Biomarkers types

Chemical Biomarker Type of Information Available Possible Applications... 

Class of Biomarker Type of Effect Specific Examples... 

Three biomarker types are the most critical, these are surrogate (disease management), stratification (companion), and early detection. The semantics is somewhat confusing as the same types of markers used during a drug trial may have different names compared to the use in clinical practice here the naming used in clinical practice is in parentheses. 

Although in vitro models clearly show that MDR transporters can protect tumor cells, their relevance in clinical oncology remains controver sial. As is the case for most potentially useful cancer biomarkers, no universally embraced guidelines for analytical or clinical validation of MDR transporters exist. Evidence linking ABCB1 Pgp/MDRl expression with poor clinical outcome is most conclusive for breast cancer, sarcoma, and certain types of leukemia. The relevance of the other MDR transporters in clinical MDR is still unclear. The prognostic implication of ABCCl/ MRPl remains controversial and very little is known clinically about ABCG2. 

Some biomarker responses provide evidence only of exposure and do not give any reliable measure of toxic effect. Other biomarkers, however, provide a measure of toxic effects, and these will be referred to as mechanistic biomarkers. Ideally, biomarker assays of this latter type monitor the primary interaction between a chemical and its site of action. However, other biomarkers operating down stream from the original toxic lesion also provide a measure of toxic action (see Figure 14.3 in Chapter 14), as, for instance, in the case of changes in the transmission of action potential... 

Four examples will now be given of such mechanistic biomarker assays that can give integrative measures of toxic action by pollutants, all of which have been described earlier in the text. Where the members of a group of pollutants share a common mode of action and their effects are additive, TEQs can, in principle, be estimated from their concentrations and then summated to estimate the toxicity of the mixture. In these examples, toxicity is thought to be simply related to the proportion of the total number sites of action occupied by the pollutants and the toxic effect additive where two or more compounds of the same type are attached to the binding site. 

There is a continuing interest in the development of biomarker assays for use in environmental risk assessment. As discussed elsewhere (Section 16.6), there are both scientific and ethical reasons for seeking to introduce in vitro assays into protocols for the regulatory testing of chemicals. Animal welfare organizations would like to see the replacement of toxicity tests by more animal-friendly alternatives for all types of risk assessment—whether for environmental risks or for human health. 

Experimental evidence in humans is based upon intervention studies with diets enriched in carotenoids or carotenoid-contaiifing foods. Oxidative stress biomarkers are measured in plasma or urine. The inhibition of low density lipoprotein (LDL) oxidation has been posmlated as one mechanism by which antioxidants may prevent the development of atherosclerosis. Since carotenoids are transported mainly via LDL in blood, testing the susceptibility of carotenoid-loaded LDL to oxidation is a common method of evaluating the antioxidant activities of carotenoids in vivo. This type of smdy is more precisely of the ex vivo type because LDLs are extracted from plasma in order to be tested in vitro for oxidative sensitivity after the subjects are given a special diet. 

Results obtained in in vivo and ex vivo experiments are of various types. Some studies have found positive effects of the consumption of carotenoids or foods containing carotenoids on the markers of in vivo oxidative stress, even in smokers. Other studies demonstrated no effects of carotenoid ingestion on oxidative stress biomarkers of lipid peroxidation. " It should be noted that for studies using food, the activity observed may also be partly due to other antioxidant molecules in the food (phenols, antioxidant vitamins) or to the combination of actions of all the antioxidants in the food. 

Microbes of differing physiologic types, acting in consortia, appear to be more destructive than monocultures. Methods for examining consortia are based on the detection of lipid biomarkers that are characteristic for different classes of microbes. These can be analyzed by gas chromatography coupled with mass spectrometry [512]. 

Quinones, lipid-soluble substances involved in electron transport, can also be used as biomarkers. Lipski et al. (155) u.sed quinone analyses, physiological tests, and fatty acid profiles to differentiate Gram-negative non-fermentative bacteria isolated from biofilters. Quinone type was found to be an efficient method to group isolates prior to the analysis of results from the physiological tests. The detection of quinones appears to be restricted to the discrimination of isolated colonies and has limited potential to the analysis of mixed populations. 

A number of biochemical markers not associated with the cell envelope allow the specific detection of individual microorganisms in environmental samples. These include secondary alcohols. For example, Mycobacterium xenopi can be detected through the hydrolysis of wax ester mycolates, which liberates 2-docosanol, a characteristic and dominant secondary alcohol, which can be detected at low levels by GC-MS. This biomarker was found to be very useful for the rapid detection of M. xenopi in drinking water (159,160). Results from the GC-MS detection of 2-docosanol were obtained within 2 days compared to the 12 weeks required for culturable detection of M. xenopi. The detection limit for this type of approach was found to be 10 colony-forming units (CFU) ml" drinking water. 

Additionally it has been our experience that mass spectrometry as a routine detection/identification technique for bacteria is not well received by microbiologists and clinicians who prefer less expensive, less complicated approaches to bacterial typing and identification, such as methods based on polymerase chain reaction (PCR) and enzyme-linked immunosorbent assays (ELISA). For that reason we have adapted our MS approach to serve as a means of biomarker discovery that feeds candidate proteins or leads into development as PCR targets or other immunoassay techniques. 

It is therefore not surprising that the interest in PyMS as a typing tool diminished at the turn of the twenty-first century and hence why taxonomists have turned to MS-based methods that use soft ionization methods such as electrospray ionization (ESI-MS) and matrix-assisted laser desorption ionization (MALDI MS). These methods generate information-rich spectra of metabolites and proteins, and because the molecular ion is seen, the potential for biomarker discovery is being realized. The analyses of ESI-MS and MALDI-MS data will still need chemometric methods, and it is hoped that researchers in these areas can look back and learn from the many PyMS studies where machine learning was absolutely necessary to turn the complex pyrolysis MS data into knowledge of bacterial identities. 

A complete physical examination and laboratory analysis are needed to rule out secondary causes and to assess kyphosis and back pain. Laboratory testing may include complete blood count, liver function tests, creatinine, urea nitrogen, calcium, phosphorus, alkaline phosphatase, albumin, thyroid-stimulating hormone, free testosterone, 25-hydroxyvitamin D, and 24-hour urine concentrations of calcium and phosphorus. Urine or serum biomarkers (e.g., cross-linked N-telopeptides of type 1 collagen, osteocalcin) are sometimes used. 

Sample type Key biomarkers Recommen- ded analytical methods Standards Advantages Disadvantages... 

---