Novel Biomarkers for Post-Liver Transplant NASH Fibrosis

Project Description (including scope of work, tasks & timeline, and deliverables): Project Overview – The scope of work to be performed at the University of Louisville for the proposal entitled “The degradome to predict post-LT NASH fibrosis” includes the mass spectrometry based peptidomic studies to characterize the circulating or plasma degradome in liver transplant donor and recipient patient samples and in mouse models of NASH fibrosis. This data will be modeled to develop rank ordered lists of peptides for subsequent confirmatory studies using human and mouse plasma specimens collected from prospective studies. This work will occur in phased approach to address human serum/plasma degradome discovery studies (Phase I), mouse serum/plasma degradome studies (Phase II) and response of the degradome to intervention (Phase III). Tasks & timeline: The timeline for these analyses, post-sample receipt and study initiation, are as follows: 1.Year 1- (A) Identification and selection of human clinical samples, (B) transfer between biorepositoryand analysis institution, (C) processing clinical samples for mass spectrometric analysis with inclusionof QA/QC steps, (D) develop unique approaches for ECM peptide quantification to address cross-linkedECM peptides 2.Year 2- (A) Collect and analyzed LCMS data on human clinical samples, (B) transfer data to Universityof Pittsburgh collaborators for modeling, (D) establish optimal protocol for mouse plasma analysis, (E)transfer mouse between biorepository and analysis institution, (F) refine and evaluate uniqueapproaches for ECM peptide quantification to address cross-linked ECM peptides in human LCMSdatasets 3.Year 3- (A) Collect LCMS data on mouse samples, (B) apply standard and cross-linked peptidebioinformatics workflow to the mouse LCMS datasets, (C) transfer data to University of Pittsburghcollaborators for modeling, (D) Process and collect LCMS data on prospectively collected humanclinical samples. 4.Year 4. (A) apply standard and cross-linked peptide bioinformatics workflow to the prospectivelycollected human clinical samples, (B) transfer data to University of Pittsburgh collaborators formodeling. 5.Year 5. (A) Develop in-silico list of targeted proteomic analysis to assess extent of partially degradedhigh-molecular weight, circulating plasma ECM proteins, (B) preliminary qualitative and quantitativedata on partially degraded high-molecular weight, circulating plasma ECM proteins Deliverables – The deliverables this study include: (1)A comprehensive list of identified human and mouse peptides with relative quantification across allanalyzed samples; (2)Standard and cross-linked peptide bioinformatics pipeline and corresponding results addressing plasmadegradomic patterning within the humans and mouse plasma peptides. (3)Standards protocols for all quantitative LCMS methods. (4)Return of excess samples to University of Pittsburgh PI.