Protein biochip systems for the clinical laboratory

Development of a dendrimer PAMAM‑based gold biochip for rapid and sensitive detection of endogenous IFN‑γ and anti‑IFN‑γ IgG in patients with hemophagocytic lymphohistiocytosis

Hemophagocytic lymphohistiocytosis (HLH) is a rare but severe disease characterized by immune hyperactivation and cytokine storm. Given the high mortality rate of HLH, there is a need for more effective diagnostic tools and treatments. The present study developed a dendrimer‑based protein biochip for rapid, sensitive and simultaneous detection of serum interferon (IFN)‑γ and endogenous anti‑IFN‑γ antibody (Ab) in patients with HLH. A gold biochip was modified with 1, 4‑phenylene diisothiocyanate (PDITC), polyamidoamine (PAMAM) or PDITC‑activated PAMAM. The optimal immobilization concentration for Ab capture and the reaction concentration for detecting Ab on the PDITC‑activated PAMAM‑modified biochip were 6.25 and 3.12 µg/ml, respectively; the limit of detection of IFN‑γ protein was 50 pg/ml. The efficiency of the protein‑probed biochip in detecting IFN‑γ and anti‑IFN‑γ Ab in serum samples from 77 patients with HLH was evaluated; the positive rates for IFN‑γ and anti‑IFN‑γ IgG Ab were 63.6% (49/77) and 61.0% (47/77), respectively. The present results demonstrated that the PDITC‑activated PAMAM‑modified biochip might be a sensitive tool for the specific detection of IFN‑γ and anti‑IFN‑γ Ab in serum, and might have clinical applicability for the diagnosis of HLH.

Availability-Driven Design of Hairpin Fuels and Small Interfering Strands for Leakage Reduction in Autocatalytic Networks

DNA-based circuits and computational tools offer great potential for advanced biomedical and technological applications. However, leakage, which is the production of an output in the absence of an input, widely exists in DNA network. As a new approach to leakage reduction, this study utilizes availability to reduce leakage in an entropy-driven autocatalytic DNA reaction networks. Here, we report the performance improvements resulting from direct tailoring of fuel strand availability through two novel approaches: (1) the addition of interfering domains to fuel strands, and (2) the introduction of separate small interfering strands. The best performing fuel designs resulted in increased performance ratios of up to 22%. Employing small interfering strands (5-12 nucleotides (nt)) improved the performance ratios by up to 21%. Furthermore, the stability of the network using either leakage reduction method matched well with computed availability and experimental results showing Spearman correlation coefficients of -0.84 for modified fuel strands and -0.92 for small interfering strands.

On-line hemodiafiltration did not induce an overproduction of oxidative stress and inflammatory cytokines in intensive care unit-acute kidney injury

Background

Though on-line intermittent hemodiafiltration (OL-IHDF) is a routine therapy for chronic dialysis patients, it is not yet widespread used in critically ill patients. This study was undergone to evaluate efficiency and tolerance of OL-IHDF and to appreciate inflammatory consequences of its use in intensive care unit (ICU)-acute kidney injury (AKI) patients.

Methods

In this prospective cohort study conducted in a medical academic ICU in France, 30 AKI patients who underwent OL-IHDF were included. OL-HDF used an ultrapure water production: AQ 1250 line with double reverse osmosis, a generator 5008 with a 1.8m² dialyzer with Polysulfone membrane (Fresenius Medical Care). Tolerance and efficiency of OL-IHDF were evaluated as well as its inflammatory risk by the measurement of plasma concentrations of proinflammatory (Interleukin 6, IL1β, IL8, Interferon γ) and anti-inflammatory (IL4, IL10) cytokines, Epidermal growth factor (EGF), Vascular Endothelial growth factor (VEGF) and Macrophage Chemoattractive Protein-1 (MCP-1) before and after sessions.

Results

Intradialytic hypotensive events were observed during 27/203 OL-IHDF sessions accounting for a mal-tolerated session’s rate at 13.3%. Mean delivered urea Kt/V per session was 1.12 ± 0.27 with a percentage of reduction for urea, creatinine, β2-microglobulin and cystatine C at 61.6 ± 8.8%, 55.3 ± 6.7%, 51.5 ± 8.7% and 44.5 ± 9.8% respectively. Production of superoxide anion by leukocytes, mean levels of pro- and anti-inflammatory cytokines and plasmatic concentrations of EGF, VEGF and MCP-1 did not differ before and after OL-IHDF sessions. We observed however a significant decrease of mean TNFα plasmatic concentrations from 8.2 ± 5.8 to 4.8 ± 3.5 pg/ml at the end of OL-IHDF.

Conclusions

OL-IHDF was not associated with an increase in pro and anti-inflammatory cytokines, oxidative stress or EGF, VEGF and MCP-1 in AKI patients and seems therefore a secure and feasible modality in ICUs.

Catch and release: integrated system for multiplexed detection of bacteria

An integrated system with automated immunomagnetic separation and processing of fluidic samples was demonstrated for multiplexed optical detection of bacterial targets. Mixtures of target-specific magnetic bead sets were processed in the NRL MagTrap with the aid of rotating magnet arrays that entrapped and moved the beads within the channel during reagent processing. Processing was performed in buffer and human serum matrixes with 10-fold dilutions in the range of 10(2)-10(6) cells/mL of target bacteria. Reversal of magnets' rotation post-processing released the beads back into the flow and moved them into the microflow cytometer for optical interrogation. Identification of the beads and the detection of PE fluorescence were performed simultaneously for multiplexed detection. Multiplexing was performed with specifically targeted bead sets to detect E. coli 0157.H7, Salmonella Common Structural Antigen, Listeria sp., and Shigella sp., dose-response curves were obtained, and limits of detection were calculated for each target in the buffer and clinical matrix. Additional tests demonstrated the potential for using the MagTrap to concentrate target from larger volumes of sample prior to the addition of assay reagents.

Low cost extraction and isothermal amplification of DNA for infectious diarrhea diagnosis

In order to counter the common perception that molecular diagnostics are too complicated to work in low resource settings, we have performed a difficult sample preparation and DNA amplification protocol using instrumentation designed to be operated without wall or battery power. In this work we have combined a nearly electricity-free nucleic acid extraction process with an electricity-free isothermal amplification assay to detect the presence of Clostridium difficile (C. difficile) DNA in the stool of infected patients. We used helicase-dependent isothermal amplification (HDA) to amplify the DNA in a low-cost, thermoplastic reaction chip heated with a pair of commercially available toe warmers, while using a simple Styrofoam insulator. DNA was extracted from known positive and negative stool samples. The DNA extraction protocol utilized an air pressure driven solid phase extraction device run using a standard bicycle pump. The simple heater setup required no electricity or battery and was capable of maintaining the temperature at 65°C±2°C for 55 min, suitable for repeatable HDA amplification. Experiments were performed to explore the adaptability of the system for use in a range of ambient conditions. When compared to a traditional centrifuge extraction protocol and a laboratory thermocycler, this disposable, no power platform achieved approximately the same lower limit of detection (1.25×10(-2) pg of C. difficile DNA) while requiring much less raw material and a fraction of the lab infrastructure and cost. This proof of concept study could greatly impact the accessibility of molecular assays for applications in global health.

Miniaturized technology for protein and nucleic acid point-of-care testing

The field of point-of-care (POC) testing technology is developing quickly and producing instruments that are increasingly reliable, while their size is being gradually reduced. Proteins are a common target for POC analyses and the detection of protein markers typically involves immunoassays aimed at detecting different groups of proteins such as tumor markers, inflammation proteins, and cardiac markers; but other techniques can also be used to analyze plasma proteins. In the case of nucleic acids, hybridization and amplification strategies can be used to record electromagnetic or electric signals. These techniques allow for the identification of specific viral or bacterial infections as well as specific cancers. In this review, we consider some of the latest advances in the analysis of specific nucleic acid and protein biomarkers, taking into account their trend toward miniaturization and paying special attention to the technology that can be implemented in future applications, such as lab-on-a-chip instruments.

A solvation-based screening approach for metabolite arrays

This paper explores a new method for screening metabolites in an array format based on relative polarity using selective solvent dissolution. A synthetic cocktail of metabolites was spotted onto a hydrophobic silicon surface, and solubilised with solvents of varying polarity. The metabolites retained on the silicon surface after the solvent treatments were detected using time-of-flight static secondary ion mass spectrometry (ToF-sSIMS). Solvent-specific metabolite retention was clearly evident on multivariate analysis of the dataset, using principal component analysis. Selective removal of metabolites was observed when solvents with different polarity were used, with the metabolite retention or removal in most cases correlating to the polarity of the solvent used, although consideration of other forces in operation may be needed to arrive at fully predictable behaviours. This approach provides the basis for development of a technique to separate complex metabolites into simpler constituents in a metabolite array prior to identification and quantification using mass spectrometry. It is an analytical approach that is intermediate between the more rapid but less informative direct analysis methods (such as DIMS) that do not involve any analyte separations and the more comprehensive but time consuming methods (such as GC- and LC-MS) that involve chromatographic or electrophoretic separations. The approach has the potential to be successfully developed for rapid, yet informative screening of metabolomes.

Particles and microfluidics merged: perspectives of highly sensitive diagnostic detection

There is a growing need for diagnostic technologies that provide laboratories with solutions that improve quality, enhance laboratory system productivity, and provide accurate detection of a broad range of infectious diseases and cancers. Recent advances in micro- and nanoscience and engineering, in particular in the areas of particles and microfluidic technologies, have advanced the "lab-on-a-chip" concept towards the development of a new generation of point-of-care diagnostic devices that could significantly enhance test sensitivity and speed. In this review, we will discuss many of the recent advances in microfluidics and particle technologies with an eye towards merging these two technologies for application in medical diagnostics. Although the potential diagnostic applications are virtually unlimited, the most important applications are foreseen in the areas of biomarker research, cancer diagnosis, and detection of infectious microorganisms.

Multiplexed detection of nucleic acids in a combinatorial screening chip

Multiplexed diagnostic testing has the potential to dramatically improve the quality of healthcare. Simultaneous measurement of health indicators and/or disease markers reduces turnaround time and analysis cost and speeds up the decision making process for diagnosis and treatment. At present, however, most diagnostic tests only provide information on a single indicator or marker. Development of efficient diagnostic tests capable of parallel screening of infectious disease markers could significantly advance clinical and diagnostic testing in both developed and developing parts of the world. Here, we report the multiplexed detection of nucleic acids as disease markers within discrete wells of a microfluidic chip using molecular beacons and total internal reflection fluorescence microscopy (TIRFM). Using a 4 × 4 array of 200 pL wells, we screened for the presence of four target single stranded oligonucleotides encoding for conserved regions of the genomes of four common viruses: human immunodeficiency virus-1 (HIV-1), human papillomavirus (HPV), Hepatitis A (Hep A) and Hepatitis B (Hep B). Target oligonucleotides are accurately detected and discriminated against alternative oligonucleotides with different sequences. This combinatorial chip represents a versatile platform for the development of clinical diagnostic tests for simultaneous screening, detection and monitoring of a wide range of biological markers of disease and health using minimal sample size.

[Highly sensitive method of detecting verotoxins produced by enterohaemorrhagic Escherichia coli O-157 : H7 using a protein chip]

Enterohaemorrhagic Escherichia coli O-157 : H7 produces verotoxins called Shiga toxin or Shiga-like toxin. The type 1 and type 2 toxins present different immunological and physicochemical characteristics, and cause symptoms such as watery diarrhea, bloody diarrhea, severe stomach ache, fever and vomiting. The toxins can be assayed by several methods, including ELISA and PCR, with some limitations as to sensitivity. In the present study, we used a ProteoChip, which requires smaller volumes of reagents and allows detection of lower concentrations of the toxins, compared with the conventional assay.

Invited Review Article: Review of centrifugal microfluidic and bio-optical disks

Spinning biodisks have advantages that make them attractive for specialized biochip applications. The two main classes of spinning biodisks are microfluidic disks and bio-optical compact disks (BioCD). Microfluidic biodisks take advantage of noninertial pumping for lab-on-a-chip devices using noninertial valves and switches under centrifugal and Coriolis forces to distribute fluids about the disks. BioCDs use spinning-disk interferometry, under the condition of common-path phase quadrature, to perform interferometric label-free detection of molecular recognition and binding. The optical detection of bound molecules on a disk is facilitated by rapid spinning that enables high-speed repetitive sampling to eliminate 1/f noise through common-mode rejection of intensity fluctuations and extensive signal averaging. Multiple quadrature classes have been developed, such as microdiffraction, in-line, phase contrast, and holographic adaptive optics. Thin molecular films are detected through the surface dipole density with a surface height sensitivity for the detection of protein spots that is approximately 1 pm. This sensitivity easily resolves a submonolayer of solid-support immobilized antibodies and their antigen targets. Fluorescence and light scattering provide additional optical detection techniques on spinning disks. Immunoassays have been applied to haptoglobin using protein A/G immobilization of antibodies and to prostate specific antigen. Small protein spots enable scalability to many spots per disk for high-throughput and highly multiplexed immonoassays.

Protein biochip array technology to monitor rituximab in rheumatoid arthritis

In rheumatoid arthritis (RA) there are currently no good indicators to predict a clinical response to rituximab. The purpose of this study was to monitor and determine the role of peripheral blood cytokine profiling in differentiating between a good versus poor response to rituximab in RA. Blood samples were collected at baseline and at 3 months from 46 RA patients who were treated with rituximab. Responders are defined by the presence of three of four American College of Rheumatology criteria: >or=20% decrease in C-reactive protein, visual analogical score of disease activity, erythrocyte sedimentation rate and improvement of the disease activity score (28) (four values) by >or=1.2 obtained at 3 months. Twelve cytokines were measured from serum collected on days 0 and 90 by proteomic array, including interleukin-6 (IL-6), tumour necrosis factor-alpha, IL-1a, IL-1b, IL-2, IL-8, interferon-gamma, IL-4, IL-10, monocyte chemoattractant protein-1, epidermal growth factor and vascular growth factor. We showed that C-reactive protein and IL-6 levels decrease significantly at 3 months in the responder group compared with baseline. At day 90 we identified a cytokine profile which differentiates responders and non-responders. High serum levels of two proinflammatory cytokines, monocyte chemoattractant protein-1 and epidermal growth factor, were significantly higher in the responder group at day 90 compared with non-responders. However, we were not able to identify a baseline cytokine profile predictive of a good response at 3 months. These findings suggest that cytokine profiling by proteomic analysis may be a promising tool for monitoring rituximab and may help in the future to identify responder RA patients.

Evolving 'omics' technologies for diagnostics of head and neck cancer

Squamous cell carcinoma of head and neck (SCCHN) is the sixth most common malignancy and is a major cause of cancer morbidity and mortality worldwide. As with most solid cancers, the cure rate for SCCHN is excellent if tumors are diagnosed early in the course of the disease. Early diagnosis of cancer remains difficult because of the lack of specific symptoms in early disease as well as the limited understanding of etiology and oncogenesis. Advances in proteomics and genomics contribute to the understanding of the pathophysiology of neoplasia, cancer diagnosis and anticancer drug discovery. The powerful 'omics' technologies have opened new avenues towards biomarker discovery, identification of signaling molecules associated with cell growth, cell death, cellular metabolism and early detection of cancer. Analysis of tumor-specific omics profiles provided a unique opportunity to diagnose, classify, and detect malignant disease; to better understand and define the behavior of specific tumors; and to provide direct and targeted therapy. These technologies however still require integration and standardization of techniques and validation against accepted clinical and pathologic parameters. This article provides a summary of technologies, potential clinical applications, and challenges of omics in head and neck cancer.

Protein biochip array technology for cytokine profiling predicts etanercept responsiveness in rheumatoid arthritis

In rheumatoid arthritis (RA) there are currently no useful indicators to predict a clinical response to tumour necrosis factor-alpha (TNF-alpha) blockade. The purpose of this study was to determine the role of peripheral blood cytokine profiling in differentiating between a good versus poor response to etanercept in RA. Peripheral blood samples were collected at baseline and at 3 months from 33 patients with active disease who were treated twice weekly by etanercept therapy. Responders are defined by the presence of three of four American College of Rheumatology criteria: > or =20% decrease in C-reactive protein (CRP), visual analogue score of disease activity, erythrocyte sedimentation rate and improvement of the disease activity score (28; four values) by > or =1.2 obtained at 3 months. Twelve cytokines were measured from serum collected on days 0 and 90 by proteomic array (protein biochip array, Investigator Evidence, Randox France), including interleukin (IL)-6, TNF-alpha, IL-1a, IL-1b, IL-2, IL-8, interferon-gamma, IL-4, IL-10, monocyte chemoattractant protein (MCP)-1, epidermal growth factor (EGF) and vascular endothelium growth factor. Our results showed that high serum levels of MCP-1 and EGF were associated with a response to etanercept. In addition, the increase of two combined parameters CRP and EGF was predictive of a response to etanercept treatment at 3 months (sensitivity: 87.5% and specificity: 75%, accuracy: 84.4%). These findings suggest that cytokine profiling by proteomic analysis before treatment initiation may help to identify a responder patient to TNF-alpha blocking agents in RA.

Synergism between particle-based multiplexing and microfluidics technologies may bring diagnostics closer to the patient

In the field of medical diagnostics there is a growing need for inexpensive, accurate, and quick high-throughput assays. On the one hand, recent progress in microfluidics technologies is expected to strongly support the development of miniaturized analytical devices, which will speed up (bio)analytical assays. On the other hand, a higher throughput can be obtained by the simultaneous screening of one sample for multiple targets (multiplexing) by means of encoded particle-based assays. Multiplexing at the macro level is now common in research labs and is expected to become part of clinical diagnostics. This review aims to debate on the “added value” we can expect from (bio)analysis with particles in microfluidic devices. Technologies to (a) decode, (b) analyze, and (c) manipulate the particles are described. Special emphasis is placed on the challenges of integrating currently existing detection platforms for encoded microparticles into microdevices and on promising microtechnologies that could be used to down-scale the detection units in order to obtain compact miniaturized particle-based multiplexing platforms.

Fine-tuning of the prediction of mortality in hemodialysis patients by use of cytokine proteomic determination

BACKGROUND AND OBJECTIVES

Inflammation-induced atherosclerosis and enhanced susceptibility to infection are linked to immune dysfunction and account for an important part of mortality in hemodialysis patients. This 4-yr prospective study aimed to use cytokine proteomic determination for predicting cardiovascular and noncardiovascular mortality in hemodialysis patients.

DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS

Levels of 12 cytokines were measured using a proteomic biochip system in 134 patients who were on stable hemodialysis and compared with a control group of 150 healthy volunteers. Cox proportional hazards regression analysis was used to determine the relationship between cytokine and clinical outcome.

RESULTS

A proinflammatory state characterized by decreased anti-/proinflammatory cytokine ratio was evidenced in hemodialysis patients compared with control subjects. After adjustment for age, gender, smoking, and high-sensitivity C-reactive protein levels, IL-6 and (IL-4+IL-10)/IL-6 ratio were associated with a significant and specific enhanced hazard ratio of cardiovascular mortality (hazard ratio 11.32 [95% confidence interval 2.52 to 50.90; P < 0.01] and hazard ratio 3.14 [95% confidence interval 1.20 to 8.22; P < 0.05], respectively, when comparing the third and first tertiles). It is interesting that (IL-4+IL-6+IL-10)/(IL-2+IFN-gamma) ratio, used as a marker of lymphocytes T helper subsets cytokine secretion, was associated only with noncardiovascular mortality (hazard ratio 4.93; 95% confidence interval 1.03 to 23.65; P < 0.05).

CONCLUSION

Beyond the strong prediction of cardiovascular mortality by IL-6, determination of cytokine ratios can be useful to identify hemodialysis patients with increased noncardiovascular mortality risk.

Ultrasensitive flow-based immunoassays using single-molecule counting

BACKGROUND

Immunoassay (IA) technology has expanded the clinical utility of protein biomarkers, but demands for increased sensitivity, dynamic reporting ranges, and small sample volumes have limited the potential clinical usefulness of many biomarkers. We assessed the performance, including limits of detection (LODs) and the dynamic reporting range, of an IA-based technology, Erenna Immunoassay System, for a series of biomarkers, including cardiac troponin I (cTnI).

METHODS

Erenna IAs were used with 10 different and clinically important biomarkers to ascertain the LOD with various sample sizes (10 microL to 200 microL).

RESULTS

The Erenna Immunoassay System generated LODs of 10-100 pg/L using 100 microL of sample. For cTnI, the LOD was 0.2 ng/L and a 10% CV was seen between 0.78 and 1.6 ng/L.

CONCLUSIONS

The Erenna IA-based technology reproducibly measures protein biomarkers with detection limits of 10-100 pg/L, with a dynamic range of >4.5 logs in sample volumes of 50-150 microL.

Microarray for serotyping of Bartonella species

Background

Bacteria of the genus Bartonella are responsible for a large variety of human and animal diseases. Serological typing of Bartonella is a method that can be used for differentiation and identification of Bartonella subspecies.

Results

We have developed a novel multiple antigenic microarray to serotype Bartonella strains and to select poly and monoclonal antibodies. It was validated using mouse polyclonal antibodies against 29 Bartonella strains. We then tested the microarray for serotyping of Bartonella strains and defining the profile of monoclonal antibodies.

Bartonella strains gave a strong positive signal and all were correctly identified. Screening of monoclonal antibodies towards the Gro EL protein of B. clarridgeiae identified 3 groups of antibodies, which were observed with variable affinities against Bartonella strains.

Conclusion

We demonstrated that microarray of spotted bacteria can be a practical tool for serotyping of unidentified strains or species (and also for affinity determination) by polyclonal and monoclonal antibodies. This could be used in research and for identification of bacterial strains.

Mass spectrometry-based "omics" technologies in cancer diagnostics

Many "omics" techniques have been developed for one goal: biomarker discovery and early diagnosis of human cancers. A comprehensive review of mass spectrometry-based "omics" approaches performed on various biological samples for molecular diagnosis of human cancers is presented in this article. Furthermore, the existing and potential problems/solutions (both de facto experimental and bioinformatic challenges), and future prospects have been extensively discussed. Although the use of present omic methods as diagnostic tools are still in their infant stage and consequently not ready for immediate clinical use, it can be envisaged that the "omics"-based cancer diagnostics will gradually enter into the clinic in next 10 years as an important supplement to current clinical diagnostics.

Microfluidic chip for fast bioassays-evaluation of binding parameters

A seven channel polystyrene (PS) microchip has been constructed using a micromilling machine and a high-temperature assembling. Protein A (PA) has been immobilized by a passive sorption on the microchannel walls. Two bioaffinity assays with human immunoglobulin G (hIgG) as a ligand have been carried out. (i) PA as the receptor and fluorescently labeled hIgG (FITC-hIgG) as the ligand, (ii) PA as the receptor with hIgG as the quantified ligand and fluorescently labeled goat anti-human IgG (FITC-gIgG) as the secondary ligand. One incubation step of the assays took only 5 min instead of hours typical for enzyme-linked immunosorbent assay applications. Calibration curves of the dependence of a fluorescence signal on the hIgG concentration in a sample have been obtained in one step due to a parallel arrangement of microchannels. A mathematical model of the PA-FITC-hIgG complex formation in the chip has been developed. The values of the kinetic constant of the PA-FITC-hIgG binding (k(on)=5.5 m(3) mol(-1) s(-1)) and the equilibrium dissociation constant of the formed complex (K(d)</=3x10(-6) mol m(-3)) have been obtained by fitting to experimental data. The proposed microchip enables fast evaluation of kinetic and equilibrium constants of ligand-receptor bioaffinity pairs and the ligand quantification. As the use of microfluidic chips for immunoassays is often limited by price, we used procedures and chemicals that allow for an inexpensive construction and operation of the microdevice, e.g., temperature assembling as a fabrication technique, detection via an ordinary digital camera, nonspecific polystyrene as a substrate, passive sorption of biomolecules as an immobilization technique, etc.