The Sentinel Within: Exploiting the Immune System for CancerBiomarkers†Karen S. Anderson‡and Joshua LaBaer*,§Dana-Farber Cancer Institute, Harvard Medical School, Boston Massachusetts, and Harvard Institute ofProteomics, Harvard Medical School, Boston Massachusetts 02115Received March 30, 2005The release of proteins from tumors triggers an immune response in cancer patients. These tumorantigens arise from several mechanisms including tumor-specific alterations in protein expression,mutation, folding, degradation, or intracellular localization. Responses to most tumor antigens are rarelyobserved in healthy individuals, making the response itself a biomarker that betrays the presence ofunderlying cancer. Antibody immune responses show promise as clinical biomarkers because antibodieshave long half-lives in serum, are easy to measure, and are stable in blood samples. However, ourunderstanding of the specificity and the impact of the immune response in early stages of cancer islimited. The immune response to cancer, whether endogenous or driven by vaccines, involves highlyspecific T lymphocytes (which target tumor-derived peptides bound to self-MHC proteins) and Blymphocytes (which generate antibodies to tumor-derived proteins). T cell target antigens have beenidentified either by expression cloning from tumor cDNA libraries, or by prediction based on patternsof antigen expression (“reverse immunology”). B cell targets have been similarly identified using theantibodies in patient sera to screen cDNA libraries derived from tumor cell lines. This review focuseson the application of recent advances in proteomics for the identification of tumor antigens. Theseadvances are opening the door for targeted vaccine development, and for using immune responsesignatures as biomarkers for cancer diagnosis and monitoring.Keywords: tumor antigen • antibody • protein array • proteomics • tumor immunology • biomarkersIntroductionThe challenge faced by our immune system resembles thatof an intelligent security system, which must continuallymonitor for the presence of foreign invaders, while recognizingand disregarding normal self. Like a vigilant sentry, im-munologic memory persists long after exposure to the threathas abated. Recognizing the value of this persistent response,clinicians have exploited it for years to test individuals forcurrent or past exposure to a wide variety of infections.Compared to other serum-derived proteins, antibodies arestable, highly specific, and readily detected with well-validatedsecondary reagents, making them ideal for such tests. Indeed,the traditional “blood test” required of couples before obtaininga marriage license is nothing more than a test for antibodiesto the spirochete T. pallidum that causes syphilis. Thus,assessing immune responses is one of the oldest and mostsuccessful forms of biomarkers in medicine.The immune system employs complex mechanisms todistinguish between self and nonself. It deletes or renderstolerant any cells which react to the constant stream of benignmacromolecules in routine circulation. The system is notfoolproof, however, and in certain diseases, the immune systemresponds to self-derived antigens, perhaps because their loca-tion, abundance, modified form, or other features appearunfamiliar. Cancer patients often produce responses to self-proteins that are expressed by their tumors, called tumorantigens, most of which are altered in some form that rendersthem immunogenic. These proteins may be unique to cancerand germ cells (the “cancer-testis” antigens), found only inspecific tumors (prostate-specific antigen)1or in most tumors(telomerase).2They may be mutated (p53),3misfolded,4over-expressed (NY-ESO-1),5aberrantly degraded,6or aberrantlyglycosylated (MUC-1).7The magnitude of the immune responseto cancer, in general, is lower than the immune response toinfectious agents and the potential number of tumor antigensencompasses the entire tumor proteome in all its variations.At present, we have a limited understanding of the breadth,extent, impact, and dynamic variation of the immune responseto cancer (the “cancer immunome”). Identifying the specifictargets of B- and T-lymphocyte immunity to cancer may (1)identify potential biomarkers for cancer diagnosis, classifica-tion, and monitoring of response, (2) determine the impact ofimmune regulation on cancer progression, and (3) identifypotential antigens and mechanisms for immunotherapy de-velopment.†Part of the Biomarkers special issue.‡Dana-Farber Cancer Institute.§Harvard Institute of Proteomics.10.1021/pr0500814 CCC: $30.25  2005 American Chemical Society Journal of Proteome Research2005, 4, 1123-11331123Published on Web 06/18/2005The natural immune response is achieved through a tightlyregulated, yet flexible network including antibodies, antigenpresenting cells, T lymphocytes, cytokines, chemokines, regula-tory systems, as well as microenvironmental signals (Figure 1).Of these responses, the targeted responses to protein (andcarbohydrate) antigens relies on the development of antibodiesand/or T lymphocytes to target epitopes. T lymphocytes canrespond to antigens derived from within cells and without. Theyprimarily recognize short peptides (8-22mer) derived fromintracellular proteins (i.e., viral antigens) bound to self-MHCmolecules for presentation to CD8+T lymphocytes. Exogenousantigens are endocytosed, degraded, and presented to CD4+lymphocytes (Figure 2). Antibody responses increase antigenpresentation by enhancing uptake through the Fcγ receptorson antigen presenting cells. As a result, antibody targets maycontain epitopes that are also recognized by T lymphocytes.This has formed the basis for using antibody responses toidentify T cell antigens for immunotherapy.Lessons from Autoimmune Diseases. Spontaneous autoan-tibodies were first identified in a series of clinical disorders inwhich the patients’ immune systems mount a vigorous re-sponse to self-antigens, in some cases leading to debilitatingsymptoms. Systemic lupus, myasthenia gravis, rheumatoidarthritis, and others all involve this process, called autoimmu-nity. In these illnesses, the titers of autoantibodies often trackwith the severity of the illness and thus have long been usedas serum biomarkers (reviewed in refs 8,9).Although post hoc arguments can usually be constructedexplaining why proven autoantigens may have appearedunfamiliar to the immune system, in general, we do