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Biomarker Discovery

The Lampe laboratory performs studies to find blood tests or protein biomarkers that can indicate if and where a person has cancer and if it is present how to best treat it. Specifically, we are working to find early detection, recurrence or response biomarkers of colon, breast, pancreas and lung cancer. Useful biomarkers can allow doctors to find and treat cancer earlier and better, saving lives, reducing costs and allowing for “personalized or precision medicine” where the treatment is specific for each person’s disease. Currently our primary approach is to utilize high density antibody arrays to determine proteomic, glycoproteomic and auto-autoantibody markers of disease. We are especially interested in markers where the level of a protein, the level of its glycosylation or whether autoantibodies are produced to it can yield multi-dimensional information on each protein. We consider specific proteins that show consistent cancer-specific changes in 2 or 3 of these measurements to be “hybrid markers”. We hypothesize these markers will suffer less variation between different individuals since one component can act to “standardize” the other measurement.

Our approach to biomarker discovery is unique in several ways. Our discovery arrays contain over 3000 antibodies printed in triplicate giving us reliable and highly consistent data. The fact that we assay proteomic, glycomic and autoantibody changes gives us broad coverage of potential biomarkers. We can screen hundreds of samples in a week reducing false positives. For early detection, we have utilized large pre-diagnostic sample sets from screening cohorts (WHI, CHS, PLCO) reducing the chance that potential early detection biomarkers are not simply related to inflammation or disease burden from people with significant disease burden. We validate in similar sized sample sets and the high denisty of the arrays allow us to test hundreds of candidate biomarkers from our research and others. Only after markers are validated in multiple sets do we spend the effort to convert them to ELISA assays Thus, their utility is more clear reducing costs and prioritizing effort.

Our array printer deposits 48 spots 3 times through all of the slides and repeats this 225 times for a total of 10800 spots per slide which represents 3600 different antibodies printed 3 times. Below is an array that was incubated with a case sample labeled with cy5 (red) and a reference sample labeled with cy3 (green).
 

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The 3 array analysis platforms we will utilize include:


Proteomics:
We use our antibody arrays to determine the level of different proteins in a blood or tissue sample by labeling the proteins in the test sample with cy5 and incubating them with a sample of reference proteins labeled with cy3. 

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Glycoproteomics: Two common cancer specific carbohydrate modifications are sialyl lewis A (the so-called CA19.9 antigen) and lewis X. We can probe the samples applied to the array with fluorescently labeled secondary antibodies that bind to sialyl Lewis A and Lewis X. 

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Autoantibodies: The presence of autoantigen-autoantibody pairs in case and control plasma samples applied to arrays can be detected with fluorescently labeled anti-human IgG or IgM.

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