Unveiling Disease-Associated Antigens: The Role of Immunoproteomics

Immunoproteomics describes a growing collection of approaches that aim to identify and analyze a subset of proteins that induce an immune response – known as the immunoproteome. Although immunoproteomics has been utilized for a longer period in the field of proteomics, it is a relatively new concept and was first coined by Peter R. Jungblut in 2001. In this infographic, we explore the role of immunoproteomics in identifying disease-associated antigens that elicit an immune response. Immunoproteomics vs immunopeptidomics: What's the difference? Immunoproteomics involves using Immunopeptidomics, utilizing MS, techniques to detect and analyze identifies peptides presented on cell antigenic proteins, leveraging advances surfaces by major histocompatibility in (e.g.) mass spectrometry (MS) to complexes (MHCs). identify immune complexes, antibody Since MHCs present antigens to T antigen interactions and antigens in cells, this approach highlights the cell blood serum. mediated immune response, crucial These methods are useful for studying for studying intracellular pathogens the immune response to specific targeted by cytotoxic T cells. antigens, but are primarily limited to the humoral immune response. Humoral immunity: Cell-mediated immunity: • An antibody-mediated response that occurs when foreign material (antigens) are detected in the body. • Does not depend on antibodies for its adaptive immune functions. • Primarily driven by B cell lymphocytes, an immune cell • Primarily driven by mature T cells, that produces antibodies after macrophages and the release of detecting a specific antigen. cytokines in response to an antigen. Typical workflow of immunoproteomics research + 1. Sample collection The collection of biological samples (e.g., blood, tissue) occurs, with a focus on those with known diseases and healthy controls for comparison. + 2. Protein extraction Extraction of proteins from the sample using specialized techniques to isolate the proteome. + 3. Identification of antigenic proteins Identification of proteins that interact with components of the immune system, such as antibodies and T cells. + 4. Analytical techniques Advanced techniques, such as MS, protein microarrays or immunoblotting (i.e., western blotting), are then applied to study the proteins of interest. These techniques can either be gel-based or gel-free immunoproteomics. + 5. Bioinformatics analysis Computational tools are applied to analyze protein data, com paring antigens between disease and healthy samples to aid identification of potential biomarkers or therapeutic targets. + 6. Validation of findings The identified antigens should be validated through replication studies, testing in larger patient cohorts and using experimental models to confirm the immune response. + 7. Application Results can be applied to different areas including: • Diagnostics: developing tests based on disease specific antigens • Therapeutics: designing vaccines or treatments targeting identified antigens • Basic research: understanding disease mechanisms and immune interactions Applications of immunoproteomics There are many potential applications of immunoproteomics, offering valuable insights into disease mechanisms. While a few key examples are outlined below, the possibilities extend far beyond these, providing a glimpse into the areas of diagnostic medicine that can benefit from immunoproteomics. 1. Vaccine efficiency and development Vaccines protect against bacterial and viral diseases by stimulating the production of neutralizing antibodies against specific pathogens. While vaccination has significantly reduced the incidence of many serious diseases, challenges remain for pathogens without vaccines or for individuals with weakened immune systems who may not respond effectively. Immunoproteomics plays a crucial role in vaccine development and efficiency by identifying highly effective immunogens and monitoring immune responses. Example: Davies et al. analyzed the humoral immune response elicited by a commercial smallpox vaccine using a viral protein array. They found >20 antigens to be immunodominant, but only half of these were potential neutralizing targets on the viral envelope. Immunoproteomics could aid monitoring of vaccination efficiency and selection of candidate antigens to generate neutralizing antigen responses. 2. Monitoring antigenicity of therapeutic drugs Immunogenicity is a significant problem associated with protein therapeutics. Due to artificial production processes, recombinant therapeutics are often not completely identical to their human native counterparts. Sometimes, these therapeutics elicit an immune response that interferes with drug affectivity. In principle, immunoproteomic approaches could be used to define the patient's immune response against a panel of related (protein) drugs to aid in selective drug application to optimize individualized treatment. 3. Diagnosis and prognosis of autoimmune diseases Autoimmune diseases arise from erroneous activation of the immune system, resulting in the attack of self-proteins within the human body. Examples of autoimmune diseases include rheumatoid arthritis, psoriasis and systemic lupus erythematosus (SLE). In all these conditions, immunoproteomics holds great promise to aid in the diagnosis, prognosis and monitoring of autoimmune diseases. Example: For the diagnosis of SLE, Li et al. constructed a multiplexed microarray with about 30 known disease-associated antigens. The use of these arrays revealed distinct clusters of immunoglobulins G/M autoreactivity in the patient’s blood serum that could be linked to SLE disease activity. This approach could aid the diagnosis of patients who are at high risk for severe organ damage and may guide treatment. 4. Early-stage cancer detection Many cancer patients produce antibodies against antigens that are specifically expressed by malignant cells. This immune response is a valuable source of diagnostic and prognostic information. Immunoproteomics can aid as a diagnostic approach for the early detection and monitoring of different types of cancer. However, the timing of antibody responses during carcinogenesis remains poorly understood, necessitating careful evaluation to minimize the risk of false-negative diagnoses. Example: Shi et al. identified six antigens as effective classifiers for prostate cancer, while gel-free LC-MS/MS revealed ovarian tumor antigens detectable in early-stage patients. However, Zeng et al. showed antibodies against a synthetic NY-ESO-1 epitope were present in only 5–10% of cancer patients, highlighting the need for a broad panel of antigens or epitopes to effectively detect cancer across diverse patient groups. Looking to the future Advances in immunoproteomics aim to bridge the gap between research and clinical application. However, a significant challenge lies in developing robust assay platforms and standardized protocols for clinical implementation. Future innovations such as specialized antigen array technologies (i.e., fluid-phase systems) may replace enzyme-linked immunosorbent assays for multiplexed antigen assays in clinical labs. Advancements in MS sensitivity enabling single-cell proteomics are also anticipated to drive progress Antigen profiling approaches have the potential to become essential clinical tools for screening, diagnosis, prognosis and monitoring therapeutic interventions.