Shotgun Immunoproteomics for Identification of Nonhuman Leukocyte Antigens Associated With Cellular Dysfunction in Heart Transplant Rejection

Report of the 2022 Banff Heart Concurrent: Focus on non-human leukocyte antigen antibodies in rejection and the pathology of "mixed" rejection

The Banff Heart Concurrent Session, held as part of the 16th Banff Foundation for Allograft Pathology Conference at Banff, Alberta, Canada, on September 21, 2022, focused on 2 major topics: non-human leukocyte antigen (HLA) antibodies and mixed rejection. Each topic was addressed in a multidisciplinary fashion with clinical, immunological, and pathology perspectives and future developments and prospectives. Following the Banff organization model and principles, the collective aim of the speakers on each topic was to • Determine current knowledge gaps in heart transplant pathology • Identify limitations of current pathology classification systems • Discuss next steps in addressing gaps and refining classification system.

Proteomics: Its Promise and Pitfalls in Shaping Precision Medicine in Solid Organ Transplantation

Solid organ transplantation is an established treatment of choice for end-stage organ failure. However, all transplant patients are at risk of developing complications, including allograft rejection and death. Histological analysis of graft biopsy is still the gold standard for evaluation of allograft injury, but it is an invasive procedure and prone to sampling errors. The past decade has seen an increased number of efforts to develop minimally invasive procedures for monitoring allograft injury. Despite the recent progress, limitations such as the complexity of proteomics-based technology, the lack of standardization, and the heterogeneity of populations that have been included in different studies have hindered proteomic tools from reaching clinical transplantation. This review focuses on the role of proteomics-based platforms in biomarker discovery and validation in solid organ transplantation. We also emphasize the value of biomarkers that provide potential mechanistic insights into the pathophysiology of allograft injury, dysfunction, or rejection. Additionally, we forecast that the growth of publicly available data sets, combined with computational methods that effectively integrate them, will facilitate a generation of more informed hypotheses for potential subsequent evaluation in preclinical and clinical studies. Finally, we illustrate the value of combining data sets through the integration of 2 independent data sets that pinpointed hub proteins in antibody-mediated rejection.

Optimization of a high-throughput shotgun immunoproteomics pipeline for antigen identification

Identification of proteins which initiate and/or perpetuate adaptive immune responses has potential to greatly impact pre-clinical and clinical work across numerous fields. To date, however, the methodologies available to identify antigens responsible for driving adaptive immune responses have been plagued by numerous issues which have drastically limited their widespread adoption. Therefore, in this study, we sought to optimize a shotgun immunoproteomics approach to alleviate these persistent issues and create a high-throughput, quantitative methodology for antigen identification. Three individual components of a previously published approach, namely the protein extraction, antigen elution, and LC-MS/MS analysis steps, were optimized in a systematic manner. These studies determined that preparation of protein extracts using a one-step tissue disruption method in immunoprecipitation (IP) buffer, eluting antigens from affinity chromatography columns with 1% trifluoroacetic acid (TFA), and TMT-labeling & multiplexing equal volumes of eluted samples for LC-MS/MS analysis, resulted in quantitative longitudinal antigen identification, with reduced variability between replicates and increased total number of antigens identified. This optimized pipeline provides a multiplexed, highly reproducible, and fully quantitative approach to antigen identification which is broadly applicable to determine the role of antigenic proteins in inciting (i.e., primary antigens) and perpetuating (i.e., secondary antigens) a wide range of diseases. SIGNIFICANCE: Using a systematic, hypothesis-driven approach, we identified potential improvements for three individual steps of a previously published approach for antigen-identification. Optimization of each step created a methodology which resolved many of the persistent issues associated with previous antigen identification approaches. The optimized high-throughput shotgun immunoproteomics approach described herein identifies more than five times as many unique antigens as the previously published method, greatly reduces protocol cost and mass spectrometry time per experiment, minimizes both inter- and intra-experimental variability, and ensures each experiment is fully quantitative. Ultimately, this optimized antigen identification approach has the potential to facilitate novel antigen identification studies, allowing evaluation of the adaptive immune response in a longitudinal manner and encourage innovations in a wide array of fields.