Dr. Michael Lenz

Dr. Michael Lenz

Advisor / Co. Advisor

Prof. Schuppert / Prof. Zenke

Dissertation

A two-scale map of global gene expression for characterising in vitro engineered cells

Contact

Michael Lenz
Aachen Institute for Advanced Study in Computational Engineering Science (AICES)
RWTH Aachen University
Schinkelstr. 2
52056 Aachen
Germany

Phone: 0241/80-99204
Email: lenz@aices.rwth-aachen.de

Education

since 01/2011 Postgraduate position at Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen
04/2009 - 11/2010 Master of Mathematics in Life Sciences, University of Applied Sciences Koblenz
03/2005 - 03/2009 Diploma in Biomathematics, University of Applied Sciences Koblenz

Professional Career

04/2009 - 09/2009 working student (Bioinformatics)Nexigen GmbH, Bonn-Bad Godesberg
08/2008 - 09/2008 Internship at Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt-Augustin
03/2008 - 06/2008 Internship at 'AG Molekulare Bioenergetik', University of Bonn
03/2006 - 02/2010 Student Assistent: Analysis I-III, Probability Theory, research projects

Research Interests

My main research focus is on the development of multifactorial biomarkers for quality control of induced pluripotent stem (iPS) cells. Induced pluripotent stem (iPS) cells are cells that are generated through reprogramming of adult cells towards a state closely related to embryonic stem cells. Like embryonic stem cells, they can divide indefinitely and differentiate into any cell types of the body. They provide unique new options for testing drugs on iPS cell-derived somatic cells that are specific to individual diseases and patients. This offers new options for drug development for disorders of the nervous system or screening of cardiac toxicity, which cannot be achieved by the established techniques due to the paucity of patient- and disease-specific cells for these organs. This work is part of the BIO.NRW funded project "StemCellFactory". “StemCellFactory” aims at the development of an integrated and automated workflow for the reprogramming of human somatic cells towards pluripotency, followed by the differentiation to cardiac and neural cellular assays for drug screening. Laborious and poorly standardized manual processes of production and expansion of the cells shall be conducted in a fully automated and standardized manner. The goal is (i) to develop an automated production facility and (ii) to produce iPS cells and iPS-cell-based products for drug development. Thus, a high quality standard as well as high throughput and parallelization of various working steps and a comprehensive quality management will be implemented in the production process. Our focus in this project is on the quality control, where we (i) try to establish biomarkers for quality control based on whole genome gene expression data and (ii) try to find surrogate markers that use less expansive and time consuming measurements, e.g. based on microscopic images, antibody staining or quantitative real time PCR. My special emphasis is on model-based analysis of microarray data, searching for large-scale patterns that are specific for pluripotent stem cells, neural cells or cardiomyocytes. Later on in the project the integration of heterogeneous data structures will be of greater importance. To this aim we plan to use sophisticated modeling methods, like, e.g., structured hybrid models, which combine machine learning with a priori established biological mechanisms.

Publications

Publications in Journals and Books

R. Wagener, M. Lenz, B. Schuldt, I. Lenz, A. Schuppert, R. Siebert, F.-J. Müller: Investigation of potential traces of pluripotency in germinal-center-derived B-cell lymphomas driven by MYC,/i> Blood Cancer Journal, 5:e317 (2015). Click here

M. Lenz, R. Goetzke, A. Schenk et al.: Epigenetic biomarker to support classification into pluripotent and non-pluripotent cells Scientific Reports 5:8973 (2015). Click here

J. Frobel, H. Hemeda, M. Lenz et al.: Epigenetic rejuvenation of mesenchymal stromal cells derived from induced pluripotent stem cells Stem Cell Reports 3:1-9 (2014). Click here

M. Lenz, B.M. Schuldt, F.-J. Müller, and A. Schuppert: PhysioSpace: Relating gene expression experiments from heterogeneous sources using shared physiological processes. PLoS ONE 8(10): e77627. doi:10.1371/journal.pone.0077627 (2013). Click here

C.A. Willmann, H. Hemeda, L.A. Pieper, M. Lenz, J. Qin, S. Joussen, S. Sontag, P. Wanek, B. Denecke, H.M. Schüler, M. Zenke, and W. Wagner: To clone or not to clone? Induced pluripotent stem cells can be generated in bulk culture. PLoS ONE 8(5): e65324. doi:10.1371/journal.pone.0065324 (2013). Click here

B.M. Schuldt, A. Guhr, M. Lenz, S. Kobold, B.D. MacArthur, A. Schuppert, P. Löser, and F.-J. Müller: Power-laws and the use of pluripotent stem cell lines. PLoS ONE 8(1): e52068 (2013). Click here

B.D. MacArthur, A. Sevilla, M. Lenz, F.-J. Müller, B.M. Schuldt, A.A. Schuppert, S.J. Ridden, P. S. Stumpf, M. Fidalgo, A. Ma'ayan, J. Wang, and I. R. Lemischka: Nanog-dependent feedback loops regulate murine embryonic stem cell heterogeneity. Nature Cell Biology 14: 1139–1147 (2012). Click here

K. Shao, C. Koch, M.K. Gupta, Q. Lin, M. Lenz, S. Laufs, B. Denecke, M. Schmidt, M. Linke, H.C. Hennies, J. Hescheler, M. Zenke, U. Zechner, T. Saric, and W. Wagner: Induced pluripotent mesenchymal stromal cell clones retain donor-derived differences in DNA methylation profiles. Molecular Therapy 21(1): 240–250 (2012). Click here

J. E. Goldmann, B. M. Schuldt, M. Lenz, and F.-J. Müller: PluriTest molecular diagnostic assay for pluripotency in human stem cells. In J.F. Loring and S.E. Peterson (eds): Human stem cell manual, second edition. Elsevier Inc. (2012). Click here

M. Lenz, M. Musso, Y. Linke, O. Tüscher, J. Timmer, C. Weiller, and B. Schelter: Joint EEG/fMRI state space model for the detection of directed interactions in human brains—a simulation study. Physiol. Meas. 32 (2011) 1725-1736. Click here


Theses

M. Lenz: Estimation of effective connectivity based on EEG and fMRI data. M. Sc. Thesis at the Freiburg Center for Data Analysis and Modeling, Freiburg (Germany), November 2010. Click here

M. Lenz: Statistische Planung von Microarray-Experimenten zur Analyse der Kationen-Homöostase in Saccharomyces cerevisiae. Diploma Thesis at the University of Applied Sciences Koblenz - RheinAhrCampus Remagen, Remagen (Germany), March 2009 (in German). Click here


Posters

M. Lenz, B.M. Schuldt, F.-J. Müller, and A. Schuppert: Physiological tracking of differentiation time series using large scale gene expression analysis 7th International Meeting of the Stem Cell Network North Rhine Westphalia, April 2013, Cologne, Germany. Click here

C. Haubenreich, P. Koch, M. Lenz, A. Schuppert, H. Chauvistré, M. Zenke, and O. Brüstle: Analysis of reprogramming-associated alterations using an isogenic human stem cell system 7th International Meeting of the Stem Cell Network North Rhine Westphalia, April 2013, Cologne, Germany.

H. Hemeda, C.A. Willmann, L.A. Pieper, M. Lenz, J. Qin, S. Joussen, S. Sontag, P. Wanek, B. Denecke, H.M. Schüler, M. Zenke, and W. Wagner: Induced pluripotent stem cells can be generated in bulk culture 7th International Meeting of the Stem Cell Network North Rhine Westphalia, April 2013, Cologne, Germany. Click here

S. Vivas, B. Schuldt, M. Lenz, and A. Schuppert: Quality control and risk assessment in mammalian systems based on genome wide pattern classification. 12th International Conference on Systems Biology, August-September 2011, Heidelberg/Mannheim, Germany. Click here

M. Lenz, B. M. Schuldt, J. E. Goldmann, and A. Schuppert: Integrating quality control in the automated generation of induced pluripotent stem cells. 6th International Meeting of the Stem Cell Network North Rhine Westphalia, April 2011, Essen, Germany. Click here