Creating Biomedical Technologies to Improve Health

2017 BESIP Project

Epithelial Systems Biology Laboratory
Mentor Name: 
Mark A. Knepper, M.D., Ph.D.
Mentor Email: 
Mentor Telephone: 

Laboratory and Project Description

The mentor, Mark Knepper, M.D., Ph.D., is a Biomedical Engineer who uses systems biology-based approaches to study how the kidney regulates water excretion. This involves use of large-scale data acquisition techniques, such as protein mass spectrometry and ‘next-generation’ nucleotide sequencing technologies to discover molecular mechanisms involved in renal water transport. Much of the focus is on regulation of molecular water channels called "aquaporins" by the hormone vasopressin. The Epithelial Systems Biology Laboratory is a small close-knit group of scientists devoted to development and exploitation of cutting-edge experimental and computational tools for these studies.
The objective is to carry out an experimental study that the student can pursue independently of other ongoing laboratory studies, generating a publication with the BESIP student as first author. The current opportunity for a BESIP student is in the category of proteomics in renal physiology. The hormone vasopressin regulates water transport in the collecting ducts of the kidney in part by regulating phosphorylation aquaporin-2 water channel and other proteins in collecting duct cells. Phosphorylation depends on protein kinase genes expressed in the cells. Of the two classes of kinases, S/T kinases and tyrosine kinases, we have only investigated how vasopressin regulates the former. The BESIP student will use techniques developed in the laboratory by a previous BESIP student, Boyang Zhao (see publication below), to identify tyrosines that become phosphorylated in response to vasopressin. The student will learn basic biochemical techniques and the principles of protein mass spectrometry. The student will also learn about strategies for bioinformatic analysis of mass spectrometry data. The student will be closely supervised by the mentor to assure rapid progress with the goal of preparing and publishing a paper based on his/her data.
Recent papers by BME students (Sachs, Harbaugh, Zhao, Huling, Liu, Claxton, Corcoran, Grady) and ChE students (Jacob, Feric, Sanghi, Pickering) in the lab include:
  • Sachs AN, Pisitkun T, Hoffert, JD, Yu MJ, Knepper MA. LC-MS/MS analysis of differential centrifugation fractions from native inner medullary collecting duct of rat. Am J Physiol Renal Physiol, 2008; 295: F 1799-806.
  • Jacob VA, Harbaugh CM, Dietz JR Fenton RA, Kim SM, Castrop H, Schnermann J, Knepper MA, Chou CL, Anderson SA. Magnetic resonance imaging of urea transporter knockout mice shows renal pelvic abnormalities. Kidney Int., 2008; 74: 1202-8.
  • Feric M, Zhao B, Hoffert JD, Pisitkun T, Knepper MA. Large-scale phosphoproteomic analysis of membrane proteins in renal proximal and distal tubule. Am J Physiol Cell Physiol. 2011; 300: C755-70.
  • Huling JC, Pisitkun T, Song JH, Yu MJ, Hoffert JD, Knepper MA. Gene expression databases for kidney epithelial cells. Am J Physiol Renal Physiol. 2012;302:F401-7.
  • Zhao B, Knepper MA, Chou CL, Pisitkun T. Large-scale phosphotyrosine proteomic profiling of rat renal collecting duct epithelium reveals predominance of proteins involved in cell polarity determination. Am J Physiol Cell Physiol. 2012;302:C27-45
  • Claxton JS, Sandoval PC, Liu G, Chou CL, Hoffert JD, Knepper MA. Endogenous carbamylation of renal medullary proteins. PLoS One. 2013 Dec 26;8(12):e82655.
  • Sanghi A, Zaringhalam M, Corcoran CC, Saeed F, Hoffert JD, Sandoval P, Pisitkun T, Knepper MA. A knowledge base of vasopressin actions in the kidney. Am J Physiol Renal Physiol. 2014;307:F747-55.
  • Pickering CM, Grady C, Medvar B, Emamian M, Sandoval PC, Zhao Y, Yang CR, Jung HJ, Chou CL, Knepper MA. Proteomic profiling of nuclear fractions from native renal inner medullary collecting duct cells. Physiol Genomics. 2016; 48:154-66.  
  • Corcoran CC, Grady CR, Pisitkun T, Parulekar J, Knepper MA. From 20th Century Metabolic Wall Charts to 21st Century Systems Biology: Database of Mammalian Metabolic Enzymes. Am J Physiol Renal Physiol. [Epub ahead of print] PMID: 27974320.
  • LeMaire SM, Raghuram V, Grady CR, Pickering CM, Chou CL, Umejiego EN, Knepper MA. Serine/threonine phosphatases and aquaporin-2 regulation in renal collecting duct. Am J Physiol Renal Physiol. 2017;312:F84-F95.