New cancer biomarkers deriving from NCI early detection research

Protective role of antioxidants capacity of Hyrtios aff. Erectus sponge extract against mixture of persistent organic pollutants (POPs)-induced hepatic toxicity in mice liver: biomarkers and ultrastructural study

The current study investigates the hepatoprotective effect of Hyrtios aff. Erectus sponge extract against POPs intoxication on endogenous antioxidant enzymes and lipid peroxidation in mice liver tissue. In the present study, the mice BALB/C were assigned into four groups: group I: received saline subcutaneously for 7 days and served as negative control; group II: received subcutaneously for 7 days, 130.6 mg/100 g/b. w/day POPs mixture(mixture of PCB 28, PCB 52,, PCB 101, PCB 118, PCB 153, PCB 138 and PCB 180, alpha-Hexachlorocyclohexane, beta-Hexachloro-cyclohexane, gamma-hexachlorocyclohexane, Aldrin, O,P'-DDE, Dieldrin, P,p DDE, O,P DDD, Endrin, P,p DDD and P,pDDT were extracted from sediments collected from Lake Mariout), and served as induced group; group III: pretreated with Hyrtios aff. Erectus sponge extract for 7 days, as a protection dose and then treated with POPs as group II and served as protective group; and group IV: received i.p Hyrtios aff. Erectus sponge extract of dose 0.7 mg/100 g b.wt/day for 7 days and served as positive control. After 7 days (experimental period), mice were scarified and the liver was harvested for biochemical estimation. Significant reduction in lipid peroxidation (p < 0.002) was noticed compared to POPs-protected group. The antioxidant biomarkers levels were significantly increase as the hepatic GSH and GST increased by 69.9 and 89.9%, respectively. Such increase was accompanied by a decrease in tyrosine kinase activity by 59.82%, additionally remarkable histopathological changes in liver tissue indicate the protective effect of Hyrtios aff. Erectus sponge extract. The results of this study revealed that the Hyrtios aff. Erectus sponge extract has the potential to diminish the destructive effect of POPs intoxication through enhancement of the endogenous antioxidant status. The hepatoprotective activity of Hyrtios aff. Erectus sponge extract is mediated, by the antioxidant effect of its active constituents. The active constituents of Hyrtios aff. Erectus sponge extract were identified by LC-MS/MS.

Expression of prostate stem cell antigen is downregulated during flavonoid-induced cytotoxicity in prostate cancer cells

Prostate stem cell antigen (PSCA) is expressed in the majority of prostate cancer cases and may be a potential therapeutic target in the treatment of prostate cancer. The present study evaluated the cytotoxicity of three flavonoids (genistein, luteolin and quercetin) towards DU145 prostate cancer cells, and investigated the effect of these flavonoids on PSCA expression. The results demonstrated that genistein, luteolin and quercetin inhibited the growth of DU145 cells in a dose-dependent manner (P<0.05) and induced morphological changes characteristic of apoptosis in DU145 cells. Flow cytometry analysis also indicated that the flavonoids induced S phase cycle arrest in DU145 cells. Notably, it was observed that expression of PSCA was inhibited at the mRNA (P<0.05) and protein levels in DU145 cells following flavonoid treatment compared with the control. These results suggest that flavonoids may be potential therapeutic agents in the treatment and prevention of prostate cancer.

Recent advances in biosensor development for the detection of cancer biomarkers

Cancer is the second largest disease throughout the world with an increasing mortality rate over the past few years. The patient's survival rate is uncertain due to the limitations of cancer diagnosis and therapy. Early diagnosis of cancer is decisive for its successful treatment. A biomarker-based cancer diagnosis may significantly improve the early diagnosis and subsequent treatment. Biosensors play a crucial role in the detection of biomarkers as they are easy to use, portable, and can do analysis in real time. This review describes various biosensors designed for detecting nucleic acid and protein-based cancer biomarkers for cancer diagnosis. It mainly lays emphasis on different approaches to use electrochemical, optical, and mass-based transduction systems in cancer biomarker detection. It also highlights the analytical performances of various biosensor designs concerning cancer biomarkers in detail.

The Role of Epigenomics in the Study of Cancer Biomarkers and in the Development of Diagnostic Tools

Epigenetics plays a key role in cancer development. Genetics alone cannot explain sporadic cancer and cancer development in individuals with no family history or a weak family history of cancer. Epigenetics provides a mechanism to explain the development of cancer in such situations. Alterations in epigenetic profiling may provide important insights into the etiology and natural history of cancer. Because several epigenetic changes occur before histopathological changes, they can serve as biomarkers for cancer diagnosis and risk assessment. Many cancers may remain asymptomatic until relatively late stages; in managing the disease, efforts should be focused on early detection, accurate prediction of disease progression, and frequent monitoring. This chapter describes epigenetic biomarkers as they are expressed during cancer development and their potential use in cancer diagnosis and prognosis. Based on epigenomic information, biomarkers have been identified that may serve as diagnostic tools; some such biomarkers also may be useful in identifying individuals who will respond to therapy and survive longer. The importance of analytical and clinical validation of biomarkers is discussed, along with challenges and opportunities in this field.

Epigenetic biomarkers in liver cancer

Liver cancer (hepatocellular carcinoma or HCC) is a major cancer worldwide. Research in this field is needed to identify biomarkers that can be used for early detection of the disease as well as new approaches to its treatment. Epigenetic biomarkers provide an opportunity to understand liver cancer etiology and evaluate novel epigenetic inhibitors for treatment. Traditionally, liver cirrhosis, proteomic biomarkers, and the presence of hepatitis viruses have been used for the detection and diagnosis of liver cancer. Promising results from microRNA (miRNA) profiling and hypermethylation of selected genes have raised hopes of identifying new biomarkers. Some of these epigenetic biomarkers may be useful in risk assessment and for screening populations to identify who is likely to develop cancer. Challenges and opportunities in the field are discussed in this chapter.

The development of nomograms for stratification of men at risk of prostate cancer prior to prostate biopsy

A main limitation of early prostate cancer (PCa) detection due to elevated PSA levels is caused by the low specificity of PSA, which is associated with a high proportion of men detected with nonmalignant findings at first or subsequent prostate biopsy (PBX). Multivariate prediction models, such as nomograms, have been developed, providing a more accurate method to prospectively determine the risk of a positive PBX. Combining established clinical risk factors with novel diagnostic markers of PCa appears promising to further improve predictive accuracy estimates. Ideally, these nomograms should be capable of identifying PCa at PBX without missing men with high-grade PCa, and preventing a significant proportion of men without, or with insignificant, PCa from undergoing PBX. The intention is to reduce disease morbidity and mortality by detecting significant PCa at an early stage, and at the same time to avoid overdiagnosis as well as overintervention.

Prostate cancer biomarkers: an update

Many aspects of prostate cancer diagnosis and treatment could be greatly advanced with new, effective biomarkers. Prostate-specific antigen (PSA) has multiple weaknesses as a biomarker, such as not distinguishing well between cancer and benign prostatic hyperplasia or between indolent and aggressive cancers, thus leading to overtreatment, especially unnecessary biopsies. PSA also often fails to indicate accurately which patients are responding to a given treatment. Yet PSA is the only prostate cancer biomarker routinely used by urologists. Here, we provide updated information on the most relevant of the other biomarkers currently in use or in development for prostate cancer. Recent research shows improvement over using PSA alone by comparing total PSA (tPSA) or free PSA (fPSA) with new, related markers, such as prostate cancer antigen (PCA) 3, the individual molecular forms of PSA (proPSA, benign PSA, and intact PSA), and kallikreins other than PSA. Promising results have also been seen with the use of the fusion gene TMPRSS2:ERG and with various forms of the urokinase plasminogen activation receptor. Initially, there were high hopes for early PCA, but those data were not reproducible and thus research on early PCA has been abandoned. Much work remains to be done before any of these biomarkers are fully validated and accepted. Currently, the only markers discussed in this paper with Food and Drug Administration-approved tests are PCA 3 and an isoform of proPSA, [-2]proPSA. Assays are in development for most of the other biomarkers described in this paper. While the biomarker validation process can be long and filled with obstacles, the rewards will be great-in terms of both patient care and costs to the health care system.

ELISA microarray technology as a high-throughput system for cancer biomarker validation

A large gap currently exists between the ability to discover potential biomarkers and the ability to assess the real value of these proteins for cancer screening. One major challenge in biomarker validation is the inherent variability in biomarker levels. This variability stems from the diversity across the human population and the considerable molecular heterogeneity between individual tumors, even those that originate from a single tissue. An additional challenge with cancer screening is that most cancers are rare in the general population, meaning that assay specificity must be very high. Otherwise, the number of false positives will be much greater than the number of true positives. Due to these challenges associated with biomarker validation, it is necessary to analyze thousands of samples in order to obtain a clear idea of the utility of a screening assay. Enzyme-linked immunosorbent assay (ELISA) microarray technology can simultaneously quantify levels of multiple proteins and, thus, has the potential to accelerate validation of protein biomarkers for clinical use. This review will discuss current ELISA microarray technology and potential advances that could help to achieve the reproducibility and throughput that are required to evaluate cancer biomarkers.

Assays for prostate cancer : changing the screening paradigm?

Prostate cancer (PCa) screening and detection have changed dramatically since the introduction of serum prostate-specific antigen (PSA) testing. Despite the resulting improvement in early PCa detection and stage migration, in clinical practice the use of PSA testing may cause overdetection and ultimately overtreatment. As a consequence, novel biomarkers are needed to increase the specificity of PCa detection. The aim of this article is to present an overview of novel blood- and urine-based biomarkers that may optimize PCa detection, with improved identification of patients with significant PCa and avoidance of unnecessary prostate biopsies. A systematic and comprehensive PubMed search was performed using the MeSH search terms 'prostate cancer', 'biomarker', 'marker', and 'detection'. Results were restricted to the English language. Several blood- and urine-based biomarkers have the potential to improve prediction of the presence and/or significance of PCa. Ideally, biomarkers should be used in combination within multivariate models, leading to superior accuracy for prediction of any PCa or clinically significant PCa, compared with the use of a single marker.

The circadian clock in cancer development and therapy

Most aspects of mammalian function display circadian rhythms driven by an endogenous clock. The circadian clock is operated by genes and comprises a central clock in the brain that responds to environmental cues and controls subordinate clocks in peripheral tissues via circadian output pathways. The central and peripheral clocks coordinately generate rhythmic gene expression in a tissue-specific manner in vivo to couple diverse physiological and behavioral processes to periodic changes in the environment. However, with the industrialization of the world, activities that disrupt endogenous homeostasis with external circadian cues have increased. This change in lifestyle has been linked to an increased risk of diseases in all aspects of human health, including cancer. Studies in humans and animal models have revealed that cancer development in vivo is closely associated with the loss of circadian homeostasis in energy balance, immune function, and aging, which are supported by cellular functions important for tumor suppression including cell proliferation, senescence, metabolism, and DNA damage response. The clock controls these cellular functions both locally in cells of peripheral tissues and at the organismal level via extracellular signaling. Thus, the hierarchical mammalian circadian clock provides a unique system to study carcinogenesis as a deregulated physiological process in vivo. The asynchrony between host and malignant tissues in cell proliferation and metabolism also provides new and exciting options for novel anticancer therapies.

Cancer proteomics

Cancer presents high mortality and morbidity globally, largely due to its complex and heterogenous nature, and lack of biomarkers for early diagnosis. A proteomics study of cancer aims to identify and characterize functional proteins that drive the transformation of malignancy, and to discover biomarkers to detect early-stage cancer, predict prognosis, determine therapy efficacy, identify novel drug targets, and ultimately develop personalized medicine. The various sources of human samples such as cell lines, tissues, and plasma/serum are probed by a plethora of proteomics tools to discover novel biomarkers and elucidate mechanisms of tumorigenesis. Innovative proteomics technologies and strategies have been designed for protein identification, quantitation, fractionation, and enrichment to delve deeper into the oncoproteome. In addition, there is the need for high-throughput methods for biomarker validation, and integration of the various platforms of oncoproteome data to fully comprehend cancer biology.

S100A9, GIF and AAT as potential combinatorial biomarkers in gastric cancer diagnosis and prognosis

PURPOSE

We have mined the gastric fluid proteome for potential gastric cancer (GC) biomarkers that may enhance disease detection and facilitate prognostic monitoring.

EXPERIMENTAL DESIGN

In biomarker discovery, a total of 12 patient gastric fluid samples (stages I, III, IV and gastritis) were analysed by 2DE for expression changes that correlated with GC status or disease progression. Gastric fluid proteins showing differential expression with GC were identified by MALDI-TOF/TOF MS as putative biomarkers. Levels of these potential biomarker candidates were independently validated by Western blotting in further 60 gastritis and GC patients. A targeted approach that recruits biomarker candidates for panel consideration was adopted to test if two or more biomarkers in combination improved diagnostic power.

RESULTS

From the 15 differentially regulated proteins identified, expression levels of S100A9, GIF and AAT in the gastric fluid clearly correlated with GC status. S100A9/AAT (AUC = 0.81) and S100A9/GIF (AUC = 0.92) were revealed as promising biomarker pairs for early GC diagnosis and disease monitoring, respectively.

CONCLUSION AND CLINICAL RELEVANCE

Early diagnosis, accurate staging and constant disease monitoring remain the prerequisites for effective treatment against GC. As current biomarkers like CA19-9 and carcinoembryonic antigen (CEA) lack sensitivity and specificity, there is a pressing need for novel GC detection and monitoring methods. To this end, S100A9, GIF and AAT from the gastric fluid may significantly augment existing methods of GC detection and monitoring, and eliminate the need for invasive tissue biopsies.

Tumor markers in prostate cancer I: blood-based markers

The introduction of total prostate specific antigen (total PSA) testing in blood has revolutionized the detection and management of men with prostate cancer (PCa). The objective of this review was to discuss the challenges of PCa biomarker research, definition of the type of PCa biomarkers, the statistical considerations for biomarker discovery and validation, and to review the literature regarding total PSA velocity and novel blood-based biomarkers.

METHODS

An English-language literature review of the Medline database (1990 to August 2010) of published data on blood-based biomarkers and PCa was undertaken.

RESULTS

The inherent biological variability of total PSA levels affects the interpretation of any single result. Men who will eventually develop PCa have increased total PSA levels years or decades before the cancer is diagnosed. Total PSA velocity improves predictiveness of total PSA only marginally, limiting its value for PCa screening and prognostication. The combination of PSA molecular forms and other biomarkers improve PCa detection substantially. Several novel blood-based biomarkers such as human glandular kallikrein 2 (hK2), urokinase plasminogen activator (uPA) and its receptor (uPAR), transforming growth factor-beta 1 (TGF-β1); interleukin-6 (IL-6) and its receptor (IL-6R) may help PCa diagnosis, staging, prognostication, and monitoring. Panels of biomarkers that capture the biologic potential of PCa are in the process of being validated for PCa prognostication.

CONCLUSIONS

PSA is a strong prognostic marker for long-term risk of clinically relevant cancer. However, there is a need for novel biomarkers that aid clinical decision making about biopsy and initial treatment. There is no doubt that progress will continue based on the integrated collaboration of researchers, clinicians and biomedical firms.

Statistical consideration for clinical biomarker research in bladder cancer

OBJECTIVE

To critically review and illustrate current methodological and statistical considerations for bladder cancer biomarker discovery and evaluation.

METHODS

Original, review, and methodological articles, and editorials were reviewed and summarized.

RESULTS

Biomarkers may be useful at multiple stages of bladder cancer management: early detection, diagnosis, staging, prognosis, and treatment; however, few novel biomarkers are currently used in clinical practice. The reasons for this disjunction are many and reflect the long and difficult pathway from candidate biomarker discovery to clinical assay, and the lack of coherent and comprehensive processes (pipelines) for biomarker development. Conceptually, the development of new biomarkers should be a process that is similar to therapeutic drug evaluation-a highly regulated process with carefully regulated phases from discovery to human applications. In a further effort to address the pervasive problem of inadequacies in the design, analysis, and reporting of biomarker prognostic studies, a set of reporting recommendations are discussed. For example, biomarkers should provide unique information that adds to known clinical and pathologic information. Conventional multivariable analyses are not sufficient to demonstrate improved prediction of outcomes. Predictive models, including or excluding any new putative biomarker, need to show clinically significant improvement of performance in order to claim any real benefit. Towards this end, proper model building, avoidance of overfitting, and external validation are crucial. In addition, it is important to choose appropriate performance measures dependent on outcome and prediction type and to avoid the use of cutpoints. Biomarkers providing a continuous score provide potentially more useful information than cutpoints since risk fits a continuum model. Combination of complementary and independent biomarkers is likely to better capture the biological potential of a tumor than any single biomarker. Finally, methods that incorporate clinical consequences such as decision curve analysis are crucial to the evaluation of biomarkers.

CONCLUSIONS

Attention to sound design and statistical practice should be delivered as early as possible and will help maximize the promise of biomarkers for patient care. Studies should include a measure of predictive accuracy and clinical decision-analysis. External validation using data from an independent cohort provides the strongest evidence that a model is valid. There is a need for adequately assessed clinical biomarkers in bladder cancer.

Electrospray ionization mass spectrometry as a critical tool for revealing new properties of snake venom phospholipase A2

Results from high-performance liquid chromatography/nano-electrospray ionization tandem mass spectrometry (HPLC/nESI-MS/MS) coupled to two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis (2D SDS-PAGE) indicated that the monomer and dimer of phospholipase A(2) (PLA(2)) coexisted in crude Chinese Agkistrodon blomhoffii Ussurensis snake venom (ABUSV). Then, an acidic PLA(2) with the accurate molecular mass of 13979.6 Da was purified from ABUSV (mo-ABUSV-aPLA(2)). MS/MS-derived peptides from ABUSV-aPLA(2) were compared with other homologous snake venom PLA(2)s, which in turn showed that ABUSV-aPLA(2) is a novel snake venom PLA(2). Meanwhile, the ABUSV-aPLA(2) dimer (di-ABUSV-aPLA(2)) was also obtained. MS/MS analysis identified the same peptides from di-ABUSV-aPLA(2) as from mo-ABUSV-aPLA(2), which indicates that di-ABUSV-aPLA(2) is a homodimer. One Ca(2+) ion is contained per ABUSV-aPLA(2). The Ca(2+) ion is critical for both the hydrolytic activity and the structure of ABUSV-aPLA(2). Pro-Q Emerald and Pro-Q Diamond specific glycoprotein and phosphoprotein staining combined with MS/MS analysis indicated that the ABUSV-aPLA(2) is both a glycoprotein and a phosphoprotein, which to our knowledge is the first such report for a snake venom PLA(2) and thus provides new threads for the study of the functions and structures of snake venom PLA(2)s. One phosphorylation site and the size of the glycan chain are determined by using HPLC/nESI-MS/MS and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS. The delicate utilization of ESI-MS can exert tremendous impact on protein sciences.

Proteomics and cancer epidemiology

Profiling of differentially expressed proteins is perhaps the most important and useful approach in developing tools for risk assessment in a population, diagnostic screening, and therapeutics. Proteomic markers have potential for identifying individuals at high risk of developing cancer; however, these markers have not been extensively used in cancer epidemiologic studies. Several markers have to be clinically validated. In this chapter, methods used in proteomic analysis of clinical samples, challenges in the proteomics and cancer epidemiology, and their potential solutions are discussed.

Performance of mitochondrial DNA mutations detecting early stage cancer

BACKGROUND

Mutations in the mitochondrial genome (mtgenome) have been associated with cancer and many other disorders. These mutations can be point mutations or deletions, or admixtures (heteroplasmy). The detection of mtDNA mutations in body fluids using resequencing microarrays, which are more sensitive than other sequencing methods, could provide a strategy to measure mutation loads in remote anatomical sites.

METHODS

We determined the mtDNA mutation load in the entire mitochondrial genome of 26 individuals with different early stage cancers (lung, bladder, kidney) and 12 heavy smokers without cancer. MtDNA was sequenced from three matched specimens (blood, tumor and body fluid) from each cancer patient and two matched specimens (blood and sputum) from smokers without cancer. The inherited wildtype sequence in the blood was compared to the sequences present in the tumor and body fluid, detected using the Affymetrix Genechip Human Mitochondrial Resequencing Array 1.0 and supplemented by capillary sequencing for noncoding region.

RESULTS

Using this high-throughput method, 75% of the tumors were found to contain mtDNA mutations, higher than in our previous studies, and 36% of the body fluids from these cancer patients contained mtDNA mutations. Most of the mutations detected were heteroplasmic. A statistically significantly higher heteroplasmy rate occurred in tumor specimens when compared to both body fluid of cancer patients and sputum of controls, and in patient blood compared to blood of controls. Only 2 of the 12 sputum specimens from heavy smokers without cancer (17%) contained mtDNA mutations. Although patient mutations were spread throughout the mtDNA genome in the lung, bladder and kidney series, a statistically significant elevation of tRNA and ND complex mutations was detected in tumors.

CONCLUSION

Our findings indicate comprehensive mtDNA resequencing can be a high-throughput tool for detecting mutations in clinical samples with potential applications for cancer detection, but it is unclear the biological relevance of these detected mitochondrial mutations. Whether the detection of tumor-specific mtDNA mutations in body fluidsy this method will be useful for diagnosis and monitoring applications requires further investigation.

High-performance liquid chromatography/nano-electrospray ionization tandem mass spectrometry, two-dimensional difference in-gel electrophoresis and gene microarray identification of lymphatic metastasis-associated biomarkers

The potential biomarkers for the lymphatic metastatic process of mouse hepatocarcinoma were investigated by using two-dimensional difference in-gel electrophoresis (2D DIGE), high-performance liquid chromatography/nano-electrospray ionization tandem mass spectrometry (HPLC/nESI-MS/MS) and GeneChip. 2D DIGE was performed to screen and quantify the differentially expressed proteins between two well-established mouse hepatocarcinoma cell lines, Hca-F with 75% and Hca-P with 25% metastasis rate of lymph node potentials. The protein spots in the gel were visualized by the highly sensitive Deep Purple (GE Healthcare) fluorescent stain. Protein identification was obtained for gel spots by HPLC/nESI-MS/MS analysis with high quality. GeneChip microarray was performed to identify genes differentially expressed at the mRNA level. Seventeen genes including the chloride intracellular channel l, caspase 3, fructose bisphosphatase 2, glutamate dehydrogenase 1, V-crk sarcoma virus CT10 oncogene homolog, N-myc downstream regulated gene1, villin2, gelsolin, enoyl coenzyme A hydratase 1, transketolase, vimentin, annexins A5 and A7, keratin complex2 basic gene7 and gene8, lactamase (bata 2) and Ero1-like protein were found abnormally regulated and expressed concordantly both at the protein and mRNA levels between the two cell lines. More than half of these genes were for the first time revealed to be involved directly in hepatocarcinoma due to the lymphatic metastasis. The interdisciplinary combination of HPLC/nESI-MS/MS with 2D DIGE and GeneChip techniques opens up the possibility for the biomarker discovery of disease with high confidence.

Mass spectrometric compatibility of Deep Purple and SYPRO Ruby total protein stains for high-throughput proteomics using large-format two-dimensional gel electrophoresis

In order to identify putative biomarkers from two-dimensional (2D) gel electrophoresis it is necessary to use a visualization technique that is sensitive, has a large dynamic range and does not interfere with the identification of the protein. As mass spectrometry increases in sensitivity more pressure is placed on visualization techniques that facilitate proteomic workflows but do not interfere with downstream processing. Two stains reported to meet these requirements are SYPRO Ruby (Invitrogen) and Deep Purple (GE Healthcare). This study examined the compatibility of these stains with protein identification by selecting spots from replicate 2D gels of human plasma and subjecting these to protein identification using liquid chromatography/tandem mass spectrometry (LC/MS/MS). Using a test of two populations of proportions it was found that proteins were statistically more likely to be identified from gels stained with Deep Purple. Additionally, the identifications from Deep Purple stained gels are of higher quality because they are based on multiple peptides.

Biomarker method validation in anticancer drug development

Over recent years the role of biomarkers in anticancer drug development has expanded across a spectrum of applications ranging from research tool during early discovery to surrogate endpoint in the clinic. However, in Europe when biomarker measurements are performed on samples collected from subjects entered into clinical trials of new investigational agents, laboratories conducting these analyses become subject to the Clinical Trials Regulations. While these regulations are not specific in their requirements of research laboratories, quality assurance and in particular assay validation are essential. This review, therefore, focuses on a discussion of current thinking in biomarker assay validation. Five categories define the majority of biomarker assays from 'absolute quantitation' to 'categorical'. Validation must therefore take account of both the position of the biomarker in the spectrum towards clinical end point and the level of quantitation inherent in the methodology. Biomarker assay validation should be performed ideally in stages on 'a fit for purpose' basis avoiding unnecessarily dogmatic adherence to rigid guidelines but with careful monitoring of progress at the end of each stage. These principles are illustrated with two specific examples: (a) absolute quantitation of protein biomarkers by mass spectrometry and (b) the M30 and M65 ELISA assays as surrogate end points of cell death.

Genetic and epigenetic biomarkers in cancer : improving diagnosis, risk assessment, and disease stratification

Gene expression patterns change during the initiation, progression, and development of cancer, as a result of both genetic and epigenetic mechanisms. Genetic changes arise due to irreversible changes in the nucleotide sequence, whereas epigenetic changes occur due to changes in chromatin conformation, histone acetylation, and methylation of the CpG islands located primarily in the promoter region of a gene. Both genetic and epigenetic markers can potentially be utilized to identify different stages of tumor development. Several such markers exhibit high sensitivity and specificity for different tumor types and can be assayed in biofluids and other specimens collected by noninvasive technologies. In spite of the availability of large numbers of diagnostic markers, only a few have been clinically validated so far. The current status and the challenges in the field of genetic and epigenetic markers in cancer diagnosis, risk assessment, and disease stratification are discussed.

A combined approach to data mining of textual and structured data to identify cancer-related targets

Background

We present an effective, rapid, systematic data mining approach for identifying genes or proteins related to a particular interest. A selected combination of programs exploring PubMed abstracts, universal gene/protein databases (UniProt, InterPro, NCBI Entrez), and state-of-the-art pathway knowledge bases (LSGraph and Ingenuity Pathway Analysis) was assembled to distinguish enzymes with hydrolytic activities that are expressed in the extracellular space of cancer cells. Proteins were identified with respect to six types of cancer occurring in the prostate, breast, lung, colon, ovary, and pancreas.

Results

The data mining method identified previously undetected targets. Our combined strategy applied to each cancer type identified a minimum of 375 proteins expressed within the extracellular space and/or attached to the plasma membrane. The method led to the recognition of human cancer-related hydrolases (on average, ~35 per cancer type), among which were prostatic acid phosphatase, prostate-specific antigen, and sulfatase 1.

Conclusion

The combined data mining of several databases overcame many of the limitations of querying a single database and enabled the facile identification of gene products. In the case of cancer-related targets, it produced a list of putative extracellular, hydrolytic enzymes that merit additional study as candidates for cancer radioimaging and radiotherapy. The proposed data mining strategy is of a general nature and can be applied to other biological databases for understanding biological functions and diseases.

Prostate cancer detection strategies

Prostate cancer is the most common malignancy in men and, as a result, there has been a nationwide emphasis on screening and detection. With the widespread use of the prostate-specific antigen (PSA), prostate cancer screening effectively detects localized prostate cancer. However, recent reports have identified a significant proportion of prostate cancer in men with low PSA levels. Many of these cancers are higher-grade malignancies. Consequently, PSA may function more effectively as a screening tool when applied over a continuum that is associated with degree of risk, rather than a binary measure. Other markers are currently being investigated. Ideally, a marker will identify the malignancy that is a clinical threat, thereby avoiding intervention for indolent disease. Prevention strategies may be employed for higher-risk patients, and these strategies eventually may be tailored to genetic or other risks.

Recent advances in biomarkers for cancer diagnosis and treatment

With the availability of new technologies and the increased interest of medical practitioners to use molecular biomarkers in early detection and diagnosis, and in the prediction of therapeutic treatment efficacy and clinical outcomes, the academic and research institutions, as well as the pharmaceutical industry, have increased their efforts to develop novel molecular biomarkers for several human diseases, including cancer. The identification of molecular biomarkers also enables the development of a new generation of diagnostic products and to integrate diagnostics and therapeutics. This integrated approach will aid in 'individualizing' the medical practice. Here, we address issues related to the development of biomarkers, novel technological platforms used for drug development, future technologies and strategies for validating biomarkers for their clinical utility.

Lifestyle and medical approaches to cancer prevention

Cancer risk can be reduced by adopting a healthy lifestyle and by medical means. Tobacco control is central to public policies for cancer prevention. Overweight and obesity in the United States may contribute to 20% of cancer deaths in women and 14% in men. Cancer prevention strategies have progressed from a predominant lifestyle approach to a model that combines clinical investigations in a medical setting with public health interventions. This change stems from advances in identifying, developing, and testing agents with the potential either to prevent cancer initiation, or to inhibit or reverse the progression of premalignant lesions to invasive cancer. Encouraging laboratory and epidemiologic studies, along with secondary endpoints in treatment trials, have provided a strong scientific rationale for the hypothesis that a pharmacologic approach--chemoprevention--can reduce cancer risk. Numerous chemopreventive agents, including naturally occurring vitamins, minerals, phytochemicals, and synthetic compounds, have proved to be safe and effective in preclinical and clinical studies. Promising results have been reported for cancers of the prostate, breast, colon, lung, bladder, cervix, oral cavity, esophagus, skin, and liver. The use of emerging technologies, identification of biomarkers of risk, and advances in genetic research are being applied to chemoprevention research. An interdisciplinary research approach to investigate molecular and genetic markers--as well as chemoprevention and lifestyle strategies--that affect cancer risk is being applied to the most common types of cancer in the United States in women (breast) and men (prostate).

Cancer chemoprevention: lessons learned and future directions

The concept of delaying or preventing epithelial transformation remains a viable and attainable goal for the future. Drug-based strategies for chemoprevention of the future may predominantly rely upon targeted therapies with tolerable but defined toxicities for treatment of individuals diagnosed with intraepithelial neoplasias. Foods, diet manipulation strategies, or nutraceuticals may be more appropriate to delay or prevent carcinogenesis progression in healthy populations with genetic or epidemiologic evidence of risk for future transformation.

Detection and quantification of mutations in the plasma of patients with colorectal tumors

The early detection of cancers through analysis of circulating DNA could have a substantial impact on morbidity and mortality. To achieve this goal, it is essential to determine the number of mutant molecules present in the circulation of cancer patients and to develop methods that are sufficiently sensitive to detect these mutations. Using a modified version of a recently developed assay for this purpose, we found that patients with advanced colorectal cancers consistently contained mutant adenomatous polyposis coli (APC) DNA molecules in their plasma. The median number of APC DNA fragments in such patients was 47,800 per ml of plasma, of which 8% were mutant. Mutant APC molecules were also detected in >60% of patients with early, presumably curable colorectal cancers, at levels ranging from 0.01% to 1.7% of the total APC molecules. These results have implications for the mechanisms through which tumor DNA is released into the circulation and for diagnostic tests based on this phenomenon.

Pancreatic cancer epidemiology

Carcinoma of the exocrine pancreas remains a challenging disease mainly due to advanced stage diagnosis, the early systemic dissemination, aggressive local tumor progression, and subsequent short patient survival. Thus, assessment of incidence markers instead of prevalence indicators is recommended because the time between diagnosis and death is usually very short. Investigations to date have led to the discovery of many rare genes and environmental factors that contribute to pancreatic cancer. However, common genes involved in genetic polymorphisms, and specific risk factors have not been identified. Furthermore, the role of gene-environment interactions on the tumorogenesis and progression of pancreatic cancer need to be further investigated. Given current therapeutic modalities, only early detection of cancer of the pancreas, followed by surgical resection, offers the possibility of lengthening survival time.

Epigenetics and cancer

Both genetics and epigenetics regulate gene expression in cancer. Regulation by genetics involves a change in the DNA sequence, whereas epigenetic regulation involves alteration in chromatin structure and methylation of the promoter region. During the initiation, development, and progression of cancer, a number of genes undergo epigenetic changes. Some of these changes can be used as biomarkers for early detection of cancer as well as to follow treatment. A panel of epigenetic biomarkers is preferred to a single biomarker in clinical assays. Changes in gene expression due to epigenetic regulation can be reversed by chemicals, and this approach opens up a novel approach in cancer prevention and treatment.

Biomarkers for risk assessment in molecular epidemiology of cancer

One out of four deaths in the USA is due to cancer. Identification of populations at risk of developing cancer is important as it provides opportunities for prevention and treatment of cancer. Biomarkers are measurable indicators of exposure effects and susceptibility or disease state, and are used to understand the mechanisms of cancer progression. In recent molecular epidemiology studies genomic, proteomic, and epigenomic markers have been utilized which exhibit high sensitivity and specificity for different tumor types and can be assayed in biofluids and other specimens collected by non-invasive technologies. The current challenges and future directions in the field are discussed in this article.

Clinical trials in cancer prevention: current results and perspectives for the future

Cancer prevention remains the ideal strategy for reducing the burden of cancer on society. Progress in cancer prevention has been accelerated as prevention clinical trials are completed and reported. A promising strategy is the identification of cancer risk factors through epidemiologic and experimental research with lifestyle and medical approaches that allow translation of clinical trial results to clinical practice. A major focus of cancer prevention clinical trials has been on modulation of hormones and nutritional modifications using natural or synthetic bioactive food components for breast and prostate cancer. Breast cancer prevention clinical trials have investigated the role of estrogen antagonists with agents such as tamoxifen, raloxifene, and newer agents such as aromatase inhibitors and bioactive food components. Among the promising bioactive food components being investigated at the National Cancer Institute in prevention clinical trials to reduce breast cancer risk are indole-3-carbinol, sulforaphanes, phytoestrogen isoflavones, perillyl alcohol, and green tea polyphenols. Prostate cancer prevention trials have focused on hormone modulation with the 5-alpha-reductase inhibitor finasteride and bioactive food components such as selenium and vitamin E. Soy isoflavones, green tea polyphenols, and doxercalciferol also are being investigated for prostate cancer prevention. Future prevention clinical trials will rely on multidisciplinary medical approaches that bring together expertise in many fields to address disease across the cancer spectrum. Nutritional science can play an important role in this effort through the use of new and emerging technologies to better understand the influence of bioactive food components on the genes, proteins, and cellular processes that are associated with cancer risk.

Translation research: from accurate diagnosis to appropriate treatment

This review article focuses on the various aspects of translational research, where research on human subjects can ultimately enhance the diagnosis and treatment of future patients. While we will use specific examples relating to the asbestos related cancer mesothelioma, it should be stressed that the general approach outlined throughout this review is readily applicable to other diseases with an underlying molecular basis. Through the integration of molecular-based technologies, systematic tissue procurement and medical informatics, we now have the ability to identify clinically applicable "genotype"-"phenotype" associations across cohorts of patients that can rapidly be translated into useful diagnostic and treatment strategies. This review will touch on the various steps in the translational pipeline, and highlight some of the most essential elements as well as possible roadblocks that can impact success of the program. Critical issues with regard to Institutional Review Board (IRB) and Health Insurance Portability and Accountability Act (HIPAA) compliance, data standardization, sample procurement, quality control (QC), quality assurance (QA), data analysis, preclinical models and clinical trials are addressed. The various facets of the translational pipeline have been incorporated into a fully integrated computational system, appropriately named Dx2Tx. This system readily allows for the identification of new diagnostic tests, the discovery of biomarkers and drugable targets, and prediction of optimal treatments based upon the underlying molecular basis of the disease.

Inter-rater agreement on chromosome 5 breakage in FISH-based mutagen sensitivity assays (MSAs)

In chromosome breakage assays, validated, universal criteria for selection of cells and classification of chromosome aberrations may enhance their utility for cancer susceptibility screening. To standardize a fluorescence in situ hybridization (FISH) modification of the mutagen sensitivity assay (MSA), scoring criteria were evaluated by web-based validation. Two hundred digital FISH images were assigned random identification numbers. With this set of images, criteria for inclusion of cells and measurement of the frequency of abnormal cells were evaluated by eight observers, all of whom had five or more years of experience. Observers included doctoral and MS/BS level cytogeneticists, and were drawn from a randomized pool of 54 volunteers. Questions addressed were: (1) how uniformly were criteria applied to analysis of a standard digital FISH image set and (2) did concordance vary with educational level? These data suggest inter-rater agreement within a factor of 2 for average breakage frequency, but revealed greater variability in cell selection. These results aid in estimating the components of assay variance due to definitions, technical parameters and biological variables.

Challenges for Biomarkers in Cancer Detection

Cancer remains the leading cause of death in the United States. Biomarkers can be used to detect cancer in different stages, initiation, development, and progression. The desirable property and utility of a biomarker lie in its ability to provide an early indication of disease progression. Biomarkers should be easy to detect, measurable across populations, and useful for detection of cancer at an early stage, identification of high-risk individuals, detection of recurrence, or monitoring endpoints in intervention studies. Recent technological advances have helped develop noninvasive, sensitive, and specific biomarkers to detect cancer at early stages of the disease.