Molecular profiling of clinical tissues specimens: feasibility and applications

Integrated Analysis Reveals ENDOU as a Biomarker in Head and Neck Squamous Cell Carcinoma Progression

Background

Head and neck squamous cell carcinoma (HNSCC) is a leading cancer with high morbidity and mortality worldwide. The aim is to identify genes with clinical significance by integrated bioinformatics analysis and investigate their function in HNSCC.

Methods

We downloaded and analyzed two gene expression datasets of GSE6631 and GSE107591 to screen differentially expressed genes (DEGs) in HNSCC. Common DEGs were functionally analyzed by Gene ontology and KEGG pathway enrichment analysis. Protein-protein interaction (PPI) network was constructed with STRING database and Cytoscape. ENDOU was overexpressed in FaDu and Cal-27 cell lines, and cell proliferation and migration capability were evaluated with MTT, scratch and transwell assay. The prognostic performance of ENDOU and expression correlation with tumor infiltrates in HNSCC were validated with TCGA HNSCC datasets.

Results

Ninety-eight genes shared common differential expression in both datasets, with core functions like extracellular matrix organization significantly enriched. 15 genes showed prognostic significance, and COBL and ENDOU serve as independent survival markers in HNSCC. In-vitro ENDOU overexpression inhibited FaDu and Cal-27 cells proliferation and migration, indicating its tumor-suppressing role in HNSCC progression. GSEA analysis indicated ENDOU down-stream pathways like DNA replication, mismatch repair, cell cycle and IL-17 signaling pathway. ENDOU showed relative lower expression in HNSCC, especially HPV-positive HNSCC samples. At last, ENDOU showed negative correlation with tumor purity and tumor infiltrating macrophages, especially M2 macrophages.

Conclusion

This study identified ENDOU as a biomarker with prognostic significance in HNSCC progression.

The Journal of Molecular Diagnostics: 20 Years Defining Professional Practice

This editorial highlights 20 years of JMD defining professional practice.

DNA Hybridization Arrays for Gene Expression Analysis of Human Oral Cancer

DNA hybridization arrays permit global gene expression profiling to be done in a single experiment. The evolution and challenges of DNA hybridization arrays are reflected in the variety of experimental platforms, probe composition, hybridization/signal detection methods, and bioinformatic interpretation. In tumor biology, DNA hybridization arrays are being used for gene/gene pathway discovery, diagnosis, and therapeutic design. Similar applications are advancing our understanding of oral cancer cell biology.

Tissue imprint for molecular mapping of deep surgical margins in patients with head and neck squamous cell carcinoma

BACKGROUND

Tissue imprinting can generate molecular marker maps of tumor cells at deep surgical margins. The purpose of this study was to evaluate the feasibility of this method for detection of residual head and neck squamous cell carcinoma (HNSCC).

METHODS

Paired fresh tissue and nitrocellulose membrane imprints of tumor and deep margins were collected from 17 HNSCC resections. DNA was amplified using quantitative methylation-specific polymerase chain reaction (qMSP) for p16, DCC, KIF1A, and EDNRB. Levels of methylation in tumors and deep margins were compared.

RESULTS

DNA from imprints was adequate for qMSP. Hypermethylation of target genes was present in 12 of 17 tumors and in 8 deep margins. Methylation level was better from margin imprints than tissue. During follow-up (median, 13 months), local or regional recurrences occurred in 6 cases of which 5 had molecularly positive margins.

CONCLUSION

Tissue imprinting is feasible for molecular detection of residual tumor at deep surgical margins and may correlate with locoregional recurrence.

Evaluation of Maxwell® 16 for automated DNA extraction from whole blood and formalin-fixed paraffin embedded (FFPE) tissue

BACKGROUND

The aim of the study was to assess the performance of Promega, Maxwell® 16 for the extraction of genomic DNA from whole blood and FFPE tissue.

METHODS

DNA was extracted from 10 whole blood and 10 FFPE specimens using six different commercial kits.

RESULTS

For whole blood, the mean DNA concentration obtained by Maxwell® 16 was significantly greater than either easyMAG® (p<0.0001) or QIAamp® Blood DNA kit (p<0.001). For FFPE, the mean DNA concentration obtained by the AllPrep® FFPE specific DNA/RNA kit was significantly greater than either the Maxwell® 16 (p<0.0001) or the general AllPrep® DNA/RNA kit (p<0.0001).

CONCLUSIONS

Comparative evaluation of the six DNA extraction kits indicated that the semi-automated Maxwell® 16 was superior for whole blood extraction while the manual AllPrep® FFPE DNA/RNA kit (Qiagen) performed better for FFPE DNA extraction in terms of quantity of DNA obtained. All six extraction methods (blood and FFPE) performed well in terms of purity. Although there were variances in the quantity of DNA obtained, there were no significant differences in the efficiency of these methods in yielding amplifiable DNA extracts, as demonstrated by β-actin for whole blood specimens. In evaluation of FFPE DNA extraction methods, the Qiagen AllPrep® FFPE DNA/RNA Mini Kit was the best for applications requiring larger amplicons, but for smaller amplicons the Maxwell was most consistent.

Why is it crucial to reintegrate pathology into cancer research?

The integration of pathology with molecular biology is vital if we are to enhance the translational value of cancer research. Pathology represents a bridge between medicine and basic biology, it remains the gold standard for cancer diagnosis, and it plays an important role in discovery studies. In the past, pathology and cancer research were closely associated; however, the molecular biology revolution has shifted the focus of investigators toward the molecular alterations of tumors. The reductionist approach taken in molecular studies is producing great insight into the inner workings of neoplasia, but it can also minimize the importance of histopathology and of understanding the disease as a whole. In turn, pathologists can underestimate the role of molecular studies in developing new ancillary techniques for clinical diagnosis. A multidisciplinary approach that integrates pathology and molecular biology within a translational research system is needed. This process will require overcoming cultural barriers and can be achieved through education, a more effective incorporation of pathology into biological research, and conversely an integration of biological research into the pathology laboratory.

Influence of hypoxia induced by minimally invasive prostatectomy on gene expression: implications for biomarker analysis

Handling and processing of clinical specimens during and after surgical resection may significantly skew the molecular data obtained from analysis of those samples. Minimally invasive prostatectomy was used as a model to specifically study effects of surgical ischemia on gene expression in human clinical samples. Normal prostatic urethra cup biopsies were procured from 12 patients at three time points during laparoscopic radical prostatectomy. Homogeneous cells (stroma and epithelium) were microdissected. Transcript analysis of 3 oxygen-dependent, 3 oxygen-independent, and 3 control class genes was performed using quantitative RT-PCR. Data were analyzed by relative quantitation and two-sided t-test. Patient demographic and time covariates were fit by a linear mixed model. VEGF, an oxygen-dependent gene, showed significant expression alterations across three time points in epithelium (p=0.008), but not in stroma (p=0.66). Expression levels of VHL, STAT5B, and CYPA showed significant changes at the p<0.05 level in the stroma only. Effects of age, PSA, prostate size, Gleason score, surgery type, total surgery time, total ischemia time, and estimated blood loss on VEGF expression over time were not significant at the p<0.01 level. Therefore, surgical manipulation and tissue processing methods need to be taken into account when assessing prostatic biomarkers; however, resection does not dramatically alter mRNA profiles in prostate specimens.

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.

Approaching solid tumor heterogeneity on a cellular basis by tissue proteomics using laser capture microdissection and biological mass spectrometry

The purpose of this study was to examine solid tumor heterogeneity on a cellular basis using tissue proteomics that relies on a functional relationship between Laser Capture Microdissection (LCM) and biological mass spectrometry (MS). With the use of LCM, homogeneous regions of cells exhibiting uniform histology were isolated and captured from fresh frozen tissue specimens, which were obtained from a human lymph node containing breast carcinoma metastasis. Six specimens approximately 50,000 cell each (three from tumor proper and three from tumor stroma) were collected by LCM. Specimens were processed directly on LCM caps, using sonication in buffered methanol to lyse captured cells, solubilize, and digest extracted proteins. Prepared samples were analyzed by LC/MS/MS resulting in more than 500 unique protein identifications. Decoy database searching revealed a false-positive rate between 5 and 10%. Subcellular localization analysis for stromal cells revealed plasma membrane 14%, cytoplasm 39%, nucleus 11%, extracellular space 27%, and unknown 9%; and tumor cell results were 5%, 58%, 26%, 4%, and 7%, respectively. Western blot analysis confirmed specific linkage of validated proteins to underlying pathology and their potential role in solid tumor heterogeneity. With continued research and optimization of this method including analysis of additional clinical specimens, this approach may lead to an improved understanding of tumor heterogeneity, and serve as a platform for solid tumor biomarker discovery.

Importance of cell-procurement methods in transforming personalized cancer treatment from concept to reality

The much-anticipated promise of personalized cancer care is to deliver therapies best suited for a patient based on the knowledge of that individual's genetics and tumor characteristics. This transformative approach will require many changes in the scientific and medical community, one of the most fundamental being the direct study of human tissue biospecimens. Biospecimens will be integral to the elucidation of biomarkers that will help identify and serve as potential diagnostic, prognostic and therapeutic targets in cancer. Despite the vast repositories of fixed-tissue biospecimens that are in existence, a number of flaws exist that hinder their reliable use as instruments from which to enable personalized cancer research and clinical care. A new view of biospecimen worth in the future will mandate that the molecules within its cells are reflective of their in vivo state, and not altered by external variables introduced during the excision and processing of the biospecimen. Research on biospecimen collection is a legitimate field of study that will be necessary for personalized cancer care to become a reality.

A comparative analysis of two tissue procurement approaches for the genomic profiling of clinical colorectal cancer samples

BACKGROUND

The basis for personalized medicine is the creation of a repository of knowledge about the genetic alterations involved in disease processes. Integral to achieving this goal is the querying of well-preserved, high-quality human tissue samples. Making these findings relevant involves the interrogation of large numbers of samples. The pace with which changes have occurred versus the potential pace with which changes can occur may be indicative of problems associated with traditional approaches on collecting biospecimens. Therefore, transforming personalized medicine from concept to reality may require an alternative approach in the field of tissue specimen procurement.

MATERIALS AND METHODS

"Exfoliation and Enrichment" (EE), a recently described rapid and cost-effective approach for procuring cells, was utilized and assessed relative to a more traditional but temporally and economically comparable approach. Material from the same tumor sample, one collected by EE but the other frozen, were procured, the DNA extracted, and the samples analyzed at the global and gene-specific level by array comparative genomic hybridization and quantitative polymerase chain reaction, respectively.

RESULTS

Both approaches resulted in the rapid procurement and retrieval of well-preserved cells and nucleic acids. The presence of "contaminating" normal cells in the more traditional approach masked the significance of genetic gains and losses, findings that were more readily apparent from the material derived by the EE method.

CONCLUSION

The EE approach represents a cost-effective alternative to traditional cell-procurement methods that results in the generation of superior genomic data.

Infrared micro-spectral imaging: distinction of tissue types in axillary lymph node histology

Background

Histopathologic evaluation of surgical specimens is a well established technique for disease identification, and has remained relatively unchanged since its clinical introduction. Although it is essential for clinical investigation, histopathologic identification of tissues remains a time consuming and subjective technique, with unsatisfactory levels of inter- and intra-observer discrepancy. A novel approach for histological recognition is to use Fourier Transform Infrared (FT-IR) micro-spectroscopy. This non-destructive optical technique can provide a rapid measurement of sample biochemistry and identify variations that occur between healthy and diseased tissues. The advantage of this method is that it is objective and provides reproducible diagnosis, independent of fatigue, experience and inter-observer variability.

Methods

We report a method for analysing excised lymph nodes that is based on spectral pathology. In spectral pathology, an unstained (fixed or snap frozen) tissue section is interrogated by a beam of infrared light that samples pixels of 25 μm × 25 μm in size. This beam is rastered over the sample, and up to 100,000 complete infrared spectra are acquired for a given tissue sample. These spectra are subsequently analysed by a diagnostic computer algorithm that is trained by correlating spectral and histopathological features.

Results

We illustrate the ability of infrared micro-spectral imaging, coupled with completely unsupervised methods of multivariate statistical analysis, to accurately reproduce the histological architecture of axillary lymph nodes. By correlating spectral and histopathological features, a diagnostic algorithm was trained that allowed both accurate and rapid classification of benign and malignant tissues composed within different lymph nodes. This approach was successfully applied to both deparaffinised and frozen tissues and indicates that both intra-operative and more conventional surgical specimens can be diagnosed by this technique.

Conclusion

This paper provides strong evidence that automated diagnosis by means of infrared micro-spectral imaging is possible. Recent investigations within the author's laboratory upon lymph nodes have also revealed that cancers from different primary tumours provide distinctly different spectral signatures. Thus poorly differentiated and hard-to-determine cases of metastatic invasion, such as micrometastases, may additionally be identified by this technique. Finally, we differentiate benign and malignant tissues composed within axillary lymph nodes by completely automated methods of spectral analysis.

Preservation of biomolecules in breast cancer tissue by a formalin-free histology system

Background

The potential problems associated with the use of formalin in histology, such as health hazards, degradation of RNA and cross-linking of proteins are well recognized. We describe the utilization of a formalin-free fixation and processing system for tissue detection of two important biopredictors in breast cancer – estrogen receptor and HER2 – at the RNA and protein levels.

Methods

Parallel sections of 62 cases of breast cancer were fixed in an alcohol-based molecular fixative and in formalin. Molecular fixative samples were processed by a novel formalin-free microwave-assisted processing system that preserves DNA, RNA and proteins. Formalin-fixed samples were processed using the conventional method. Estrogen receptor was assessed by immunohistochemistry and real-time PCR. HER2 was assessed by immunohistochemistry, FISH, CISH and real-time PCR.

Results

The immunohistochemical reaction for estrogen receptor was similar in molecular- and formalin-fixed samples (Spearman Rank R = 0.83, p < 0.05). Also HER2 result was similar to that of formalin-fixed counterparts after elimination of antigen retrieval step (Spearman Rank R = 0.84, p < 0.05). The result of HER2 amplification by FISH and CISH was identical in the molecular fixative and formalin-fixed samples; although a shorter digestion step was required when using the former fixative. Real-time PCR for both estrogen receptor and HER2 were successful in all of the molecular fixative specimens.

Conclusion

The formalin-free tissue fixation and processing system is a practical platform for evaluation of biomolecular markers in breast cancer and it allows reliable DNA and RNA and protein studies.

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.

Laser-capture microdissection

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 thorough molecular analysis, one must be able to analyze specific cell populations within the context of their heterogeneous tissue microecology. Laser-capture microdissection (LCM) is a method to procure subpopulations of tissue cells under direct microscopic visualization. LCM 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 (LOH) analysis, RNA transcript profiling, cDNA library generation, proteomics discovery and signal-pathway profiling. Herein we provide a thorough description of LCM techniques, with an emphasis on tips and troubleshooting advice derived from LCM users. The total time required to carry out this protocol is typically 1-1.5 h.

An exfoliation and enrichment strategy results in improved transcriptional profiles when compared to matched formalin fixed samples

Background

Identifying the influence formalin fixation has on RNA integrity and recovery from clinical tissue specimens is integral to determining the utility of using archival tissue blocks in future molecular studies. For clinical material, the current gold standard is unfixed tissue that has been snap frozen. Fixed and frozen tissue however, both require laser capture microdissection to select for a specific cell population to study. The recent development of a sampling method capable of obtaining a viable, enriched cell population represents an alternative option in procuring cells from clinical material for molecular research purposes. The expression profiles of cells obtained by using this procurement approach, in conjunction with the profiles from cells laser capture microdissected from frozen tissue sections, were compared to the expression profiles from formalin fixed cells to determine the influence fixation has on expression profiles in clinical material.

Methods

Triplicate samples of non-neoplastic colonic epithelial cells were recovered from a hemicolectomy specimen using three different procurement methods from the same originating site: 1) an exfoliation and enrichment strategy 2) laser capture microdissection from formalin fixed tissue and 3) laser capture microdissection from frozen tissue. Parameters currently in use to assess RNA integrity were utilized to assess the quality of recovered RNA. Additionally, an expression microarray was performed on each sample to assess the influence each procurement technique had on RNA recovery and degradation.

Results

The exfoliation/enrichment strategy was quantitatively and qualitatively superior to tissue that was formalin fixed. Fixation negatively influenced the expression profile of the formalin fixed group compared to both the frozen and exfoliated/enrichment groups.

Conclusion

The exfoliation/enrichment technique represents a superior alternative in tissue procurement and RNA recovery relative to formalin fixed tissue. None of the deleterious effects associated with formalin fixation are encountered in the exfoliated/enriched samples because of the absence of its use in this protocol. The exfoliation/enrichment technique also represents an economical alternative that will yield comparable results to cells enriched by laser capture microdissection from frozen tissue sections.

Genome-controlled reverse transcriptase-polymerase chain reaction for targeted gene-expression analysis

OBJECTIVE

Although gene-expression profiling has an important part to play in the classification of tumours and premalignant conditions, reproducibility of the present polymerase chain reaction (PCR)-based quantitative techniques needs to be improved for diagnostic purposes and to enable analysis of gene expression in formalin-fixed paraffin-embedded (FFPE) tissue samples. We have developed reverse transcriptase-PCR-based technology for quantitative assessment of the relative content of multiple mRNA transcripts in small tissue or cell samples.

MATERIAL AND METHODS

A multiplexed sequence modifying cDNA synthesis reaction is performed with this technique to create a 4-5 degrees increase in the melting temperature of subsequent short (56-64 bp) PCR amplicons. Each cDNA template is competitively co-amplified with genomic DNA, which serves as a universal internal standard. The relative amounts of cDNA and genomic DNA-derived amplicons are quantified in-tube by homogeneous melting curve analysis.

RESULTS

The dynamic range of the assay was three orders of magnitude, while the detection limit was 100 cDNA molecules. A prototype assay, consisting of the analysis of eight genes, displayed good reproducibility (inter-assay CV 5-20 %) compared to the TaqMan assay (inter-assay CV 7-43 %). Gene-expression analysis could be performed in 20 of 20 (100 %) archival frozen samples, in 30 of 35 (86 %) archival FFPE samples and in 26 of 27 (96 %) endoscopic biopsies.

CONCLUSIONS

We demonstrate that this new technique enables accurate analysis of mRNA expression in cultured cells and endoscopic tissue biopsies. Sensitive analysis FFPE tissue is also possible thanks to the short PCR amplicons.

Tissue detection of biomolecular predictors in breast cancer

One of the promises of modern biotechnology is to improve medical care by providing accurate diagnosis and targeted treatment to patients who will derive the maximum benefit. Delivery of this promise in the 21st century is the result of major advances in biotechnology over the past 20 years. Sequencing of the human genome and other high-volume data discovery has become possible, owing to relatively inexpensive computation power and automation. The same forces that drove the human genome project are now being focused on cataloging various disease processes at the DNA, RNA and protein levels. As these high-throughput technologies are entering the clinical care environment, the major task at hand is to integrate the complex data and derive clinically useful information. In spite of major breakthroughs in molecular approaches to the diagnosis and prognostication of cancer, there remain significant obstacles in applying these technologies to clinical samples. The time-honored conventional histopathology, for example, is still the backbone of tumor diagnosis and prognostication. The traditional fixation and processing methods are, however, rapidly losing ground, as they do not protect important tissue macromolecules. Formalin, the common universal fixative, is losing its place in histopathology. In addition to its toxicity, it alters macromolecules and renders the tissue unfit for most advanced molecular studies. This has prompted the use of fresh or fresh-frozen biopsy material for most biomolecular discoveries and clinical assays. This of course is impractical, or even impossible, in most clinical settings, particularly since tumors are being detected earlier and smaller. Also, many preneoplastic conditions are impossible to triage for freezing since their accurate diagnosis requires the use of the entire sample for detailed microscopic examination. The focus in this report is on breast cancer, where the value of the innovative approaches of the tissue detection of biomolecular predictors is examined. To this end, novel tissue handling platforms are introduced that are not only suitable for histological diagnosis, but allow the detection of tumor proteome and expression profiles on the same biopsy sample.

Targeted gene-expression analysis by genome-controlled reverse transcription-PCR

BACKGROUND

For gene-expression analysis, which is anticipated to play an important role in classification of tumors and premalignant conditions, PCR-based quantitative assays must have increased diagnostic quantitative accuracy and reproducibility and enable analysis of gene expression in formalin-fixed paraffin-embedded (FFPE) tissue samples.

METHODS

We developed a reverse transcription-PCR-based quantitative assay that modifies the cDNA sequence to increase the melting temperature of short (56-64 bp) PCR amplicons, enabling their quantification in-tube by homogeneous melting-curve analysis. We used this method to analyze the expression of 8 genes, 7 potential colon cancer markers, and 1 control in samples obtained from 3 colon carcinoma cell lines, endoscopic biopsy from 8 patients undergoing gastroscopy for Barrett esophagus, and archival FFPE and frozen tissue from 20 patients who underwent surgery for colon carcinoma.

RESULTS

The detection limit of the assay, when optimized for FFPE samples, was 100 copies of cDNA, and the dynamic range was 3 orders of magnitude. A prototype assay containing a panel of 8 genes displayed good reproducibility compared with the commercially available TaqMan assay (interassay CVs, 5%-20% vs 7%-43%, respectively). Gene-expression analysis was performed successfully in 26 (96%) of 27 endoscopic biopsy specimens, 30 (86%) of 35 archival FFPE samples, and 20 (100%) of 20 archival frozen samples.

CONCLUSIONS

This new technology combines the reproducibility of competitive PCR with accurate quantitative detection by in-tube melting-curve analysis, enabling efficient analysis of mRNA profiles in samples with small numbers of cells or small amounts of tissue, as well as in archival FFPE tissues.

Reliable amplification method for bacterial RNA

DNA microarray technology has been increasingly applied for studies of clinical samples. Frequently, RNA probes from clinical samples are available in limited amounts. We describe a reliable amplification method for bacterial RNA. We verified this method on mycobacterial RNA applying mycobacterial genome-directed primers (mtGDPs). Glass slide-based oligoarrays were employed to assess the quality of the amplification method. We observed a relatively small bias in amplified RNA pool when compared to the unamplified one. Up to 1000-fold linear RNA amplification in a single amplification round was obtained. To our knowledge, this study describes the first amplification method for mycobacterial RNA.

Grating-coupled surface plasmon resonance: a cell and protein microarray platform

Grating-coupled surface plasmon resonance (GCSPR) is a method for the accurate assessment of analyte in a multiplexed format using small amounts of sample. In GCSPR, the analyte is flowed across specific receptors (e.g. antibodies or other proteins) that have been immobilized on a sensor chip. The chip surface is illuminated with p-polarized light that couples to the gold surface's electrons to form a surface plasmon. At a specific angle of incidence, the GCSPR angle, the maximum amount of coupling occurs, thus reducing the intensity of reflected light. Shifts in the GCSPR angle can be correlated with refractive index increases following analyte capture by chip-bound receptors. Because regions of the chip can be independently analyzed, this system can assess 400 interactions between analyte and receptor on a single chip. We have used this label-free system to assess a number of molecules of immunological interest. GCSPR can simultaneously detect an array of cytokines and other proteins using the same chip. Moreover, GCSPR is also compatible with assessments of antigen expression by intact cells, detecting cellular apoptosis and identifying T cells and B cells. This technology represents a powerful new approach to the analysis of cells and molecular constituents of biological samples.

Manual exfoliation plus immunomagnetic bead separation as an initial step toward translational research

CONTEXT

The development of biotechnologic platforms capable of high throughput analysis has ushered in a promising new era of translational medicine. However, most studies to date are based on in vitro cell lines or substitute models for human disease. Although these model systems have proven insightful, it is readily becoming apparent that human clinical tissue must be studied in order to fully understand all the nuances of human disease. Studies that are based on human tissue, however, are limited by qualitative and quantitative issues, factors often precluding their use in high throughput studies.

OBJECTIVE

To develop a simple and rapid tissue procurement protocol for use in obtaining a homogeneous epithelial cell population from clinical tissue and the recovery of nucleic acids and proteins of high quality and quantity. Also, to determine if the technique preserves tissue, thereby allowing morphologic correlation with molecular findings.

DESIGN

Performance of manual exfoliation to procure cells from clinical resection specimens and use of immunomagnetic beads embedded with the antibody ber-Ep4 for the positive enrichment of a homogeneous epithelial cell population. Nucleic acids and proteins are then separated using a phenol plus guanidine thiocyante solution. Nucleic acids and proteins are quantitated and qualitatively analyzed using standard laboratory techniques.

RESULTS

Nucleic acids and proteins of high quality and quantity were recovered following manual exfoliation and immunomagnetic bead separation. Tissue architecture was not destroyed, thus permitting histologic and molecular correlation.

CONCLUSIONS

A simple and reproducible protocol is presented that may enable the molecular profiling of clinically resected tissue. Although the technique is currently limited to certain tissue and tumor types, further research will broaden its overall application.

Manual exfoliation of fresh tissue obviates the need for frozen sections for molecular profiling

BACKGROUND

Simple, rapid tissue processing that preserves macromolecules will enhance translational research capabilities. Traditional fixative-based approaches for specimen preservation are ideal for histologic evaluation but are not conducive to molecular studies of nucleic acids and protein. Tissue cryosections preserve macromolecule integrity, but the process is labor intensive and technically challenging. To the authors' knowledge to date, an alternative method capable of retrieving cells while providing adequate histologic detail yet preserving macromolecule integrity has been lacking. In the current study, the authors evaluated the utility of using manual exfoliation of clinical tissue samples as a means of obtaining cells for molecular analysis. This technique possesses the advantages of fixed and frozen tissue sections without their drawbacks. This simple, rapid, nonfixative based technique is capable of preparing cells from human clinical material for further isolation without compromising the preservation of macromolecules in the tissue.

METHODS

Cells from a variety of clinical resection specimens from solid tumors were directly scraped from the tissue samples using the edge of a glass microscope slide and smeared onto another slide for cytologic evaluation. The manually exfoliated cells were evaluated microscopically for cytologic quality and cellular quantity. Pure cell populations were procured by laser capture microdissection (LCM) with subsequent extraction of nucleic acids and proteins. The integrity and suitability of the recovered nucleic acids and proteins for molecular analysis were evaluated using the polymerase chain reaction (PCR), reverse transcriptase-PCR, and reverse-phase protein microarray, respectively.

RESULTS

Manual exfoliation permits the selection of homogeneous cell populations by LCM based on well established cytologic characteristics. DNA and mRNA, of comparable quality to frozen sections, can be amplified from the manual exfoliation cells. Proteins of similar quality can be recovered using this technique and quantitated via reverse-phase protein microarray.

CONCLUSIONS

Molecular macromolecules of high quality and sufficient quantity can be retrieved from human clinical samples using manual exfoliation and LCM to procure specific cell populations. The manual exfoliation technique does not destroy the original tissue source, thereby allowing subsequent formalin tissue fixation. The technique of manual exfoliation in conjunction with LCM can enable the molecular profiling of a sampled selected cell population. Because it does not destroy the original tissue, histologic correlation can be combined with molecular profiling.

Microarrays in veterinary diagnostics

Microarrays have numerous applications in the clinical setting, and these uses are not confined to the study of common human diseases. Indeed, the high-throughput technology affects clinical diagnostics in a variety of contexts, and this is reflected in the increasing use of microarray-based tools in the development of diagnostic and prognostic tests and in the identification of novel therapeutic targets. While much of the value of microarray-based experimentation has been derived from the study of human disease, there is equivalent potential for its role in veterinary medicine. Even though the resources devoted to the study of animal molecular diagnostics may be less than those available for human research, there is nonetheless a growing appreciation of the value of genome-wide information as it applies to animal disease. Therefore, this review focuses on the basics of microarray experimentation, and how this technology lends itself to a variety of diagnostic approaches in veterinary medicine.

Combined laser capture microdissection and serial analysis of gene expression from human tissue samples

Cell-specific gene expression profiling from heterogeneous human tissues is confounded by cell purification limitations. Here, we describe a technique to generate gene expression profiles of pure populations of prostate cancer cells obtained from fresh-frozen prostatectomy specimens and small initial quantities of RNA by combining laser capture microdissection and microserial analysis of gene expression (LCM-microSAGE). Two microSAGE libraries were obtained from approximately 100,000 laser pulses, estimated to contain fewer than 3 x 10(5) cells and 20-30 ng mRNA. Two libraries were sequenced to a depth of 10,111 and 10,463 unique tags from normal and cancer cells, representing 6453 and 6923 genes, respectively. Most transcripts were expressed at similar levels, but cancer cells compared with normal cells had increased expression of 385 tags and decreased expression of 389 tags. A total of 20 genes were differentially expressed (P<0.05); five of these genes were upregulated and 15 were downregulated in cancer cells. Quantitative reverse transcriptase-polymerase chain reaction results from three selected genes corroborated the existence of cell-specific gene expression in LCM-microSAGE-derived libraries. In conclusion, the LCM-microSAGE approach demonstrates that large-scale expression profiles of known and unknown transcripts can be generated from pure populations of target cells obtained from human tissue samples comprised of heterogeneous mixtures of cell types.

Serum, salivary and tissue proteomics for discovery of biomarkers for head and neck cancers

Initial clinically oriented applications of emerging proteomic technologies that aim to identify biomarkers for head and neck squamous cell carcinoma diagnostics have yielded promising results. The development of new proteomic diagnostics remains critical for the early detection of head and neck squamous cell carcinoma at more treatable stages. Prognostic markers for disease recurrence and treatment sensitivities are also required. In this overview of current biomarker identification strategies for head and neck squamous cell carcinoma, different combinations of mass spectrometry platforms, laser capture microscopy and 2D gel electrophoresis procedures are summarized as applied to readily available clinical specimens (tissue, blood and saliva). Issues related to assay reproducibility, management of large data sets and future improvements in clinical proteomics are also addressed.

Tissue-print and print-phoresis as platform technologies for the molecular analysis of human surgical specimens: mapping tumor invasion of the prostate capsule

Molecular profiling of human biopsies and surgical specimens is frequently complicated by their inherent biological heterogeneity and by the need to conserve tissue for clinical diagnosis. We have developed a set of novel 'tissue print' and 'print-phoresis' technologies to facilitate tissue and tumor-marker profiling under these circumstances. Tissue printing transfers cells and extracellular matrix components from a tissue surface onto nitrocellulose membranes, generating a two-dimensional anatomical image on which molecular markers can be visualized by specific protein and RNA- and DNA-detection techniques. Print-phoresis is a complementary new electrophoresis method in which thin strips from the print are subjected to polyacrylamide gel electrophoresis, providing a straightforward interface between the tissue-print image and gel-based proteomic techniques. Here we have utilized these technologies to identify and characterize markers of tumor invasion of the prostate capsule, an event generally not apparent to the naked eye that may result in tumor at the surgical margins ('positive margins'). We have also shown that tissue-print technologies can provide a general platform for the generation of marker maps that can be superimposed directly onto histopathological and radiological images, permitting molecular identification and classification of individual malignant lesions.

Genomics and proteomics: application of novel technology to early detection and prevention of cancer

Advances in molecular biology over the past decade have helped to enhance our understanding of the complex interplay between genetic, transcriptional and translational alterations in human cancers. These molecular changes are the basis for an evolving field of high-throughput cancer discovery techniques using microscopic amounts of patient-based materials. Laser capture microdissection allows pure populations of cells to be isolated from both the tumor and stroma in order to identify subtle differences in RNA and protein expression. Comparative analysis of these alterations between normal, pre-invasive, and invasive tissue using powerful bioinformatics programs has allowed us to identify novel tumor markers, profile complex protein pathways, and develop new molecular-based therapies. Continued refinement of such high-throughput microtechnologies will enable us to rapidly query patient specimens to identify novel methods for early detection, treatment, and follow-up of a wide array of human cancers.

Differential expression profiling of head and neck squamous carcinoma: significance in their phenotypic and biological classification

The genetic events associated with the development and progression of head and neck squamous carcinoma (HNSC) are largely unknown. We analysed 12 matched pairs of histologically normal squamous mucosa and tumor specimens from six conventional and six phenotypic variants HNSC to define the differentially expressed genes in these tumors. Parallel expression analysis of 8055 unique genes was performed, and the level of the hybridization signal for each gene was measured after normalization. Hierarchical cluster analysis of the expressed genes showed distinct inter- and intra-tumoral patterns in and between conventional squamous carcinoma and squamous carcinoma variants. We also identified 26 (0.32%) differentially expressed genes that were consistently different between matched pairs of normal and tumor specimens; a selected set of the overexpressed genes was validated using real-time quantitative RT-PCR. The majority of the genes were associated with differentiation and proliferation. Our study defines a set of genes that could form the basis for the construction of limited HNSC targeted expression array and in-depth studies and further highlights gene profile differences that may be useful in pathobiologic classification of HNSC.

Identification of single nucleotide polymorphisms in the human kallikrein 10 (KLK10) gene and their association with prostate, breast, testicular, and ovarian cancers

BACKGROUND

The KLK10 gene (also known as the normal epithelial cell-specific 1 gene) is a member of the expanded human kallikrein gene family. Recently, it has been reported that KLK10 is a tumor suppressor gene and that its expression is downregulated in various forms of cancer and cancer cell lines. KLK10 is also upregulated in ovarian cancer. We thus hypothesized that the KLK10 gene may be a target for mutations in various cancers.

METHODS

We sequenced the five coding exons of the KLK10 gene using genomic DNA from various tumors, normal tissues, and blood, by PCR amplification and automated sequencing.

RESULTS

In none of the tumor-derived DNAs, we identified somatic mutations that could inactivate this gene. However, we identified a prevalent germline single nucleotide variation at codon 50 (exon 3) of this gene [GCC (alanine) to TCC (serine)]. The GCC genotype was less prevalent in prostatic cancer patients in comparison to control subjects (P = 0.027) but no differences were seen with testicular, ovarian, and breast cancer. We also identified four genetic variations in exon 4, at codons106 [GGC (glycine) to GGA (glycine)], codon 112 [ACG (threonine) to ACC (threonine)], codon 141 [CTA (leucine) to CTG (leucine)], and at codon 149 [CCG (proline) to CTG (leucine)]. None of these variations was significantly different between normal subjects and cancer groups.

CONCLUSIONS

We found no evidence for somatic mutations of the KLK10 gene in cancers of the prostate, breast, ovary, and testis. The single nucleotide variation at codon 50 appears to be associated with prostate cancer risk.

Application of genome-wide gene expression profiling by high-density DNA arrays to the treatment and study of inflammatory bowel disease

Identification of factors involved in the initiation, amplification, and perpetuation of the chronic immune response and the identification of markers for the characterization of patient subgroups remain critical objectives for ongoing research in inflammatory bowel disease (IBD). The Human Genome Project and the development of the expressed sequence tag (EST) clone collection and database have made possible a new revolution in gene expression analysis. Instead of measuring one or a few genes, parallel DNA microarrays are capable of simultaneously measuring expression of thousands of genes, providing a glimpse into the logic and functional grouping of gene programs encoded by our genome. Applied to clinical specimens from affected and normal individuals, this methodology has the potential to provide a new level of information about disease pathogenesis not previously possible. Two dominant platforms for the construction of high-density microarrays have emerged: cDNA arrays and GeneChips. The first involves robotic spotting of DNA molecules, often derived from EST clone collections, onto a suitable solid phase matrix such as a glass slide. The second involves direct in situ synthesis of sets of gene-specific oligonucleotides on a silicon wafer by an eloquent derivative of the photolithography process. Both cDNA and oligonucleotide arrays are interrogated by hybridization with a fluorescent-labeled cDNA or cRNA representation of the original tissue mRNA. This enables measurement of the expression levels for thousands of mucosal genes in a single experiment. These technologies have recently become less expensive and more widely accessible to all researchers. This review details the principles and methods behind DNA array technology, data analysis and mining, and potential application to research and treatment of IBD.

DNA microarrays in prostate cancer

DNA microarray technology provides a means to examine large numbers of molecular changes related to a biological process in a high throughput manner. This review discusses plausible utilities of this technology in prostate cancer research, including definition of prostate cancer predisposition, global profiling of gene expression patterns associated with cancer initiation and progression, identification of new diagnostic and prognostic markers, and discovery of novel patient classification schemes. The technology, at present, has only been explored in a limited fashion in prostate cancer research. Some hurdles to be overcome are the high cost of the technology, insufficient sample size and repeated experiments, and the inadequate use of bioinformatics. With the completion of the Human Genome Project and the advance of several highly complementary technologies, such as laser capture microdissection, unbiased RNA amplification, customized functional arrays (eg, single-nucleotide polymorphism chips), and amenable bioinformatics software, this technology will become widely used by investigators in the field. The large amount of novel, unbiased hypotheses and insights generated by this technology is expected to have a significant impact on the diagnosis, treatment, and prevention of prostate cancer. Finally, this review emphasizes existing, but currently underutilized, data-mining tools, such as multivariate statistical analyses, neural networking, and machine learning techniques, to stimulate wider usage.

The future of colon cancer prevention

Chemoprevention science is in flux owing to rapid advances in postgenomic technology. We have witnessed enormous advances in the areas of early detection and molecular profiling of colorectal carcinogenesis; however, unique interpretive and technologic challenges persist. Neoplastic hallmarks must be iteratively tested and validated as markers of risk, targets for intervention, and/or markers of response in order to expedite the development of preventive interventions. In this review, we highlight several of the technologies that are revolutionizing our understanding of carcinogenesis and our approach to colorectal cancer prevention.

The Cancer Genome Anatomy Project: new resources for reading the molecular signatures of cancer

The Cancer Genome Anatomy Project (CGAP) has built informational, technological, and physical resources to interface genomics with basic and clinical cancer research. The CGAP web site (http://cgap.nci.nih.gov) provides informatics tools for in silico analysis of the CGAP datasets as well as information for accessing each of the CGAP resources. Published in 2001 by John Wiley & Sons, Ltd.