Epithelial Systems Biology Laboratory

 Home Page Research Water Balance
Disorders
Vasopressin and its
Receptors
Aquaporins Systems Biology Protein Mass
Spectrometry
Phosphoproteomics Deep Sequencing
in Epithelia
Bioinformatic/
Computational Tools
Proteomics &
Transcriptomics Databases
Integrated Antibody Design Kidney Systems Biology Project Isolated Perfused
Tubule
AbDesigner

Next Generation Sequencing in Renal Epithelial Cells

Vasopressin regulates Aqp2 gene expression as part of a broader transcriptional response (9). The Epithelial Systems Biology Laboratory (ESBL) is utilizing next-generation DNA sequencing to investigate vasopressin signaling and transcriptional regulation in microdissected renal tubule segments (1-3), single cells isolated from mouse kidneys (5) and cultured mouse collecting duct cells (mpkCCD) (4, 6, 7).

To provide a resource for the renal research community, ESBL members have recently published a study identifying every transcript in every renal tubule segment using a combination of single-tubule micro-dissection and RNA-seq (8). The data can be viewed here.

References:

  1. Sung CC, Chen L, Limbutara K, Jung HJ, Gilmer GG, Yang CR, Lin SH, Khositseth S, Chou CL, Knepper MA. RNA-Seq and protein mass spectrometry in microdissected kidney tubules reveal signaling processes initiating lithium-induced nephrogenic diabetes insipidus. Kidney Int. 2019. [Epub ahead of print] PMID: 31146973.

  2. Clark JZ, Chen L, Chou CL, Jung HJ, Lee JW, Knepper MA. Representation and relative abundance of cell-type selective markers in whole-kidney RNA-Seq data. Kidney Int. 2019; 95: 787-796. PMID: 30826016.

  3. Lee JW, Alsady M, Chou CL, de Groot T, Deen PMT, Knepper MA, Ecelbarger CM. Single-tubule RNA-Seq uncovers signaling mechanisms that defend against hyponatremia in SIADH. Kidney Int. 2018; 93: 128-146. PMID: 28843412.

  4. Jung HJ, Raghuram V, Lee JW, Knepper MA. Genome-Wide Mapping of DNA Accessibility and Binding Sites for CREB and C/EBPβ in Vasopressin-Sensitive Collecting Duct Cells. J Am Soc Nephrol. 2018; 29: 1490-1500. PMID: 29572403.

  5. Chen L, Lee JW, Chou CL, Nair AV, Battistone MA, Păunescu TG, Merkulova M, Breton S, Verlander JW, Wall SM, Brown D, Burg MB, Knepper MA. Transcriptomes of major renal collecting duct cell types in mouse identified by single-cell RNA-seq. Proc Natl Acad Sci USA. 2017; 114:E9989-E9998. PMID: 29089413 .

  6. Isobe K, Jung HJ, Yang CR, Claxton J, Sandoval P, Burg MB, Raghuram V, Knepper MA. Systems-level identification of PKA-dependent signaling in epithelial cells. Proc Natl Acad Sci USA. 2017; 114: E8875-E8884. PMID: 28973931.

  7. Sandoval PC, Claxton JS, Lee JW, Saeed F, Hoffert JD, Knepper MA. Systems-level analysis reveals selective regulation of Aqp2 gene expression by vasopressin. Sci Rep. 2016; 6:34863. PMID: 27725713.

  8. Lee JW, Chou CL, Knepper MA. Deep sequencing in microdissected renal tubules identifies nephron segment-specific transcriptomes. J Am Soc Nephrol. 2015; 26: 2669-77. PMID: 25817355.

  9. Khositseth S, Pisitkun T, Slentz DH, Wang G, Hoffert JD, Knepper MA, Yu MJ. Quantitative protein and mRNA profiling shows selective post-transcriptional control of protein expression by vasopressin in kidney cells. Mol Cell Proteomics. 2011; 10: M110.004036 PMID: 20940332.