Breast cancer diagnosis using a microfluidic multiplexed immunohistochemistry platform

Au-decorated Ti3C2Tx/porous carbon immunoplatform for ECM1 breast cancer biomarker detection with machine learning computation for predictive accuracy

Electrochemical immunosensors, surpassing conventional diagnostics, exhibit significant potential for cancer biomarker detection. However, achieving a delicate balance between signal sensitivity and operational stability, especially at the heterostructure interface, is crucial for practical immunosensors. Herein, porous carbon (PC) integration with Ti3C2Tx-MXene (MX) and gold nanoparticles (Au NPs) constructs a versatile immunosensing platform for detecting extracellular matrix protein-1 (ECM1), a breast cancer-associated biomarker. The inclusion of PC provided robust structural support, enhancing electrolytic diffusion with an expansive surface area while synergistically facilitating charge transfer with Ti3C2Tx. The biosensor optimized with 1.0 mg PC demonstrates a robust electrochemical redox response to the surface-bound thionine (th) redox probe, utilizing an inhibition-based strategy for ECM1 detection. The robust antibody-antigen interactions across the PC-integrated Ti3C2Tx-Au NPs platform (MX-Au-C-1) enabled robust ECM1 detection within 0.1-7.5 nM, with a low limit of detection (LOD) of 0.012 nM. The constructed biosensor shows improved operational stability with a 98.6 % current retention over 1 h, surpassing MXene-integrated (MX-Au) and pristine Au NPs (63.2 % and 44.3 %, respectively) electrodes. Moreover, the successful adaptation of the artificial neural network (ANN) model for predictive analysis of the generated DPV data further validates the accuracy of the biosensor, promising its future application in AI-powered remote health monitoring.

Delineating intra-tumoral heterogeneity and tumor evolution in breast cancer using precision-based approaches

The burden of breast cancer continues to increase worldwide as it remains the most diagnosed tumor in females and the second leading cause of cancer-related deaths. Breast cancer is a heterogeneous disease characterized by different subtypes which are driven by aberrations in key genes such as BRCA1 and BRCA2, and hormone receptors. However, even within each subtype, heterogeneity that is driven by underlying evolutionary mechanisms is suggested to underlie poor response to therapy, variance in disease progression, recurrence, and relapse. Intratumoral heterogeneity highlights that the evolvability of tumor cells depends on interactions with cells of the tumor microenvironment. The complexity of the tumor microenvironment is being unraveled by recent advances in screening technologies such as high throughput sequencing; however, there remain challenges that impede the practical use of these approaches, considering the underlying biology of the tumor microenvironment and the impact of selective pressures on the evolvability of tumor cells. In this review, we will highlight the advances made thus far in defining the molecular heterogeneity in breast cancer and the implications thereof in diagnosis, the design and application of targeted therapies for improved clinical outcomes. We describe the different precision-based approaches to diagnosis and treatment and their prospects. We further propose that effective cancer diagnosis and treatment are dependent on unpacking the tumor microenvironment and its role in driving intratumoral heterogeneity. Underwriting such heterogeneity are Darwinian concepts of natural selection that we suggest need to be taken into account to ensure evolutionarily informed therapeutic decisions.

The 2D microfluidics cookbook - modeling convection and diffusion in plane flow devices

A growing number of microfluidic systems operate not through networks of microchannels but instead through using 2D flow fields. While the design rules for channel networks are already well-known and exposed in microfluidics textbooks, the knowledge underlying transport in 2D microfluidics remains scattered piecemeal and is not easily accessible to experimentalists and engineers. In this tutorial review, we formulate a unified framework for understanding, analyzing and designing 2D microfluidic technologies. We first show how a large number of seemingly different devices can all be modelled using the same concepts, namely flow and diffusion in a Hele-Shaw cell. We then expose a handful of mathematical tools, accessible to any engineer with undergraduate level mathematics knowledge, namely potential flow, superposition of charges, conformal transforms and basic convection-diffusion. We show how these tools can be combined to obtain a simple "recipe" that models almost any imaginable 2D microfluidic system. We end by pointing to more advanced topics beyond 2D microfluidics, namely interface problems and flow and diffusion in the third dimension. This forms the basis of a complete theory allowing for the design and operation of new microfluidic systems.

Efficient AC electrothermal flow (ACET) on-chip for enhanced immunoassays

Biochemical reaction rates in microfluidic systems are known to be limited by the diffusional transport of reagents, leading often to lowered sensitivity and/or longer detection times in immunoassays. Several methods, including electrically powering electrodes to generate AC electrothermal flow (ACET) on-chip, have been adopted to enhance the mass transport of the reagents and improve microfluidic mixing. Here, we report a novel ACET electrode design concept for generating in-plane microfluidic mixing vortices that act over a large volume close to the reaction surface of interest. This is different from the traditional ACET parallel electrode design that provides rather local vertical mixing vortices directly above the electrodes. Both numerical simulation and experimental studies were performed to validate the new design. Moreover, numerical simulation was carried out to show the effects of experimental factors such as the reaction kinetics (association constant) and the reagent concentration on the ACET-enhanced surface-based assays. As a proof of concept, the new design for the ACET-enhanced immunoassays was used to improve the immunostaining signal of the HER2 (human epidermal growth factor receptor 2) cancer biomarker on breast cancer cells. Finally, the concept of scaling up the design has been validated by experiments (immunoassays on breast cancer cells for different ACET power and different assay times). In particular, we show that larger ACET in-plane designs can agitate and mix the fluid over large microfluidic volumes, which further enhances the immunoassay's output. We have achieved a 6-times enhancement in the assay signal with a 75% reduction in assay time.

Hydrogel Stamping for Rapid, Multiplexed, Point-of-Care Immunostaining of Cells and Tissues

In the era of precision oncology, multicolor fluorescence imaging has become a core technology for multiplexed molecular analysis of cellular and tissue specimens. However, conventional solution-based staining is labor-intensive and time-consuming and requires considerable expertise to yield optimal results, which creates difficulties for employing this technology in resource-limited settings. Here, we report a new immunostaining method based on hydrogel stamping, which is simple, fast, easy to use, and reproducible. We showed that a hydrophilic hydrogel stamp could effectively transfer fluorescent antibodies to targets and withdraw an excess solution when the reaction is completed, obviating the need for extra washing. This unique property allows for quality immunostaining in 5 min for cells using one-eighth of antibody consumption compared to the conventional solution-based method. Furthermore, we implemented fluorescence quenching and immunocycling with hydrogel staining for multiplexed analysis of 9 protein markers at a single cell level. Finally, we applied the immunocycling method to human breast cancer tissue samples and showed quality immunostaining over a large area (∼2 cm²) in 30 min for molecular subtyping of breast cancer. The hydrogel immunostaining could open new opportunities for rapid, automated, and multiplexed profiling in compact point-of-care systems for molecular cancer diagnosis.

Use of some cost-effective technologies for a routine clinical pathology laboratory

Classically, the need for highly sophisticated instruments with important economic costs has been a major limiting factor for clinical pathology laboratories, especially in developing countries. With the aim of making clinical pathology more accessible, a wide variety of free or economical technologies have been developed worldwide in the last few years. 3D printing and Arduino approaches can provide up to 94% economical savings in hardware and instrumentation in comparison to commercial alternatives. The vast selection of point-of-care-tests (POCT) currently available also limits the need for specific instruments or personnel, as they can be used almost anywhere and by anyone. Lastly, there are dozens of free and libre digital tools available in health informatics. This review provides an overview of the state-of-the-art on cost-effective alternatives with applications in routine clinical pathology laboratories. In this context, a variety of technologies including 3D printing and Arduino, lateral flow assays, plasmonic biosensors, and microfluidics, as well as laboratory information systems, are discussed. This review aims to serve as an introduction to different technologies that can make clinical pathology more accessible and, therefore, contribute to achieve universal health coverage.

Biomarker barcodes: multiplexed microfluidic immunohistochemistry enables high-throughput analysis of tissue microarray

We present a multiplexed microfluidic immunohistochemistry (IHC) technology that enables high-throughput analysis of tissue microarrays (TMAs) using the patterns of biomarker barcodes, which consist of a series of expressed linear patterns of specific biomarkers. A multichannel poly(dimethylsiloxane) microfluidic device was reversibly assembled by the pressure of simple equipment for multiplexed IHC on each core of TMA or cell microarray (CMA) section slides. By injecting primary antibodies from different biomarkers independently into each channel, multiplexed immunostaining can be performed on each core of TMA. We confirmed the equal immunostaining quality regardless of the channel orders and core positions in the slide. Four different biomarkers (ER, PR, HER2, and Ki67) were used for the demonstration of distinctive expression patterns on CMAs which consist of six different breast cancer cell lines, and it was confirmed that these bar-like signals could be a biomarker barcode for the TMA core. A biomarker barcode of breast cancer patient-derived TMA was quickly scanned by a slide scanner and compared to the conventional method for breast cancer diagnosis. This "barcode-IHC" concept, which has been verified by performing multiplexed microfluidic IHC on CMA and TMA samples, provides high reproducibility and the potential of high-throughput screening with molecular diagnostic capability.

A versatile microfluidic device for multiple ex vivo/in vitro tissue assays unrestrained from tissue topography

Precision-cut tissue slices are an important in vitro system to study organ function because they preserve most of the native cellular microenvironments of organs, including complex intercellular connections. However, during sample manipulation or slicing, some of the natural surface topology and structure of these tissues is lost or damaged. Here, we introduce a microfluidic platform to perform multiple assays on the surface of a tissue section, unhindered by surface topography. The device consists of a valve on one side and eight open microchannels located on the opposite side, with the tissue section sandwiched between these two structures. When the valve is actuated, eight independent microfluidic channels are formed over a tissue section. This strategy prevents cross-contamination when performing assays and enables parallelization. Using irregular tissues such as an aorta, we conducted multiple in vitro and ex vivo assays on tissue sections, including short-term culturing, a drug toxicity assay, a fluorescence immunohistochemistry staining assay, and an immune cell assay, in which we observed the interaction of neutrophils with lipopolysaccharide (LPS)-stimulated endothelium. Our microfluidic platform can be employed in other disciplines, such as tissue physiology and pathophysiology, morphogenesis, drug toxicity and efficiency, metabolism studies, and diagnostics, enabling the conduction of several assays with a single biopsy sample.

Reconfigurable microfluidics: real-time shaping of virtual channels through hydrodynamic forces

To break the current paradigm in microfluidics that directly links device design to functionality, we introduce microfluidic "virtual channels" that can be dynamically shaped in real-time. A virtual channel refers to a flow path within a microfluidic flow cell, guiding an injected reagent along a user-defined trajectory solely by hydrodynamic forces. Virtual channels dynamically reproduce key microfluidic functionality: directed transport of minute volumes of liquid, splitting, merging and mixing of flows. Virtual channels can be formed directly on standard biological substrates, which we demonstrate by sequential immunodetection at arrays of individual reaction sites on a glass slide and by alternating between local and global processing of surface-adherent cell-block sections. This approach is simple, versatile and generic enough to form the basis of a new class of microfluidic techniques.

Electrokinetic Scanning Probe

The theoretical analysis and experimental demonstration of a new concept are presented for a non-contact scanning probe, in which transport of fluid and molecules is controlled by electric fields. The electrokinetic scanning probe (ESP) enables local chemical and biochemical interactions with surfaces in liquid environments. The physical mechanism and design criteria for such a probe are presented, and its compatibility with a wide range of processing solutions and pH values are demonstrated. The applicability of the probe is shown for surface patterning in conjunction with localized heating and 250-fold analyte stacking.

Rapid micro-immunohistochemistry

We present a new and versatile implementation of rapid and localized immunohistochemical staining of tissue sections. Immunohistochemistry (IHC) comprises a sequence of specific biochemical reactions and allows the detection of specific proteins in tissue sections. For the rapid implementation of IHC, we fabricated horizontally oriented microfluidic probes (MFPs) with functionally designed apertures to enable square and circular footprints, which we employ to locally expose a tissue to time-optimized sequences of different biochemicals. We show that the two main incubation steps of IHC protocols can be performed on MDAMB468-1510A cell block sections in less than 30 min, compared to incubation times of an hour or more in standard protocols. IHC analysis on the timescale of tens of minutes could potentially be applied during surgery, enabling clinicians to react in more dynamically and efficiently. Furthermore, this rapid IHC implementation along with conservative tissue usage has strong potential for the implementation of multiplexed assays, allowing the exploration of optimal assay conditions with a small amount of tissue to ensure high-quality staining results for the remainder of the sample.

Paper-based multiplexed vertical flow assay for point-of-care testing

We developed a multiplexed point-of-care immunodiagnostic assay for antibody detection in human sera made through the vertical stacking of functional paper layers. In this multiplexed vertical flow immunodiagnostic assay (xVFA), a colorimetric signal is generated by gold nanoparticles captured on a spatially-multiplexed sensing membrane containing specific antigens. The assay is completed in 20 minutes, following which the sensing membrane is imaged by a cost-effective mobile-phone reader. The images are sent to a server, where the results are rapidly analyzed and relayed back to the user. The performance of the assay was evaluated by measuring Lyme-specific antibodies in human sera as model target antibodies. The presented platform is rapid, simple, inexpensive, and allows for simultaneous and quantitative measurement of multiple antibodies and/or antigens making it a suitable point-of-care platform for disease diagnostics.

Vertically sheathing laminar flow-based immunoassay using simultaneous diffusion-driven immune reactions

Simultaneous infusion of primary and secondary antibodies of different diffusivity into vertical laminar flows enables the improved immune reactions.

Microfluidics-based immunofluorescence for fast staining of ALK in lung adenocarcinoma

Background

Anaplastic lymphoma kinase (ALK) is a key oncogenic driver in lung adenocarcinoma patients and its fusion proteins are routinely assessed. The microfluidic tissue processor (MTP) device is based on a chip-confined low-volume technology allowing for rapid immunohistochemistry/immunofluorescence (IHC/IF) stainings of formalin-fixed paraffin-embedded (FFPE) or frozen tissue samples.

Methods

A novel ALK IF protocol was developed for the MTP device using the primary mouse anti-human ALK antibody clone 5A4. FFPE tumor whole sections from 14 resected lung adenocarcinoma patients documented to be ALK positive (ALK+) by automated chromogenic IHC and/or FISH were used. MTP-derived IF immunoreactivity was measured by computerized analysis of digitalized images on individual frames of tumor epithelia and surrounding stroma, using an ImageJ plug-in.

Results

The 5A4 antibody yielded saturated immunoreactivity at an incubation time of 4 min on a titration curve ranging from 2 to 32 min. Total staining time on the MTP device was 18 min including secondary IgG Alexa Fluor 647. MTP-based ALK IF confirmed all 12 cases; with epithelial signal above stromal staining based on computerized pixel-based measurement. MTP-IF (mean intensity levels 458 to 1301) and chromogenic IHC (H-score 120 to 300) showed an equal range of variation of 2.8 and 2.5 folds, respectively, and a trend for direct correlation (p-value 0.051).

Conclusion

The newly developed protocol for immunofluorescent detection of ALK protein with the MTP device confirms chromogenic IHC results on FFPE lung adenocarcinoma specimens. MTP-based IF is fast and reliable. We foresee this study to be a first step opening the road for further realization of microfluidic-based assays for rapid simultaneous detection of targetable oncogenic and immune-system related markers in their topographical context to investigate tumour heterogeneity and micro-environmental interactions.

Electronic supplementary material

The online version of this article (10.1186/s13000-018-0757-1) contains supplementary material, which is available to authorized users.

Microfluidic on-chip immunohistochemistry directly from a paraffin-embedded section

We present here a novel microfluidic platform that can perform microfluidic on-chip immunohistochemistry (IHC) processes on a formalin-fixed paraffin-embedded section slide. Unlike previous microfluidic IHC studies, our microfluidic chip made of organic solvent-resistant polyurethane acrylate (PUA) is capable of conducting on-chip IHC processes consecutively. A narrow channel wall structure of the PUA chip shows effective sealing by pressure-based reversible assembly with a section slide. We performed both on-chip IHC and conventional IHC processes and compared the IHC results based on the immunostaining intensity. The result showed that the effects of the on-chip deparaffinization, antigen retrieval, and immunoreaction processes on the IHC result were equivalent to conventional methods while reducing the total process time to less than 1/2. The experiment with breast cancer tissue shows that human epidermal growth factor receptor 2 (HER2) classification can be performed by obtaining a clearly distinguishable immunostaining intensity according to the HER2 expression level. We expect our on-chip microfluidic platform to provide a facile technique suitable for miniaturized, automated, and precise diagnostic devices, including a point-of-care device.

Direct Surface and Droplet Microsampling for Electrospray Ionization Mass Spectrometry Analysis with an Integrated Dual-Probe Microfluidic Chip

Ambient mass spectrometry (MS) has revolutionized the way of MS analysis and broadened its application in various fields. This paper describes the use of microfluidic techniques to simplify the setup and improve the functions of ambient MS by integrating the sampling probe, electrospray emitter probe, and online mixer on a single glass microchip. Two types of sampling probes, including a parallel-channel probe and a U-shaped channel probe, were designed for dry-spot and liquid-phase droplet samples, respectively. We demonstrated that the microfabrication techniques not only enhanced the capability of ambient MS methods in analysis of dry-spot samples on various surfaces, but also enabled new applications in the analysis of nanoliter-scale chemical reactions in an array of droplets. The versatility of the microchip-based ambient MS method was demonstrated in multiple different applications including evaluation of residual pesticide on fruit surfaces, sensitive analysis of low-ionizable analytes using postsampling derivatization, and high-throughput screening of Ugi-type multicomponent reactions.

Microfluidics for rapid cytokeratin immunohistochemical staining in frozen sections

Frozen sections (FS) of tumor samples represent a cornerstone of pathological intraoperative consultation and have an important role in the microscopic analysis of specimens during surgery. So far, immunohistochemical (IHC) stainings on FS have been demonstrated for a few markers using manual methods. Microfluidic technologies have proven to bring substantial improvement in many fields of diagnostics, though only a few microfluidic devices have been designed to improve the performance of IHC assays. In this work, we show optimization of a complete pan-cytokeratin chromogenic immunostaining protocol on FS using a microfluidic tissue processor into a protocol taking <12 min. Our results showed specificity and low levels of background. The dimensions of the microfluidic prototype device are compatible with the space constraints of an intraoperative pathology laboratory. We therefore anticipate that the adoption of microfluidic technologies in the field of surgical pathology can significantly improve the way FSs influence surgical procedures.

Tissue lithography: Microscale dewaxing to enable retrospective studies on formalin-fixed paraffin-embedded (FFPE) tissue sections

We present a new concept, termed tissue lithography (TL), and its implementation which enables retrospective studies on formalin-fixed paraffin-embedded tissue sections. Tissue lithography uses a microfluidic probe to remove microscale areas of the paraffin layer on formalin-fixed paraffin-embedded biopsy samples. Current practices in sample utilization for research and diagnostics require complete deparaffinization of the sample prior to molecular testing. This imposes strong limitations in terms of the number of tests as well as the time when they can be performed on a single sample. Microscale dewaxing lifts these constraints by permitting deprotection of a fraction of a tissue for testing while keeping the remaining of the sample intact for future analysis. After testing, the sample can be sent back to storage instead of being discarded, as is done in standard workflows. We achieve this microscale dewaxing by hydrodynamically confining nanoliter volumes of xylene on top of the sample with a probe head. We demonstrate micrometer-scale, chromogenic and fluorescence-based immunohistochemistry against multiple biomarkers (p53, CD45, HER2 and β-actin) on tonsil and breast tissue sections and microarrays. We achieve stain patterns as small as 100 μm × 50 μm as well as multiplexed immunostaining within a single tissue microarray core with a 20-fold time reduction for local dewaxing as compared to standard protocols. We also demonstrate a 10-fold reduction in the rehydration time, leading to lower processing times between different stains. We further show the potential of TL for retrospective studies by sequentially dewaxing and staining four individual cores within the same tissue microarray over four consecutive days. By combining tissue lithography with the concept of micro-immunohistochemistry, we implement each step of the IHC protocol—dewaxing, rehydration and staining—with the same microfluidic probe head. Tissue lithography brings a new level of versatility and flexibility in sample processing and budgeting in biobanks, which may alleviate current sample limitations for retrospective studies in biomarker discovery and drug screening.

Demonstration of Interposed Modular Hydrogel Sheet for Multicellular Analysis in a Microfluidic Assembly Platform

Hydrogel sheets have emerged as a promising biomaterial scaffold for the encapsulation and transfer of multicellular structures. Although the improvement of the chemical interactions and the design of micro-scaled geometry have contributed to the development of multipurpose hydrogel scaffolds, the application of hydrogel sheets to assess multicellular structures is still challenging. To expand the technical applicability of hydrogel sheets, we here demonstrate that a single layer of the hydrogel sheet can be integrated as an interposed module in a microfluidic device for multicellular analysis. As a cell culture unit, encapsulated pancreatic insulinoma (MIN6) cells in the hydrogel sheet were labeled and examined via multiple microchannels. After obtaining simultaneously multi-labeled cells in the hydrogel sheet that had been incorporated into the microfluidic device, each modular hydrogel sheet was also recoverable and re-cultured without any distortion. The modular hydrogel sheet can be simply manipulated and conserved as a multicellular module in a three-dimensional (3D) in vitro culture platform. Using the modular concept of hydrogel sheets capable of cell culture and/or assay, an integrated multicellular analysis in the microfluidic device is expected to improve accessibility, scalability, and practicality for end users.

A Microfluidic Immunostaining System Enables Quality Assured and Standardized Immunohistochemical Biomarker Analysis

Immunohistochemistry (IHC) plays an important role in biomarker-driven cancer therapy. Although there has been a high demand for standardized and quality assured IHC, it has rarely been achieved due to the complexity of IHC testing and the subjective validation-based process flow of IHC quality control. We present here a microfluidic immunostaining system for the standardization of IHC by creating a microfluidic linearly graded antibody (Ab)-staining device and a reference cell microarray. Unlike conventional efforts, our system deals primarily with the screening of biomarker staining conditions for quantitative quality assurance testing in IHC. We characterized the microfluidic matching of Ab staining intensity using three HER2 Abs produced by different manufacturers. The quality of HER2 Ab was also validated using tissues of breast cancer patients, demonstrating that our system is an efficient and powerful tool for the standardization and quality assurance of IHC.

Pipetting-driven microfluidic immunohistochemistry to facilitate enhanced immunoreaction and effective use of antibodies

Immunohistochemistry (IHC), which has been used to detect antigens in cells of a tissue section using an immunoreaction between an antibody and an antigen, is a practical tool for identifying the type and stage of diseases in cancer diagnosis and scientific research. However, conventional IHC requires long, laborious process times and high costs. Although microfluidic IHC platforms have been developed to overcome these limitations, the application of microfluidic IHC in real-world environments is still limited due to the additional equipment needed to operate the microfluidic systems. In addition, continuous flow in a microfluidic channel leads to a waste of unbound antibodies. In this study, we demonstrate a novel and easy-to-use microfluidic IHC platform operated only using a manual pipette that is commonly available in research laboratories or hospitals. No other device such as a pump or a controller is required to operate our system. Bidirectional flows of the antibody solution in a microfluidic device are induced by repetitive manual pipetting which facilitates the enhanced antigen-antibody reaction and enables the effective use of a limited amount of antibody. When breast cancer cell and tissue sections are reacted with antibodies using our platform, pipetting for less than 2 min is sufficient to obtain immunostaining results without damaging the sample. The staining intensity by our method is similar to that of the sample stained for 1 h by a conventional batch process. We believe that this pipetting-based approach to the operation of a microfluidic system allows end users to use microfluidic IHC more conveniently and easily in real-world environments.

Centimeter-Scale Surface Interactions Using Hydrodynamic Flow Confinements

We present a device and method for selective chemical interactions with immersed substrates at the centimeter-scale. Our implementations enable both, sequential and simultaneous delivery of multiple reagents to a substrate, as well as the creation of gradients of reagents on surfaces. The method is based on localizing submicroliter volumes of liquids on an immersed surface with a microfluidic probe (MFP) using a principle termed hydrodynamic flow confinement (HFC). We here show spatially defined, multiplexed surface interactions while benefiting from the probe capabilities such as non-contact scanning operation and convection-enhanced reaction kinetics. Three-layer glass-Si-glass probes were developed to implement slit-aperture and aperture-array designs. Analytical and numerical analysis helped to establish probe designs and operating parameters. Using these probes, we performed immunohistochemical analysis on individual cores of a human breast-cancer tissue microarray. We applied α-p53 antibodies on a 2 mm diameter core within 2.5 min using a slit-aperture probe (HFC dimension: 0.3 mm × 1.2 mm). Further, multiplexed treatment of a tissue core with α-p53 and α-β-actin antibodies was performed using four adjacent HFCs created with an aperture-array probe (HFC dimension: 4 × 0.3 mm × 0.25 mm). The ability of these devices and methods to perform multiplexed assays, present sequentially different liquids on surfaces, and interact with surfaces at the centimeter-scale will likely spur new and efficient surface assays.

Multiplex Gene Expression Profiling of 16 Target Genes in Neoplastic and Non-Neoplastic Canine Mammary Tissues Using Branched-DNA Assay

Mammary gland tumors are one of the most common neoplasms in female dogs, and certain breeds are prone to develop the disease. The use of biomarkers in canines is still restricted to research purposes. Therefore, the necessity to analyze gene profiles in different mammary entities in large sample sets is evident in order to evaluate the strength of potential markers serving as future prognostic factors. The aim of the present study was to analyze the gene expression of 16 target genes (BRCA1, BRCA2, FOXO3, GATA4, HER2, HMGA1, HMGA2, HMGB1, MAPK1, MAPK3, MCL1, MYC, PFDN5, PIK3CA, PTEN, and TP53) known to be involved in human and canine mammary neoplasm development. Expression was analyzed in 111 fresh frozen (FF) and in 170 formalin-fixed, paraffin-embedded (FFPE) specimens of neoplastic and non-neoplastic canine mammary tissues using a multiplexed branched-DNA (b-DNA) assay. TP53, FOXO3, PTEN, and PFDN5 expression revealed consistent results with significant low expression in malignant tumors. The possibility of utilizing them as predictive factors as well as for assisting in the choice of an adequate gene therapy may help in the development of new and improved approaches in canine mammary tumors.

193 nm Ultraviolet Photodissociation Mass Spectrometry for Phosphopeptide Characterization in the Positive and Negative Ion Modes

Advances in liquid chromatography tandem mass spectrometry (LC-MS/MS) have permitted phosphoproteomic analysis on a grand scale, but ongoing challenges specifically associated with confident phosphate localization continue to motivate the development of new fragmentation techniques. In the present study, ultraviolet photodissociation (UVPD) at 193 nm is evaluated for the characterization of phosphopeptides in both positive and negative ion modes. Compared to the more standard higher energy collisional dissociation (HCD), UVPD provided more extensive fragmentation with improved phosphate retention on product ions. Negative mode UVPD showed particular merit for detecting and sequencing highly acidic phosphopeptides from alpha and beta casein, but was not as robust for larger scale analysis because of lower ionization efficiencies in the negative mode. HeLa and HCC70 cell lysates were analyzed by both UVPD and HCD. While HCD identified more phosphopeptides and proteins compared to UVPD, the unique matches from UVPD analysis could be combined with the HCD data set to improve the overall depth of coverage compared to either method alone.

A Comparison of Fresh Frozen vs. Formalin-Fixed, Paraffin-Embedded Specimens of Canine Mammary Tumors via Branched-DNA Assay

Mammary neoplasms are the tumors most affecting female dogs and women. Formalin-fixed, paraffin-embedded (FFPE) tissues are an invaluable source of archived biological material. Fresh frozen (FF) tissue is considered ideal for gene expression analysis. However, strategies based on FFPE material offer several advantages. Branched-DNA assays permit a reliable and fast workflow when analyzing gene expression. The aim of this study was to assess the comparability of the branched-DNA assay when analyzing certain gene expression patterns between FF and FFPE samples in canine mammary tumors. RNA was isolated from 109 FFPE samples and from 93 FF samples of different canine mammary tissues. Sixteen (16) target genes (Tp53; Myc; HMGA1; Pik3ca; Mcl1; MAPK3; FOXO3; PTEN; GATA4; PFDN5; HMGB1; MAPK1; BRCA2; BRCA1; HMGA2; and Her2) were analyzed via branched-DNA assay (b-DNA). ACTB, GAPDH, and HPRT1 were used as data normalizers. Overall, the relative gene expression of the two different origins of samples showed an agreement of 63%. Still, care should be taken, as FFPE specimens showed lower expression of the analyzed targets when compared to FF samples. The fact that the gene expression in FFPE proved to be lower than in FF specimens is likely to have been caused by the effect of storage time. ACTB had the best performance as a data normalizer.

Status and perspective of lab-on-a-chip systems for common diseases: a systematic review from 2003 to 2013

BACKGROUND

Lab-on-a-chip systems (LOCs) are a useful aid for the individualization of therapeutic algorithms at the point-of-care.

MATERIALS & METHODS

We performed a systematic literature review on LOCs for diseases with a global impact for healthcare.

RESULTS

A total of 1007 articles matched the previously specified search criteria, thereof 65 studies could be included in this review. A total of 55 different LOCs were evaluated, most for diagnosis or monitoring of cancer (n = 24). For other diseases we found considerably less analyzed LOCs. The analytical performance of the LOCs was usually very good, 37 (67%) LOCs had a sensitivity higher than 90%.

CONCLUSION

Although LOC systems performance has been positively evaluated in the great majority of studies, the testing was mostly limited to the research laboratory setting rather than real-world scenarios.

Retina-on-a-chip: a microfluidic platform for point access signaling studies

We report on a microfluidic platform for culture of whole organs or tissue slices with the capability of point access reagent delivery to probe the transport of signaling events. Whole mice retina were maintained for multiple days with negative pressure applied to tightly but gently bind the bottom of the retina to a thin poly-(dimethylsiloxane) membrane, through which twelve 100 μm diameter through-holes served as fluidic access points. Staining with toluidine blue, transport of locally applied cholera toxin beta, and transient response to lipopolysaccharide in the retina demonstrated the capability of the microfluidic platform. The point access fluidic delivery capability could enable new assays in the study of various kinds of excised tissues, including retina.

3D liver models on a microplatform: well-defined culture, engineering of liver tissue and liver-on-a-chip

The liver, the largest organ in the human body, is a multi-functional organ with diverse metabolic activities that plays a critical role in maintaining the body and sustaining life. Although the liver has excellent regenerative and recuperative properties, damages caused by chronic liver diseases or viral infection may lead to permanent loss of liver functions. Studies of liver disease mechanism have focused on drug screening and liver tissue engineering techniques, including strategies based on in vitro models. However, conventional liver models are plagued by a number of limitations, which have motivated the development of 'liver-on-a-chip' and microplatform-based bioreactors that can provide well-defined microenvironments. Microtechnology is a promising tool for liver tissue engineering and liver system development, as it can mimic the complex in vivo microenvironment and microlevel ultrastructure, by using a small number of human cells under two-dimensional (2D) and three-dimensional (3D) culture conditions. These systems provided by microtechnology allow improved liver-specific functions and can be expanded to encompass diverse 3D culture methods, which are critical for the maintenance of liver functions and recapitulation of the features of the native liver. In this review, we provide an overview of microtechnologies that have been used for liver studies, describe biomimetic technologies for constructing microscale 2D and 3D liver models as well as liver-on-a-chip systems and microscale bioreactors, and introduce applications of liver microtechnology and future trends in the field.

Recent developments in multiplexing techniques for immunohistochemistry

Methods to detect immunolabeled molecules at increasingly higher resolutions, even when present at low levels, are revolutionizing immunohistochemistry (IHC). These technologies can be valuable for the management and examination of rare patient tissue specimens, and for improved accuracy of early disease detection. The purpose of this article is to highlight recent multiplexing methods that are candidates for more prevalent use in clinical research and potential translation to the clinic. Multiplex IHC methods, which permit identification of at least 3 and up to 30 discrete antigens, have been divided into whole-section staining and spatially-patterned staining categories. Associated signal enhancement technologies that can enhance performance and throughput of multiplex IHC assays are also discussed. Each multiplex IHC technique, detailed herein, is associated with several advantages as well as tradeoffs that must be taken into consideration for proper evaluation and use of the methods.

Expanding imaging capabilities for microfluidics: applicability of darkfield internal reflection illumination (DIRI) to observations in microfluidics

Microfluidics is used increasingly for engineering and biomedical applications due to recent advances in microfabrication technologies. Visualization of bubbles, tracer particles, and cells in a microfluidic device is important for designing a device and analyzing results. However, with conventional methods, it is difficult to observe the channel geometry and such particles simultaneously. To overcome this limitation, we developed a Darkfield Internal Reflection Illumination (DIRI) system that improved the drawbacks of a conventional darkfield illuminator. This study was performed to investigate its utility in the field of microfluidics. The results showed that the developed system could clearly visualize both microbubbles and the channel wall by utilizing brightfield and DIRI illumination simultaneously. The methodology is useful not only for static phenomena, such as clogging, but also for dynamic phenomena, such as the detection of bubbles flowing in a channel. The system was also applied to simultaneous fluorescence and DIRI imaging. Fluorescent tracer beads and channel walls were observed clearly, which may be an advantage for future microparticle image velocimetry (μPIV) analysis, especially near a wall. Two types of cell stained with different colors, and the channel wall, can be recognized using the combined confocal and DIRI system. Whole-slide imaging was also conducted successfully using this system. The tiling function significantly expands the observing area of microfluidics. The developed system will be useful for a wide variety of engineering and biomedical applications for the growing field of microfluidics.

Aqueous two-phase system-mediated antibody micropatterning enables multiplexed immunostaining of cell monolayers and tissues

Conventional immunostaining methods consume large quantities of expensive antibodies and are limited in terms of the number of antigens that can be detected from a single sample. In order to achieve multiplexed immunostaining, we micropatterned antibodies using aqueous two-phase systems (ATPS) formed from polyethylene glycol (PEG) and dextran. Multiple antigens can be detected on a single fixed sample by incorporating antibodies within dextran solutions, which are then patterned by micropipetting at specific sites on the sample in a solution of PEG. The antibodies are retained within the dextran phase due to biomolecular partitioning, allowing multiple protein markers to be visualized simultaneously by way of chromogenic, chemiluminescent, or immunofluorescent detection. This aqueous two-phase system-mediated antibody micropatterning approach allows antibody dilutions to be easily optimized, reduces the consumption of expensive primary antibodies and can prevent antibody cross-reactions, since the antibodies are retained at separate sites within the dextran microdroplets.

A compact and versatile microfluidic probe for local processing of tissue sections and biological specimens

The microfluidic probe (MFP) is a non-contact, scanning microfluidic technology for local (bio)chemical processing of surfaces based on hydrodynamically confining nanoliter volumes of liquids over tens of micrometers. We present here a compact MFP (cMFP) that can be used on a standard inverted microscope and assist in the local processing of tissue sections and biological specimens. The cMFP has a footprint of 175 × 100 × 140 mm(3) and can scan an area of 45 × 45 mm(2) on a surface with an accuracy of ±15 μm. The cMFP is compatible with standard surfaces used in life science laboratories such as microscope slides and Petri dishes. For ease of use, we developed self-aligned mounted MFP heads with standardized "chip-to-world" and "chip-to-platform" interfaces. Switching the processing liquid in the flow confinement is performed within 90 s using a selector valve with a dead-volume of approximately 5 μl. We further implemented height-compensation that allows a cMFP head to follow non-planar surfaces common in tissue and cellular ensembles. This was shown by patterning different macroscopic copper-coated topographies with height differences up to 750 μm. To illustrate the applicability to tissue processing, 5 μm thick M000921 BRAF V600E+ melanoma cell blocks were stained with hematoxylin to create contours, lines, spots, gradients of the chemicals, and multiple spots over larger areas. The local staining was performed in an interactive manner using a joystick and a scripting module. The compactness, user-friendliness, and functionality of the cMFP will enable it to be adapted as a standard tool in research, development and diagnostic laboratories, particularly for the interaction with tissues and cells.

A trachea-inspired bifurcated microfilter capturing viable circulating tumor cells via altered biophysical properties as measured by atomic force microscopy

Circulating tumor cells (CTCs), though exceedingly rare in the blood, are nonetheless becoming increasingly important in cancer diagnostics. Despite this keen interest and the growing number of potential clinical applications, there has been limited success in developing a CTC isolation platform that simultaneously optimizes recovery rates, purity, and cell compatibility. Herein, a novel tracheal carina-inspired bifurcated (TRAB) microfilter system is reported, which uses an optimal filter gap size satisfying both 100% theoretical recovery rate and purity, as determined by biomechanical analysis and fluid-structure interaction (FSI) simulations. Biomechanical properties are also used to clearly discriminate between cancer cells and leukocytes, whereby cancer cells are selectively bound to melamine microbeads, which increase the size and stiffness of these cells. Nanoindentation experiments are conducted to measure the stiffness of leukocytes as compared to the microbead-conjugated cancer cells, with these parameters then being used in FSI analyses to optimize the filter gap size. The simulation results show that given a flow rate of 100 μL min(-1), an 8 μm filter gap optimizes the recovery rate and purity. MCF-7 breast cancer cells with solid microbeads are spiked into 3 mL of whole blood and, by using this flow rate along with the optimized microfilter dimensions, the cell mixture passes through the TRAB filter, which achieves a recovery rate of 93% and purity of 59%. Regarding cell compatibility, it is verified that the isolation procedure does not adversely affect cell viability, thus also confirming that the re-collected cancer cells can be cultured for up to 8 days. This work demonstrates a CTC isolation technology platform that optimizes high recovery rates and cell purity while also providing a framework for functional cell studies, potentially enabling even more sensitive and specific cancer diagnostics.

Microfluidics in the "open space" for performing localized chemistry on biological interfaces

Local interactions between (bio)chemicals and biological interfaces play an important role in fields ranging from surface patterning to cell toxicology. These interactions can be studied using microfluidic systems that operate in the "open space", that is, without the need for the sealed channels and chambers commonly used in microfluidics. This emerging class of techniques localizes chemical reactions on biological interfaces or specimens without imposing significant "constraints" on samples, such as encapsulation, pre-processing steps, or the need for scaffolds. They therefore provide new opportunities for handling, analyzing, and interacting with biological samples. The motivation for performing localized chemistry is discussed, as are the requirements imposed on localization techniques. Three classes of microfluidic systems operating in the open space, based on microelectrochemistry, multiphase transport, and hydrodynamic flow confinement of liquids are presented.

Microfluidic processor allows rapid HER2 immunohistochemistry of breast carcinomas and significantly reduces ambiguous (2+) read-outs

Biomarker analysis is playing an essential role in cancer diagnosis, prognosis, and prediction. Quantitative assessment of immunohistochemical biomarker expression on tumor tissues is of clinical relevance when deciding targeted treatments for cancer patients. Here, we report a microfluidic tissue processor that permits accurate quantification of the expression of biomarkers on tissue sections, enabled by the ultra-rapid and uniform fluidic exchange of the device. An important clinical biomarker for invasive breast cancer is human epidermal growth factor receptor 2 [(HER2), also known as neu], a transmembrane tyrosine kinase that connotes adverse prognostic information for the patients concerned and serves as a target for personalized treatment using the humanized antibody trastuzumab. Unfortunately, when using state-of-the-art methods, the intensity of an immunohistochemical signal is not proportional to the extent of biomarker expression, causing ambiguous outcomes. Using our device, we performed tests on 76 invasive breast carcinoma cases expressing various levels of HER2. We eliminated more than 90% of the ambiguous results (n = 27), correctly assigning cases to the amplification status as assessed by in situ hybridization controls, whereas the concordance for HER2-negative (n = 31) and -positive (n = 18) cases was 100%. Our results demonstrate the clinical potential of microfluidics for accurate biomarker expression analysis. We anticipate our technique will be a diagnostic tool that will provide better and more reliable data, onto which future treatment regimes can be based.

Microfluidic probes for use in life sciences and medicine

Microfluidic probes (MFPs) combine the concepts of microfluidics and of scanning probes and constitute a contact-free and channel-free microfluidic system. Whereas classically the sample is introduced into the microfluidic device, with a MFP, the microfluidic stream is applied to the sample. MFPs use hydrodynamic flow confinement instead of walls to constrain a microfluidic stream between the MFP tip and a substrate. Because MFPs are free to move, they can be used to process large areas and samples in a selective manner. The development of MFP technology is recent and has numerous potential applications in several fields, most notably in the life sciences. In this review, we discuss the concept of MFPs and highlight their application in surface biopatterning, controlling the cellular microenvironments, local processing of tissue slices, and generating concentration gradients of biochemicals. We hope that this manuscript will serve as an interdisciplinary guide for both engineers as they further develop novel MFPs and applications and for life scientists who may identify novel uses of the MFP for their research.

Breast cancer diagnostics using microfluidic multiplexed immunohistochemistry

A quantitative, reproducible, fast and inexpensive multiplexed immunohistochemistry (IHC) system might play a locomotive role in drug screening and personalized medicine. Currently, fully automated IHC machines and sequential multiplexed IHC methods based upon multiple color reagents have been developed, with the evolution of such methods having revealed novel biological findings over the conventional IHC method, which is time consuming and labor intensive. We describe a novel parallel multiplexed IHC method using a microfluidic multiplexed immunohistochemistry (MMIHC) device for quantitative pathological diagnosis of breast cancer. The key factors for success of parallel multiplexed IHC are the fabrication of a robust microfluidic device, the interface between the device and a tissue slide, and an accurate fluidic control for multiple IHC reagents. In order to apply conventional thin-section tissues into on-chip systems without any additional modification process, a tissue slide-compatible assembler was developed for optimal compatibility of conventional IHC methods. With this approach, a perfect fluid control for various solutions was demonstrated without any leakage, bubble formation or cross-contamination. The results presented in this chapter indicate that the microfluidic IHC protocol developed can provide the possibility of tailored cancer treatments as well as precise histopathological diagnosis using numerous specific biomarkers.

Protein analytical assays for diagnosing, monitoring, and choosing treatment for cancer patients

Cancer treatment is often hindered by inadequate methods for diagnosing the disease or insufficient predictive capacity regarding therapeutic efficacy. Targeted cancer treatments, including Bcr-Abl and EGFR kinase inhibitors, have increased survival for some cancer patients but are ineffective in other patients. In addition, many patients who initially respond to targeted inhibitor therapy develop resistance during the course of treatment. Molecular analysis of cancer cells has emerged as a means to tailor treatment to particular patients. While DNA analysis can provide important diagnostic information, protein analysis is particularly valuable because proteins are more direct mediators of normal and diseased cellular processes. In this review article, we discuss current and emerging protein assays for improving cancer treatment, including trends toward assay miniaturization and measurement of protein activity.

Micro-fluidic chip platform for the characterization of breast cancer cells using aptamer-assisted immunohistochemistry

We demonstrated a new QIHC (Quantitative Immunohistochemistry) microfluidic PDMS (Polydimethylsiloxane) platform by the introduction of the aptamer specific to the Fc region of the IgG antibody as a reporting probe. The aptamer was designed and synthesized. Various breast cancer cell lines were prepared as paraffin block slides, which were covered by a microfluidic PDMS platform to form a micro-reaction chamber. Primary antibodies specific to marker proteins (HER2, ER, PR, and ki-67) for breast cancer characterization were loaded in the micro-fluidic chip prior to the introduction of the aptamer. A master mixture of QNASBA (Quantitative Nucleic Acid Sequence Based Amplification) was used to quantify marker proteins by real time amplification of the aptamers. The quantitative results of aptamer amplification were linearly proportional to the concentrations of 4 different primary antibodies. The characterization results of the aptamer-assisted IHC using the microfluidic platform were well-correlated with those of conventional IHC for breast cancer cell lines (SK-BR-3, MCF-7, MDA-MB-231). Objective quantitative evaluations were carried out and compared with conventional results for real clinical samples.

Analysis of arecoline in Semen Arecae decoction pieces by microchip capillary electrophoresis with contactless conductivity detection

A new method for the determination of arecoline in Semen Arecae decoction pieces by microchip capillary electrophoresis with contactless conductivity detection (MCE-CCD) was proposed. The effects of various electrophoretic operating parameters on the analysis of arecoline were studied. Under the optimal conditions, arecoline was rapidly separated and detected in 1 min with good linearity over the concentration range of 20–1500 μM (r²=0.9991) and the detection limit of 5 μM (S/N=3). The method was used for the analysis of arecoline satisfactorily with a recovery of 96.8–104%.

Integrating contextual miRNA and protein signatures for diagnostic and treatment decisions in cancer

The promise of personalized medicine is highly dependent on the identification of biomarkers that inform diagnostic decisions and treatment options, as well as on the accurate, rapid and cost-effective detection and interpretation of these biomarkers. miRNAs, which are short noncoding regulatory RNAs, are rapidly emerging as a novel class of biomarkers with a unique set of biological and chemical properties that makes them very appealing candidates for theranostic applications in cancer. Since the utility of some protein-encoding gene biomarkers is already exploited in routine clinical practice, it will be important to identify areas in which miRNAs provide complementary or superior information to these existing (and other translational) biomarkers to enhance the diagnostic, prognostic and predictive power of molecular characterization of tumors. In this article, the challenges and opportunities for integration of miRNA-based assays in the clinical toolkit to improve care and management of patients afflicted with solid tumors will be discussed.

HistoFlex--a microfluidic device providing uniform flow conditions enabling highly sensitive, reproducible and quantitative in situ hybridizations

A microfluidic device (the HistoFlex) designed to perform and monitor molecular biological assays under dynamic flow conditions on microscope slide-substrates, with special emphasis on analyzing histological tissue sections, is presented. Microscope slides were reversibly sealed onto a cast polydimethylsiloxane (PDMS) insert, patterned with distribution channels and reaction chambers. Topology optimization was used to design reaction chambers with uniform flow conditions. The HistoFlex provided uniform hybridization conditions, across the reaction chamber, as determined by hybridization to microscope slides of spotted DNA microarrays when applying probe concentrations generally used in in situ hybridization (ISH) assays. The HistoFlex's novel ability in online monitoring of an in situ hybridization assay was demonstrated using direct fluorescent detection of hybridization to 18S rRNA. Tissue sections were not visually damaged during assaying, which enabled adapting a complete ISH assay for detection of microRNAs (miRNA). The effects of flow based incubations on hybridization, antibody incubation and Tyramide Signal Amplification (TSA) steps were investigated upon adapting the ISH assay for performing in the HistoFlex. The hybridization step was significantly enhanced using flow based incubations due to improved hybridization efficiency. The HistoFlex device enabled a fast miRNA ISH assay (3 hours) which provided higher hybridization signal intensity compared to using conventional techniques (5 h 40 min). We further demonstrate that the improved hybridization efficiency using the HistoFlex permits more complex assays e.g. those comprising sequential hybridization and detection of two miRNAs to be performed with significantly increased sensitivity. The HistoFlex provides a new histological analysis platform that will allow multiple and sequential assays to be performed under their individual optimum assay conditions. Images can subsequently be recorded either in combination or sequentially through the ability of the HistoFlex to monitor assays without disassembly.

[Recent development of microfluidic diagnostic technologies]

Microfluidic devices exhibit a great promising development in clinical diagnosis and disease screening due to their advantages of precise controlling of fluid flow, requirement of miniamount sample, rapid reaction speed and convenient integration. In this paper, the improvements of microfluidic diagnostic technologies in recent years are reviewed. The applications and developments of on-chip disease marker detection, microfluidic cell selection and cell drug metabolism, and diagnostic micro-devices are discussed.