection even in the presence of nAbs, the viral titer should be kept as low as possible. As such, there is a delicate balance between the infection duration and viral titer to define a window of specificity. The infection rate of droplets was studied for different viral titers over a period of 48 hours after host cell injection (Fig. 4d). In general, the higher the picoinjected viral titer, the greater the percentage of infected droplets at all time points. Additionally, the infection rate appeared to plateau after 24 hours regardless of viral titer used. Based on the results, a viral titer of 75 kPFU μL−1 was selected to be used for the single-cell neutralization assay as it provided a high droplet infection rate at 93.2% beyond 20 hours. As a positive control for the presence of nAbs, droplets containing 9 μg mL−1 of 8B10 nAbs (to simulate the average concentrations of Abs accumulated in droplets after 24 hours) are injected with 75 kPFU μL−1 CHIKV virus, followed by host cell injection for infection. We observed that the percentage of droplets with infected cells is consistently lower at all times when droplets contain nAbs, demonstrating their protective effects against CHIKV infection in this droplet-based assay. In this way, collection of droplets containing cells exhibiting a lower level of infection is expected to enrich for nAbs.
The relatively modest enrichment ratio of virus neutralization assay compared to antibody affinity assays is well within expectations. Unlike antigen-binding assay involves simple molecular interactions between antigen and antibody, virus neutralization assay is much more complicated involving the binding of antibody to the right epitope, and requires complex cellular mechanisms that determines virus infectivity and host cell permissiveness. Incomplete permissiveness of the host cells (also seen in bulk neutralization assay, where ∼30% of cells are uninfected even when there is no neutralizing Ab (Fig. 2C)) could result in false positive droplets being selected, thereby reducing the enrichment ratio. Nevertheless, this is the first demonstration of high-throughput virus neutralizing antibody enrichment in a semiautomatic microfluidics platform, and could already be used as a first enrichment step to provide a coarse selection of nAb secreting cells. We believe that this demonstration sets the foundation to its future use for a variety of viral diseases.
Finally, in view of the encouraging results of ASC enrichment from non-secreting cells using DROP-PEARL, we asked if similar enrichment of specific neutralizing antibody secreting cells can be achieved in more complex scenarios that better resembles physiological samples. We focus on two important aspects: 1) the proportion of neutralizing antibody secreting cells are low (0.1–2%) in convalescent/immunized patients, 2) there is an excess of B cells secreting unrelated antibodies in patient samples. In order to simulate these conditions, we performed an experiment where we prepared two kinds of cells secreting different monoclonal antibodies (8B10 is CHIKV neutralizing antibody, and 5A6 is a non-relevant SARS-COV-2 neutralizing antibody). ASCs secreting 8B10 (labelled red) and 5A6 (labelled blue) were mixed at a 1:
50 ratio and the DROP-PEARL sorting experiment was performed as above. Representative images of the droplets before sorting, as well as sorted droplets from the top collection and bottom waste channel are shown in Fig. 7a–c. As before, the unsorted droplets consist of mostly virus infected cells and a mixture of specific (red) and non-relevant (blue) antibody secreting cells. Droplets recovered from the top collection channel contains predominantly uninfected cells, and an observable enrichment of specific CHIKV neutralizing antibodies (red). Upon FACS analysis of the recovered cells, we observed that the DROP-PEARL sorted cells contains 6.27% of CHIKV neutralizing antibody secreting cells, up from 2.69% in the unsorted population (Fig. 7d). This enrichment ratio of 2.42 at sorting threshold of 0.4 V is similar to what we obtained in the earlier proof-of-concept experiment. Our results showed that DROP-PEARL retain the ability to enrich for neutralizing antibody secreting cells even when they are present at low frequencies, and that the enrichment was not negatively impacted by the presence of large number of cells secreting non-relevant antibodies. The demonstration of successful application of DROP-PEARL in a scenario that better simulates physiological condition is an important milestone towards clinical implementation of this platform.
This is the first time an in-droplet virus neutralization assay has been demonstrated in the context of an infectious human disease where there is clinical evidence for the therapeutic benefits of exogenously administered nAb.23 Previous reports on in-droplet virus neutralization assay are only limited to characterizing the functional activities of ASCs, as it lack droplet sorting ability. In this report, we successfully developed and optimized the DROP-PEARL platform with functional ASC retrieval as an end goal, in order to realize its true potential for accelerating high throughput discovery of virus nAbs. Cells secreting monoclonal antibodies are used to validate the DROP-PEARL platform to statistically evaluate the in-droplet virus neutralizing activities. As virus neutralizing activity is performed at the single antibody-secreting cell level, it is compatible with rapid method to generating antibody-secreting cells (e.g. transient transfection) that does not require lengthy cell immortalization. On the other hand, there is also great potential to apply this method for enrichment of functional population from polyclonal antibody secreting cells, such as what would be typically found from convalescent patients.
In this proof of concept, we demonstrate that a single round of DROP-PEARL workflow enriches functional ASCs relative to non-Ab-secreting cells by 1.90–2.75 fold. Similar enrichment of specific ASC was also achieved when they were at a low proportion (∼2%) within large excess of cells secreting a irrelevant antibody, indicating a promising prospect of applying this method for enriching functional antibodies from primary samples. The relatively modest enrichment factor is consistent with a partially permissive host cell that we have used in this proof of concept. Various literature have shown the choice of host cells and reporter virus could have a significant impact on the sensitivities of virus neutralization assay.31 We believe there are significant opportunities for host cell and reporter virus engineering that could improve their permissiveness and infectivity for droplet based virus neutralization assay. For example, knocking out antiviral genes in host cells (e.g. STAT1) could drastically improve virus infection rates, as shown in dengue virus.32 Overexpression of viral receptors in host cells (e.g. ACE2 and TMPRSS2 for SARS-CoV-2,33 MXRA8 for CHIKV34) could also significantly increase the efficiency of virus entry into host cells. Engineering approaches to improve virus capsid stability and improved virus manufacturing process to reduce empty capsids35 would also increase the infection rates of virus. These approaches would be expected to significantly increase the specificity of DROP-PEARL for selection of virus-neutralizing ASCs by reducing the false positives.
DROP-PEARL is not intended to be a one-size-fits-all solution for neutralizing antibody discovery in all diseases. Due to the very different infection models and varied considerations for different viruses, the parameters in DROP-PEARL should be optimized for specific applications. Nonetheless, we expect enrichments to be achieved in majority of cases. Notwithstanding the additional specificities that could be gained from host cells and reporter virus engineering, application of DROP-PEARL to enrich for functional ASCs from convalescent individuals or immunized animals already represents a significant advance on yielding a subpopulation of ASCs secreting more potent polyclonal nAbs for immediate applications. We note that despite our best efforts to follow the conventional virus neutralizing assay steps in the single cell droplet workflow, there are unavoidable differences. Among them, the variabilities between the number of target cells, as well as heterogeneity among the antibody-secreting cells and virus, will be accentuated when they are present in small numbers within a droplet. As such, we envision DROP-PEARL as the first enrichment step to provide a coarse selection of neutralizing antibody producing cells. If desired, this enriched population could be used to generate polyclonal antibodies with better functionalities compared to the unsorted populations. A second round of DROP-PEARL workflow on the collected cells can also be performed to improve on the enrichment of ASCs. Furthermore, we envision that the DROP-PEARL workflow can be performed with ASCs enriched from previously reported Ab binding affinity assays,17,18,36 in order to obtain nAbs with high affinity. Finally, RNA sequencing of the antibody-coding genes can be performed on cells that are enriched using DROP-PEARL workflow. Antibody sequences that are enriched relative to the initial population can be identified. Such approaches have been very successfully used to identify therapeutic antibodies even when the specific ASCs constitute a small fraction of the circulating cells (e.g. from convalescence patient).37 A combination of DROP-PEARL enrichment and RNA sequencing is expected to enable rapid identification of functional antibodies from a polyclonal mixture.
In summary, we present a complete platform for the rapid discovery and retrieval of functional ASCs. We successfully demonstrated a proof of concept of the DROP-PEARL workflow to enrich for cells secreting nAbs against the CHIKV virus. In reality, the DROP-PEARL platform is versatile for rapid screening of biologics for treatment of various viral infections. We envision that it will be of great interest to the scientific community seeking to characterize nAbs against particular viruses, and biotechnology companies interested in adopting a new paradigm for rapid functional biologics discovery.
A typical 60 μm height, 3-inlet flow-focusing channel design was used for droplet generation and single-cell encapsulation processes. The aqueous and oil channel widths were designed to be at 50 μm, which then constricted to 40 μm at the outlet to facilitate droplet breakup. 70 μm diameter droplets were generated by infusion of aqueous and oil. Next, to deliver CHIKV and host cells into droplets, 45 μm height/width picoinjectors with a 40 μm picoinjector nozzle width were used (ESI† Fig. S1). To generate the electric field required to disrupt the stable interface of reinjected droplets for picoinjection to occur, a 1 Vpp 20 kHz sinusoidal wave was amplified 100-fold and passed into the electrodes of the picoinjector. Lastly, to sort droplets after CHIKV infection, 100 μm height droplet sorters modified from Gielen et al.39 were used (ESI† Fig. S2). To ensure that droplets preferentially enter the top outlet channel in the absence of an electric field, the bottom outlet channel was lengthened such that its resistance is approximately 2 times the top channel. Additional shielding electrodes were included around the device to prevent undesired coalescence of droplets from the sorting electric pulses.
To fabricate the master moulds needed to create the microfluidic devices, SU-8 2050 negative photoresist (Kayaku Advanced Materials, Westborough, MA) was first spin coated onto silicon wafers. Subsequent UV exposure via a mask aligner (MJB4, SUSS MicroTec, Germany) and development was performed according to the SU-8 product sheet's recommended settings. The retrieved moulds were then surface-treated with trichloro-(1H,1H,2H,2H-perfluorooctyl)silane (Sigma-Aldrich, St. Louis, MO) in a dessicator overnight. PDMS (Sylgard 184™, Dow Corning Inc, Midland, MI) was then added over the moulds, degassed, and cured. The cured PDMS microchannels are then removed from the moulds using a scalpel, followed by creation of inlets and outlets using a 1 mm biopsy punch. The microchannels were then cleaned by ultrasonication for 10 minutes, dried, and irreversibly bonded to a substrate using a plasma cleaner (PDC-32G, Harrick Plasma, Ithaca, NY). Glass slides which were spin-coated with PDMS were used as the substrate for droplet generators, whereas uncoated glass slides were used as the substrate for picoinjectors and sorters. After plasma bonding, to create the electrodes required for the picoinjectors and sorters, a low-melting point indium alloy wire (WIREBN-52189, Indium Corporation, Clinton, NY) was melted into the electrode inlet channels, then connected to wires and secured with UV-curable glue (Uni-Seal™ 6322, Incure, Asheville, SC).
In the purified nAb in-droplet neutralization experiment, purified 8B10 nAbs diluted with growth media to obtain a concentration of 18 μg mL−1 was used as the first aqueous phase. After dilution with the secondary aqueous phase, a final in-droplet nAb concentration of 9 μg mL−1 was obtained. The droplets were then subjected to the above mentioned in-droplet infection workflow to determine the infection rate of nAb-containing droplets over time.
Voltage signals obtained from the PMT were parallelized into two outputs for sorting and signal recording. For signal recording, the PMT analog signals were converted to digital signals using a data acquisition card (USB-6002, National Instruments, USA) and recorded using the in-built Analog Input Recorder application in MATLAB (R2019b, MathWorks, USA). For sorting, PMT signals were processed in real-time using an Arduino DUE microprocessor (Arduino, USA) to determine if a particular droplet signal exceeds a pre-defined threshold. The DUE microprocessor was used to control an Arduino UNO microprocessor (Arduino, USA) responsible for generating 8 Vpp, 10 kHz square waves which were amplified 100-fold through a high-voltage amplifier before they were passed into the sorter's electrodes. Upon detection of a PMT signal which exceeds the threshold, sorting waves were switched on for 1750 μs to actuate the droplet towards the bottom sorting channel.
For ROC curve characterization, a 50:
50 mixed pool of infected and non-infected droplets were sorted at 11 different thresholds ranging from 0.12 to 3.24 V. 0.5 μL of droplets from each sorting condition was then sampled and fluorescently imaged to identify the number of true and false positives.
To evaluate the performance of DROP-PEARL for enrichment of specific functional ASCs in the presence of large excess of cells secreting irrelevant antibodies, 8B10 ASCs (secreting CHIKV nAbs) and 5A6 ASCs (secreting non-relevant SARS-COV-2 nAbs) are subject to the DROP-PEARL workflow as described above. An initial cell population comprising of 8B10 and 5A6 ASCs at a ratio of 1:
50 was first encapsulated in 70 μm diameter droplets to achieve a single-cell occupancy rate of 20%. The droplets were then incubated to allow the accumulation of Abs within the droplets over a period of 24 h. The droplets were then picoinjected with 75 kPFU uL−1 of CHIKV, incubated for 3 h to allow Ab neutralization of CHIKV, before a second picoinjection step to deliver 293T host cells at a cell density of 100 million per mL. The droplets were then incubated for 20 h to allow infection to take place before they were dielectrophoretically sorted at a 0.4/0.6 V signal threshold.
Footnotes |
† Electronic supplementary information (ESI) available. See DOI: https://doi.org/10.1039/d2lc00018k |
‡ These authors contributed equally. |
This journal is © The Royal Society of Chemistry 2022 |