Molecular profiling of tissue samples using laser capture microdissection

Combining laser microdissection and microRNA expression profiling to unmask microRNA signatures in complex tissues

Neglecting tissue heterogeneity during the analysis of microRNA (miRNA) levels results in average signals from an unknown mixture of different cell types that are difficult to interpret. Here we demonstrate the technical requirements needed to obtain high-quality, quantitative miRNA expression information from tumor tissue compartments obtained by laser microdissection (LMD). Furthermore, we show the significance of disentangling tumor tissue heterogeneity by applying the newly developed protocols for combining LMD of tumor tissue compartments with RT-qPCR analysis to reveal compartment-specific miRNA expression signatures. An important advantage of this strategy is that the miRNA signature can be directly linked to histopathology. In summary, combining LMD and RT-qPCR is a powerful approach for spatial miRNA expression analysis in complex tissues, enabling discovery of disease mechanisms, biomarkers and drug candidates.

Combine Phage Antibody Display Library Selection on Patient Tissue Specimens with Laser Capture Microdissection to Identify Novel Human Antibodies Targeting Clinically Relevant Tumor Antigens

A functional approach to generate tumor-targeting human monoclonal antibodies is through selection of phage antibody display libraries directly on tumor cells. Although technically convenient, the use of cancer cell lines for the selection has limitations as those cell lines often undergo genetic and epigenetic changes during prolonged in vitro culture and alter their cell surface antigen expression profile. The key is to develop a technology that allows selection of phage antibody display libraries on tumor cells in situ residing in their natural tissue microenvironment. Laser capture microdissection (LCM) permits the precise procurement of tumor cells from human cancer patient tissue sections. Here, we describe a LCM-based method for selecting phage antibodies against tumor cells in situ using both fresh frozen and paraffin-embedded tissues. To restrict the selection to antibodies that bind internalizing epitopes, the method utilizes a polyclonal phage population pre-enriched for internalizing phage antibodies. The ability to recognize tumor cells in situ residing in their natural tissue microenvironment and to deliver payload intracellularly makes these LCM-selected antibodies attractive candidates for the development of targeted cancer therapeutics.

Laser Capture Microdissection of Epithelium from a Wound Healing Model for MicroRNA Analysis

MicroRNAs are ~22 nucleotide-long noncoding RNAs influencing many cellular processes (including wound healing) by their regulatory functions on gene expression. The ability to analyze microRNA in different cells at the wound site is essential for understanding the critical role(s) of microRNA during various phases of wound healing. Laser capture micro-dissection (LCM) is an effective method to distinguish between relevant and non-relevant cells or tissues and enables the researcher to obtain homogeneous, ultra-pure samples from heterogeneous starting material. We present here our protocol for procuring epithelial cells from a mouse wound healing model using a Leica LMD7000 Laser Microdissection system, as well as the RNA isolation and downstream microRNA analysis. Using this method, researchers can selectively and routinely analyze regions of interest down to single cells to obtain results that are relevant, reproducible, and specific.

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.

Optimal molecular profiling of tissue and tissue components: defining the best processing and microdissection methods for biomedical applications

Isolation of well-preserved pure cell populations is a prerequisite for sound studies of the molecular basis of any tissue-based biological phenomenon. This updated chapter reviews current methods for obtaining anatomically specific signals from molecules isolated from tissues, a basic requirement for productive linking of phenotype and genotype. The quality of samples isolated from tissue and used for molecular analysis is often glossed over or omitted from publications, making interpretation and replication of data difficult or impossible. Fortunately, recently developed techniques allow life scientists to better document and control the quality of samples used for a given assay, creating a foundation for improvement in this area. Tissue processing for molecular studies usually involves some or all of the following steps: tissue collection, gross dissection/identification, fixation, processing/embedding, storage/archiving, sectioning, staining, microdissection/annotation, and pure analyte labeling/identification and quantification. We provide a detailed comparison of some current tissue microdissection technologies and provide detailed example protocols for tissue component handling upstream and downstream from microdissection. We also discuss some of the physical and chemical issues related to optimal tissue processing and include methods specific to cytology specimens. We encourage each laboratory to use these as a starting point for optimization of their overall process of moving from collected tissue to high-quality, appropriately anatomically tagged scientific results. Improvement in this area will significantly increase life science quality and productivity. The chapter is divided into introduction, materials, protocols, and notes subheadings. Because many protocols are covered in each of these sections, information relating to a single protocol is not contiguous. To get the greatest benefit from this chapter, readers are advised to read through the entire chapter first, identify protocols appropriate to their laboratory for each step in their workflow, and then reread entries in each section pertaining to each of these single protocols.

Genetics of psychiatric disorders methods: molecular approaches

The practice of psychiatry has long suffered from the limited information available on the biological basis of mental disorders. This limitation is now coming to an end. Advances in DNA analysis technologies and in our understanding of the human genome, together with our new knowledge of the properties of the genome and significant efforts toward generating large patient and control sample collections, have paved the way for successful genome-wide association studies. As a result, reports now appear in the literature every week identifying new genes for complex disorders. Next-generation sequencing methods, combined with the results of association and perhaps linkage studies, will help us uncover missing heritability factors, achieve a better understanding of the genetic aspects of psychiatric disease, and devise the best strategies for incorporating genetics in the service of patients.

Genetics of psychiatric disorders methods: molecular approaches

The practice of psychiatry has long suffered from the limited information available on the biological basis of mental disorders. This limitation is now coming to an end. Advances in DNA analysis technologies and in our understanding of the human genome, together with our new knowledge of the properties of the genome and significant efforts toward generating large patient and control sample collections, have paved the way for successful genome-wide association studies. As a result, reports now appear in the literature every week identifying new genes for complex disorders. Next-generation sequencing methods, combined with the results of association and perhaps linkage studies, will help us uncover missing heritability factors, achieve a better understanding of the genetic aspects of psychiatric disease, and devise the best strategies for incorporating genetics in the service of patients.

Quantitative RT-PCR gene expression analysis of laser microdissected tissue samples

Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) is a valuable tool for measuring gene expression in biological samples. However, unique challenges are encountered when studies are performed on cells microdissected from tissues derived from animal models or the clinic, including specimen-related issues, variability of RNA template quality and quantity, and normalization. qRT-PCR using small amounts of mRNA derived from dissected cell populations requires adaptation of standard methods to allow meaningful comparisons across sample sets. The protocol described here presents the rationale, technical steps, normalization strategy and data analysis necessary to generate reliable gene expression measurements of transcripts from dissected samples. The entire protocol from tissue microdissection through qRT-PCR analysis requires approximately 16 h.

Tissue sample collection for proteomics analysis

Successful collection of tissue samples for molecular analysis requires critical considerations. We describe here our procedure for tissue specimen collection for proteomic purposes with emphasis on the most important steps, including timing issues and the procedures for immediate freezing, storage, and microdissection of the cells of interest or "tissue targets" and the lysates for protein isolation for SELDI, MALDI, and 2DGE applications. The pathologist is at the cornerstone of this process and is an invaluable collaborator. In most institutions, pathologists are responsible for "tissue custody," and they closely supervise the tissue bank. In addition, they are optimally trained in histopathology in order to they assist investigators to correlate tissue morphology with molecular findings. In recent years, the advent of the laser capture microscope, a tool ideally designed for pathologists, has tremendously facilitated the efficiency of collecting tissue targets for molecular analysis.

Clinical proteomics: discovery of cancer biomarkers using mass spectrometry and bioinformatics approaches--a prostate cancer perspective

Prostate cancer (PCa) is an intractable disease, where diagnosis and clinical prediction of the disease course and response to treatment is compromised by the lack of objective and robust biomarker assays. In late stage metastatic disease, treatment options are limited, although it is recognized that some patients may benefit from immunotherapy and in particular vaccine therapy. However, research into biomarkers that correlate with the clinical outcome of immunotherapy has lagged behind vaccine development. Thus, proteomic tools are increasingly being utilized for the discovery of biomarkers which will allow us to make clinical decisions about patient treatment at an earlier stage and should aid in shortening the development time for vaccines. In this review we will summarize the various proteomic platforms used to investigate new biomarkers in PCa for better patient diagnosis, prognosis, patient stratification, treatment monitoring and clinical surrogate endpoints. We will discuss method limitations and highlight the key areas of research required for understanding the etiology of PCa.

Tissue microdissection

Procurement of pure populations of cells from heterogeneous histological sections can be accomplished utilizing tissue microdissection. At present, a variety of different manual and laser-based dissection tools are available and each method has particular strengths and weaknesses. The types of biomolecular analyses that can be performed on microdissected cells depend not only on the method of cell procurement, but also on the effects of upstream tissue handling and processing. Tissue preparation protocols include two major approaches; snap-freezing, or, fixation and embedding. Snap-freezing generally provides the best quality tissue for subsequent study, including proteomic analyses such as two-dimensional polyacrylamide gel electrophoresis (2D-PAGE). Tissue fixatives include either precipitating reagents or biomolecular cross-linkers. The fixed samples are then further processed and embedded in a wax medium. In general, the biomolecules recovered from fixed and embedded tissue specimens are lower in both quantity and quality than those from snap-frozen specimens, although they are useful for certain types of analyses. The protocols provided here for tissue handling and processing, preparation of tissue sections, and microdissection are derived from our experience at the Pathogenetics Unit of the National Cancer Institute.

Preservation of skin DNA for oligonucleotide array CGH studies: a feasibility study

Array-based comparative genomic hybridization (a-CGH) is a promising tool for clinical genomic studies. However, pre-analytical sample preparation methods have not been fully evaluated for this purpose. Parallel sections of normal male human skin biopsy samples were collected and immediately immersed in saline, formalin and a molecular fixative for 8, 12 and 24 h. Genomic DNA was isolated from the samples and subjected to amplification and labeling. Labeled samples were then co-hybridized with normal reference female DNA to Agilent oligonucleotide-based a-CGH 44k slides. Pre-analytic parameters such as DNA yield, quality of genomic DNA and labeling efficacy were evaluated. Also microarray analytical variables, including the feature signal intensity, data distribution dynamic range, signal to noise ratio and background intensity levels were assessed for data quality. DNA yield and quality of genomic DNA--as evaluated by spectrophotometry and gel electrophoresis--were similar for fresh and molecular fixative-exposed samples. In addition, labeling efficacy of dye incorporation was not drastically different. There was no difference between fresh and molecular fixative material comparing scan parameters and stem plot analysis of a-CGH result. Formalin-fixed samples, on the other hand, showed various errors such as oversaturation, non-uniformity in replicates, and decreased signal to noise ratio. Overall, the a-CGH result of formalin samples was not interpretable. DNA extracted from formalin-fixed tissue samples is not suitable for oligonucleotide-based a-CGH studies. On the other hand, the molecular fixative preserves tissue DNA similar to its fresh state with no discernable analytical differences.

Extracting quantitative information from tissue--an industrial perspective

The focus of this article is to provide an overview of the current technologies for the pharmaceutical and biotech industry. Disease processes express themselves in the functional and structural disturbance of cellular systems. Cells and their metabolites constitute the building blocks of tissues and entire organisms. Studying the spatial and temporal phenotype of disease processes in tissues at the cellular level reveals a multitude of information about the progress and status of a disease. Detailed exploration of tissues by slide-based cytometry is an important source of information about disease processes. Technological and analytical advances allow us to shed a new light on tissues and to come to a better understanding of the complexity of disease processes. Dealing with complex multidimensional datasets from tissue samples requires an advanced approach to image processing and data management. The increase in computing power and the continuing research into imaging algorithms allow us to improve the exploration of the data content of tissues.

Quantitative expression profile of PSGR in prostate cancer

PSGR is a novel member of the G-protein-coupled olfactory receptor family. Our initial report showed predominant expression of the PSGR in human prostate gland and significant alterations of PSGR expression in primary prostate cancer (CaP) specimens. The aim of this study was to provide in-depth evaluations of the expression profile of PSGR in prostatic epithelial cells of CaP patients and to evaluate the association of PSGR expression characteristics with clinico-pathologic features. In total, 220 RNA specimens, from laser capture microdissected paired benign and malignant prostatic epithelial cells of 110 CaP patients, were analyzed for PSGR expression by quantitative real-time PCR. The differential expression of PSGR between the prostatic epithelial cells of malignant and benign glands was statistically significant (P<0.0001). Comparison of PSGR expression between paired benign and tumor cells revealed prostate tumor cell-specific overexpression in 67.2% of tumor specimens (74 of 110), decreased expression in 20.9% of tumor specimens (23 of 110) and no difference of PSGR expression between tumor and normal cells in 11.8% of specimens (13 of 110). In representative cases, PSGR expression patterns were independently confirmed by in situ RNA hybridization. The PSGR overexpression associated with higher percentage of pathologic stage, pT3, and a higher level of preoperative serum PSA. CaP cells of African-American CaP patients exhibited about two-fold increase of PSGR expression in comparison to the Caucasian American CaP patients. Strikingly high-percentage CaP cells overexpress PSGR warrants further studies of PSGR expression alterations to define subsets of CaPs.

Optimal molecular profiling of tissue and tissue components: defining the best processing and microdissection methods for biomedical applications

Isolation of well-preserved pure cell populations is a prerequisite for sound studies of the molecular basis of any tissue-based biological phenomenon. This article reviews current methods for obtaining anatomically specific signals from molecules isolated from tissues, a basic requirement for productive linking of phenotype and genotype. The quality of samples isolated from tissue and used for molecular analysis is often glossed over or omitted from publications, making interpretation and replication of data difficult or impossible. Fortunately, recently developed techniques allow life scientists to better document and control the quality of samples used for a given assay, creating a foundation for improvement in this area. Tissue processing for molecular studies usually involves some or all of the following steps: tissue collection, gross dissection/identification, fixation, processing/embedding, storage/archiving, sectioning, staining, microdissection/annotation, and pure analyte labeling/identification and quantification. We provide a detailed comparison of some current tissue microdissection technologies, and provide detailed example protocols for tissue component handling upstream and downstream from microdissection. We also discuss some of the physical and chemical issues related to optimal tissue processing, and include methods specific to cytology specimens. We encourage each laboratory to use these as a starting point for optimization of their overall process of moving from collected tissue to high quality, appropriately anatomically tagged scientific results. In optimized protocols is a source of inefficiency in current life science research. Improvement in this area will significantly increase life science quality and productivity. The article is divided into introduction, materials, protocols, and notes sections. Because many protocols are covered in each of these sections, information relating to a single protocol is not contiguous. To get the greatest benefit from this article, readers are advised to read through the entire article first, identify protocols appropriate to their laboratory for each step in their workflow, and then reread entries in each section pertaining to each of these single protocols.

Emerging technologies for the identification of therapeutic targets for the management of pre-eclampsia

Pre-eclampsia is a common and serious complication of pregnancy characterised by hypertension and proteinuria. Genetic and environmental factors influence the occurrence and progression of the disease. Emerging experimental systems and increasingly specific analytical methods for the study of differences between normal and pre-eclamptic placentae are close to identifying specific indicators of disease, which may allow early diagnosis and intervention and reveal targets against which therapeutic agents can be developed.

Selective capture of prostatic basal cells and secretory epithelial cells for proteomic and genomic analysis☆

Basal cells play an undefined role in signaling the growth and differentiation of normal secretory epithelial cells in the human prostate. Because basal cells disappear during malignant transformation, we hypothesize that loss of basal cell function may have a permissive role in progression of prostate intraepithelial neoplasia into invasive carcinoma. We describe an immuno-laser capture microdissection approach to selectively capture basal cells. Using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry, we identified several protein candidates selectively expressed in microdissected basal cells. We also demonstrate that the RNA derived form this technique is an excellent source for gene-array studies. Thus, we provide evidence that proteomic and microgenomic techniques can be successfully applied to investigate the expression profiles of basal and secretory cells after immuno-capture.

Molecular analysis of gene expression in tumor pathology

Human cancers are diverse in their pathology and responsiveness to clinical treatment. This diversity is at least in part due to variations in cellular gene expression programs. Although the analyis of proteins--the key players in cells and potential drug targets--is advancing rapidly, there are situations in which the analysis of RNA rather than proteins can provide valuable information for the diagnosis of cancer. These situations include absense of an antibody for the protein of interest, expression of functionally defective proteins, expressed small nucleotide polymorphisms (SNPs), analysis of alternatively or abnormally spliced molecules, and functional analysis of splice site mutations. In this chapter we will focus on the analysis of RNA from clinical samples and will summarize how gene expression studies on the RNA level using a variety of new tools can be useful for discovering new classes of tumors, for predicting clinical outcome or therapy response, and for designing novel personalized clinical interventions that can not be achieved with histology alone.

Development of rapid staining protocols for laser-capture microdissection of brain vessels from human and rat coupled to gene expression analyses

Laser-capture microdissection (LCM) is a technique that enables selective extraction of desired cells from heterogeneous tissues compatible with subsequent molecular analyses. The specific visualization of desired cell types prior to LCM is essential for achieving selective capture. We have developed rapid and selective staining protocols for LCM extraction of microvessels from human and rat brain. Vessels in human and rat brain sections were visualized by a 2 min exposure to fluorescein-labeled lectins Ulex Europeaus Agglutinin I (UEA I) and Ricinus Communis Agglutinin I (RCA I), respectively. Immunohistochemical staining for the endothelial-specific marker, Factor VIII-related antigen (FVIII-rAg), co-localized with that for either UEA I or RCA I, confirming the selective staining of vascular structures with these lectins. Both brain vessels and perivascular parenchyma were captured using LCM, followed by RNA isolation. RT-PCR analyses demonstrated the enrichment of LCM-captured vessels and parenchyma in FVIII-rAg and GFAP mRNA, respectively. LCM-captured human vessels also expressed the tight junction-specific gene, zonula occludens 1 (ZO-1). LCM extraction of vessels from brain sections can be used to perform molecular fingerprinting of neurovascular unit in various brain pathologies.

Advantages and limitations of microarray technology in human cancer

Cancer is a highly variable disease with multiple heterogeneous genetic and epigenetic changes. Functional studies are essential to understanding the complexity and polymorphisms of cancer. The final deciphering of the complete human genome, together with the improvement of high throughput technologies, is causing a fundamental transformation in cancer research. Microarray is a new powerful tool for studying the molecular basis of interactions on a scale that is impossible using conventional analysis. This technique makes it possible to examine the expression of thousands of genes simultaneously. This technology promises to lead to improvements in developing rational approaches to therapy as well as to improvements in cancer diagnosis and prognosis, assuring its entry into clinical practice in specialist centers and hospitals within the next few years. Predicting who will develop cancer and how this disease will behave and respond to therapy after diagnosis will be one of the potential benefits of this technology within the next decade. In this review, we highlight some of the recent developments and results in microarray technology in cancer research, discuss potentially problematic areas associated with it, describe the eventual use of microarray technology for clinical applications and comment on future trends and issues.

Chapter 5: Viral and host factors in human papillomavirus persistence and progression

Understanding the interdependent roles that host and viral factors play in cervical cancer pathogenesis is important for distinguishing women at the highest risk of human papillomavirus (HPV) persistence and progression to cervical cancer. Ongoing research on viral factors such as viral variants is providing important clues regarding HPV oncogenesis; the comprehensive characterization of the HPV genome and the function of viral genes by HPV type and variant will further this understanding. Although the biologic importance of viral integration and viral load measurements in cervical neoplasia is still being debated, available data are difficult to interpret because of methodologic limitations; to sufficiently address the importance of these events will require further methods validation and subsequent application in epidemiologic studies. Continued and expanded investigation of host immune responses-humoral, cellular, and innate immunity-should specifically address the outcomes of HPV persistence and progression to cervical cancer. Molecularly based assays paired with functional assays will be integral toward the identification and validation of key immune pathways and genes specifically relevant to cervical cancer pathogenesis. Novel technologies such as gene expression microarrays will further allow comprehensive identification of relevant genes that are important at various stages of cervical pathogenesis. The study of viral and host factors will undoubtedly lead to markers that may hold diagnostic and/or prognostic value; the clinical validity and utility of these molecular events will, therefore, need to be carefully assessed before implementation in a population setting.

Identification of genes up-regulated in urothelial tumors: the 67-kd laminin receptor and tumor-associated trypsin inhibitor

Studies investigating changes in gene expression in urothelial carcinoma have generally compared tumors of different stages and grades but comparisons between low-grade, noninvasive tumors and normal urothelium are needed to identify genes involved in early tumor development. We isolated the urothelium from a low-grade tumor and corresponding normal mucosa by laser capture microdissection on frozen sections. The RNA extracted was amplified to generate suppressive subtractive cDNA libraries. Random sequencing of cDNA clones identified approximately 100 unique species. Of these 83% were known genes, 15% had homology to genes with an unknown function in humans, and 2% did not show homology to any published gene sequence. Two of the known genes, the 67-kd laminin receptor (67LR) and tumor-associated trypsin inhibitor (TATI), had previously been associated with metastatic progression in many tumor types, although 67LR has not been investigated in urothelial tumors. Immunolabeling of the original tissue with antibodies against these two genes confirmed overexpression, validating our strategy: 67LR was not expressed in the normal urothelium but was present in the tumor, whereas TATI expression was confined to umbrella cells in the normal urothelium, but extended to all cell layers in the tumor. We investigated both markers further in a separate series of tumors of different stages and grades. TATI was more consistently overexpressed than 67LR in all tumor grades and stages. Levels of secreted TATI were significantly higher in urine samples from patients with tumors compared to controls. Our strategy, combining laser capture microdissection and cDNA library construction, has identified genes that may be involved in the early phases of urothelial tumor development rather than with disease progression, highlighting the importance of comparing tumor with normal rather than just tumors of different stages and grades.

Combined histomorphometric and gene-expression profiling applied to toxicology

We have developed a unique methodology for the combined analysis of histomorphometric and gene-expression profiles amenable to intensive data mining and multisample comparison for a comprehensive approach to toxicology. This hybrid technology, termed extensible morphometric relational gene-expression analysis (EMeRGE), is applied in a toxicological study of time-varied vehicle- and carbon-tetrachloride (CCl4)-treated rats, and demonstrates correlations between specific genes and tissue structures that can augment interpretation of biological observations and diagnosis.

Gene expression profiling using laser capture microdissection

Human disease is governed by a complex array of cellular populations and sub-population. Gene expression profiling is proving an important means of understanding and classifying pathophysiologic processes by identifying genes, gene pathways and pathway networks not previously known to be associated with particular diseases. However, disease-associated gene expression can be obscured by surrounding 'normal' tissue. Laser capture microdissection allows gene expression analysis of pooled single cells, cell subpopulations and cell populations. Analysis of laser capture microdissection-procured cells will allow a better understanding of the cellular components of disease.

Banking of fresh-frozen prostate tissue: methods, validation and use

OBJECTIVE

To describe the establishment, methods, validation and use of a bank of fresh-frozen human prostate tissue.

MATERIALS AND METHODS

On obtaining informed patient consent, protocols were followed for banking prostate tissue from any type of prostatectomy or cystoprostatectomy. A pseudobanking procedure was devised to determine the accuracy of assessing the histopathological status of the banked tissue. RNA was extracted, its quality assessed and used for quantitative real-time reverse transcription-polymerase chain reaction for the serine protease hepsin.

RESULTS

To date prostate tissue from 112 patients has been banked, with pseudobanking in 58. The histopathological assessment showed pseudobanked tissue matched adjacent unbanked tissue in 98% of cases for benign vs malignant diagnoses, and in 92% of carcinomas for the Gleason score. Hepsin expression was significantly higher in malignant than in benign tissues (P < 0.0001).

CONCLUSION

We established a validated method for banking human fresh-frozen prostate tissue and applied it successfully. Hepsin expression can be used to differentiate malignant and benign prostate tissue, and as an indicator of tissue heterogeneity.

Differential analysis of DNA microarray gene expression data

Here, we review briefly the sources of experimental and biological variance that affect the interpretation of high-dimensional DNA microarray experiments. We discuss methods using a regularized t-test based on a Bayesian statistical framework that allow the identification of differentially regulated genes with a higher level of confidence than a simple t-test when only a few experimental replicates are available. We also describe a computational method for calculating the global false-positive and false-negative levels inherent in a DNA microarray data set. This method provides a probability of differential expression for each gene based on experiment-wide false-positive and -negative levels driven by experimental error and biological variance.

Monoclonal antibodies as therapeutics in oncology

The specificity of antibodies has been harnessed to target cancer cells and the first therapeutic antibodies for use in oncology are now finding application in the clinic. Studies are currently under way to develop new and improved antibodies. Recent developments have been made in the identification of novel targets, including the use of genomic and proteomic technologies. Several methods are also being developed to enhance antibody efficacy.

Nuclear matrix proteins as biomarkers for breast cancer

Breast cancer remains a leading cause of cancer death in women despite widespread screening, in part because screening mammography has high rates of false-negative results and because many women decline to have routine mammograms. The development of sensitive and specific assays for breast tumor markers would improve detection and facilitate screening, diagnosis, therapeutic monitoring and surveillance for recurrence. Nuclear matrix proteins (NMPs) are promising candidates for tumor markers because they are involved in malignant transformation. Therefore, they may be useful for screening and early diagnosis of small tumors. Proteomic analysis was used to demonstrate that a 28.3 kD serum protein, designated NMP66, can distinguish malignant disease from benign conditions and normal controls. NMP66 is now being evaluated as a potential biomarker for early breast cancer detection in large-scale clinical trials.