Studies in the Epithelial Systems Biology Laboratory of the Systems Biology Center (NHLBI) are focused on developing and understanding of the mechanistic basis of vasopressin-mediated regulation of water transport across the epithelium of the renal collecting duct. To do this, we are using a systems biology approach. Specifically, we are addressing the scientific problem by investigating networks of proteins that carry out the relevant regulatory tasks in the cell rather than focusing on any single protein such as the vasopressin V2 receptor or the water channel, aquaporin-2. For this we are using methods of large scale biology, viz, protein mass spectrometry and deep sequencing of DNA, coupled with mathematical methods for analysis of the data. A large part of our efforts are in the area of bioengineering, both with regard to the large-scale biological methods deployed and the computational methods that are used to analyze the data. Much of our current work focuses on development of methods for quantitative tandem mass spectrometry applied to proteins. Guided by a generalized mathematical model of cell signaling processes, we are using quantitative protein mass spectrometry-based proteomics for large-scale assessment of changes in post-translational modifications (esp. phosphorylation), intracellular localization, abundance, and binding to other proteins in renal collecting duct cells. After critical proteins and protein modifications in vasopressin signaling are identified with 'discovery' approaches, we will track these critical processes using targeted mass spectrometry. Because we have found that many of the commercially available tools for analysis of large-scale biological data are imperfect or not appropriate for the tasks at hand, we are developing custom Java- and C++-based software tools for the analysis of proteomic and array data, with the objective of sharing these tools with the community. Regulation of transport in the collecting duct also involves transcriptional regulation. The laboratory has added RNA-Seq and ChIP-Seq approaches to hone in on the regulatory molecules that mediate vasopressin-regulated transcriptional changes in the renal collecting duct. RNA-Seq in single microdissected renal tubules is allowing us to discover signaling mechanisms responsible for transcriptional changes in animal models of water balance disorders such as the syndrome of inappropriate antidiuresis and lithium-induced nephrogenic diabetes insipidus.
| Guillén-Gómez, Elena; Bardají-de-Quixano, Beatriz; Ferrer, Sílvia et al. (2018) Urinary Proteome Analysis Identified Neprilysin and VCAM as Proteins Involved in Diabetic Nephropathy. J Diabetes Res 2018:6165303 |
| Saethang, Thammakorn; Hodge, Kenneth; Kimkong, Ingorn et al. (2018) AbDesigner3D: a structure-guided tool for peptide-based antibody production. Bioinformatics 34:2158-2160 |
| Briggs, Josephine; Palevsky, Paul; Knepper, Mark (2018) JASN this Month: Something Old, Something New. J Am Soc Nephrol 29:1345-1346 |
| Chen, Lihe; Lee, Jae Wook; Chou, Chung-Lin et al. (2018) Reply to Edemir: Physiological regulation and single-cell RNA sequencing. Proc Natl Acad Sci U S A 115:E351-E352 |
| Hyndman, Kelly A; Yang, Chin-Rang; Jung, Hyun Jun et al. (2018) Proteomic determination of the lysine acetylome and phosphoproteome in the rat native inner medullary collecting duct. Physiol Genomics 50:669-679 |
| Jung, Hyun Jun; Raghuram, Viswanathan; Lee, Jae Wook et al. (2018) Genome-Wide Mapping of DNA Accessibility and Binding Sites for CREB and C/EBP? in Vasopressin-Sensitive Collecting Duct Cells. J Am Soc Nephrol 29:1490-1500 |
| Lee, Jae Wook; Alsady, Mohammad; Chou, Chung-Lin et al. (2018) Single-tubule RNA-Seq uncovers signaling mechanisms that defend against hyponatremia in SIADH. Kidney Int 93:128-146 |
| Gilmer, Gabrielle G; Deshpande, Venkatesh; Chou, Chung-Ling et al. (2018) Flow Resistance along the Rat Renal Tubule. Am J Physiol Renal Physiol : |
| Rinschen, Markus M; Limbutara, Kavee; Knepper, Mark A et al. (2018) From Molecules to Mechanisms: Functional Proteomics and Its Application to Renal Tubule Physiology. Physiol Rev 98:2571-2606 |
| Chou, Chung-Lin; Hwang, Gloria; Hageman, Daniel J et al. (2018) Identification of UT-A1- and AQP2-interacting proteins in rat inner medullary collecting duct. Am J Physiol Cell Physiol 314:C99-C117 |
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