Dr. John Lee, an Assistant Professor in Medicine at Weill Cornell Medical College, seeks to achieve an academic career as a patient-oriented researcher in the field of kidney transplantation. His overall goal is to become a translational researcher who will develop biomarkers for the diagnosis and prognostication of kidney transplant related complications with the aim of developing targeted therapies for these complications. His research will focus on characterizing the relationship between the gut microbiome and post-transplant complications in kidney transplant recipients. This application describes a series of planned steps to further his development into an independent physician-scientist over the next five years. The gut microbiota (the community of bacteria in the gut) is increasingly being recognized as having an important role in regulating the immune system and in drug metabolism. Little, however, is known about the changes in the gut microbiome after kidney transplantation or about the gut microbiome's contribution to post-transplantation complications. Through a KL2 Scholars Award, Dr. Lee conducted a pilot study on characterizing the gut microbiota after kidney transplantation and reported the gut microbiota's associations with acute rejection (an immune process that can lead to transplant failure), with tacrolimus dosing requirements (a key immunosuppressive drug used to prevent acute rejection), and with post-transplant diarrhea. Based upon this preliminary data, Dr. Lee proposes the following specific aims in this K23 application:
Aim 1 : To characterize microbial profiles associated with AR and develop novel diagnostic and prognostic AR biomarkers;
Aim 2 : To investigate whether gut microbiome profiles predict future tacrolimus dosing requirements;
Aim 3 : To characterize microbial profiles associated with post-transplant diarrhea. To achieve Aim 1, Dr. Lee will collect and profile stool specimens from kidney transplant recipients at the time of kidney transplant biopsy using 16S rRNA deep sequencing, shotgun metagenomic sequencing, and metabolite profiling. He will determine whether gut microbial profiles distinguish kidney transplant recipients with acute cellular rejection (N=40) from those with graft dysfunction but no AR (N=40) and from those with normal biopsies (N=40). Based upon the results, he will develop a PCR-based fecal assay for the rapid diagnosis of ACR. To achieve Aim 2, Dr. Lee plans to recruit 110 kidney transplant recipients prospectively after transplantation and collect weekly fecal specimens in the first month of transplantation and monthly specimen during post-transplant month 2 and 3. He will profile the post- transplant week 1 fecal specimens and will determine whether post-transplant week 1 fecal Faecalibacterium prausnitzii, other bacterial species, genes, and metabolites are associated with tacrolimus dosing requirements at 1 month post-transplantation and based upon the results, will develop a PCR-based fecal assay that will predict 1-month tacrolimus dosing requirements. To achieve Aim 3, Dr. Lee will utilize the same prospective cohort and will profile fecal specimens associated with post-transplant diarrhea and compare them to time- matched fecal specimens from transplant recipients who do not develop diarrhea. He will determine whether Bacteroides, other bacterial species, genes, and metabolites are associated with post-transplant diarrhea. The proposed project should elucidate novel biomarkers for diagnosing AR and for predicting tacrolimus dosing requirements as well as yield mechanistic insight into AR, tacrolimus dosing, and post-transplant diarrhea. Armed with a novel understanding of the gut microbiome's role in kidney transplantation, it will be possible to design new therapies to prevent acute rejection, optimize tacrolimus dosing, and minimize post-transplant diarrhea. The proposed project will build upon Dr. Lee's preliminary 16S rRNA deep sequencing study and further develop his expertise in conducting translational research. Dr. Lee has formed a Scholarship Advisory Committee that will guide him in completing the proposed project. Dr. Manikkam Suthanthiran, an expert in conducting translational studies in kidney transplantation, will be Dr. Lee's primary mentor. Dr. Eric Pamer will be a co- mentor and provide expertise in the gut microbiome profiling techniques. Dr. Joao Xavier, an expert computational biologist, will assist Dr. Lee in gut microbiome specific bioinformatics. Dr. Joseph Schwartz, an expert biostatistician, will assist Dr. Lee with biostatistical analyses. Dr. David Artis, a leading expert in characterizing the link between commensal bacteria and immune regulation, will provide expertise in interpreting the microbiome findings as well as designing future mechanistic experiments. Throughout the 5-year period, Dr. Lee will meet regularly with members of his Scholarship Advisory Committee who will oversee the project's progress as well as his development into an independent physician scientist. He will supplement his training with structured meetings and with formal coursework through his current enrollment in a Master's Degree in Clinical and Translational Investigation. Weill Cornell Medical College is committed to Dr. Lee's development into a physician scientist and has provided institutional start-up funds and dedicated research personnel as well as a commitment for him to devote at least 75% effort to the proposed project. By the end of the 5-year award period, Dr. Lee will have gained expertise in conducting a large translational study, gut microbiome profiling, and advanced bioinformatical and biostatistical analyses, which will allow him to achieve independent status as a translational researcher, able to investigate the gut microbiome's associations with post-transplant complications as well as to investigate modulation of the gut microbiota to favor beneficial outcomes in kidney transplantation.

Public Health Relevance

This project examines the role of gut bacteria in acute rejection of a transplant kidney, dosing of a transplant medication called tacrolimus, and post-transplant diarrhea in kidney transplant recipients. This research will provide fundamental insights into these critical and unresolved issues in kidney transplantation and will allow for the development of improved strategies to prevent acute rejection, to optimize tacrolimus dosing, and to minimize post-transplant diarrhea.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Mentored Patient-Oriented Research Career Development Award (K23)
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Transplantation Biology & Immunology-2 (AITC)
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Gondre-Lewis, Timothy A
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Weill Medical College of Cornell University
Internal Medicine/Medicine
Schools of Medicine
New York
United States
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Lee, John Richard; Magruder, Matthew; Zhang, Lisa et al. (2018) Gut microbiota dysbiosis and diarrhea in kidney transplant recipients. Am J Transplant :
Burnham, Philip; Dadhania, Darshana; Heyang, Michael et al. (2018) Urinary cell-free DNA is a versatile analyte for monitoring infections of the urinary tract. Nat Commun 9:2412