New approaches to molecular profiling of tissue samples

Altered protein expression in endometrial carcinogenesis

We have discovered several protein biomarkers that are altered during carcinogenesis of the human uterine endometrium. Proteins prepared from 19 endometrial carcinomas (Group A), and 20 normal endometria obtained from benign gynecological conditions (Group B), were investigated by Surface Enhanced Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (SELDI-TOF-MS). Two proteins, EC1 and EC2, were consistently expressed differentially. EC1 had an increased level of expression in carcinomas (P<0.001), while EC2 was expressed at a lower level (P=0.004). The isoelectric points of EC1 and EC2 were approximately pH 5.0 and 7.0, respectively. These proteins are thus potential biomarkers for detection of endometrial carcinoma.

Proteomic evaluation of archival cytologic material using SELDI affinity mass spectrometry: potential for diagnostic applications

Proteomic studies of cells via surface-enhanced laser desorption/ionization spectrometry (SELDI) analysis have enabled rapid, reproducible protein profiling directly from crude samples. We applied this technique to archival cytology material to determine whether distinct, reproducible protein fingerprints could be identifiedfor potential diagnostic purposes in blinded specimens. Rapid Romanowsky-stained cytocentrifuged specimens from fine-needle aspirates of metastatic malignant melanoma (with both known cutaneous primary and unknown primary sites), clear cell sarcoma, and renal cell carcinoma and reactive effusions were examined using the SELDI technology. A unique characteristic fingerprint was identified for each disease entity. Fifteen "blinded" unknown samples then were analyzed. When the protein profilefingerprints were plotted against the known fingerprints for the aforementioned diagnoses, the appropriate match or diagnosis was obtained in 13 (87%) of 15 cases. These preliminary findings suggest a substantial potential for SELDI applications to specific pathologic diagnoses.

Proteomics in cancer research

With the human genome sequence now determined, the field of molecular medicine is moving beyond genomics to proteomics. In the field of cancer research, the key question is: how can oncologists best use techniques of proteomics in basic research and clinical application? In the postgenomic era, proteomics promises the discovery of biomarkers and tumor markers for early detection and diagnosis, novel protein-based drug targets for anticancer therapy, and new endpoints for the assessment of therapeutic efficacy and toxicity. This review paper will explore key themes in proteomics and their application in clinical cancer research.

Cancer Biomarkers: Easier Said Than Done

Background: Biological and technical advances have led to greatly increased research and development of cancer biomarkers. This overview lists some of the challenges and barriers to developing novel effective cancer biomarkers and enablers to facilitate cancer biomarker development.

Methods: Current scientific literature regarding development of biomarkers for cancer and other diseases was reviewed.

Results: Challenges to developing cancer biomarkers include better understanding of biological heterogeneity, including host/tumor heterogeneity; analytical factors, such as interferences and analytical sensitivity; clinical pathologic factors, such as current histopathologic standards; and health service and market factors. More standardized biomarker definitions, standardization of cancer biology terminology, and high-quality reference materials (specimen and clinical data repositories) were identified as factors required to support advances in cancer biomarkers.

Conclusions: With the above enablers, novel cancer biomarkers may be useful, both for assessing early and established neoplasia more precisely and for contributing data toward development of novel practical concepts regarding cancer biology.

Human prostate epithelial cell-type cDNA libraries and prostate expression patterns

BACKGROUND

Transcriptome analysis is a powerful approach to uncovering genes responsible for diseases such as prostate cancer. Ideally, one would like to compare the transcriptomes of a cancer cell and its normal counterpart for differences.

METHODS

Prostate luminal and basal epithelial cell types were isolated and cell-type-specific cDNA libraries were constructed. Sequence analysis of cDNA clones generated 505 luminal cell genes and 560 basal cell genes. These sequences were deposited in a public database for expression analysis.

RESULTS

From these sequences, 119 unique luminal expressed sequence tags (ESTs) were extracted and assembled into a luminal-cell transcriptome set, while 154 basal ESTs were extracted and assembled into a basal-cell set. Interlibrary comparison was performed to determine representation of these sequences in cDNA libraries constructed from prostate tumors, PIN, cell lines.

CONCLUSIONS

Our analysis showed that a significant number of epithelial cell genes were not represented in the various transcriptomes of prostate tissues, suggesting that they might be underrepresented in libraries generated from tissue containing multiple cell types. Although both luminal and basal cell types are epithelial, their transcriptomes are more divergent from each other than expected, underscoring their functional difference (secretory vs. nonsecretory). Tumor tissues show different expression of luminal and basal genes, with perhaps a trend towards expression of basal genes in advanced diseases.

High resolution spatial analysis of plant systems

Analysis of organisms using techniques that provide high spatial and temporal resolution is of increasing interest in many disciplines of biomedical research. Although the examination of animal tissues has been the main focus to date, the recent development and improvement of methods for the sampling and handling of single cells and for their biochemical analysis now provide tools for investigating plant as well as animal cells.