Background:
The kidney tubule consists of different epithelial cell
types (e. g. proximal tubule, distal tubule, collecting duct epithelial cells), which are characterized by marked
differences in their paracellular transport characteristics and their tight junction composition. These epithelia
and their barrier characteristics are important for central aspects of kidney function, including blood pressure
control and osmoregulation.
PhD project:
In this project we aim to comprehensively assess the molecular composition of
epithelial barriers within cell types of the kidney using systems biology approaches. The goal will be to produce
an atlas of tight junction component-encoding gene expression in the healthy and diseased kidney and to elucidate
transcriptional networks associated with their gene expression control.
The project will focus on integration of multi-omics
technologies, including single cell transcriptomics and spatially resolved transcriptomics, followed by focused
validation experiments. A strong focus will be placed on bioinformatic integration of systems data. The successful
candidate will work in an interdisciplinary environment including biologists, computer scientists, mathematicians
and clinicians. Initial tasks will include setting up, applying and developing bioinformatics platforms and
computational pipelines for the analysis of single cell and spatial transcriptomics and integrated downstream
analyses.
The successful candidate will interact within a
multidisciplinary environment of biologists, clinicians, computational scientists within the graduate school
"TJ-Train" at Charité – Universitätsmedizin Berlin and at the Max-Delbrück Center for Molecular Medicine.
Requirements:
Profound background in molecular biology, strong interest in computational data
analysis, basic skills in programming (especially the R programming language and in scripting languages such as
Perl/Python) are a plus.
2nd cohort PhD doctoral student
Shuang Cao
1st cohort PhD doctoral student
Janna Leiz
Promotion Sept 30, 2022: "Molecular functions of the transcriptional regulator AP-2 alpha (TFAP2A) in the renal collecting duct".
-
Leiz J*, Hinze C* (*shared first authorship), Boltengagen A, Braeuning C, Kocks C, Rajewsky N,
Schmidt-Ott KM (2021) Nuclei isolation from adult mouse kidney for single-nucleus RNA-sequencing. J. Vis. Exp. 175
doi: 10.3791/62901 (IF
1.4)
-
Leiz J, Schmidt-Ott K (2020) Claudins
in the renal collecting duct.
Int. J. Mol. Sci.
21(1): 221 (11 pages) (Review)
[PubMed] [WebPage]
[PDF]
(IF 5.9)
1st cohort MD doctoral student
Alexander Holler
Project-related publications
If
a paper is not accessible, please mail to
.
1. Vukićević
T*, Hinze C*, Baltzer S, Himmerkus N, Quintanova C, Zühlke K, Compton F, Ahlborn R, Dema A, Eichhorst J, Wiesner
B, Bleich M, Schmidt-Ott KM**, Klussmann E**. Fluconazole Increases Osmotic Water Transport in Renal Collecting
Duct through Effects on Aquaporin-2 Trafficking. J. Am. Soc. Nephrol. 2019, 30: 795-810.
*Co-first, **Corresponding authors.
2. Vigolo E*,
Marko L*, Hinze C, Müller DN**, Schmidt-Ullrich R**, Schmidt-Ott KM**. Canonical BMP signaling in tubular cells
mediates recovery after acute kidney injury. Kidney Int. 2019, 95:108-122. *Co-first, **Equally
contributing principal investigators.
3. Hinze C*,
Ruffert J*(Co-first), Walentin K*(Co-first), Himmerkus N, Nikpey E, Tenstad O, Wiig H, Mutig K, Yurtdas ZY, Klein
JD, Sands JM, Branchi F, Schumann M, Bachmann S, Bleich M, Schmidt-Ott KM. GRHL2 is required for collecting duct
epithelial barrier function and renal osmoregulation. J. Am. Soc. Nephrol. 2018, 29:
857-868.
4. Werth, M.*,
Schmidt-Ott, K.M.* (co-first), Leete, T., Qiu, A., Hinze, C., Viltard, M., Paragas, N., Shawber, C.J., Yu, W.,
Lee, P., Chen, X., Sarkar, A., Mu, W., Rittenberg, A., Lin, C.S., Kitajewski, J., Al-Awqati, Q., Barasch, J.
(2017). Transcription factor TFCP2L1 patterns cells in the mouse kidney collecting ducts. eLife 6, e24265.
5. Paragas N*,
Kulkarni R*, Werth M*, Schmidt-Ott KM*, Forster C, Deng R, Zhang Q, Singer E, Klose AD, Shen TH, Francis KP, Ray
S, Vijayakumar S, Seward S, Bovino ME, Xu K, Takabe Y, Amaral FE, Mohan S, Wax R, Corbin K, Sanna-Cherchi S, Mori
K, Johnson L, Nickolas T, D'Agati V, Lin CS, Qiu A, Al-Awqati Q, Ratner AJ, Barasch J. α-Intercalated cells defend
the urinary system from bacterial infection. J. Clin. Invest. 2014, 124:2963-76. *Equal
contribution.
6. Marko L*,
Vigolo E*, Hinze C, Park JK, Roel G, Balogh A, Choi M, Wuebken A, Cording J, Blasig IE, Luft FC, Scheidereit C,
Schmidt-Ott KM**, Schmidt-Ullrich R**, Muller DN**. Tubular Epithelial NF-kB Activity Regulates Ischemic AKI.
J. Am. Soc. Nephrol. 2016, 27:2658-69. *Co-first, **Equally contributing principal
investigators.
7. Aue A,
Hinze C, Walentin K, Ruffert J, Yurtdas ZY, Werth M, Chen W, Rabien A, Kilic E, Schulzke JD, Schumann M,
Schmidt-Ott KM. A grainyhead-like 2/ovo-like 2 pathway regulates renal epithelial barrier function and lumen
expansion. J. Am. Soc. Nephrol. 2015, 26:2704-15.
8. Walentin K,
Hinze C, Werth M, Haase N, Varma S, Morell R, Aue A, Pötschke E, Warburton D, Qiu A, Barasch J, Purfürst B,
Dieterich C, Popova E, Bader M, Dechend R, Staff AC, Yurtdas ZY, Kilic E, Schmidt-Ott KM. A Grhl2-dependent gene
network controls trophoblast branching morphogenesis. Development 2015, 142:1125-36.
9. Werth, M.,
Walentin, K., Aue, A., Schonheit, J., Wuebken, A., Pode-Shakked, N., Vilianovitch, L., Erdmann, B., Dekel, B.,
Bader, M., Barasch, J., Rosenbauser, F., Luft, F.C., and Schmidt-Ott, K.M. The transcription factor
grainyhead-like 2 (Grhl2) regulates the molecular composition of the epithelial apical junctional complex.
