The goal in our first of three aims is to integrate data and sample collection from subjects enrolled in the ongoing CTOT-08 trial. On this cohort, additional discovery genomics will be performed, including alternative splicing, mlRNA profiling, epigenetics, multiple single reaction monitoring proteomics of cells and plasma, multiparameter flow cytometry genomics and target gene, pathway-centered genetics. The first objective of this Aim will be to understand what additional discoveries, in terms of biomarkers and mechanisms, are possible by integration of these latest genomic/proteomic technologies. The second objective of this Aim will be to identify patients with specific clinical events and outcomes (e.g. acute rejection and aggressive chronic rejection) that can be studied with freshly purified and activated T and B cell subsets in the context of functional pathways and immunosuppressive therapies identified by the deep sequencing genetics in Project #4, the functional genomics in Project #1, and phosphoproteomlcs in Project #2.
Our second aim will be to discover a new set of biomarker signatures that correlate with the outcomes of patients undergoing kidney transplantation with known levels of anti-donor HLA-specific antibodies following desensitization protocols. Third, we will test the hypothesis that there are common, unifying mechanisms of immunity and inflammation that mechanistically link chronic kidney transplant rejection with the significantly increased risk of catastrophic cardiac events post-transplantation and can be followed by new profiles of blood and/or plasma biomarkers.

Public Health Relevance

The proposed projects have broad relevance for all transplant recipient populations given the burden of chronic immune injury to transplants and the associated systemic effects on the transplant recipients. By advancing the understanding of immune mechanisms involved in transplant rejection while identifying better biomarkers for early diagnosis and intervention, we hope to impact long term survival for these patients.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Research Program--Cooperative Agreements (U19)
Project #
Application #
Study Section
Special Emphasis Panel (ZAI1-MFH-I)
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Scripps Research Institute
La Jolla
United States
Zip Code
Leventhal, J R; Mathew, J M; Salomon, D R et al. (2016) Nonchimeric HLA-Identical Renal Transplant Tolerance: Regulatory Immunophenotypic/Genomic Biomarkers. Am J Transplant 16:221-34
LaMere, S A; Thompson, R C; Komori, H K et al. (2016) Promoter H3K4 methylation dynamically reinforces activation-induced pathways in human CD4 T cells. Genes Immun 17:283-97
Modena, B D; Milam, R; Harrison, F et al. (2016) Changes in Urinary Microbiome Populations Correlate in Kidney Transplants With Interstitial Fibrosis and Tubular Atrophy Documented in Early Surveillance Biopsies. Am J Transplant :
Savaryn, John P; Toby, Timothy K; Catherman, Adam D et al. (2016) Comparative top down proteomics of peripheral blood mononuclear cells from kidney transplant recipients with normal kidney biopsies or acute rejection. Proteomics 16:2048-58
Weinsheimer, Shantel; Bendjilali, Nasrine; Nelson, Jeffrey et al. (2016) Genome-wide association study of sporadic brain arteriovenous malformations. J Neurol Neurosurg Psychiatry 87:916-23
Kurian, S M; Fouraschen, S M G; Langfelder, P et al. (2015) Genomic profiles and predictors of early allograft dysfunction after human liver transplantation. Am J Transplant 15:1605-14
Norden-Krichmar, Trina M; Gizer, Ian R; Phillips, Evelyn et al. (2015) Variants Near CCK Receptors are Associated With Electrophysiological Responses to Pre-pulse Startle Stimuli in a Mexican American Cohort. Twin Res Hum Genet 18:727-37
Magdeldin, Sameh; Blaser, Rachel E; Yamamoto, Tadashi et al. (2015) Behavioral and proteomic analysis of stress response in zebrafish (Danio rerio). J Proteome Res 14:943-52
Komori, H Kiyomi; Hart, Traver; LaMere, Sarah A et al. (2015) Defining CD4 T cell memory by the epigenetic landscape of CpG DNA methylation. J Immunol 194:1565-79
Routh, Andrew; Head, Steven R; Ordoukhanian, Phillip et al. (2015) ClickSeq: Fragmentation-Free Next-Generation Sequencing via Click Ligation of Adaptors to Stochastically Terminated 3'-Azido cDNAs. J Mol Biol 427:2610-6

Showing the most recent 10 out of 66 publications