An automated microfluidic gene-editing platform for deciphering cancer genes

Integrating microfluidics and synthetic biology: advancements and diverse applications across organisms

Synthetic biology is the design and modification of biological systems for specific functions, integrating several disciplines like engineering, genetics, and computer science. The field of synthetic biology is to understand biological processes within host organisms through the manipulation and regulation of their genetic pathways and the addition of biocontrol circuits to enhance their production capabilities. This pursuit serves to address global challenges spanning diverse domains that are difficult to tackle through conventional routes of production. Despite its impact, achieving precise, dynamic, and high-throughput manipulation of biological processes is still challenging. Microfluidics offers a solution to those challenges, enabling controlled fluid handling at the microscale, offering lower reagent consumption, faster analysis of biochemical reactions, automation, and high throughput screening. In this review, we diverge from conventional focus on automating the synthetic biology design-build-test-learn cycle, and instead, focus on microfluidic platforms and their role in advancing synthetic biology through its integration with host organisms - bacterial cells, yeast, fungi, animal cells - and cell-free systems. The review illustrates how microfluidic devices have been instrumental in understanding biological systems by showcasing microfluidics as an essential tool to create synthetic genetic circuits, pathways, and organisms within controlled environments. In conclusion, we show how microfluidics expedite synthetic biology applications across diverse domains including but not limited to personalized medicine, bioenergy, and agriculture.

A low-temperature digital microfluidic system used for protein-protein interaction detection

The occurrence, development and prediction of various biological processes and diseases are inseparable from the protein-protein interaction (PPI), so it is extremely meaningful to perfect PPI networks. However, shortcomings of traditional detection methods, such as protein degradation, long detection time, complex operation, poor automation and high cost, restrict the rapid development of PPI networks. Here, a low-temperature digital microfluidic (LTDMF) system-based PPI detection box (LTDMF-PPI-Box) was developed to achieve rapid, lossless and efficient PPI detection. It consists of a PMMA shell, LTDMF-PPI and an integrated temperature control system. LTDMF reduces the PPI detection time from tens of hours to 1.5 hours by programmatically controlling the movement of droplets. Moreover, an integrated thermoelectric cooler (TEC) ensures an operating temperature of 4 °C, resulting in a protein protection up to 90%. The interaction between RILP protein and Rab26 protein which has a close connection to insulin secretion was demonstrated as a prototype to illustrate the feasibility of the LTDMF-PPI-Box. LTDMF with automation characteristics is capable of meeting the requirement of high-throughput screening of interacting proteins; therefore, the LTDMF-PPI-Box is expected to accelerate the establishment of the PPI network in the future.

Lab-on-a-chip systems for cancer biomarker diagnosis

Lab-on-a-chip (LOC) or micro total analysis system is one of the microfluidic technologies defined as the adaptation, miniaturization, integration, and automation of analytical laboratory procedures into a single instrument or "chip". In this article, we review developments over the past five years in the application of LOC biosensors for the detection of different types of cancer. Microfluidics encompasses chemistry and biotechnology skills and has revolutionized healthcare diagnosis. Superior to traditional cell culture or animal models, microfluidic technology has made it possible to reconstruct functional units of organs on chips to study human diseases such as cancer. LOCs have found numerous biomedical applications over the past five years, including integrated bioassays, cell analysis, metabolomics, drug discovery and delivery systems, tissue and organ physiology and disease modeling, and personalized medicine. This review provides an overview of the latest developments in microfluidic-based cancer research, with pros, cons, and prospects.

Digital microfluidics for biological analysis and applications

Digital microfluidics (DMF) is an emerging liquid-handling technology based on arrays of microelectrodes for the precise manipulation of discrete droplets. DMF offers the benefits of automation, addressability, integration and dynamic configuration ability, and provides enclosed picoliter-to-microliter reaction space, making it suitable for lab-on-a-chip biological analysis and applications that require high integration and intricate processes. A review of DMF bioassays with a special emphasis on those actuated by electrowetting on dielectric (EWOD) force is presented here. Firstly, a brief introduction is presented on both the theory of EWOD actuation and the types of droplet motion. Subsequently, a comprehensive overview of DMF-based biological analysis and applications, including nucleic acid, protein, immunoreaction and cell assays, is provided. Finally, a discussion on the strengths, challenges, and potential applications and perspectives in this field is presented.

Integrating machine learning and digital microfluidics for screening experimental conditions

Digital microfluidics (DMF) has the signatures of an ideal liquid handling platform - as shown through almost two decades of automated biological and chemical assays. However, in the current state of DMF, we are still limited by the number of parallel biological or chemical assays that can be performed on DMF. Here, we report a new approach that leverages design-of-experiment and numerical methodologies to accelerate experimental optimization on DMF. The integration of the one-factor-at-a-time (OFAT) experimental technique with machine learning algorithms provides a set of recommended optimal conditions without the need to perform a large set of experiments. We applied our approach towards optimizing the radiochemistry synthesis yield given the large number of variables that affect the yield. We believe that this work is the first to combine such techniques which can be readily applied to any other assays that contain many parameters and levels on DMF.

Viral Generation, Packaging, and Transduction on a Digital Microfluidic Platform

Viral-based systems are a popular delivery method for introducing exogenous genetic material into mammalian cells. Unfortunately, the preparation of lentiviruses containing the machinery to edit the cells is labor-intensive, with steps requiring optimization and sensitive handling. To mitigate these challenges, we introduce the first microfluidic method that integrates lentiviral generation, packaging, and transduction. The new method allows the production of viral titers between 10⁶ and 10⁷ (similar to macroscale production) and high transduction efficiency for hard-to-transfect cell lines. We extend the technique for gene editing applications and show how this technique can be used to knock out and knock down estrogen receptor gene─a gene prominently responsible for 70% of breast cancer cases. This new technique is automated with multiplexing capabilities, which have the potential to standardize the methods for viral-based genome engineering.

CRISPR-Powered Microfluidics in Diagnostics: A Review of Main Applications

In the past few years, the CRISPR (clustered regularly interspaced short palindromic repeats) applications in medicine and molecular biology have broadened. CRISPR has also been integrated with microfluidic-based biosensors to enhance the sensitivity and selectivity of medical diagnosis due to its great potentials. The CRISPR-powered microfluidics can help quantify DNAs and RNAs for different diseases such as cancer, and viral or bacterial diseases among others. Here in this review, we discussed the main applications of such tools along with their advantages and limitations.

Digital Microfluidic Thermal Control Chip-Based Multichannel Immunosensor for Noninvasively Detecting Acute Myocardial Infarction

Rapid and automated detection of acute myocardial infarction (AMI) at its developing stage is very important due to its high mortality rate. To quantitatively diagnose AMI, Myo, CK-MB, and cTnI are chosen as three biomarkers, which are usually detected through an immunosorbent assay, such as the enzyme-linked immunosorbent assay. However, the approach poses many drawbacks, such as long detection time, the cumbersome process, the need for professionals, and the difficulty of realizing automatic operation. Here, a multichannel digital microfluidic (DMF) thermal control chip integrated with a sandwich-based immunoassay strategy is proposed for the automated, rapid, and sensitive detection of AMI biomarkers. A miniaturized temperature control module is integrated on the back of the DMF chip, meeting the temperature requirement for the immunoassay. With this DMF thermal control chip, sample and reagent consumption are reduced to several microliters, significantly alleviating reagent consumption and sample dependence, and the automated and multichannel detection of biomarkers can be achieved. In this work, the simultaneously noninvasive detection of the human serum sample containing the three biomarkers of AMI is also achieved within 30 min, which improves the diagnostic accuracy of AMI. Due to the features of automation and miniaturization, the multichannel immunosensor can be used in community hospitals to increase the speed of diagnosis of patients with various acute diseases.

Expanding the limits towards 'one-pot' DNA assembly and transformation on a rapid-prototype microfluidic device

DNA assembly and transformation are crucial to the building process in synthetic biology. These steps are significant roadblocks when engineering increasingly complex biological systems. To address this, recent development of widespread 'biofoundry' facilities has employed automation equipment to expedite the synthetic biology workflow. Despite significant progress, there is a clear demand for lower-cost and smaller-footprint automation equipment. The field of microfluidics have emerged to provide automation capabilities to meet this demand. However, we still lack devices capable of building large multi-gene systems in a consolidated process. In response to this challenge, we have developed a digital microfluidic platform that performs "one-pot" Golden Gate DNA assembly of large plasmids and transformation of E coli. The system features a novel electrode geometry and modular design, which make these devices simple to fabricate and use, thus improving the accessibility of microfluidics. This device incorporates an impedance-based adaptive closed loop water replenishment system to compensate for droplet evaporation and maintain constant assembly reaction concentrations, which we found to be crucial to the DNA assembly efficiency. We also showcase a closed-loop temperature control system that generates precise thermodynamic profiles to optimize heat shock transformation. Moreover, we validated the system by assembling and transforming large and complex plasmids conferring a biosynthetic pathway, resulting in performance comparable to those of standard techniques. We propose that the methods described here will contribute to a new generation of accessible automation platforms aimed at speeding up the 'building' process, lowering reagent consumption and removing manual work from synthetic biology.

Auto-Panning: a highly integrated and automated biopanning platform for peptide screening

Biopanning, a common affinity selection approach in phage display, has evolved numerous ligands for diagnosis, imaging, delivery, and therapy applications. However, traditional biopanning has suffered from time-consuming processes, highly-repetitive procedures and labor-intensive manual operation. Herein, a highly integrated and automated biopanning platform (Auto-Panning) is proposed. Based on digital microfluidics (DMF), biopanning processes are integrated on a chip with highly reproducible, precise, automated liquid manipulation. Therefore, 3 rounds of Auto-Panning can be accomplished within 16 h, instead of nearly a week of complicated manual operations. Auto-Panning has been used to evolve a specific peptide against cancer biomarker EphA2 with excellent cellular penetrating ability and significant invasion suppression biofunction, successfully demonstrating the practicality of the platform. Overall, as an automated programmable molecular screening platform, Auto-Panning will further promote the discovery and applications of novel ligands.

CRISPR-Associated (CAS) Effectors Delivery via Microfluidic Cell-Deformation Chip

Identifying new and even more precise technologies for modifying and manipulating selectively specific genes has provided a powerful tool for characterizing gene functions in basic research and potential therapeutics for genome regulation. The rapid development of nuclease-based techniques such as CRISPR/Cas systems has revolutionized new genome engineering and medicine possibilities. Additionally, the appropriate delivery procedures regarding CRISPR/Cas systems are critical, and a large number of previous reviews have focused on the CRISPR/Cas9-12 and 13 delivery methods. Still, despite all efforts, the in vivo delivery of the CAS gene systems remains challenging. The transfection of CRISPR components can often be inefficient when applying conventional delivery tools including viral elements and chemical vectors because of the restricted packaging size and incompetency of some cell types. Therefore, physical methods such as microfluidic systems are more applicable for in vitro delivery. This review focuses on the recent advancements of microfluidic systems to deliver CRISPR/Cas systems in clinical and therapy investigations.

Microfluidics in Biotechnology: Quo Vadis

The emerging technique of microfluidics offers new approaches for precisely controlling fluidic conditions on a small scale, while simultaneously facilitating data collection in both high-throughput and quantitative manners. As such, the so-called lab-on-a-chip (LOC) systems have the potential to revolutionize the field of biotechnology. But what needs to happen in order to truly integrate them into routine biotechnological applications? In this chapter, some of the most promising applications of microfluidic technology within the field of biotechnology are surveyed, and a few strategies for overcoming current challenges posed by microfluidic LOC systems are examined. In addition, we also discuss the intensifying trend (across all biotechnology fields) of using point-of-use applications which is being facilitated by new technological achievements.

μCB-seq: microfluidic cell barcoding and sequencing for high-resolution imaging and sequencing of single cells

Single-cell RNA sequencing (scRNA-seq) enables the investigation of complex biological processes in multicellular organisms with high resolution. However, many phenotypic features that are critical to understanding the functional role of cells in a heterogeneous tissue or organ are not directly encoded in the genome and therefore cannot be profiled with scRNA-seq. Quantitative optical microscopy has long been a powerful approach for characterizing diverse cellular phenotypes including cell morphology, protein localization, and chemical composition. Combining scRNA-seq with optical imaging has the potential to provide comprehensive single-cell analysis, allowing for functional integration of gene expression profiling and cell-state characterization. However, it is difficult to track single cells through both measurements; therefore, coupling current scRNA-seq protocols with optical measurements remains a challenge. Here, we report microfluidic cell barcoding and sequencing (μCB-seq), a microfluidic platform that combines high-resolution imaging and sequencing of single cells. μCB-seq is enabled by a novel fabrication method that preloads primers with known barcode sequences inside addressable reaction chambers of a microfluidic device. In addition to enabling multi-modal single-cell analysis, μCB-seq improves gene detection sensitivity, providing a scalable and accurate method for information-rich characterization of single cells.

Is microfluidics the "assembly line" for CRISPR-Cas9 gene-editing?

Acclaimed as one of the biggest scientific breakthroughs, the technology of CRISPR has brought significant improvement in the biotechnological spectrum-from editing genetic defects in diseases for gene therapy to modifying organisms for the production of biofuels. Since its inception, the CRISPR-Cas9 system has become easier and more versatile to use. Many variants have been found, giving the CRISPR toolkit a great range that includes the activation and repression of genes aside from the previously known knockout and knockin of genes. Here, in this Perspective, we describe efforts on automating the gene-editing workflow, with particular emphasis given on the use of microfluidic technology. We discuss how automation can address the limitations of gene-editing and how the marriage between microfluidics and gene-editing will expand the application space of CRISPR.

One Cell, One Drop, One Click: Hybrid Microfluidics for Mammalian Single Cell Isolation

Generating a stable knockout cell line is a complex process that can take several months to complete. In this work, a microfluidic method that is capable of isolating single cells in droplets, selecting successful edited clones, and expansion of these isoclones is introduced. Using a hybrid microfluidics method, droplets in channels can be individually addressed using a co-planar electrode system. In the hybrid microfluidics device, it is shown that single cells can be trapped and subsequently encapsulate them on demand into pL-sized droplets. Furthermore, droplets containing single cells are either released, kept in the traps, or merged with other droplets by the application of an electric potential to the electrodes that is actuated through an in-house user interface. This high precision control is used to successfully sort and recover single isoclones to establish monoclonal cell lines, which is demonstrated with a heterozygous NCI-H1299 lung squamous cell population resulting from loss-of-function eGFP and RAF1 gene knockout transfections.

Role of Digital Microfluidics in Enabling Access to Laboratory Automation and Making Biology Programmable

Digital microfluidics (DMF) is a liquid handling technique that has been demonstrated to automate biological experimentation in a low-cost, rapid, and programmable manner. This review discusses the role of DMF as a "digital bioconverter"-a tool to connect the digital aspects of the design-build-learn cycle with the physical execution of experiments. Several applications are reviewed to demonstrate the utility of DMF as a digital bioconverter, namely, genetic engineering, sample preparation for sequencing and mass spectrometry, and enzyme-, immuno-, and cell-based screening assays. These applications show that DMF has great potential in the role of a centralized execution platform in a fully integrated pipeline for the production of novel organisms and biomolecules. In this paper, we discuss how the function of a DMF device within such a pipeline is highly dependent on integration with different sensing techniques and methodologies from machine learning and big data. In addition to that, we examine how the capacity of DMF can in some cases be limited by known technical and operational challenges and how consolidated efforts in overcoming these challenges will be key to the development of DMF as a major enabling technology in the computer-aided biology framework.

Auto-affitech: an automated ligand binding affinity evaluation platform using digital microfluidics with a bidirectional magnetic separation method

The dissociation constant (Kd) is a crucial parameter for characterizing binding affinity in molecular recognition, including antigen-antibody, DNA-protein, and receptor-ligand interactions. However, conventional methods for Kd characterization usually involve a multi-step process and time-consuming operations for incubation, washing, and detection, thus causing problems, such as time delays, microbead loss, degradation of sensitive molecules, and personal errors. Here we demonstrate an automated ligand binding affinity evaluation platform (Auto-affitech) using digital microfluidics (DMF), with individual droplets at the microliter level, programmed to rapidly perform the incubation and separation of target-beads and binding ligands. Because the loss of the beads influences the detection results, we propose a new strategy for magnetic bead separation using DMF, termed the bidirectional separation method. By splitting one droplet into two asymmetric droplets, high bead retention efficiency (89.57% ± 0.05%) and high washing efficiency (99.59% ± 0.17%, with four washings) were obtained. We demonstrate the determination of Kd of an aptamer-protein system (EpCAM and its corresponding aptamer SYL3C) and an antigen-antibody system (H5N1 antigen and antibody), proving the capability and universality of Auto-affitech in various receptor-ligand systems. Integrating all the sample processing procedures, the Auto-affitech not only saves manual labor and minimizes personal errors, but also conserves samples and shortens analysis time. Overall, this platform successfully demonstrates to be an automated approach for dissociation constant evaluation and exhibits great potential for highly efficient screening of ligands.

Electric and Electrochemical Microfluidic Devices for Cell Analysis

Microfluidic devices are widely used for cell analysis, including applications for single-cell analysis, healthcare, environmental monitoring, and organs-on-a-chip that mimic organs in microfluidics. Moreover, to enable high-throughput cell analysis, real-time monitoring, and non-invasive cell assays, electric and electrochemical systems have been incorporated into microfluidic devices. In this mini-review, we summarize recent advances in these systems, with applications from single cells to three-dimensional cultured cells and organs-on-a-chip. First, we summarize microfluidic devices combined with dielectrophoresis, electrophoresis, and electrowetting-on-a-dielectric for cell manipulation. Next, we review electric and electrochemical assays of cells to determine chemical section activity, and oxygen and glucose consumption activity, among other applications. In addition, we discuss recent devices designed for the electric and electrochemical collection of cell components from cells. Finally, we highlight the future directions of research in this field and their application prospects.

A fucosyltransferase inhibition assay using image-analysis and digital microfluidics

Sialyl-LewisX and LewisX are cell-surface glycans that influence cell-cell adhesion behaviors. These glycans are assembled by α(1,3)-fucosyltransferase enzymes. Their increased expression plays a role in inflammatory disease, viral and microbial infections, and cancer. Efficient screens for specific glycan modifications such as those catalyzed by fucosyltransferases are tended toward costly materials and large instrumentation. We demonstrate for the first time a fucosylation inhibition assay on a digital microfluidic system with the integration of image-based techniques. Specifically, we report a novel lab-on-a-chip approach to perform a fluorescence-based inhibition assay for the fucosylation of a labeled synthetic disaccharide, 4-methylumbelliferyl β-N-acetyllactosaminide. As a proof-of-concept, guanosine 5'-diphosphate has been used to inhibit Helicobacter pylori α(1,3)-fucosyltransferase. An electrode shape (termed "skewed wave") is designed to minimize electrode density and improve droplet movement compared to conventional square-based electrodes. The device is used to generate a 10 000-fold serial dilution of the inhibitor and to perform fucosylation reactions in aqueous droplets surrounded by an oil shell. Using an image-based method of calculating dilutions, referred to as "pixel count," inhibition curves along with IC₅₀ values are obtained on-device. We propose the combination of integrating image analysis and digital microfluidics is suitable for automating a wide range of enzymatic assays.