Quantitative multiplexed quantum dot immunohistochemistry

A manual multiplex immunofluorescence method for investigating neurodegenerative diseases

BACKGROUND

Neurodegenerative diseases feature stereotypical deposits of protein aggregates that selectively accumulate in vulnerable cells. The ability to simultaneously localize multiple targets in situ is critical to facilitate discovery and validation of pathogenic molecular pathways. Immunostaining methods enable in situ detection of specific targets. Effective stripping of antibodies, allowing successive rounds of staining while maintaining tissue adhesion and antigen integrity, is the main roadblock for enabling multiplex immunostaining in standard labs. Furthermore, stripping techniques require antibody-specific optimization, validation, and quality control steps.

NEW METHOD

Aiming to create protocols for multiplex localization of neurodegenerative-related processes, without the need for specialized equipment, we evaluated several antibody stripping techniques. We also recommend quality control steps to validate stripping efficacy and ameliorate concerns of cross-reactivity and false positives based on extensive testing.

RESULTS

A protocol using β-mercaptoethanol and SDS consistently enables reliable antibody stripping across multiple rounds of staining and minimizes the odds of cross-reactivity while preserving tissue adhesion and antigen integrity in human postmortem tissue.

COMPARISON WITH EXISTING METHODS

Our proposed method is optimal for standard lab settings and shows consistent efficacy despite the intricacies of suboptimal human postmortem tissue and the need to strip markers bound to highly aggregated proteins. Additionally, it incorporates quality control steps to validate antibody stripping.

CONCLUSIONS

Multiplex immunofluorescence methods for studying neurodegenerative diseases in human postmortem tissue are feasible even in standard laboratories. Nevertheless, evaluation of stripping parameters during optimization and validation phases of experiments is prudent.

Inhibition of DPP4 enhances inhibitory synaptic transmission through activating the GLP-1/GLP-1R signaling pathway in a rat model of febrile seizures

Dipeptidyl peptidase-IV (DPP4) is a cell surface serine peptidase widely expressed in the brain. Recent studies suggest that DPP4 contributes to the development of febrile seizures (FS); however, the underlying mechanism is still unclear. Thus, we investigated the role of DPP4 in the progression of FS at the molecular and electrophysiological levels using FS models in vivo and in vitro. Herein, we found that both the mRNA and protein levels of DPP4 were upregulated in the FS model. Administration of the pharmacological DPP4 inhibitor sitagliptin suppressed the hyperthermia-induced neuronal excitability as determined via whole-cell patch-clamp recordings in vitro. Interestingly, sitagliptin administration activated the glucagon-like peptide-1 (GLP-1)/GLP-1 receptor (GLP-1R) pathway by increasing the expression of GLP-1 and GLP-1R in a rat model of FS. Moreover, administration of the GLP-1R inhibitor exendin9-39 increased seizure severity, and sitagliptin reversed the effect, as shown in the electroencephalogram (EEG) and patch-clamp results in a rat model of FS. Furthermore, the GLP-1R-mediated reduction in GABAergic transmission was enhanced by sitagliptin and DPP4 knockdown through increasing miniature inhibitory post-synaptic currents (mIPSCs) in vitro accompanied by increased synaptic release of GABA in vivo. Taken together, our results demonstrate a role of DPP4 in regulating GABAergic transmission via the GLP-1/GLP-1R pathway. These findings indicated that DPP4 may represent a novel therapeutic strategy and target for FS.

A Kv1.3 channel-specific blocker alleviates neurological impairment through inhibiting T-cell activation in experimental autoimmune encephalomyelitis

AIM

Multiple sclerosis (MS) is a neurological autoimmune disorder characterized by mistaken attacks of inflammatory cells against the central nervous system (CNS), resulting in demyelination and axonal damage. Kv1.3 channel blockers can inhibit T-cell activation and have been designed for MS therapy. However, little is known about the effects of Kv1.3 blockers on protecting myelin sheaths/axons in MS. This study aimed at investigating the neuroprotection efficacy of a selective Kv1.3 channel blocker ImKTx88 (ImK) in MS animal model.

METHODS

Experimental autoimmune encephalomyelitis (EAE) rat model was established. The neuroprotective effect of ImK was assessed by immunohistochemistry and transmission electron microscopy (TEM). In addition, the antiinflammatory effect of ImK by suppressing T-cell activation was assessed by flow cytometry and ELISA in vitro.

RESULTS

Our results demonstrated that ImK administration ameliorated EAE clinical severity. Moreover, ImK increased oligodendrocytes survival, preserved axons, and myelin integrity and reduced the infiltration of activated T cells into the CNS. This protective effect of the peptide may be related to its suppression of autoantigen-specific T-cell activation via calcium influx inhibition.

CONCLUSION

ImK prevents neurological damage by suppressing T-cell activation, suggesting the applicability of this peptide in MS therapy.

Emerging Themes in Image Informatics and Molecular Analysis for Digital Pathology

Pathology is essential for research in disease and development, as well as for clinical decision making. For more than 100 years, pathology practice has involved analyzing images of stained, thin tissue sections by a trained human using an optical microscope. Technological advances are now driving major changes in this paradigm toward digital pathology (DP). The digital transformation of pathology goes beyond recording, archiving, and retrieving images, providing new computational tools to inform better decision making for precision medicine. First, we discuss some emerging innovations in both computational image analytics and imaging instrumentation in DP. Second, we discuss molecular contrast in pathology. Molecular DP has traditionally been an extension of pathology with molecularly specific dyes. Label-free, spectroscopic images are rapidly emerging as another important information source, and we describe the benefits and potential of this evolution. Third, we describe multimodal DP, which is enabled by computational algorithms and combines the best characteristics of structural and molecular pathology. Finally, we provide examples of application areas in telepathology, education, and precision medicine. We conclude by discussing challenges and emerging opportunities in this area.

Quantum dot as probe for disease diagnosis and monitoring

Semiconductor quantum dots (QD) possess unique optical and electric properties like size-tunable light emission, narrow emission range, high brightness and photostability. Recent research advances have minimized the toxicity of QDs and they are successfully used in in vitro and in vivo imaging. Encapsulation of QDs into polymeric nanoparticles and linking them with targeting ligands enabled the detection of tumors and cancer cells in vivo. QD-antibody conjugates were successfully used in monitoring and diagnosis of HIV and myocardial infarction. Application of near infrared (NIR) QDs was found to minimize the absorption and scattering of light by native tissues thus rendering them suitable in deep tissue analysis. Aggregation and endosomal sequestration of QDs pose major challenges for the effective delivery of QDs to the cell cytosol. Toxicity minimization and effective delivery strategies may further increase their suitability for utilization in disease diagnosis. New synthesis of QDs may provide new types of bioconjugates of QDs to biomolecules, which leads to a variety of applications to many challenged research areas. QDs with narrow emission wavelength ranges are very suitable for monitoring multiple cellular targets simultaneously, and still remain the best known probes for imaging as an alternative to traditional fluorophores in disease diagnosis.

Quantum dots: bright and versatile in vitro and in vivo fluorescence imaging biosensors

Colourful cells and tissues: semiconductor quantum dots and their versatile applications in multiplexed bioimaging research.

Addressing Key Technical Aspects of Quantum Dot Probe Preparation for Bioassays

Fluorescent semiconductor nanoparticles, or quantum dots, have become a promising platform for the engineering of biofunctional probes for a variety of biomedical applications, ranging from multicolor imaging to single-molecule tracking to traceable drug delivery. Advances in organometallic synthesis have enabled preparation of hydrophobic quantum dots with high quantum yields and narrow size distribution, offering bright optical materials with narrow size-tunable emission profiles. At the same time, polymer encapsulation procedures provided a simple and versatile methodology for transferring hydrophobic nanoparticles into physiologically-relevant aqueous buffers. Taken together, hydrophobic nanoparticle platforms and polymer encapsulation should offer great flexibility for implementation of novel probe designs. However, the success of the encapsulation and purification depends on many factors often overlooked in the scientific literature, such as close match between nanoparticle and polymer physicochemical properties and dimensions, slow dynamics of polymer arrangement on the nanoparticle surface, and the size and charge similarity of resultant polymer-coated quantum dots and empty byproduct polymer micelles. To make this general hydrophobic nanoparticle modification strategy accessible by a broad range of biomedical research groups, we focus on the important technical aspects of nanoparticle polymer encapsulation, purification, bioconjugation, and characterization.

Spraying quantum dot conjugates in the colon of live animals enabled rapid and multiplex cancer diagnosis using endoscopy

The detection of colon cancer using endoscopy is widely used, but the interpretation of the diagnosis is based on the clinician's naked eye. This is subjective and can lead to false detection. Here we developed a rapid and accurate molecular fluorescence imaging technique using antibody-coated quantum dots (Ab-QDs) sprayed and washed simultaneously on colon tumor tissues inside live animals, subsequently excited and imaged by endoscopy. QDs were conjugated to matrix metalloproteinases (MMP) 9, MMP 14, or carcinoembryonic antigen (CEA) Abs with zwitterionic surface coating to reduce nonspecific bindings. The Ab-QD probes can diagnose tumors on sectioned mouse tissues, fresh mouse colons stained ex vivo and also in vivo as well as fresh human colon adenoma tissues in 30 min and can be imaged with a depth of 100 μm. The probes successfully detected not only cancers that are readily discernible by bare eyes but also hyperplasia and adenoma regions. Sum and cross signal operations provided postprocessed images that can show complementary information or regions of high priority. This multiplexed quantum dot, spray-and-wash, and endoscopy approach provides a significant advantage for detecting small or flat tumors that may be missed by conventional endoscopic examinations and bestows a strategy for the improvement of cancer diagnosis.

Multiplexed immunohistochemistry, imaging, and quantitation: a review, with an assessment of Tyramide signal amplification, multispectral imaging and multiplex analysis

Tissue sections offer the opportunity to understand a patient's condition, to make better prognostic evaluations and to select optimum treatments, as evidenced by the place pathology holds today in clinical practice. Yet, there is a wealth of information locked up in a tissue section that is only partially accessed, due mainly to the limitations of tools and methods. Often tissues are assessed primarily based on visual analysis of one or two proteins, or 2-3 DNA or RNA molecules. Even while analysis is still based on visual perception, image analysis is starting to address the variability of human perception. This is in contrast to measuring characteristics that are substantially out of reach of human perception, such as parameters revealed through co-expression, spatial relationships, heterogeneity, and low abundance molecules. What is not routinely accessed is the information revealed through simultaneous detection of multiple markers, the spatial relationships among cells and tissue in disease, and the heterogeneity now understood to be critical to developing effective therapeutic strategies. Our purpose here is to review and assess methods for multiplexed, quantitative, image analysis based approaches, using new multicolor immunohistochemistry methods, automated multispectral slide imaging, and advanced trainable pattern recognition software. A key aspect of our approach is presenting imagery in a workflow that engages the pathologist to utilize the strengths of human perception and judgment, while significantly expanding the range of metrics collectable from tissue sections and also provide a level of consistency and precision needed to support the complexities of personalized medicine.

Antigen retrieval, blocking, detection and visualisation systems in immunohistochemistry: a review and practical evaluation of tyramide and rolling circle amplification systems

To achieve specificity and sensitivity using immunohistochemistry it is necessary to combine the application of validated primary antibodies with optimised pre-treatment, detection and visualisation steps. The influence of these surrounding procedures is reviewed. A practical evaluation of tyramide signal amplification and rolling circle amplification detection methods is provided in which formalin fixed paraffin embedded sections of adenocarcinomas of breast, colon and lung together with squamous metaplasia of lung were immunostained with CD20 and CK19 primary antibodies. The results indicate that the detection systems are of comparable sensitivity and specificity.

A novel, automated technology for multiplex biomarker imaging and application to breast cancer

AIMS

Multiplexed immunofluorescence is a powerful tool for validating multigene assays and understanding the complex interplay of proteins implicated in breast cancer within a morphological context. We describe a novel technology for imaging an extended panel of biomarkers on a single, formalin-fixed paraffin-embedded breast sample and evaluating biomarker interaction at a single-cell level, and demonstrate proof-of-concept on a small set of breast tumours, including those which co-express hormone receptors with Her2/neu and Ki-67.

METHODS AND RESULTS

Using a microfluidic flow cell, reagent exchange was automated and consisted of serial rounds of staining with dye-conjugated antibodies, imaging and chemical deactivation. A two-step antigen retrieval process was developed to satisfy all epitopes simultaneously, and key parameters were optimized. The imaging sequence was applied to seven breast tumours, and compared with conventional immunohistochemistry. Single-cell correlation analysis was performed with automated image processing.

CONCLUSIONS

We have described a novel platform for evaluating biomarker co-localization. Expression in multiplexed images is consistent with conventional immunohistochemistry. Automation reduces inconsistencies in staining and positional shifts, while the fluorescent dye cycling approach dramatically expands the number of biomarkers which can be visualized and quantified on a single tissue section.

Multispectral Imaging

The field of anatomic pathology has changed significantly over the last decades and, as a result of the technological developments in molecular pathology and genetics, has had increasing pressures put on it to become quantitative and to provide more information about protein expression on a cellular level in tissue sections. Multispectral imaging (MSI) has a long history as an advanced imaging modality and has been used for over a decade now in pathology to improve quantitative accuracy, enable the analysis of multicolor immunohistochemistry, and drastically reduce the impact of contrast-robbing tissue autofluorescence common in formalin-fixed, paraffin-embedded tissues. When combined with advanced software for the automated segmentation of different tissue morphologies (eg, tumor vs stroma) and cellular and subcellular segmentation, MSI can enable the per-cell quantitation of many markers simultaneously. This article covers the role that MSI has played in anatomic pathology in the analysis of formalin-fixed, paraffin-embedded tissue sections, discusses the technological aspects of why MSI has been adopted, and provides a review of the literature of the application of MSI in anatomic pathology.

Multicolor multicycle molecular profiling with quantum dots for single-cell analysis

Here we present a detailed protocol for molecular profiling of individual cultured mammalian cells using multicolor multicycle immunofluorescence with quantum dot probes. It includes instructions for cell culture growth and processing (2 h + 48-72 h for cell growth), preparation and characterization of universal quantum dot probes (4.5 h + overnight incubation), cyclic cell staining (∼4.5 h per cycle) and image analysis (varies by application). The use of quantum dot fluorescent probes enables highly multiplexed, robust quantitative molecular imaging with a conventional fluorescence microscopy setup, whereas the probe preparation methodology, using a self-assembly between protein A-decorated universal quantum dots and intact primary antibodies, offers a fast, simple and purification-free route for an on-demand preparation of antibody-functionalized quantum dot libraries. As a result, this protocol can be used by biomedical researchers for a variety of cell staining applications, and, with further optimization, for staining of other biological specimens (e.g., clinical tissue sections).

Quantum dot imaging for HSP70 and HSF‑1 kinetics in SCC‑25 cells with or without leucine deprivation following heat shock

The aim of this study was to develop a quantum dot-based approach for heat shock protein 70 (HSP70) and heat shock factor 1 (HSF-1) kinetics following heat shock, and to discover approaches to thermotherapy based on disrupting the effect of activation of HSF-1 and the accumulation of HSP70 by leucine deprivation. SCC-25 cells cultured with limiting leucine or normal leucine were stressed at 42˚C for 30 min, and were cultured for 2, 4, 6, 8 and 10 h, respectively. The expression of HSP70 and HSF-1 was observed using confocal laser microscopy and semi-quantitative analysis was performed by Image-Pro Plus. At 6 h after heating, HSF-1 in cells cultured with normal leucine was activated and translocated from the cytosol to the nucleus, and the synthesis of HSP70 reached the maximum value and had a tendency to gather in the nucleus. However, in cells cultured with limiting leucine, HSF-1 activity decreased and accumulation of HSP70 was not found. Leucine deprivation results in the inactivation of HSF-1 leading to slight accumulation of HSP70 and no tendency to gather in the nucleus. Thus, HSF-1 may serve as a novel therapeutic target in the treatment of oral cancer.

Induction of brain CYP2E1 by chronic ethanol treatment and related oxidative stress in hippocampus, cerebellum, and brainstem

Ethanol is one of the most commonly abused substances, and oxidative stress is an important causative factor in ethanol-induced neurotoxicity. Cytochrome P450 2E1 (CYP2E1) is involved in ethanol metabolism in the brain. This study investigates the role of brain CYP2E1 in the susceptibility of certain brain regions to ethanol neurotoxicity. Male Wistar rats were intragastrically treated with ethanol (3.0 g/kg, 30 days). CYP2E1 protein, mRNA expression, and catalytic activity in various brain regions were respectively assessed by immunoblotting, quantitative quantum dot immunohistochemistry, real-time RT-PCR, and LC-MS. The generation of reactive oxygen species (ROS) was analyzed using a laser confocal scanning microscope. The hippocampus, cerebellum, and brainstem were selectively damaged after ethanol treatment, indicated by both lactate dehydrogenase (LDH) activity and histopathological analysis. Ethanol markedly increased the levels of CYP2E1 protein, mRNA expression, and activity in the hippocampus and cerebellum. CYP2E1 protein and activity were significantly increased by ethanol in the brainstem, with no change in mRNA expression. ROS levels induced by ethanol paralleled the enhanced CYP2E1 proteins in the hippocampus, granular layer and white matter of cerebellum as well as brainstem. Brain CYP2E1 activity was positively correlated with the damage to the hippocampus, cerebellum, and brainstem. These results suggest that the selective sensitivity of brain regions to ethanol neurodegeneration may be attributed to the regional and cellular-specific induction of CYP2E1 by ethanol. The inhibition of CYP2E1 levels may attenuate ethanol-induced oxidative stress via ROS generation.

Tapping the potential of quantum dots for personalized oncology: current status and future perspectives

Cancer is one of the most serious health threats worldwide. Personalized oncology holds potential for future cancer care in clinical practice, where each patient could be delivered individualized medicine on the basis of key biological features of an individual tumor. One of the most urgent problems is to develop novel approaches that incorporate the increasing molecular information into the understanding of cancer biological behaviors for personalized oncology. Quantum dots are a heterogeneous class of engineered fluorescent nanoparticles with unique optical and chemical properties, which make them promising platforms for biomedical applications. With the unique optical properties, the utilization of quantum dot-based nanotechnology has been expanded into a wide variety of attractive biomedical applications for cancer diagnosis, monitoring, pathogenesis, treatment, molecular pathology and heterogeneity in combination with cancer biomarkers. Here, we focus on the clinical application of quantum dot-based nanotechnology in personalized oncology, covering topics on individualized cancer diagnosis and treatment by in vitro and in vivo molecular imaging technologies, and in-depth understanding of the biological behaviors of tumors from a nanotechnology perspective. In addition, the major challenges in translating quantum dot-based nanotechnology into clinical application and promising future directions in personalized oncology are also discussed.

The use of quantum dots for immunochemistry applications

Immunocytochemistry and histochemistry are two most valuable immunochemistry techniques routinely used in biological laboratories. These techniques rely on the use of antibodies to label epitopes of interest in cells. At present, there is a wide range of commercially available organic dyes for labeling antibodies. However, limited extinction coefficients of organic dyes often make it difficult to achieve the optimal exposure and therefore fluorescence detection limit. Quantum dots (QDs) are fluorescent semiconductor nanocrystals which are advantageous over the organic fluorescent dyes in many aspects, principally their long-term luminescence stability, high brightness, and multicolor detection. Here, we describe the use of QDs for immunocytochemistry applications. We used three different antibodies-anti-β-tubulin monoclonal antibody for visualizing the microtubule network, the GM130 antibody for staining the Golgi complex, and the EEA1 antibody for detecting the endosomal system. We use the anti-mouse IgG antibody directly conjugated to QD655 quantum dots or anti-mouse IgG conjugated to biotin for tertiary detection with streptavidin-conjugated QD655.

Semiconductor quantum dots for in vitro diagnostics and cellular imaging

The need for companion diagnostics, point-of-care testing (POCT) and high-throughput screening in clinical diagnostics and personalized medicine has pushed the need for more biological information from a single sample at extremely low concentrations and volumes. Optical biosensors based on semiconductor quantum dots (QDs) can answer these requirements because their unique photophysical properties are ideally suited for highly sensitive multiplexed detection. Many different biological systems have been successfully scrutinized with a large variety of QDs over the past decade but their future as widely applied commercial biosensors is still open. In this review, we highlight recent in vitro diagnostic and cellular imaging applications of QDs and discuss milestones and obstacles on their way toward integration into real-life diagnostic and medical applications.

Bioconjugated and cross-linked bionanostructures for bifunctional immunohistochemical labeling

The present study describes the development and use of a new bioconjugate combining targeted quantum dot labeling with an immunoperoxidase method and explores whether these bioconjugates could specifically and effectively label Cu/Zn superoxide dismutase (SOD1). The new bioconjugate is designed for the examination of samples both under fluorescent and bright-field microscopy at the same time. For this purpose chlorobis(2-2'-bipyridyl) methacryloyl tyrosine-ruthenium(II) and bis (2-2'-bipyridyl) methacryloyltyrosine-methacryloyltryptophan-ruthenium (II) photosensitive monomers and photosensitive poly(Bis (2-2'-bipyridyl)) methacryloyltyrosine-methacryloyltryptophan-ruthenium(II) were synthesized and characterized. The anti-SOD1 antibody and horseradish peroxidase (HRD) conjugated quantum dots were prepared by using this polymer. The anti-SOD1 antibody and HRD conjugated quantum dots were used in labeling and imaging of SOD1 in rat liver sections. Quantum dot particles were observed as a bright fluorescence in their specific binding locations inside the hepatocytes. The HRD-diaminobenzidine reaction product was observed as brown-colored particles at the same locations under bright-field microscopy. Structural details of the tissue sections could be examined at the same time. The conjugation protocol is simple; the bioconjugate is applicable for efficient cell labeling and can be adapted for imaging of other targets in different tissues. Also, the prepared nanobioconjugates have mechanic stability and can be used for a long period.

Multiplexed quantum dot labeling of activated c-Met signaling in castration-resistant human prostate cancer

The potential application of multiplexed quantum dot labeling (MQDL) for cancer detection and prognosis and monitoring therapeutic responses has attracted the interests of bioengineers, pathologists and cancer biologists. Many published studies claim that MQDL is effective for cancer biomarker detection and useful in cancer diagnosis and prognosis, these studies have not been standardized against quantitative biochemical and molecular determinations. In the present study, we used a molecularly characterized human prostate cancer cell model exhibiting activated c-Met signaling with epithelial to mesenchymal transition (EMT) and lethal metastatic progression to bone and soft tissues as the gold standard, and compared the c-Met cell signaling network in this model, in clinical human prostate cancer tissue specimens and in a castration-resistant human prostate cancer xenograft model. We observed c-Met signaling network activation, manifested by increased phosphorylated c-Met in all three. The downstream survival signaling network was mediated by NF-κB and Mcl-1 and EMT was driven by receptor activator of NF-κB ligand (RANKL), at the single cell level in clinical prostate cancer specimens and the xenograft model. Results were confirmed by real-time RT-PCR and western blots in a human prostate cancer cell model. MQDL is a powerful tool for assessing biomarker expression and it offers molecular insights into cancer progression at both the cell and tissue level with high degree of sensitivity.

CdTe and CdSe quantum dots cytotoxicity: a comparative study on microorganisms

Quantum dots (QDs) are colloidal semiconductor nanocrystals of a few nanometers in diameter, being their size and shape controlled during the synthesis. They are synthesized from atoms of group II–VI or III–V of the periodic table, such as cadmium telluride (CdTe) or cadmium selenium (CdSe) forming nanoparticles with fluorescent characteristics superior to current fluorophores. The excellent optical characteristics of quantum dots make them applied widely in the field of life sciences. Cellular uptake of QDs, location and translocation as well as any biological consequence, such as cytotoxicity, stimulated a lot of scientific research in this area. Several studies pointed to the cytotoxic effect against micoorganisms. In this mini-review, we overviewed the synthesis and optical properties of QDs, and its advantages and bioapplications in the studies about microorganisms such as protozoa, bacteria, fungi and virus.

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.

Louis ZE, Becker-Catania SG. Simplistic attachment and multispectral imaging with semiconductor nanocrystals

Advances in spectral deconvolution technologies are rapidly enabling researchers to replace or enhance traditional epifluorescence microscopes with instruments capable of detecting numerous markers simultaneously in a multiplexed fashion. While significantly expediting sample throughput and elucidating sample information, this technology is limited by the spectral width of common fluorescence reporters. Semiconductor nanocrystals (NC’s) are very bright, narrow band fluorescence emitters with great potential for multiplexed fluorescence detection, however the availability of NC’s with facile attachment chemistries to targeting molecules has been a severe limitation to the advancement of NC technology in applications such as immunocytochemistry and immunohistochemistry. Here we report the development of simple, yet novel attachment chemistries for antibodies onto NC’s and demonstrate how spectral deconvolution technology enables the multiplexed detection of 5 distinct NC-antibody conjugates with fluorescence emission wavelengths separated by as little as 20 nm.

MALDI tissue imaging: from biomarker discovery to clinical applications

Matrix-assisted laser desorption ionization (MALDI) imaging mass spectrometry (IMS) is a powerful tool for the generation of multidimensional spatial expression maps of biomolecules directly from a tissue section. From a clinical proteomics perspective, this method correlates molecular detail to histopathological changes found in patient-derived tissues, enhancing the ability to identify candidates for disease biomarkers. The unbiased analysis and spatial mapping of a variety of molecules directly from clinical tissue sections can be achieved through this method. Conversely, targeted IMS, by the incorporation of laser-reactive molecular tags onto antibodies, aptamers, and other affinity molecules, enables analysis of specific molecules or a class of molecules. In addition to exploring tissue during biomarker discovery, the integration of MALDI-IMS methods into existing clinical pathology laboratory practices could prove beneficial to diagnostics. Querying tissue for the expression of specific biomarkers in a biopsy is a critical component in clinical decision-making and such markers are a major goal of translational research. An important challenge in cancer diagnostics will be to assay multiple parameters in a single slide when tissue quantities are limited. The development of multiplexed assays that maximize the yield of information from a small biopsy will help meet a critical challenge to current biomarker research. This review focuses on the use of MALDI-IMS in biomarker discovery and its potential as a clinical diagnostic tool with specific reference to our application of this technology to prostate cancer.

Multiparametric luminescence method for quantitative cell surface protein expression analysis and imaging

A luminometric method for quantitative cell surface protein expression analysis has been developed in a microtiter plate format. The method is based on immunocytochemistry, the use of long-lived europium(III) and terbium(III) chelates and platinum(II) porphyrin luminescence labels in addition to short-lived syto13 DNA stain, and detection of photoluminescence emission from adhered cells by both time-resolved luminescence and conventional fluorescence. After the immunoreactions, the wells were evaporated to dryness, allowing repeated and postponed luminescence analysis even after months and cellular protein localization studies by microscopy imaging. The multiparametric method assayed the cell surface expression of ß1-integrin, E-selectin and intercellular adhesion molecule 1 (ICAM-1) in HUVE cells (human umbilical vein endothelial cells). The expression of E-selectin and ICAM-1 was enhanced by treating HUVECs with tumor necrosis factor α (TNF-α), while the expression level of ß1-integrin remained unchanged. The sensitivity limit of TNF-α detection by the method was ca. 1 pg/ml and the Z'-factors for the quantification of E-selectin and ICAM-1 were >0.7 suggesting a highly robust method. The novel approach proposed in this paper can be potentially applied to cell surface protein expression analysis in screening applications combined with localization studies of the target proteins by fluorescence microscopy imaging.

Quantum dots brighten biological imaging

Quantum dots (QDs) are novel photostable semiconductor nanocrystals possessing wide excitation spectra and narrow, symmetrical emission spectra and can be conjugated to a wide range of biological targets, including proteins, antibodies and nucleic acid probes. These characteristics have provoked considerable interest in their use for bioimaging. Much investigation has been performed into their use for multiplex immunohistochemistry and in situ hybridisation which, when combined with multispectral imaging, has enabled quantitation and colocalisation of gene expression in clinical tissue. Many advances have recently been made using QDs for live cell and in vivo imaging, in which QD-labelled molecules can be tracked and visualised in 3-D. This review aims to outline the beneficial properties presented by QDs along with important advances in their biological application.

Multiplexed detection and characterization of rare tumor cells in Hodgkin's lymphoma with multicolor quantum dots

The multicolor and multiplexing capabilities of semiconductor quantum dots (QDs) are most promising for improving the sensitivity and specificity of in vitro molecular and cellular diagnostics. Here, we report the use of multiplexed QDs and wavelength-resolved imaging to detect and characterize a class of low-abundant tumor cells in Hodgkin's lymphoma. Known as the Hodgkin's and Reed-Sternberg (HRS) cells, this class of malignant cells is a pathological hallmark in clinical diagnosis, but it comprises only about 1% of the heterogeneous infiltrating cells in lymph node tissues. To overcome this cellular heterogeneity and rarity problem, we have developed multicolor QD-antibody conjugates to simultaneously detect a panel of four protein biomarkers (CD15, CD30, CD45, and Pax5) directly on human tissue biopsies. This multiplexing approach allows rapid detection and differentiation of rare HRS cells from infiltrating immune cells such as T and B lymphocytes. We have also carried out clinical translation studies involving six confirmed Hodgkin's lymphoma patients, two suspicious lymphoma cases, and two patients with reactive lymph nodes (but not lymphoma). The results indicate that a distinct QD staining pattern (CD15 positive, CD30 positive, CD45 negative, and Pax5 positive) can be used to not only detect Hodgkin's lymphoma but also differentiate it from benign lymphoid hyperplasia.

Adding value to liver (and allograft) biopsy evaluation using a combination of multiplex quantum dot immunostaining, high-resolution whole-slide digital imaging, and automated image analysis

Various technologies including nucleic acid, protein, and metabolic array analyses of blood, liver tissue, and bile are emerging as powerful tools in the study of hepatic pathophysiology. The entire lexicon of liver disease, however, has been written using classical hematoxylin-eosin staining and light microscopic examination. The authors' goal is to develop new tools to enhance histopathologic examination of liver tissue that would enrich the information gained from liver biopsy analysis, enable quantitative analysis, and bridge the gap between various "-omics" tools and interpretation of routine liver biopsy results. This article describes the progress achieved during the past 2 years in developing multiplex quantum dot (nanoparticle) staining and combining it with high-resolution whole-slide imaging using a slide scanner equipped with filters to capture 9 distinct fluorescent signals for multiple antigens. The authors first focused on precise characterization of leukocyte subsets, but soon realized that the data generated were beyond the practical limits that could be properly evaluated, analyzed, and interpreted visually by a pathologist. Therefore, the authors collaborated with the open source FARSIGHT image analysis project (http://www.farsight-toolkit.org). FARSIGHT's goal is to develop and disseminate the next-generation toolkit of automated image analysis methods to enable quantification of molecular biomarkers on a cell-by-cell basis from multiparameter images. The resulting data can be used for histocytometric studies of the complex and dynamic tissue microenvironments that are of biomedical interest. The authors envisage that these tools will eventually be incorporated into the routine practice of surgical pathology and precipitate a revolution in the specialty.

Use of IgY antibodies and semiconductor nanocrystal detection in cancer biomarker quantitation

Biomarkers play a pivotal role in the early detection and diagnosis of cancer. Accurate quantitation of certain biomarkers is crucial to reach correct treatment decisions. In practice, immunohistochemistry (IHC) remains the most important diagnostic technique to evaluate protein biomarker expression in tissue biopsies. However, IHC has largely been qualitative. Low specificity of the mammalian IgG antibodies used to capture the analytes and instability of fluorescence from the organic dyes used as the detecting agents are among the major factors that have impeded the development of quantitative IHC. Avian IgY antibodies have many attractive biochemical, immunological and production advantages over IgGs and are, therefore, better substitutes in diagnostic applications. Using IgY in immunoassays can potentially eliminate false positives and often results in low background and interference. Quantum dots (QDs) have recently emerged as a novel class of fluorophores, promising for many biomedical imaging applications. Fluorescence from QDs is significantly brighter and more photostable than organic dyes. In addition, QDs offer the capacity of multiplexed detection of several biomarkers simultaneously. Combining the high sensitivity and specificity of IgY antibodies and the high brightness and photostability of QDs in IHC has been demonstrated to improve biomarker detection and quantitation.

Molecular mapping of tumor heterogeneity on clinical tissue specimens with multiplexed quantum dots

Tumor heterogeneity is one of the most important and challenging problems not only in studying the mechanisms of cancer development but also in developing therapeutics to eradicate cancer cells. Here we report the use of multiplexed quantum dots (QDs) and wavelength-resolved spectral imaging for molecular mapping of tumor heterogeneity on human prostate cancer tissue specimens. By using a panel of just four protein biomarkers (E-cadherin, high-molecular-weight cytokeratin, p63, and alpha-methylacyl CoA racemase), we show that structurally distinct prostate glands and single cancer cells can be detected and characterized within the complex microenvironments of radical prostatectomy and needle biopsy tissue specimens. The results reveal extensive tumor heterogeneity at the molecular, cellular, and architectural levels, allowing direct visualization of human prostate glands undergoing structural transitions from a double layer of basal and luminal cells to a single layer of malignant cells. For clinical diagnostic applications, multiplexed QD mapping provides correlated molecular and morphological information that is not available from traditional tissue staining and molecular profiling methods.

Breast cancer diagnosis using a microfluidic multiplexed immunohistochemistry platform

Background

Biomarkers play a key role in risk assessment, assessing treatment response, and detecting recurrence and the investigation of multiple biomarkers may also prove useful in accurate prediction and prognosis of cancers. Immunohistochemistry (IHC) has been a major diagnostic tool to identify therapeutic biomarkers and to subclassify breast cancer patients. However, there is no suitable IHC platform for multiplex assay toward personalized cancer therapy. Here, we report a microfluidics-based multiplexed IHC (MMIHC) platform that significantly improves IHC performance in reduction of time and tissue consumption, quantification, consistency, sensitivity, specificity and cost-effectiveness.

Methodology/Principal Findings

By creating a simple and robust interface between the device and human breast tissue samples, we not only applied conventional thin-section tissues into on-chip without any additional modification process, but also attained perfect fluid control for various solutions, without any leakage, bubble formation, or cross-contamination. Four biomarkers, estrogen receptor (ER), human epidermal growth factor receptor 2 (HER2), progesterone receptor (PR) and Ki-67, were examined simultaneously on breast cancer cells and human breast cancer tissues. The MMIHC method improved immunoreaction, reducing time and reagent consumption. Moreover, it showed the availability of semi-quantitative analysis by comparing Western blot. Concordance study proved strong consensus between conventional whole-section analysis and MMIHC (n = 105, lowest Kendall's coefficient of concordance, 0.90). To demonstrate the suitability of MMIHC for scarce samples, it was also applied successfully to tissues from needle biopsies.

Conclusions/Significance

The microfluidic system, for the first time, was successfully applied to human clinical tissue samples and histopathological diagnosis was realized for breast cancers. Our results showing substantial agreement indicate that several cancer-related proteins can be simultaneously investigated on a single tumor section, giving clear advantages and technical advances over standard immunohistochemical method. This novel concept will enable histopathological diagnosis using numerous specific biomarkers at a time even for small-sized specimens, thus facilitating the individualization of cancer therapy.

In situ visualization of gene expression using polymer-coated quantum-dot-DNA conjugates

Imaging of specific mRNA targets in cells is of great importance in understanding gene expression and cell signaling processes. Subcellular localization of mRNA is known as a universal mechanism for cells to sequester specific mRNA for high production of required proteins. Various gene expressions in Drosophila cells are studied using quantum dots (QDs) and the fluorescence in situ hybridization (FISH) method. The excellent photostability and highly luminescent properties of QDs compared to conventional fluorophores allows reproducible obtainment of quantifiable mRNA gene expression imaging. Amine-modified oligonucleotide probes are designed and covalently attached to the carboxyl-terminated polymer-coated QDs via EDC chemistry. The resulting QD-DNA conjugates show sequence-specific hybridization with target mRNAs. Quantitative analysis of FISH on the Diptericin gene after lipopolysaccharide (LPS) treatment shows that the intensity and number of FISH signals per cell depends on the concentration of LPS and correlates well with quantitative real-time PCR results. In addition, our QD-DNA probes exhibit excellent sensitivity to detect the low-expressing Dorsal-related immunity factor gene. Importantly, multiplex FISH of Ribosomal protein 49 and Actin 5C using green and red QD-DNA conjugates allows the observation of cellular distribution of the two independent genes simultaneously. These results demonstrate that highly fluorescent and stable QD-DNA probes can be a powerful tool for direct localization and quantification of gene expression in situ.

Quantum dots light up pathology

Quantum dots (QDs) are novel nanocrystal fluorophores with extremely high fluorescence efficiency and minimal photobleaching. They also possess a constant excitation wavelength together with sharp and symmetrical tunable emission spectra. These unique optical properties make them near-perfect fluorescent markers and there has recently been rapid development of their use for bioimaging. QDs can be conjugated to a wide range of biological targets, including proteins, antibodies, and nucleic acid probes, rendering them of particular interest to pathology researchers. They have been used in multiplex immunohistochemistry and in situ hybridization, which when combined with multispectral imaging, has enabled quantitative measurement of gene expression in situ. QDs have also been used for live in vivo animal imaging and are now being applied to an ever-increasing range of biological problems. These are detailed in this review, which also acts to outline the important advances that have been made in their range of applications. The relative novelty of QDs can present problems in their practical use and guidelines for their application are given.