Mass spectrometry-based proteomics for advancing solid organ transplantation research

Abstract

Scarcity of high-quality organs, suboptimal organ quality assessment, unsatisfactory pre-implantation procedures, and poor long-term organ and patient survival are the main challenges currently faced by the solid organ transplant (SOT) field. New biomarkers for assessing graft quality pre-implantation, detecting, and predicting graft injury, rejection, dysfunction, and survival are critical to provide clinicians with invaluable prediction tools and guidance for personalized patients' treatment. Additionally, new therapeutic targets are also needed to reduce injury and rejection and improve transplant outcomes. Proteins, which underlie phenotypes, are ideal candidate biomarkers of health and disease statuses and therapeutic targets. A protein can exist in different molecular forms, called proteoforms. As the function of a protein depends on its exact composition, proteoforms can offer a more accurate basis for connection to complex phenotypes than protein from which they derive. Mass spectrometry-based proteomics has been largely used in SOT research for identification of candidate biomarkers and therapeutic intervention targets by so-called "bottom-up" proteomics (BUP). However, such BUP approaches analyze small peptides in lieu of intact proteins and provide incomplete information on the exact molecular composition of the proteins of interest. In contrast, "Top-down" proteomics (TDP), which analyze intact proteins retaining proteoform-level information, have been only recently adopted in transplantation studies and already led to the identification of promising proteoforms as biomarkers for organ rejection and dysfunction. We anticipate that the use of top-down strategies in combination with new technological advancements in single-cell and spatial proteomics could drive future breakthroughs in biomarker and therapeutic target discovery in SOT.

Keywords: biomarkers; bottom-up mass spectrometry; proteoforms; proteomics; solid organ transplantation; top-down mass spectrometry.

Figure 1

Translational MS-based proteomics for identifying novel biomarkers and therapeutic targets in SOT research. (A) Overview of mechanisms contributing to SOT outcomes. (B) Workflow of translational bottom-up and top-down MS-based proteomics approaches in SOT.

Figure 2

BUP and TDP strategies for biomarker and therapeutic target identification. Workflows of BUP (A), TDP (B) and spatial proteomics (C) using mass spectrometry imaging approaches.