Electrochemical aptasensors for the detection of hepatocellular carcinoma-related biomarkers

Recent progress in electrochemical aptasensors for the detection of HCC-related biomarkers, including cancer cells, proteins, cell-derived exosomes, and nucleic acids, is reviewed.

Investigation of cancer drug resistance mechanisms by phosphoproteomics

Cancer cell mutations can be identified by genomic and transcriptomic techniques. However, they are not sufficient to understand the full complexity of cancer heterogeneity. Analyses of proteins expressed in cancers and their modification profiles show how these mutations could be translated at the functional level. Protein phosphorylation is a major post-translational modification critical for regulating several cellular functions. The covalent addition of phosphate groups to serine, threonine, and tyrosine is catalyzed by protein kinases. Over the past years, kinases were strongly associated with cancer, thus inhibition of protein kinases emanated as novel cancer treatment. However, cancers frequently develop drug resistance. Therefore, a better understanding of drug effects on tumors is urgently needed. In this perspective, phosphoproteomics arose as advanced tool to monitor cancer therapies and to discover novel drugs. This review highlights the role of phosphoproteomics in predicting sensitivity or resistance of cancers towards tyrosine kinase inhibitors and cytotoxic drugs. It also shows the importance of phosphoproteomics in identifying biomarkers that could be applied in clinical diagnostics to predict responses to drugs.

Aptamer based recognition of cancer cells: Recent progress and challenges in bioanalysis

Rapid and accurate monitoring of cancer cells with high sensitivity is essential for a successful cancer treatment. As high-affinity nucleic acid ligands, aptamers can improve the properties of detection methods by conjugating with intracellular or extracellular cancer biomarkers. Despite the advances in the early detection and treatment of cancer cells, lacking effective early detection tools is one of the causes of a high mortality rate. Aptasensors, which are based on the specificity of aptamer-target recognition, with transduction for analytical purposes have received particular attention due to their high sensitivity and selectivity, simple instrumentation, as well as low production cost. In this review, some selective and sensitive methods were summarized based on advanced nanomaterials towards aptasensing of cancer cells, such as blood, breast, cervical, colon, gastric, liver, and lung cancer cells. This review summarizes advances from 2010 to June 2020 in the development of aptasensors for cancer cell detection. Various aptasensing strategies are assessed according to their potential for reaching relevant limits of sensitivity, specificity, and degrees of multiplexing. Furthermore, we address the remaining challenges and opportunities to integrate aptasensing platforms into point-of-care solutions. Finally, the advantages and limitations of aptamer-based aptasensing strategies were reviewed.

Klotho Protects Dopaminergic Neuron Oxidant-Induced Degeneration by Modulating ASK1 and p38 MAPK Signaling Pathways

Klotho transgenic mice exhibit resistance to oxidative stress as measured by their urinal levels of 8-hydroxy-2-deoxyguanosine, albeit this anti-oxidant defense mechanism has not been locally investigated in the brain. Here, we tested the hypothesis that the reactive oxygen species (ROS)-sensitive apoptosis signal-regulating kinase 1 (ASK1)/p38 MAPK pathway regulates stress levels in the brain of these mice and showed that: 1) the ratio of free ASK1 to thioredoxin (Trx)-bound ASK1 is relatively lower in the transgenic brain whereas the reverse is true for the Klotho knockout mice; 2) the reduced p38 activation level in the transgene corresponds to higher level of ASK1-bound Trx, while the KO mice showed elevated p38 activation and lower level of-bound Trx; and 3) that 14-3-3ζ is hyper phosphorylated (Ser-58) in the transgene which correlated with increased monomer forms. In addition, we evaluated the in vivo robustness of the protection by challenging the brains of Klotho transgenic mice with a neurotoxin, MPTP and analyzed for residual neuron numbers and integrity in the substantia nigra pars compacta. Our results show that Klotho overexpression significantly protects dopaminergic neurons against oxidative damage, partly by modulating p38 MAPK activation level. Our data highlight the importance of ASK1/p38 MAPK pathway in the brain and identify Klotho as a possible anti-oxidant effector.

Single electrode biosensor for simultaneous determination of interferon gamma and lysozyme

Simultaneous detection of multiple biomarkers holds great promise for acute leukemia evaluation. Here, a novel biosensor is developed for simultaneous electrochemical detection of interferon gamma (IFN-γ) and lysozyme (Lys) based on aptamer recognition by coupling "signal-on" and "signal-off" modes. On one Au electrode, two kinds of signaling probes labeled by the thiolated ferrocene (Fc)- and methy blue (MB)- were designed to hybridize with IFN-γ and Lys aptamers respectively to form partial complementary DNA duplexes. In the presence of IFN-γ and Lys, the target-aptamer interaction led to the release of aptamer from duplex DNA structure. The single-stranded signaling probes thus suffered from the conformation changes, which resulted in the decreased (or increased) oxidation peak current of Fc (or MB) according to the "signal-off (or signal-on)" mode. Electrodes were characterized using cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). Under the optimized conditions, the signal changes were quantified using square wave voltammetry (SWV). This proposed biosensor for IFN-γ and Lys possessed linear detection range from 0.01 to 10 nM and 0.1 to 100 nM, with the detection limits of 1.14×10(-3) nM and 0.0164 nM, respectively. Moreover, this biosensor was readily regenerated and proved successful toward the practical analysis. The proposed strategy could provide more integrated and reliable information for acute leukemia evaluation.

Investigational agents for epithelial ovarian cancer

Ovarian cancer is the leading cause of gynecologic cancer deaths and accounts for 4% of women's cancer diagnoses and 5% of all cancer mortalities. Despite the ability of current chemotherapy and cytoreductive surgery to put patients in remission, most patients with advanced cancer will eventually relapse. Many advances in the treatment of ovarian cancer have been reported in the past several years and a historical background is provided. Attention will then turn to analogs of current chemotherapeutic agents, new cytotoxic drugs, targeted molecular therapy, intraperitoneal therapy and immunotherapy. This review will give a perspective on current drugs, potential agents and upcoming clinical trials.

Laser capture microdissection for the investigative pathologist

An important step in translational research is the validation of molecular findings from in vitro experiments using tissue specimens. However, tissue specimens are complex and contain a multitude of diverse cell populations that interfere with the molecular profiling data of a specific cell type. Laser capture microdissection (LCM) alleviates this issue by providing a valuable tool for the enrichment of a specific cell type within complex tissue samples. However, LCM and molecular analysis from tissue specimens can be complex and challenging due to numerous issues related with the tissue processing and its impact on the integrity of biomolecules in the specimen. The intricate nature of this application highlights the essential role a pathologist plays in translational research by contributing an expertise in histopathology, tissue handling, tissue analysis techniques, and clinical correlation of biological findings. The present review examines key practical aspects in tissue handling, specimen selection, quality control, and sample preparation for LCM and downstream molecular analyses that are a primary objective of the investigative pathologist.

Laser-assisted microdissection in translational research: theory, technical considerations, and future applications

Molecular profiling already exerts a profound influence on biomedical research and disease management. Microdissection technologies contribute to the molecular profiling of diseases, enabling investigators to probe genetic characteristics and dissect functional physiology within specific cell populations. Laser-capture microdissection (LCM), in particular, permits collation of genetic, epigenetic, and gene expression differences between normal, premalignant, and malignant cell populations. Its selectivity for specific cell populations promises to greatly improve the diagnosis and management of many human diseases. LCM has been extensively used in cancer research, contributing to the understanding of tumor biology by mutation detection, clonality analysis, epigenetic alteration assessment, gene expression profiling, proteomics, and metabolomics. In this review, we focus on LCM applications for DNA, RNA, and protein analysis in specific cell types and on commercially available LCM platforms. These analyses could clinically be used as aids to cancer diagnosis, clinical management, genomic profile studies, and targeted therapy. In this review, we also discuss the technical details of tissue preparation, analytical yields, tissue selection, and selected applications using LCM.

Everolimus in colorectal cancer

INTRODUCTION

There has been a strong preclinical rationale for studying mammalian target of rapamycin (mTOR) inhibitors as single agents or in combination, in multiple malignancies and colorectal cancer in particular.

AREAS COVERED

The authors summarize the complete clinical experience to date of all trials, both published and in abstract form, of everolimus in colorectal cancer. While initial Phase I trials showed promise, further studies have confirmed that single agent everolimus is not active in advanced metastatic colorectal carcinoma with trials showing single agent tolerability, but without significant hints of efficacy in terms of either objective tumor responses or prolonged stable disease. Combination regimens, including combinations with cytotoxic chemotherapy, and inhibitors of VEGF, EGFR and HDAC have been tested specifically in the colorectal setting in Phase I and Phase II clinical trials. The authors discuss the potential reasons for mixed results and suggest future directions for the development of everolimus in colorectal malignancies.

EXPERT OPINION

Studies demonstrate limited clinical activity of everolimus for the treatment of advanced colorectal cancer and have been complicated by increases in toxicity. However, the central role of the PI3K/mTOR pathway in cancer biology suggests that other drug combinations with mTOR inhibition may still merit evaluation.

The promise of mTOR inhibitors in the treatment of colorectal cancer

INTRODUCTION

Recently, deregulation of protein synthesis has begun to gain attention as a major player in cancer development and progression. Specifically, deregulation of the process of translation initiation appears to play a key role in oncogenesis. The PI3K/Akt/mTOR pathway is vital for cellular metabolism, growth and proliferation and thus an attractive therapeutic target in oncology. Accordingly, several mTOR inhibitors are currently being tested in many cancers including colorectal cancer (CRC).

AREAS COVERED

In this review, the key components of the PI3K/Akt/mTOR pathways, their molecular alterations and the inhibitors targeting the mTOR pathway in CRC are described. Complex interactions with other pathways such as the MAPK pathway are analyzed, as are possible drug combinations that target this pathway. In addition, novel strategies for use of mTOR pathway inhibitors in CRC treatment are introduced.

EXPERT OPINION

Clinical trials of mTOR inhibitors have been investigated in CRC. mTOR inhibitors may represent an attractive antitumor target in combination with strategies to target other pathways that may overcome resistance. Further research is needed to identify critical molecular effector mechanisms, molecular markers that predict responsiveness and potential toxicities.

A simple, cost-effective and flexible method for processing of snap-frozen tissue to prepare large amounts of intact RNA using laser microdissection

Understanding the molecular basis of disease requires gene expression profiling of normal and pathological tissue. Although the advent of laser microdissection (LMD) has greatly facilitated the procurement of specific cell populations, often only small amounts of low quality RNA is recovered. This precludes the use of global approaches of gene expression profiling which require sizable amounts of high quality RNA. Here we report a method for processing of snap-frozen tissue to prepare large amounts of intact RNA using LMD. Portions of small intestine from piglets (n = 6) were snap-frozen in Optimum Cutting Temperature compound (experimental) and in RNAlater (control). A randomly selected sample was laser microdissected using the developed protocol in multiple sessions totalling 4 h each day on four consecutive days. RNAs were extracted from these samples and its control and their quality (RIN) determined. RINs of the experimental samples were independent of time (p = 0.12) and day (p = 0.56) of the microdissection thereby suggesting that their RNA quality remained unaltered. These samples exhibited high quality (RIN ≥ 8) with good recovery (81.2%) and excellent yield (1539 ng/1.2 × 10(7) μm(2)). Their overall RIN, 8.029 ± 0.116, was not significantly different from 8.2 (p = 0.123), the value obtained from the control, non-laser microdissected, sample. This indicated that the RNA quality from the laser microdissected and non-microdissected samples was comparable. The method allowed LMD for up to 4 h each day for a total of four days. The microdissected samples can be pooled thereby increasing amount of RNA at least by ten-fold. The procedure did not require any expensive limited-shelf life RNase inhibitors, RNA protectors, staining kits or toxic chemicals. Furthermore, it was flexible and enabled the processing without affecting routine laboratory workflow. The method developed was simple, inexpensive and provided substantial amounts of high quality RNA suitable for gene expression profiling and other cellular and molecular analyses for biology and molecular medicine.

Construction and hyperspectral imaging of quantum dot lysate arrays

The emerging field of proteomic molecular profiling will be driven by new technologies that can measure dozens to hundreds of proteins from a small sample input from a patient's biopsy. Lysate arrays, or reverse-phase protein microarrays, provide a platform for complex mixtures of proteins extracted from cells and tissues to be directly immobilized onto a solid support (such as a biochip with protein binding capacity) in diminutive volumes (picoliter-to-nanoliter). The proteins are spotted using precision robotics and then quantitatively assayed using primary antibodies; important posttranslational modifications, such as phosphorylations that are important for protein activation, may also be assayed to provide an estimate of the regulation of cellular signaling. Until recently, chromogenic signals and fluorescence (using organic fluorophores) detection were two strategies relied upon for signal detection. Emerging regents such as quantum dots (Qdot® nanocrystals; QD) are now employed for improved performance. QD embody a more versatile detection system because the robust signals may be time averaged and the narrow spectral emissions enable many protein targets to be quantified within the same lysate spot. Previously, we found that commercially available pegylated, streptavidin-conjugated QD were effective detection agents, with low-background affinities to spurious components within heterogeneous protein mixtures. Hyperspectral imaging allows the simultaneous detection of the different colored QD reagents within a single lysate spot. Here, we described the construction and imaging of QD lysate arrays. This technology is an emerging, enabling tool within the exciting, clinically oriented field of clinical tissue proteomics.

A electrogenerated chemiluminescence biosensor for Ramos cancer cell using DNA encapsulated Ru(bpy)₃Cl₂ as signal probe

A label-free sensing technology for detection of Ramos cell was developed based on a signal probe Ru(bpy)3Cl2 (Ru) encapsulated by DNA. Gold electrode or magnetic bead as the sensing surface was firstly modified with long-strand DNA with five repeating units. Then two kinds of short-strand DNA are grafted onto the long-strand DNA to form DNA strands A and B (L-A and L-B) through the hybridization, respectively. The addition of aptamer initiates hybridization of L-A and L-B with the aptamer sequence. As the hybridization proceeds, the four kinds of DNA would finally transform into a three-dimensional network structure and the signal probe Ru was encapsulated by DNA simultaneously. When Ramos cells are introduced to interact with the aptamer, the signal probe is released. In order to confirm the generality of this method the ferrocenecarboxylic acid and luminol selected as a signal probe mode were also tested. The Ru used as a signal probe for electrogenerated chemiluminescence (ECL) detection was detailedly studied. With this ECL biosensor, detection limit as low as 58 cells/mL was achieved for Ramos cell. The biosensor also exhibited excellent sensitivity and selectivity.

Phosphoproteomic biomarkers predicting histologic nonalcoholic steatohepatitis and fibrosis

The progression of nonalcoholic fatty liver disease (NAFLD) has been linked to deregulated exchange of the endocrine signaling between adipose and liver tissue. Proteomic assays for the phosphorylation events that characterize the activated or deactivated state of the kinase-driven signaling cascades in visceral adipose tissue (VAT) could shed light on the pathogenesis of nonalcoholic steatohepatitis (NASH) and related fibrosis. Reverse-phase protein microarrays (RPMA) were used to develop biomarkers for NASH and fibrosis using VAT collected from 167 NAFLD patients (training cohort, N = 117; testing cohort, N = 50). Three types of models were developed for NASH and advanced fibrosis: clinical models, proteomics models, and combination models. NASH was predicted by a model that included measurements of two components of the insulin signaling pathway: AKT kinase and insulin receptor substrate 1 (IRS1). The models for fibrosis were less reliable when predictions were based on phosphoproteomic, clinical, or the combination data. The best performing model relied on levels of the phosphorylation of GSK3 as well as on two subunits of cyclic AMP regulated protein kinase A (PKA). Phosphoproteomics technology could potentially be used to provide pathogenic information about NASH and NASH-related fibrosis. This information can lead to a clinically relevant diagnostic/prognostic biomarker for NASH.

Aptamer-based and DNAzyme-linked colorimetric detection of cancer cells

This paper reports a novel method to detect human leukemic lymphoblasts (CCRF-CEM cells). While the aptamer of the cancer cells was employed as the recognition element to target cancer cells, peroxidase-active DNAzyme was used as the sensing element to produce catalysis-induced colorimetric signals. The elegant architecture integrating the aptamer and DNAzyme made it feasible to detect cancer cells easily and rapidly by the color change of the substrate for DNAzyme. Experimental results showed that 500 cells can well indicate the cancer, while as control, 250,000 Islet Island Beta cells only show tiny signals, suggesting that the method proposed in this paper has considerable sensitivity and selectivity. Furthermore, since it does not require expensive apparatus, or modification or label of DNA chains, the method we present here is also cost-effective and conveniently operated, implying potential applications in future cancer diagnosis.

New frontiers for ovarian cancer risk evaluation: proteomics and contrast-enhanced ultrasound

OBJECTIVE

The grim ovarian cancer statistics are attributed to the fact that most women typically present with widespread disease at the time of initial diagnosis. Our current diagnostic tools, such as pelvic examination and standard ultrasound, are inadequate to detect early-stage epithelial ovarian cancer. In recent years there has been an explosion of important advances in biomedical engineering, proteomic technologies, and computational analyses that has led to the identification of hundreds of previously unknown proteins unique to the pathophysiology of ovarian cancer, some of which are currently under clinical validation. At present, no one biomarker exists with 100% specificity and sensitivity for the accurate detection of early-stage epithelial ovarian cancer.

CONCLUSION

As the search for a panel of biomarkers detecting cancer, let alone early-stage disease, progresses, diagnostic imaging will continue to play a critical role to confirm or refute these biomarker assays. Interestingly, recent studies using contrast-enhanced ultrasound have shown potential as an early-detection tool by detecting the aberrant vascularity required for tumor growth before the development of a mass. Thus, we propose that the use of proteomic-based biomarker discovery and contrast-enhanced ultrasound may serve as a promising combination to help accurately identify early-stage epithelial ovarian cancer to improve women's health care.

Laser capture microdissection of cervical human papillomavirus infections: copy number of the virus in cancerous and normal tissue and heterogeneous DNA methylation

Research on the pathogenicity of human papillomaviruses (HPVs) during cervical carcinogenesis often relies on the study of homogenized tissue or cultured cells. This approach does not detect molecular heterogeneities within the infected tissue. It is desirable to understand molecular properties in specific histological contexts. We asked whether laser capture microdissection (LCM) of archival cervical tumors in combination with real-time polymerase chain reaction and bisulfite sequencing permits (i) sensitive DNA diagnosis of small clusters of formalin-fixed cells, (ii) quantification of HPV DNA in neoplastic and normal cells, and (iii) analysis of HPV DNA methylation, a marker of tumor progression. We analyzed 26 tumors containing HPV-16 or 18. We prepared DNA from LCM dissected thin sections of 100 to 2000 cells, and analyzed aliquots corresponding to between nine and 70 cells. We detected nine to 630 HPV-16 genome copies and one to 111 HPV-18 genome copies per tumor cell, respectively. In 17 of the 26 samples, HPV DNA existed in histologically normal cells distant from the margins of the tumors, but at much lower concentrations than in the tumor, suggesting that HPVs can infect at low levels without pathogenic changes. Methylation of HPV DNA, a biomarker of integration of the virus into cellular DNA, could be measured only in few samples due to limited sensitivity, and indicated heterogeneous methylation patterns in small clusters of cancerous and normal cells. LCM is powerful to study molecular parameters of cervical HPV infections like copy number, latency and epigenetics.

Combined inhibition of MEK and mTOR signaling inhibits initiation and progression of colorectal cancer

The role of the mTOR signal pathway in colorectal cancer (CRC) pathogenesis remains unclear, and the combination effect of PD98059 (an inhibitor for MEK) and rapamycin (an inhibitor for mTOR) on CRC is still unknown. Here, we found that combination treatment with PD98059 and rapamycin suppressed the proliferation of CRC cells, induced apoptosis, arrested cell cycle, and reduced the incidence and volume of CRC in mice, as well as inhibited phosphorylation of mTOR and the MEK signal pathway components, of which the effects were more significant than single-drug treatments. These findings indicate that PD98059 combined with rapamycin appears to be a promising strategy for inhibiting the initiation, and progression of CRC, which may provide a novel strategy for CRC prevention.

The critical role of histology in an era of genomics and proteomics: a commentary and reflection

The role of histologic examination in lymphoma diagnosis has been called into question by proponents of new technologies, such as genomics and proteomics. We review the history and salient features of morphologic evaluation in lymphoid diseases, and discuss the general and specific limitations of mature ancillary techniques, such as immunohistochemistry, flow cytometry, and molecular studies. We then speculate on the future relationship between morphology and the new genomic and proteomic technologies as they become integrated into clinical practice.

A ribonuclease protection assay-based approach for analysis of angiogenic gene expression in archival tissues

Archival, formalin-fixed and paraffin-embedded tissues routinely stored in pathology departments represent an invaluable resource for retrospective molecular biology studies for diagnostic and prognostic purposes. In such specimens extraction of transcriptionally competent RNA to be analyzed by conventional techniques, such as reverse transcription-polymerase chain reaction, is a challenging task. Therefore, we developed a novel methodological approach that allows successful detection and semiquantitative analysis of specific mRNAs obtained from archival formalin-fixed, paraffin-embedded specimens by ribonuclease protection assay. Specifically, we measured a panel of 7 angiogenic markers in selected archival tissues stored at room temperature and retrieved over a wide time span (10 y). The study series consisted in samples of benign and malignant melanocytic lesions. In our model, expression of FLT-1, the vascular-endothelial growth factor receptor-1, correlated with the expression of mRNAs encoding other tyrosine kinase receptors, such as TIE-1 and TIE-2, as well as with angiopoietin and with the protease-activated receptor-1 and vascular-endothelial growth factor itself. Relative to control (normal skin), in melanoma the expression of the selected angiogenic markers was significantly higher. In conclusion, our study provides evidence that ribonuclease protection assay on archival specimens would be highly valuable for retrospective studies, for diagnosis or prognosis.

Reverse-phase protein microarrays: application to biomarker discovery and translational medicine

Mapping of protein signaling networks within tumors can identify new targets for therapy and provide a means to stratify patients for individualized therapy. Kinases are important drug targets, as such kinase network information could become the basis for development of therapeutic strategies for improving treatment outcome. An urgent clinical goal is to identify functionally important molecular networks associated with subpopulations of patients that may not respond to conventional combination chemotherapy. Reverse-phase protein microarrays are a technology platform designed for quantitative, multiplexed analysis of specific phosphorylated, cleaved, or total (phosphorylated and nonphosphorylated) forms of cellular proteins from a limited amount of sample. This class of microarray can be used to interrogate cellular samples, serum or body fluids. This review focuses on the application of reverse-phase protein microarrays for translational research and therapeutic drug target discovery.

Laser capture microdissection technology

Deciphering the cellular and molecular interactions that drive disease within the tissue microenvironment holds promise for discovering drug targets of the future. In order to recapitulate the in vivo interactions through molecular analysis, one must be able to analyze specific cell populations within the context of their heterogeneous tissue microecology. Laser capture microdissection is a method to procure subpopulations of tissue cells under direct microscopic visualization. Laser capture microdissection technology can harvest the cells of interest directly or can isolate specific cells by cutting away unwanted cells to give histologically pure enriched cell populations. A variety of downstream applications exist: DNA genotyping and loss-of-heterozygosity analysis, RNA transcript profiling, cDNA library generation, mass spectrometry proteomics discovery and signal pathway profiling.

Proteomics in cancer

Proteomic studies have generated numerous datasets of potential diagnostic, prognostic, and therapeutic significance in human cancer. Two key technologies underpinning these studies in cancer tissue are two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and mass spectrometry (MS). Although surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF)-MS is the mainstay for serum or plasma analysis, other methods including isotope-coded affinity tag technology, reverse-phase protein arrays, and antibody microarrays are emerging as alternative proteomic technologies. Because there is little overlap between studies conducted with these approaches, confirmation of these advanced technologies remains an elusive goal. This problem is further exacerbated by lack of uniform patient inclusion and exclusion criteria, low patient numbers, poor supporting clinical data, absence of standardized sample preparation, and limited analytical reproducibility (in particular of 2D-PAGE). Despite these problems, there is little doubt that the proteomic approach has the potential to identify novel diagnostic biomarkers in cancer. In therapeutic proteomics, the challenge is significant due to the complexity systems under investigation (i.e., cells generate over 10(5) different polypeptides). However, the most significant contribution of therapeutic proteomics research is expected to derive not from single experiments, but from the synthesis and comparison of large datasets obtained under different conditions (e.g., normal, inflammation, cancer) and in different tissues and organs. Thus, standardized processes for storing and retrieving data obtained with different technologies by different research groups will have to be developed. Shifting the emphasis of cancer proteomics from technology development and data generation to careful study design, data organization, formatting, and mining is crucial to answer clinical questions in cancer research.

Quantitative fluorescence imaging analysis for cancer biomarker discovery: application to beta-catenin in archived prostate specimens

The surprising disparity between the number of protein-encoding genes ( approximately 30,000) in the human genome and the number of proteins ( approximately 300,000) in the human proteome has inspired the development of translational proteomics aimed at protein expression profiling of disease states. Translational proteomics, which offers the promise of early disease detection and individualized therapy, requires new methods for the analysis of clinical specimens. We have developed quantitative fluorescence imaging analysis (QFIA) for accurate, reproducible quantification of proteins in slide-mounted tissues. The method has been validated for the analysis of beta-catenin in archived prostate specimens fixed in formalin. QFIA takes advantage of the linearity of fluorescence antibody signaling for tissue epitope content, a feature validated for beta-catenin in methacarn-fixed prostate specimens analyzed by reverse-phase protein array analysis and QFIA (r = 0.97). QFIA of beta-catenin in formaldehyde-fixed tissues correlated directly with beta-catenin content (r = 0.86). Application of QFIA in a cross-sectional study of biopsies from 42 prostate cancer (PC) cases and 42 matched controls identified beta-catenin as a potential field marker for PC. Receiver operating characteristic plots revealed that beta-catenin expression in the normal-appearing acini of cancerous glands identified 42% (95% confidence intervals, 26-57%) of cancer cases, with 88% (95% confidence intervals, 80-96%) specificity. The marker may contribute to a PC biomarker panel. In conclusion, we report the development and validation of a new method for fluorescence quantification of proteins in archived tissues and its application to archived specimens for an evaluation of beta-catenin expression as a biomarker for PC.

A systems biology approach to the pathogenesis of obesity-related nonalcoholic fatty liver disease using reverse phase protein microarrays for multiplexed cell signaling analysis

Nonalcoholic fatty liver disease (NAFLD) is a common cause of chronic liver disease. Omental adipose tissue, a biologically active organ secreting adipokines and cytokines, may play a role in the development of NAFLD. We tested this hypothesis with reverse-phase protein microarrays (RPA) for multiplexed cell signaling analysis of adipose tissue from patients with NAFLD. Omental adipose tissue was obtained from 99 obese patients. Liver biopsies obtained at the time of surgery were all read by the same hepatopathologist. Adipose tissue was exposed to rapid pressure cycles to extract protein lysates. RPA was used to investigate intracellular signaling. Analysis of 54 different kinase substrates and cell signaling endpoints showed that an insulin signaling pathway is deranged in different locations in NAFLD patients. Furthermore, components of insulin receptor-mediated signaling differentiate most of the conditions on the NAFLD spectrum. For example, PKA (protein kinase A) and AKT/mTOR (protein kinase B/mammalian target of rapamycin) pathway derangement accurately discriminates patients with NASH from those with the non-progressive forms of NAFLD. PKC (protein kinase C) delta, AKT, and SHC phosphorylation changes occur in patients with simple steatosis. Amounts of the FKHR (forkhead factor Foxo1)phosphorylated at S256 residue were significantly correlated with AST/ALT ratio in all morbidly obese patients. Furthermore, amounts of cleaved caspase 9 and pp90RSK S380 were positively correlated in patients with NASH. Specific insulin pathway signaling events are altered in the adipose tissue of patients with NASH compared with patients with nonprogressive forms of NAFLD.

CONCLUSION

These findings provide evidence for the role of omental fat in the pathogenesis, and potentially, the progression of NAFLD.

Laser-assisted microdissection (LAM) in developmental biology

The analysis of gene expression in developing organs is a valuable tool for the assessment of genetic fingerprints during the various stages of differentiation. Complex processes in developing tissues are particularly difficult to understand in terms of biochemical phenomena. Laser-assisted microdissection (LAM) allows the efficient and precise capture of cells or groups of cells from developing tissues in sufficient quantities and within the context of time and space to permit the subsequent molecular characterization of the targeted tissue. The technique development has dramatically increased the ease of isolating specific cells which, together with progress in tissue preparation and microextraction protocols, allows for broad-range down-stream applications in the fields of genomics, transcriptomics and proteomics. This review gives an overview of the LAM technology and its application in developmental biology.

Aptamers evolved from cultured cancer cells reveal molecular differences of cancer cells in patient samples

BACKGROUND

Molecular-level differentiation of neoplastic cells is essential for accurate and early diagnosis, but effective molecular probes for molecular analysis and profiling of neoplastic cells are not yet available. We recently developed a cell-based SELEX (systematic evolution of ligands by exponential enrichment) strategy to generate aptamers (designer DNA/RNA probes) as molecular probes to recognize neoplastic cells.

METHODS

We tested 6 cell-SELEX-generated aptamers with equilibrium dissociation constants in the nanomolar to subnanomolar range: sgd5, selected from Toledo cells, a human diffuse large-cell lymphoma cell line (B-cell), and sgc8, sgc3, sgc4, sgd2, and sgd3 from CCRF-CEM cells, a human precursor T cell acute lymphoblastic leukemia (T-ALL) cell line. Aptamers were labeled with fluorescein isothiocyanate fluorophores and then used to recognize, by flow cytometric analysis, neoplastic cells in cultured hematopoietic cell lines and clinical samples.

RESULTS

Aptamer sgd5 recognized only its target cells. Aptamers sgc3, sgd2, sgd3, sgc4, and sgc8, selected from a T-cell leukemia cell line, identified all of the cultured T-cell leukemia cell lines with relatively high fluorescence intensity. Aptamers sgc8, sgc3, and sgd3 showed good selectivity toward T-ALL cells and almost no binding to normal hematopoietic cells or lymphoma and myeloma cells. Selected aptamers also detected targets on the cell membranes of neoplastic cells in patient samples.

CONCLUSIONS

Aptamers selected against cultured neoplastic cells can effectively be used as molecular probes for recognition of neoplastic cells in patient samples. Cell-based aptamer selection can be used to generate aptamer probes to obtain molecular signatures of neoplastic cells in patient samples.

Quantitative protein analysis from formalin-fixed tissues: implications for translational clinical research and nanoscale molecular diagnosis

Owing to its cross-linking effects, it is currently believed that formalin fixation of routinely processed tissues in the clinic prevents protein extraction and profiling. The aim of our study was to develop a robust, fast, standardized, and easy to use technique for the solubilization of non-degraded, full length, and immunoreactive proteins from formalin-fixed tissues for western blot and protein microarray analysis. Sections of routinely processed formalin-fixed and paraffin-embedded tissues of various origin were analysed. After deparaffination, tissues were manually dissected from the slides and transferred into an optimized protein extraction buffer system. Proteins were solubilized and subsequently analysed by western blot and reverse phase protein microarrays. We succeeded in isolating non-degraded, soluble, and immunoreactive proteins from routinely processed formalin-fixed tissues. We were able to detect membrane, cytoplasmic and nuclear proteins at the expected molecular weight. No differences were found in the protein yield and protein abundances between fresh frozen and formalin-fixed tissues. Using western blots and reverse phase protein microarrays, the receptor tyrosine kinase HER2, an important protein target for antibody based cancer treatment, was reliably measured in formalin-fixed breast cancer biopsy samples when compared with measurement by immunohistochemistry and fluorescence in situ hybridization; remarkably, immunohistochemically equivocal cases (score 2+) can be categorized according to HER2 protein abundance. Our new clinically orientated multiplexed protein measurement system may be generally applicable to determine the relative abundances of known disease-related proteins in small amounts of routinely processed formalin-fixed tissue samples for research and diagnosis. This technique may also be used to identify, characterize, and validate known and new protein markers in a variety of human diseases.

Novel targeted therapies in epithelial ovarian cancer: from basic research to the clinic

The development of new molecularly targeted therapies represents a high priority for the treatment of epithelial ovarian cancer. P-glycoprotein overexpression has been associated with multidrug resistance, and the use of multidrug resistance modulators, such as valspodar, is being explored in combination with chemotherapy. Human epidermal receptor (HER) family members are attractive targets for biological therapies. The addition of erlotinib or cetuximab to first-line paclitaxel- plus carboplatin-based chemotherapy is feasible and well tolerated. Gefitinib is able to inhibit the proliferation of ovarian clear-cell carcinoma in in vitro and in vivo experimental models. Single-agent trastuzumab has a limited value for recurrent epithelial ovarian cancer owing to the low frequency of HER2 overexpression and the low rate of objective responses among HER2-overexpressing patients. A Gynecologic Oncology Group Phase II trial of the proteasome inhibitor bortezomib in recurrent epithelial ovarian cancer is currently ongoing, and the combination of bortezomib and chemotherapeutic agents should be assessed. The mammalian target of rapamycin (mTOR) plays an important role in stimulating the translation of mRNAs encoding key proteins for cell growth and angiogenesis, and mTOR inhibitors, such as AP-23573 (ARIAD), deserve to be tested in selected epithelial ovarian cancer patients. The addition of intraperitoneal treatment with adenovirus containing human wild-type p53 to standard paclitaxel- plus carboplatin-based chemotherapy failed to improve the clinical outcome of patients with mutated p53 epithelial ovarian cancer. The Gynecologic Oncology Group is conducting a Phase II trial of single-agent bevacizumab (antivascular endothelial growth factor monoclonal antibody) in platinum-resistant disease. In conclusion, emerging drugs for epithelial ovarian cancer include agents designed to overcome chemoresistance, HER-targeting agents, proteasome inhibitors, mTOR inhibitors and angiogenesis inhibitors. A new paradigm of treatment could consist of chemotherapy combined with a biological agent for six cycles, and followed by chronic maintenance therapy with the biological agent alone. Advances in genomics and proteomics will elucidate the molecular mechanisms of ovarian carcinogenesis, which will hopefully lead to individualized molecular medicine in the next years.

Molecular targets in gynaecological cancers

The application of high throughput expression profiling and other advanced molecular biology laboratory techniques has revolutionised the management of cancers and is gaining attention in the field of gynaecological cancers. Such new approaches may help to improve our understanding of carcinogenesis and facilitate screening and early detection of gynaecological cancers and their precursors. Individualised prediction of patients' responses to therapy and design of personalised molecular targeted therapy is also possible. The studies of various molecular targets involved in the various signal pathways related to carcinogenesis are particularly relevant to such applications. At the moment, the application of detection and genotyping of human papillomavirus in management of cervical cancer is one of the most well established appliances of molecular targets in gynaecological cancers. Methylation, telomerase and clonality studies are also potentially useful, especially in assisting diagnosis of difficult clinical scenarios. This post-genomic era of clinical medicine will continue to make a significant impact in routine pathology practice. The contribution of pathologists is indispensable in analysis involving tissue microarray. On the other hand, both pathologists and bedside clinicians should be aware of the limitation of these molecular targets. Interpretation must be integrated with clinical and histopathological context to avoid misleading judgement. The importance of quality assurance of all such molecular techniques and their ethical implications cannot be over-emphasised.

Multilectin Affinity Chromatography for Characterization of Multiple Glycoprotein Biomarker Candidates in Serum from Breast Cancer Patients

Background: Glycoproteins are often associated with cancer and are important in serum studies, for which glycosylation is a common posttranslational modification.

Methods: We used multilectin affinity chromatography (M-LAC) to isolate glycoproteins from the sera of breast cancer patients and controls. The proteins were identified by HPLC–tandem mass spectrometry (MS/MS) analysis of the corresponding tryptic digests. We used the FuncAssociate Gene Ontology program for association analysis of the identified proteins. Biomarker candidates in these groups were comparatively quantitated by use of peak area measurements, with inclusion of an internal standard. We analyzed data for concordance within the ontology association groups for vector of change with the development of breast cancer.

Results: Detection of the known low-concentration biomarker HER-2 (8–24 μg/L) enabled us to establish a dynamic range of 106, relative to the amount of albumin, for the depletion step. We then used ELISA to confirm this range. Proteins associated with lipid transport and metabolism, cell growth and maintenance, ion homeostasis, and protease inhibition were found to be differentially regulated in serum from women with breast cancer compared with serum from women without breast cancer.

Conclusions: M-LAC for isolation of the serum glycoproteome, coupled with liquid chromatography–MS/MS and the use of gene ontology associations, can be used to characterize large panels of candidate markers, which can then be evaluated in a particular patient population.

Aptamers evolved from live cells as effective molecular probes for cancer study

Using cell-based aptamer selection, we have developed a strategy to use the differences at the molecular level between any two types of cells for the identification of molecular signatures on the surface of targeted cells. A group of aptamers have been generated for the specific recognition of leukemia cells. The selected aptamers can bind to target cells with an equilibrium dissociation constant (K(d)) in the nanomolar-to-picomolar range. The cell-based selection process is simple, fast, straightforward, and reproducible, and, most importantly, can be done without prior knowledge of target molecules. The selected aptamers can specifically recognize target leukemia cells mixed with normal human bone marrow aspirates and can also identify cancer cells closely related to the target cell line in real clinical specimens. The cell-based aptamer selection holds a great promise in developing specific molecular probes for cancer diagnosis and cancer biomarker discovery.

Preservation of RNA and destruction of infectivity in microdissected brain tissues of Lewis rats infected with the Borna disease virus

Laser microdissection combined with real-time RT-PCR presents an advanced tool to quantify particular RNA species in defined tissue areas. Dealing with infectious tissue samples increases the need to overcome the risk of infectivity and contamination during laser microdissection. Here, an useful method to control infectivity of frozen brain sections infected with the Borna disease virus (BDV), an enveloped RNA virus, is described. Various pre-treatments were applied prior to laser microdissection and subsequent real-time RT-PCR. Brain sections were incubated with Vennotrade mark Vet 1 super 1% or 70% ethanol for 30, 60 and 90min, followed by quantification of infectious virus and RNA recovery using laser microdissection. Total RNA specific for the BDV nucleoprotein (BDV-N) and the cellular genes glyceraldehyde-3-phosphate dehydrogenase (GAPDH), succinate-ubiquinone reductase (SDHA) and hypoxanthine phosphoribosyl-transferase-1 (HPRT) was measured by real-time RT-PCR and compared to BDV-infected control samples. After 30 min incubation with both disinfectants, no infectious virus was isolated, while sufficient cDNA copy numbers were amplified. As tissue morphology was best preserved after ethanol treatment, 30min incubation with 70% ethanol was selected as the method of choice to prevent infectivity of BDV. This procedure represents a suitable pre-treatment option to ensure adequate safety of virus infected central nervous system tissue.

Array-based proteomics: mapping of protein circuitries for diagnostics, prognostics, and therapy guidance in cancer

The human proteome, due to the enormity of post-translational permutations that result in large numbers of isoforms, is much more complex than the genome and alterations in cancer can occur in ways that are not predictable by translational analysis alone. Proteomic analysis therefore represents a more direct way of investigating disease at the individual patient level. Furthermore, since most novel therapeutic targets are proteins, proteomic analysis potentially has a central role in patient care. At the same time, it is becoming clear that mapping entire networks rather than individual markers may be necessary for robust diagnostics as well as tailoring of therapy. Consequently, there is a need for high-throughput multiplexed proteomic techniques, with the capability of scanning multiple cases and analysing large numbers of endpoints. New types of protein arrays combined with advanced bioinformatics are currently being used to identify molecular signatures of individual tumours based on protein pathways and signalling cascades. It is envisaged that analysing the cellular 'circuitry' of ongoing molecular networks will become a powerful clinical tool in patient management.

Proteomics and clinical surgery

This article concludes the Journal's "Scientific Surgery" series of leaders. The series, published throughout 2005, has highlighted areas of bioscience that may soon be transferred from the laboratory into the clinical sphere. In this final paper Roblick and Auer consider the future role of the surgeon in the era of the "diagnostic chip".

Embryonic stem cells in predictive cardiotoxicity: laser capture microscopy enables assay development

Embryonic stem (ES) cells offer unprecedented opportunities for in vitro drug discovery and safety assessment of compounds. Cardiomyocytes derived from ES cells enable development of predictive cardiotoxicity models to increase the safety of novel drugs. Heterogeneity of differentiated ES cells limits the development of reliable in vitro models for compound screening. We report an innovative and robust approach to isolate ES-derived cardiomyocytes using laser microdissection and pressure catapulting (LMPC). LMPC cells were readily applied onto 96-well format in vitro pharmacology assays. The expression of developmental and functional cardiac markers, Nkx 2.5, MLC2V, GATA-4, Connexin 43, Connexin 45, Serca-2a, cardiac alpha actin, and phospholamban, among others, was confirmed in LMPC ES-derived cardiomyocytes. Functional assays exhibited cardiac-like response to increased extracellular calcium (5.4 mM extracellular Ca2+) and L-type calcium channel antagonist (1 microM nifedipine). In conclusion, laser microdissection and pressure catapulting is a robust technology to isolate homogeneous ES-derived cell types from heterogeneous populations applicable to assay development.

The role of proteomics in the diagnosis and treatment of ovarian cancer

Ovarian cancer is the leading cause of gynecologic cancer death in the Western world and more than 70% of patients are diagnosed with advanced stage disease. The high mortality rate is due to the difficulty in the early detection of ovarian cancer. Current screening strategies lack the necessary sensitivity and specificity to reliably and accurately diagnose affected women, prompting investigators to seek alternative means of analysis found in protein pathways and networks. Proteomics seeks to advance the understanding of how proteins interact in cancer and may provide a mechanism for early stage diagnosis. The proteomic techniques of laser capture microdissection, mass spectrometry and tissue lysate arrays have led to the discovery of new biomarkers and the identification, development and approval of a number of targeted therapeutic agents. Following validation through clinical trials, the application of these techniques will contribute to the changing paradigm of cancer detection and treatment toward personalized medicine.